Latest publications

• Marszałek-Grabska, Marta; Hułas-Stasiak, Monika; Bekenova, Saadat; Grenda, Anna; Szulc, Michał & Esguerra, Camila [Show all 9 contributors for this article] (2026). Lithium pretreatment does not affect pilocarpine-induced seizure-like activity in zebrafish larvae. Pharmacological Reports. ISSN 1734-1140. doi: 10.1007/s43440-026-00905-y. Full text in Research Archive Show summary

  Background Recently, it has been reported that pilocarpine (PILO) induces seizures in zebrafish larvae. It has also been shown that acute PILO-induced convulsions result in unprovoked seizure-like discharges 24 hours later. Since lithium (Li) pretreatment potentiates the convulsions induced by PILO in rodents, this study was undertaken to evaluate the effect of Li on PILO-induced seizures in zebrafish larvae. Methods Experiments were conducted on zebrafish larvae up to 5 days post-fertilization. Larvae were pre-exposed to Li and then exposed to PILO. Local field potentials from the optic tectum were recorded and subjected to quantitative spectral analysis, including power spectral density estimation, band-specific power analysis, and automated ictal-event detection based on root mean square thresholding. Locomotor activity, followed by quartile-based population analysis as a potential behavioral correlate of seizure activity, was investigated. TUNEL-based apoptosis quantification and mRNA expression of neuronal activity markers npas4α and c-fos were examined. Results It was found, that pre-exposure to Li does not affect PILO-induced seizures. PILO induced seizure-like discharges in Li-pretreated larvae comparable to those evoked by PILO alone, and similarly to PILO, resulted in spontaneous, unprovoked paroxysmal brain activity 24 hours post-exposure. Spectral analysis revealed persistent increases in theta, alpha, and beta band power at the 24-hour time point, accompanied by brain apoptosis. At this time, an increase in npas4α expression was found in naïve larvae exposed to PILO. Results of quartile-based locomotor analysis, but not aggregate distance measures, correlate with seizure-like activity. Conclusions Both PILO and Li+PILO zebrafish paradigms offer a reproducible, ethically advantageous platform for conducting research related to early-onset epilepsy and for antiseizure medication screening targeting this age group.

• Schmieder, Stefanie S; Cordara, Gabriele; Kersten, Flore; Steiner, Kevin; Samim, Clara H & Plaza, David F [Show all 13 contributors for this article] (2026). Structure and function of a fungal AB toxin-like chimerolectin involved in anti-nematode defense. EMBO Journal. ISSN 0261-4189. 45(13), p. 4786–4786. doi: 10.1038/s44318-026-00812-1. Full text in Research Archive Show summary

  Abstract Fungal defense against predators largely relies on protein toxins, many of which are lectins. We previously showed that the production of the nematotoxin CCTX2 is upregulated in the Agaricomycete Coprinopsis cinerea upon predation by nematodes. Here, we classify CCTX2 as the founding member of a previously unknown family of fungal chimerolectins. Cryo-EM analysis to 3.2 Å resolution reveals five domains, with the four N-terminal β-trefoil fold (BTF) domains cradling a C-terminal domain, which exhibits an unusual α + β protein fold with some similarity to killer protein 4. Mutational analysis suggests that both terminal domains are functionally required for nematotoxicity. The first two BTF domains enable CCTX2 binding to glycosphingolipids with LacNAc or LacdiNAc glycoepitopes on nematode intestinal epithelial cells, whereas the biochemical function of the C-terminal domain remains unknown. Experiments in the model nematode Caenorhabditis elegans demonstrate that CCTX2 exploits the endocytic and retrograde trafficking machinery of cells in the intestinal epithelium to exert its toxicity and access the yet-to-be-identified intracellular target of the non-lectin domain. Our findings thus show that the molecular architecture and mode of action of CCTX2 is reminiscent of bacterial and plant AB toxins.

• Kersten, Flore; Cortés, Natalia Mojica; Serrano, Albert; Heim, Joel Benjamin; Guyette, Jessica L. & Cezar, Henrique Musseli [Show all 11 contributors for this article] (2026). A Single Amino Acid in the A2 Linker of Cholera Toxin Affects the Efficiency of Toxin Disassembly and Resulting Toxicity. ACS Omega. 11(38), p. 57763–57780. doi: 10.1021/acsomega.6c07022. Full text in Research Archive Show summary

  Abstract Cholera toxin (CT) from Vibrio cholerae and heat-labile enterotoxin (LT) from enterotoxigenic Escherichia coli are highly related AB5-type protein toxins that contain a catalytic A1 subunit, an A2 linker, and a cell-binding homopentamer of B subunits. The two proteins bind the same GM1 receptor and have similar levels of enzymatic activity toward their shared Gsα target, yet CT is more potent than LT. This difference has been mapped to a sequence of 11 amino acids (residues 226–236) near the C-terminus of the A2 linker. We now identify a single amino acid, aspartic acid at position 229, as a key contributor to the function of CT: substituting it for glutamic acid 229 from LT reduced the toxicity of CT to the level of LT. Toxin disassembly by protein disulfide isomerase (PDI), which is an essential event in the intoxication process, was less efficient for CTD229E and LT than for wild-type CT. This was further confirmed by a CT variant, in which four residues were converted into the LT sequence (D229E, I230V, T232I, and H233Y). To test our previous hypothesis that the positioning of the A1 subunit over the B pentamer critically determines toxin disassembly and thus potency, we determined crystal structures of both toxin variants to 1.6 Å resolution and calculated the angle at which the A2 linker exits the pore. The conformations of the two toxin chimeras lie between CT and LT, with the A2 C-terminus of the CT quadruple variant adopting essentially the same fold as LT. The A subunits of the toxin variants as well as that of LT showed a higher conformational freedom than CT as determined by molecular dynamics simulations, suggesting that a more rigid positioning of the A subunit drives toxin disassembly and potency. Our collective data uncover the critical role of D229 in toxin folding and structural dynamics, which in turn impacts toxin potency through effects on the efficiency of PDI-driven toxin disassembly.

• Labun, Kornel; Rio, Oline Eriksen; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia; Valen, Eivind & Haapaniemi, Emma Maria (2026). SNIPSNP: precision design of CRISPR/Cas9 knock-in reagents for variant correction and disease modeling. Nucleic Acids Research (NAR). ISSN 0305-1048. 54(W1). doi: 10.1093/nar/gkag409. Full text in Research Archive Show summary

  Abstract We present SNIPSNP (crisprtools.org/snipsnp), a comprehensive bioinformatics pipeline for designing experiments for CRISPR-induced homology-directed repair (HDR). The tool addresses the critical challenge of Cas9 re-cleavage by simplifying the selection of “blocking” silent variants that are effective at inhibiting RNP binding upon donor-templated editing. SNIPSNP handles complex edits, including indels, and uses multi-objective optimization to balance editing efficiency with biological safety. From user-defined wild-type and desired HDR alleles, the pipeline identifies candidate guides, annotating them with integrated efficiency scores and genome-wide off-target assessments. Uniquely, SNIPSNP evaluates guide binding against the post-edit genome to determine whether the therapeutic variant alone disrupts repeated Cas9 recognition. When necessary, it introduces synonymous blocking variants, prioritizing PAM and seed regions to minimize re-cleavage probability and editing of the wild-type (WT) allele when editing heterozygous variants. All candidate modifications undergo safety profiling and prioritization of known benign variants from dbSNP. We experimentally validated SNIPSNP and benchmarked it on pathogenic inborn error of immunity variants in primary patient T-cells. Across loci, SNIPSNP-designed templates outperform standard “correction-only” strategies, demonstrating enhanced precision editing, and reduced re-cleavage, establishing SNIPSNP as a robust platform for genome editing and disease modeling.

• Nothnagel, Patrizia Maria Christiane; Meslin, Paul-Arthur Richard; Wik, Jonas Aakre; Dufour, Damien; Strøm, Yunna Erika & Bjørås, Magnar [Show all 11 contributors for this article] (2026). Transient SUMOylation inhibition in human pre-adipocytes stably imprints a transcriptional beiging fate. Nucleic Acids Research (NAR). ISSN 0305-1048. 54(6), p. 1–22. doi: 10.1093/nar/gkag232. Full text in Research Archive Show summary

  SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how perturbation of the SUMOylation pathway impacts adipocyte plasticity remains unclear. Here, we show that brief pharmacologic inhibition of SUMOylation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Transient TAK-981 exposure produces changes in the transcriptome and metabolism of mature adipocytes, including robust induction of canonical beiging markers like UCP1 and increased mitochondrial respiration. Mechanistically, ATAC-seq and RNA-sequencing revealed immediate chromatin remodeling and early mobilization of CEBP family members, followed by stable activation of CEBPA and PPARG regulatory networks. ChIP experiments demonstrated loss of H3K27me3 and gain of H3K27ac at PPAR response elements at thermogenic enhancers, and increased PPARG occupancy across the UCP1 regulatory unit. This mechanism is enforced by enhanced cAMP-PKA-p38 signaling and stabilization of beiging transcription activators. We propose that transient relief of SUMO-mediated repression unlocks dominant regulatory units, notably the UCP1 enhancer cluster, producing a monomorphic reprogramming toward adaptive thermogenesis. These findings identify SUMOylation as a reversible epigenetic barrier to adipocyte beiging and suggest that temporally controlled SUMO pathway inhibition combined with PPARG activation could be exploited to modulate adipose tissue thermogenic capacity.

• Lindeman, Ida; Officer, Aengus; Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Hjort, Rebecka & Lundin, Knut [Show all 9 contributors for this article] (2026). A predisposing effect of HLA class II genes in celiac disease by skewing the naive CD4⁺T cell receptor repertoire. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 123(26). doi: 10.1073/pnas.2520636123. Full text in Research Archive
• Darbandi, Sara; Urbanucci, Alfonso; Hakkola, Sini; Gujral, Juanita; Darbandi, Mahsa & Eraky, Ahmed [Show all 10 contributors for this article] (2026). Happening in the Prostate Tumor Microenvironment: Ion Channels and Extrachromosomal DNA Driving Phenotypic Plasticity. The Prostate. ISSN 0270-4137. 86(6), p. 636–636. doi: 10.1002/pros.70139. Full text in Research Archive Show summary

  ABSTRACT Background Plasticity of cancer, including epithelial–mesenchymal transition (EMT), cancer stem cell (CSC) self‐renewal, and microenvironmental adaptation, drives metastasis, therapy resistance, and poor outcomes in prostate cancer (PCa). Ion channels and extrachromosomal DNA (ecDNA) have emerged as key drivers of such adaptive processes by influencing signaling, metabolism, and immune interactions. Methods We evaluated available evidence on ion channel biology, ecDNA dynamics, and their roles in tumor plasticity and drug resistance in PCa. Further, we analyzed two publicly accessible single‐cell RNA‐sequencing (scRNA‐seq) datasets (primary PCa and castration‐resistant PCa) to determine ion channel and transporter expression profiles in tumor and stromal cell populations. Results Our analysis showed cell type–specific expression of many ion channels, including KCNJ10, CACNA1H, and CLIC1, and identification of six transporters (SLC25A1, SLC25A10, SLC25A33, SLC25A42, SLC29A2, SLC7A11) strongly enriched in luminal tumor cells. The discovered genes regulate mitochondrial metabolism, redox homeostasis, nucleotide biosynthesis, immune modulation, and resistance to ferroptosis, all contributing to tumor growth. ecDNA facilitates oncogene amplification (e.g., MYC, EGFR), induction of EMT, and immune evasion, driving intratumoral heterogeneity and therapy‐resistant clones. Conclusions Ion channels and ecDNA are central to the disease progression and treatment resistance of PCa through regulation of EMT, CSC phenotype, and tumor microenvironment (TME) interactions. Targeting the drivers—through ion channel modulators, ferroptosis induction, and ecDNA‐targeting interventions (BET/HDAC inhibitors, CRISPR‐based methods) offers a promising way to overcome resistance. Integration of multi‐omics, and combination treatments will be key to construct precision medicine strategies and improve clinical outcomes in advanced PCa.

• Wei, Qian; Hajjar, Ehsan; Cornillot‐Clément, Selma; Solli, Elise; Diaz, Nuria Garcia & Landskron, Johannes [Show all 9 contributors for this article] (2026). High-Throughput Phenotypic Screen to Identify FoxP3 Regulators in Primary T Cells. ACS Chemical Biology. ISSN 1554-8929. 21(4), p. 764–778. doi: 10.1021/acschembio.5c01019. Full text in Research Archive Show summary

  FoxP3+ regulatory T cells (Tregs) maintain immune homeostasis by suppressing excessive antiself-immunity of effector T cells (Teffs) and thereby regulate autoimmunity and inhibit antitumor immune responses. Thus, Treg-targeting is a popular therapeutic strategy for both autoimmune diseases and cancer treatment. However, specific regulators of Tregs are needed to bypass adverse effects elicited by strategies that target molecules with overlapping expression between Tregs and other T cell subsets. We aim to identify small molecules that specifically target the key Treg lineage-defining transcription factor FoxP3. Here, we describe a high-throughput, flow-cytometry-based phenotypic screening assay, its data processing pipeline, and downstream methods for compound validation. We developed a set of algorithms to easily exclude compounds with high toxicity and to filter out autofluorescent compounds. Our screening assay is performed on human primary T cells by measuring FoxP3 levels in CD4+ T cells, using an automated liquid handling pipeline. Selected hit candidates from the screening were validated and assessed through functional analyses. From screening a library of approved drugs, we identified several candidates that regulate Treg functions through FoxP3. Seventeen chemical analogs of one hit compound were identified and characterized in cell-based assays, revealing structure–activity relationships and identifying compounds with more potent effects on the regulation of FoxP3 levels and Treg function. We conclude that this novel screening method could successfully identify FoxP3 regulators with an effect on Treg functions.

• Holme, Andreas Næss; Moen, Line Victoria; Sallinen, Mikael; Nilsen, Kristian Bernhard; Boccara, Charlotte & Phillips, Andrew JK [Show all 8 contributors for this article] (2026). Adaptation across consecutive night shifts at 71°N under Arctic summer daylight and winter darkness. Effects on alertness, sleepiness, and fatigue. Scandinavian Journal of Work, Environment and Health. ISSN 0355-3140. 52(4), p. 403–414. doi: 10.5271/sjweh.4295. Full text in Research Archive Show summary

  Objectives: This study aimed to investigate how alertness, sleepiness, and fatigue change across consecutive night compared to morning shifts among Arctic shift workers and whether these effects differ between seasons of midnight sun and polar night. Methods: We conducted an observational crossover study of 118 shift workers from an industrial plant at a high latitude (71°N) in northern Norway. Eighty-one individuals participated in both the light (near 24-hour daylight) and dark (minimal natural light) seasons. Work schedules included blocks of seven consecutive morning shifts and seven consecutive night shifts, separated by four rest days. Alertness (psychomotor vigilance test), subjective sleepiness (Karolinska Sleepiness Scale), and subjective fatigue were measured at the end of shifts on days 1, 3, and 6 of each shift block. We analyzed data using multilevel mixed-effects regression models with season, shift type (morning/night), and consecutive workday number as fixed effects. Results: Night shifts were linked to lower alertness and higher sleepiness and fatigue in both seasons, with the largest impairments on the first night. Across six consecutive night shifts, alertness improved and sleepiness and fatigue decreased, with similar trajectories in both seasons. There was no evidence that season significantly affected alertness, sleepiness, or fatigue. Conclusions: Night shifts generally impair alertness and increase sleepiness and fatigue, yet outcomes improved across consecutive nights. Despite the well-established effects of natural light on circadian rhythms, the seasonal photoperiod altered neither the shift-related impairments in alertness, sleepiness or fatigue nor the subsequent improvements across consecutive nights; workers showed similar adaptation in both seasons.

• Shrestha, Asmita; van_Son, Maren; Hashim, Adnan; Rouzbehani, Soudabeh; Gilfillan, Gregor & Berge, Urszula [Show all 8 contributors for this article] (2026). Sperm RNA landscape during sexual maturation in Duroc boars. BMC Genomics. 27(1). doi: 10.1186/s12864-025-12490-0. Full text in Research Archive Show summary

  Background Sexual maturation in boars impacts reproductive efficiency in swine production, yet the molecular mechanisms underlying this developmental transition remain poorly understood. This study aimed to investigate the transcriptomic changes in sperm from Duroc boars during sexual maturation, conducting a longitudinal analysis. The total RNA and miRNA profiles from the same individuals (n = 6) at puberty (7.24 ± 0.39 months) and sexual maturity (10 ± 0.40 months) were compared, identifying molecular signatures associated with reproductive development. Total RNA sequencing (Illumina NovaSeq-6000) and miRNA sequencing (Illumina NextSeq-500) were performed on all 12 paired samples (6 boars at 2 time points), followed by differential expression analysis using a paired statistical model in DESeq2 to account for repeated measures. Results Differential expression analysis identified 60 differentially expressed genes using stringent criteria (adj P < 0.05, |log2FC| ≥ 0.5), with 65% upregulated in sperm of boars 10-months versus 7-months of age. Key upregulated genes included NCLN, RGS12, CIB2, FOXP4, PHC1, CDC25B and AKAP1, while HSP90AA1, EVI5, FSIP2, VDAC3, and ALMS1 were key downregulated genes. Furthermore, Gene ontology analysis revealed significant enrichment of 11 biological processes, mostly related to reproductive development, and four molecular functions (transferase activity, transferring phosphorus-containing groups, protein serine/threonine kinase activity, protein kinase activity and signal sequence binding). Additionally, our miRNA analysis identified six differentially abundant miRNAs (adj P < 0.05 & |log2FC| ≥ 0.5); ssc-miR-193a-5p, ssc-miR-574-3p, ssc-miR-126-3p, ssc-miR-196a, ssc-miR-210 were upregulated, and ssc-miR-338 showed downregulation in 10-months age. Integrated analysis of differentially expressed mRNA and predicted miRNA targets identified 18 miRNA-mRNA regulatory pairs, enriched in pathways related to cell cycle processes and chromatin binding, suggesting coordinated regulation across RNA biotypes in sperm during sexual maturation. Conclusions Our study reveals coordinated transcriptomic shifts in boar sperm during sexual maturation. Most genes show increased RNA abundance at 10 months of age, with enrichment in terms of reproductive development. Several miRNAs appear to regulate these changes through targeted mRNA interactions. These findings expand our understanding of the biological processes underlying sexual maturation in pigs.

• Officer, Aengus; Watson, Corey T.; Engelbrecht, Eric; Dahal-Koirala, Shiva; Risnes, Louise Fremgaard & Lundin, Knut [Show all 9 contributors for this article] (2026). Immunoglobulin gene polymorphisms shape the naïve B-cell receptor repertoire; relevance to celiac disease. Genes and Immunity. ISSN 1466-4879. 27, p. 210–222. doi: 10.1038/s41435-026-00384-4. Full text in Research Archive
• Sørensen, Henrik Vinther; Canals, Mateu Montserrat; Coder, Ayla Steffensen; Prévost, Sylvain; Krueger, Susan & Vaaje-Kolstad, Gustav [Show all 9 contributors for this article] (2026). Tangled Up in Fibers: How a Multidomain Lytic Polysaccharide Monooxygenase Binds Its Chitin Substrate. ACS Applied Materials & Interfaces. ISSN 1944-8244. doi: 10.1021/acsami.5c24418. Full text in Research Archive Show summary

  Lytic polysaccharide monooxygenases (LPMOs) are redox enzymes that bind to and oxidize insoluble carbohydrate substrates such as chitin or cellulose. This class of enzymes has attracted considerable attention due to their ability to convert biomaterials of high abundance into oligosaccharides that can be useful for producing biofuels and bioplastics. However, processes at the interface between solution and insoluble substrates represent a major challenge to biochemical and structural characterization. Here, we investigated the four-domain LPMO from Vibrio cholerae, N-acetyl glucosamine binding protein A (GbpA), to elucidate how it docks onto its insoluble substrate with its two terminal domains. First, we developed a protocol that allowed GbpA and chitin to form a stable complex in suspension, overcoming incompatibilities of the two binding partners with respect to pH. After determining the small-angle neutron scattering (SANS) contrast match point for chitin (47% D2O), we characterized the mesoscale structure of GbpA in complex with chitin by SANS and complemented the results with negative-stain electron microscopy. We found that GbpA binds rapidly to chitin, where it coats the chitin fibers and smooths their surface. In some locations, GbpA binding induces the formation of protein–chitin clumps containing a large number of GbpA molecules. Together, this suggests how the secretion of GbpA efficiently prepares the ground for microcolony formation by the bacteria.

• Tiusanen, Ville; Patel, Divyeshkumar Amrubthai; Xia, Jihan; Xu, Chi; Datta, Subhamoy & Yun, Ji [Show all 13 contributors for this article] (2026). Classical enhancers couple cis-regulatory logic with transcriptional condensates and 3D genome architecture. bioRxiv - the preprint server for biology. doi: 10.64898/2026.01.23.701252. Full text in Research Archive Show summary

  Abstract Deciphering the regulatory logic of enhancers remains a central question in understanding cell- and tissue-specific gene expression in multicellular organisms. This is particularly pertinent at multipartite enhancer clusters such as super-enhancers, where multiple enhancers contribute to the expression of a single gene. Gene expression has been studied largely through sequence-dependent recruitment of transcription factors (TF) and co-activators, whereas 3D chromatin structure has been attributed to architectural proteins such as cohesion and CTCF 1–3 . However, the contribution of DNA sequence encoded in enhancers to shaping higher-order genome organization remains poorly understood. Here we show that classical enhancers, embedded within multipartite super-enhancer structures, act as determinant regulatory elements that initiate the gene regulatory cascade by linking DNA sequence recognition to 3D chromatin architecture. Classical enhancers are more evolutionarily conserved and display stronger regulatory activity than facilitator elements, which lack intrinsic enhancer activity but potentiate classical enhancer function. We show that classical enhancers are selectively bound by specific TFs with strong intrinsically disordered regions, such as NFE2L2 in liver cancer cells, capable of driving transcriptional condensate formation through phase separation. NFE2L2 depletion reduced enhancer activity and induced widespread chromatin reorganization, characterized by increased cohesin and CTCF occupancy at super-enhancer boundaries and beyond. This “cohesin clogging” impaired DNA loop extrusion, led to formation of smaller topologically associated domains, and weakened enhancer–promoter contacts. These findings highlight that sequence-specific TFs have multifaceted roles beyond transcriptional control, establishing a direct mechanistic link between enhancer sequence, TF binding, condensate formation, and 3D genome organization, with the regulatory logic being encoded in the DNA sequence itself.

• Ferenc, Katalin Terezia; Martini, Lorenzo; Rauluseviciute, Ieva; Sandve, Geir Kjetil Ferkingstad & Mathelier, Anthony (2026). inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btag026. Full text in Research Archive Show summary

  The accurate development, assessment, interpretation, and benchmarking of bioinformatics frameworks for analyzing transcriptional regulatory grammars rely on controlled simulations to validate the underlying methods. However, existing simulators often lack end-to-end flexibility or ease of integration, which limits their practical use. We present inMOTIFin, a lightweight, modular, and user-friendly Python-based software that addresses these gaps by providing versatile and efficient simulation and modification of DNA regulatory sequences. inMOTIFin enables users to simulate or modify regulatory sequences efficiently for the customizable generation of motifs and insertion of motif instances with precise control over their positions, co-occurrences, and spacing, as well as direct modification of real sequences, facilitating a comprehensive evaluation of motif-based methods and interpretation tools. We demonstrate inMOTIFin applications for the assessment of de novo motif discovery, the analysis of transcription factor cooperativity, and the support of explainability analyses for deep learning models. inMOTIFin ensures robust and reproducible analyses for studying transcriptional regulatory grammars.

• Mikkelsen, Nanna S.; Ravendran, Sujan; Broksø, Amalie D.; Skjelbostad, Sigrid Fu; Pedersen, Maya G. & Fang, Hongyu [Show all 9 contributors for this article] (2025). Orthogonal CRISPR systems for targeted integration and multiplex base editing enable nonviral engineering of allogeneic CAR-T cells. Molecular Therapy. ISSN 1525-0016. 33(12), p. 6100–6100. doi: 10.1016/j.ymthe.2025.08.032. Full text in Research Archive Show summary

  Multiple genomic modifications, including targeted transgene integrations and knockouts, may be required to develop potent, allogeneic chimeric antigen receptor (CAR)-T cell therapies. Conventional CRISPR-Cas systems generate double-strand breaks (DSBs) associated with genomic rearrangements and genotoxicities. DSB-free base editing reduces these risks. Here, we facilitate multiplex editing by combining Staphylococcus aureus Cas9 (SaCas9) mRNA base editors for DSB-free knockout of B2M and REGNASE-1 with Streptococcus pyogenes Cas9 nucleases for targeted integration of an anti-CD19 CAR transgene at the T cell receptor α constant locus. Combined, these edits have been reported to generate safer allogeneic CAR-T cells with enhanced activity and persistence. We demonstrate multiplex gene editing in primary human T cells with B2M and REGNASE-1 base editing frequencies reaching 66% and 84%, respectively, while integrating the anti-CD19 CAR transgene in up to 36% or 71% of cells using nonviral single-stranded DNA repair templates or viral vector templates (AAV6), respectively. Importantly, no detrimental effects on CAR-T cell function were observed in vitro or in vivo, and knockout by base editing reduced rates of balanced chromosomal translocations by 210-fold. This orthogonal CRISPR-Cas engineering approach represents a novel and safer strategy for nonviral, multiplexed genetic engineering of CAR-T cells.

• Grist, Emily; Dutey-Magni, Peter; Parry, Marina A.; Mendes, Larissa; Sachdeva, Ashwin & Proudfoot, James A. [Show all 47 contributors for this article] (2025). Tumor transcriptome-wide expression classifiers predict treatment sensitivity in advanced prostate cancers. Cell. ISSN 0092-8674. 188(20), p. 5734–5734. doi: 10.1016/j.cell.2025.07.042. Full text in Research Archive
• Yamaguchi, Takafumi N.; Houlahan, Kathleen E.; Zhu, Helen; Kurganovs, Natalie; Livingstone, Julie & Fox, Natalie S. [Show all 82 contributors for this article] (2025). The Germline and Somatic Origins of Prostate Cancer Heterogeneity. Cancer Discovery. ISSN 2159-8274. 15(5), p. 988–1017. doi: 10.1158/2159-8290.CD-23-0882. Full text in Research Archive
• Lam, Suk Wai; Belova, Tatiana; Franceschini, Natasja; Akker, Brendy van den; IJzendoorn, David G.P. van & Mikkers, Harald M.M. [Show all 11 contributors for this article] (2025). Truncated FOS impairs osteogenic differentiation and induces prostaglandin and NFκB signalling in an in vitro cell-of-origin model for osteoid osteoma and osteoblastoma. Journal of Pathology. ISSN 0022-3417. 268(3), p. 263–275. doi: 10.1002/path.70010. Full text in Research Archive
• Arcos-Encarnación, Bolivar; Cortes-Flores, Eladio; Barón-Mendoza, Isabel; Almazán, Jorge L.; Valle-García, David & León-Guerrero, Sol Díaz de [Show all 15 contributors for this article] (2025). KChIP3 fosters neuroinflammation and synaptic dysfunction in the 5XFAD mouse model of Alzheimer’s disease. Journal of Neuroinflammation. doi: 10.1186/s12974-025-03426-2. Full text in Research Archive Show summary

  Alzheimer’s disease (AD) is a progressive neurodegenerative disorder marked by β-amyloid (βA) accumulation, neuroinflammation, excessive synaptic pruning, and cognitive decline. Despite extensive research, effective treatments remain elusive. Here, we identify potassium channel-interacting protein 3 (KChIP3) as a key driver of AD pathology using the 5XFAD mouse model. KChIP3 levels were significantly elevated in the hippocampus of 5XFAD mice, correlating with βA burden and neuroinflammation. This upregulation was triggered by inflammatory signaling via the NLRP3 inflammasome and Caspase-1 activation. Notably, genetic deletion of KChIP3 (5XFAD/KChIP3−/−) markedly reduced βA plaque deposition, pro-inflammatory cytokines, reactive gliosis, and expression of inflammation-related proteins (APO, CLU, MDK). Transcriptomic and proteomic analyses revealed restored synaptic markers (CD47, CD200, CACNB4, GDA) and a shift of the disease-associated microglial (DAM-1) phenotype. Mechanistically, we propose that KChIP3 amplifies AD pathology through two key mechanisms: (1) sustaining neuroinflammation by upregulating pro-inflammatory genes and (2) impairing synaptic integrity by repressing genes critical for neuronal function. Consistently, KChIP3 deletion enhanced dendritic complexity, synaptic plasticity, and cognitive performance in 5XFAD mice. These findings position KChIP3 as a potential therapeutic target for mitigating neuroinflammation and synaptic dysfunction in AD and highlight its potential as a biomarker for disease progression. Graphical abstract

• Gupta, Kushol; Sekulic, Nikolina; Allu, Praveen Kumar; Sapp, Nicklas; Huang, Qingqiu & Sarachan, Kathryn [Show all 13 contributors for this article] (2025). Solution conformational differences between conventional and CENP-A nucleosomes are accentuated by reversible deformation under high pressure. Chromosome Research. ISSN 0967-3849. 33(1). doi: 10.1007/s10577-025-09769-z. Full text in Research Archive Show summary

  Abstract Solution-based interrogation of the physical nature of nucleosomes has its roots in X-ray and neutron scattering experiments, including those that provided the initial observation that DNA wraps around core histones. In this study, we performed a comprehensive small-angle scattering study to compare canonical nucleosomes with variant centromeric nucleosomes harboring the histone variant, CENP-A. We used nucleosome core particles (NCPs) assembled on an artificial positioning sequence (Widom 601) and compared these to those assembled on a natural α-satellite DNA from human centromeres. We establish the native solution properties of octameric H3 and CENP-A NCPs using analytical ultracentrifugation (AUC), small-angle X-ray scattering (SAXS), and contrast variation small-angle neutron scattering (CV-SANS). Using high-pressure SAXS (HP-SAXS), we discovered that both histone and DNA sequence have an impact on the stability of octameric nucleosomes in solution under high pressure (300 MPa), with evidence of reversible unwrapping in these experimental conditions. Both canonical nucleosomes harboring conventional histone H3 and their centromeric counterparts harboring CENP-A have a substantial increase in their radius of gyration, but this increase is much less prominent for centromeric nucleosomes. More broadly for chromosome-related research, we note that as HP-SAXS methodologies expand in their utility, we anticipate this will provide a powerful solution-based approach to study nucleosomes and higher-order chromatin complexes.

• Sankaranarayanan, Sundar Ram; Ulmer, Jonathan; Mørch, Anna; Ahmad, Ahmad Ali; Sekulic, Nikolina & Drinnenberg, Ines Anna (2025). Insects evolved a monomeric histone-fold domain in the CENP-T protein family. EMBO Reports. ISSN 1469-221X. 26(23), p. 5825–5825. doi: 10.1038/s44319-025-00603-5. Full text in Research Archive Show summary

  Abstract The histone-fold domain (HFD) is a conserved protein interaction module that requires stabilization through a handshake interaction with an HFD partner. All HFD proteins known to date form obligate dimers to shield the extensive hydrophobic residues along the HFD. Here, we find that the lepidopteran kinetochore protein CENP-T is soluble as a monomer. We attribute this stability to a structural rearrangement, which leads to the repositioning of the HFD helix α3. This brings a conserved two-helical extension closer to the histone fold, where it takes over the position and function of the CENP-T partner CENP-W. This change has no effect on the DNA-binding ability of the lepidopteran CENP-T. Our analysis suggests that the monomeric HFD originated in the last common ancestor of insects, with a possible second independent origin in Acariformes, both of which lack CENP-W. Our study highlights an unexpected structural variation in a protein module as conserved and optimized as the HFD, providing a unique perspective on the evolution of protein structure and the forces driving it.

• Cieslar-Pobuda, Artur Grzegorz & Caglayan, Safak (2025). Loss of dynamin 1-like protein impairs mitochondrial function and self-renewal, and activates the integrated stress response in human embryonic stem cells. Frontiers in Genetics. 16. doi: 10.3389/fgene.2025.1628178. Full text in Research Archive Show summary

  Dynamin 1-like protein (DNM1L/DRP1) is a crucial regulator of mitochondrial fission in cells and pathogenic mutations in DNM1L are linked to developmental and metabolic disorders in humans. While the role of DNM1L has been described in patient-derived fibroblasts, its function in early human development remains unclear. In this study, we generated DNM1L deficient human embryonic stem cells (hESCs) using CRISPR/Cas9 to investigate the consequences of DNM1L deficiency and impaired mitochondrial fission on stem cell function. DNM1L−/− hESCs exhibited hyperfused mitochondrial networks, reduced mitochondrial membrane potential, and elevated oxidative stress, indicating compromised mitochondrial fitness. Functionally, DNM1L−/− hESCs showed diminished self-renewal, and reduced expression of the core pluripotency factor OCT4, while NANOG expression was unaffected. We further found that differentiation potential toward the early ectodermal lineage was impaired, whereas early endodermal and mesodermal differentiation remained intact. Notably, integrated stress response (ISR) pathway was activated in DNM1L−/− hESCs, as shown by increased phosphorylated eIF2a and upregulation of downstream targets including activating transcription factor 4 (ATF4), ATF3, ATF5, and DDIT3. Restoring DNM1L expression by reintroduction of DNM1L into the AAVS1 locus rescued mitochondrial morphology and function, normalized ISR activation, and restored self-renewal and OCT4 expression in DNM1L−/− hESCs. These findings demonstrate that DNM1L is essential for maintaining mitochondrial homeostasis, stress response, self-renewal, and pluripotency in hESCs, and emphasize the importance of mitochondrial fission in stem cell function.

• Lehtonen, Johanna; Hakonen, Anna H; Hassinen, Antti; Lurås, Sanne Iversen; Kaustio, Meri & Glumoff, Virpi [Show all 19 contributors for this article] (2025). Genome sequencing reveals CCDC88A variants in malformations of cortical development and immune dysfunction. Human Molecular Genetics. ISSN 0964-6906. 34(15), p. 1294–1312. doi: 10.1093/hmg/ddaf081. Full text in Research Archive Show summary

  Abstract Malformations of cortical development (MCDs) encompass a diverse group of genetic and clinical disorders. Here, we aimed to determine a genetic etiology for two siblings manifesting MCD, microcephaly, epilepsy, intellectual disability, and susceptibility to infections. A missense variant (NM_018084:c.929A &gt; C, p.Asp310Ala) and an intragenic deletion (exons 14–16) in CCDC88A were identified as compound heterozygous in patients by genome sequencing. Truncating homozygous CCDC88A variants are known to cause an ultra-rare syndrome manifesting with MCD, microcephaly, seizures, and severe neurological impairment. CCDC88A encodes girdin, which is essential for various cell functions, such as actin remodeling and cell proliferation. Western blot analysis showed that the missense variant allele was expressed in fibroblasts at a level compatible with a heterozygous allele, whereas a truncated protein from the deletion allele was barely detectable. Proliferation and wound-healing assays revealed that girdin-deficient fibroblasts proliferated faster and migrated slower than controls. High-content imaging highlighted girdin-deficient fibroblasts as smaller and their actin remodeling disrupted, leading to perinuclear accumulation of endolysosomal organelles. To confirm these cellular phenotypes resulted from girdin loss, CRISPR-Cas9 edited knockout models of healthy fibroblasts were created, replicating the observations in patient cells. Additionally, the siblings exhibited reduced monocytoid and plasmacytoid dendritic cells, suggesting compromised immunity due to girdin deficiency. In summary, the study describes the first case of a CCDC88A missense variant and intragenic deletion associated with MCD. It demonstrates altered immunity and girdin-related cellular changes, such as cell morphology and proliferation-migration dichotomy, in patient and knockout fibroblasts, reinforcing the pathogenic relevance of these variants.

