Siste publikasjoner

• Mohammadzadeh, Naiyereh; Melleby, Arne Olav; Palmero, Sheryl; Sjaastad, Ivar; Chakravarti, Shukti; Engebretsen, Kristin V Thunheim; Christensen, Geir Arve; Lunde, Ida Gjervold & Tønnessen, Theis (2020). Moderate Loss of the Extracellular Matrix Proteoglycan Lumican Attenuates Cardiac Fibrosis in Mice Subjected to Pressure Overload. Cardiology.  ISSN 0008-6312.  145(3), s 187- 198 . doi: 10.1159/000505318
• Pladsen, Arne Valebjørg; Nilsen, Gro; Rueda, Oscar M.; Aure, Miriam Ragle; Borgan, Ørnulf; Liestøl, Knut; Vitelli, Valeria; Frigessi Di Rattalma, Arnoldo; Langerød, Anita; Mathelier, Anthony; Engebråten, Olav; Kristensen, Vessela N.; Wedge, David C.; Van Loo, Peter; Caldas, Carlos; Børresen-Dale, Anne-Lise; Russnes, Hege Elisabeth Giercksky & Lingjærde, Ole Christian (2020). DNA copy number motifs are strong and independent predictors of survival in breast cancer. Communications Biology.  ISSN 2399-3642.  3 . doi: 10.1038/s42003-020-0884-6
• Gawel, Kinga Aurelia; Langlois, Melanie; Martins, Teresa G.; van der Ent, Wietske; Tiraboschi, Ettore; Jacmin, Maxime; Crawford, Alexander Dettmar & Esguerra, Camila V. (2020). Seizing the moment: Zebrafish epilepsy models. Neuroscience and Biobehavioral Reviews.  ISSN 0149-7634.  116, s 1- 20 . doi: 10.1016/j.neubiorev.2020.06.010
• Banono, Nancy Saana & Esguerra, Camila (2020). Pharmacological Validation of the Prepulse Inhibition of Startle Response in Larval Zebrafish using a Commercial Automated System and Software. Journal of Visualized Experiments.  ISSN 1940-087X.  161 . doi: 10.3791/61423
• Ramonet Jimenez, Jose David & Dietz, Gunnar P.H. (2020). Novel cell-based assay for identification of LRRK2 inhibitors using its aberrant regulation of a pluripotency gene. SLAS Discovery.  ISSN 2472-5552.  25(1), s 104- 112 . doi: 10.1177/2472555219864086
• Waszak, Sebastian Martin (2020). Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung. BioRxiv.  ISSN 0362-4331. . doi: 10.1101/2020.04.01.018861 Vis sammendrag

  The complexity of the lung microenvironment together with changes in cellular composition during disease progression make it exceptionally hard to understand the molecular mechanisms leading to the development of chronic lung diseases. Although recent advances in cell type resolved and single-cell sequencing approaches hold great promise for studying complex diseases, their implementation greatly relies on local access to fresh tissue, as traditional methods to process and store tissue do not allow viable cell isolation. To overcome these hurdles, we developed a novel, versatile workflow that allows long-term storage of human lung tissue with high cell viability, permits thorough sample quality check before cell isolation, and is compatible with next generation sequencing-based profiling, including single-cell approaches. We demonstrate that cryopreservation is suitable for isolation of multiple cell types from different lung locations and is applicable to both healthy and diseased tissue, including COPD and tumor samples. Basal cells isolated from cryopreserved airways retain the ability to differentiate, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for -omics profiling of human lung cells. In addition, we obtained high-quality single-cell RNA sequencing data of cells isolated from cryopreserved human lung, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our cryopreservation workflow is well-suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to human tissue.

• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie Maria; Lucas, Christin; Vekterud, Kristin; Soedling, Helen; Matthews, Jason; Lemma, Roza Berhanu; Gabrielsen, Odd Stokke; Bindesbøll, Christian; Ulven, Stine Marie; Nebb, Hilde Irene; Grønning-Wang, Line Mariann & Sæther, Thomas (2020). LXRα Regulates ChREBPα Transactivity in a Target Gene-Specific Manner through an Agonist-Modulated LBD-LID Interaction. Cells.  ISSN 2073-4409.  9(5) . doi: 10.3390/cells9051214 Fulltekst i vitenarkiv. Vis sammendrag

  The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in the liver. More knowledge of their mechanistic interplay is needed to understand their role in pathological conditions like fatty liver disease and insulin resistance. In the current study, LXR and ChREBP co-occupancy was examined by analyzing ChIP-seq datasets from mice livers. LXR and ChREBP interaction was determined by Co-immunoprecipitation (CoIP) and their transactivity was assessed by real-time quantitative polymerase chain reaction (qPCR) of target genes and gene reporter assays. Chromatin binding capacity was determined by ChIP-qPCR assays. Our data show that LXRα and ChREBPα interact physically and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; the low glucose inhibitory domain (LID) of ChREBPα and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα in responding to nutritional cues that was overlooked due to LXR lipogenesis-promoting function.

• Khalid, Khalisanni; Tan, Xuefei; Mohd Zaid, Hayyiratul Fatimah; Tao, Yang; Lye Chew, Chien; Chu, Dinh Toi; Lam, Man Kee; Ho, Yeek-Chia; Lim, Jun Wei & Chin Wei, Lai (2020). Advanced in developmental organic and inorganic nanomaterial: a review. Bioengineered.  ISSN 2165-5979.  11(1), s 328- 355 . doi: 10.1080/21655979.2020.1736240
• Chu, Dinh Toi; Phuong, Thuy Nguyen Thi; Tien, Nguyen Le Bao; Tran, Dang Khoa; Thanh, Vo Van; Quang, Thuy Luu; Truong, Dang Tien; Pham, Van-Huy; Ngoc, Vo Truong Nhu; Chu-Dinh, Thien & Kushekhar, Kushi (2020). An update on the progress of isolation, culture, storage, and clinical application of human bone marrow mesenchymal stem/stromal cells. International Journal of Molecular Sciences.  ISSN 1422-0067.  21:708(3), s 1- 27 . doi: 10.3390/ijms21030708
• Lindner, Paula Maria; Christensen, Søren Brøgger; Nissen, Poul; Møller, Jesper Vuust & Engedal, Nikolai (2020). Cell death induced by the ER stressor thapsigargin involves death receptor 5, a non-autophagic function of MAP1LC3B, and distinct contributions from unfolded protein response components. Cell Communication and Signaling.  ISSN 1478-811X.  18(1), s 1- 23 . doi: 10.1186/s12964-019-0499-z
• Martîn, Ruth Martîn; Stonyte, Vilte & Lopez Aviles, Sandra (2020). Protein phosphatases in G1 regulation. International Journal of Molecular Sciences.  ISSN 1422-0067.  21:395(2), s 1- 15 . doi: 10.3390/ijms21020395
• Meås, Hany Zakaria; Haug, Markus; Beckwith, Marianne Sandvold; Louet, Claire; Ryan, Liv; Hu, Zhenyi; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Yin, Hang; Damås, Jan Kristian & Flo, Trude Helen (2020). Sensing of HIV-1 by TLR8 activates human T cells and reverses latency. Nature Communications.  ISSN 2041-1723.  11 . doi: https://doi.org/10.1038/s41467-019-13837-4 Fulltekst i vitenarkiv. Vis sammendrag

  During HIV infection, cell-to-cell transmission results in endosomal uptake of the virus by target CD4+ T cells and potential exposure of the viral ssRNA genome to endosomal Toll-like receptors (TLRs). TLRs are instrumental in activating inflammatory responses in innate immune cells, but their function in adaptive immune cells is less well understood. Here we show that synthetic ligands of TLR8 boosted T cell receptor signaling, resulting in increased cytokine production and upregulation of surface activation markers. Adjuvant TLR8 stimulation, but not TLR7 or TLR9, further promoted T helper cell differentiation towards Th1 and Th17. In addition, we found that endosomal HIV induced cytokine secretion from CD4+ T cells in a TLR8-specific manner. TLR8 engagement also enhanced HIV-1 replication and potentiated the reversal of latency in patient-derived T cells. The adjuvant TLR8 activity in T cells can contribute to viral dissemination in the lymph node and low-grade inflammation in HIV patients. In addition, it can potentially be exploited for therapeutic targeting and vaccine development.

• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie Maria; Lucas, Christin; Vekterud, Kristin; Soedling, Helen; Matthews, Jason; Lemma, Roza Berhanu; Gabrielsen, Odd Stokke; Bindesbøll, Christian; Ulven, Stine Marie; Nebb, Hilde Irene; Grønning-Wang, Line Mariann & Sæther, Thomas (2019). Open the LID: LXRα regulates ChREBPα transactivity in a target gene-specific manner through an agonist-modulated LBD-LID interaction. BioRxiv.  ISSN 0362-4331. . doi: 10.1101/2019.12.20.869974 Vis sammendrag

  The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in liver. We have previously shown that LXR regulates ChREBP transcription and activity; however, the underlying mechanisms are unclear. In the current study, we demonstrate that LXRα and ChREBPα interact physically, and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα, and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP, but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; ChREBPα’s low glucose inhibitory domain (LID) and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα that was overlooked due to LXR lipogenesis-promoting function.

• Connell, Shea P; Yazbek-Hanna, Marcelino; McCarthy, Frank; Hurst, Rachel; Webb, Martyn; Curley, Helen; Walker, Helen; Mills, Rob; Ball, Richard Y; Sanda, Martin G.; Pellegrini, Kathryn L; Patil, Dattatraya; Perry, Antoinette; Schalken, Jack A.; Pandha, Hardev; Whitaker, Hayley; Dennis, Nening; Stuttle, Christine; Mills, Ian Geoffrey; Guldvik, Ingrid; Parker, Chris; Brewer, Daniel; Cooper, Colin S. & Clark, Jeremy P. (2019). A four‐group urine risk classifier for predicting outcomes in patients with prostate cancer. BJU International.  ISSN 1464-4096.  124(4), s 609- 620 . doi: 10.1111/bju.14811 Fulltekst i vitenarkiv.
• Keskitalo, Salla; Haapaniemi, Emma M.; Glumoff, Virpi; Liu, Xiaonan; Lehtinen, Ville; Fogarty, Christopher; Rajala, Hanna; Chiang, Samuel C.; Mustjoki, Satu; Kovanen, Panu; Lohi, Jouko; Bryceson, Yenan; Seppänen, Mikko; Kere, Juha; Heiskanen, Kaarina & Varjosalo, Markku (2019). Dominant TOM1 mutation associated with combined immunodeficiency and autoimmune disease. NPJ GENOMIC MEDICINE.  ISSN 2056-7944.  4:14, s 1- 7 . doi: 10.1038/s41525-019-0088-5 Fulltekst i vitenarkiv.
• Joemetsa, Silver; Spustová, Karolina; Kustanovich, Kiryl; Ainla, Alar; Schindler, Severin; Eigler, Siegfried; Lobovkina, Tatsiana; Lara-Avila, Samuel; Jesorka, Aldo & Gözen, Irep (2019). Molecular Lipid Films on Microengineering Materials. Langmuir.  ISSN 0743-7463.  35(32), s 10286- 10298 . doi: 10.1021/acs.langmuir.9b01120
• Kustanovich, Kiryl; Yantchev, Ventsislav; Doosti, Baharan Ali; Gözen, Irep & Jesorka, Aldo (2019). A microfluidics-integrated impedance/surface acoustic resonance tandem sensor. Sensing and Bio-Sensing Research.  25 . doi: 10.1016/j.sbsr.2019.100291
• Vo, Truong Nhu Ngoc; Chu, Dinh Toi; Duong, Duc Long; Bui, Van Nhon; Tong, Minh Son; Nguyen, Thi Thu Phuong; Le, Quynh-Anh; Nguyen, Khanh-Hoang; Pham, Van-Huy & Chu-Dinh, Thien (2019). Efficacy of electrochemically activated water solution in gingivitis treatment. Journal of Pharmaceutical Investigation (JPI).  ISSN 2093-5552.  49(3), s 323- 329 . doi: 10.1007/s40005-018-00419-7
• Truong-Nhu-Ngoc, Vo; Vu-Thai-Lien, Nguyen; Minh-Hang, Luong; Thanh-Tung, Doan; Thi-Nga, Vu; Pham-The, Hai & Chu, Dinh Toi (2019). Radicular cyst in a primary molar following pulp therapy with gutta percha: A case report and literature review. Journal of Clinical and Experimental Dentistry.  11(1), s e85- e90 . doi: 10.4317/jced.55309
• Gawel, Kinga Aurelia; Turski, Waldemar A.; van der Ent, Wietske; Mathai, Benan John; Kirstein-Smardzewska, Karolina Joanna; Simonsen, Anne & Esguerra, Camila V. (2019). Phenotypic Characterization of Larval Zebrafish (Danio rerio) with Partial Knockdown of the cacna1a Gene. Molecular Neurobiology.  ISSN 0893-7648. . doi: 10.1007/s12035-019-01860-x Fulltekst i vitenarkiv.
• Kamiński, Krzysztof; Socała, Katarzyna; Zagaja, Mirosław; Andres-Mach, Marta; Abram, Michał; Jakubiec, Marcin; Pieróg, Mateusz; Nieoczym, Dorota; Rapacz, Anna; Esguerra, Camila V.; Gawel, Kinga Aurelia; Latacz, Gniewomir; Lubelska, Annamaria; Szulczyk, Bartłomiej; Szewczyk, Aleksandra; Łuszczki, Jarogniew Jacek & Wlaź, Piotr (2019). N-Benzyl-(2,5-dioxopyrrolidin-1-yl)propanamide (AS-1) with Hybrid Structure as a Candidate for a Broad-Spectrum Antiepileptic Drug. Neurotherapeutics.  ISSN 1933-7213. . doi: 10.1007/s13311-019-00773-w Fulltekst i vitenarkiv.
• Fromm, Bastian; Domanska, Diana Ewa; Høye, Eirik; Ovchinnikov, Vladimir; Kang, Wenjing; Aparicio-Puerta, Ernesto; Johansen, Morten; Flatmark, Kjersti; Mathelier, Anthony; Hovig, Eivind; Hackenberg, Michael; Friedländer, Marc R. & Peterson, Kevin J. (2019). MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Research.  ISSN 0305-1048.  48(D1), s D132- D141 . doi: 10.1093/nar/gkz885 Fulltekst i vitenarkiv.
• Skånland, Sigrid Strand & Cieslar-Pobuda, Artur (2019). Off-label uses of drugs for depression. European Journal of Pharmacology.  ISSN 0014-2999.  865 . doi: 10.1016/j.ejphar.2019.172732 Fulltekst i vitenarkiv.
• Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana; Holden, Lars; Gheorghe, Marius; Mathelier, Anthony; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics.  ISSN 1467-5463.  s 1- 8 . doi: 10.1093/bib/bbz083 Vis sammendrag

  The generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of similarity measures have been proposed for this problem in other fields like ecology. However, while several of these measures have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated. We show that the choice of similarity measure may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly altered by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less influenced by dataset size, but one should be aware of increased variance for small datasets. All results on simulated and real data can be inspected and reproduced at https://hyperbrowser.uio.no/sim-measure.

