Laura Rodriguez de la Ballina

• Ballina, Laura Rodriguez de la; Walther, Christa G.; Condon, Nicholas D.; Felder, Alessandro A.; Schätz, Martin & Schmerl, Bettina [Show all 18 contributors for this article] (2026). GloBIAS survey results – An insight into the global bioimage analysis community. Journal of Microscopy. ISSN 0022-2720. p. 1–10. doi: 10.1111/jmi.70153. Full text in Research Archive
• Theart, Rensu P.; Levet, Florian; Hernández-Herrera, Paul; Leterrier, Christophe & Ballina, Laura R. de la (2025). Presynaptic actin nanostructures: A reproducibility case study. bioRxiv - the preprint server for biology. doi: 10.64898/2025.12.18.695210. Full text in Research Archive Show summary

  ABSTRACT In an effort to assess the reproducibility of bioimage analyses in current publications, we took part in a Global BioImage Analysts’ Society (GloBIAS) initiative to try and reproduce results from published articles. We attempted to reproduce core findings from the work of Bingham et al. , which investigates the actin organisation in presynaptic structures by using diffraction-limited and super-resolution microscopy. While the original paper unveiled clear biological insight, it lacked sufficient detail in the bioimage analysis methodological approach, limiting the depth of reproducibility we could achieve. Through frequent contacts with the corresponding author, we managed to replicate qualitative aspects of the analysis of actin nanostructures in bead-induced presynapses. We performed image reconstruction from super-resolution microscopy data, automatic image registration and visual inspection, followed by manual annotation of structures of interest in ∼35 images. Our experience with this exercise highlights the importance of transparent data sharing and accessibility, as well as the need to adhere to bioimage analysis standards that ensure the reproducibility of nowadays complex biological image analysis studies. It also shows how crucial interdisciplinary collaboration is, since many biology labs are simply unaware of these standards, which are often easy to implement and would likely be widely adopted if their value was better understood or known.

• Corbat, Agustin Andres; Walther, Christa G; Ballina, Laura R de la; Condon, Nicholas David; Felder, Alessandro A & Schätz, Martin [Show all 17 contributors for this article] (2025). GloBIAS: strengthening the foundations of BioImage Analysis. arXiv. doi: 10.48550/ARXIV.2507.06407. Full text in Research Archive Show summary

  There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of biological images. Turning these data into scientific discoveries requires people with effective data management skills and knowledge of state-of-the-art image processing and data analysis, in other words, BioImage Analysts. The Global BioImage Analysts’ Society (GloBIAS) aims to enhance the profile of BioImage Analysts as a key role in science and research. Its vision encompasses fostering a global network, democratising access to BIA by providing educational resources tailored to various proficiency levels and disciplines, while also establishing guidelines for BIA courses. By collaboratively shaping the education of BioImage Analysts, GloBIAS aims to unlock the full potential of BIA in advancing life science research and to consolidate BIA as a career path. To better understand the needs and geographical representation of the BIA community, a worldwide survey was conducted and 291 responses were collected across people from all career stages and continents. This work discusses how GloBIAS aims to address community-identified shortcomings in work environment, funding, and scientific activities. The survey underscores a strong interest from the BIA community in activities proposed by GloBIAS and their interest to actively contribute. With 72% of respondents willing to pay for membership, the community’s enthusiasm for both online and in-person events is set to drive the growth and sustainability of GloBIAS.

• Timmer, Romy; Bellanger, Aurélie Nathalie Pascale; Peeters, Sarah; Kim, Hera; Ballina, Laura Rodriguez de la & Eikvar, Sissel [Show all 11 contributors for this article] (2025). LRRC59 cooperates with nuclear transporters to restrain the nuclear envelope repair machinery and safeguard genome integrity. Nature Communications. 16(1). doi: 10.1038/s41467-025-65994-4. Full text in Research Archive Show summary