• Pukaj, Albert; Harroud, Adil; Shchetynsky, Klementy; Wirsching, Laura; Peters, Lucy & Andlauer, Till F.M. [Show all 52 contributors for this article] (2025). Genetic Risk Variants for Multiple Sclerosis and Other Loci Linked to Intrathecal Immunoglobulin G Synthesis. Neurology: Neuroimmunology and neuroinflammation. 12(6). doi: 10.1212/nxi.0000000000200499. Full text in Research Archive Show summary

  Background and Objectives Intrathecal synthesis of immunoglobulin G (IgG) is a key feature of multiple sclerosis (MS) and a prognostic marker for the disease course. Although previous studies identified 2 genetic regions—the major histocompatibility complex (MHC) region on chromosome 6 and the immunoglobulin heavy chain constant (IGHC) locus on chromosome 14—associated with intrathecal IgG synthesis in MS, the genetic underpinnings remain insufficiently understood. Methods We conducted a genome-wide association study on intrathecal IgG synthesis using the IgG index to identify individuals with (≥0.7) or without (<0.7) quantitative intrathecal synthesis. We used logistic regression models adjusting for sex, age, and population structure. We performed secondary analyses to examine associations between identified loci and the extent of intrathecal IgG synthesis and the presence and extent of intrathecal immunoglobulin A and M synthesis. We further conducted association analyses for imputed human leukocyte antigen alleles and analyzed whether a higher genetic burden for MS risk—quantified through polygenic risk scores—is associated with intrathecal IgG synthesis. Results In the discovery cohort (n = 3,934), we identified a novel genome-wide significant association of the intronic variant rs844586 (p = 1.48 × 10−8) in the sterile alpha motif domain containing 5 (SAMD5) gene on chromosome 6, with intrathecal IgG synthesis. We could confirm this association in a replication cohort (n = 1,094) and demonstrated that it is independent of a previously described association signal at the MHC region. In a subset (n = 1,413), we further identified rs1407 as a potential causal variant (p = 3.80 × 10−11, posterior inclusion probability = 0.92) for the previously reported association signal at the IGHC locus with the extent of intrathecal IgG synthesis. In addition, we demonstrated that a higher genetic burden for MS susceptibility, both within and outside of the MHC region, is associated with a higher likelihood of and a more pronounced intrathecal IgG synthesis. Discussion Our study revealed a previously unknown association between an intronic variant in SAMD5 with intrathecal IgG synthesis and identified a potential causal variant within the IGHC locus. It further provides evidence for possible effects of known MS risk variants on disease severity through their effect on the intrathecal humoral immune response, a prognostic marker for the disease course.

• Kalinichenko, Artem; Huemer, Jakob; Humer, Theresa; Haimel, Matthias; Svaton, Michael & Socquet-Juglard, Nicolas [Show all 31 contributors for this article] (2025). Protein palmitoylation and sphingolipid metabolism control regulated exocytosis in cytotoxic lymphocytes. Science immunology. 10(112). doi: 10.1126/sciimmunol.ado3825. Full text in Research Archive Show summary

  Regulated exocytosis controls key cellular functions ranging from neurotransmitter release to the secretion of immune mediators, and its disruption is associated with numerous pathologies. The cytotoxic activity of lymphocytes is particularly dependent on regulated and polarized lytic granule delivery toward infected or malignant cells. Although genetic and mechanistic studies have identified factors regulating exocytosis in cytotoxic lymphocytes, a systematic mapping of the relevant factors and their relationships is lacking. Through a genome-scale CRISPR knockout screen in a human natural killer cell line, we characterized a complex genetic network regulating cytotoxic granule exocytosis, with lipid metabolism and protein lipidation among the most prominent pathways. By combining global protein palmitoylation and lipidomic studies, we found that ZDHHC17 drives palmitoylation of the core SNARE complex protein SNAP23 to target cytotoxic granules to GM1-rich lipid rafts whose assembly is controlled by serine palmitoyltransferase. In summary, our study identifies previously unrecognized factors essential for cytotoxic function in human lymphocytes and uncovers how lipid metabolism and protein palmitoylation are involved in the process of regulated exocytosis.

• Koski, Yrjö; Patel, Divyesh; Koch, Natalia Kakko von; Jouhten, Paula; Aaltonen, Lauri & Palin, Kimmo [Show all 8 contributors for this article] (2025). Compound-specific DNA adduct profiling with nanopore sequencing and IonStats. bioRxiv - the preprint server for biology. doi: 10.1101/2025.10.31.685820. Full text in Research Archive Show summary

  A bstract Covalently bound DNA adducts are mutation precursors that contribute to aging and diseases such as cancer. Accurate detection of adducts in the genome will shed light on tumorigenesis. Commonly used detection methods are unable to pinpoint the exact genomic locations of adducts. Long-read nanopore sequencing has the potential to accurately detect multiple types of DNA adducts at single-nucleotide precision. In this study, we developed a novel statistical toolkit, IonStats, to profile DNA adducts in nanopore sequencing data. With IonStats, we investigated the effects of four adduct-inducing genotoxic compounds on nanopore sequencing, and found both shared and compound-specific perturbations in base quality scores, ionic current profiles, and translocation dynamics. Notably, aristolochic acid II and melphalan treatments profoundly altered nanopore readouts and led to substantial sequence-specific read interruptions. Our study shows that nanopore sequencing can be effectively employed to detect and characterize DNA adducts, paving the way for high-resolution, high-throughput profiling of DNA damage and the exposome.

• Tuohinto, Krista; Graus, Matthew S.; Staab, Peyton; Tiusanen, Ville; Fei, Liangru & Pradhan, Susav [Show all 20 contributors for this article] (2025). Oncogenic virus hijacks SOX18 pioneer function to enhance viral persistence. bioRxiv - the preprint server for biology. doi: 10.1101/2025.06.28.662102. Full text in Research Archive Show summary

  Abstract Kaposi’s sarcoma herpesvirus (KSHV) establishes lifelong oncogenic infection in lymphatic endothelial cells (LECs) by ensuring episomal maintenance of its genome via the viral protein LANA. Efficient viral genome maintenance typically involves host DNA replication and episome tethering, but the extent of cell-type-specific regulation remains unclear. Here, we identify that KSHV hijacks the pioneering function of the endothelial-specific transcription factor SOX18 to facilitate persistence of viral episomes. Upon infection, LANA co-opts SOX18 to recruit the SWI/SNF chromatin-remodeling complex via its ATPase subunit BRG1, enhancing chromatin accessibility and enabling efficient viral genome persistence. Disruption of SOX18 or BRG1—genetically or pharmacologically—leads to reduced episome load and attenuated hallmarks of virus infection. This work highlights how viruses can harness lineage-specific transcriptional regulators to establish persistent nuclear retention of their episome into the host genome.

• Kauko, Otto; Turunen, Mikko; Pihlajamaa, Päivi; Häkkinen, Antti; Queiroz, Rayner M.L. & Pääkkönen, Mirva [Show all 19 contributors for this article] (2025). Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer. Science Advances. 11(34). doi: 10.1126/sciadv.adt1798. Full text in Research Archive Show summary

  Mutations in numerous genes contribute to human cancer, with different oncogenic lesions prevalent in different cancer types. However, the malignant phenotype is simple, characterized by unrestricted cell growth, invasion, and often metastasis. One possible hypothesis explaining this dichotomy is that cancer genes regulate common targets, which then function as master regulators of essential cancer phenotypes. To identify mechanisms that drive the most fundamental feature shared by all tumors—unrestricted cell proliferation—we used a multiomic approach, which identified translation and ribosome biogenesis as common targets of major oncogenic pathways across cancer types. Proteomic analysis of tumors and functional studies of cell cultures established nucleolar and coiled-body phosphoprotein 1 as a key node, whose convergent regulation, both transcriptionally and posttranslationally, is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways regulate the same set of targets for growth control, revealing key downstream nodes that could be targeted for therapy or chemoprevention.

• Nossum, Baard; Liverud, Anders Erik; Dapsance, Florian Albert; Annavini, Eis; Modi, Brijesh & Hafting, Torkel [Show all 8 contributors for this article] (2025). A Lightweight FPGA-Based Platform for Low-Power Neural Recording in Freely Moving Animals. In Redaktørkomite (Eds.), 2025 47th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE (Institute of Electrical and Electronics Engineers). ISSN 9798331586188. doi: 10.1109/embc58623.2025.11253988. Full text in Research Archive Show summary

  Understanding the neural mechanisms of sleep is critical for advancing treatments for neurodegenerative diseases. To investigate these mechanisms, long-term electrophysiological studies are conducted in animal models, where brain activity can be monitored continuously under controlled conditions. However, electrophysiological recordings from freely moving animals are typically performed using a tethered setup, which imposes constraints on natural behaviour. As a first step towards a miniaturised, wireless neural implant, we present a low-power system that enables direct control of the Intan RHD2132 electrophysiology chip using a custom FPGA-based stack. A light-weight yet robust implementation ensures efficient operation while maintaining the necessary flexibility for future integration into a compact, wireless system. The FPGA handles real-time signal processing and data transmission, with support for closed-loop stimulation and onboard data compression. Our system achieves continuous multi-channel recording at 20 kHz, with real-time wireless streaming and long-term data storage. The hardware design prioritises low power consumption, with the aim of enabling extended operation for uninterrupted sleep monitoring over 24 hoursClinical Relevance— This technology enables long-term, high-resolution sleep monitoring, which is essential for understanding the role of sleep in neurodegenerative disorders such as Alzheimer’s and Parkinson’s. By providing continuous, naturalistic brain recordings, this system may help identify early electrophysiological biomarkers of cognitive decline, with potential translational and therapeutics applications.

• Dufour, Damien; Bryne, Sandra Kristine Stølen; Dapsance, Florian; Ferrito, Noemi; Plotton, Ingrid & Dalen, Knut Tomas [Show all 9 contributors for this article] (2025). Mechanisms of sexually dimorphic adipose tissue remodelling upon prolonged breastfeeding. bioRxiv (preprint article). doi: 10.1101/2025.09.05.674416. Full text in Research Archive Show summary

  Early developmental cues exert lasting influence on the adipose tissue function and the metabolic health throughout adulthood. In mice, adipose tissue remodelling during the weaning transition programs long-term tissue plasticity, setting its capacity for expansion and thermogenesis in response to environmental stimuli. However, the mechanisms driving this remodelling, and the role of weaning-associated dietary changes in this process, are unknown. Here, we characterise the emergence of sexually dimorphic patterns of adipose tissue distribution and function during the post-weaning period. As subcutaneous adipocytes acquire a white phenotype, the tissue microenvironment undergoes a coordinated remodelling, including reduced innervation and an increase in immune cell content. Using a model of prolonged breastfeeding, we show that it promotes adipose tissue expansion through sex-dependent mechanisms, stimulating progenitor proliferation in males and adipocyte hypertrophy in females. In males, this is accompanied by accelerated tissue whitening, which we link to enhanced clearance of extracellular noradrenaline by mature adipocytes. Our findings reveal sex- and diet-dependent mechanisms governing adipose tissue maturation and highlight how early life nutritional cues shape the microenvironment and function of mature adipocytes. Highlights - The peri-weaning period associates with sexually dimorphic remodelling of the adipose tissue - Whitening of the adipose tissue associates with immune infiltration and decrease innervation in both sexes - Prolonged breastfeeding prevents drop in proliferation in males - Whitening is accelerated in males during prolonged breastfeeding

• Kumar, Vipin; Rossini, Roberto; Paulsen, Jonas & Mathelier, Anthony (2025). BHiCect 2.0: Multi-resolution clustering of Hi-C data. EarthArXiv preprint platform. doi: 10.48550/ARXIV.2512.17512. Full text in Research Archive
• Puig, Rafael Riudavets; Brorson, Ina Skaara; O’Mahony, Denise; Kristensen, Vessela N. & Mathelier, Anthony (2025). HiFIseek: gene-specific enrichment of high-impact mutations in associated genomic regions. bioRxiv (preprint article). doi: 10.1101/2025.06.12.659305. Full text in Research Archive Show summary

  Transcription is regulated through the sequence-specific binding of transcription factors (TFs) to cis-regulatory regions (CRRs). Although scattered along the genome, multiple CRRs are brought in close spatial proximity to the genes they regulate through the formation of DNA loops. The sequence component of transcriptional regulation suggests that DNA variants in CRRs could disrupt TF-DNA interactions and gene regulatory networks through a cascading effect. To date, only a few cases of recurrent cis-regulatory variants have been described. As an alternative to variant recurrence, some methods utilize genomic annotations that indicate the functional impact (FI) of a variant and the CRRs of each gene to detect the enrichment of high-impact cis-regulatory variants (CRVs). However, the agreement across the different associations and FI scoring methods remains unexplored. This work demonstrates that gene-CRR and FI scoring methods exhibit little consensus, highlighting the impact of the choice of a specific CRR-score combination in a given analysis. In addition, we demonstrate that cancer genes exhibit a higher frequency of FI variants compared to non-cancer genes. Based on this, we developed HiFIseek, a Snakemake pipeline exploring the enrichment of FI variants in associated genomic regions using all region-score combinations and two enrichment detection methods. We apply HiFIseek to detect genes exhibiting high FI CRVs in eight cancer cohorts and a set of breast cancer risk-associated single-nucleotide polymorphisms (SNPs). In the cancer cohorts, we observe a small degree of agreement across CRR-score combinations. Although HiFIseek detected known cancer-related genes with FI CRVs, most of them did not show significant changes in their expression. In the SNPs cohort, HiFIseek found small consensus across CRR-score combinations. However, one of the combinations returned 18 known cancer-related genes, including BRCA1 , showing an enrichment of high-impact CRVs.

• Nothnagel, Patrizia Maria Christiane; Meslin, Paul-Arthur Richard; Wik, Jonas Aakre; Strøm, Yunna Erika; Bjørås, Magnar & Enserink, Jorrit [Show all 10 contributors for this article] (2025). Transient SUMOylation Inhibition In Human Pre-adipocytes Stably Imprints a Transcriptional Beiging Fate. bioRxiv (preprint article). 54(6). doi: 10.1101/2025.03.07.642034. Full text in Research Archive Show summary

  Abstract SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how transient perturbation of the SUMO pathway impacts adipocyte plasticity remains unclear. Here we show that brief pharmacologic inhibition of SUMO conjugation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Transient TAK-981 exposure before adipogenic induction produces long-lasting changes in the transcriptome and metabolism of mature adipocytes, including robust induction of canonical beiging markers like UCP1 and increased mitochondrial respiration. Mechanistically, ATAC-seq and transcription factor footprinting revealed immediate and durable chromatin remodeling and early mobilization of CEBP family members, followed by stable activation of CEBPA and PPARG regulatory networks. ChIP experiments demonstrated loss of H3K27me3 and gain of H3K27ac at PPAR response elements within key thermogenic enhancers, with increased PPARG occupancy across the UCP1 regulatory unit. This mechanism is enforced by enhanced cAMP-PKA-p38 signaling, and stabilization of beiging transcriptional activators. Our data support a model in which transient relief of SUMO-mediated repression unlocks dominant regulatory units, notably the UCP1 enhancer cluster, producing a monomorphic, cell type specific reprogramming toward adaptive thermogenesis. These findings identify SUMOylation as a reversible epigenetic barrier to adipocyte beiging and suggest that temporally controlled SUMO pathway inhibition combined with PPARG activation could be exploited to modulate adipose tissue thermogenic capacity. Graphical abstract SUMOylation restricts de novo differentiation of pre-adipocytes into beige adipocytes by repressing cAMP signaling and preventing epigenetic and transcriptional reprogramming of white adipocytes.

• Zeitlinger, Julia; Roy, Sushmita; Ay, Ferhat; Mathelier, Anthony; Medina-Rivera, Alejandra & Mahony, Shaun [Show all 8 contributors for this article] (2025). Perspective on recent developments and challenges in regulatory and systems genomics. Bioinformatics Advances. 5(1). doi: 10.1093/bioadv/vbaf106. Full text in Research Archive Show summary

  Abstract Summary: Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective, we discuss recent computational progress and challenges toward solving this fundamental problem. We describe how cis-regulatory elements are mapped with various genomics assays and how studies of the 3D chromatin organization could help identifying long-range regulatory effects. We discuss how the cis-regulatory sequence rules can be learned and interpreted with sequence-to-function neural networks, with the goal of identifying genetic variants in human disease. We also describe current methods for mapping gene regulatory networks to describe biological processes. We point out current gaps in knowledge along with technical limitations and benchmarking challenges of computational methods. Finally, we discuss newly emerging technologies, such as spatial transcriptomics, and outline strategies for creating a more general model of the cis-regulatory code that is more broadly applicable across cell types and individuals.

• Baydar, Damla Övek; Rauluseviciute, Ieva; Aronsen, Dina Ruud; Blanc-Mathieu, Romain; Bonthuis, Ine & de Beukelaer, Herman [Show all 34 contributors for this article] (2025). JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models. Nucleic Acids Research (NAR). ISSN 0305-1048. 54(D1), p. D184–D193. doi: 10.1093/nar/gkaf1209. Full text in Research Archive Show summary

  Abstract JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding profiles for transcription factors (TFs) as position frequency matrices (PFMs) for over 20 years. We expanded the CORE (306 new profiles, 12% increase) and UNVALIDATED (433, 60% increase) collections with new PFMs and updated 13 existing profiles. We updated the TF binding site predictions and genome tracks for eight species. TF binding profile clusters and familial TF binding sites were updated accordingly. We integrate the inMOTIFin software to easily simulate regulatory sequences using JASPAR PFMs. To enrich TFs’ annotations, we provide scientific literature-based human TF target information. Notably, this release features a deep learning (DL) collection, providing a paradigm shift in modeling and characterizing TF–DNA interactions with 1259 BPNet models trained on Homo sapiens ENCODE chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from 240 TFs and interpreted to reveal predictive motif patterns for the models. The motifs associated with the same TF were clustered to provide a summary of the binding properties, resulting in 240 primary and 113 alternative motif patterns in the DL collection. The JASPAR 2026 collections lay a foundation for future endeavors in genomic research, serving the scientific community in uncovering the mechanisms of gene regulation.

• Canals, Mateu Montserrat; Schnelle, Kilian; Leipart, Vilde; Halskau, Øyvind; Amdam, Gro Vang & Moeller, Arne [Show all 8 contributors for this article] (2025). Cryo-EM structure of native honey bee vitellogenin. Nature Communications. 16(1). doi: 10.1038/s41467-025-58575-y. Full text in Research Archive Show summary

  Vitellogenin (Vg) is the main yolk precursor lipoprotein in almost all egg-laying animals. In addition, along its evolutionary history, Vg has developed a range of new functions in different taxa. In the honey bee, Vg has functions related to immunity, antioxidant protection, social behavior and longevity. However, the molecular mechanisms underlying Vg functionalities are still poorly understood. Here, we report the cryo-EM structure of full-length honey bee Vg, one-step purified directly from hemolymph. The structure provides structural insights into the overall domain architecture, including the lipid binding cavity and the previously uncharacterized von Willebrand factor type D domain. A domain of unknown function has been identified as a C-terminal cystine knot domain based on structural homology. Information about post-translational modifications, cleavage products, metal and lipid binding allow an improved understanding of the mechanisms underlying the range of Vg functionalities. The findings have numerous implications for the structure-function relationship of vitellogenins of other species as well as members of the same protein superfamily, which share the same structural elements.

• Ahmad, Ahmad Ali; Mors, Mira; Carrer, Manuel; Li, Xinmeng; Bilokapić, Silvija & Halić, Mario [Show all 8 contributors for this article] (2025). Structure and dynamics of 2x(CENP-A/H4)2 octasome reveal a possible intermediate in centromeric chromatin. Life Science Alliance (LSA). 9(3). doi: 10.26508/lsa.202503377. Full text in Research Archive Show summary

  The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the constitutive centromere-associated network (CCAN) of proteins. In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently, the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryo-EM structure of 2x(CENP-A/H4)2 octasomes assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)2 tetrasomes might serve as a platform for CCAN organization.

• Labun, Kornel; Rio, Oline Eriksen; Tjeldnes, Håkon; Swirski, Michał; Komisarczuk, Anna Zofia & Haapaniemi, Emma Maria [Show all 7 contributors for this article] (2025). CHOPOFF: symbolic alignments enable fast and sensitive CRISPR off-target detection. bioRxiv - the preprint server for biology. doi: 10.1101/2025.01.06.603201. Full text in Research Archive Show summary

  ABSTRACT CRISPR/Cas systems offer powerful tools for genome editing, but their therapeutic application is hampered by the risk of unintended off-target mutations. Many molecular methods have been established to detect off-target editing, however, their sensitivity depends on first identifying potential sites using in silico methods. However, these in silico prediction methods are challenged by a trade-off between speed and sensitivity, and can fail to comprehensively detect all edited off-target sites. Here, we demonstrate that ignoring bulges has led to missing editing at off-target sites in previous studies and that continuing this practice can lead to inflated claims of fidelity. As a solution, we introduce the concept of symbolic alignments to efficiently identify off-targets without sacrificing sensitivity. We further present specialized data structures that enable rapid, alignment-free probabilistic ranking of guide RNAs based on their predicted off-target burden. Implemented in the tool CHOPOFF, these innovations accommodate mismatches, bulges (insertions/deletions), and incorporate genomic sequence variants for personalized off-target assessment. Benchmarking demonstrates that CHOPOFF significantly outperforms state-of-the-art tools in both prediction accuracy and computational speed. Availability CHOPOFF command line available at https://github.com/JokingHero/CHOPOFF.jl CHOPOFF web server available at https://crisprtools.org/chopoff

• Kopcil, Pavel; Ervik, Carolina W.; Reint, Ganna; Mamia, Katariina; Szymanska, Monika & Dahal-Koirala, Shiva [Show all 17 contributors for this article] (2025). Editing of ADA2 Point Mutation in Human Hematopoietic Stem Cells. bioRxiv (preprint article). doi: 10.1101/2025.08.14.670303. Full text in Research Archive Show summary

  Abstract Background The homozygous ADA2 : c.506G>A (p.Arg169Gln; p.R169Q) variant accounts for majority of Deficiency in Adenosine Deaminase 2 (DADA2). This monogenic disorder may be amenable to ex vivo gene therapy by correcting the pathogenic mutation in CD34+ hematopoietic stem and progenitor cells (HSPCs). Objective To apply CRISPR-Cas9 and homology-directed repair (HDR) as a surrogate strategy to model correction of the pathogenic ADA2 c.506G>A variant in healthy cord blood HSPCs. Methods HSPCs were electroporated with optimised CRISPR-Cas9 editing reagents, and editing outcomes, including HDR and on-target deletions, were quantified by ddPCR. Cell functionality was assessed through colony-forming unit (CFU) assays and by xenotransplantation into NOD SCID Gamma (NSG) mice. Two HDR enhancement strategies were tested: (1) genetic inhibitors of p53 and non-homologous end joining (NHEJ) pathways, and (2) pharmacological NHEJ inhibition. Results Small-molecule NHEJ inhibitors increased HDR efficiency approximately two-fold (from ∼40 % to ∼80 %). Edited HSPCs retained normal CFU capacity and successfully engrafted in NSG mice. However, up to 8 % of edited cells exhibited on-target chromosome loss, though this declined over time. Up to 40 % of T cells and fibroblasts demonstrated similar losses under NHEJ inhibitors treatment. In contrast, genetically encoded inhibitors did not improve HDR. Conclusion The ADA2 p. c.506G>A variant can be effectively edited employing surrogate strategy in HSPCs without impairing functionality. Although pharmacological inhibition of NHEJ enhances HDR efficiency, it also increases the risk of on-target chromosome aberrations, highlighting the need for careful consideration of the associated risks and benefits in therapeutic gene editing. Key messages 1) The ADA2 p.R169Q variant can be efficiently corrected via HDR, and the edited CD34+ HSPCs retain their engraftment capability in NSG mice. 2) Pharmacological inhibition of NHEJ using small-molecule inhibitors increases HDR efficiency but is associated with significant on-target deletions and chromosomal arm loss, particularly in differentiated cell types, and in a donor-dependent manner. Capsule summary The ADA2 p.R169Q variant is a viable target for precision gene editing in hematopoietic stem cells. Although inhibition of NHEJ improves HDR efficiency, it concomitantly increases the risk of large on-target deletions, particularly in differentiated cells.

• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Labun, Kornel; Li, Zhuokun; Komisarczuk, Anna Zofia & Keskitalo, Salla [Show all 32 contributors for this article] (2025). Precision T cell correction platform for Inborn Errors of Immunity. Molecular Therapy. ISSN 1525-0016. 33(11), p. 5624–5643. doi: 10.1016/j.ymthe.2025.08.018. Full text in Research Archive Show summary

  CRISPR/Cas9 gene editing is a promising tool to correct pathogenic variants for autologous cell therapies targeting Inborn errors of immunity (IEI). Current strategies, such as gene knockout or cDNA knock-in, address many single-gene defects but can disrupt gene expression, highlighting the need for precise correction platforms. While transplanting corrected autologous hematopoietic stem cells is a curative approach, it is unsuitable for patients with advanced disease, inflammation or acute infections. As correcting T cells is an alternative therapeutic strategy for lymphoid IEIs, we present an efficient T cell single nucleotide variant (SNV) correction platform based on homology-directed repair (HDR). By using STAT1 gain-of-function (STAT1-GOF), Cartilage Hair Hypoplasia (CHH), Deficiency of ADA2 (DADA2), and Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) as IEI models, we demonstrate that our platform achieves up to 80% correction, with resultant functional correction of the disease phenotype in the selected models. Furthermore, we performed safety profiling using GUIDE-seq, single-cell RNA sequencing, long-read genome sequencing, and proteomics analysis and detected no genomic, transcriptomic, or proteomic aberrations. This study establishes HDR-based SNV editing as a portable method for developing clinical autologous T cell therapies and represents a promising step toward a broad-spectrum gene correction platform for treating diverse monogenic immune disorders.

• Kaustio, Meri; Szymanska, Monika; Li, Weiwei; Braathen, Ragnhild Selvig; Campbell, Tessa M. & Haugen, Frida Loe [Show all 23 contributors for this article] (2025). Heterozygous loss of MAP4K1 causes immune dysregulation by amplifying T-cell responses. Journal of Allergy and Clinical Immunology. ISSN 0091-6749. 156(4), p. 1024–1037. doi: 10.1016/j.jaci.2025.07.010. Full text in Research Archive Show summary

  Background MAP4K1 encodes hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase that negatively regulates T-cell receptor signaling via phosphorylation of the adaptor proteins SLP-76 (Src homology 2 domain-containing leukocyte protein of 76 kDa) and Gads. While common MAP4K1 variants have been implicated in polygenic immune-mediated diseases, the impact of rare germline variants on human immunity remains undefined. Objective We investigated the immunologic and functional consequences of HPK1 deficiency in individuals with suspected inborn errors of immunity. Methods We performed genomic linkage analysis and exome sequencing to identify disease-associated variants in patients with inborn errors of immunity. Immunophenotyping, RNA sequencing, and functional assays were conducted on patient-derived lymphocytes, complemented by CRISPR-Cas9–mediated MAP4K1 disruption and correction in primary T cells. Results Heterozygous MAP4K1 loss-of-function variants were identified in two kindreds presenting with diverse immune dysregulatory symptoms, including recurrent fevers, inflammatory arthritis, Epstein-Barr virus–related complications, and nephritis. These variants led to reduced HPK1 protein levels and SLP-76Ser376 phosphorylation. While lymphocyte development was largely preserved, T cells from HPK1-deficient individuals displayed hyperresponsiveness to T-cell receptor stimulation, characterized by elevated secretion of proinflammatory cytokines, particularly IFN-γ and TNF. CRISPR-Cas9–mediated knockout recapitulated, and variant correction partially reversed this phenotype. Transcriptomic profiling of stimulated CD4+ T cells further revealed upregulation of immune signaling pathways—including NF-κB, JAK/STAT, and AP-1—as well as increased expression of multiple T-cell cytokines, consistent with enhanced T-cell receptor signaling and T-cell responses in HPK1-deficient individuals. Conclusion HPK1 deficiency, caused by heterozygous loss of MAP4K1, is a novel monogenic cause of immune dysregulation. Increased T-cell activation and proinflammatory cytokine production are implicated in disease pathogenesis

• Hovan, Ladislav & Kuijjer, Marieke (2025). SPONGE: Simple Prior Omics Network GEnerator. Bioinformatics. ISSN 1367-4803. 41(7). doi: 10.1093/bioinformatics/btaf320. Full text in Research Archive Show summary

  Gene regulatory networks modelled from experimental data can be improved through the use of prior biological knowledge, e.g. transcription factor binding. There are several tools that utilize this information. However, the prior networks used with them are often not updated and may fail to reflect the most up-to-date information. Here we present SPONGE, a Python module designed to access information across biological databases, chiefly JASPAR and STRING, to model two types of networks—a prior gene regulatory network mapping transcription factors to genes based on their predicted binding sites, and a prior protein-protein interaction network mapping potential interactions between transcription factors. SPONGE is mainly designed to work with the PANDA algorithm and the corresponding NetZoo family of tools. However, the networks are provided in an easily adaptable format for other tools. SPONGE was designed with ease of use in mind, and it provides sensible default values for all of its parameters while giving the users the freedom to fine-tune them. Availability and implementation The code for the Python module and the documentation can be found in our GitHub repository.

• Luis, Almazán, Jorge; Bolivar, Arcos-Encarnación,; Isabel, Barón-Mendoza,; Nohemi, Camacho-Concha,; Eladio, Cortes-Flores, & Sol, Díaz de León-Guerrero, [Show all 15 contributors for this article] (2025). KChIP3 fosters neuroinflammation and synaptic dysfunction in the 5XFAD mouse model of Alzheimer’s disease | Journal of Neuroinflammation | Full Text. Journal of Neuroinflammation. 22(160). doi: 10.1186/s12974-025-03426-2. Full text in Research Archive Show summary

  Alzheimer’s disease (AD) is a progressive neurodegenerative disorder marked by β-amyloid (βA) accumulation, neuroinflammation, excessive synaptic pruning, and cognitive decline. Despite extensive research, effective treatments remain elusive. Here, we identify potassium channel-interacting protein 3 (KChIP3) as a key driver of AD pathology using the 5XFAD mouse model. KChIP3 levels were significantly elevated in the hippocampus of 5XFAD mice, correlating with βA burden and neuroinflammation. This upregulation was triggered by inflammatory signaling via the NLRP3 inflammasome and Caspase-1 activation. Notably, genetic deletion of KChIP3 (5XFAD/KChIP3−/−) markedly reduced βA plaque deposition, pro-inflammatory cytokines, reactive gliosis, and expression of inflammation-related proteins (APO, CLU, MDK). Transcriptomic and proteomic analyses revealed restored synaptic markers (CD47, CD200, CACNB4, GDA) and a shift of the disease-associated microglial (DAM-1) phenotype. Mechanistically, we propose that KChIP3 amplifies AD pathology through two key mechanisms: (1) sustaining neuroinflammation by upregulating pro-inflammatory genes and (2) impairing synaptic integrity by repressing genes critical for neuronal function. Consistently, KChIP3 deletion enhanced dendritic complexity, synaptic plasticity, and cognitive performance in 5XFAD mice. These findings position KChIP3 as a potential therapeutic target for mitigating neuroinflammation and synaptic dysfunction in AD and highlight its potential as a biomarker for disease progression.

• Pop, Romana Tabita; Hsieh, Ping-Han; Belova, Tatiana; Mathelier, Anthony & Kuijjer, Marieke (2025). Gene regulatory network integration with multi-omics data enhances survival predictions in cancer. Briefings in Bioinformatics. ISSN 1467-5463. 26(4). doi: 10.1093/bib/bbaf315. Full text in Research Archive Show summary

  The emergence of high-throughput omics technologies has resulted in their wide application to cancer studies, greatly increasing our understanding of the disruptions occurring at different molecular levels. To fully harness these data, integrative approaches have emerged as essential tools, enabling the combination of multiple omics modalities to uncover disease mechanisms. However, many such approaches overlook gene regulatory mechanisms, which play a central role in the development and progression of cancer. Patient-specific gene regulatory networks (GRNs), representing interactions between regulators (such as transcription factors) and their target genes in each individual tumour, offer a powerful framework to bridge this gap and investigate the regulatory landscape of cancer. In this study, we introduce a novel approach for integrating patient-specific GRNs with multi-omic data and assess whether their inclusion in joint dimensionality reduction models improves survival prediction across multiple cancer types. By applying our method on ten cancer datasets from The Cancer Genome Atlas, we demonstrate that incorporating GRNs enhances associations with patient survival in several cancer types. Focusing on liver cancer, with validation in independent data, our methodology identifies potential mechanisms of gene regulatory dysregulation associated with cancer progression. These were linked to dysregulated fatty acid metabolism, and identified JUND as a potential novel transcriptional regulator driving these processes. Our findings highlight the value of network-based multi-omics integration for uncovering clinically relevant regulatory mechanisms and improving our understanding of cancer biology at the patient-specific level.

• Ullern, Halvor; Schnur, Paulina; Boccara, Charlotte & Knævelsrud, Helene (2025). Rest, Repair, Repeat: The Complex Relationship of Autophagy and Sleep. Journal of Molecular Biology (JMB). ISSN 0022-2836. 437(18). doi: 10.1016/j.jmb.2025.169227. Full text in Research Archive Show summary

  Autophagy and sleep are two evolutionary conserved mechanisms across the animal kingdom. Autophagy is a pathway for the degradation of cytoplasmic material in the lysosome, playing important roles in the homeostasis and health of the organism. On the other hand, sleep is a homeostatically regulated state with numerous presumed essential roles, including the restoration of tissue and physiological functions, such as brain waste clearance via the activation of the glymphatic systems. Given that sleep and autophagy are crucial processes tightly linked to homeostasis and maintenance of good health, understanding how they interact is of great interest, especially as sleep quality decreases in our modern 24-hour societies. Autophagy represents a promising target for therapeutic interventions in this context. Here, we review the contrasted and complementary roles of autophagy and sleep in maintaining homeostasis. Specifically, we focus on recent evidence suggesting that sleep impairment may increase autophagy, while autophagosome levels may modulate the amount of sleep. We discuss outstanding questions at the intersection of these two fields, highlighting methodological shortcomings in the current literature. Overcoming these limitations will be instrumental to design new experiments with the aim of answering one of the greatest mysteries of our time – why do we sleep?

• Patel, Divyeshkumar Amrubthai; Tiusanen, Ville; Karttunen, Konsta; Pihlajamaa, Paivi & Sahu, Biswajyoti (2025). Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes. Communications Biology. 8. doi: 10.1038/s42003-025-08413-0. Full text in Research Archive Show summary

  Derepression of transposable elements (TE) by epigenetic therapy leads to the activation of immune response in cancer cells. However, the molecular mechanism of TE regulation by distinct chromatin modifier enzymes (CME) in context of p53 is still elusive. Here, we used FDA-approved epigenetic drugs to systematically inhibit distinct CMEs in p53 wild-type and p53-mutant colorectal, esophageal, and prostate cancer cells. We show that distinct TE subfamilies are derepressed by inhibition of different CMEs in cell type-specific manner. Co-inhibition of DNMT and HDAC (DNMTi-HDACi) had the most consistent effect across cancer types. Loss of p53 results in stronger TE activation and TE-chimeric transcript expression and this effect is largely mediated by the non-genomic actions of p53. Robust immune response elicited by DNMTi-HDACi is due to induced inverted repeat Alu expression concomitant with reduced ADAR1-mediated Alu RNA editing. Collectively, our systematic analyses provide insights for rational use of epigenetic therapies in distinct cancers.