• Barnett, Ian; Nishant, Malik; Kuijjer, Marieke Lydia; Mucha, Peter & Onnela, Jukka-Pekka (2019). Feature-based classification of networks. Network Science.  ISSN 2050-1242.  7(3), s 438- 444 . doi: https://doi.org/10.1017/nws.2019.21
• Fagny, Maud; Platig, John; Kuijjer, Marieke Lydia; Lin, Xihong & Quackenbush, John (2019). Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. British Journal of Cancer.  ISSN 0007-0920. . doi: 10.1038/s41416-019-0614-3 Fulltekst i vitenarkiv.
• Kuijjer, Marieke Lydia; Hsieh, Ping-Han; Quackenbush, John & Glass, Kimberly (2019). lionessR: single sample network inference in R. BMC Cancer.  ISSN 1471-2407.  19(1003) . doi: 10.1186/s12885-019-6235-7 Fulltekst i vitenarkiv.
• Kuijjer, Marieke Lydia; Tung, Matthew George; Yuan, GuoCheng; Quackenbush, John & Glass, Kimberly (2019). Estimating Sample-Specific Regulatory Networks. iScience.  ISSN 2589-0042.  14, s 226- 240 . doi: 10.1016/j.isci.2019.03.021 Fulltekst i vitenarkiv.
• Wong, Kim; van der Weyden, Louise; Schott, Courtney R.; Foote, Alastair; Constantino-Casas, Fernando; Smith, Sionagh; Dobson, Jane M.; Murchison, Elizabeth P.; Wu, Hong; Yeh, Iwei; Fullen, Douglas R.; Joseph, Nancy; Bastian, Boris C.; Patel, Rajiv M.; Martincorena, Inigo; Robles-Espinoza, Carla Daniela; Iyer, Vivek; Kuijjer, Marieke Lydia; Arends, Mark J.; Brenn, Thomas; Harms, Paul W.; Wood, Geoffrey A. & Adams, David J. (2019). Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. Nature Communications.  ISSN 2041-1723.  10(353), s 1- 14 . doi: 10.1038/s41467-018-08081-1 Fulltekst i vitenarkiv.
• Zhen, Yan; Spangenberg, Helene; Munson, Michael Joseph; Brech, Andreas; Schink, Kay Oliver; Tan, Kia Wee; Sørensen, Vigdis; Wenzel, Eva; Radulovic, Maja; Engedal, Nikolai; Simonsen, Anne; Raiborg, Camilla & Stenmark, Harald (2019). ESCRT-mediated phagophore sealing during mitophagy. Autophagy.  ISSN 1554-8627.  s 1- 16 . doi: 10.1080/15548627.2019.1639301 Fulltekst i vitenarkiv.
• Handle, Florian; Prekovic, Stefan; Helsen, Christine; van den Broeck, Thomas; Smeets, Elien; Moris, Lisa; Eerlings, Roy; El Kharraz, Sarah; Urbanucci, Alfonso; Mills, Ian Geoffrey; Joniau, Steven; Attard, Gerhardt & Claessens, Frank (2019). Drivers of AR indifferent anti-androgen resistance in prostate cancer cells. Scientific Reports.  ISSN 2045-2322.  9(13786), s 1- 11 . doi: 10.1038/s41598-019-50220-1 Fulltekst i vitenarkiv.
• Ha, Thomas J.; Zhang, Peter G.Y.; Robert, Remi; Yeung, Joanna; Swanson, Douglas J.; Mathelier, Anthony; Wasserman, Wyeth W.; Im, Sujin; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Daub, Carsten O.; Arner, Erik; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R.R. & Goldowitz, Daniel (2019). Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics.  ISSN 1471-2164.  20(718), s 1- 17 . doi: 10.1186/s12864-019-6063-9 Fulltekst i vitenarkiv.
• Vu, Le Nguyen; Nghia, Nguyen Quang; Thanh, Do Truong; Giang, Tran Binh; Nga, Vu Thi; Bui, Le Minh & Chu, Dinh Toi (2019). Laparoscopic living donor right nephrectomy: Assessment of outcome and association of BMI to length of right renal vein. Actas Urológicas Españolas.  ISSN 0210-4806.  43(10), s 536- 542 . doi: 10.1016/j.acuro.2019.05.005
• Behringer, Sidney; Wingert, Victoria; Oria, Victor; Schumann, Anke; Grünert, Sarah; Cieslar-Pobuda, Artur; Kölker, Stefan; Lederer, Ann-Kathrin; Jacobsen, Donald W.; Stärk, Judith; Schilling, Oliver; Spiekerkoetter, Ute & Hannibal, Luciana (2019). Targeted metabolic profiling of methionine cycle metabolites and redox thiol pools in mammalian plasma, cells and urine. Metabolites.  ISSN 2218-1989.  9:235(10), s 1- 27 . doi: 10.3390/metabo9100235 Fulltekst i vitenarkiv.
• Copmans, Daniëlle; Kildgaard, Sara; Rasmussen, Silas A.; Ślęzak, Monika; Dirkx, Nina; Partoens, Michèle; Esguerra, Camila Vicencio; Crawford, Alexander Dettmar; Larsen, Thomas O. & de Witte, Peter A.M. (2019). Zebrafish-based discovery of antiseizure compounds from the north sea: Isoquinoline alkaloids TMC-120A and TMC-120B. Marine Drugs.  ISSN 1660-3397.  17:607(11), s 1- 20 . doi: 10.3390/md17110607 Fulltekst i vitenarkiv.
• Nielsen, Nis Valentin; Roedel, Elfie; Manna, Dipankar; Etscheid, Michael; Morth, Jens Preben & Kanse, Sandip (2019). Characterization of the enzymatic activity of the serine protease domain of Factor VII activating protease (FSAP). Scientific Reports.  ISSN 2045-2322.  9(1) . doi: 10.1038/s41598-019-55531-x Fulltekst i vitenarkiv.
• Braadland, Peder Rustøen; Ramberg, Håkon Andre; Grytli, Helene Hartvedt; Urbanucci, Alfonso; Nielsen, Heidi Kristin; Guldvik, Ingrid Jenny; Engedahl, Andreas; Ketola, Kirsi; Wanzhong, Wang; Svindland, Aud; Mills, Ian Geoffrey; Bjartell, Anders & Tasken, Kristin Austlid (2019). The β2-adrenergic receptor is a molecular switch for neuroendocrine transdifferentiation of prostate cancer cells. Molecular Cancer Research.  ISSN 1541-7786.  17(11), s 2154- 2168 . doi: 10.1158/1541-7786.MCR-18-0605
• Tepekule, Burcu; Abel zur Wiesch, Pia; Kouyos, Roger D. & Bonhoeffer, Sebastian (2019). Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America.  ISSN 0027-8424.  116(46), s 23106- 23116 . doi: 10.1073/pnas.1912188116 Fulltekst i vitenarkiv.
• Skånland, Sigrid Strand; Cremaschi, Andrea; Bendiksen, Henrik; Hermansen, Johanne Uthus; Thimiri Govinda Raj, Deepak Balaji; Munthe, Ludvig Andre; Tjønnfjord, Geir Erland & Tasken, Kjetil (2019). An in vitro assay for biomarker discovery and dose prediction applied to ibrutinib plus venetoclax treatment of CLL. Leukemia.  ISSN 0887-6924. . doi: 10.1038/s41375-019-0569-7
• Korecki, Andrea J; Hickmott, Jack W; Lam, Siu Ling; Dreolini, Lisa; Mathelier, Anthony; Baker, Oliver; Kuehne, Claudia; Bonaguro, Russell J; Smith, Jillian; Tan, Chin-Vern; Zhou, Michelle; Goldowitz, Daniel; Deussing, Jan M; Stewart, A. Francis; Wasserman, Wyeth W.; Holt, Robert A & Simpson, Elizabeth M (2019). Twenty-seven tamoxifen-inducible icre-driver mouse strains for eye and brain, including seventeen carrying a new inducible-first constitutive-ready allele. Genetics.  ISSN 0016-6731.  211(4), s 1155- 1177 . doi: 10.1534/genetics.119.301984
• Halnes, Geir; Pettersen, Klas Henning; Øyehaug, Leiv; Rognes, Marie Elisabeth & Einevoll, Gaute (2019). Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow, In Hugues Berry & Maurizio De Pittà (ed.),  Computational Glioscience.  Springer Nature.  ISBN 978-3-030-00817-8.  Chapter.  s 363 - 391
• Mayer, Alexander E.; Löffler, Mona C; Valdés, Angel E Loza; Schmitz, Werner; El-Merahbi, Rabih; Viera, Jonathan Trujillo; Erk, Manuela; Zhang, Tianzhou; Braun, Ursula Barbara; Heikenwalder, Mathias; Leitges, Michael; Schulze, Almut & Sumara, Grzegorz (2019). The kinase PKD3 provides negative feedback on cholesterol and triglyceride synthesis by suppressing insulin signaling. Science Signaling.  ISSN 1945-0877.  12(593) . doi: 10.1126/scisignal.aav9150
• Sisodiya, Sanjay M.; Fowler, Hayley J.; Lake, Iain; Nanji, Rosemary Ogwen; Gawel, Kinga Aurelia; Esguerra, Camila Vicencio; Newton, Charles & Foley, Aideen (2019). Climate change and epilepsy: Time to take action. Epilepsia Open.  ISSN 2470-9239.  4(4), s 524- 536 . doi: 10.1002/epi4.12359 Fulltekst i vitenarkiv.
• Fornes, Oriol; Castro Mondragón, Jaime Abraham; Khan, Aziz; Robin van der, Lee; Zhang, Xi; A. Richmond, Phillip; P. Modi, Bhavi; Correard, Solenne; Gheorghe, Marius; Baranasic, Damir; Santana-Garcia, Walter; Tan, Ge; Cheneby, Jeanne; Ballester, Benoit; Parcy, François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W. & Mathelier, Anthony (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research.  ISSN 0305-1048.  48, s 87- 92 . doi: 10.1093/nar/gkz1001 Vis sammendrag

  JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.

• Gawel, Kinga Aurelia; Banono, Nancy Saana; Michalak, Agnieszka & Esguerra, Camila Vicencio (2019). A critical review of zebrafish schizophrenia models: Time for validation?. Neuroscience and Biobehavioral Reviews.  ISSN 0149-7634.  107, s 6- 22 . doi: 10.1016/j.neubiorev.2019.08.001
• Rydmark, Marcella Orwick; Christensen, Mikkel; Köksal, Elif; Kantarci, Ilayda; Kustanovich, Kiryl; Yantchev, Ventsislav; Jesorka, Aldo & Gözen, Irep (2019). Styrene maleic acid copolymer induces pores in biomembranes. Soft Matter.  ISSN 1744-683X.  15(39), s 7934- 7944 . doi: 10.1039/C9SM01407A Fulltekst i vitenarkiv.
• Gözen, Irep (2019). A Hypothesis for Protocell Division on the Early Earth. ACS Nano.  ISSN 1936-0851.  13(10), s 10869- 10871 . doi: 10.1021/acsnano.9b06584
• Post, Joakim Iver; Leergaard, Trygve B.; Ratz, Veronika; Walaas, S. Ivar; von Hörsten, Stephan & Nissen-Meyer, Lise Sofie Haug (2019). Differential Levels and Phosphorylation of Type 1 Inositol 1,4,5-Trisphosphate Receptor in Four Different Murine Models of Huntington Disease. Journal of Huntington's Disease.  ISSN 1879-6397.  8(3), s 271- 289 . doi: 10.3233/JHD-180301
• Köksal, Elif; Belletati, Patrícia Fernandes; Reint, Ganna; Olsson, Ragni; Leitl, Kira; Kantarci, Ilayda & Gözen, Irep (2019). Spontaneous Formation and Rearrangement of Artificial Lipid Nanotube Networks as a Bottom-Up Model for Endoplasmic Reticulum. Journal of Visualized Experiments.  ISSN 1940-087X.  2019(143), s 1- 9 . doi: 10.3791/58923 Fulltekst i vitenarkiv.
• Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Anderssen, Petter Inge; Kuivanen, Suvi; Teppor, Mona; Zusinaite, Eva; Dumpis, Uga; Vitkauskiene, Astra; Cox, Rebecca Jane; Kallio-Kokko, Hannimari; Bergqvist, Anders; Tenson, Tanel; Merits, Andres; Oksenych, Valentyn; Bjørås, Magnar; Anthonsen, Marit Walbye; Shum, David H.K.; Kaarbø, Mari; Vapalahti, Olli; Windisch, Marc P.; Superti-Furga, Giulio; Snijder, Berend; Kainov, Denis & Kandasamy, Richard Kumaran (2019). Common nodes of virus-host interaction revealed through an integrated network analysis. Frontiers in Immunology.  ISSN 1664-3224.  10 . doi: 10.3389/fimmu.2019.02186 Fulltekst i vitenarkiv.
• Ali Ahmad, Ahmad; Bilokapic, Silvija; Schafer, Ingmar B; Halic, Mario & Sekulic, Nikolina (2019). CENP‐C unwraps the human CENP‐A nucleosome through the H2A C‐terminal tail. EMBO Reports.  ISSN 1469-221X. . doi: 10.15252/embr.201948913 Fulltekst i vitenarkiv.
• Dung, Truong Manh; Ngoc, Vo Truong Nhu; Hiep, Nguyen Hung; Khoi, Truong Dinh; Xiem, Vu Van; Chu-Dinh, Thien; Cieslar-Pobuda, Artur; Stoufi, Eleana; Show, Pau Loke; Tao, Yang; Bac, Nguyen Duy; Van Ba, Nguyen; Le, Quynh-Anh; Pham, Van-Huy & Chu, Dinh Toi (2019). Evaluation of dental arch dimensions in 12 year-old Vietnamese children - A cross-sectional study of 4565 subjects. Scientific Reports.  ISSN 2045-2322.  9(1) . doi: 10.1038/s41598-019-39710-4 Fulltekst i vitenarkiv.
• Köksal, Elif; Liese, Susanne; Kantarci, Ilayda; Olsson, Ragni; Carlson, Andreas & Gözen, Irep (2019). Nanotube-Mediated Path to Protocell Formation. ACS Nano.  ISSN 1936-0851.  13(6), s 6867- 6878 . doi: 10.1021/acsnano.9b01646 Fulltekst i vitenarkiv.
• Horowitz, Viva R; Chambers, Zachary C; Gözen, Irep; Dimiduk, Thomas G & Manoharan, Vinothan N (2019). Active colloidal particles in emulsion droplets: a model system for the cytoplasm. The European Physical Journal Special Topics.  ISSN 1951-6355.  227(17), s 2413- 2424 . doi: 10.1140/epjst/e2019-800026-y Vis sammendrag