  Nuclear envelope (NE) rupture is a hallmark of cancer cells, and persistent NE damage drives genome instability and inflammation. NE repair relies on activation of the endosomal sorting complex required for transport (ESCRT)-III repair machinery by the LEMD2-CHMP7 compartmentalization sensor, but little is known beyond these core factors. Here, we use convergent proximity proteomics to inventorise proteins mobilized to the NE upon assembly of LEMD2-CHMP7 and activation of ESCRT-III. Within this NE repairome, we identify LRRC59 as a critical regulator of LEMD2 accumulation at NE ruptures. We find that LRRC59, together with the nuclear transporters KPNB1 and XPO1, restricts the assembly of LEMD2-CHMP7 complexes to the site of rupture. Disruption of this regulatory axis escalates LEMD2-CHMP7 spreading across the NE, driving torsional DNA damage in ruptured nuclei and micronuclei. Thus, our work identifies a central regulatory layer of NE repair centered on LRRC59 and KPNB1. We propose that altered LRRC59 levels and deregulated nuclear transport coordinately compromise NE repair, driving genome instability and cancer development.

• Mauthe, Mario; Beek, Nicole van de; Mari, Muriel; Korsten, Giel; Nobari, Parisa & Castelino, Kennith B. [Show all 17 contributors for this article] (2025). A chaperone-proteasome-based fragmentation machinery is essential for aggrephagy. Nature Cell Biology. ISSN 1465-7392. 27(9), p. 1448–1464. doi: 10.1038/s41556-025-01747-1. Full text in Research Archive Show summary

  Perturbations in protein quality control lead to the accumulation of misfolded proteins and protein aggregates, which can compromise health and lifespan. One key mechanism eliminating protein aggregates is aggrephagy, a selective type of autophagy. Here we reveal that fragmentation is required before autophagic clearance of various types of amorphous aggregates. This fragmentation requires both the 19S proteasomal regulatory particle and the DNAJB6-HSP70-HSP110 chaperone module. These two players are also essential for aggregate compaction that leads to the clustering of the selective autophagy receptors, which initiates the autophagic removal of the aggregates. We also found that the same players delay the formation of disease-associated huntingtin inclusions. This study assigns a novel function to the 19S regulatory particle and the DNAJB6-HSP70-HSP110 module, and uncovers that aggrephagy entails a piecemeal process, with relevance for proteinopathies.

• Kaur, Namrita; Ballina, Laura R de la; Haukaas, Håvard Styrkestad; Torgersen, Maria Lyngaas; Radulovic, Maja & Munson, Michael J [Show all 11 contributors for this article] (2023). TECPR1 is activated by damage-induced sphingomyelin exposure to mediate noncanonical autophagy. EMBO Journal. ISSN 0261-4189. 42(17), p. 1–19. doi: 10.15252/embj.2022113105. Full text in Research Archive Show summary

  Abstract Cells use noncanonical autophagy, also called conjugation of ATG8 to single membranes (CASM), to label damaged intracellular compartments with ubiquitin‐like ATG8 family proteins in order to signal danger caused by pathogens or toxic compounds. CASM relies on E3 complexes to sense membrane damage, but so far, only the mechanism to activate ATG16L1‐containing E3 complexes, associated with proton gradient loss, has been described. Here, we show that TECPR1‐containing E3 complexes are key mediators of CASM in cells treated with a variety of pharmacological drugs, including clinically relevant nanoparticles, transfection reagents, antihistamines, lysosomotropic compounds, and detergents. Interestingly, TECPR1 retains E3 activity when ATG16L1 CASM activity is obstructed by the Salmonella Typhimurium pathogenicity factor SopF. Mechanistically, TECPR1 is recruited by damage‐induced sphingomyelin (SM) exposure using two DysF domains, resulting in its activation and ATG8 lipidation. In vitro assays using purified human TECPR1‐ATG5‐ATG12 complex show direct activation of its E3 activity by SM, whereas SM has no effect on ATG16L1‐ATG5‐ATG12. We conclude that TECPR1 is a key activator of CASM downstream of SM exposure.