• Begum, Most Champa; Belova, Tatiana; Dieseth, Jon Arne; Yang, Ennian; Mosleth, Ellen Færgestad & Uhlen, Anne Kjersti [Show all 7 contributors for this article] (2025). QTL mapping of preharvest sprouting resistance in bread wheat population SHA3/CBRD by Naxos confirms a negative effect of the 1BL.1RS translocation on falling number. Crop Science. ISSN 0011-183X. 65(1), p. 1–18. doi: 10.1002/csc2.21320. Full text in Research Archive Show summary

  Preharvest sprouting (PHS) is a serious problem in wheat (Triticum aestivum L.)production areas with rainy harvest conditions. To explore the genetic control ofPHS resistance, a population of 166 recombinant inbred lines from a cross betweenSHA3/CBRD and Naxos was evaluated in a total of eight field trials in Norway andChina. PHS resistance was evaluated with both germination index (GI) and fallingnumber (FN). A total of 15 PHS-related quantitative trait loci (QTLs) were detected atchromosome arms 1RS, 2DL, 3BL, 4AL, 4BS, and 7BL. At 2DL and 3BL, QTLs forboth GI and FN were detected in proximity to each other with PHS resistance fromSHA3/CBRD, indicating a common genetic control of the two traits at these loci.At 4AL, a significant QTL for GI was detected with seed dormancy contributed byNaxos. Moreover, the Rht-B1b dwarfing allele contributed by SHA3/CBRD showeda positive association with FN. On the other hand, QFN.nmbu-1RS, carried by the1BL.1RS translocation in SHA3/CBRD showed consistent negative effects on FNacross all field trials where FN was measured. However, it did not have any notableeffect on GI. The negative effect of QFN.nmbu-1RS on FN was validated on a set of113 wheat cultivars and breeding lines, where lines carrying the 1BL.1RS translo-cation showed significantly lower FN in 12 out of 14 independent field trials. TheQTL and associated markers identified in this study will aid the breeding of morePHS-resistant wheat cultivars.

• Wei, Qian; Foyn, Håvard; Landskron, Johannes; Wang, Shixiong; Rye, Inga Hansine & Skånland, Sigrid S [Show all 10 contributors for this article] (2025). Identification of a group of 9-amino-acridines that selectively downregulate regulatory T cell functions through FoxP3. iScience. 28(3). doi: 10.1016/j.isci.2025.111931. Full text in Research Archive Show summary

  FoxP3+ regulatory T cells (Tregs) are responsible for immune homeostasis by suppressing excessive anti-self-immunity. Tregs facilitate tumor growth by inhibiting anti-tumor immunity. Here, we explored the targeting of FoxP3 as a basis for new immunotherapies. In a high-throughput phenotypic screening of a drug repurposing library using human primary T cells, we identified quinacrine as a FoxP3 downregulator. In silico searches based on the structure of quinacrine, testing of sub-libraries of analogs in vitro, and validation identified a subset of 9-amino-acridines that selectively abrogated Treg suppressive functions. Mechanistically, these acridines interfered with the DNA-binding activity of FoxP3 and inhibited FoxP3-regulated downstream gene regulation. Release from Treg suppression by 9-amino-acridines increased anti-tumor immune responses both in cancer patient samples and in mice in a syngeneic tumor model. Our study highlights the feasibility of screening for small molecular inhibitors of FoxP3 as an approach to pursuing Treg-based immunotherapy.

• Souza, Suiane Lima de; Asano, Takaki; Glumoff, Virpi; Keskitalo, Salla; Pikkarainen, Keela & Martelius, Timi [Show all 19 contributors for this article] (2025). Pulmonary Aspergillosis and Low HIES Score in a Family with STAT3 N-Terminal Domain Mutation. Journal of Clinical Immunology. ISSN 0271-9142. 45(1). doi: 10.1007/s10875-025-01867-1. Full text in Research Archive
• Lautrup, Sofie Hindkjær; Zhang, Shi-qi; Funayama, Shinichiro; Lirussi, Lisa; Visnovska, Martina & Cheung, Hoi-Hung [Show all 19 contributors for this article] (2025). Decreased mitochondrial NAD+ in WRN deficient cells links to dysfunctional proliferation. Aging. 17(4), p. 937–959. doi: 10.18632/aging.206236. Full text in Research Archive
• Petersson, Marcus; Zingl, Franz G.; Rodriguez-Rodriguez, Everardo; Rendsvig, Jakob K. H.; Heinsøe, Heidi & Arendrup, Emma Wenzel [Show all 16 contributors for this article] (2025). Orally delivered toxin–binding protein protects against diarrhoea in a murine cholera model. Nature Communications. 16. doi: 10.1038/s41467-025-57945-w. Full text in Research Archive Show summary

  The ongoing seventh cholera pandemic, which began in 1961, poses an escalating threat to public health. There is a need for new cholera control measures, particularly ones that can be produced at low cost, for the one billion people living in cholera-endemic regions. Orally delivered VHHs, functioning as target-binding proteins, have been proposed as a potential approach to control gastrointestinal pathogens. Here, we describe the development of an orally deliverable bivalent VHH construct that binds to the B-pentamer of cholera toxin, showing that it inhibits toxin activity in a murine challenge model. Infant mice given the bivalent VHH prior to V. cholerae infection exhibit a significant reduction in cholera toxin–associated intestinal fluid secretion and diarrhoea. In addition, the bivalent VHH reduces V. cholerae colonization levels in the small intestine by a factor of 10. This cholera toxin–binding protein holds promise for protecting against severe diarrhoea associated with cholera.

• Clarke, Alexander W.; Høye, Eirik; Hembrom, Anju Angelina; Paynter, Vanessa Molin; Vinther, Jakob & Wyrozemski, Lukasz [Show all 22 contributors for this article] (2025). MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models. Nucleic Acids Research (NAR). ISSN 0305-1048. 53(D1), p. D116–D128. doi: 10.1093/nar/gkae1094. Full text in Research Archive
• Ciani, Elia; Stormoen, Marit; Antonsen, Stein Ivar; Nilsen, Frank; Jørgensen, Even & Komisarczuk, Anna Zofia (2025). Optimization of calcium oxide treatment against salmon louse (Lepeophtheirus salmonis). A controlled laboratory study. Aquaculture Reports. 43. doi: 10.1016/j.aqrep.2025.102894. Full text in Research Archive
• Mera, Aurora Bernal; Cuminetti, Vincent; Serulla, Marc; Florit, Adrian; Konieczny, Joanna & Golnarnik, Golnaz [Show all 12 contributors for this article] (2025). Bone marrow sympathetic neuropathy is a hallmark of hematopoietic malignancies and it involves severe ultrastructural damage. Experimental Hematology & Oncology. 14. doi: 10.1186/s40164-025-00614-x. Full text in Research Archive Show summary

  The hematopoietic stem cell (HSC) niche in the bone marrow (BM) supports HSC function, fate and numbers [1]. Sympathetic fibres innervate the BM and are components of the hematopoietic stem and progenitor cell (HSPC) niche [2]. Neuropathy of the HSPC niche is present and essential for disease development in experimental models of JAK2V617F+ myeloproliferative neoplasms (MPN) and MLL-AF9+ acute myeloid leukemia (AML), and it is present in the BM of human MPN and AML patients [3–6]. Neuropathy contributes to mutant HSC expansion and represents an effective therapeutic target to block disease progression in JAK2V617F+ MPN mice [3]. The sympathomimetic agonist mirabegron restored nestin+ cells and reduced reticulin fibrosis in MPN patients [7]. Here, we show that neuropathy of the HSPC niche emerges in two additional experimental models of hematological disease including pre-leukemic myelopoiesis driven by NRASG12D and lymphoma/lymphoblastic leukemia driven by p53 deletion. Neuropathy involves severe ultrastructural damage in NRASG12D+ mice and AML patients as shown by electron microscopy. When further reinforced chemically, neuropathy has a profound impact on the experimental NRASG12D mouse model, promoting myeloid bias, reducing HSPC numbers and inducing changes in the stem cell microenvironment that include reduced numbers of mesenchymal stromal cells (MSC) and increased presence of morphologically abnormal blood vessels in BM. Together, BM neuropathy is a prevalent factor in hematopoietic malignancies that involves important degradation of sympathetic fibres and contributes to disease in a different manner depending on the driver mutation. This should be taken in consideration in the clinic, given that chemotherapy induces neuropathy of the HSC niche [8] and it is the most frequent first line treatment for AML, acute lymphoblastic leukemia and MPN patients.

• Diaz, Nuria Garcia; Solli, Elise; Hajjar, Ehsan; Cornillot‐Clément, Selma; Landskron, Johannes & Ahmad, Rafi [Show all 8 contributors for this article] (2025). MAPK and STAT3 Inhibitors Modulate FoxP3 Expression and Regulatory T Cell Function. European Journal of Immunology. ISSN 0014-2980. 55(2). doi: 10.1002/eji.202451225. Full text in Research Archive Show summary

  Regulatory T cells (Tregs) are a subset of T cells defined by the expression of Forkhead box protein P3 (FoxP3) playing a crucial role in regulating effector T cell activity. Tregs accumulate in the tumor microenvironment facilitating tumor growth. Thus, targeting FoxP3+ Tregs could improve cancer immunotherapies. Here, we conducted a high-throughput, phenotypic screening of a drug repurposing library to identify compounds downregulating FoxP3 expression in human primary T cells. We identified the tyrosine kinase inhibitor bosutinib and the STAT3 inhibitor nifuroxazide effectively downregulating FoxP3 expression. To identify more potent compounds, structural analogs of these two compounds were searched and validated. These analogs were found to reduce FoxP3 expression in a similar- or more potent manner than the original hits. All compounds inhibited Treg suppressive functions and reduced the expression of Treg activation markers. Importantly, bosutinib disrupted FAK and CaMKII signaling more potently in Tregs, whilst nifuroxazide and its analog NA16 targeted STAT3 protein levels more effectively in Tregs. Additionally, bosutinib and NA16 targeted effector Tregs more effectively than other Treg subsets. In summary, bosutinib, nifuroxazide, and their analogs inhibited FoxP3 expression, Treg suppressive abilities, and Treg activation effectively, which could serve as tools for the improvement of current cancer immunotherapies.

• Ryskulov, Ruslan; Pedrueza-Villalmanzo, Esteban; Tatli, Yagiz Alp; Gözen, Irep & Jesorka, Aldo (2024). Complete de-wetting of lipid membranes on silicon carbide. The European Physical Journal Special Topics (EPJ - Special Topics (EPJ ST)). ISSN 1951-6355. doi: 10.1140/epjs/s11734-024-01259-3. Full text in Research Archive
• Struck, Eike Christopher; Belova, Tatiana; Hsieh, Ping-Han; Odeberg, Jacob Olof; Kuijjer, Marieke & Dusart, Philip James [Show all 7 contributors for this article] (2024). Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF. Journal of Immunology. ISSN 0022-1767. 212(1), p. 117–129. doi: 10.4049/jimmunol.2300419. Full text in Research Archive Show summary

  The vascular endothelium acts as a dynamic interface between blood and tissue. TNF-α, a major regulator of inflammation, induces endothelial cell (EC) transcriptional changes, the overall response dynamics of which have not been fully elucidated. In the present study, we conducted an extended time-course analysis of the human EC response to TNF, from 30 min to 72 h. We identified regulated genes and used weighted gene network correlation analysis to decipher coexpression profiles, uncovering two distinct temporal phases: an acute response (between 1 and 4 h) and a later phase (between 12 and 24 h). Sex-based subset analysis revealed that the response was comparable between female and male cells. Several previously uncharacterized genes were strongly regulated during the acute phase, whereas the majority in the later phase were IFN-stimulated genes. A lack of IFN transcription indicated that this IFN-stimulated gene expression was independent of de novo IFN production. We also observed two groups of genes whose transcription was inhibited by TNF: those that resolved toward baseline levels and those that did not. Our study provides insights into the global dynamics of the EC transcriptional response to TNF, highlighting distinct gene expression patterns during the acute and later phases. Data for all coding and noncoding genes is provided on the Web site (http://www.endothelial-response.org/). These findings may be useful in understanding the role of ECs in inflammation and in developing TNF signaling–targeted therapies.

• Osorio, Daniel; Capasso, Anna; Eckhardt, S. Gail; Giri, Uma; Somma, Alexander & Pitts, Todd M. [Show all 14 contributors for this article] (2024). Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. Nature Computational Science. doi: 10.1038/s43588-024-00597-5. Full text in Research Archive Show summary

  Single-cell technologies enable high-resolution studies of phenotype-defining molecular mechanisms. However, data sparsity and cellular heterogeneity make modeling biological variability across single-cell samples difficult. Here we present SCORPION, a tool that uses a message-passing algorithm to reconstruct comparable gene regulatory networks from single-cell/nuclei RNA-sequencing data that are suitable for population-level comparisons by leveraging the same baseline priors. Using synthetic data, we found that SCORPION outperformed 12 existing gene regulatory network reconstruction techniques. Using supervised experiments, we show that SCORPION can accurately identify differences in regulatory networks between wild-type and transcription factor-perturbed cells. We demonstrate SCORPION’s scalability to population-level analyses using a single-cell RNA-sequencing atlas containing 200,436 cells from colorectal cancer and adjacent healthy tissues. The differences between tumor regions detected by SCORPION are consistent across multiple cohorts as well as with our understanding of disease progression, and elucidate phenotypic regulators that may impact patient survival.

• Nieoczym, Dorota; Marszalek-Grabska, Marta; Szalak, Radoslaw; Kundap, Uday; Kaczor, Agnieszka A. & Wrobel, Tomasz M. [Show all 16 contributors for this article] (2024). A comprehensive assessment of palmatine as anticonvulsant agent – In vivo and in silico studies. Biomedicine & Pharmacotherapy. ISSN 0753-3322. 172. doi: 10.1016/j.biopha.2024.116234. Full text in Research Archive
• Ferenc, Katalin Terezia; Rauluseviciute, Ieva; Hovan, Ladislav; Kumar, Vipin; Kuijjer, Marieke & Mathelier, Anthony (2024). Improving bioinformatics software quality through teamwork. Bioinformatics. ISSN 1367-4803. 40(11). doi: 10.1093/bioinformatics/btae632. Full text in Research Archive Show summary

  Since high-throughput techniques became a staple in biological science laboratories, computational algorithms, and scientific software have boomed. However, the development of bioinformatics software usually lacks software development quality standards. The resulting software code is hard to test, reuse, and maintain. We believe that the root of inefficiency in implementing the best software development practices in academic settings is the individualistic approach, which has traditionally been the norm for recognizing scientific achievements and, by extension, for developing specialized software. Software development is a collective effort in most software-heavy endeavors. Indeed, the literature suggests teamwork directly impacts code quality through knowledge sharing, collective software development, and established coding standards. In our computational biology research groups, we sustainably involve all group members in learning, sharing, and discussing software development while maintaining the personal ownership of research projects and related software products. We found that group members involved in this endeavor improved their coding skills, became more efficient bioinformaticians, and obtained detailed knowledge about their peers’ work, triggering new collaborative projects. We strongly advocate for improving software development culture within bioinformatics through collective effort in computational biology groups or institutes with three or more bioinformaticians.

• Imbery, John Franklin; Wiik, Celina Marie; Heinzelbecker, Julia; Jebsen, Jenny Karoline; Dobbing, Mia K. & Bottini, Nunzio [Show all 12 contributors for this article] (2024). CD38 regulates chronic lymphocytic leukemia proliferation via CD45 phosphatase activity. Molecular Therapy: Oncology. 32(3), p. 1–15. doi: 10.1016/j.omton.2024.200841. Full text in Research Archive Show summary

  Chronic lymphocytic leukemia (CLL) growth is dependent on both B cell receptor (BCR) signaling and signals from microenvironmental T helper (Th) cells. We previously described a mechanism where Th cells enhance BCR signaling and proliferation through CD45 phosphatase activity regulation via galectin-1 and CD43. The CLL negative prognostic indicator CD38 is linked to BCR signaling and proliferation, with its expression induced by Th cells. Here, we explore a link between CD38 and CD45 phosphatase activity regulation using patient-derived material in a Th-CLL cell co-culture model. Results demonstrate CD43 and galectin-1 are co-expressed with CD38, defining proliferative CLL cells with augmented CD45 activity. CD38 enzymatic and receptor inhibition regulated CD43 and galectin-1 expression, CD45 activityhi populations, and CLL proliferation, while leaving Th cells largely unaffected. Mechanistically, CD38- or LGALS1 (galectin-1)-deficient malignant B cell lines further confirmed CD38-mediated regulation of CD45 activity and BCR signaling through CD43 expression and galectin-1 surface binding, while galectin-1 contributed to CD43/CD45 colocalization. Together, this highlights CD38 as an important regulator of CD45 activity via CD43 and galectin-1, in turn acting as a positive modulator of CLL proliferation. Ultimately, the CD38/CD45 molecular hub could be an important therapeutic target in CLL.

• Schiffer, Philipp H.; Natsidis, Paschalis; Leite, Daniel J.; Robertson, Helen E.; Lapraz, François & Marlétaz, Ferdinand [Show all 20 contributors for this article] (2024). Insights into early animal evolution from the genome of the xenacoelomorph worm Xenoturbella bocki. eLIFE. 13. doi: 10.7554/eLife.94948. Full text in Research Archive Show summary

  The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data can provide important comparative data and help understand the evolution and biology of enigmatic species better. Here, we assemble and analyze the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian evolution. Our highly contiguous genome assembly of X. bocki has a size of ~111 Mbp in 18 chromosome-like scaffolds, with repeat content and intron, exon, and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signaling pathways are also largely complete and most bilaterian miRNAs are present. Overall, we conclude that X. bocki has a complex genome typical of bilaterians, which does not reflect the apparent simplicity of its body plan that has been so important to proposals that the Xenacoelomorpha are the simple sister group of the rest of the Bilateria.

• Lincoln, Matthew R.; Connally, Noah; Axisa, Pierre-Paul; Gasperi, Christiane; Mitrovic, Mitja & Heel, David van [Show all 53 contributors for this article] (2024). Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nature Genetics. ISSN 1061-4036. 56(5), p. 838–845. doi: 10.1038/s41588-024-01732-8. Full text in Research Archive
• Brugger, Melanie; Lauri, Antonella; Zhen, Yan; Gramegna, Laura L.; Zott, Benedikt & Sekulic, Nikolina [Show all 40 contributors for this article] (2024). Bi-allelic variants in SNF8 cause a disease spectrum ranging from severe developmental and epileptic encephalopathy to syndromic optic atrophy. American Journal of Human Genetics. ISSN 0002-9297. 111(3), p. 594–613. doi: 10.1016/j.ajhg.2024.02.005. Full text in Research Archive Show summary

  The endosomal sorting complex required for transport (ESCRT) machinery is essential for membrane remodeling and autophagy and it comprises three multi-subunit complexes (ESCRT I-III). We report nine individuals from six families presenting with a spectrum of neurodevelopmental/neurodegenerative features caused by bi-allelic variants in SNF8 (GenBank: NM_007241.4), encoding the ESCRT-II subunit SNF8. The phenotypic spectrum included four individuals with severe developmental and epileptic encephalopathy, massive reduction of white matter, hypo-/aplasia of the corpus callosum, neurodevelopmental arrest, and early death. A second cohort shows a milder phenotype with intellectual disability, childhood-onset optic atrophy, or ataxia. All mildly affected individuals shared the same hypomorphic variant, c.304G>A (p.Val102Ile). In patient-derived fibroblasts, bi-allelic SNF8 variants cause loss of ESCRT-II subunits. Snf8 loss of function in zebrafish results in global developmental delay and altered embryo morphology, impaired optic nerve development, and reduced forebrain size. In vivo experiments corroborated the pathogenicity of the tested SNF8 variants and their variable impact on embryo development, validating the observed clinical heterogeneity. Taken together, we conclude that loss of ESCRT-II due to bi-allelic SNF8 variants is associated with a spectrum of neurodevelopmental/neurodegenerative phenotypes mediated likely via impairment of the autophagic flux.

• Fernandez, Javier Gutierrez; Hersleth, Hans-Petter & Hammerstad, Marta (2024). The crystal structure of myco­thiol di­sulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria. Acta Crystallographica Section D: Structural Biology. 80(3), p. 181–193. doi: 10.1107/S205979832400113X. Full text in Research Archive Show summary

  Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reduc- tases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future anti- tuberculosis drug development.

• Moussavi, Nastaran; Ent, Wietske van der; Diallo, Drissa; Sanogo, Rokia; Malterud, Karl Egil & Esguerra, Camila V. [Show all 7 contributors for this article] (2024). Inhibition of Seizure-Like Paroxysms and Toxicity Effects of Securidaca longepedunculata Extracts and Constituents in Zebrafish Danio rerio. ACS Chemical Neuroscience. 15(3), p. 617–628. doi: 10.1021/acschemneuro.3c00642. Full text in Research Archive
• Flynn, Aidan; Waszak, Sebastian Martin & Weischenfeldt, Joachim (2024). Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Molecular Systems Biology. doi: 10.1038/s44320-024-00054-5. Full text in Research Archive
• Meijer, Debora M.; Ruano, Dina; Briaire-de Bruijn, Inge H.; Wijers-Koster, Pauline M.; Sande, Michiel A. J. van de & Gelderblom, Hans [Show all 10 contributors for this article] (2024). The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis. Genes, Chromosomes and Cancer. ISSN 1045-2257. 63(7). doi: 10.1002/gcc.23253. Full text in Research Archive
• Ankill, Jørgen; Zhao, Zhi; Tekpli, Xavier; Kure, Elin Wenche Hegland; Kristensen, Vessela N. & Mathelier, Anthony [Show all 7 contributors for this article] (2024). Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. PLoS Computational Biology. ISSN 1553-734X. 20:e1012565(11), p. 1–33. doi: 10.1371/journal.pcbi.1012565. Full text in Research Archive Show summary

  Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations’ precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylation Quantitative Trait Loci (emQTL) analysis to identify deregulated cancer-driving transcriptional networks linked to CpG demethylation pan-cancer. By analyzing 33 cancer types from The Cancer Genome Atlas, we identified and confirmed significant correlations between CpG methylation and gene expression (emQTL) in cis and trans, both across and within cancer types. Bipartite network analysis of the emQTL revealed groups of CpGs and genes related to important biological processes involved in carcinogenesis including proliferation, metabolism and hormone-signaling. These bipartite communities were characterized by loss of enhancer methylation in specific transcription factor binding regions (TFBRs) and the CpGs were topologically linked to upregulated genes through chromatin loops. Penalized Cox regression analysis showed a significant prognostic impact of the pan-cancer emQTL in many cancer types. Taken together, our integrative pan-cancer analysis reveals a common architecture where hallmark cancer-driving functions are affected by the loss of enhancer methylation and may be epigenetically regulated.

• Karttunen, Konsta; Patel, Divyesh & Sahu, Biswajyoti (2024). Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer. Bioessays. ISSN 0265-9247. 46(10). doi: 10.1002/bies.202400059. Full text in Research Archive Show summary

  Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.

• Urbanucci, Alfonso (2024). Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nature Communications. doi: 10.1038/s41467-021-25624-1. Full text in Research Archive
• Rauluseviciute, Ieva; Launay, Timothée; Barzaghi, Guido; Nikumbh, Sarvesh; Lenhard, Boris & Krebs, Arnaud Regis [Show all 8 contributors for this article] (2024). Identification of transcription factor co-binding patterns with non-negative matrix factorization. Nucleic Acids Research (NAR). ISSN 0305-1048. 52(18), p. e85–e85. doi: 10.1093/nar/gkae743. Full text in Research Archive Show summary

  Transcription factor (TF) binding to DNA is critical to transcription regulation. Although the binding properties of numerous individual TFs are well-documented, a more detailed comprehension of how TFs interact cooperatively with DNA is required. We present COBIND, a novel method based on non-negative matrix factorization (NMF) to identify TF co-binding patterns automatically. COBIND applies NMF to one-hot encoded regions flanking known TF binding sites (TFBSs) to pinpoint enriched DNA patterns at fixed distances. We applied COBIND to 5699 TFBS datasets from UniBind for 401 TFs in seven species. The method uncovered already established co-binding patterns and new co-binding configurations not yet reported in the literature and inferred through motif similarity and protein-protein interaction knowledge. Our extensive analyses across species revealed that 67% of the TFs shared a co-binding motif with other TFs from the same structural family. The co-binding patterns captured by COBIND are likely functionally relevant as they harbor higher evolutionarily conservation than isolated TFBSs. Open chromatin data from matching human cell lines further supported the co-binding predictions. Finally, we used single-molecule footprinting data from mouse embryonic stem cells to confirm that the COBIND-predicted co-binding events associated with some TFs likely occurred on the same DNA molecules.

• Green, Darrell; Ewijk, Roelof van; Tirtei, Elisa; Andreou, Dimosthenis; Baecklund, Fredrik & Baumhoer, Daniel [Show all 56 contributors for this article] (2024). Biological Sample Collection to Advance Research and Treatment: A Fight Osteosarcoma Through European Research and Euro Ewing Consortium Statement. Clinical Cancer Research. ISSN 1078-0432. 30(16), p. 3395–3406. doi: 10.1158/1078-0432.CCR-24-0101. Full text in Research Archive
• Canals, Mateu Montserrat; Bjerregaard-Andersen, Kaare; Sørensen, Henrik Vinther; Kommedal, Eirik; Cordara, Gabriele & Vaaje-Kolstad, Gustav [Show all 7 contributors for this article] (2024). Calcium-binding site in AA10 LPMO from Vibrio cholerae suggests modulating effects during environmental survival and infection. QRB Discovery. 5. doi: 10.1017/qrd.2024.14. Full text in Research Archive Show summary

  Despite major efforts toward its eradication, cholera remains a major health threat and economic burden in many low- and middle-income countries. Between outbreaks, the bacterium responsible for the disease, Vibrio cholerae, survives in aquatic environmental reservoirs, where it commonly forms biofilms, for example, on zooplankton. N-acetyl glucosamine-binding protein A (GbpA) is an adhesin that binds to the chitinaceous surface of zooplankton and breaks its dense crystalline packing thanks to its lytic polysaccharide monooxygenase (LPMO) activity, which provides V. cholerae with nutrients. In addition, GbpA is an important colonization factor associated with bacterial pathogenicity, allowing the binding to mucins in the host intestine. Here, we report the discovery of a cation-binding site in proximity of the GbpA active site, which allows Ca2+, Mg2+, or K+ binding close to its carbohydrate-binding surface. In addition to the X-ray crystal structures of cation-LPMO complexes (to 1.5 Å resolution), we explored how the presence of ions affects the stability and activity of the protein. Calcium and magnesium ions were found to bind to GbpA specifically, with calcium ions – abundant in natural sources of chitin – having the strongest effect on protein stability. When the cation-binding site was rendered non-functional, a decrease in activity was observed, highlighting the importance of the structural elements stabilized by calcium. Our findings suggest a cation-binding site specific to GbpA and related LPMOs that may fine-tune binding and activity for its substrates during environmental survival and host infection.

• Bischof, Katharina; Cremaschi, Andrea; Eroukhmanoff, Lena; Landskron, Johannes; Flage-Larsen, Lise-Lotte & Gade, Alexandra [Show all 9 contributors for this article] (2024). Patient-derived acellular ascites fluid affects drug responses in ovarian cancer cell lines through the activation of key signalling pathways. Molecular Oncology. ISSN 1574-7891. 19(1). doi: 10.1002/1878-0261.13726. Full text in Research Archive Show summary

  Malignant ascites is commonly produced in advanced epithelial ovarian cancer (EOC) and serves as unique microenvironment for tumour cells. Acellular ascites fluid (AAF) is rich in signalling molecules and has been proposed to play a role in the induction of chemoresistance. Through in vitro testing of drug sensitivity and by assessing intracellular phosphorylation status in response to mono- and combination treatment of five EOC cell lines after incubation with AAFs derived from 20 different patients, we investigated the chemoresistance-inducing potential of ascites. We show that the addition of AAFs to the culture media of EOC cell lines has the potential to induce resistance to standard-of-care drugs (SCDs). We also show that AAFs induce time- and concentration-dependent activation of downstream signalling to signal transducer and activator of transcription 3 (STAT3), and concomitantly altered phosphorylation of mitogen-activated protein kinase kinase (MEK), phosphoinositide 3-kinase (PI3K)–protein kinase B (AKT) and nuclear factor NF-kappa-B (NFκB). Antibodies targeting the interleukin-6 receptor (IL6R) effectively blocked phosphorylation of STAT3 and STAT1. Treatments with SCDs were effective in reducing cell viability in only a third of 30 clinically relevant conditions examined, defined as combinations of drugs, different cell lines and AAFs. Combinations of SCDs and novel therapeutics such as trametinib, fludarabine or rapamycin were superior in another third. Notably, we could nominate effective treatment combinations in almost all conditions except in 4 out of 30 conditions, in which trametinib or fludarabine showed higher efficacy alone. Taken together, our study underscores the importance of the molecular characterisation of individual patients' AAFs and the impact on treatment resistance as providing clinically meaningful information for future precision treatment approaches in EOC.

• Demko, Viktor; Belova, Tatiana; Messerer, Maxim; Hvidsten, Torgeir Rhoden; Perroud, Pierre-François & Ako, Ako Eugene [Show all 10 contributors for this article] (2024). Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Communications Biology. 7(1). doi: 10.1038/s42003-024-05933-z. Full text in Research Archive Show summary

  Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.

• Lehtonen, Johanna; Sulonen, Anna-Maija; Almusa, Henrikki; Lehtokari, Vilma-Lotta; Johari, Mridul & Palva, Aino [Show all 14 contributors for this article] (2024). Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield. Scientific Reports. 14(1). doi: 10.1038/s41598-024-54866-4. Full text in Research Archive
• Shahrouzi, Parastoo; Forouz, Farzaneh; Mathelier, Anthony; Kristensen, Vessela N. & Duijf, Pascal Hubertus Gerardus (2024). Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends in Molecular Medicine. ISSN 1471-4914. 30(8), p. 750–764. doi: 10.1016/j.molmed.2024.04.017. Full text in Research Archive Show summary

  Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.

• Nurmi, Katariina; Silventoinen, Kristiina; Keskitalo, Salla; Rajamäki, Kristiina; Kouri, Vesa-Petteri & Kinnunen, Matias [Show all 32 contributors for this article] (2024). Truncating NFKB1 variants cause combined NLRP3 inflammasome activation and type I interferon signaling and predispose to necrotizing fasciitis. Cell Reports Medicine. 5(4). doi: 10.1016/j.xcrm.2024.101503. Full text in Research Archive Show summary

  In monogenic autoinflammatory diseases, mutations in genes regulating innate immune responses often lead to uncontrolled activation of inflammasome pathways or the type I interferon (IFN-I) response. We describe a mechanism of autoinflammation potentially predisposing patients to life-threatening necrotizing soft tissue inflammation. Six unrelated families are identified in which affected members present with necrotizing fasciitis or severe soft tissue inflammations. Exome sequencing reveals truncating monoallelic loss-of-function variants of nuclear factor κ light-chain enhancer of activated B cells (NFKB1) in affected patients. In patients’ macrophages and in NFKB1-variant-bearing THP-1 cells, activation increases both interleukin (IL)-1β secretion and IFN-I signaling. Truncation of NF-κB1 impairs autophagy, accompanied by the accumulation of reactive oxygen species and reduced degradation of inflammasome receptor nucleotide-binding oligomerization domain, leucine-rich repeat-containing protein 3 (NLRP3), and Toll/IL-1 receptor domain-containing adaptor protein inducing IFN-β (TRIF), thus leading to combined excessive inflammasome and IFN-I activity. Many of the patients respond to anti-inflammatory treatment, and targeting IL-1β and/or IFN-I signaling could represent a therapeutic approach for these patients.

• Burkert, Martin; Blanc, Eric; Thiessen, Nina; Weber, Christiane; Toedling, Joern & Monti, Remo [Show all 16 contributors for this article] (2024). Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma. iScience. 27(10), p. 1–22. doi: 10.1016/j.isci.2024.110918. Full text in Research Archive Show summary

  Telomere maintenance in neuroblastoma is linked to poor outcome and caused by either telomerase reverse transcriptase (TERT) activation or through alternative lengthening of telomeres (ALT). In contrast to TERT activation, commonly caused by genomic rearrangements or MYCN amplification, ALT is less well understood. Alterations at the ATRX locus are key drivers of ALT but only present in ∼50% of ALT tumors. To identify potential new pathways to telomere maintenance, we investigate allele-specific gene dosage effects from whole genomes and transcriptomes in 115 primary neuroblastomas. We show that copy-number dosage deregulates telomere maintenance, genomic stability, and neuronal pathways and identify upregulation of variants of histone H3 and H2A as a potential alternative pathway to ALT. We investigate the interplay between TERT activation, overexpression and copy-number dosage and reveal loss of imprinting at the RTL1 gene associated with poor clinical outcome. These results highlight the importance of gene dosage in key oncogenic mechanisms in neuroblastoma.

• Hsieh, Ping-Han; Hsiao, Ru-Xiu; Ferenc, Katalin; Mathelier, Anthony; Burkholz, Rebekka & Chen, Chien-Yu [Show all 9 contributors for this article] (2024). CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data. arXiv.org. ISSN 2331-8422. doi: 10.48550/arXiv.2405.18655. Full text in Research Archive
• Karabiyik, Gizem; Jesorka, Aldo & Gözen, Irep (2024). Ring-shaped nanoparticle assembly and cross-linking on lipid vesicle scaffolds. Soft Matter. ISSN 1744-683X. 20(45), p. 8947–8951. doi: 10.1039/d4sm01010h. Full text in Research Archive
• Fei, Liangru; Zhang, Kaiyang; Hautaniemi, Sampsa & Sahu, Biswajyoti (2024). Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach. STAR Protocols. 5(3). doi: 10.1016/j.xpro.2024.103148. Full text in Research Archive Show summary

  Ectopic expression of lineage-specific transcription factors (TFs) of another cell type can induce cell fate reprogramming. However, the heterogeneity of reprogramming cells has been a challenge for data interpretation and model evaluation. Here, we present a protocol to characterize cells expressing defined factors during direct cell reprogramming using a factor-indexing approach based on single-nuclei multiome sequencing (FI-snMultiome-seq). We describe the steps for barcoding TFs, converting human fibroblasts to pancreatic ductal-like cells using defined TFs, and preparing library for FI-snMultiome-seq analysis. For complete details on the use and execution of this protocol, please refer to Fei et al.1

• Rose, Maddison; Burgess, Joshua T.; Cheong, Chee Man; Adams, Mark N.; Shahrouzi, Parastoo & O’Byrne, Kenneth J. [Show all 8 contributors for this article] (2024). The expression and role of the Lem-D proteins Ankle2, Emerin, Lemd2, and TMPO in triple-negative breast cancer cell growth. Frontiers in Oncology. 14:1222698, p. 1–14. doi: 10.3389/fonc.2024.1222698. Full text in Research Archive Show summary

  Background: Triple-negative breast cancer (TNBC) is a sub-classification of breast carcinomas, which leads to poor survival outcomes for patients. TNBCs do not possess the hormone receptors that are frequently targeted as a therapeutic in other cancer subtypes and, therefore, chemotherapy remains the standard treatment for TNBC. Nuclear envelope proteins are frequently dysregulated in cancer cells, supporting their potential as novel cancer therapy targets. The Lem-domain (Lem-D) (LAP2, Emerin, MAN1 domain, and Lem-D) proteins are a family of inner nuclear membrane proteins, which share a ~45-residue Lem-D. The Lem-D proteins, including Ankle2, Lemd2, TMPO, and Emerin, have been shown to be associated with many of the hallmarks of cancer. This study aimed to define the association between the Lem-D proteins and TNBC and determine whether these proteins could be promising therapeutic targets. Methods: GENT2, TCGA, and KM plotter were utilized to investigate the expression and prognostic implications of several Lem-D proteins: Ankle2, TMPO, Emerin, and Lemd2 in publicly available breast cancer patient data. Immunoblotting and immunofluorescent analysis of immortalized non-cancerous breast cells and a panel of TNBC cells were utilized to establish whether protein expression of the Lem-D proteins was significantly altered in TNBC. SiRNA was used to decrease individual Lem-D protein expression, and functional assays, including proliferation assays and apoptosis assays, were conducted. Results: The Lem-D proteins were generally overexpressed in TNBC patient samples at the mRNA level and showed variable expression at the protein level in TNBC cell lysates. Similarly, protein levels were generally negatively correlated with patient survival outcomes. siRNA-mediated depletion of the individual Lem-D proteins in TNBC cells induced aberrant nuclear morphology, decreased proliferation, and induced cell death. However, minimal effects on nuclear morphology or cell viability were observed following Lem-D depletion in non-cancerous MCF10A cells. Conclusion: There is evidence to suggest that Ankle2, TMPO, Emerin, and Lemd2 expressions are correlated with breast cancer patient outcomes, but larger patient sample numbers are required to confirm this. siRNA-mediated depletion of these proteins was shown to specifically impair TNBC cell growth, suggesting that the Lem-D proteins may be a specific anti-cancer target.