  In living cells, molecular motors create activity that enhances the diffusion of particles throughout the cytoplasm, and not just ones attached to the motors. We demonstrate initial steps toward creating artificial cells that mimic this phenomenon. Our system consists of active, Pt-coated Janus particles and passive tracers confined to emulsion droplets. We track the motion of both the active particles and passive tracers in a hydrogen peroxide solution, which serves as the fuel to drive the motion. We first show that correcting for bulk translational and rotational motion of the droplets induced by bubble formation is necessary to accurately track the particles. After drift correction, we find that the active particles show enhanced diffusion in the interior of the droplets and are not captured by the droplet interface. At the particle and hydrogen peroxide concentrations we use, we observe little coupling between the active and passive particles. We discuss the possible reasons for lack of coupling and describe ways to improve the system to more effectively mimic cytoplasmic activity.

• Leong, Yoong Kit; Show, Pau Loke; Lan, John Chi-Wei; Krishnamoorthy, Rambabu; Chu, Dinh Toi; Nagarajan, Dillirani; Yen, Hong-Wei & Chang, Jo-Shu (2019). Application of thermo-separating aqueous two-phase system in extractive bioconversion of polyhydroxyalkanoates by Cupriavidus necator H16. Bioresource Technology.  ISSN 0960-8524.  287, s 1- 5 . doi: 10.1016/j.biortech.2019.121474
• Martinecz, Antal; Clarelli, Fabrizio; Abel, Sören & Abel zur Wiesch, Pia (2019). Reaction Kinetic Models of Antibiotic Heteroresistance. International Journal of Molecular Sciences.  ISSN 1422-0067.  20(16) . doi: 10.3390/ijms20163965 Fulltekst i vitenarkiv.
• Luhr, Morten; Torgersen, Maria Lyngaas; Szalai, Paula; Hashim, Adnan; Brech, Andreas; Stärk, Judith & Engedal, Nikolai (2019). The kinase PERK and the transcription factor ATF4 play distinct and essential roles in autophagy resulting from tunicamycin-induced ER stress. Journal of Biological Chemistry.  ISSN 0021-9258.  294(20), s 8197- 8217 . doi: 10.1074/jbc.RA118.002829 Fulltekst i vitenarkiv.
• Stiksrud, Birgitte; Aass, Hans Christian Dalsbotten; Lorvik, Kristina Berg; Ueland, Thor; Trøseid, Marius & Dyrhol-Riise, Anne Ma (2019). Activated dendritic cells and monocytes in HIV immunological nonresponders: HIV-induced interferon-inducible protein-10 correlates with low future CD4+ recovery. AIDS (London).  ISSN 0269-9370.  33(7), s 1117- 1129 . doi: 10.1097/QAD.0000000000002173 Fulltekst i vitenarkiv.
• van IJzendoorn, David G.P.; Szuhai, Karoly; Briaire-De Bruijn, Inge H; Kostine, Marie; Kuijjer, Marieke Lydia & Bovée, Judith V.M.G. (2019). Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. PLoS Computational Biology.  ISSN 1553-734X.  15(2), s 1- 19 . doi: 10.1371/journal.pcbi.1006826 Fulltekst i vitenarkiv.
• Gupta, Abhay; Gözen, Irep & Taylor, Michael (2019). A cellular automaton for modeling non-trivial biomembrane ruptures. Soft Matter.  ISSN 1744-683X.  15(20), s 4178- 4186 . doi: 10.1039/c8sm02032a Fulltekst i vitenarkiv.
• Itkonen, Harri; Poulose, Ninu; Walker, Suzanne & Mills, Ian Geoffrey (2019). CDK9 Inhibition Induces a Metabolic Switch that Renders Prostate Cancer Cells Dependent on Fatty Acid Oxidation. Neoplasia.  ISSN 1522-8002.  21(7), s 713- 720 . doi: 10.1016/j.neo.2019.05.001 Fulltekst i vitenarkiv.
• Banerjee, Debarshi; Cieslar-Pobuda, Artur; Zhu, Geyunjian Harry; Wiechec, Emilia & Patra, Hirak K. (2019). Adding Nanotechnology to the Metastasis Treatment Arsenal. TIPS - Trends in Pharmacological Sciences.  ISSN 0165-6147.  40(6), s 403- 418 . doi: 10.1016/j.tips.2019.04.002
• Feng, Huijuan; Bao, Suying; Rahman, Mohammad Alinoor; Weyn-Vanhentenryck, Sebastien M.; Khan, Aziz; Wong, Justin YY; Shah, Ankeeta; Flynn, Elise D.; Krainer, Adrian R. & Zhang, Chaolin (2019). Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. Molecular Cell.  ISSN 1097-2765.  74(6), s 1189- 1204 . doi: 10.1016/j.molcel.2019.02.002 Vis sammendrag

  RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence motifs in their target transcripts, but precisely defining their binding specificity remains challenging. Crosslinking and immunoprecipitation (CLIP) allows for mapping of the exact protein-RNA crosslink sites, which frequently reside at specific positions in RBP motifs at single-nucleotide resolution. Here, we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the discovered motifs by genome-wide analysis of allelic binding sites. Our analyses revealed that the prototypical SR protein SRSF1 recognizes clusters of GGA half-sites in addition to its canonical GGAGGA motif. Therefore, SRSF1 regulates splicing of a much larger repertoire of transcripts than previously appreciated, including HNRNPD and HNRNPDL, which are involved in multivalent protein assemblies and phase separation.