• Holme, Børge; Bjørnerud, Birgitte; Pedersen, Nina Marie; Ballina, Laura Rodriguez de la; Wesche, Jørgen & Haugsten, Ellen Margrethe (2023). Automated tracking of cell migration in phase contrast images with CellTraxx. Scientific Reports. 13(1). doi: 10.1038/s41598-023-50227-9. Full text in Research Archive Show summary

  The ability of cells to move and migrate is required during development, but also in the adult in processes such as wound healing and immune responses. In addition, cancer cells exploit the cells’ ability to migrate and invade to spread into nearby tissue and eventually metastasize. The majority of cancer deaths are caused by metastasis and the process of cell migration is therefore intensively studied. A common way to study cell migration is to observe cells through an optical microscope and record their movements over time. However, segmenting and tracking moving cells in phase contrast time-lapse video sequences is a challenging task. Several tools to track the velocity of migrating cells have been developed. Unfortunately, most of the automated tools are made for fluorescence images even though unlabelled cells are often preferred to avoid phototoxicity. Consequently, researchers are constrained with laborious manual tracking tools using ImageJ or similar software. We have therefore developed a freely available, user-friendly, automated tracking tool called CellTraxx. This software makes it easy to measure the velocity and directness of migrating cells in phase contrast images. Here, we demonstrate that our tool efficiently recognizes and tracks unlabelled cells of different morphologies and sizes (HeLa, RPE1, MDA-MB-231, HT1080, U2OS, PC-3) in several types of cell migration assays (random migration, wound healing and cells embedded in collagen). We also provide a detailed protocol and download instructions for CellTraxx.

• Creamer, Adam; Fiego, Alessandra Lo; Agliano, Alice; Prados-Martin, Lino; Høgset, Håkon & Najer, Adrian [Show all 26 contributors for this article] (2023). Modular Synthesis of Semiconducting Graft Copolymers to Achieve “Clickable” Fluorescent Nanoparticles with Long Circulation and Specific Cancer Targeting. Advanced Materials. ISSN 0935-9648. doi: 10.1002/adma.202300413. Full text in Research Archive Show summary

  Semiconducting polymer nanoparticles (SPNs) are explored for applications in cancer theranostics because of their high absorption coefficients, photostability, and biocompatibility. However, SPNs are susceptible to aggregation and protein fouling in physiological conditions, which can be detrimental for in vivo applications. Here, a method for achieving colloidally stable and low‐fouling SPNs is described by grafting poly(ethylene glycol) (PEG) onto the backbone of the fluorescent semiconducting polymer, poly(9,9′‐dioctylfluorene‐5‐fluoro‐2,1,3‐benzothiadiazole), in a simple one‐step substitution reaction, postpolymerization. Further, by utilizing azide‐functionalized PEG, anti‐human epidermal growth factor receptor 2 (HER2) antibodies, antibody fragments, or affibodies are site‐specifically “clicked” onto the SPN surface, which allows the functionalized SPNs to specifically target HER2‐positive cancer cells. In vivo, the PEGylated SPNs are found to have excellent circulation efficiencies in zebrafish embryos for up to seven days postinjection. SPNs functionalized with affibodies are then shown to be able to target HER2 expressing cancer cells in a zebrafish xenograft model. The covalent PEGylated SPN system described herein shows great potential for cancer theranostics.

• Søreng, Kristiane; Pankiv, Serhiy; Bergsmark, Camilla; Haugsten, Ellen Margrethe; Dahl, Anette Kathinka & Ballina, Laura R de la [Show all 9 contributors for this article] (2022). ALFY localizes to early endosomes and cellular protrusions to facilitate directional cell migration. Journal of Cell Science. ISSN 0021-9533. 135(4). doi: 10.1242/jcs.259138. Full text in Research Archive Show summary

  ABSTRACT Cell migration is a complex process underlying physiological and pathological processes such as brain development and cancer metastasis. The autophagy-linked FYVE protein (ALFY; also known as WDFY3), an autophagy adaptor protein known to promote clearance of protein aggregates, has been implicated in brain development and neural migration during cerebral cortical neurogenesis in mice. However, a specific role of ALFY in cell motility and extracellular matrix adhesion during migration has not been investigated. Here, we reveal a novel role for ALFY in the endocytic pathway and in cell migration. We show that ALFY localizes to RAB5- and EEA1-positive early endosomes in a PtdIns(3)P-dependent manner and is highly enriched in cellular protrusions at the leading and lagging edge of migrating cells. We find that cells lacking ALFY have reduced attachment and altered protein levels and glycosylation of integrins, resulting in the inability to form a proper leading edge and loss of directional cell motility.