• Khosravizad, Beyayna Vahramians; Ruud, Anja Karine; Belova, Tatiana; Windju, Susanne Skinnehaugen; Dieseth, Jon Arne & Yang, Ennian [Show all 7 contributors for this article] (2024). A major falling number locus on chromosome 4B governs resistance to pre-harvest sprouting in bread wheat line Soru#1. Euphytica. ISSN 0014-2336. 220(11). doi: 10.1007/s10681-024-03430-2. Full text in Research Archive Show summary

  Pre-harvest sprouting (PHS) is a serious threat to wheat quality and occurs when maturing seeds on plants encounter substantial rain before harvest. In the present study, the genetics of PHS resistance were studied using a population of 131 recombinant inbred lines (RILs) from a cross between Soru#1 and Naxos. The population was genotyped with the Illumina 90 K and Axiom 35 K wheat SNP arrays and tested in field trials across two locations in Norway and one in China. Seed dormancy as a measure of sprouting damage was evaluated using germination index (GI) and falling number (FN). Days to heading, days to maturity, and plant height were also recorded to evaluate their potential impact on PHS. Thirteen PHS-related quantitative trait loci (QTL) were detected. The most consistent QTL for FN, contributed by Soru#1, on the long arm of chromosome 4B explained 10.0–19.2% of the phenotypic variation across trials. Other important PHS resistance QTL from Soru#1 detected on chromosome arms 2AL, 2BL, and 4BS, affected both GI and FN. Naxos carried favorable QTL alleles for PHS resistance on chromosome arm 4AS and the Phs1 allele on 4AL. The reduced height Rht-D1 and vernalization Vrn-A1 alleles were the major determinants of plant height and earliness; however, these traits had minimal impact on the genetic control of PHS resistance in this population. Thus, both parents contributed valuable alleles for improving PHS resistance in breeding programs.

• Ünal, Bilal; Kuzu, Omer; Yang, Jin; Osorio, Daniel; Kildal, Wanja & Pradhan, Manohar [Show all 14 contributors for this article] (2024). Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer. Nature Communications. 15(1), p. 1–21. doi: 10.1038/s41467-024-53039-1. Full text in Research Archive Show summary

  Unfolded protein response (UPR) is a central stress response pathway that is hijacked by tumor cells for their survival. Here, we find that IRE1α signaling, one of the canonical UPR arms, is increased in prostate cancer (PCa) patient tumors. Genetic or small molecule inhibition of IRE1α in syngeneic mouse PCa models and an orthotopic model decreases tumor growth. IRE1α ablation in cancer cells potentiates interferon responses and activates immune system related pathways in the tumor microenvironment (TME). Single-cell RNA-sequencing analysis reveals that targeting IRE1α in cancer cells reduces tumor-associated macrophage abundance. Consistently, the small molecule IRE1α inhibitor MKC8866, currently in clinical trials, reprograms the TME and enhances anti-PD-1 therapy. Our findings show that IRE1α signaling not only promotes cancer cell growth and survival but also interferes with anti-tumor immunity in the TME. Thus, targeting IRE1α can be a promising approach for improving anti-PD-1 immunotherapy in PCa.

• Hautala, Nina Maria; Joensuu, Maija; Paakkola, Teija; Glumoff, Virpi; Kettunen, Kaisa & Saarela, Janna Saija [Show all 10 contributors for this article] (2024). Recurrent ocular toxoplasmosis is associated with interferon-gamma deficiency possibly due to genetic origin. BMJ Open Ophthalmology. 9(1). doi: 10.1136/bmjophth-2024-001769. Full text in Research Archive
• Taboada-Castro, Hermenegildo; Hernández-Álvarez, Alfredo José; Mondragon, Jaime Abraham Castro & Encarnación-Guevara, Sergio (2024). RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites. Bioinformatics and Biology Insights. 18. doi: 10.1177/11779322241272395. Full text in Research Archive
• Palmio, Johanna; Kiviranta, Panu; Hartikainen, Päivi H.; Isohanni, Pirjo; Auranen, Mari & Videman, Karoliina [Show all 13 contributors for this article] (2024). Homozygosity of a Founder Variant c.1508dupC in DOK7 Causes Congenital Myasthenia With Variable Severity. Neurology: Genetics. 10(3). doi: 10.1212/NXG.0000000000200155. Full text in Research Archive
• Melikishvili, Gia; Striano, Pasquale; Shojaeinia, Elham; Gachechiladze, Tamar; Kurua, Ekaterine & Tabatadze, Nazhi [Show all 18 contributors for this article] (2024). Effectiveness of add-on acetazolamide in children with drug-resistant CHD2-related epilepsy and in a zebrafish CHD2 model. Epilepsia Open. 9(5). doi: 10.1002/epi4.13034. Full text in Research Archive Show summary

  CHD2-related epilepsy is characterized by early-onset photosensitive myoclonic epilepsy with developmental delay and a high rate of pharmacoresistance. We sought to evaluate the efficacy of acetazolamide (ACZ) in CHD2-related epilepsy, due to ACZ's unexpected efficacy in our first patient harboring a pathogenic CHD2 variant. We collected patients from different Eastern European countries with drug-resistant CHD2-related epilepsy who were then treated with ACZ. Patients underwent video EEG before and during ACZ treatment. In a zebrafish model of CHD2-related epilepsy, ictal-like events were recorded 5 days post-fertilization after overnight ACZ exposure. Developmental delay preceded the onset of seizures in 10 of the 12 patients. Four had ataxia, and 6 exhibited autistic features. Seizures, primarily myoclonic, began at an average age of 3.4 years and were photosensitive in all 12 patients. Add-on ACZ treatment controlled photosensitive seizures in all patients: 6 became seizure-free, and in the remaining 6, seizure frequency decreased by over 75%. Four patients transitioned to ACZ monotherapy. The median follow-up was 13 months. In the zebrafish model, ACZ exposure reduced ictal-like events by 72%. ACZ, a well-tolerated and cost-effective medication, could be a good option for CHD2-related epilepsy, predominantly manifesting with myoclonic seizures and photosensitivity.

• Doboszewska, Urszula; Socała, Katarzyna; Pieróg, Mateusz; Nieoczym, Dorota; Sawicki, Jan & Szafarz, Małgorzata [Show all 18 contributors for this article] (2023). TC-G 1008 facilitates epileptogenesis by acting selectively at the GPR39 receptor but non-selectively activates CREB in the hippocampus of pentylenetetrazole-kindled mice. Cellular and Molecular Life Sciences (CMLS). ISSN 1420-682X. 80. doi: 10.1007/s00018-023-04766-z. Full text in Research Archive Show summary

  Abstract The pharmacological activation of the GPR39 receptor has been proposed as a novel strategy for treating seizures; however, this hypothesis has not been verified experimentally. TC-G 1008 is a small molecule agonist increasingly used to study GPR39 receptor function but has not been validated using gene knockout. Our aim was to assess whether TC-G 1008 produces anti-seizure/anti-epileptogenic effects in vivo and whether the effects are mediated by GPR39. To obtain this goal we utilized various animal models of seizures/epileptogenesis and GPR39 knockout mice model. Generally, TC-G 1008 exacerbated behavioral seizures. Furthermore, it increased the mean duration of local field potential recordings in response to pentylenetetrazole (PTZ) in zebrafish larvae. It facilitated the development of epileptogenesis in the PTZ-induced kindling model of epilepsy in mice. We demonstrated that TC-G 1008 aggravated PTZ-epileptogenesis by selectively acting at GPR39. However, a concomitant analysis of the downstream effects on the cyclic-AMP-response element binding protein in the hippocampus of GPR39 knockout mice suggested that the molecule also acts via other targets. Our data argue against GPR39 activation being a viable therapeutic strategy for treating epilepsy and suggest investigating whether TC-G 1008 is a selective agonist of the GPR39 receptor.

• Hsieh, Ping-Han; Lopes-Ramos, Camila Miranda; Zucknick, Manuela; Sandve, Geir Kjetil Ferkingstad; Glass, Kimberly & Kuijjer, Marieke (2023). Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics. ISSN 1367-4803. 39(10). doi: 10.1093/bioinformatics/btad610. Full text in Research Archive Show summary

  Abstract Motivation Gene co-expression measurements are widely used in computational biology to identify coordinated expression patterns across a group of samples. Coordinated expression of genes may indicate that they are controlled by the same transcriptional regulatory program, or involved in common biological processes. Gene co-expression is generally estimated from RNA-Sequencing data, which are commonly normalized to remove technical variability. Here, we demonstrate that certain normalization methods, in particular quantile-based methods, can introduce false-positive associations between genes. These false-positive associations can consequently hamper downstream co-expression network analysis. Quantile-based normalization can, however, be extremely powerful. In particular, when preprocessing large-scale heterogeneous data, quantile-based normalization methods such as smooth quantile normalization can be applied to remove technical variability while maintaining global differences in expression for samples with different biological attributes. Results We developed SNAIL (Smooth-quantile Normalization Adaptation for the Inference of co-expression Links), a normalization method based on smooth quantile normalization specifically designed for modeling of co-expression measurements. We show that SNAIL avoids formation of false-positive associations in co-expression as well as in downstream network analyses. Using SNAIL, one can avoid arbitrary gene filtering and retain associations to genes that only express in small subgroups of samples. This highlights the method’s potential future impact on network modeling and other association-based approaches in large-scale heterogeneous data. Availability and implementation The implementation of the SNAIL algorithm and code to reproduce the analyses described in this work can be found in the GitHub repository https://github.com/kuijjerlab/PySNAIL.

• Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Mondragon, Jaime Abraham Castro; Ferenc, Katalin Terezia & Kumar, Vipin [Show all 20 contributors for this article] (2023). JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. 52(D1), p. D174–D182. doi: 10.1093/nar/gkad1059. Full text in Research Archive Show summary

  JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.

• Weikum, Julia; Dyck, Jeroen F. van; Subramani, Saranya; Klebl, David P.; Storflor, Merete & Muench, Stephen P. [Show all 9 contributors for this article] (2023). The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species. BBA - Molecular Cell Research. ISSN 0167-4889. 1871(1). doi: 10.1016/j.bbamcr.2023.119614. Full text in Research Archive Show summary

  The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg²⁺ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and antibacterial resistance in Salmonella strains. Here, we show that MgtA has functional specificity for cardiolipin 18:1. Still, it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. Native mass spectrometry indicates the presence of two binding sites for cardiolipin, agreeing with the kinetic studies revealing that a cooperative relationship likely exists between the two cardiolipin variants. This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg²⁺ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.

• Haas-Kogan, Daphne A.; Aboian, Mariam S.; Minturn, Jane E.; Leary, Sarah E S; Abdelbaki, Mohamed S. & Goldman, Stewart [Show all 20 contributors for this article] (2023). Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial. Journal of Clinical Oncology. ISSN 0732-183X. 42(4), p. 441–451. doi: 10.1200/JCO.23.01838. Full text in Research Archive Show summary

  Purpose The PNOC001 phase II single-arm trial sought to estimate progression-free survival (PFS) associated with everolimus therapy for progressive/recurrent pediatric low-grade glioma (pLGG) on the basis of phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway activation as measured by phosphorylated-ribosomal protein S6 and to identify prognostic and predictive biomarkers. Patients and Methods Patients, age 3-21 years, with progressive/recurrent pLGG received everolimus orally, 5 mg/m2 once daily. Frequency of driver gene alterations was compared among independent pLGG cohorts of newly diagnosed and progressive/recurrent patients. PFS at 6 months (primary end point) and median PFS (secondary end point) were estimated for association with everolimus therapy. Results Between 2012 and 2019, 65 subjects with progressive/recurrent pLGG (median age, 9.6 years; range, 3.0-19.9; 46% female) were enrolled, with a median follow-up of 57.5 months. The 6-month PFS was 67.4% (95% CI, 60.0 to 80.0) and median PFS was 11.1 months (95% CI, 7.6 to 19.8). Hypertriglyceridemia was the most common grade ≥3 adverse event. PI3K/AKT/mTOR pathway activation did not correlate with clinical outcomes (6-month PFS, active 68.4% v nonactive 63.3%; median PFS, active 11.2 months v nonactive 11.1 months; P = .80). Rare/novel KIAA1549::BRAF fusion breakpoints were most frequent in supratentorial midline pilocytic astrocytomas, in patients with progressive/recurrent disease, and correlated with poor clinical outcomes (median PFS, rare/novel KIAA1549::BRAF fusion breakpoints 6.1 months v common KIAA1549::BRAF fusion breakpoints 16.7 months; P < .05). Multivariate analysis confirmed their independent risk factor status for disease progression in PNOC001 and other, independent cohorts. Additionally, rare pathogenic germline variants in homologous recombination genes were identified in 6.8% of PNOC001 patients. Conclusion Everolimus is a well-tolerated therapy for progressive/recurrent pLGGs. Rare/novel KIAA1549::BRAF fusion breakpoints may define biomarkers for progressive disease and should be assessed in future clinical trials.

• Nieoczym, Dorota; Banono, Nancy Saana; Stępnik, Katarzyna; Kaczor, Agnieszka A.; Szybkowski, Przemysław & Esguerra, Camila [Show all 8 contributors for this article] (2023). In Silico Analysis, Anticonvulsant Activity, and Toxicity Evaluation of Schisandrin B in Zebrafish Larvae and Mice. International Journal of Molecular Sciences. ISSN 1661-6596. 24(16). doi: 10.3390/ijms241612949. Full text in Research Archive Show summary

  The aim of this study is to evaluate the anticonvulsant potential of schisandrin B, a main ingredient of Schisandra chinensis extracts. Schisandrin B showed anticonvulsant activity in the zebrafish larva pentylenetetrazole acute seizure assay but did not alter seizure thresholds in the intravenous pentylenetetrazole test in mice. Schisandrin B crosses the blood–brain barrier, which we confirmed in our in silico and in vivo analyses; however, the low level of its unbound fraction in the mouse brain tissue may explain the observed lack of anticonvulsant activity. Molecular docking revealed that the anticonvulsant activity of the compound in larval zebrafish might have been due to its binding to a benzodiazepine site within the GABAA receptor and/or the inhibition of the glutamate NMDA receptor. Although schisandrin B showed a beneficial anticonvulsant effect, toxicological studies revealed that it caused serious developmental impairment in zebrafish larvae, underscoring its teratogenic properties. Further detailed studies are needed to precisely identify the properties, pharmacological effects, and safety of schisandrin B.

• Guebila, Marouen Ben; Wang, Tian; Lopes-Ramos, Camila M.; Fanfani, Viola; Weighill, Des & Burkholz, Rebekka [Show all 25 contributors for this article] (2023). The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. ISSN 1474-7596. 24(1). doi: 10.1186/s13059-023-02877-1. Full text in Research Archive Show summary

  Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

• Belova, Tatiana; Biondi, Nicola; Hsieh, Ping-Han; Lutsik, Pavlo; Chudasama, Priya & Kuijjer, Marieke (2023). Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer. 5(3). doi: 10.1093/narcan/zcad037. Full text in Research Archive Show summary

  Abstract Characterizing inter-tumor heterogeneity is crucial for selecting suitable cancer therapy, as the presence of diverse molecular subgroups of patients can be associated with disease outcome or response to treatment. While cancer subtypes are often characterized by differences in gene expression, the mechanisms driving these differences are generally unknown. We set out to model the regulatory mechanisms driving sarcoma heterogeneity based on patient-specific, genome-wide gene regulatory networks. We developed a new computational framework, PORCUPINE, which combines knowledge on biological pathways with permutation-based network analysis to identify pathways that exhibit significant regulatory heterogeneity across a patient population. We applied PORCUPINE to patient-specific leiomyosarcoma networks modeled on data from The Cancer Genome Atlas and validated our results in an independent dataset from the German Cancer Research Center. PORCUPINE identified 37 heterogeneously regulated pathways, including pathways representing potential targets for treatment of subgroups of leiomyosarcoma patients, such as FGFR and CTLA4 inhibitory signaling. We validated the detected regulatory heterogeneity through analysis of networks and chromatin states in leiomyosarcoma cell lines. We showed that the heterogeneity identified with PORCUPINE is not associated with methylation profiles or clinical features, thereby suggesting an independent mechanism of patient heterogeneity driven by the complex landscape of gene regulatory interactions.

• Giesecke, Astrid; Johnstone, Peter S.; Lamaze, Angelique; Landskron, Johannes; Atay, Ezgi & Chen, Ko-Fan [Show all 9 contributors for this article] (2023). A novel period mutation implicating nuclear export in temperature compensation of the Drosophila circadian clock. Current Biology. ISSN 0960-9822. 33(2), p. 336–350. doi: 10.1016/j.cub.2022.12.011. Full text in Research Archive
• Houlahan, Kathleen E.; Livingstone, Julie; Fox, Natalie S.; Kurganovs, Natalie; Zhu, Helen & Penington, Jocelyn Sietsma [Show all 21 contributors for this article] (2023). A polygenic two-hit hypothesis for prostate cancer. Journal of the National Cancer Institute. ISSN 0027-8874. 115(4), p. 468–472. doi: 10.1093/jnci/djad001. Full text in Research Archive
• Perdreau-Dahl, Harmonie; Lipsett, David Bruce; Frisk, Michael; Kermani, Fatemeh; Carlson, Cathrine Rein & Brech, Andreas [Show all 19 contributors for this article] (2023). BIN1, Myotubularin, and Dynamin-2 Coordinate T-Tubule Growth in Cardiomyocytes. Circulation Research. ISSN 0009-7330. 132(11), p. E188–E205. doi: 10.1161/CIRCRESAHA.122.321732. Full text in Research Archive
• Pena, Dario Segura; Hovet, Oda; Gogoi, Hemanga; Dawicki-Mckenna, Jennine; Wøien, Stine Malene Hansen & Carrer, Manuel [Show all 9 contributors for this article] (2023). The structural basis of the multi-step allosteric activation of Aurora B kinase. eLIFE. 12. doi: 10.7554/eLife.85328. Full text in Research Archive Show summary

  Aurora B, together with IN-box, the C-terminal part of INCENP, forms an enzymatic complex that ensures faithful cell division. The [Aurora B/IN-box] complex is activated by autophosphorylation in the Aurora B activation loop and in IN-box, but it is not clear how these phosphorylations activate the enzyme. We used a combination of experimental and computational studies to investigate the effects of phosphorylation on the molecular dynamics and structure of [Aurora B/IN-box]. In addition, we generated partially phosphorylated intermediates to analyze the contribution of each phosphorylation independently. We found that the dynamics of Aurora and IN-box are interconnected, and IN-box plays both positive and negative regulatory roles depending on the phosphorylation status of the enzyme complex. Phosphorylation in the activation loop of Aurora B occurs intramolecularly and prepares the enzyme complex for activation, but two phosphorylated sites are synergistically responsible for full enzyme activity.

• Kolodziejczak, Anna S.; Guerrini-Rousseau, Lea; Planchon, Julien Masliah; Ecker, Jonas; Selt, Florian & Mynarek, Martin [Show all 73 contributors for this article] (2023). Clinical outcome of pediatric medulloblastoma patients with Li-Fraumeni syndrome. Neuro-Oncology. ISSN 1522-8517. 25(12), p. 2273–2286. doi: 10.1093/neuonc/noad114. Full text in Research Archive
• Karttunen, Konsta; Patel, Divyesh; Xia, Jihan; Fei, Liangru; Palin, Kimmo & Aaltonen, Lauri [Show all 7 contributors for this article] (2023). Transposable elements as tissue-specific enhancers in cancers of endodermal lineage. Nature Communications. 14. doi: 10.1038/s41467-023-41081-4. Full text in Research Archive Show summary

  Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we utilize unbiased massively parallel reporter assay data using a whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identify distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

• Challal, Soura; Skiba, Adrianna; Langlois, Mélanie; Esguerra, Camila V.; Wolfender, Jean-Luc & Crawford, Alexander Dettmar [Show all 7 contributors for this article] (2023). Natural product-derived therapies for treating drug-resistant epilepsies: From ethnopharmacology to evidence-based medicine. Journal of Ethnopharmacology. ISSN 0378-8741. 317. doi: 10.1016/j.jep.2023.116740. Full text in Research Archive
• Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina Maria; Castañeda, Fernando Rodriguez-; Eskeland, Ragnhild & Gabrielsen, Odd Stokke (2023). MYB regulates the SUMO protease SENP1 and its novel interaction partner UXT, modulating MYB target genes and the SUMO landscape. Journal of Biological Chemistry. ISSN 0021-9258. 299(9). doi: 10.1016/j.jbc.2023.105062. Full text in Research Archive Show summary

  SUMOylation is a post-translational modification frequently found on nuclear proteins, including transcription factors (TFs) and coactivators. By controlling the activity of several TFs, SUMOylation may have far-reaching effects. MYB is an example of a developmental TF subjected to SUMO-mediated regulation, through both SUMO conjugation and SUMO binding. How SUMO affects MYB target genes is unknown. Here, we explored the global effect of reduced SUMOylation of MYB on its downstream gene programs. RNA-Seq in K562 cells after MYB knockdown and rescue with mutants having an altered SUMO status revealed a number of differentially regulated genes and distinct gene ontology term enrichments. Clearly, the SUMO status of MYB both quantitatively and qualitatively affects its regulome. The transcriptome data further revealed that MYB upregulates the SUMO protease SENP1, a key enzyme that removes SUMO conjugation from SUMOylated proteins. Given this role of SENP1 in the MYB regulome, we expanded the analysis, mapped interaction partners of SENP1, and identified UXT as a novel player affecting the SUMO system by acting as a repressor of SENP1. MYB inhibits the expression of UXT suggesting that MYB is able not only to control a specific gene program directly but also indirectly by affecting the SUMO landscape through SENP1 and UXT. These findings suggest an autoactivation loop whereby MYB, through enhancing SENP1 and reducing UXT, is itself being activated by a reduced level of repressive SUMOylation. We propose that overexpressed MYB, seen in multiple cancers, may drive this autoactivation loop and contribute to oncogenic activation of MYB.

• Fei, Liangru; Zhang, Kaiyang; Poddar, Nikita; Hautaniemi, Sampsa & Sahu, Biswajyoti (2023). Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells. Developmental Cell. ISSN 1534-5807. 58(18), p. 1701–1715. doi: 10.1016/j.devcel.2023.08.023. Full text in Research Archive Show summary

  Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TFs). However, the exact cell state transitions during transdifferentiation are still poorly understood. Here, we have generated pancreatic exocrine cells of ductal epithelial identity from human fibroblasts using a set of six TFs. We mapped the molecular determinants of lineage dynamics using a factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: an endodermal progenitor state defined by activation of HHEX with FOXA2 and SOX17 and a temporal GATA4 activation essential for the maintenance of pancreatic cell fate program. Collectively, our data suggest that transdifferentiation—although being considered a direct cell fate conversion method—occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs.

• Pop, Romana Tabita; Pisante, Alessandra; Nagy, Dorka; Martin, Patrick C. N.; Mikheeva, Liudmila A. & Hayat, Ateequllah [Show all 8 contributors for this article] (2023). Identification of mammalian transcription factors that bind to inaccessible chromatin. Nucleic Acids Research (NAR). ISSN 0305-1048. 51(16), p. 8480–8495. doi: 10.1093/nar/gkad614. Full text in Research Archive Show summary

  Abstract Transcription factors (TFs) are proteins that affect gene expression by binding to regulatory regions of DNA in a sequence specific manner. The binding of TFs to DNA is controlled by many factors, including the DNA sequence, concentration of TF, chromatin accessibility and co-factors. Here, we systematically investigated the binding mechanism of hundreds of TFs by analysing ChIP-seq data with our explainable statistical model, ChIPanalyser. This tool uses as inputs the DNA sequence binding motif; the capacity to distinguish between strong and weak binding sites; the concentration of TF; and chromatin accessibility. We found that approximately one third of TFs are predicted to bind the genome in a DNA accessibility independent fashion, which includes TFs that can open the chromatin, their co-factors and TFs with similar motifs. Our model predicted this to be the case when the TF binds to its strongest binding regions in the genome, and only a small number of TFs have the capacity to bind dense chromatin at their weakest binding regions, such as CTCF, USF2 and CEBPB. Our study demonstrated that the binding of hundreds of human and mouse TFs is predicted by ChIPanalyser with high accuracy and showed that many TFs can bind dense chromatin.

• Jackson, Evangeline R.; Duchatel, Ryan J.; Staudt, Dilana E.; Persson, Mika L.; Mannan, Abdul & Yadavilli, Sridevi [Show all 48 contributors for this article] (2023). ONC201 in Combination with Paxalisib for the Treatment of H3K27-Altered Diffuse Midline Glioma. Cancer Research. ISSN 0008-5472. 83(14), p. 2421–2437. doi: 10.1158/0008-5472.CAN-23-0186. Full text in Research Archive Show summary

  Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPG), are the most lethal of childhood cancers. Palliative radiotherapy is the only established treatment, with median patient survival of 9 to 11 months. ONC201 is a DRD2 antagonist and ClpP agonist that has shown preclinical and emerging clinical efficacy in DMG. However, further work is needed to identify the mechanisms of response of DIPGs to ONC201 treatment and to determine whether recurring genomic features influence response. Using a systems-biological approach, we showed that ONC201 elicits potent agonism of the mitochondrial protease ClpP to drive proteolysis of electron transport chain and tricarboxylic acid cycle proteins. DIPGs harboring PIK3CA mutations showed increased sensitivity to ONC201, whereas those harboring TP53 mutations were more resistant. Metabolic adaptation and reduced sensitivity to ONC201 was promoted by redox-activated PI3K/Akt signaling, which could be counteracted using the brain penetrant PI3K/Akt inhibitor, paxalisib. Together, these discoveries coupled with the powerful anti-DIPG/DMG pharmacokinetic and pharmacodynamic properties of ONC201 and paxalisib have provided the rationale for the ongoing DIPG/DMG phase II combination clinical trial NCT05009992. Significance: PI3K/Akt signaling promotes metabolic adaptation to ONC201-mediated disruption of mitochondrial energy homeostasis in diffuse intrinsic pontine glioma, highlighting the utility of a combination treatment strategy using ONC201 and the PI3K/Akt inhibitor paxalisib.

• Bonner, Erin R.; Dawood, Adam; Gordish-Dressman, Heather; Eze, Augustine; Bhattacharya, Surajit & Yadavilli, Sridevi [Show all 9 contributors for this article] (2023). Pan-cancer atlas of somatic core and linker histone mutations. NPJ GENOMIC MEDICINE. 8(1). doi: 10.1038/s41525-023-00367-8. Full text in Research Archive Show summary

  Abstract Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the prevalence and the clinical and biological implications of histone gene mutations in malignant tumors remain incompletely defined. To address these knowledge gaps, we analyzed somatic mutations in 88 linker and core histone genes across 12,743 tumors from pediatric, adolescent and young adult (AYA), and adult cancer patients. We established a pan-cancer histone mutation atlas contextualized by patient age, survival outcome, and tumor location. Overall, 11% of tumors harbored somatic histone mutations, with the highest rates observed among chondrosarcoma (67%), pediatric high-grade glioma (pHGG, &gt;60%), and lymphoma (&gt;30%). Previously unreported histone mutations were discovered in pHGG and other pediatric brain tumors, extending the spectrum of histone gene alterations associated with these cancers. Histone mutation status predicted patient survival outcome in tumor entities including adrenocortical carcinoma. Recurrent pan-cancer histone mutation hotspots were defined and shown to converge on evolutionarily conserved and functional residues. Moreover, we studied histone gene mutations in 1700 pan-cancer cell lines to validate the prevalence and spectrum of histone mutations seen in primary tumors and derived histone-associated drug response profiles, revealing candidate drugs targeting histone mutant cancer cells. This study presents the first-of-its-kind atlas of both core and linker histone mutations across pediatric, AYA, and adult cancers, providing a framework by which specific cancers may be redefined in the context of histone and chromatin alterations.

• Frioux, Clémence; Ansorge, Rebecca; Özkurt, Ezgi; Nedjad, Chabname Ghassemi; Fritscher, Joachim & Quince, Christopher [Show all 8 contributors for this article] (2023). Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host and Microbe. ISSN 1931-3128. 31(7), p. 1111–1125.e6. doi: 10.1016/j.chom.2023.05.024. Full text in Research Archive Show summary

  The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is “core” in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.

• Chlubnova, Marketa; Christophersen, Asbjørn Otto; Sandve, Geir Kjetil Ferkingstad; Lundin, Knut Erik Aslaksen; Jahnsen, Jørgen & Dahal-Koirala, Shiva [Show all 7 contributors for this article] (2023). Identification of gluten T cell epitopes driving celiac disease. Science Advances. 9(4), p. 1–8. doi: 10.1126/sciadv.ade5800. Full text in Research Archive Show summary

  CD4+ T cells specific for cereal gluten proteins are key players in celiac disease (CeD) pathogenesis. While several CeD-relevant gluten T cell epitopes have been identified, epitopes recognized by a substantial proportion of gluten-reactive T cells remain unknown. The identification of such CeD-driving gluten epitopes is important for the food industry and in clinical settings. Here, we have combined the knowledge of a distinct phenotype of gluten-reactive T cells and key features of known gluten epitopes for the discovery of unknown epitopes. We tested 42 wheat gluten–reactive T cell clones, isolated on the basis of their distinct phenotype and with no reactivity to known epitopes, against a panel of synthetic peptides bioinformatically identified from a wheat gluten protein database. We were able to assign reactivity to 10 T cell clones and identified a 9-nucleotide oligomer core region of five previously uncharacterized gliadin/glutenin epitopes. This work represents an advance in the effort to identify CeD-driving gluten epitopes.

• Sanjaya, Prima; Maljanen, Katri; Katainen, Riku; Waszak, Sebastian Martin; Stegle, Oliver & Korbel, Jan O. [Show all 50 contributors for this article] (2023). Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. Genome Medicine. 15(1). doi: 10.1186/s13073-023-01204-4. Full text in Research Archive Show summary

  Abstract Background Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatric tumours. Moreover, the ability to leverage deep representation learning in discovery of tumour entities remains unknown. Methods We introduce here Mutation-Attention (MuAt), a deep neural network to learn representations of simple and complex somatic alterations for prediction of tumour types and subtypes. In contrast to many previous methods, MuAt utilizes the attention mechanism on individual mutations instead of aggregated mutation counts. Results We trained MuAt models on 2587 whole cancer genomes (24 tumour types) from the Pan-Cancer Analysis of Whole Genomes (PCAWG) and 7352 cancer exomes (20 types) from the Cancer Genome Atlas (TCGA). MuAt achieved prediction accuracy of 89% for whole genomes and 64% for whole exomes, and a top-5 accuracy of 97% and 90%, respectively. MuAt models were found to be well-calibrated and perform well in three independent whole cancer genome cohorts with 10,361 tumours in total. We show MuAt to be able to learn clinically and biologically relevant tumour entities including acral melanoma, SHH-activated medulloblastoma, SPOP -associated prostate cancer, microsatellite instability, POLE proofreading deficiency, and MUTYH -associated pancreatic endocrine tumours without these tumour subtypes and subgroups being provided as training labels. Finally, scrunity of MuAt attention matrices revealed both ubiquitous and tumour-type specific patterns of simple and complex somatic mutations. Conclusions Integrated representations of somatic alterations learnt by MuAt were able to accurately identify histological tumour types and identify tumour entities, with potential to impact precision cancer medicine.

• Cortés, Natalia Mojica; Kersten, Flore; Canals, Mateu Montserrat; III, G. Robb Huhn; Tislevoll, Abelone & Cordara, Gabriele [Show all 8 contributors for this article] (2023). Using Vibrio natriegens for High-Yield Production of Challenging Expression Targets and for Protein Perdeuteration. Biochemistry. ISSN 0006-2960. doi: 10.1021/acs.biochem.3c00612. Full text in Research Archive Show summary

  Production of soluble proteins is essential for structure/function studies; however, this usually requires milligram amounts of protein, which can be difficult to obtain with traditional expression systems. Recently, the Gram-negative bacterium Vibrio natriegens emerged as a novel and alternative host platform for production of proteins in high yields. Here, we used a commercial strain derived from V. natriegens (Vmax X2) to produce soluble bacterial and fungal proteins in milligram scale, which we struggled to achieve in Escherichia coli. These proteins include the cholera toxin (CT) and N-acetyl glucosamine-binding protein A (GbpA) from Vibrio cholerae, the heat-labile enterotoxin (LT) from E. coli and the fungal nematotoxin CCTX2 from Coprinopsis cinerea. CT, GbpA, and LT are secreted by the Type II secretion system in their natural hosts. When these three proteins were produced in Vmax, they were also secreted and could be recovered from the growth media. This simplified the downstream purification procedure and resulted in considerably higher protein yields compared to production in E. coli (6- to 26-fold increase). We also tested Vmax for protein perdeuteration using deuterated minimal media with deuterium oxide as solvent and achieved a 3-fold increase in yield compared to the equivalent protocol in E. coli. This is good news, since isotopic labeling is expensive and often ineffective but represents a necessary prerequisite for some structural biology techniques. Thus, Vmax represents a promising host for production of challenging expression targets and for protein perdeuteration in amounts suitable for structural biology studies.

• Harroud, Adil; Stridh, Pernilla; McCauley, Jacob L.; Saarela, Janna Saija; Bosch, Aletta M. R. van den & Engelenburg, Hendrik J. [Show all 120 contributors for this article] (2023). Locus for severity implicates CNS resilience in progression of multiple sclerosis. Nature. ISSN 0028-0836. 619(7969), p. 323–331. doi: 10.1038/s41586-023-06250-x. Full text in Research Archive
• Skogestad, Jonas; Albert, Ingrid; Hougen, Karina; Lothe, Gustav B; Lunde, Marianne & Eken, Olav Søvik [Show all 25 contributors for this article] (2023). Disruption of Phosphodiesterase 3A Binding to SERCA2 Increases SERCA2 Activity and Reduces Mortality in Mice with Chronic Heart Failure. Circulation. ISSN 0009-7322. 147(16), p. 1221–1236. doi: 10.1161/CIRCULATIONAHA.121.054168. Full text in Research Archive
• Gawriyski, Lisa; Jouhilahti, Eeva-Mari; Yoshihara, Masahito; Fei, Liangru; Weltner, Jere & Airenne, Tomi T. [Show all 20 contributors for this article] (2023). Comprehensive characterization of the embryonic factor LEUTX. iScience. 26(3). doi: 10.1016/j.isci.2023.106172. Full text in Research Archive Show summary

  The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.

• Perälä, Miia; Kaustio, Meri; Salava, Alexander; Jakkula, Eveliina; Pelkonen, Anna S. & Saarela, Janna Saija [Show all 8 contributors for this article] (2023). Relevance of Coding Variation in FLG And DOCK8 in Finnish Pediatric Patients with Early-Onset Moderate-To-Severe Atopic Dermatitis. JID Innovations. 3(4). doi: 10.1016/j.xjidi.2023.100203. Full text in Research Archive Show summary

  Early-onset, persistent atopic dermatitis (AD) is proposed as a distinct subgroup that may have specific genotypic features. FLG gene loss-of-function variants are the best known genetic factors contributing to epidermal barrier impairment and eczema severity. In a cohort of 140 Finnish children with early-onset moderate-to-severe AD, we investigated the effect of coding variation in FLG and 13 other genes with epidermal barrier or immune function through the use of targeted amplicon sequencing and genotyping. A FLG loss-of-function variant (Arg501Ter, Ser761fs, Arg2447Ter, or Ser3247Ter) was identified in 20 of 140 patients showing higher transepidermal water loss values than patients without these variants. Total FLG loss-of-function variant frequency (7.14%) was significantly higher than in the general Finnish population (2.34%). When tested separately, only Arg2447Ter showed a significant association with AD (P = 0.003104). In addition, a modest association with moderate-to-severe pediatric AD was seen for rs12730241 and rs6587667 (FLG2:Gly137Glu). Loss-of-function variants, previously reported pathogenic variants, or statistically significant enrichment of nonsynonymous coding region variants were not found in the 13 candidate genes studied by amplicon sequencing. However, higher IgE and eosinophil counts were found in carriers of potentially pathogenic DOCK8 missense variants, suggesting that the role of DOCK8 variation in AD should be further investigated in larger cohorts.