• Chellappa, Stalin; Kushekhar, Kushi; Munthe, Ludvig Andre; Tjønnfjord, Geir Erland; Aandahl, Einar Martin; Okkenhaug, Klaus & Tasken, Kjetil (2019). The PI3K p110δ isoform inhibitor idelalisib preferentially inhibits human regulatory T cell function. Journal of Immunology.  ISSN 0022-1767.  202(5), s 1397- 1405 . doi: 10.4049/jimmunol.1701703
• Cuminetti, Vincent & Arranz, Lorena (2019). Bone Marrow Adipocytes: The Enigmatic Components of the Hematopoietic Stem Cell Niche. Journal of Clinical Medicine.  ISSN 2077-0383.  8(5), s 707 . doi: 10.3390/jcm8050707 Fulltekst i vitenarkiv.
• Goodridge, Jodie; Jacobs, Benedikt Marcel; Sætersmoen, Michelle Lu; Clement, Dennis; Hammer, Quirin; Clancy, Trevor; Skarpen, Ellen; Brech, Andreas; Landskron, Johannes; Grimm, Christian; Pfefferle, Aline; Meza, Leonardo Zepeda; Lorenz, Susanne; Wiiger, Merete Thune; Louch, William Edward; Ask, Eivind Heggernes; Liu, Lisa L.; Oei, Vincent Yi Sheng; Kjällquist, Una; Linnarsson, Sten; Patel, Sandip; Tasken, Kjetil; Stenmark, Harald & Malmberg, Karl-Johan (2019). Remodeling of secretory lysosomes during education tunes functional potential in NK cells. Nature Communications.  ISSN 2041-1723.  10:14, s 1- 15 . doi: 10.1038/s41467-019-08384-x Fulltekst i vitenarkiv.
• Nieoczym, Dorota; Socala, Katarzyna; Gawel, Kinga Aurelia; Esguerra, Camila Vicencio; Wyska, Elzbieta & Wlaz, Piotr (2019). Anticonvulsant Activity of Pterostilbene in Zebrafish and Mouse Acute Seizure Tests. Neurochemical Research.  ISSN 0364-3190.  44(5), s 1043- 1055 . doi: 10.1007/s11064-019-02735-2 Fulltekst i vitenarkiv.
• Subbannayya, Yashwanth; Pinto, Sneha; Bösl, Korbinian; Prasad, T. S. Keshava & Kandasamy, Richard Kumaran (2019). Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling. International Journal of Molecular Sciences.  ISSN 1422-0067.  20(9), s 1- 22 . doi: 10.3390/ijms20092086 Fulltekst i vitenarkiv.
• Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony; Thiede, Bernd; Walker, Suzanne & Mills, Ian Geoffrey (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics.  ISSN 1838-7640.  9(8), s 2183- 2197 . doi: 10.7150/thno.30834 Fulltekst i vitenarkiv.
• Engedal, Nikolai; Luhr, Morten; Szalai, Paula & Seglen, Per O. (2019). Measurement of Bulk Autophagy by a Cargo Sequestration Assay. Methods in molecular biology.  ISSN 1064-3745.  1880, s 307- 313 . doi: 10.1007/978-1-4939-8873-0_20
• Abudu, Yakubu Princely; Pankiv, Serhiy; Mathai, Benan John; Lystad, Alf Håkon; Bindesbøll, Christian; Brenne, Hanne Britt; Ng, Matthew Yoke Wui; Thiede, Bernd; Yamamoto, Ai; Nthiga, Thaddaeus Mutugi; Lamark, Trond; Esguerra, Camila Vicencio; Johansen, Terje & Simonsen, Anne (2019). NIPSNAP1 and NIPSNAP2 act as “eat-me signal” for mitophagy. Developmental Cell.  ISSN 1534-5807.  49(4), s 509- 525.e12 . doi: 10.1016/j.devcel.2019.03.013 Fulltekst i vitenarkiv.
• Szwed, Marzena; Sønstevold, Tonje; Øverbye, Anders; Engedal, Nikolai; Grallert, Beata; Mørch, Ýrr Asbjørg; Sulheim, Einar; Iversen, Tore Geir; Skotland, Tore; Sandvig, Kirsten & Torgersen, Maria Lyngaas (2019). Small variations in nanoparticle structure dictate differential cellular stress responses and mode of cell death. Nanotoxicology.  ISSN 1743-5390.  13(6), s 761- 782 . doi: 10.1080/17435390.2019.1576238 Fulltekst i vitenarkiv.
• Khan, Aziz & Zhang, Xuegong (2019). Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers. Scientific Reports.  ISSN 2045-2322.  9(1), s 1- 15 . doi: 10.1038/s41598-019-38979-9 Fulltekst i vitenarkiv.
• Brennecke, Philip; Rasina, Dace; Aubi Catevilla, Oscar; Herzog, Katja; Landskron, Johannes; Cautain, Bastien; Vicente, Francisca; Quintana, Jordi; Mestres, Jordi; Stechmann, Bahne; Ellinger, Bernhard; Brea, Jose; Kolanowski, Jacek L.; Pilarski, Radosław; Orzáez, Mar; Pineda-Lucena, Antonio; Laraia, Luca; Nami, Faranak; Zielenkiewicz, Piotr; Paruch, Kamil; Hansen, Espen; von Kries, Jens P.; Neuenschwander, Martin; Specker, Edgar; Bartunek, Petr; Šímová, Šárka; Leśnikowski, Zbigniew; Krauss, Stefan; Lehtiö, Lari; Bilitewski, Ursula; Brönstrup, Mark; Tasken, Kjetil; Jirgensons, Aigars; Lickert, Heiko; Clausen, Mads H.; Andersen, Jeanette hammer; Vicent, Maria J.; Genilloud, Olga; Martinez, Aurora; Nazaré, Marc; Fecke, Wolfgang & Gribbon, Philip (2019). EU-OPENSCREEN: A novel collaborative approach to facilitate chemical biology. SLAS Discovery.  ISSN 2472-5552.  24(3), s 398- 413 . doi: 10.1177/2472555218816276 Fulltekst i vitenarkiv.
• Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research.  ISSN 0305-1048.  47(4), s e21 . doi: 10.1093/nar/gky1210 Fulltekst i vitenarkiv.
• Wang, Shixiong; Singh, Sachin Kumar; Katika, MR; Lopez Aviles, Sandra & Hurtado, Antoni (2018). High Throughput Chemical Screening Reveals Multiple Regulatory Proteins on FOXA1 in Breast Cancer Cell Lines. International Journal of Molecular Sciences.  ISSN 1422-0067. . doi: 10.3390/ijms19124123
• Kang, Tianyu; Zarringhalam, Kourosh; Kuijjer, Marieke Lydia; Chen, Ping; Quackenbush, John & Ding, Wei (2018). Clustering on Sparse Data in Non-Overlapping Feature Space with Applications toCancer Subtyping. IEEE International Conference on Data Mining. Proceedings.  ISSN 1550-4786. . doi: 10.1109/ICDM.2018.00138
• Gerhauser, Clarissa; Favero, Francesco; Risch, Thomas; Simon, Ronald; Feuerbach, Lars; Assenov, Yassen; Heckmann, Doreen; Sidiropoulos, Nikos; Waszak, Sebastian M.; Hübschmann, Daniel; Urbanucci, Alfonso; Girma, Etsehiwot G.; Kuryshev, Vladimir; Klimczak, Leszek J.; Saini, Natalie; Stütz, Adrian M.; Weichenhan, Dieter; Böttcher, Lisa-Marie; Toth, Reka; Hendriksen, Josephine D.; Koop, Christina; Lutsik, Pavlo; Matzk, Sören; Warnatz, Hans-Jörg; Amstislavskiy, Vyacheslav; Feuerstein, Clarissa; Raeder, Benjamin; Bogatyrova, Olga; Schmitz, Eva-Maria; Hube-Magg, Claudia; Kluth, Martina; Huland, Hartwig; Graefen, Markus; Lawerenz, Chris; Henry, Gervaise H.; Yamaguchi, Takafumi N.; Malewska, Alicia; Meiners, Jan; Schilling, Daniela; Reisinger, Eva; Eils, Roland; Schlesner, Matthias; Strand, Douglas W.; Bristow, Robert G.; Boutros, Paul C.; von Kalle, Christof; Gordenin, Dmitry; Sültmann, Holger; Brors, Benedikt; Sauter, Guido; Plass, Christoph; Yaspo, Marie-Laure; Korbel, Jan O.; Schlomm, Thorsten & Weischenfeldt, Joachim (2018). Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories. Cancer Cell.  ISSN 1535-6108.  34(6), s 996- 1011.e8 . doi: 10.1016/j.ccell.2018.10.016
• Roest, Gemma; Hesemans, Evelien; Welkenhuyzen, Kirsten; Luyten, Tomas; Engedal, Nikolai; Bultynck, Geert & Parys, Jan B. (2018). The ER Stress Inducer L-Azetidine-2-Carboxylic Acid Elevates the Levels of Phospho-eIF2α and of LC3-II in a Ca2+-Dependent Manner. Cells.  ISSN 2073-4409.  7(12), s 239 . doi: 10.3390/cells7120239 Fulltekst i vitenarkiv.
• Tsui, Carlson; Martínez-Martín, Nuria; Gaya, Mauro; Maldonado, Paula; Llorian, Miriam; Legrave, Nathalie M.; Rossi, Merja; MacRae, James I.; Cameron, Angus J.; Parker, Peter J.; Leitges, Michael; Bruckbauer, Andreas & Batista, Facundo D. (2018). Protein kinase C-β dictates B cell fate by regulating mitochondrial remodeling, metabolic reprogramming, and heme biosynthesis. Immunity.  ISSN 1074-7613.  48(6), s 1144- 1159.e5 . doi: 10.1016/j.immuni.2018.04.031 Fulltekst i vitenarkiv.
• Nguyen, Nga Thi Thuy; Contreras-Moreira, Bruno; Castro Mondragón, Jaime Abraham; Santana-Garcia, Walter; Ossio, Raul; Robles-Espinoza, Carla Daniela; Bahin, Mathieu; Collombet, Samuel; Vincens, Pierre; Thieffry, Denis; van Helden, Jacques; Medina-Rivera, Alejandra & Thomas-Chollier, Morgane (2018). RSAT 2018: Regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research.  ISSN 0305-1048.  46(1), s W209- W214 . doi: 10.1093/nar/gky317 Fulltekst i vitenarkiv.
• Colgan, Lesley A; Hu, Mo; Misler, Jaime A; Parra-Bueno, Paula; Moran, Corey M; Leitges, Michael & Yasuda, Ryohei (2018). PKCα integrates spatiotemporally distinct Ca2+ and autocrine BDNF signaling to facilitate synaptic plasticity. Nature Neuroscience.  ISSN 1097-6256.  21(8), s 1027- 1037 . doi: 10.1038/s41593-018-0184-3
• Aourz, Najat; Serruys, Ann-Sophie K.; Chabwine, Joelle N.; Balegamire, Pascal Byenda; Afrikanova, Tatiana; Edrada-Ebel, RuAngelie; Grey, Alexander I.; Kamuhabwa, Appolinary R.; Walrave, Laura; Esguerra, Camila V.; van Leuven, Fred; De Witte, Peter A.M.; Smolders, Ilse & Crawford, Alexander D. (2018). Identification of GSK‑3 as a Potential Therapeutic Entry Point for Epilepsy. ACS Chemical Neuroscience.  ISSN 1948-7193. . doi: 10.1021/acschemneuro.8b00281
• Fornes, Oriol; Gheorghe, Marius; Richmond, Phillip A.; Arenillas, David J.; Wasserman, Wyeth W. & Mathelier, Anthony (2018). MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Scientific Data.  ISSN 2052-4463.  5:180141, s 1- 7 . doi: 10.1038/sdata.2018.141 Fulltekst i vitenarkiv.