• Munson, Michael Joseph; Mathai, Benan John; Ng, Matthew; Moncho, Laura Cristina Trachsel; Ballina, Laura R de la & Simonsen, Anne Gjøen (2022). GAK and PRKCD kinases regulate basal mitophagy. Autophagy. ISSN 1554-8627. 18(2), p. 467–469. doi: 10.1080/15548627.2021.2015154. Full text in Research Archive Show summary

  The removal of mitochondria in a programmed or stress-induced manner is essential for maintaining cellular homeostasis. To date, much research has focused upon stress-induced mitophagy that is largely regulated by the E3 ligase PRKN, with limited insight into the mechanisms regulating basal “housekeeping” mitophagy levels in different model organisms. Using iron chelation as an inducer of PRKN-independent mitophagy, we recently screened an siRNA library of lipid-binding proteins and determined that two kinases, GAK and PRKCD, act as positive regulators of PRKN-independent mitophagy. We demonstrate that PRKCD is localized to mitochondria and regulates recruitment of ULK1-ATG13 upon induction of mitophagy. GAK activity, by contrast, modifies the mitochondrial network and lysosomal morphology that compromise efficient transport of mitochondria for degradation. Impairment of either kinase in vivo blocks basal mitophagy, demonstrating the biological relevance of our findings.

• Maestro, Inés; Ballina, Laura R de la; Porras, Gracia; Corrochano, Silvia; Lago, Eva de & Simonsen, Anne Gjøen [Show all 8 contributors for this article] (2022). Discovery of Mitophagy Inhibitors with Therapeutic Potential in Different Familial Amyotrophic Lateral Sclerosis Mutations. International Journal of Molecular Sciences. ISSN 1661-6596. 23(20). doi: 10.3390/ijms232012676. Full text in Research Archive Show summary

  Mitophagy is the selective degradation of mitochondria by autophagy. It promotes the turnover of mitochondria and prevents the accumulation of dysfunctional mitochondria, which can lead to cellular degeneration. Mitophagy is known to be altered in several pathological conditions, especially in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). We recently demonstrated an increase in autophagy flux in lymphoblasts from ALS patients bearing a mutation in SOD1. Thus, the identification of mitophagy inhibitors may be a therapeutic option to recover mitochondrial homeostasis. Here, using a phenotypic mitophagy assay, we identified a new mitophagy inhibitor, the small molecule named IGS2.7 from the MBC library. Interestingly, the treatment of different cellular and in vivo models of ALS with mutations on SOD1 and TARDBP with this inhibitor restores autophagy to control levels. These results point mitophagy inhibitors, especially IGS2.7, to a new therapeutic approach for familial ALS patients.

• Munson, Michael Joseph; Mathai, Benan J.; Ng, Matthew; Moncho, Laura Cristina Trachsel; Ballina, Laura R de la & Schultz, Sebastian W. [Show all 13 contributors for this article] (2021). GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nature Communications. 12(1). doi: 10.1038/s41467-021-26331-7. Full text in Research Archive Show summary

  The mechanisms involved in programmed or damage-induced removal of mitochondria by mitophagy remains elusive. Here, we have screened for regulators of PRKN-independent mitophagy using an siRNA library targeting 197 proteins containing lipid interacting domains. We identify Cyclin G-associated kinase (GAK) and Protein Kinase C Delta (PRKCD) as regulators of PRKN-independent mitophagy, with both being dispensable for PRKN- dependent mitophagy and starvation-induced autophagy. We demonstrate that the kinase activity of both GAK and PRKCD are required for efficient mitophagy in vitro, that PRKCD is present on mitochondria, and that PRKCD facilitates recruitment of ULK1/ATG13 to early autophagic structures. Importantly, we demonstrate in vivo relevance for both kinases in the regulation of basal mitophagy. Knockdown of GAK homologue (gakh-1) in C. elegans or knockout of PRKCD homologues in zebrafish led to significant inhibition of basal mitophagy, highlighting the evolutionary relevance of these kinases in mitophagy regulation.