• Papadopoulos, Nicolas; Pristavec, Ajda; Nédélec, Audrey; Levy, Gabriel; Staerk, Judith & Constantinescu, Stefan N. (2023). Modulation of human thrombopoietin receptor conformations uncouples JAK2 V617F-driven activation from cytokine-induced stimulation. Blood. ISSN 0006-4971. doi: 10.1182/blood.2022019580. Full text in Research Archive Show summary

  Abstract The thrombopoietin receptor (TpoR) plays a central role in myeloproliferative neoplasms (MPNs). Mutations in JAK2, calreticulin, or TpoR itself drive the constitutive activation of TpoR and uncontrolled proliferation and differentiation of hematopoietic stem cells and progenitors. The JAK2 V617F mutation is responsible for most MPNs, and all driver mutants induce pathologic TpoR activation. Existing therapeutic strategies have focused on JAK2 kinase inhibitors that are unable to differentiate between the mutated MPN clone and healthy cells. Surprisingly, the targeting of TpoR itself has remained poorly explored despite its central role in pathology. Here, we performed a comprehensive characterization of human TpoR activation under physiological and pathological conditions, focusing on the JAK2 V617F mutant. Using a system of controlled dimerization of the transmembrane and cytosolic domains of TpoR, we discovered that human TpoR (hTpoR) adopts different dimeric conformations upon Tpo-induced vs JAK2 V617F–mediated activation. We identified the amino acids and specific dimeric conformation of hTpoR responsible for activation in complex with JAK2 V617F and confirmed our findings in the full-length receptor context in hematopoietic cell lines and primary bone marrow cells. Remarkably, we found that the modulation of hTpoR conformations by point mutations allowed for specific inhibition of JAK2 V617F–driven activation without affecting Tpo-induced signaling. Our results demonstrate that modulation of the hTpoR conformation is a viable therapeutic strategy for JAK2 V617F–positive MPNs and set the path for novel drug development by identifying precise residues of hTpoR involved in JAK2 V617F–specific activation.

• Nagpal, Harsh; Ahmad, Ahmad Ali; Hirano, Yasuhiro; Cai, Wei; Halic, Mario & Fukagawa, Tatsuo [Show all 8 contributors for this article] (2023). CENP-A and CENP-B collaborate to create an open centromeric chromatin state. Nature Communications. 14(1). doi: 10.1038/s41467-023-43739-5. Full text in Research Archive Show summary

  Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore assemble, connecting the centromere to spindle microtubules during cell division. The DNA-binding centromeric protein CENP-B is involved in maintaining centromere stability and, together with CENP-A, shapes the centromeric chromatin state. The nanoscale organization of centromeric chromatin is not well understood. Here, we use single-molecule fluorescence and cryoelectron microscopy (cryoEM) to show that CENP-A incorporation establishes a dynamic and open chromatin state. The increased dynamics of CENP-A chromatin create an opening for CENP-B DNA access. In turn, bound CENP-B further opens the chromatin fiber structure and induces nucleosomal DNA unwrapping. Finally, removal of CENP-A increases CENP-B mobility in cells. Together, our studies show that the two centromere-specific proteins collaborate to reshape chromatin structure, enabling the binding of centromeric factors and establishing a centromeric chromatin state.

• Olkinuora, Alisa; Nieminen, Taina T.; Douglas, Suvi; Kauppinen, Anni; Kontro, Mika & Väänänen, Juho [Show all 20 contributors for this article] (2023). Identification of DHX40 as a candidate susceptibility gene for colorectal and hematological neoplasia. Leukemia. ISSN 0887-6924. doi: 10.1038/s41375-023-02021-9. Full text in Research Archive
• Clarke, Mary L.; Lemma, Roza Berhanu; Walton, David Scott; Volpe, Giacomo; Noyvert, Boris & Gabrielsen, Odd Stokke [Show all 7 contributors for this article] (2023). MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia. Blood. ISSN 0006-4971. 141(15), p. 1858–1870. doi: 10.1182/blood.2022019138. Full text in Research Archive Show summary

  MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of leukemias, although inherited noncoding variants of the MYB gene are a susceptibility factor for many hematological conditions, including myeloproliferative neoplasms (MPN). The mechanisms that connect variations in MYB levels to disease predisposition, especially concerning age dependency in disease initiation, are completely unknown. Here, we describe a model of Myb insufficiency in mice that leads to MPN, myelodysplasia, and leukemia in later life, mirroring the age profile of equivalent human diseases. We show that this age dependency is intrinsic to HSC, involving a combination of an initial defective cellular state resulting from small effects on the expression of multiple genes and a progressive accumulation of further subtle changes. Similar to previous studies showing the importance of proteostasis in HSC maintenance, we observed altered proteasomal activity and elevated proliferation indicators, followed by elevated ribosome activity in young Myb-insufficient mice. We propose that these alterations combine to cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation.

• Haapaniemi, Emma Maria; Leiding, Jennifer W.; Vogel, Tiphanie P.; Santarlas, Valentine G.J.; Mhaskar, Rahul & Smith, Madison R. [Show all 51 contributors for this article] (2023). Monogenic early-onset lymphoproliferation and autoimmunity: Natural history of STAT3 gain-of-function syndrome. Journal of Allergy and Clinical Immunology. ISSN 0091-6749. doi: 10.1016/j.jaci.2022.09.002. Full text in Research Archive
• Santaniemi, Wenny; Åström, Pirjo; Glumoff, Virpi; Pernaa, Nora; Tallgren, Ella-Noora & Palosaari, Sanna [Show all 14 contributors for this article] (2023). Inflammation and Neutrophil Oxidative Burst in a Family with NFKB1 p.R157X LOF and Sterile Necrotizing Fasciitis. Journal of Clinical Immunology. ISSN 0271-9142. 43, p. 1007–1018. doi: 10.1007/s10875-023-01461-3. Full text in Research Archive Show summary

  Abstract Loss-of-function (LOF) mutations in NFKB1 , coding for p105, may cause common variable immunodeficiency due to dysregulation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κΒ) pathway. Monoallelic LOF variants of NFKB1 can predispose to uncontrolled inflammation including sterile necrotizing fasciitis or pyoderma gangrenosum. In this study, we explored the impact of a heterozygous NFKB1 c.C936T/p.R157X LOF variant on immunity in sterile fasciitis patients and their family members. The p50 or p105 protein levels were reduced in all variant carriers. Interleukin-1β (IL-1β) and interleukin-8 (IL-8) levels were elevated in vitro, potentially contributing to the very high neutrophil counts observed during fasciitis episodes. Phosphorylation of p65/RelA was reduced in p.R157X neutrophils suggesting defective activation of canonical NF-κB. Oxidative burst after NF-κB-independent phorbol 12-myristate 13-acetate (PMA) stimulation was similar in both p.R157X and control neutrophils. Comparable amounts of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex subunits were found in p.R157X and control neutrophils. However, a compromised oxidative burst was observed in p.R157X neutrophils following activation of NF-κB-dependent mechanisms following stimulation of toll-like receptor 2 (TLR2) and Dectin-1. Neutrophil extracellular trap formation was not affected by p.R157X. In summary, the NFKB1 c.C936T/p.R157X LOF variant has an impact on inflammation and neutrophil function and may play a role in the pathogenesis of sterile necrotizing fasciitis.

• Venneti, Sriram; Kawakibi, Abed Rahman; Ji, Sunjong; Waszak, Sebastian Martin; Sweha, Stefan R. & Mota, Mateus [Show all 84 contributors for this article] (2023). Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways. Cancer Discovery. ISSN 2159-8274. 13(11), p. 2370–2393. doi: 10.1158/2159-8290.CD-23-0131. Full text in Research Archive Show summary

  Patients with H3K27M-mutant diffuse midline glioma (DMG) have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this finding remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/cerebrospinal fluid (CSF) correlate samples from patients treated in two completed multisite clinical studies. Patients treated with ONC201 following initial radiation but prior to recurrence demonstrated a median overall survival of 21.7 months, whereas those treated after recurrence had a median overall survival of 9.3 months. Radiographic response was associated with increased expression of key tricarboxylic acid cycle–related genes in baseline tumor sequencing. ONC201 treatment increased 2-hydroxyglutarate levels in cultured H3K27M-DMG cells and patient CSF samples. This corresponded with increases in repressive H3K27me3 in vitro and in human tumors accompanied by epigenetic downregulation of cell cycle regulation and neuroglial differentiation genes. Overall, ONC201 demonstrates efficacy in H3K27M-DMG by disrupting integrated metabolic and epigenetic pathways and reversing pathognomonic H3K27me3 reduction. Significance: The clinical, radiographic, and molecular analyses included in this study demonstrate the efficacy of ONC201 in H3K27M-mutant DMG and support ONC201 as the first monotherapy to improve outcomes in H3K27M-mutant DMG beyond radiation. Mechanistically, ONC201 disrupts integrated metabolic and epigenetic pathways and reverses pathognomonic H3K27me3 reduction.

• Katke, Chinmay; Pedrueza-Villalmanzo, Esteban; Spustova, Karolina; Ryskulov, Ruslan; Kaplan, C. Nadir & Gözen, Irep (2023). Colony-like Protocell Superstructures. ACS Nano. ISSN 1936-0851. 17(4), p. 3368–3382. doi: 10.1021/acsnano.2c08093. Full text in Research Archive Show summary

  We report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate nonenzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nanotethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature “exocompartments”, which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed suggests that a plausible driving force behind subcompartment formation is attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 236 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the “lipid world hypothesis”, protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.

• Lin, Xiaolin; Wang, Wei; Yang, Mingyi; Damseh, Nadirah; Sousa, Mirta & Jacob, Fadi [Show all 29 contributors for this article] (2023). A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial–temporal regulation of histone arginine methylation in neurodevelopment. Genome Biology. ISSN 1465-6906. 24(1). doi: 10.1186/s13059-023-03037-1. Full text in Research Archive Show summary

  Background Oxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pathways, cell cycle, neuronal protection, and arginine methylation. In 2019, five patients from three families carrying four biallelic loss-of-function variants in OXR1 were reported to be associated with cerebellar atrophy. However, the impact of OXR1 on cellular functions and molecular mechanisms in the human brain is largely unknown. Notably, no human disease models are available to explore the pathological impact of OXR1 deficiency. Results We report a novel loss-of-function mutation in the TLDc domain of the human OXR1 gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generate patient-derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identify that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1-dependent mechanisms regulating gene expression during neurodevelopment. We model the function of OXR1 in early human brain development using patient-derived brain organoids revealing that OXR1 contributes to the spatial–temporal regulation of histone arginine methylation in specific brain regions. Conclusions This study provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency in patients.

• Fornes, Oriol; Av-Shalom, Tamar V; Korecki, Andrea J; Farkas, Rachelle A; Arenillas, David J & Mathelier, Anthony [Show all 8 contributors for this article] (2023). OnTarget: In silico design of MiniPromoters for targeted delivery of expression. Nucleic Acids Research (NAR). ISSN 0305-1048. 51(W1), p. W379–W386. doi: 10.1093/nar/gkad375. Full text in Research Archive Show summary

  Abstract MiniPromoters, or compact promoters, are short DNA sequences that can drive expression in specific cells and tissues. While broadly useful, they are of high relevance to gene therapy due to their role in enabling precise control of where a therapeutic gene will be expressed. Here, we present OnTarget (http://ontarget.cmmt.ubc.ca), a webserver that streamlines the MiniPromoter design process. Users only need to specify a gene of interest or custom genomic coordinates on which to focus the identification of promoters and enhancers, and can also provide relevant cell-type-specific genomic evidence (e.g. accessible chromatin regions, histone modifications, etc.). OnTarget combines the provided data with internal data to identify candidate promoters and enhancers and design MiniPromoters. To illustrate the utility of OnTarget, we designed and characterized two MiniPromoters targeting different cell populations relevant to Parkinson Disease.

• Skiba, Adrianna; Kozioł, Ewelina; Luca, Simon Vlad; Budzyńska, Barbara; Podlasz, Piotr & Ent, Wietske van der [Show all 12 contributors for this article] (2023). Evaluation of the Antiseizure Activity of Endemic Plant Halfordia kendack Guillaumin and Its Main Constituent, Halfordin, on a Zebrafish Pentylenetetrazole (PTZ)-Induced Seizure Model. International Journal of Molecular Sciences. ISSN 1661-6596. 24(3). doi: 10.3390/ijms24032598. Full text in Research Archive Show summary

  Epilepsy is a neurological disease that burdens over 50 million people worldwide. Despite the considerable number of available antiseizure medications, it is estimated that around 30% of patients still do not respond to available treatment. Herbal medicines represent a promising source of new antiseizure drugs. This study aimed to identify new drug lead candidates with antiseizure activity from endemic plants of New Caledonia. The crude methanolic leaf extract of Halfordia kendack Guillaumin (Rutaceae) significantly decreased (75 μg/mL and 100 μg/mL) seizure-like behaviour compared to sodium valproate in a zebrafish pentylenetetrazole (PTZ)-induced acute seizure model. The main coumarin compound, halfordin, was subsequently isolated by liquid-liquid chromatography and subjected to locomotor, local field potential (LFP), and gene expression assays. Halfordin (20 μM) significantly decreased convulsive-like behaviour in the locomotor and LFP analysis (by 41.4% and 60%, respectively) and significantly modulated galn, and penka gene expression.

• Pelin, Katarina; Sagath, Lydia; Lehtonen, Johanna; Kiiski, Kirsi; Tynninen, Olli & Paetau, Anders [Show all 10 contributors for this article] (2023). Novel Compound Heterozygous Splice-Site Variants in TPM3 Revealed by RNA Sequencing in a Patient with an Unusual Form of Nemaline Myopathy: A Case Report. Journal of Neuromuscular Diseases. ISSN 2214-3599. 10(5), p. 977–984. doi: 10.3233/JND-230026. Full text in Research Archive Show summary

  Background: Pathogenic variants in the TPM3 gene, encoding slow skeletal muscle α-tropomyosin account for less than 5% of nemaline myopathy cases. Dominantly inherited or de novo missense variants in TPM3 are more common than recessive loss-of-function variants. The recessive variants reported to date seem to affect either the 5’ or the 3’ end of the skeletal muscle-specific TPM3 transcript. Objectives: The aim of the study was to identify the disease-causing gene and variants in a Finnish patient with an unusual form of nemaline myopathy. Methods: The genetic analyses included Sanger sequencing, whole-exome sequencing, targeted array-CGH, and linked-read whole genome sequencing. RNA sequencing was done on total RNA extracted from cultured myoblasts and myotubes of the patient and controls. TPM3 protein expression was assessed by Western blot analysis. The diagnostic muscle biopsy was analyzed by routine histopathological methods. Results: The patient had poor head control and failure to thrive, but no hypomimia, and his upper limbs were clearly weaker than his lower limbs, features which in combination with the histopathology suggested TPM3-caused nemaline myopathy. Muscle histopathology showed increased fiber size variation and numerous nemaline bodies predominantly in small type 1 fibers. The patient was found to be compound heterozygous for two splice-site variants in intron 1a of TPM3: NM_152263.4:c.117+2_5delTAGG, deleting the donor splice site of intron 1a, and NM_152263.4:c.117 + 164 C&gt;T, which activates an acceptor splice site preceding a non-coding exon in intron 1a. RNA sequencing revealed inclusion of intron 1a and the non-coding exon in the transcripts, resulting in early premature stop codons. Western blot using patient myoblasts revealed markedly reduced levels of the TPM3 protein. Conclusions: Novel biallelic splice-site variants were shown to markedly reduce TPM3 protein expression. The effects of the variants on splicing were readily revealed by RNA sequencing, demonstrating the power of the method.

• Lee, Pui Y.; Davidson, Brad A.; Abraham, Roshini S.; Alter, Blanche; Arostegui, Juan I. & Bell, Katherine [Show all 41 contributors for this article] (2023). Evaluation and Management of Deficiency of Adenosine Deaminase 2: An International Consensus Statement. JAMA Network Open. 6(5), p. e2315894–e2315894. doi: 10.1001/jamanetworkopen.2023.15894. Full text in Research Archive Show summary

  Importance Deficiency of adenosine deaminase 2 (DADA2) is a recessively inherited disease characterized by systemic vasculitis, early-onset stroke, bone marrow failure, and/or immunodeficiency affecting both children and adults. DADA2 is among the more common monogenic autoinflammatory diseases, with an estimate of more than 35 000 cases worldwide, but currently, there are no guidelines for diagnostic evaluation or management. Objective To review the available evidence and develop multidisciplinary consensus statements for the evaluation and management of DADA2. Evidence Review The DADA2 Consensus Committee developed research questions based on data collected from the International Meetings on DADA2 organized by the DADA2 Foundation in 2016, 2018, and 2020. A comprehensive literature review was performed for articles published prior to 2022. Thirty-two consensus statements were generated using a modified Delphi process, and evidence was graded using the Oxford Center for Evidence-Based Medicine Levels of Evidence. Findings The DADA2 Consensus Committee, comprising 3 patient representatives and 35 international experts from 18 countries, developed consensus statements for (1) diagnostic testing, (2) screening, (3) clinical and laboratory evaluation, and (4) management of DADA2 based on disease phenotype. Additional consensus statements related to the evaluation and treatment of individuals with DADA2 who are presymptomatic and carriers were generated. Areas with insufficient evidence were identified, and questions for future research were outlined. Conclusions and Relevance DADA2 is a potentially fatal disease that requires early diagnosis and treatment. By summarizing key evidence and expert opinions, these consensus statements provide a framework to facilitate diagnostic evaluation and management of DADA2.

• Brandt, E.; Harjama, L.; Elomaa, O.; Saarela, Janna Saija; Donner, K. & Lappalainen, K. [Show all 11 contributors for this article] (2023). A novel SERPINA12 variant and first European patients with diffuse palmoplantar keratoderma. Journal of the European Academy of Dermatology and Venereology. ISSN 0926-9959. doi: 10.1111/jdv.19498. Full text in Research Archive Show summary

  Abstract Background Hereditary palmoplantar keratodermas (hPPKs) comprise a heterogeneous group of skin disorders characterized by persistent palmoplantar hyperkeratosis. Loss‐of‐function variants in a serine peptidase inhibitor, SERPINA12 , have recently been implicated in autosomal recessive diffuse hPPK. The disorder appears to share similarities with another hPPK associated with protease overactivity, namely Nagashima‐type PPK (NPPK) caused by biallelic variants in SERPINB7 . Objectives The aim of this study was to enhance the understanding of the clinical and genetic characteristics of serine protease‐related hPPKs caused by variants in SERPINA12 and SERPINB7 . Methods Whole‐exome sequencing (WES) was performed for hPPK patients. Haplotype analysis was completed for the patients with identified recessive SERPINA12 variants and their available family members. In addition, the current literature of SERPINA12 ‐ and SERPINB7 ‐related hPPKs was summarized. Results The phenotype of SERPINA12 ‐related hPPK was confirmed by reporting three new SERPINA12 patients, the first of European origin. A novel SERPINA12 c.1100G&gt;A p.(Gly367Glu) missense variant was identified confirming that the variant spectrum of SERPINA12 include both truncating and missense variants. The previously reported SERPINA12 c.631C&gt;T p.(Arg211*) was indicated enriched in the Finnish population due to a plausible founder effect. In addition, SERPINA12 hPPK patients were shown to share a similar phenotype to patients with recessive variants in SERPINB7 . The shared phenotype included diffuse transgradient PPK since birth or early childhood and frequent palmoplantar hyperhidrosis, aquagenic whitening and additional hyperkeratotic lesions in non‐palmoplantar areas. SERPINA12 and SERPINB7 hPPK patients cannot be distinguished without genetic analysis. Conclusions Recessive variants in SERPINA12 and SERPINB7 leading to protease overactivity and hPPK produce a similar phenotype, indistinguishable without genetic analysis. SERPINA12 variants should be assessed also in non‐Asian patients with diffuse transgradient PPK. Understanding the role of serine protease inhibitors will provide insights into the complex proteolytic network in epidermal homeostasis.

• DeMarzio, Margherita; Glass, Kimberly & Kuijjer, Marieke (2023). Single-sample network modeling on omics data. BMC Biology. doi: 10.1186/s12915-023-01783-z. Full text in Research Archive Show summary

  Modeling networks for single samples can facilitate discoveries in biology that go beyond those found when analyzing an “aggregate” network, i.e., one that merges information across all the samples in an omics data set. In this commentary article, we discuss the history, current state, and future directions of the field of single-sample network modeling using omics data.

• Sørensen, Henrik Vinther; Canals, Mateu Montserrat; Loose, Jennifer Sarah Maria; Fisher, S. Zoë; Moulin, Martine & Blakeley, Matthew P. [Show all 9 contributors for this article] (2023). Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. ACS Omega. 8(32), p. 29101–29112. doi: 10.1021/acsomega.3c02168. Full text in Research Archive Show summary

  Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen’s large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using N-acetylglucosamine-binding protein A (GbpA) from Vibrio cholerae as a target. GbpA is a multifunctional protein that is secreted by the bacteria to colonize and degrade chitin. We developed an efficient deuteration protocol, which yields >10 mg of pure 97% deuterated protein per liter expression media, which was scaled up further at international facilities. The deuterated protein retains its catalytic activity and structure, as demonstrated by small-angle X-ray and neutron scattering studies of full-length GbpA and X-ray crystal structures of its LPMO domain (to 1.1 Å resolution), setting the stage for neutron scattering experiments with its substrate chitin.

• Sørensen, Henrik Vinther; Montserrat-Canals, Mateu; Prévost, Sylvain François; Vaaje-Kolstad, Gustav; Bjerregaard-Andersen, Kaare & Lund, Reidar [Show all 7 contributors for this article] (2023). Tangled up in fibers: How a lytic polysaccharide monooxygenase binds its chitin substrate. BioRxiv. ISSN 0362-4331. doi: 10.1101/2023.09.21.558757. Full text in Research Archive
• Desalegn, Anteneh Assefa; Ent, Wietske van der; Lenters, Virissa Claire; Torcelino-Iszatt, Nina Louise; Stigum, Hein & Lyche, Jan Ludvig [Show all 10 contributors for this article] (2023). Perinatal exposure to potential endocrine disrupting chemicals and autism spectrum disorder: From Norwegian birth cohort to zebrafish studies. Environment International. ISSN 0160-4120. 181. doi: 10.1016/j.envint.2023.108271. Full text in Research Archive Show summary

  Background The etiology of autism spectrum disorder (ASD) is multifactorial, involving genetic and environmental contributors such as endocrine-disrupting chemicals (EDCs). Objective To evaluate the association between perinatal exposure to 27 potential EDCs and ASD among Norwegian children, and to further examine the neurodevelopmental toxicity of associated chemicals using zebrafish embryos and larvae. Method 1,199 mothers enrolled in the prospective birth-cohort (HUMIS, 2002–2009) study. Breastmilk levels of 27 chemicals were measured: polychlorinated biphenyls, organochlorine pesticides, polybrominated diphenyl ethers, and perfluoroalkyl substances as a proxy for perinatal exposure. We employed multivariable logistic regression to determine association, utilized elastic net logistic regression as variable selection method, and conducted an in vivo study with zebrafish larvae to confirm the neurodevelopmental effect. Results A total of 20 children had specialist confirmed diagnosis of autism among 1,199 mother–child pairs in this study. β-Hexachlorocyclohexane (β-HCH) was the only chemical associated with ASD, after adjusting for 26 other chemicals. Mothers with the highest levels of β-HCH in their milk had a significant increased risk of having a child with ASD (OR = 1.82, 95 % CI: 1.20, 2.77 for an interquartile range increase in ln-transformed β-HCH concentration). The median concentration of β-HCH in breast milk was 4.37 ng/g lipid (interquartile range: 2.92–6.47), and the estimated daily intake (EDI) for Norwegian children through breastfeeding was 0.03 µg/kg of body weight. The neurodevelopmental and social behavioral effects of β-HCH were established in zebrafish embryos and larvae across various concentrations, with further analysis suggesting that perturbation of dopaminergic neuron development may underlie the neurotoxicity associated with β-HCH. Conclusions Prenatal exposure to β-HCH was associated with an increased risk of specialist-confirmed diagnoses of ASD among Norwegian children, and the EDI surpasses the established threshold. Zebrafish experiments confirm β-HCH neurotoxicity, suggesting dopaminergic neuron disruption as a potential underlying mechanism.

• Tran, Dang-Khoa; Phuong, Thuy Nguyen Thi; Bui, Nhat-Le; Singh, Vijai; Looi, Qi Hao & Koh, Benson [Show all 11 contributors for this article] (2023). Exploring the potential of stem cell-based therapy for aesthetic and plastic surgery. IEEE Reviews in Biomedical Engineering (RBME). ISSN 1941-1189. 16, p. 386–402. doi: 10.1109/RBME.2021.3134994. Full text in Research Archive
• Rauluseviciute, Ieva; Launay, Timothée; Barzaghi, Guido; Nikumbh, Sarvesh; Lenhard, Boris & Krebs, Arnaud Regis [Show all 8 contributors for this article] (2023). Identification of transcription factor co-binding patterns with non-negative matrix factorization. BioRxiv. ISSN 0362-4331. doi: 10.1101/2023.04.28.538684. Full text in Research Archive
• Dapsance, Florian; Hou, Jie; Dufour, Damien; Boccara, Charlotte; Briand, Nolwenn & Martinsen, Ørjan Grøttem (2023). Adipose Tissue Characterization With Electrical Impedance Spectroscopy and Machine Learning. IEEE Sensors Letters. 7(10). doi: 10.1109/LSENS.2023.3317921. Full text in Research Archive Show summary

  Biological tissues have variable passive electrical properties depending on their cellular constitution. Electrical impedance spectroscopy (EIS) is commonly used to monitor cell and tissue characteristics. By measuring the impedance of a sample at various frequencies, it is possible to collect information regarding cell size and shape, cell membrane properties, or cytoplasm conductivity. From the perspective of longitudinal structural monitoring, bioimpedance measurements outrank traditional tissue analysis methods, such as fixation and slicing, owing to their nondestructive nature. Machine learning can be used to automatically process the impedance data and make real-time classifications of tissue types. Here, we present preliminary results on ex-vivo mouse adipose tissue measurements using EIS and further data processing and classification using machine learning models.

• Waszak, Sebastian Martin (2022). Germline determinants of the prostate tumor genome. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.11.16.516773. Full text in Research Archive
• Przystal, Justyna M.; Cosentino, Chiara Cianciolo; Yadavilli, Sridevi; Zhang, Jie; Laternser, Sandra & Bonner, Erin R. [Show all 26 contributors for this article] (2022). Imipridones affect tumor bioenergetics and promote cell lineage differentiation in diffuse midline gliomas. Neuro-Oncology. ISSN 1522-8517. 24(9), p. 1438–1451. doi: 10.1093/neuonc/noac041. Full text in Research Archive
• Chica-Balaguera, Nathalia; Portantier, Marina; Nyquist-Andersen, Mari; Burriel, Silvia Espada & Aviles, Sandra Lopez (2022). Uncoupling of Mitosis and Cytokinesis Upon a Prolonged Arrest in Metaphase Is Influenced by Protein Phosphatases and Mitotic Transcription in Fission Yeast. Frontiers in Cell and Developmental Biology. 10. doi: 10.3389/fcell.2022.876810. Full text in Research Archive Show summary

  Depletion of the Anaphase-Promoting Complex/Cyclosome (APC/C) activator Cdc20 arrests cells in metaphase with high levels of the mitotic cyclin (Cyclin B) and the Separase inhibitor Securin. In mammalian cells this arrest has been exploited for the treatment of cancer with drugs that engage the spindle assembly checkpoint and, recently, with chemical inhibitors of the APC/C. While most cells arrested in mitosis for prolonged periods undergo apoptosis, others skip cytokinesis and enter G1 with unsegregated chromosomes. This process, known as mitotic slippage, generates aneuploidy and increases genomic instability in the cancer cell. Here, we analyze the behavior of fission yeast cells arrested in mitosis through the transcriptional silencing of the Cdc20 homolog slp1 . While depletion of slp1 readily halts cells in metaphase, this arrest is only transient and a majority of cells eventually undergo cytokinesis and show steady mitotic dephosphorylation. Notably, this occurs in the absence of Cyclin B (Cdc13) degradation. We investigate the involvement of phosphatase activity in these events and demonstrate that PP2A-B55 Pab1 is required to prevent septation and, during the arrest, its CDK-mediated inhibition facilitates the induction of cytokinesis. In contrast, deletion of PP2A-B56 Par1 completely abrogates septation. We show that this effect is partly due to this mutant entering mitosis with reduced CDK activity. Interestingly, both PP2A-B55 Pab1 and PP2A-B56 Par1 , as well as Clp1 (the homolog of the budding yeast mitotic phosphatase Cdc14) are required for the dephosphorylation of mitotic substrates during the escape. Finally, we show that the mitotic transcriptional wave controlled by the RFX transcription factor Sak1 facilitates the induction of cytokinesis and also requires the activity of PP2A-B56 Par1 in a mechanism independent of CDK.

• Gözen, Irep; Köksal, Elif; Põldsalu, Inga; Xue, Lin; Spustova, Karolina & Pedrueza-Villalmanzo, Esteban [Show all 9 contributors for this article] (2022). Protocells: Milestones and Recent Advances. Small. ISSN 1613-6810. 18(18). doi: 10.1002/smll.202106624. Full text in Research Archive Show summary

  The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

• Pihlajamaa, Päivi; Kauko, Otto; Sahu, Biswajyoti; Kivioja, Teemu & Taipale, Jussi (2022). A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites. Nature Biotechnology. ISSN 1087-0156. Full text in Research Archive
• Xue, Lin; Stephenson, Anna B. & Gözen, Irep (2022). Liposome-assisted in-situ cargo delivery to artificial cells and cellular subcompartments. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.04.27.489538. Full text in Research Archive
• Arranz, Lorena (2022). The Hematology of Tomorrow Is Here-Preclinical Models Are Not: Cell Therapy for Hematological Malignancies. Cancers. 14(3). doi: 10.3390/cancers14030580. Full text in Research Archive Show summary

  The purpose of this review is to present the current knowledge on the clinical use of several forms of cell therapy in hematological malignancies and the preclinical models available for their study. In the context of allogeneic hematopoietic stem cell transplants, mesenchymal stromal cells are pursued to help stem cell engraftment and expansion, and control graft versus host disease. We further summarize the status of promising forms of cellular immunotherapy including CAR T cell and CAR NK cell therapy aimed at eradicating the cells of origin of leukemia, i.e., leukemia stem cells. Updates on other forms of cellular immunotherapy, such as NK cells, CIK cells and CAR CIK cells, show encouraging results in AML. The considerations in available in vivo models for disease modelling and treatment efficacy prediction are discussed, with a particular focus on their strengths and weaknesses for the study of healthy and diseased hematopoietic stem cell reconstitution, graft versus host disease and immunotherapy. Despite current limitations, cell therapy is a rapidly evolving field that holds the promise of improved cure rates, soon. As a result, we may be witnessing the birth of the hematology of tomorrow. To further support its development, improved preclinical models including humanized microenvironments in mice are urgently needed.

• Tuovinen, Elina A.; Kuismin, Outi; Soikkonen, Leila; Martelius, Timi; Kaustio, Meri & Hamalainen, Sari [Show all 15 contributors for this article] (2022). Long-term follow up of families with pathogenic NFKB1 variants reveals incomplete penetrance and frequent inflammatory sequelae. Clinical Immunology. ISSN 1521-6616. doi: 10.1016/j.clim.2022.109181. Full text in Research Archive Show summary

  Nuclear factor κ light-chain enhancer of activated B cells (NF-κB) family of evolutionarily conserved transcription factors are involved in key cellular signaling pathways. Previously, hypogammaglobulinemia and common variable immunodeficiency (CVID)-like phenotypes have been associated with NFKB1 variants and loss-of-function NFKB1 variants have been reported as the most common monogenic cause for CVID among Europeans. Here, we describe a Finnish cohort of NFKB1 carriers consisting of 31 living subjects in six different families carrying five distinct heterozygous variants. In contrast to previous reports, the clinical penetrance was not complete even with advancing age and the prevalence of CVID/hypogammaglobulinemia was significantly lower, whereas (auto)inflammatory manifestations were more common (42% of the total cohort). At current stage of knowledge, routine genetic screening of asymptomatic individuals is not recommended, but counseling of potential adult carriers seems necessary.

• Fernandez, Javier Gutierrez; Javaid, Faiza; Rossi, Giulia De; Chudasama, Vijay; Greenwood, John & Moss, Stephen E [Show all 7 contributors for this article] (2022). Structural basis of human LRG1 recognition by Magacizumab, a humanized monoclonal antibody with therapeutic potential. Acta Crystallographica Section D: Structural Biology. 78, p. 725–734. doi: 10.1107/S2059798322004132. Full text in Research Archive Show summary

  The formation of new dysfunctional blood vessels is a crucial stage in the development of various conditions such as macular degeneration, diabetes, cardiovascular disease, neurological disease and inflammatory disorders, as well as during tumor growth, eventually contributing to metastasis. An important factor involved in pathogenic angiogenesis is leucine-rich α-2-glycoprotein 1 (LRG1), the antibody blockade of which has been shown to lead to a reduction in both choroidal neovascularization and tumor growth in mouse models. In this work, the structural interactions between the LRG1 epitope and the Fab fragment of Magacizumab, a humanized function-blocking IgG4 against LRG1, are analysed, determining its specific binding mode and the key residues involved in LRG1 recognition. Based on these structural findings, a series of mutations are suggested that could be introduced into Magacizumab to increase its affinity for LRG1, as well as a model of the entire Fab–LRG1 complex that could enlighten new strategies to enhance affinity, consequently leading towards an even more efficient therapeutic.

• Merklinger, Lisa; Bauer, Johannes; Pedersen, Per A.; Damgaard, Rune Busk & Morth, Jens Preben (2022). Phospholipids alter activity and stability of mitochondrial membrane-bound ubiquitin ligase MARCH5. Life Science Alliance (LSA). 5(8), p. 1–13. doi: 10.26508/lsa.202101309. Full text in Research Archive Show summary

  Mitochondrial homeostasis is tightly controlled by ubiquitination. The mitochondrial integral membrane ubiquitin ligase MARCH5 is a crucial regulator of mitochondrial membrane fission, fusion, and disposal through mitophagy. In addition, the lipid composition of mitochondrial membranes can determine mitochondrial dynamics and organelle turnover. However, how lipids influence the ubiquitination processes that control mitochondrial homeostasis remains unknown. Here, we show that lipids common to the mitochondrial membranes interact with MARCH5 and affect its activity and stability depending on the lipid composition in vitro. As the only one of the tested lipids, cardiolipin binding to purified MARCH5 induces a significant decrease in thermal stability, whereas stabilisation increases the strongest in the presence of phosphatidic acid. Furthermore, we observe that the addition of lipids to purified MARCH5 alters the ubiquitination pattern. Specifically, cardiolipin enhances auto-ubiquitination of MARCH5. Our work shows that lipids can directly affect the activity of ubiquitin ligases and suggests that the lipid composition in mitochondrial membranes could control ubiquitination-dependent mechanisms that regulate the dynamics and turnover of mitochondria.