Se alle arbeider i Cristin

• Ahrens, Theresa Dorothee; Caglayan, Safak; Staerk, Judith & Cieslar-Pobuda, Artur (2018). Transdifferentiation – changing cell identity. Academic Press.  ISBN 9780128122785.  249 s.
• Caglayan, Safak; Ahrens, Theresa Dorothee; Cieslar-Pobuda, Artur & Staerk, Judith (2018). Modern ways of obtaining stem cells. Academic Press.  ISBN 9780128122785.  249 s.

Se alle arbeider i Cristin

• Sharapova, Svetlana O.; Haapaniemi, Emma; Sakovich, Inga S.; Kostyuchenko, Larysa V.; Donkó, Agnes; Dulau-Florea, Alina; Malko, Oksana; Bondarenko, Anastasia V.; Stegantseva, Maria V.; Leto, Thomas L.; Uygun, Vedat; Karasu, Gülsün Tezcan; Holland, Steven M.; Hsu, Amy P. & Aleinikova, Olga V. (2019). Heterozygous activating mutation in RAC2 causes infantile-onset combined immunodeficiency with susceptibility to viral infections. Clinical Immunology.  ISSN 1521-6616.  205, s 1- 5 . doi: 10.1016/j.clim.2019.05.003
• Lopes-ramos, Camila; Kuijjer, Marieke Lydia; Ogino, Shuji; Fuchs, Charles S.; DeMeo, Dawn L.; Glass, Kimberly & Quackenbush, John (2019). Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research.  ISSN 0008-5472.
• Meås, Hany Zakaria; Haug, Markus; Beckwith, Marianne Sandvold; Louet, Claire; Ryan, Liv; Hu, Z.; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Yin, H. H.; Damås, Jan Kristian & Flo, Trude Helen (2019). Sensing of HIV-1 by TLR8 activates human T cells and reverses latency.
• Haug, Markus; Meås, Hany Zakaria; Beckwith, Marianne Sandvold; Louet, Claire; Ryan, Liv; Hu, Z.; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Yin, H. H.; Damås, Jan Kristian & Flo, Trude Helen (2019). Sensing of HIV-1 by TLR8 in human CD4+ T cells. Vis sammendrag

  Cell-to-cell transmission of HIV can result in endosomal uptake of HIV by CD4+ T cells with possible exposure of viral ssRNA genome to endolysosomal Toll-like receptors (TLRs). TLRs are central in activating inflammatory responses in innate immune cells, but their function in CD4+ T cells is less well understood. Here we show that combined TLR8 ligand and T cell receptor (TCR) stimulation boosted CD4+ T cell activation by enhancing NF-B and MAPK signaling. This led to increased production of inflammatory cytokines and surface activation marker expression. Adjuvant TLR8 stimulation, but not TLR7 or TLR9, promoted interleukin (IL)-17 and interferon (IFN)- effector cytokine production, indicating lineage commitment towards the pro-inflammatory T helper (Th)1 and Th17 axis. Using a cell-to-cell transmission model, we found that endosomal HIV induced cytokine secretion from CD4+ T cells, which could be significantly reduced by a TLR8 specific inhibitor. TLR8 engagement also enhanced HIV replication in CD4+ T cells and potentiated the reversal of latency in patient-derived CD4+ T cells. Taken together, our results reveal a previously unknown function of TLR8 in human primary CD4+ T cells in shaping immunity and modulating HIV-1 infection. This adjuvant TLR8 activity can contribute to low-grade inflammation seen in HIV patients and may also have implications for therapeutic targeting and vaccine development.