• Kline, Cassie; Jain, Payal; Kilburn, Lindsay; Bonner, Erin R.; Gupta, Nalin & Crawford, John R. [Show all 28 contributors for this article] (2022). Upfront Biology-Guided Therapy in Diffuse Intrinsic Pontine Glioma: Therapeutic, Molecular, and Biomarker Outcomes from PNOC003. Clinical Cancer Research. ISSN 1078-0432. 28(18), p. 3965–3978. doi: 10.1158/1078-0432.CCR-22-0803. Full text in Research Archive Show summary

  Abstract Purpose: PNOC003 is a multicenter precision medicine trial for children and young adults with newly diagnosed diffuse intrinsic pontine glioma (DIPG). Patients and Methods: Patients (3–25 years) were enrolled on the basis of imaging consistent with DIPG. Biopsy tissue was collected for whole-exome and mRNA sequencing. After radiotherapy (RT), patients were assigned up to four FDA-approved drugs based on molecular tumor board recommendations. H3K27M-mutant circulating tumor DNA (ctDNA) was longitudinally measured. Tumor tissue and matched primary cell lines were characterized using whole-genome sequencing and DNA methylation profiling. When applicable, results were verified in an independent cohort from the Children's Brain Tumor Network (CBTN). Results: Of 38 patients enrolled, 28 patients (median 6 years, 10 females) were reviewed by the molecular tumor board. Of those, 19 followed treatment recommendations. Median overall survival (OS) was 13.1 months [95% confidence interval (CI), 11.2–18.4] with no difference between patients who followed recommendations and those who did not. H3K27M-mutant ctDNA was detected at baseline in 60% of cases tested and associated with response to RT and survival. Eleven cell lines were established, showing 100% fidelity of key somatic driver gene alterations in the primary tumor. In H3K27-altered DIPGs, TP53 mutations were associated with worse OS (TP53mut 11.1 mo; 95% CI, 8.7–14; TP53wt 13.3 mo; 95% CI, 11.8–NA; P = 3.4e−2), genome instability (P = 3.1e−3), and RT resistance (P = 6.4e−4). The CBTN cohort confirmed an association between TP53 mutation status, genome instability, and clinical outcome. Conclusions: Upfront treatment-naïve biopsy provides insight into clinically relevant molecular alterations and prognostic biomarkers for H3K27-altered DIPGs.

• Santana-Garcia, Walter; Mondragon, Jaime Abraham Castro; Padilla-Gálvez, Mónica; Nguyen, Nga Thi Thuy; Elizondo-Salas, Ana & Ksouri, Najla [Show all 13 contributors for this article] (2022). RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(1), p. W670–W676. doi: 10.1093/nar/gkac312. Full text in Research Archive Show summary

  Abstract RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/.

• Ferenc, Katalin Terezia; Otto, Konrad; Neto, Francisco Gomes de Oliveira; López, Marcela Dávila; Horkoff, Jennifer & Schliep, Alexander (2022). Empirical study on software and process quality in bioinformatics tools. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.03.10.483804. Full text in Research Archive
• Guebila, Marouen Ben; Morgan, Daniel C.; Glass, Kimberly; Kuijjer, Marieke; Demeo, Dawn L. & Quackenbush, John (2022). gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genomics and Bioinformatics. 4(1). doi: 10.1093/nargab/lqac002. Full text in Research Archive Show summary

  Abstract Gene regulatory network inference allows for the modeling of genome-scale regulatory processes that are altered during development, in disease, and in response to perturbations. Our group has developed a collection of tools to model various regulatory processes, including transcriptional (PANDA, SPIDER) and post-transcriptional (PUMA) gene regulation, as well as gene regulation in individual samples (LIONESS). These methods work by postulating a network structure and then optimizing that structure to be consistent with multiple lines of biological evidence through repeated operations on data matrices. Although our methods are widely used, the corresponding computational complexity, and the associated costs and run times, do limit some applications. To improve the cost/time performance of these algorithms, we developed gpuZoo which implements GPU-accelerated calculations, dramatically improving the performance of these algorithms. The runtime of the gpuZoo implementation in MATLAB and Python is up to 61 times faster and 28 times less expensive than multi-core CPU implementation of the same methods. gpuZoo is available in MATLAB through the netZooM package https://github.com/netZoo/netZooM and in Python through the netZooPy package https://github.com/netZoo/netZooPy.

• Bjørklund, Sunniva; Aure, Miriam Ragle; Häkkinen, Jari; Vallon-Christersson, Johan; Kumar, Surendra & Evensen, Katrine Bull [Show all 34 contributors for this article] (2022). Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Communications Biology. 5(1), p. 1–14. doi: 10.1038/s42003-022-03559-7. Full text in Research Archive Show summary

  Abstract Long non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer.

• Guerrini-Rousseau, Lea; Masliah-Planchon, Julien; Waszak, Sebastian Martin; Alhopuro, Pia; Benusiglio, Patrick R & Bourdeaut, Franck [Show all 28 contributors for this article] (2022). Cancer risk and tumour spectrum in 172 patients with a germline SUFU pathogenic variation: A collaborative study of the SIOPE Host Genome Working Group. Journal of Medical Genetics. ISSN 0022-2593. doi: 10.1136/jmedgenet-2021-108385. Full text in Research Archive Show summary

  Background Little is known about risks associated with germline SUFU pathogenic variants (PVs) known as a cancer predisposition syndrome. Methods To study tumour risks, we have analysed data of a large cohort of 45 unpublished patients with a germline SUFU PV completed with 127 previously published patients. To reduce the ascertainment bias due to index patient selection, the risk of tumours was evaluated in relatives with SUFU PV (89 patients) using the Nelson-Aalen estimator. Results Overall, 117/172 (68%) SUFU PV carriers developed at least one tumour: medulloblastoma (MB) (86 patients), basal cell carcinoma (BCC) (25 patients), meningioma (20 patients) and gonadal tumours (11 patients). Thirty-three of them (28%) had multiple tumours. Median age at diagnosis of MB, gonadal tumour, first BCC and first meningioma were 1.5, 14, 40 and 44 years, respectively. Follow-up data were available for 160 patients (137 remained alive and 23 died). The cumulative incidence of tumours in relatives was 14.4% (95% CI 6.8 to 21.4), 18.2% (95% CI 9.7 to 25.9) and 44.1% (95% CI 29.7 to 55.5) at the age of 5, 20 and 50 years, respectively. The cumulative risk of an MB, gonadal tumour, BCC and meningioma at age 50 years was: 13.3% (95% CI 6 to 20.1), 4.6% (95% CI 0 to 9.7), 28.5% (95% CI 13.4 to 40.9) and 5.2% (95% CI 0 to 12), respectively. Sixty-four different PVs were reported across the entire SUFU gene and inherited in 73% of cases in which inheritance could be evaluated. Conclusion Germline SUFU PV carriers have a life-long increased risk of tumours with a spectrum dominated by MB before the age of 5, gonadal tumours during adolescence and BCC and meningioma in adulthood, justifying fine-tuned surveillance programmes.

• Sekulic, Nikolina; Hovet, Oda; Gogoi, Hemanga; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen & Carrer, Manuel [Show all 8 contributors for this article] (2022). The structural basis of the multi-step allosteric activation of Aurora B kinase. BioRxiv. ISSN 0362-4331. Full text in Research Archive
• Köksal, Elif; Põldsalu, Inga; Friis, Henrik; Mojzsis, Stephen J; Bizzarro, Martin & Gözen, Irep (2022). Spontaneous formation of prebiotic compartment colonies on Hadean Earth and pre-Noachian Mars. ChemSystemsChem. 4(3). doi: 10.1002/syst.202100040. Full text in Research Archive Show summary

  Prominent among the models for protocells is the spherical biosurfactant shell, freely suspended in aqueous media. This model explains initial, but not subsequent events in the development process towards structured protocells. Taking into consideration the involvement of naturally occurring surfaces, which were abundant on the early Earth, feasible and productive pathways for the development of primitive cells are reported. Surfaces intrinsically possess energy, easily utilized by the interfacing amphiphiles, such as lipids, to attain self-organization and spontaneous transformations. This work shows that the physical interaction of phospholipid pools with 20 Hadean Earth analogue materials as well as a Martian meteorite composed of fused regolith representing the ancient crust of Mars consistently lead to the shape transformation and autonomous formation of surfactant compartment assemblies. Dense, colony-like protocell populations grow from these lipid deposits, predominantly at the grain boundaries or cleavages of the investigated natural surfaces, and remain there for several days. The model protocells in this study are able to autonomously develop, transform and pseudo-divide, and encapsulate RNA as well as DNA. Moreover, they can accommodate non-enzymatic, DNA strand displacement reactions. These findings suggest a feasible route towards the transformation from non-living to living entities, and provide fresh support for the ‘Lipid World’ hypothesis.

• Cancellieri, Samuele (2022). Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature Genetics. ISSN 1061-4036. doi: 10.1038/s41588-022-01257-y. Full text in Research Archive
• Rossini, Roberto; Kumar, Vipin; Mathelier, Anthony; Rognes, Torbjørn & Paulsen, Jonas (2022). MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biology. ISSN 1465-6906. 23(1). doi: 10.1186/s13059-022-02815-7. Full text in Research Archive Show summary

  DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.

• Modi, Brijesh; Guardamagna, Matteo; Stella, Federico; Griguoli, Marilena; Cherubini, Enrico & Battaglia, Francesco (2022). State Dependent Coupling of Hippocampal Oscillations. BioRxiv. ISSN 0362-4331. Full text in Research Archive
• Messinger, Dana; Harris, Micah K; Cummings, Jessica R; Chase, Thomas; Yang, Tao & Sweha, Stefan R [Show all 38 contributors for this article] (2022). Therapeutic targeting of prenatal pontine ID1 signaling in diffuse midline glioma. Neuro-Oncology. ISSN 1522-8517. doi: 10.1093/neuonc/noac141. Full text in Research Archive Show summary

  Abstract Background Diffuse midline gliomas (DMG) are highly invasive brain tumors with rare survival beyond two years past diagnosis and limited understanding of the mechanism behind tumor invasion. Previous reports demonstrate upregulation of the protein ID1 with H3K27M and ACVR1 mutations in DMG, but this has not been confirmed in human tumors or therapeutically targeted. Methods Whole exome, RNA, and ChIP-sequencing was performed on the ID1 locus in DMG tissue. Scratch-assay migration and transwell invasion assays of cultured cells were performed following shRNA-mediated ID1-knockdown. In vitro and in vivo genetic and pharmacologic [cannabidiol (CBD)] inhibition of ID1 on DMG tumor growth was assessed. Patient-reported CBD dosing information was collected. Results Increased ID1 expression in human DMG and in utero electroporation (IUE) murine tumors is associated with H3K27M mutation and brainstem location. ChIP-sequencing indicates ID1 regulatory regions are epigenetically active in human H3K27M-DMG tumors and prenatal pontine cells. Higher ID1-expressing astrocyte-like DMG cells share a transcriptional program with oligo/astrocyte-precursor cells (OAPCs) from the developing human brain and demonstrate upregulation of the migration regulatory protein SPARCL1. Genetic and pharmacologic (CBD) suppression of ID1 decreases tumor cell invasion/migration and tumor growth in H3.3/H3.1K27M PPK-IUE and human DIPGXIIIP* in vivo models of pHGG. The effect of CBD on cell proliferation appears to be non-ID1 mediated. Finally, we collected patient-reported CBD treatment data, finding that a clinical trial to standardize dosing may be beneficial. Conclusions H3K27M-mediated re-activation of ID1 in DMG results in a SPARCL1+ migratory transcriptional program that is therapeutically targetable with CBD.

• Waszak, Sebastian Martin (2022). Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.08.16.504100. Full text in Research Archive
• Kratz, Christian P.; Smirnov, Dmitrii; Autry, Robert; Jäger, Natalie; Waszak, Sebastian Martin & Großhennig, Anika [Show all 13 contributors for this article] (2022). Heterozygous BRCA1 and BRCA2 and Mismatch Repair Gene Pathogenic Variants in Children and Adolescents With Cancer. Journal of the National Cancer Institute. ISSN 0027-8874. 114(11), p. 1523–1532. doi: 10.1093/jnci/djac151. Full text in Research Archive Show summary

  Abstract Background Genetic predisposition is has been identified as a cause of cancer, yet little is known about the role of adult cancer predisposition syndromes in childhood cancer. We examined the extent to which heterozygous pathogenic germline variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, MSH2, MSH6, MLH1, and PMS2 contribute to cancer risk in children and adolescents. Methods We conducted a meta-analysis of 11 studies that incorporated comprehensive germline testing for children and adolescents with cancer. ClinVar pathogenic or likely pathogenic variants (PVs) in genes of interest were compared with 2 control groups. Results were validated in a cohort of mainly European patients and controls. We employed the Proxy External Controls Association Test to account for different pipelines. Results Among 3975 children and adolescents with cancer, statistically significant associations with cancer risk were observed for PVs in BRCA1 and 2 (26 PVs vs 63 PVs among 27 501 controls, odds ratio = 2.78, 95% confidence interval = 1.69 to 4.45; P &amp;lt; .001) and mismatch repair genes (19 PVs vs 14 PVs among 27 501 controls, odds ratio = 7.33, 95% confidence interval = 3.64 to 14.82; P &amp;lt;.001). Associations were seen in brain and other solid tumors but not in hematologic neoplasms. We confirmed similar findings in 1664 pediatric cancer patients primarily of European descent. Conclusion These data suggest that heterozygous PVs in BRCA1 and 2 and mismatch repair genes contribute with reduced penetrance to cancer risk in children and adolescents. No changes to predictive genetic testing and surveillance recommendations are required.

• Waszak, Sebastian Martin (2022). Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.03.15.483816. Full text in Research Archive

View all works in NVA

• Komisarczuk, Anna Zofia (2026). Genome editing with designer nucleases. Full text in Research Archive
• Karabulut, Hatice; Ervik, Carolina Wieczorek; Flister, Renate Sæther; Kopcil, Pavel; Szymanska, Monika & Hedhili, Dalila [Show all 12 contributors for this article] (2026). Chasing Better Models: Human HSPC Engraftment in Mouse Models (PRIMA). Full text in Research Archive
• Skjelbostad, Sigrid Fu (2026). Engineering T-cells with optimized TCR knock-in and enhanced tumor-killing capacity. Full text in Research Archive
• Skjelbostad, Sigrid Fu (2026). Creating stronger cancer-fighting immune cells. Full text in Research Archive
• Rio, Oline Eriksen; Labun, Kornel; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia; Valen, Eivind & Haapaniemi, Emma Maria (2026). SNIPSNP: precision design of CRISPR reagents. Full text in Research Archive
• Dahal-Koirala, Shiva (2026). Precision T cell correction platform for inborn errors of immunity. Full text in Research Archive
• Karabulut, Hatice; Ervik, Carolina Wieczorek; Flister, Renate Sæther; Kopcil, Pavel; Szymanska, Monika & Hedhili, Dalila [Show all 12 contributors for this article] (2026). Chasing Better Models: Human HSPC Engraftment in Mouse Models. Full text in Research Archive
• Strand, Tor A; Averina, Maria; Bakken, Kjersti Sletten; Basnet, Sudha; Böttcher, Yvonne & Huber, Sandra [Show all 16 contributors for this article] (2026). Early-Life Exposures, Neurodevelopment, and Health Outcomes: Protocol for a Birth Cohort Study. doi: 10.2196/78593. Full text in Research Archive Show summary

  Background Negative early-life exposures, particularly during the first 1000 days of life, may disrupt organ development and lead to lifelong negative health consequences. Objective Using an exposome and deep phenotyping framework, this study aims to characterize established early-life risk factors, including environmental pollutants and nutritional status during pregnancy and infancy, and identify associated short- and long-term health and developmental outcomes. Methods We leverage a pregnancy cohort of 800 mother-infant pairs in Bhaktapur, Nepal, nested within a randomized controlled trial (ClinicalTrials.gov: NCT03071666) that evaluated daily vitamin B12 supplementation from before 15 weeks of gestation until 6 months post partum. The primary outcomes of the original trial were linear growth and neurodevelopment at 12 months. In this follow-up, children will be evaluated up to school age to obtain more robust estimates of long-term health outcomes. Exposures include clinical, dietary, cognitive, demographic, and anthropometric variables during pregnancy and infancy, as well as analyses of environmental pollutants, inflammation, micronutrient status, and hormonal status. Outcomes comprise neurodevelopment, morbidity, mental health, vaccine responses, thyroid function, growth, body composition, lung function, and biomarkers of health and development. Our main research questions for this phase of the project are: (1) what are the most common environmental pollutants among Nepalese women and children? (2) Is there a social gradient in exposure to these pollutants? (3) To what extent are these exposures associated with nutritional status, growth, neurodevelopment, and clinical outcomes? Associations will be examined using cross-sectional, case-control, and cohort designs applying advanced statistical methods to address confounding and complex exposure patterns. Results Enrollment began in March 2017, and the first child was born in August of the same year. More than 90% of the original cohort (734/800, 91.8%) have provided data up to the children’s fourth birthday. By December 2025, the project will have funding until July 2027, and the papers addressing the main research questions will be submitted for publication before the end of 2026. Conclusions This study draws on a well-characterized mother-child cohort in a South Asian setting with repeated biological samples from blood, breast milk, and urine and extensive high-quality longitudinal data on health, growth, and neurodevelopment. By integrating data on environmental exposures, nutrition, inflammation, and biological responses, the project aims to improve understanding of early-life determinants of health and inform policies and potential interventions to protect vulnerable women and children in marginalized settings. While the exploratory nature of exposome analyses entails a risk of spurious associations, careful interpretation and transparent communication of uncertainty will be prioritized. International Registered Report Identifier (IRRID) DERR1-10.2196/78593

• Holme, Andreas Næss; Moen, Line Victoria; Sallinen, Mikael; Nilsen, Kristian Bernhard; Boccara, Charlotte & Haugen, Fred [Show all 7 contributors for this article] (2026). Night Shift Work as an Arctic Hazard: Do Seasonal Light Extremes Affect Alertness, Sleepiness, and Fatigue? Full text in Research Archive Show summary

  Introduction: Light is the primary entrainment mechanism (‘zeitgeber’) of the circadian clock. Its sensitivity to light means that seasonal changes in photoperiod can affect circadian entrainment in shift workers, potentially influencing their adaptation to night work. At high latitudes, such as the Arctic, extreme daylight variations across seasons provide a unique context for studying consequences of such light sensitivity. Polar nights and midnight sun may further challenge circadian entrainment mechanisms. Whether shift work and seasonal variations cumulate or combine their effect in the photoperiodic zeitgeber remains unclear. This study investigates how seasonal variations may interact with consecutive morning and night shifts to impact alertness, sleepiness and fatigue in shift workers. Methods: We recruited 112 three-shift process operators at 71°N, among which 81 participated during both the dark and light seasons. The work schedule included seven consecutive morning shifts and seven consecutive night shifts, separated by four rest days. Objective alertness was measured by the 3-minute Psychomotor Vigilance Task (PVT-B), using lapses (omissions ≥355ms) and response speed (inverse response time) as outcome variables. Subjective sleepiness and fatigue were assessed by the Karolinska Sleepiness Scale (KSS) and a separate question to assess mental fatigue, respectively. Tests were conducted at the end of shift on days 1, 3, and 6 of each 7-day shift block. Data were analysed using multilevel linear mixed-effects regression models with season, shift type (morning/night) and consecutive workday number as fixed effects. Results: Night shifts were associated with lower alertness and higher levels of sleepiness and fatigue, especially on the first night shift, compared to morning shifts. Furthermore, the results indicated significant improvements in alertness and reduced sleepiness and fatigue over the consecutive six night shifts. There was no effect of season on any of the outcome variables. Conclusion: These findings suggest that while night shifts generally impair alertness, as well as increase sleepiness and fatigue, workers may gradually adapt over consecutive shifts, as evidenced by improvements by the sixth night. The lack of significant seasonal effects on sleepiness and fatigue suggests that workers might adapt equally well to night shifts regardless of the photoperiod.

• Ervik, Carolina Wieczorek; Kopcil, Pavel; Szymanska, Monika; Kristiansen, Oddrun; Mamia, Katariina Aino Inkeri & Dahal-Koirala, Shiva [Show all 11 contributors for this article] (2025). ENHANCING CRISPR GENE CORRECTION IN HEMATOPOIETIC STEM/PROGENITOR CELLS. Full text in Research Archive Show summary

  CRISPR/Cas9 is a powerful tool for precise gene correction of monogenic blood diseases, such as deficiency of adenosine deaminase 2 (DADA2), a rare disorder that causes recurrent inflammation and vascular damage. However, the efficiency of homology-directed repair (HDR) in CD34+ hematopoietic stem/progenitor cells (HSPCs) is low and limits the therapeutic potential of this approach. In this study, we used a Finnish founder mutation (R169Q) in ADA2 as a model locus for gene correction. We introduced four silent single nucleotide polymorphisms (SNPs) by electroporation using RNPs (ribonucleoproteins) and single-stranded oligodeoxynucleotide (ssODN) repair template in wild-type CD34+ cells isolated from umbilical cord blood. We evaluated the effect of IDT HDR Enhancer v2, and two PKc inhibitors (KU0060684 and AZD7648) on enhancing HDR in CD34+ cells. We measured the colony forming unit (CFU) output of edited cells was compared: a solid assay based on morphology and pigment of cells, and a liquid assay based on cell surface markers (CD14, CD15, CD235), enabling a higher-throughput setup. Using droplet digital PCR as a method to quantify edited cells, we found that PKc inhibitors increased HDR up to 80% in CD34+ cells. Our results suggest that PKc inhibitors is a promising HDR modulator for gene correction in HSPCs. Viability and proliferation were affected in IDT and KU0060684, but in AZD7648 function as well as mock and control. In conclusion, our preliminary results indicates that AZD7648 could lead to the development of more effective gene therapies for monogenic blood diseases in the future. Furthermore, we are optimizing the in vitro culturing of the long-term repopulating hematopoietic stem cells to keep stemness and potentially expanding this population. While initial in vivo testing has been performed, we will also create a novel human xenograft model for modelling diseases e.g. monogenetic disease and leukemia that are irradiation free.

• Bryne, Sandra Kristine Stølen; Dufour, Damien; Briand, Nolwenn & Boccara, Charlotte (2025). Does poor sleep during adolescence lead to metabolic disorders later in life? – Targeted chemogenetic models of sleep deprivation in mice. Full text in Research Archive Show summary

  Poor sleep and obesity are concurrent health epidemics in adolescents. This is especially concerning given that adolescents are getting less and less sleep as technology invades their bedrooms. Several studies point to adolescence as a critical period for sleep and adipose tissue development, implying that poor sleep during this period might alter the normal development of adipose tissue and cause metabolic imbalance. To investigate whether adolescent sleep quality contributes to the emergence of metabolic dysfunctions later in life, we propose to establish new rodent models of reversible sleep deprivation for which we can turn on and off sleep quality/quantity at specific developmental windows. Here we present preliminary data of our new chemogenetic model for which we can disturb sleep at specific time points between postnatal day P21 and P54 by targeting brain nuclei promoting wakefulness through the stimulation of GABAergic neurons in the ventral pallidum. We assessed the sleep amounts and quality of these animals by recording their neural (EEG) and muscular (EMG) activity. Metabolic parameters during and after sleep disturbances were assessed with metabolic cages (energy expenditure, respiratory exchange rate, food intake, weight, activity), adipose tissue histology and plasma collection (hormones and proteins). Our preliminary results indicate successful sleep deprivation concomitant with decreased respiratory exchange rate indicating a shift toward lipid oxidation as a primary energy source.

• Bryne, Sandra Kristine Stølen; Dufour, Damien; Briand, Nolwenn & Boccara, Charlotte (2025). Can poor sleep during adolescence lead to metabolic disorders later in life?- Targeted chemogenetic models of sleep deprivation in mice. Full text in Research Archive Show summary

  Obesity and poor sleep are concurrent health epidemics in adolescents. This is especially concerning given that adolescents are getting less and less sleep as technology invades their bedrooms. Several studies point to adolescence as a critical period for sleep and adipose tissue development, implying that poor sleep during this period might alter the normal development of adipose tissue. To investigate whether adolescent sleep quality contributes to the emergence of metabolic dysfunctions later in life, we propose to establish new rodent models of reversible sleep deprivation for which we can turn on/off sleep quality/quantity at specific developmental windows. Here we present preliminary data of our new chemogenetic model for which we can disturb sleep at specific time points between postnatal day P21 and P54 by targeting brain nuclei promoting wakefulness through the stimulation of GABAergic neurons in the ventral pallidum. We assessed the sleep amounts and quality of these animals by recording their neural (EEG) and muscular (EMG) activity. Metabolic parameters during and after sleep disturbances were assessed with metabolic cages (energy expenditure, respiratory exchange rate, food/water intake, weight), adipose tissue histology and plasma collection (hormones and proteins). Our preliminary results indicate successful sleep deprivation concomitant with decreased respiratory exchange rate indicating a shift toward lipid oxidation as a primary energy source.

• Risnes, Louise Fremgaard; Dahal-Koirala, Shiva; Hjort, Rebecka; Bolstad, Nils; Lundin, Knut & Ness-Jensen, Eivind [Show all 7 contributors for this article] (2025). Detection of gluten-specific CD4+ T cells with tetramer test among anti-transglutaminase seropositive participants in the HUNT4 study. Full text in Research Archive
• Holme, Andreas Næss; Moen, Line Victoria; Sallinen, Mikael; Nilsen, Kristian Bernhard; Boccara, Charlotte & Haugen, Fred [Show all 7 contributors for this article] (2025). Night Work During Midnight Sun and Polar Nights: Impact on Alertness, Sleepiness and Fatigue. doi: 10.1055/s-0045-1812737. Full text in Research Archive Show summary

  Introduction: The circadian clock's sensitivity to light means that seasonal changes in photoperiod can affect circadian entrainment in shift workers, thus influencing their adaptation to night work. At high latitudes, such as the Arctic, extreme daylight variations across seasons, provide a unique context for studying such circadian disruption. Polar nights and midnight sun may further challenge circadian entrainment mechanisms. Whether shift work and seasonal variations cumulate or combine their effect in the photoperiodic zeitgeber remains unclear. This study investigates how seasonal variations may interact with consecutive morning and night shifts to impact alertness, sleepiness and fatigue. Methods: We recruited 112 three-shift process operators at 71°N, among which 84 participated during both the dark and light seasons. Their work schedule included blocks of seven consecutive morning shifts and seven consecutive night shifts, separated by four rest days. Alertness was measured by the 3-minute Psychomotor Vigilance Task (PVT-B), using lapses (omissions ≥355ms) and response speed (inverse response time) as outcome variables. Sleepiness was assessed by the Karolinska Sleepiness Scale (KSS). A separate question was used to assess mental fatigue. Tests were conducted at the end of the operators’ shift on days 1, 3, and 6 of each shift block. KSS was also assessed at the start and end of all shifts. Data were analyzed using multilevel mixed-effects regression models with season, shift type (morning/night) and consecutive workday number as fixed effects. Results: Night shifts were linked to lower alertness, as well as higher sleepiness and fatigue, especially on the first night shift. Interaction effects indicated improved response speed, fewer lapses, and reduced sleepiness and fatigue over six-night shifts, with significant differences between night 1 and night 6. These patterns were similar for both seasons across all variables. However, PVT-tests showed that the overall contrast between morning and night shifts was only significant during the dark season (response speed: p < 0.0001, lapses: p≈0.005), but not during the light season. Neither sleepiness, nor fatigue, were significantly affected by seasons. Conclusion: These findings suggest that while night shifts generally impair alertness, as well as increase sleepiness and fatigue, workers may gradually adapt over consecutive shifts, as evidenced by improvements by the sixth night. The lack of significant seasonal effects on sleepiness and fatigue suggests that workers might adapt equally well to night shifts regardless of the photoperiod. However, the more pronounced differences in alertness between morning and night shifts during the dark season highlight the potential interplay between reduced daylight’s influence on circadian rhythms and adaptability to work night shifts.

• Moen, Line Victoria; Holme, Andreas Næss; Matre, Dagfinn & Haugen, Fred (2025). SEASONAL IMPACTS ON SLEEP IN ARCTIC SHIFT WORKERS: INSIGHTS FROM WEARABLE MONITORING. Full text in Research Archive Show summary

  Introduction Studies suggest that seasons may influence sleep, though findings are inconsistent. In Arctic settings, the extreme light conditions including polar night (dark season) and midnight sun (light season) may have a distinct impact on the relationship between shift work and sleep. This observational cross-over study aimed to examine seasonal variations in sleep among Arctic shift workers using both subjective and objective sleep measures. Methods A cohort of 112 rotational shift working process operators (mean age 32 ± 11.3 years, 21% women) from an industrial plant at 71°N in Norway participated during both light and dark seasons. Their work schedule included seven consecutive morning shifts and seven consecutive night shifts, separated by four rest days. Objective sleep duration was measured over 20 days with the Oura smart ring, while subjective sleep was measured over 25 days by sleep diary. Results Preliminary results indicate that objectively measured sleep duration (minutes; mean ± SEM) after night shifts was slightly longer in the dark season 385 ± 4 compared to the light season 374 ± 4. The opposite trend was observed for seasonal effects on sleep after morning shifts: 379 ± 3 in the dark season; 387 ± 3 in the light season. Sleep on free days followed the same pattern as morning shifts, with shorter duration in the dark season (443 ± 6) compared to the light season (452 ± 6). Overall, our findings indicate that sleep duration tends to be longer on free days than on workdays. The timing of sleep measured objectively as mid-sleep (hours past midnight), was similar after night shifts across dark and light seasons; at 11.6 and 11.5, respectively. Mid-sleep during the dark and light seasons after morning shifts occurred at 3.0 and 3.3; and on free days, at 5.7 and 6.0; respectively. Subjective sleep duration (minutes; mean ± SEM) in dark and light season after night shifts was 404 ± 5 and 406 ± 5; after morning shifts 411 ± 5 and 404 ± 4; and on free days 492 ± 8 and 489 ± 6, respectively. These subjective ratings were somewhat higher than the objective measures. Conclusion Our data suggests that night shifts and seasonal variations have only a minor impact on objective and subjective measures of total sleep duration among these Arctic shift workers. Follow-up analyses will explore potential underlying factors, day-to-day variation and individual variability. Support (if any) This research is supported by the RRESEARCH COUNCIL OF NORWAY; the PETROMAKS2 program ID# 326291

• Signorelli, Letizia; Korchynska, Solomiia & Boccara, Charlotte (2025). A robust pipeline for sleepscoring in developing rodents. Full text in Research Archive
• Ervik, Carolina Wieczorek; Kopcil, Pavel; Szymanska, Monika; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva & Komisarczuk, Anna Zofia [Show all 10 contributors for this article] (2025). Enhancing CRISPR gene correction in hematopoetic stem/progenitor cells. doi: https:/iuis2025.org/. Full text in Research Archive Show summary

  CRISPR/Cas9 is a powerful tool for precise gene correction of monogenic blood diseases, such as deficiency of adenosine deaminase 2 (DADA2), a rare disorder that causes recurrent inflammation and vascular damage. However, the efficiency of homology-directed repair (HDR) in CD34+ hematopoietic stem/progenitor cells (HSPCs) is low and limits the therapeutic potential of this approach. In this study, we used a Finnish founder mutation (R169Q) in ADA2 as a model locus for gene correction. We introduced four silent single nucleotide polymorphisms (SNPs) by electroporation using RNPs (ribonucleoproteins) and single-stranded oligodeoxynucleotide (ssODN) repair template in wild-type CD34+ cells isolated from umbilical cord blood. We evaluated the effect of IDT HDR Enhancer v2, and two PKc inhibitors (KU0060684 and AZD7648) on enhancing HDR in CD34+ cells. We measured the colony forming unit (CFU) output of edited cells was compared: a solid assay based on morphology and pigment of cells, and a liquid assay based on cell surface markers (CD14, CD15, CD235), enabling a higher-throughput setup. Using droplet digital PCR as a method to quantify edited cells, we found that PKc inhibitors increased HDR up to 80% in CD34+ cells. Our results suggest that PKc inhibitors is a promising HDR modulator for gene correction in HSPCs. Viability and proliferation were affected in IDT and KU0060684, but in AZD7648 function as well as mock and control. In conclusion, our preliminary results indicates that AZD7648 could lead to the development of more effective gene therapies for monogenic blood diseases in the future. Furthermore, we are optimizing the in vitro culturing of the long-term repopulating hematopoietic stem cells to keep stemness and potentially expanding this population. While initial in vivo testing has been performed, we will also create a novel human xenograft model for modelling diseases e.g. monogenetic disease and leukemia that are irradiation free.

• Haugen, Frida Loe; Mamia, Katariina Aino Inkeri; Rio, Oline Eriksen; Sollano, Anniken Solveig Matheson; Li, Zhuokun & Labun, Kornel [Show all 20 contributors for this article] (2025). CRISPR/Cas9-based pipeline to introduce custom edits in autologous T cells. Full text in Research Archive
• Haugen, Frida Loe; Mamia, Katariina Aino Inkeri; Rio, Oline Eriksen; Sollano, Anniken Solveig Matheson; Li, Zhuokun & Labun, Kornel [Show all 20 contributors for this article] (2025). CRISPR-Cas9 pipeline for custom editing in autologous T cells. doi: https:/event.fourwaves.com/crisprmed25/abstracts/b5911e8e-de8e-4ee4-b8e2-9f08cc2f31d8. Full text in Research Archive Show summary

  CRISPR/Cas9 gene editing technology is a promising tool for correcting pathogenic variants in Inborn Errors of Immunity (IEIs). Current IEI correction strategies rely on cDNA knock-in or gene knockout, which can disrupt gene expression and need extensive optimization. To address this, we developed a safe, efficient CRISPR/Cas9-based T cell editing pipeline using HDR for SNV correction. We observe a rapid and selective expansion of CD3+ T cells from patient peripheral blood following an 8-day cytokine stimulation. To enhance HDR outcomes, we explored multiple strategies and developed an optimized T cell pipeline capable of achieving up to 80% HDR. We found no pre-malignant off-target effects or karyotypic, transcriptomic, or proteomic abnormalities in patient T cells analysed with GUIDE-seq, scRNA-seq, long-read WGS, and proteomics. We observed functional correction of the disease phenotype in patient T cells demonstrated on transcriptomic level by single cell RNA sequencing, on proteomic level by Mass Spectrometry and in cell culture-based assays. So far, we have implemented the pipeline and corrected 12 unique SNV mutations causing 8 diverse IEIs. This platform is designed to streamline CRISPR tool discovery/optimization and can be further developed into a GMP-compatible, scaled-up process for salvage therapy in T cell-related IEIs.

• Ervik, Carolina Wieczorek (2025). Establishing GMP-Compatible Culture to Preserve LT-HSC Function and Support Gene Correction for Autologous CRISPR Therapies. Full text in Research Archive Show summary

  Hematopoietic stem cell transplantation (HSCT) offers curative potential for malignant and non-malignant diseases, but expansion and genetic correction of bona fide long-term hematopoietic stem cells (LT-HSCs) remains a major challenge. Homology-directed repair (HDR)-based CRISPR editing is inefficient in quiescent LT-HSCs, and current culture protocols often compromise stemness. To address this, we benchmarked the commercial StemSpan AOF medium against a novel polymer-based, albumin-free medium (Wilkinson homebrew, W-HB) under both atmospheric (20% O₂) and physiologic (10% O₂) conditions. Key findings: CD34⁺ viability: W-HB consistently maintained ≥90% CD34⁺ viability, meeting the in vivo cut-off for transplantation, while AOF dropped below this threshold by day 10. LT-HSC phenotype (CD34⁺CD90⁺EPCR⁺CD45RA⁻CD41⁻): W-HB preserved ~2–2.5× higher LT-HSC frequency compared to AOF over culture, even after electroporation. Proliferation kinetics: W-HB supported slower but steadier proliferation (doubling time ~2.5–3 days), with consistent donor-to-donor trends. Colony-forming assays: W-HB cultures retained more primitive CFU-GEMM colonies, indicating broader multilineage potential. Editing efficiency (ddPCR at ADA2 locus): HDR and NHEJ rates were comparable between AOF and W-HB, demonstrating that editing is not compromised by the albumin-free formulation. Viability post-editing: AOF showed better short-term recovery in the RNP condition, whereas W-HB cultures were more sensitive to electroporation-induced stress — highlighting an area for optimization. Conclusion: The Wilkinson polymer-based medium (W-HB) maintains CD34⁺ viability and LT-HSC phenotype significantly better than the commercial AOF medium, without reducing CRISPR editing efficiency. However, further work is needed to improve post-editing viability in W-HB. These findings support the clinical potential of defined, albumin-free media for autologous CRISPR-based HSC therapies.

• Haugen, Frida Loe (2024). Gene Therapy Innovations: from science and manufacturing to patient benefit. [Internet]. med.uio.no. doi: https:/www.med.uio.no/ncmbm/english/news-and-events/news/2024/gene-therapy-innovations-from-science-and-manufact.html. Full text in Research Archive
• Kopcil, Pavel; Ervik, Carolina Wieczorek; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Szymanska, Monika & Komisarczuk, Anna Zofia [Show all 8 contributors for this article] (2024). Enhancing CRISPR Gene Correction In Hematopoietic Stem/Progenitor Cells. Full text in Research Archive Show summary

  CRISPR/Cas9 is a powerful tool for precise gene correction of monogenic blood diseases, such as deficiency of adenosine deaminase 2 (DADA2), a rare disorder that causes recurrent inflammation and vascular damage. However, the efficiency of homology-directed repair (HDR) in CD34+ hematopoietic stem/progenitor cells (HSPCs) is low and limits the therapeutic potential of this approach. In this study, we used a Finnish founder mutation (R169Q) in ADA2 as a model locus for gene correction. We introduced four silent single nucleotide polymorphisms (SNPs) by electroporation using RNPs (ribonucleoproteins) and single-stranded oligodeoxynucleotide (ssODN) repair template in wild-type CD34+ cells isolated from umbilical cord blood. We evaluated the effect of Compound X, a small molecule inhibitor selected from a chemical compounds screen in T cells, on enhancing HDR in CD34+ cells. We also compared two methods for measuring the colony forming unit (CFU) output of edited cells: a solid assay based on morphology and pigment of cells, and a liquid assay based on cell surface markers (CD14, CD15, CD235), enabling a higher-throughput setup. Using droplet digital PCR (ddPCR) as a method to quantify edited cells, we found that Compound X increased HDR up to 80% in CD34+ cells, but reduced CFU output by 2-3 folds. Our results suggest that Compound X is a promising HDR modulator for gene correction in HSPCs, and could lead to the development of more effective gene therapies for monogenic blood diseases in the near future; however, its side effects need to be further investigated. We are currently performing in vivo experiments with Compound X and exploring novel editing strategies, while also working to align our protocols with current good manufacturing practice (cGMP) standards. Furthermore, we aim to assess and optimize the efficacy of Compound X, as well as similar compounds, in long-term repopulating hematopoietic stem cells (LT-HSCs), given their significant clinical importance and the crucial need to enhance editing efficiency in these cells.

• Kopcil, Pavel; Ervik, Carolina Wieczorek; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Szymanska, Monika & Komisarczuk, Anna Zofia [Show all 8 contributors for this article] (2024). Enhancing CRISPR Gene Correction in Hematopoietic Stem/Progenitor Cells. Full text in Research Archive Show summary

  CRISPR/Cas9 is a powerful tool for precise gene correction of monogenic blood diseases, such as deficiency of adenosine deaminase 2 (DADA2), a rare disorder that causes recurrent inflammation and vascular damage. However, the efficiency of homology-directed repair (HDR) in CD34+ hematopoietic stem/progenitor cells (HSPCs) is low and limits the therapeutic potential of this approach. In this study, we used a Finnish founder mutation (R169Q) in ADA2 as a model locus for gene correction. We introduced four silent single nucleotide polymorphisms (SNPs) by electroporation using RNPs (ribonucleoproteins) and single-stranded oligodeoxynucleotide (ssODN) repair template in wild-type CD34+ cells isolated from umbilical cord blood. We evaluated the effect of Compound X, a small molecule inhibitor selected from a chemical compounds screen in T cells, on enhancing HDR in CD34+ cells. We also compared two methods for measuring the colony forming unit (CFU) output of edited cells: a solid assay based on morphology and pigment of cells, and a liquid assay based on cell surface markers (CD14, CD15, CD235), enabling a higher-throughput setup. Using droplet digital PCR (ddPCR) as a method to quantify edited cells, we found that Compound X increased HDR up to 80% in CD34+ cells, but reduced CFU output by 2-3 folds. Our results suggest that Compound X is a promising HDR modulator for gene correction in HSPCs, and could lead to the development of more effective gene therapies for monogenic blood diseases in the near future; however, its side effects need to be further investigated. We are currently performing in vivo experiments with Compound X and exploring novel editing strategies, while also working to align our protocols with current good manufacturing practice (cGMP) standards. Furthermore, we aim to assess and optimize the efficacy of Compound X, as well as similar compounds, in long-term repopulating hematopoietic stem cells (LT-HSCs), given their significant clinical importance and the crucial need to enhance editing efficiency in these cells.

• Dahal-Koirala, Shiva (2024). CRISPR/Cas9-based autologous T cell editing pipeline for Inborn Errors of Immunity. Full text in Research Archive
• Ervik, Carolina Wieczorek (2024). Personal Introduction & Research Focus: CRISPR-Based Therapies in HSPCs. Full text in Research Archive Show summary

  This presentation introduced Carolina Wieczorek Ervik and the Haapaniemi Lab to the Wilkinson group. Carolina shared her academic and professional background, including her training in medical biology, stem cell biology, GMP cell production, and CRISPR gene editing. The talk highlighted the lab’s overall mission to develop CRISPR-based therapies for inborn errors of immunity, with a focus on optimizing editing protocols in hematopoietic stem and progenitor cells (HSPCs), studying the functionality of edited cells in animal models, scaling up protocols, and translating them into clinical settings. Carolina outlined her specific role in the stem cell team, working on LT-HSC culture optimization, gene editing, flow cytometry, and functional assays, with the ultimate goal of personalized stem cell correction for patients.

• Wang, Heling; Siow, Richard; Schmauck-Medina, Tomás Alejandro; Zhang, Jianying; Sandset, Per Morten & Filshie, Clare [Show all 38 contributors for this article] (2024). Meeting Summary of The NYO3 5th NO-Age/AD Meeting and the 1st Norway-UK Joint Meeting on Aging and Dementia: Recent Progress on the Mechanisms and Interventional Strategies. The journals of gerontology. Series A, Biological sciences and medical sciences. ISSN 1079-5006. 79(4), p. 1–10. doi: 10.1093/gerona/glae029. Full text in Research Archive Show summary

  Unhealthy aging poses a global challenge with profound healthcare and socioeconomic implications. Slowing down the aging process offers a promising approach to reduce the burden of a number of age-related diseases, such as dementia, and promoting healthy longevity in the old population. In response to the challenge of the aging population and with a view to the future, Norway and the United Kingdom are fostering collaborations, supported by a “Money Follows Cooperation agreement” between the 2 nations. The inaugural Norway–UK joint meeting on aging and dementia gathered leading experts on aging and dementia from the 2 nations to share their latest discoveries in related fields. Since aging is an international challenge, and to foster collaborations, we also invited leading scholars from 11 additional countries to join this event. This report provides a summary of the conference, highlighting recent progress on molecular aging mechanisms, genetic risk factors, DNA damage and repair, mitophagy, autophagy, as well as progress on a series of clinical trials (eg, using NAD+ precursors). The meeting facilitated dialogue among policymakers, administrative leaders, researchers, and clinical experts, aiming to promote international research collaborations and to translate findings into clinical applications and interventions to advance healthy aging.

• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun; Reint, Ganna; Komisarczuk, Anna Zofia & Haugen, Frida Høsøien [Show all 21 contributors for this article] (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. Full text in Research Archive
• Boccara, Charlotte (2024). New perspectives on sleep functions. Full text in Research Archive
• Boccara, Charlotte (2024). Beyond space: Hippocampal representations of novelty and reward. Full text in Research Archive
• Boccara, Charlotte (2024). Active memory system – Entorhinal replay during sleep. Full text in Research Archive
• Boccara, Charlotte; Korchynska, Solomiia & Signorelli, Letizia (2024). Recording and analysing sleep and brain activity in laboratory rodents across development. Full text in Research Archive
• Korchynska, Solomiia; Signorelli, Letizia; Modi, Brijesh; Annavini, Eis; Okinina, Lina & Boccara, Charlotte (2024). MICROSTRUCTURE OF SLEEP AND SLEEP OSCILLATION DYNAMICS ACROSS DEVELOPMENT. Full text in Research Archive
• Bryne, Sandra Kristine Stølen; Dufour, Damien; Briand, Nolwenn & Boccara, Charlotte (2024). Inducible mouse models of adolescent sleep deprivation: the role of sleep in metabolic health. Full text in Research Archive
• Boccara, Charlotte (2024). Different dynamics of learning in entorhinal and hippocampal cortices. Full text in Research Archive
• Boccara, Charlotte (2024). Hippocampal and Cortical Dynamics across Learning and Development. Full text in Research Archive
• Modi, Brijesh; Korchynska, Solomiia; Okinina, Lina; Signorelli, Letizia & Boccara, Charlotte (2024). Maturation of Sharp Wave Ripples and Cortical Dynamics during Developmental Sleep. Full text in Research Archive
• Horn, Solveig; Modi, Brijesh & Boccara, Charlotte (2024). BEHAVIORAL METHODS TO INFER COGNITIVE DEVELOPMENT IN RODENTS. Full text in Research Archive
• Boccara, Charlotte (2024). The ERC, funding support for investigator-driven research in Europe. Full text in Research Archive
• Helmersen, Mats; Korchynska, Solomiia & Boccara, Charlotte (2024). Assessing social behaviour in developing rats. Full text in Research Archive
• Boccara, Charlotte; Korchynska, Solomiia & Signorelli, Letizia (2024). Can we automatically discriminate between NREM 1 2 and 3 in rodents across their lifespan? Full text in Research Archive
• Boccara, Charlotte; Korchynska, Solomiia & Signorelli, Letizia (2024). Maturation of REM sleep neural dynamics across development. Full text in Research Archive
• Ervik, Carolina Wieczorek; Kopcil, Pavel; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia & Bak, Rasmus O. [Show all 7 contributors for this article] (2024). Enhancing CRISPR Gene Correction In Hematopoietic Stem/Progenitor Cells. Full text in Research Archive Show summary

  CRISPR/Cas9 is a powerful tool for precise gene correction of monogenic blood diseases, such as deficiency of adenosine deaminase 2 (DADA2), a rare disorder that causes recurrent inflammation and vascular damage. However, the efficiency of homology-directed repair (HDR) in CD34+ hematopoietic stem/progenitor cells (HSPCs) is low and limits the therapeutic potential of this approach. In this study, we used a Finnish founder mutation (R169Q) in ADA2 as a model locus for gene correction. We introduced four silent single nucleotide polymorphisms (SNPs) by electroporation using RNPs (ribonucleoproteins) and single-stranded oligodeoxynucleotide (ssODN) repair template in wild-type CD34+ cells isolated from umbilical cord blood. We evaluated the effect of Compound X, a small molecule inhibitor selected from a chemical compounds screen in T cells, on enhancing HDR in CD34+ cells. We also compared two methods for measuring the colony forming unit (CFU) output of edited cells: a solid assay based on morphology and pigment of cells, and a liquid assay based on cell surface markers (CD14, CD15, CD235), enabling a higher-throughput setup. Using droplet digital PCR (ddPCR) as a method to quantify edited cells, we found that Compound X increased HDR up to 80% in CD34+ cells, but reduced CFU output by 2-3 folds. Our results suggest that Compound X is a promising HDR modulator for gene correction in HSPCs, and could lead to the development of more effective gene therapies for monogenic blood diseases in the near future; however, its side effects need to be further investigated. We are currently performing in vivo experiments with Compound X and exploring novel editing strategies, while also working to align our protocols with current good manufacturing practice (cGMP) standards. Furthermore, we aim to assess and optimize the efficacy of Compound X, as well as similar compounds, in long-term repopulating hematopoietic stem cells (LT-HSCs), given their significant clinical importance and the crucial need to enhance editing efficiency in these cells.

• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun; Reint, Ganna; Komisarczuk, Anna Zofia & Haugen, Frida Høsøien [Show all 21 contributors for this article] (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. Full text in Research Archive
• Rio, Oline Eriksen (2024). CRISPR corrected T-cells for personalized therapy of IEIs. Full text in Research Archive
• Haapaniemi, Emma Maria; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia; Mamia, Katariina Aino Inkeri; Rio, Oline Eriksen & Haugen, Frida Høsøien [Show all 10 contributors for this article] (2024). Presentation of precision pediatrics and gene editing group. Full text in Research Archive
• Dahal-Koirala, Shiva (2024). CRISPR/Cas9-based autologous T cell editing pipeline for Inborn Errors of Immunity. Full text in Research Archive
• Cortés, Natalia Mojica; Kersten, Flore; Krengel, Ute; Cordara, Gabriele; Serrano, Albert & Heim, Joel Benjamin [Show all 7 contributors for this article] (2024). Molecular insights into the differential toxicity of cholera toxin and heat-labile enterotoxin. Full text in Research Archive
• Meijer, Debora; Oost, Siddh van; Roelands, Jessica P; Ruano, Dina; Bruijn, Inge H Briaire-de & Akker, Brendy E van den [Show all 19 contributors for this article] (2024). Enhanced immune responses are accompanied by increased MAGEA expression in osteosarcoma metastases. BMJ Oncology. 3(1). doi: 10.1136/bmjonc-2024-000472. Full text in Research Archive
• Osorio, Daniel & Kuijjer, Marieke (2024). Enabling comparative gene regulatory network analysis on single-cell data with SCORPION. Nature Computational Science. doi: 10.1038/s43588-024-00615-6. Full text in Research Archive
• Canals, Mateu Montserrat; Sekulic, Nikolina & Krengel, Ute (2024). UiO structural biology core facilities. Full text in Research Archive
• Risnes, Louise Fremgaard; Dahal-Koirala, Shiva; Hjort, Rebecka Louise; Bolstad, Nils; Christophersen, Asbjørn Otto & Sarna, Vikas Kumar [Show all 9 contributors for this article] (2024). Påvisning av glutenspesifikke CD4+ T-celler med tetramertest blant anti-transglutaminase seropositive deltakere i HUNT4-studien. Full text in Research Archive
• Korchynska, Solomiia; Signorelli, Letizia; Modi, Brijesh; Annavini, Eis; Okinina, Lina & Boccara, Charlotte (2024). MICROSTRUCTURE OF SLEEP AND SLEEP OSCILLATION DYNAMICS ACROSS DEVELOPMENT. Full text in Research Archive
• Kersten, Flore; Cordara, Gabriele & Krengel, Ute (2024). Cryo-EM structure of a fungal chimerolectin. Full text in Research Archive
• Mamia, Katariina Aino Inkeri; Kolbeinsdottir, Solrun; Li, Zhuokun; Reint, Ganna; Komisarczuk, Anna Zofia & Haugen, Frida Høsøien [Show all 21 contributors for this article] (2024). CRISPR/Cas9 T cell editing pipeline for monogenic primary immunodeficiency disorders. Full text in Research Archive
• Søraas, Arne; Holland, Petter & Dahl, John Arne (2024). Epigenetic aging of human blood cells is influenced by the age of the host body. Aging Cell. ISSN 1474-9718. doi: 10.1111/acel.14112. Full text in Research Archive
• Banono, Nancy Saana; Gawel, Kinga Aurelia; Mäki-Marttunen, Tuomo; Ent, Wietske van der; Kukula-Koch, Wirginia & Fyhn, Marianne [Show all 10 contributors for this article] (2023). Novel zebrafish model for studying neurodevelopment in Timothy syndrome. Full text in Research Archive
• Connors, Craig; Mastracci, Teresa; Devinsky, Orrin; Shojaeinia, Elham; Esguerra, Camila Vicencio & Crawford, Alexander Dettmar (2023). Zebrafish embryos with reduced deoxyhypusine synthase exhibit dysmorphology, epileptiform activity, and reduced GABAergic neuronal arborization. Full text in Research Archive
• Ent, Wietske van der; Kirstein-Smardzewska, Karolina Joanna; Gawel, Kinga Aurelia; Banono, Nancy Saana; Eggesbø, Merete Åse & Esguerra, Camila Vicencio (2023). Evaluation of Developmental Neurotoxicity in Zebrafish (Danio rerio) by Endocrine Disrupting Chemical β-HCH. Full text in Research Archive
• Ent, Wietske van der; Kirstein-Smardzewska, Karolina Joanna; Gawel, Kinga Aurelia; Banono, Nancy Saana; Eggesbø, Merete Åse & Esguerra, Camila Vicencio (2023). Evaluation of Developmental Neurotoxicity in Zebrafish (Danio rerio) by Endocrine Disrupting Chemical β-HCH. Full text in Research Archive
• Yuan, Yuan; Ju, Young Seok; Kim, Youngwook; Li, Jun; Wang, Yumeng & Yoon, Christopher J. [Show all 1,339 contributors for this article] (2023). Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics. ISSN 1061-4036. 55(5), p. 893–893. doi: 10.1038/s41588-020-0587-4. Full text in Research Archive
• Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A.; Shapira, Ofer & Tiao, Grace [Show all 1,616 contributors for this article] (2023). Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Nature, (2020), 578, 7793, (102-111), 10.1038/s41586-020-1965-x). Nature. ISSN 0028-0836. 614(7948), p. E40–E40. doi: 10.1038/s41586-022-05599-9. Full text in Research Archive
• Komisarczuk, Anna Zofia (2023). Genome editing with designer nucleases. Full text in Research Archive
• Komisarczuk, Anna Zofia (2023). CRISPR technology in advanced medicine. Full text in Research Archive
• Zapatka, Marc; Borozan, Ivan; Brewer, Daniel S.; Iskar, Murat; Grundhoff, Adam & Alawi, Malik [Show all 1,354 contributors for this article] (2023). Author Correction: The landscape of viral associations in human cancers (Nature Genetics, (2020), 52, 3, (320-330), 10.1038/s41588-019-0558-9). Nature Genetics. ISSN 1061-4036. 55(6), p. 1077–1077. doi: 10.1038/s41588-023-01316-y. Full text in Research Archive
• Kriener, Birgit; Mueller, Sabine; Phillips, Joanna J. & Waszak, Sebastian Martin (2023). A deep learning-approach to infer somatic alterations in glioma using digital tissue slides. Full text in Research Archive
• Calabrese, Claudia; Davidson, Natalie R.; Demircioğlu, Deniz; Fonseca, Nuno A.; He, Yao & Kahles, André [Show all 1,459 contributors for this article] (2023). Author Correction: Genomic basis for RNA alterations in cancer (Nature, (2020), 578, 7793, (129-136), 10.1038/s41586-020-1970-0). Nature. ISSN 0028-0836. 614(7948), p. E37–E37. doi: 10.1038/s41586-022-05596-y. Full text in Research Archive
• Yakneen, Sergei; Waszak, Sebastian Martin; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A. & Boyce, Rich [Show all 1,439 contributors for this article] (2023). Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes (Nature Biotechnology, (2020), 38, 3, (288-292), 10.1038/s41587-019-0360-3). Nature Biotechnology. ISSN 1087-0156. 41(4), p. 577–577. doi: 10.1038/s41587-022-01554-1. Full text in Research Archive
• Sajib, Saikat Das; Florholmen-Kjær, Åse; Brun, Vegard; Mortensen, Elin Synnøve; Hovd, Aud-Malin Karlsson & Tekpli, Xavier [Show all 10 contributors for this article] (2023). Epithelial-to-mesenchymal transition (EMT) is a major contributor to intratumor heterogeneity in lymph node metastasis in breast cancer. Full text in Research Archive
• Akdemir, Kadir C.; Le, Victoria T.; Chandran, Sahaana; Li, Yilong; Verhaak, Roel G. & Beroukhim, Rameen [Show all 1,405 contributors for this article] (2023). Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (Nature Genetics, (2020), 52, 3, (294-305), 10.1038/s41588-019-0564-y). Nature Genetics. ISSN 1061-4036. 55(6), p. 1079–1079. doi: 10.1038/s41588-023-01318-w. Full text in Research Archive
• Yuan, Yuan; Ju, Young Seok; Kim, Youngwook; Li, Jun; Wang, Yumeng & Yoon, Christopher J. [Show all 1,340 contributors for this article] (2023). Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics. ISSN 1061-4036. 55(6), p. 1078–1078. doi: 10.1038/s41588-023-01317-x. Full text in Research Archive
• Cortés-Ciriano, Isidro; Lee, Jake June-Koo; Xi, Ruibin; Jain, Dhawal; Jung, Youngsook L. & Yang, Lixing [Show all 1,402 contributors for this article] (2023). Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (Nature Genetics, (2020), 52, 3, (331-341), 10.1038/s41588-019-0576-7). Nature Genetics. ISSN 1061-4036. 55(6), p. 1076–1076. doi: 10.1038/s41588-023-01315-z. Full text in Research Archive
• Rio, Oline Eriksen; Komisarczuk, Anna Zofia; Labun, Kornel & Haapaniemi, Emma Maria (2023). CRISPR-Cas9 corrected T cells for personalized primary immunodeficiency disease (PIDD) therapy. Full text in Research Archive
• Arranz, Lorena & Rasmussen, Nikoline Lander (2023). NCMM Associate Investigator collaboration leads to important findings on the development of acute myeloid leukemia. [Internet]. https://www.med.uio.no/ncmm/. Full text in Research Archive
• Hovan, Ladislav (2023). Role of computational tools in drug discovery. Full text in Research Archive
• Sahu, Biswajyoti (2023). A molecular approach to genetic and epigenetic gene regulation, from basic research to the clinic. Full text in Research Archive
• Mathelier, Anthony (2023). Insights into the disruption of gene regulatory programs in cancers. Full text in Research Archive
• Pongcharoen, Sutatip; Spurkland, Anne & Baldari, Cosima T. (2023). Editorial: Community series in adaptor molecules in T cell signaling, volume II. Frontiers in Immunology. 14. doi: 10.3389/fimmu.2023.1243039. Full text in Research Archive
• Rio, Oline Eriksen; Komisarczuk, Anna Zofia; Labun, Kornel & Haapaniemi, Emma Maria (2023). CRISPR-Cas9 corrected T cells for personalized primary immunodeficiency disease (PIDD) therapy. Full text in Research Archive
• Rio, Oline Eriksen; Haapaniemi, Emma Maria; Komisarczuk, Anna Zofia & Labun, Kornel (2023). CRISPR-Cas9 corrected T cells for personalized primary immunodeficiency disease (PIDD) therapy. Full text in Research Archive
• Lehtonen, Johanna & Hassinen, Antti (2023). FIMM High Content Imaging and Analysis Unit Phenotyping Rare Neurological Disease Variants Using High-Content Imaging. Full text in Research Archive
• Sahu, Biswajyoti (2023). Single Cell Biology: From Development to Cancer. Full text in Research Archive
• Sahu, Biswajyoti (2023). Multi-omic data analysis and integration for precision medicine. Full text in Research Archive
• Sahu, Biswajyoti (2023). Molecular approach to study human cancers and the role of epigenome reprogramming. Full text in Research Archive
• Modi, Brijesh; Annavini, Eis & Boccara, Charlotte (2023). Benchmarking algorithms to automatically detect sharp wave ripples. Full text in Research Archive
• Thiyagaraja, Maivizhi & Gözen, Irep (2023). Thermoresponsive artificial cells. Biophysical Journal. ISSN 0006-3495. 122(3), p. 227a–227a. doi: 10.1016/j.bpj.2022.11.1555. Full text in Research Archive
• Kersten, Flore Marie Colette; Cordara, Gabriele & Krengel, Ute (2023). Cryo-EM reveals a novel domain fold of a fungal toxin. Full text in Research Archive
• Pop, Romana Tabita (2023). Integrating gene regulatory networks and multi-omics data using joint dimensionality reduction. Full text in Research Archive
• Gonzalez, Alicia Elena Villatoro; Cuminetti, Vincent; Mera, Aurora Bernal; Torroja, Carlos; Cossío, Itziar & Benguría, Alberto [Show all 22 contributors for this article] (2023). Author Correction: Endogenous IL-1 receptor antagonist restricts healthy and malignant myeloproliferation (Nature Communications, (2023), 14, 1, (12), 10.1038/s41467-022-35700-9). Nature Communications. 14(1). doi: 10.1038/s41467-023-39601-3. Full text in Research Archive
• Berge, Anne Kristin Mclaren; Sellæg, Kjersti; Figenschau, Stine; Sajib, Saikat Das; Olsvik, Hallvard Lauritz & Perander, Maria [Show all 8 contributors for this article] (2023). TRIM32 in Head and Neck Cancer. Full text in Research Archive
• Christou, Maria; Hultman, Maria Thérése; Esguerra, Camila Vicencio; Lillicrap, Adam David & Song, You (2023). Using Automated Size Measurement Software as a Possible New Approach Methodology to Support Adverse Outcome Pathway. Full text in Research Archive
• Pop, Romana Tabita (2023). Integrating gene regulatory networks and multi-omics data using joint dimensionality reduction. Full text in Research Archive
• Gerstung, Moritz; Jolly, Clemency; Leshchiner, Ignaty; Dentro, Stefan C.; Gonzalez, Santiago & Rosebrock, Daniel [Show all 1,440 contributors for this article] (2023). Author Correction: The evolutionary history of 2,658 cancers (Nature, (2020), 578, 7793, (122-128), 10.1038/s41586-019-1907-7). Nature. ISSN 0028-0836. 614(7948), p. E42–E42. doi: 10.1038/s41586-022-05601-4. Full text in Research Archive
• Ervik, Carolina Wieczorek (2023). Clinical Translation of Optimized CRISPR Editing Protocols for Primary Immunodeficiency Diseases. Full text in Research Archive Show summary

  Primary immunodeficiency diseases (PIDDs) are an umbrella term for more than 250 rare monogenic disorders that affect the function and/or development of the immune system. Hematopoietic stem cell transplantation (HSCT) is the standard treatment for many PIDDs, but many are limited to allogenic HSCT due to their pathophysiology. Because of the risks carried with allogeneic HSCT, ex vivo gene therapy where the patients’ own hematopoietic stem and progenitor cells (HSPCs) are corrected using the CRISPR/Cas9 genome editing tool and re-introduced to the patient would be the ideal way of treatment. However, the efficiency of CRISPR editing in HSPCs need to be optimized and evaluated for clinical translation, as well as the clinical- grade scale-up of these cells. Here we aim to develop an optimized CRISPR editing protocol for PIDDs using HSPCs from various sources. We will use multiple strategies to enhance homology-directed repair (HDR) efficiency and optimize stem cell expansion using clinical-grade reagents. Furthermore, we will establish a good manufacturing practice (GMP) compliant pipeline for scaled-up editing protocols using automated devices such as CliniMACS Prodigy® and MaxCyte GTx. The results will facilitate a start-to-finish approach for future CRISPR gene therapies of clinical relevance for PIDDs. We will use DADA2 (deficient in ADA2) as a model disease, but our protocols can be extended and applied to other PIDDs with different genetic mutations. By improving the efficacy and safety of CRISPR editing in HSPCs, we hope to provide curative treatments for PIDD patients who lack suitable donors or have poor outcomes with HSCT.