• Haug, Markus; Meås, Hany Zakaria; Beckwith, Marianne Sandvold; Louet, Claire; Ryan, Liv; Hu, Z.; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Yin, H. H.; Damås, Jan Kristian & Flo, Trude Helen (2019). Sensing of HIV-1 nucleic acids by TLR8 in human CD4+ T cells. Vis sammendrag

  During HIV-infection, cell-to-cell transmission results in endosomal uptake of the virus by target CD4+ T cells and potential exposure of the viral ssRNA genome to endolysosomal Toll-like receptors (TLRs). TLRs are instrumental in activating inflammatory responses in innate immune cells, but their function in adaptive immune cells is less well understood. Here we show that combined TLR8 ligand and T cell receptor (TCR) stimulation boosted CD4+ T cell activation by enhancing NF-kB and MAPK signaling. This led to increased production of inflammatory cytokines and surface activation marker expression. Adjuvant TLR8 stimulation, but not TLR7 or TLR9, promoted interleukin (IL)-17 and interferon (IFN)-g effector cytokine production, indicating lineage commitment towards the pro-inflammatory T helper (Th)1 and Th17 axis. Using a cell-to-cell transmission model, we found that endosomal HIV-1 induced cytokine secretion from CD4+ T cells, which could be significantly reduced by a TLR8 specific inhibitor. TLR8 engagement also enhanced HIV-1 replication in CD4+ T cells and potentiated the reversal of latency in patient-derived CD4+ T cells. Taken together, our results reveal a previously unknown function of TLR8 in human primary CD4+ T cells in shaping immunity and modulating HIV-1 infection. This adjuvant TLR8 activity can contribute to low-grade inflammation seen in HIV patients and may have broad implications for therapeutic targeting and vaccine development.

• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie Maria; Lucas, Christin; Vekterud, Kristin; Södling, Helen; Matthews, Jason; Lemma, Roza Berhanu; Gabrielsen, Odd Stokke; Bindesbøll, Christian; Ulven, Stine Marie; Nebb, Hilde Irene; Grønning-Wang, Line Mariann & Sæther, Thomas (2019). LXRα interacts with the glucose-sensing transcription factor ChREBPα to regulate its transcriptional activity.. Vis sammendrag

  The cholesterol-sensing nuclear receptor Liver X Receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in the regulation of glucose and lipid metabolism. LXR does this job in part by regulating the expression of ChREBP. We have previously shown that LXR also regulates ChREBP activity. To get a better understanding of mechanisms at play, we asked if LXR and ChREBP interact physically. Interestingly, LXRα binds to ChREBPα, but not the shorter isoform ChREBPβ. Co-immunoprecipitation (CoIP) of different LXR and ChRBEP domains shows that it is ChREBPα’s low glucose inhibitory domain (LID), which is lacking in ChREBPβ, that interacts with the ligand-binding domain (LBD) of LXRα. In line with this, we see a surprisingly high co-occupancy of LXR and ChREBP on regulatory regions in the mouse genome when re-analysing two independently published chromatin immunoprecipitation-sequencing (ChIP-seq) datasets. Moreover, Functional studies show that LXRα is able to co-activate together with ChREBPα, but not ChREBPβ, and increase ChREBP-specific target gene expression in vitro and in vivo. Unexpectedly however, ligand-engaged LXR exhibits a repressive effect on the expression of the same genes in primary mouse hepatocytes, in contrast to what we observe with target genes that are common to LXR and ChREBP. Performing CoIP and ChIP on selected target genes, we demonstrate mechanistically that the repressive effect most likely is due to a weakened ChREBPα:LXRα interaction and reduced binding of ChREBP to chromatin. Altogether, the novel transcriptional complex comprising ChREBPα and LXRα adds to the intricate integration of nutrient signals in glucose and lipid metabolism.

• Haug, Markus; Meås, Hany Zakaria; Beckwith, Marianne Sandvold; Louet, Claire; Ryan, Liv; Hu, Z.; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Yin, H. H.; Damås, Jan Kristian & Flo, Trude Helen (2019). P1511 - Sensing of HIV-1 nucleic acids by TLR8 in human CD4+ T cells. European Journal of Immunology.  ISSN 0014-2980.  43, s 1- 2223 . doi: https://doi.org/10.1002/eji.201970400
• Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Andersen, Petter I.; Kuivanen, Suvi; Mona, Teppor; Zusinaite, Eva; Dumpis, Uga; Vitkauskiene, Astra; Cox, Rebecca J.; Kallio-Kokko, Hannimari; Bergqvist, Anders; Tenson, Tanel; Merits, Andres; Oksenych, Valentyn; Bjørås, Magnar; Anthonsen, Marit Walbye; Shum, David H.K.; Kaarbø, Mari; Vapalahti, Olli; Windisch, Marc P; Superti-Furga, Giulio; Snijder, Berend; Kainov, Denis & Kandasamy, Richard Kumaran (2019). Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis.
• Meås, Hany Zakaria; Haug, Markus; Beckwith, Marianne; Louet, Claire; Ryan, Liv; Landskron, Johannes; Nordbø, Svein Arne; Tasken, Kjetil; Damås, Jan Kristian & Flo, Trude Helen (2019). Sensing of HIV-1 by TLR8 activates human T cells and reverses Latency.
• Bösl, Korbinian; Ianevski, Aleksandr; Than, Thoa T.; Andersen, Petter I.; Teppor, Mona; Zusinaite, Eva; Dumpis, Uga; Vitkauskiene, Astra; Cox, Rebecca Jane; Kallio-Kokko, Hannimari; Bergqvist, Anders; Tenson, Tanel; Merits, Andres; Oksenych, Valentyn; Bjørås, Magnar; Anthonsen, Marit Walbye; Shum, David H.K.; Kaarbø, Mari; Windisch, Marc P.; Superti-Furga, Giulio; Snijder, Berend; Kainov, Denis & Kandasamy, Richard Kumaran (2019). Critical Nodes of Viral Modulation Revealed Through an Integrated Network Analysis of Host-Virus Interaction Landscape.
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ulven, Stine Marie; Lucas, Christin; Bindesbøll, Christian; Lemma, Roza Berhanu; Gabrielsen, Odd Stokke; Grønning-Wang, Line Mariann; Nebb, Hilde Irene & Sæther, Thomas (2018). LXRα interacts with the glucose-sensing transcription factor ChREBPα and increases its transcriptional activity.
• Luecke, Hartmut (2018). Structure, function, and inhibitors of the Helicobacter pylori acid acclimation system, an essential component for chronic infection.
• Luecke, Hartmut (2018). Cryo EM.
• Luecke, Hartmut (2018). Membrane protein crystallization.

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