• Kriener, Birgit; Mueller, Sabine & Waszak, Sebastian Martin (2023). DIGITAL PATHOLOGY IN NEURO-ONCOLOGY. Full text in Research Archive
• Sellæg, Kjersti; Hofsten, Susannah Beatrice von; Berge, Anne Kristin McLaren; Ligtenberg, Lennart Maximilian van; Mauseth, Marcus Moe & Kournoutis, Athanasios [Show all 8 contributors for this article] (2023). Autofagi: cellenes spareblussmodus. Full text in Research Archive
• Ervik, Carolina Wieczorek; Kopcil, Pavel; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia & Bak, Rasmus O. [Show all 7 contributors for this article] (2023). Enhancing CRISPR Gene Correction In Hematopoietic Stem/Progenitor Cells. Full text in Research Archive
• Ervik, Carolina Wieczorek; Kopcil, Pavel; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia & Bak, Rasmus O. [Show all 7 contributors for this article] (2023). Enhancing CRISPR Gene Correction In Hematopoietic Stem/Progenitor Cells. Full text in Research Archive
• Li, Yilong; Roberts, Nicola D.; Wala, Jeremiah A.; Shapira, Ofer; Schumacher, Steven E. & Kumar, Kiran [Show all 1,410 contributors for this article] (2023). Author Correction: Patterns of somatic structural variation in human cancer genomes (Nature, (2020), 578, 7793, (112-121), 10.1038/s41586-019-1913-9). Nature. ISSN 0028-0836. 614(7948), p. E38–E38. doi: 10.1038/s41586-022-05597-x. Full text in Research Archive
• Kopcil, Pavel (2023). Genome editing for founder diseases: Lesson from DADA2. Full text in Research Archive
• Sekulic, Nikolina & Ahmad, Ahmad Ali (2023). Cryo-EM insights into the structure of the centromeric chromatin. Full text in Research Archive
• Sekulic, Nikolina; Teigen, Kelly Yong Kreutzmann; Strømme, Alexandra Nathalie & Wøien, Stine Malene Hansen (2023). Praktisk arbeid på utplassering. [Internet]. https://skolesamarbeid.oslocancercluster.no/. Full text in Research Archive
• Sekulic, Nikolina; Krengel, Ute & Brech, Andreas (2023). Minisymposium on CryoEM and CryoET: From knowledge to cures. Full text in Research Archive
• Sekulic, Nikolina (2023). Hydrogen-deuterium exchange (HDX) for monitoring protein interactions and conformational changes. Full text in Research Archive
• Sakovich, Inga S.; Haapaniemi, Emma Maria; Aleshkevich, Svetlana N.; Pakhomava, Iryna V.; Belobokova, Victoria D. & Poliakova, Ekaterina A. [Show all 15 contributors for this article] (2023). Clinical Course and Family History of Adult Patient with Novel MYSM1 Variant. Journal of Clinical Immunology. ISSN 0271-9142. 44(1). doi: 10.1007/s10875-023-01609-1. Full text in Research Archive
• Mathelier, Anthony (2023). Insights into the disruption of gene regulatory programs in cancers. Full text in Research Archive
• Cunha, Eva Mariana de Sousa; Chen, Xiaorui; Gaitero, Marta Sanz; Mills, Deryck J. & Lücke, Hartmut (2023). Author Correction: Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution (Nature Communications, (2021), 12, 1, (230), 10.1038/s41467-020-20485-6). Nature Communications. 14(1). doi: 10.1038/s41467-023-36404-4. Full text in Research Archive
• Alexandrov, Ludmil B.; Kim, Jaegil; Haradhvala, Nicholas J.; Huang, Mi Ni; Ng, Alvin Wei Tian & Wu, Yang [Show all 1,383 contributors for this article] (2023). Author Correction: The repertoire of mutational signatures in human cancer (Nature, (2020), 578, 7793, (94-101), 10.1038/s41586-020-1943-3). Nature. ISSN 0028-0836. 614(7948), p. E41–E41. doi: 10.1038/s41586-022-05600-5. Full text in Research Archive
• Shojaeinia, Elham (2023). Acetazolamide – an old drug but potentially also a first precision medicine for CHD2-related epilepsy? Full text in Research Archive
• Shojaeinia, Elham; Melikishvili, Gia; Kurua, Ekaterine; Tabatadze, Nazhi; Gachechiladze, Tamar & Melikishvili, Mariam [Show all 10 contributors for this article] (2023). Acetazolamide – an old drug but potentially also a first precision medicine for CHD2-related epilepsy? Full text in Research Archive
• Beraneck, Mathieu; Elliott, Karen L.; Glover, Joel Clinton & Straka, Hans (2023). Editorial: Development of the vestibular system. Frontiers in Neurology. 14. doi: 10.3389/fneur.2023.1191086. Full text in Research Archive
• Fernandez, Javier Gutierrez; Hammerstad, Marta & Hersleth, Hans-Petter (2023). Structural determination of Mycobacterium smegmatis and Rhodococcus erythropolis mycothiol disulphide reductases. Full text in Research Archive
• Sulonen, Anna-Maija; Lehtonen, Johanna; Kaustio, Meri; Edgren, Henrik; Almusa, Henrikki & Ellonen, Pekka [Show all 15 contributors for this article] (2023). Copy number variations from exome sequencing of Finnish inborn errors of immunity cohort. Full text in Research Archive
• Kopcil, Pavel; Ervik, Carolina Wieczorek; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia & Bak, Rasmus O. [Show all 7 contributors for this article] (2023). Enhancing CRISPR gene correction in hematopoietic stem/progenitor cells. Full text in Research Archive
• Dahal-Koirala, Shiva (2023). CRISPR-Cas9 T cell editing for correcting monogenic mutations. Full text in Research Archive
• Sakovich, Inga S.; Haapaniemi, Emma Maria; Aleshkevich, Svetlana N.; Pakhomava, Iryna V.; Belobokova, Victoria D. & Poliakova, Ekaterina A. [Show all 15 contributors for this article] (2023). Clinical Course and Family History of Adult Patient with Novel MYSM1 Variant. Journal of Clinical Immunology. ISSN 0271-9142. doi: 10.1007/s10875-023-01609-1. Full text in Research Archive
• Aaltonen, Lauri A.; Abascal, Federico; Abeshouse, Adam; Aburatani, Hiroyuki; Adams, David J. & Agrawal, Nishant [Show all 1,324 contributors for this article] (2023). Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6). Nature. ISSN 0028-0836. 614(7948), p. E39–E39. doi: 10.1038/s41586-022-05598-w. Full text in Research Archive
• Kumar, Vipin (2023). BootTHiC: Integrating HiC and transcriptomics to detect transcriptional hubs. Full text in Research Archive
• Kopcil, Pavel; Ervik, Carolina Wieczorek; Mamia, Katariina Aino Inkeri; Dahal-Koirala, Shiva; Komisarczuk, Anna Zofia & Bak, Rasmus O [Show all 7 contributors for this article] (2023). Enhancing CRISPR Gene Correction In Hematopoietic Stem/Progenitor Cells. Full text in Research Archive
• Modi, Brijesh; Annavini, Eis & Boccara, Charlotte (2023). Benchmarking algorithms to automatically detect sharp wave ripples. Full text in Research Archive
• Boccara, Charlotte; Nardin, Michele; Stella, Federico & Csicsvari, Jozsef (2023). Learning and sleep: hippocampal-parahippocampal differential roles in updating and consolidating mnemonic traces. Full text in Research Archive
• Boccara, Charlotte (2023). Research on rodents and significance as a model organism in studying sleep. Full text in Research Archive
• Boccara, Charlotte (2023). How memories can be stored and modified: decoding hippocampal algorithms during learning and sleep. Full text in Research Archive
• Korchynska, Solomiia; Modi, Brijesh & Boccara, Charlotte (2023). Maturation of sleep architecture across development. Full text in Research Archive
• Yuan, Yuan; Ju, Young Seok; Kim, Youngwook; Li, Jun; Wang, Yumeng & Yoon, Christopher J. [Show all 1,340 contributors for this article] (2023). Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics. ISSN 1061-4036. 55(5), p. 892–892. doi: 10.1038/s41588-020-0629-y. Full text in Research Archive
• Rodriguez-Martin, Bernardo; Alvarez, Eva G.; Baez-Ortega, Adrian; Zamora, Jorge; Supek, Fran & Demeulemeester, Jonas [Show all 1,445 contributors for this article] (2023). Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (Nature Genetics, (2020), 52, 3, (306-319), 10.1038/s41588-019-0562-0). Nature Genetics. ISSN 1061-4036. 55(6), p. 1080–1080. doi: 10.1038/s41588-023-01319-9. Full text in Research Archive
• Boccara, Charlotte (2023). Sleep: a new target for precision medicine. Full text in Research Archive
• Boccara, Charlotte & Skrøder, Karoline (2023). Dårlig søvn: Kan ha sammenheng med ADHD og autisme. [Journal]. Oslo – VG. Full text in Research Archive
• Kriener, Birgit; Albada, Sacha van; Djurfeldt, Mikael & Senk, Johanna (2023). Connectivity concepts in neuronal network modeling. Full text in Research Archive
• Kriener, Birgit & Waszak, Sebastian Martin (2023). A deep learning approach to infer somatic alterations in glioma using digital tissue slides. Full text in Research Archive
• Fernandez, Javier Gutierrez; Hammerstad, Marta & Hersleth, Hans-Petter (2023). Structural determination of Mycobacterium smegmatis and Rhodococcus erythropolis mycothiol disulphide reductases. Full text in Research Archive
• Fernandez, Javier Gutierrez; Hammerstad, Marta & Hersleth, Hans-Petter (2023). Structural determination of Mycobacterium smegmatis and Rhodococcus erythropolis mycothiol disulphide reductases. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Mapping the genetic and cellular origin of DIPG/DMG in clinical trials. Full text in Research Archive
• Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri & Mamia, Katariina Aino Inkeri [Show all 19 contributors for this article] (2022). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. Full text in Research Archive
• Sahu, Biswajyoti (2022). Sequence determinants of human gene regulatory elements and the role of transcription factors in cell fate control and cancer. Full text in Research Archive
• Sahu, Biswajyoti (2022). A novel factor indexing multiome approach to dissect determinants of cell fate control. Full text in Research Archive
• Kuijjer, Marieke (2022). Gene regulatory networks in precision medicine. Full text in Research Archive
• Modi, Brijesh; Guardamagna, Matteo; Stella, Federico; Griguoli, Marilena; Cherubini, Enrico & Battaglia, Francesco (2022). Intrinsic Organization of Hippocampal Oscillations. Full text in Research Archive
• Boccara, Charlotte (2022). Decoding hippocampal representation. Full text in Research Archive
• Kuijjer, Marieke (2022). A network approach to personalized medicine. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Reconstructing the past, predicting the future: mapping the genetic and cellular origin of brain tumors. Full text in Research Archive
• Kuijjer, Marieke (2022). Modeling regulatory network rewiring in cancer. Full text in Research Archive
• Kuijjer, Marieke (2022). Modeling genome-wide regulatory network rewiring in healthy tissues and cancer. Full text in Research Archive
• Modi, Brijesh; Guardamagna, Matteo; Stella, Federico; Griguoli, Marilena; Cherubini, Enrico & Battaglia, Francesco (2022). State Dependent Coupling of Hippocampal Oscillations. Full text in Research Archive
• Kersten, Flore Marie Colette; Cordara, Gabriele & Krengel, Ute (2022). Cryo-EM structure of a fungal chimerolectin. Full text in Research Archive
• Kriener, Birgit & Waszak, Sebastian Martin (2022). Digital pathology in neuro-oncology: Towards deep learning-based prediction of clinically-actionable genomic alterations from histopathological images. Full text in Research Archive
• Kriener, Birgit (2022). Parvalbumin interneuron dendrites enhance gamma oscillations. Full text in Research Archive
• Kriener, Birgit; Mueller, Sabine & Waszak, Sebastian Martin (2022). Digital pathology in pediatric neuro-oncology: deep learning-based prediction of clinically-actionable genomic alterations from histopathological images. Full text in Research Archive
• Schito, Giulia (2022). Modeling large scale personalized omics networks to characterize breast cancer evolution in response to neoadjuvant chemotherapy with and without bevacizumab. Full text in Research Archive
• Belova, Tatiana (2022). Studying heterogeneity in the gene regulatory landscape of cancer. Full text in Research Archive
• Belova, Tatiana (2022). Studying heterogeneity in the gene regulatory landscape of cancer. Full text in Research Archive
• Annavini, Eis; Korchynska, Solomiia; Babursah, Ela; Hafting, Torkel & Boccara, Charlotte (2022). A benchmark for sharp wave-ripple detection algorithms. Full text in Research Archive
• Hsieh, Ping-Han (2022). Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration. Full text in Research Archive
• Belova, Tatiana (2022). Studying heterogeneity in the gene regulatory landscape of cancer. Full text in Research Archive
• Schito, Giulia (2022). Modeling large scale personalized omics networks to characterize breast cancer evolution in response to neoadjuvant chemotherapy with and without bevacizumab. Full text in Research Archive
• Hovan, Ladislav (2022). STOAT: Generating gene regulatory networks from spatially resolved transcriptomic data. Full text in Research Archive
• Landskron, Johannes (2022). Basics of Chemical Biology and High throughput screening. Full text in Research Archive
• Landskron, Johannes (2022). Hit Selection. Full text in Research Archive
• Kriener, Birgit (2022). Digital pathology in neuro-oncology: Towards deep learning-based prediction of clinically-actionable genomic alterations from histopathological images. Full text in Research Archive
• Kriener, Birgit; Mueller, Sabine & Waszak, Sebastian Martin (2022). Digital pathology in neuro-oncology: deep learning-based prediction of clinically-actionable genomic alterations from histopathological images. Full text in Research Archive
• Hsieh, Ping-Han (2022). Cell Cluster Analysis with Variational Autoencoder using Conditional Hierarchy of Latent Representation. Full text in Research Archive
• Pop, Romana-Tabita (2022). Integrating gene regulatory networks with multi-omics data with MOFA+. Full text in Research Archive
• Schito, Giulia (2022). Modeling large scale personalized omics networks to characterize breast cancer evolution in response to neoadjuvant chemotherapy with and without bevacizumab. Full text in Research Archive
• Schito, Giulia (2022). Modeling large scale personalized omics networks to characterize breast cancer evolution in response to neoadjuvant chemotherapy with and without bevacizumab. Full text in Research Archive
• Pop, Romana-Tabita (2022). ELAND: Desparsifying somatic mutations based on network communities. Full text in Research Archive
• Hsieh, Ping-Han (2022). Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration. Full text in Research Archive
• Mottl, Sophie; Sill, Martin; Northcott, Paul A.; Jäger, Natalie; Pfister, Stefan M & Waszak, Sebastian Martin (2022). Parent-of-origin-specific genetic predisposition to medulloblastoma. Full text in Research Archive
• Mottl, Sophie; Sill, Martin; Northcott, Paul A.; Jäger, Natalie; Pfister, Stefan M & Waszak, Sebastian Martin (2022). Molecular landscape of GNAS-associated pediatric brain tumors. Full text in Research Archive
• Fernandez, Javier Gutierrez; Hammerstad, Marta & Hersleth, Hans-Petter (2022). Structural determination of Mycobacterium tuberculosis and Rhodococcus erythropolis mycothiol disulphide reductases. Full text in Research Archive
• Sekulic, Nikolina & Segura-Pena, Dario (2022). Hydrogen-deuterium exchange (HDX) coupled to mass spectrometry for analysis of protein conformations and protein-ligand interactions. Full text in Research Archive
• Bjørgo, Elisa; Solheim, Silje Anette; Abrahamsen, Hilde; Baillie, George S.; Brown, Kim M. & Berge, Torunn [Show all 9 contributors for this article] (2022). Erratum: Cross Talk between Phosphatidylinositol 3-Kinase and Cyclic AMP (cAMP)-Protein Kinase A Signaling Pathways at the Level of a Protein Kinase B/b-Arrestin/cAMP Phosphodiesterase 4 Complex (Molecular and Cellular Biology (2010) 30:7 (1660–1672) DOI: 10.1128/MCB.00696-09). Molecular and Cellular Biology. ISSN 0270-7306. 42(2). doi: 10.1128/mcb.00556-21. Full text in Research Archive
• Sekulic, Nikolina & Segura-Pena, Dario (2022). Hydrogen-deuterium exchange (HDX) coupled to mass spectrometry for analysis of protein conformations and protein-ligand interactions. Full text in Research Archive
• Korchynska, Solomiia; Annavini, Eis; Modi, Brijesh; Vharegui, Luca & Boccara, Charlotte (2022). Sleep architecture dynamics across the lifespan. Full text in Research Archive
• Shuai, Shimin; Abascal, Federico; Amin, Samirkumar B.; Bader, Gary D.; Bandopadhayay, Pratiti & Barenboim, Jonathan [Show all 1,455 contributors for this article] (2022). Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower (Nature Communications, (2020), 11, 1, (734), 10.1038/s41467-019-13929-1). Nature Communications. 13(1). doi: 10.1038/s41467-022-32343-8. Full text in Research Archive
• Annavini, Eis; Korchynska, Solomiia; Babursah, Ela; Hafting, Torkel & Boccara, Charlotte (2022). A benchmark for sharp wave-ripple detection algorithms. Full text in Research Archive
• Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony & Sandve, Geir Kjetil Ferkingstad (2022). Method development for the identification of cis-regulatory signatures of cell types. Full text in Research Archive
• Ferenc, Katalin Terezia; Mathelier, Anthony; Hsieh, Ping-Han & Sandve, Geir Kjetil Ferkingstad (2022). Method development for the identification of cis-regulatory signatures of cell types. Full text in Research Archive
• Lehtonen, Johanna (2022). A summary of the 20th Biennial meeting of the European Society for Immunodeficiencies. Full text in Research Archive
• Guebila, Marouen Ben; Weighill, Deborah; Lopes-Ramos, Camila M.; Burkholz, Rebekka; Pop, Romana-Tabita & Palepu, Kalyan [Show all 14 contributors for this article] (2022). An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. ISSN 1548-7091. 19, p. 511–513. doi: 10.1038/s41592-022-01479-2. Full text in Research Archive
• Lehtonen, Johanna & Batlle-Masó, Laura (2022). Genetic studies in autoimmune lymphoproliferative syndrome pediatric patients. Full text in Research Archive
• Boccara, Charlotte (2022). Panel discussion related to the path to research excellence. Full text in Research Archive
• Sekulic, Nikolina; Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen & Black, Ben E. [Show all 7 contributors for this article] (2022). Aurora B activation requires synchronized internal motion initiated by IN-box phosphorylation. Full text in Research Archive
• Boccara, Charlotte (2022). Uncovering the mechanisms linking sleep and health. [Internet]. Nordic EMBL Partnership website. Full text in Research Archive
• Boccara, Charlotte (2022). Du er faktisk en mattenerd. [Internet]. forskning.no. Full text in Research Archive
• Boccara, Charlotte (2022). Natteangst: Slik får du sove. [Internet]. Dagbladet. Full text in Research Archive
• Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen; Black, Ben E. & Cascella, Michele [Show all 7 contributors for this article] (2022). The structural basis of the multi-step allosteric activation of Aurora B kinase. Full text in Research Archive
• Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen; Black, Ben E. & Cascella, Michele [Show all 7 contributors for this article] (2022). HDX and MD as tools to elucidate Aurora B kinase activation mechanism. Full text in Research Archive
• Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony & Sandve, Geir Kjetil Ferkingstad (2022). Method development for the identification of cis-regulatory signatures of cell types. Full text in Research Archive
• Boccara, Charlotte (2022). Norske forskere: Hjernen din har superceller! [Internet]. VG. Full text in Research Archive
• Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen; Black, Ben E. & Cascella, Michele [Show all 7 contributors for this article] (2022). Phosphorylation structurally organizes the [Aurora B/IN-box] complex and introduces a synchronised internal motion of the enzyme resulting in activation. Full text in Research Archive
• Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen; Black, Ben E. & Cascella, Michele [Show all 7 contributors for this article] (2022). The structural basis of the multi-step allosteric activation of Aurora B kinase. Full text in Research Archive
• Segura-Pena, Dario; Hovet, Oda; Dawicki-McKenna, Jennine; Wøien, Stine Malene Hansen; Black, Ben E. & Cascella, Michele [Show all 7 contributors for this article] (2022). The structural basis of the multi-step allosteric activation of Aurora B kinase. Full text in Research Archive
• Burkert, Christian Martin & Waszak, Sebastian Martin (2022). Novel computational approaches to infer the cellular origin of somatic genomes. Full text in Research Archive
• Fatima, Nazeefa; Lemma, Roza Berhanu; Rauluseviciute, Ieva; Belova, Tatiana; Kumar, Vipin & Hsieh, Ping-Han [Show all 12 contributors for this article] (2022). Developing Bioinformatics Societies in Norway and Nordic. Full text in Research Archive Show summary

  With the increasing amount of biological data, the need for computational skills has become prominent. Interdisciplinary fields such as computational biology require interdisciplinary collaborations; in order to create an environment for sharing skills and experiences, opportunities for funding and training, career path advice, and research ideas. Creating such environments also help to establish an inclusive platform where students and early-career researchers in computational biology can socialise and help each other in an informal setting. Currently, this is achieved locally at department level at a university or industrial company. The social interactions between students and established scientists are, therefore, consequently limited to the geographical locations of their institutions. The Regional Study Group Norway (RSG-Norway), part of the International Society of Computational Biology (ISCB), aims to create a country-wide platform, to bring together aspiring and established bioinformaticians and to develop an active presence in the Norwegian bioinformatics community. Regional level communities such as RSG-Norway are particularly helpful for students to broaden training and career opportunities. It can also help foreign researchers and students, in settling as new arrivals, through building contacts with those who are familiar with studying and working in Norway. Finally, the study group can be a channel for students and trainees to initiate and/or realise their own ideas regarding social and professional communication with fellow bioinformaticians. RSG-Norway works together with Nordic Computational Biology (NCB), which serves as a resource and knowledge-exchange hub to bring together people from industries and academia as well as local communities such as Regional Student Groups across the Nordics. As part of the NCB, Nordic RSGs are able to build cross-border collaborations and organise open events that reach a wider audience strengthening the community's knowledge-base. The presentation for this abstract will include information on past events and initiatives by RSG-Norway and NCB, their future activities and plans, and how to get involved as a member and an advisor to help develop the computational biology community in Norway and the Nordics.

• Kersten, Flore Marie Colette; Cordara, Gabriele & Krengel, Ute (2022). Cryo-EM structure of a fungal toxin. Full text in Research Archive
• Boccara, Charlotte (2022). Goal encoding during sleep. Full text in Research Archive
• Lemma, Roza Berhanu; Castro-Mondragon, Jaime Abraham & Mathelier, Anthony (2022). Large-scale investigation of noncoding elements associated with transcriptional deregulation involved in carcinogenesis. Full text in Research Archive
• Kersten, Flore Marie Colette; Cordara, Gabriele & Krengel, Ute (2022). Cryo-EM structure of a fungal toxin. Full text in Research Archive
• Song, You; Lillicrap, Adam David; Esguerra, Camila Vicencio; Villeneuve, Daniel L.; Ng, Daniel & Rundberget, Jan Thomas [Show all 15 contributors for this article] (2022). Quantitative Adverse Outcome Pathways Assisted Next Generation Risk Assessment of Mitochondrial Toxicants. Full text in Research Archive
• Christou, Maria; Hultman, Maria Thérése; Esguerra, Camila Vicencio; Lillicrap, Adam David & Song, You (2022). Adverse outcome pathway guided hazard assessment of mitochondrial uncouplers: a tiered testing strategy using zebrafish in vitro assays and embryo toxicity assays. Full text in Research Archive
• Sekulic, Nikolina; Repasky, Gretchen & Segura-Pena, Dario (2022). Uncovering protein dynamics with hydrogen/deuterium exchange mass spectrometry in the Nordics. [Internet]. https://projects.au.dk/nordic-embl-partnership/show-news/art. Full text in Research Archive
• Hashem, Hasan; Bucciol, Giorgia; Ozen, Seza; Unal, Sule; Bozkaya, Ikbal Ok & Akarsu, Nurten [Show all 51 contributors for this article] (2022). Correction to: Hematopoietic Cell Transplantation Cures Adenosine Deaminase 2 Deficiency: Report on 30 Patients (Journal of Clinical Immunology, (2021), 41, 7, (1633-1647), 10.1007/s10875-021-01098-0). Journal of Clinical Immunology. ISSN 0271-9142. doi: 10.1007/s10875-022-01280-y. Full text in Research Archive
• Cmero, Marek; Yuan, Ke; Ong, Cheng Soon; Schröder, Jan; Adams, David J. & Anur, Pavana [Show all 1,399 contributors for this article] (2022). Author Correction: Inferring structural variant cancer cell fraction (Nature Communications, (2020), 11, 1, (730), 10.1038/s41467-020-14351-8). Nature Communications. 13(1). doi: 10.1038/s41467-022-32338-5. Full text in Research Archive
• Sekulic, Nikolina; Yuen, Karen Wing Yee; Kelly, Alexander & Meraldi, Patrick (2022). Editor for research topic: Dynamic kinetochore. Frontiers in Cell and Developmental Biology. Full text in Research Archive
• Sekulic, Nikolina & Krengel, Ute (2022). PX-Oslo: Structural Biology Core Facilities. Full text in Research Archive
• Zhang, Yiqun; Chen, Fengju; Fonseca, Nuno A.; He, Yao; Fujita, Masashi & Nakagawa, Hidewaki [Show all 1,480 contributors for this article] (2022). Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (Nature Communications, (2020), 11, 1, (736), 10.1038/s41467-019-13885-w). Nature Communications. 13(1). doi: 10.1038/s41467-022-32333-w. Full text in Research Archive
• Ent, Wietske van der (2022). Toward novel therapeutic interventions for rare pediatric epilepsies. Full text in Research Archive
• Mamia, Katariina Aino Inkeri; Saarela, Janna Saija; Li, Zhuokun; Reint, Ganna; Fatkhutdinov, Nail & Haugen, Frida Høsøien [Show all 13 contributors for this article] (2022). CRISPR-Cas9 T cell editing pipeline for Finnish founder diseases. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Genetic origin and somatic evolution of childhood medulloblastoma. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Genetic origin and somatic evolution of childhood medulloblastoma. Full text in Research Archive
• Ent, Wietske van der (2022). Toward novel therapeutic interventions for rare pediatric epilepsies. Full text in Research Archive
• Ent, Wietske van der (2022). Modelling SNAREopathies in Zebrafish. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Medulloblastoma predisposition syndromes: molecular mechanisms and clinical implications. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Reconstructing the past, predicting the future: using somatic genomes to identify the cellular origin of childhood cancers. Full text in Research Archive
• Waszak, Sebastian Martin (2022). Genetic Origin and Somatic Evolution of Childhood Medulloblastoma. Full text in Research Archive
• Waszak, Sebastian Martin (2022). RECONSTRUCTING THE PAST, PREDICTING THE FUTURE: MAPPING THE GENETIC AND CELLULAR ORIGIN OF PEDIATRIC AND ADULT BRAIN TUMORS. Full text in Research Archive
• Rauluseviciute, Ieva; Castro-Mondragon, Jaime A. & Mathelier, Anthony (2022). Identification of transcription factor co-binding patterns with non-negative matrix factorization. Full text in Research Archive
• Lemma, Roza Berhanu (2022). Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Full text in Research Archive Show summary

  Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression–methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.

• Waszak, Sebastian Martin (2022). Genetic origin and somatic evolution of childhood brain tumors. Full text in Research Archive
• Naseri, Nafasgol; Dahal-Koirala, Shiva; Haapaniemi, Emma Maria & Falnes, Pål (2026). Investigation of on-target Chromosomal deletions and loss during HDR-enhanced CRISPR-Cas9 correction of a CARMIL2 point mutation in patient-derived T cells. University of Oslo (UiO). Full text in Research Archive
• Borg, Nora Helene Hammersten; Komisarczuk, Anna Zofia; Falnes, Pål & Haapaniemi, Emma Maria (2026). Development of a Multimodal Screening Platform for Comparative Evaluation of Prime Editing Efficiency. Establishing an experimental framework through reporter cell line generation, prime editing vector construction, and detection assay development. Universitetet i Oslo. Full text in Research Archive Show summary

  --- Abstract will be published: 2027-05-19

• Flister, Renate Sæther; Fahlquist-Hagert, Cecilia & Prydz, Kristian (2026). Comparison of finding an optimal model for human xenografts. A comparative study of NSG-SGM3 and NBSGW mouse strains and the effect of Busulfan conditioning on human hematopoietic engraftment. Universitetet i Oslo. Full text in Research Archive Show summary

  Hematopoietic stem cell transplantation (HSCT) is reserved for patients with malignant and non-malignant hematological disorders, in whom other therapeutic options are ineffective. To improve the translational value of HSCT research, robust pre-clinical models are needed to capture human hematopoietic reconstitution niche dependent engraftment. Humanized mouse models provide a useful system for studying the interaction between donor hematopoietic stem (HSC) and progenitor cells and the bone marrow niche. This thesis compares the engraftment efficiency and multilineage reconstitution supported by the NSG-SGM3 and NBSGW mice. Highly purified cord blood-derived CD34+ cells were transplanted into both strains, with groups receiving either busulfan preconditioning (2x 20mg/kg) or no conditioning. Human hematopoietic reconstitution was analyzed in bone marrow, spleen and peripheral blood using conventional and spectral flow cytometry. In addition, donor-host sex matching and sample fixation were evaluated as biological and technical variables affecting data interpretation. Both strains supported human engraftment, but with distinct lineage biases. NSG-SGM3 favored primitive and myeloid-associated output, where NBSGW supported a more lymphoid output, with higher frequence of lymphoid-primed multipotent (LMPP) and pre-B-cell. Busulfan preconditioning provided only limited additional benefits and, in some cases, did not improve human chimerism. Donor-host sex matching did not produce a statistically significant effect, through a trend toward higher cell frequencies in sex-matched was observed. Sample fixation, however clearly reduced marker detection and introduced epitope masking, showing that fresh cells analysis is preferable for reliable high-parameter flow. Overall, the findings indicate that neither NSG-SGM3 nor NBSGW is universally superior. Rather, each model is suited to different biological questions and engraftment success, depending on host background, donor quality, conditioning strategy and analytical workflow. This has a direct relevance for translational HSCT research, where model choice can shape experimental conclusions. The most useful humanized mouse model is therefore not that one performs best in all settings, but the one whose bias best matches the question being asked.

• Pop, Romana Tabita (2026). Omics data integration with gene regulatory networks in health and disease. Universitetet i Oslo. ISSN 9788234807817. Full text in Research Archive Show summary

  This thesis lies at the intersection of computational biology, network science, and cancer systems biology. It investigates whether gene regulatory networks (GRNs) can improve multi-omics data integration, enhance prediction of cancer patient survival, and be analyzed more effectively using scalable network methods. It also examines how accessibility and reproducibility of GRN analyses can be strengthened. To address these questions, sample-specific GRNs were integrated with ten cancer multi-omics datasets from TCGA using the MOFA+ framework, with validation in an independent liver cancer cohort. A new algorithm, HEDGEHOG, was developed to detect hierarchical and overlapping communities in large bipartite biological networks and applied to 34 tissue-specific GRNs from GTEx. In parallel, an online platform, NetBooks, was created to provide reproducible workflows, code, and tutorials. Results show that incorporating GRNs into multi-omics models improves associations with patient survival in several cancer types and highlights biologically meaningful pathways, including fatty-acid metabolism in liver cancer. HEDGEHOG identifies hundreds of stable network communities per tissue, many corresponding to known biological processes, demonstrating its value for interpreting large regulatory systems. The reproducibility resources further support transparent and reusable analyses. Overall, the thesis demonstrates that integrating regulatory network information with multi-omics data yields more informative models of disease biology and that scalable network methods combined with open tools can substantially advance systems-level cancer research.

• Boccara, Charlotte; Einevoll, Gaute & Nikolaisen, Myrland, Henriette (2025). Methods for Sleep Deprivation in Laboratory Rodent Models: A Systematic Review. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  Sleep is an essential and conserved biological function, yet its specific functions remain difficult to pinpoint, and much of our current knowledge on the subject comes from clinical studies. While these studies were essential to establish what general functions sleep may support, they often fail to identify the underlying mechanisms that explain why sleep is essential to health or demonstrate causal links between sleep issues and pathological outcomes. Rodent sleep deprivation models offer a unique opportunity to study these mechanisms and establish how sleep perturbations may directly cause dysfunction. However, rodent sleep deprivation methods to perturbate sleep differ in precision, efficiency and interpretability, and a comprehensive, comparative overview has been lacking. My aim with this thesis is to address that knowledge gap by systematically cataloguing and comparing different rodent sleep deprivation methods. I conducted a systematic review and meta-analysis of 100 papers and 161 experiments to compare mechanical paradigms, lesions, pharmacologic interventions, gene editing, optogenetics, and chemogenetics across wake, NREM and REM sleep. I quantified method effectiveness by sleep state and mapped typical brain area targets to identify how these choices may shape outcomes. The analyses reveal a precision-efficiency trade-off. Tools that target specific areas and circuits tend to be less efficient in wake and sleep-state changes, whereas broad approaches produce larger but less selective effects. I integrated these findings into a decision framework to align method selection with research aims, emphasizing state targeting goals, anatomical targeting and practical constraints. Overall, this thesis offers a structured, transparent comparison of rodent sleep deprivation tools, balancing precision against the magnitude and reliability of sleep state-specific effects. It sets the necessary framework to outline future priorities for sleep deprivation-based research that I predict likely to focus on naturalistic design, transparency and broader coverage across development and sex.

• Boccara, Charlotte & Gaupseth, Ane Mæsted (2025). Characterisation of Temperature Dynamics across Brain Development in Rodents. Universitetet i Oslo. Full text in Research Archive
• Mamia, Katariina Aino Inkeri & Haapaniemi, Emma Maria (2025). Precision T cell correction platform for Inborn Errors of Immunity. Universitetet i Oslo. Full text in Research Archive Show summary

  In this study, Katariina Mamia and colleagues developed an efficient and safe gene editing platform that can correct genetic “typos” in human T cells. This platform can correct single-gene mistakes in T cells from patients with rare diseases affecting the immune system, also known as Inborn Errors of Immunity (IEI). Currently, some IEIs can be treated with stem cell transplants from healthy donors, but this approach carries serious risks and is not an option for everyone. To address this unmet need, Katariina and colleagues used CRISPR/Cas9 gene editing technology to modify the patients’ own T cells instead. In this approach, T cells are isolated from blood samples, corrected in a laboratory – and one day, transplanted back into the patients. The platform achieved up to 80% correction efficiency and was shown to improve T cell functions in the corrected T cells. Extensive safety testing detected no harmful effects or unwanted genetic changes within the methods used. This study presents a first-generation T cell correction platform that can repair various single-gene defects with one workflow. This study presents a first-generation T cell correction platform that can repair various single-gene defects with one workflow. It represents an early step towards clinical translation of gene therapies for IEI patients who currently have limited treatment options.

• Saarela, Janna Saija; Szymanska, Monika; Bøhn, Siv Kjølsrud & Lurås, Sanne Iversen (2024). Deciphering ADA2 Deficiency: Creating an ADA2 deficiency model using CRISPR/Cas genome editing. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  Mangel på adenosindeaminase 2 (DADA2) er en sjelden autoinflammatorisk lidelse forårsaket av bialleliske mutasjoner i adenosindeaminase 2 (ADA2) genet. Pasienter med DADA2 viser et bredt spekter av kliniske manifestasjoner, og tilstanden kan være livstruende. Sykdomsmekanismene til DADA2 er i stor grad ukjente og for å øke kunnskapen i dette feltet, hadde denne studien som mål å lage DADA2-cellemodeller og studere effekten av nedslått ADA2 genuttrykk på to sentrale immune celle mekanismer: proliferasjon av monocytter og makrofagpolarisering. For å gen redigere ADA2 ble guide RNA (gRNA) og CRISPR-assosiert protein 9 (Cas9) introdusert inn i THP-1 celler ved bruk av elektroporering. De gen redigerte cellene ble videre sortert ved bruk av fluorescensaktivert cellesortering (FACS), hvor til slutt fire av de utvalgte klonene viste en homozygot delesjon i ADA2-genet som er forventet å forårsake en leseramme forskyvning i budbringer-RNA (mRNA). En proliferasjon analyse som ble utført på ADA2-redigerte, ikke-sorterte celler ved bruk av Incucyte S3 viste at de redigerte cellene hadde en signifikant lavere proliferasjon sammenlignet med kontroll celler. Effekten av DADA2 på makrofagpolarisering ble testet på sorterte ADA2-redigerte celler og evaluert med spesifikke markører ved hjelp av kvantitativ PCR (qPCR). Cellene ble først differensiert til M0 og deretter polarisert til M1 og M2a makrofager. Resultatene indikerte at DADA2-cellemodeller viste en favorisert polarisering mot M1 makrofager. Eksperimentelle begrensninger oppsto, og ytterligere testing må gjøres for å trekke pålitelige konklusjoner.

• Komisarczuk, Anna Zofia; Ganeshan, Janaarthan; Haapaniemi, Emma Maria & Winge, Per (2024). epegRNA Screening Platform for Primary Immunodeficiency Mutations in HEK293 cells and Hematopoietic Stem and Progenitory Cells (HSPCs). Norges teknisk-naturvitenskapelige universitet. Full text in Research Archive Show summary

  Mangel på adenosindeaminase (DADA2) er en primær immunsvikt forårsaket av autosomale recessive mutasjoner i adenosindeaminasegen (CECR1, ADA2). Korrekte behandlingsmetoder er først og fremst avhengig av sykdomsfenotypen, og understreker behovet for målrettet genkorreksjon. Prime editing (PE) er et allsidig genomredigeringsverktøy som er i stand til å introdusere innsetting, sletting, alle 12 typer nukleotidendringer og kombinasjoner derav. PE kan potensielt korrigere opptil 90 % av genetiske lidelser, inkludert primære immunsvikt. Evaluering av redigeringseffektiviteten til prime-redigeringsguidRNA (pegRNA) krever imidlertid betydelig innsats. I denne studien beskriver vi en optimalisert prime-redigeringsscreeningsplattform for å vurdere redigeringseffektiviteten til grunnleggende (pegRNA) og konstruert pegRNA (epegRNA) rettet mot pR169Q-mutasjon i ADA2 (ENSG00000093072). Vi evaluerte sekvensriktigheten til epegRNA- og pegRNA-plasmidbiblioteket ved Sanger-sekvensering og genererte lentivirusbiblioteker. Vi evaluerte også den smittsomme titeren ved bruk av digital dråpe-PCR (ddPCR), genererte cellebiblioteker for stabil ekspresjon av epegRNA og pegRNA, og optimaliserte PCR-forholdene for dyp amplikonsekvensering. Vi demonstrerte en ddPCR-basert tilnærming for å kvantifisere lentivirus-kopinummer med høy sensitivitet og lavt standardavvik. Det dynamiske området for ddPCR var mellom 300 og 30 000 målkopier per reaksjon, som ble brukt til estimering av kopiantallvariasjon, beregning av infeksiøs titer og infeksjonsmangfold for epegRNA- og pegRNA-cellebibliotek-preparat. Vi observerte at PCR-tilstanden brukt med epegRNA-plasmid ikke var forenlig med gDNA oppnådd fra cellebiblioteket når biblioteket ble klargjort for amplikonsekvensering. Oppsummert la denne studien grunnlaget for pålitelig og effektiv screening av epegRNA og pegRNA. Vi fremhevet viktigheten av å optimalisere PCR-forhold for amplikonsekvensering. Implementering av denne optimaliserte plattformen lover å effektivisere prosessen med å teste pegRNA-er for monogene mutasjoner.

• Boccara, Charlotte & Adrian, Engberg (2024). THE EFFECTS OF IN UTERO EXPOSURE TO ANTIDEPRESSANTS ON SLEEP ARCHITECTURE DEVELOPMENT. University of Copenhagen. Full text in Research Archive Show summary

  BLC807

• Dahal-Koirala, Shiva (2024). Correction of a Signal Transducer and Activator of Transcription 1 (STAT1) gain-of-function mutation in T cells by applying the CRISPR-Cas9 technique. OsloMet - storbyuniversitetet. Full text in Research Archive
• Sundell, Tuva; Carlsen, Harald & Haapaniemi, Emma Maria (2023). The impact of ADA2 downregulation on T-cell functioning of CRISPR/Cas9 edited PBMCs. Norges miljø- og biovitenskapelige universitet (NMBU). Full text in Research Archive Show summary

  Adenosine Deaminase 2 Deficiency (DADA2) is a rare autosomal genetic syndrome characterized by auto-inflammatory symptoms, where the development of T lymphocytes and B lymphocytes is malfunctioning. The deficiency is caused by the loss of function mutations in the CECR1 gene, which encodes the enzyme adenosine deaminase 2. Adenosine Deaminase 2 (ADA2) is involved in the metabolism of adenosine and has a role in regulating the immune response, and in addition it has been linked to the regulation of T-cell activation and differentiation. Recent studies suggest that downregulation of ADA2 can lead to altered T-cell activation and proliferation. The pathogenesis of the disease is still not completely understood. The aim of this study was to study the effect of knock out of ADA2 and knock in of ADA2 R169Q mutation on the activity and expression of the ADA2 gene. and study the impact of ADA2 downregulation on T-cells functioning. The editing on T-cells was done to understand more of the mechanism of DADA2. Electroporation was used as delivery method for CRISPR/Cas9 in PBMCs (Peripheral Blood Mononuclear Cells) to knock out the ADA2 gene and knock in a mutation of ADA2 (R169Q), a mutation linked to the development of ADA2 deficiency. Further the cells were analyzed to evaluate ADA2 enzyme activity and gene expression, and the effect of ADA2 knockout and R169Q mutation on T-cells were studied using flow cytometry in T-cell activation and proliferation downstream assays. A decrease in ADA2 activity and gene expression were observed for the ADA2 KO and KI of R169Q samples compared to the non-edited samples. However, for the study of T-cell functioning, some problems occurred for long cultivation of the edited T-cells, which was further discussed and compared with cells undergoing a shorter cultivation period. Thus, future experiments are needed with a wider set of samples from multiple donors with enhanced editing efficiency. It is crucial to optimize the experimental procedures for utilizing edited cells to gain deeper insights into the effects of ADA2 downregulation on T-cell functionality. Taking these factors into consideration will contribute to a more comprehensive understanding of the impact of ADA2 downregulation on the functioning of T-cells.

• Mørch, Anna; Sekulic, Nikolina & Ali-Ahmad, Ahmad (2023). Structural and Functional Studies of Centromeric Protein CENP-T from Bombyx mori. Universitetet i Oslo. Full text in Research Archive
• Fløgstad, Ole Magnus; Sekulic, Nikolina & Segura-Pena, Dario (2023). Optimization of mass spectrometry techniques for epitope characterization of the interaction between HER2 and trastuzumab. Universitetet i Oslo. Full text in Research Archive Show summary

  Antibodies are well established in therapeutic treatment of cancers, autoimmune disorders, and infections for a wide variety of diseases. However, the establishment of new antibody treatments is a long process relaying on initial generation of antibodies in animal models and further optimization. To avoid the time and resource demanding process in monoclonal antibody development many attempts have been made to computationally engineer antibodies with desired binding affinities and optimal biochemical properties. Recently, the prediction of antigen-antibody specificity through deep learning has been applied to a well categorized antibody-antigen system: Human epidermal growth factor receptor 2 (HER2) and the anti-HER2 monoclonal antibody (Trastuzumab) (Mason, Friedensohn et al. 2021) (Shanehsazzadeh, Bachas et al. 2023). Binding assays of the predicted variants of trastuzumab show similar or even higher binding affinity compared to the original antibody. Interestingly, some of the predicted variant antibodies with high affinity binding have a large sequence difference, compared to the original trastuzumab, in the complementarity determining region of the heavy chain 3 (CDRH3) that is major player in epitope recognition. This observation opens the possibility that the developed antibodies bind the epitope in a different way, but the experimental techniques required to explore this possibility are limited and cumbersome. In this study, we used two mass spectrometry-based epitope mapping techniques: Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) and epitope excision to characterize HER2-trastuzumab interaction and whether they are useful for characterizing antibody variants. We have successfully established experimental conditions for studying the complex interaction with HDX-MS, while the epitope excision method poses some challenges for the given antibody-antigen system. The results of our study are consistent with the available high-resolution structures of HER2-trastuzumab and provide the basis for future studies on the interactions between engineered antibodies and HER2.

• Boccara, Charlotte; Gosse, Laure; Briand, Nolwenn & Dufour, Damien (2023). Innervation of adipose tissue in mice. Sorbone Universite. Full text in Research Archive
• Boccara, Charlotte; Saigal, Ruchi; Korchynska, Solomiia & Komisarczuk, Anna Zofia (2023). Optimizing cellular tools to engineer a CRISPR-mediated REM-sleep deprivation model. OsloMet. Full text in Research Archive
• Mørch, Anna & Sekulic, Nikolina (2023). Structural and Functional Studies of Centromeric Protein CENP-T from Bombyx mori. Kjemisk Institutt, Universitetet i Oslo. Full text in Research Archive
• Boccara, Charlotte & Babursah, Ela (2022). MASTER 1 NEUROSCIENCE Research Internship Report – A comparison of automatic sharp wave ripple detection algorithms. Université de Paris Cité. Full text in Research Archive

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