• Maestro, Inés; Ballina, Laura R de la; Simonsen, Anne Gjøen; Boya, Patricia & Martinez, Ana (2021). Phenotypic Assay Leads to Discovery of Mitophagy Inducers with Therapeutic Potential for Parkinson's Disease. ACS Chemical Neuroscience. 12(24), p. 4512–4523. doi: 10.1021/acschemneuro.1c00529. Full text in Research Archive Show summary

  Mitophagy, the selective degradation of mitochondria by autophagy, involved in important physiological processes and defects in pathways has been reported in pathological conditions, such as neurodegeneration. Thus, mitophagy is an interesting target for drug discovery programs. In this investigation, we used robust phenotypic assay to screen a set of 50 small heterocyclic compounds to identify inducers of mitophagy. We identified two compounds, VP07 and JAR1.39, that induce Parkin-dependent mitophagy. Based on structure–activity relationship studies, we proposed the ability of the compounds to act as light chain 3 (LC3) interactors, similar to cardiolipin or ceramide, triggering mitophagy via Pink1/Parkin. Finally, we show promising therapeutic applicability in a cellular model of Parkinson’s disease.

• Holdgaard, Søs Grønbæk; Cianfanelli, Valentina; Pupo, Emanuela; Lambrughi, Matteo; Lubas, Michal & Nielsen, Julie C. [Show all 28 contributors for this article] (2019). Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites. Nature Communications. 10:4176, p. 1–19. doi: 10.1038/s41467-019-12094-9. Full text in Research Archive Show summary

  The centrosome is the master orchestrator of mitotic spindle formation and chromosome segregation in animal cells. Centrosome abnormalities are frequently observed in cancer, but little is known of their origin and about pathways affecting centrosome homeostasis. Here we show that autophagy preserves centrosome organization and stability through selective turnover of centriolar satellite components, a process we termed doryphagy. Autophagy targets the satellite organizer PCM1 by interacting with GABARAPs via a C-terminal LIR motif. Accordingly, autophagy deficiency results in accumulation of large abnormal centriolar satellites and a resultant dysregulation of centrosome composition. These alterations have critical impact on centrosome stability and lead to mitotic centrosome fragmentation and unbalanced chromosome segregation. Our findings identify doryphagy as an important centrosome-regulating pathway and bring mechanistic insights to the link between autophagy dysfunction and chromosomal instability. In addition, we highlight the vital role of centriolar satellites in maintaining centrosome integrity.

• Lystad, Alf Håkon; Carlsson, Sven R; Ballina, Laura Rodriguez de la; Kauffman, Karlina J; Nag, Shanta & Yoshimori, Tamotsu [Show all 8 contributors for this article] (2019). Distinct functions of ATG16L1 isoforms in membrane binding and LC3B lipidation in autophagy-related processes. Nature Cell Biology. ISSN 1465-7392. 21(3), p. 372–383. doi: 10.1038/s41556-019-0274-9. Full text in Research Archive Show summary

  Covalent modification of LC3 and GABARAP proteins to phosphatidylethanolamine in the double-membrane phagophore is a key event in the early phase of macroautophagy, but can also occur on single-membrane structures. In both cases this involves transfer of LC3/GABARAP from ATG3 to phosphatidylethanolamine at the target membrane. Here we have purified the full-length human ATG12-5–ATG16L1 complex and show its essential role in LC3B/GABARAP lipidation in vitro. We have identified two functionally distinct membrane-binding regions in ATG16L1. An N-terminal membrane-binding amphipathic helix is required for LC3B lipidation under all conditions tested. By contrast, the C-terminal membrane-binding region is dispensable for canonical autophagy but essential for VPS34-independent LC3B lipidation at perturbed endosomes. We further show that the ATG16L1 C-terminus can compensate for WIPI2 depletion to sustain lipidation during starvation. This C-terminal membrane-binding region is present only in the β-isoform of ATG16L1, showing that ATG16L1 isoforms mechanistically distinguish between different LC3B lipidation mechanisms under different cellular conditions.

• Cano-Crespo, Sara; Chillarón, Josep; Junza, Alexandra; Fernández-Miranda, Gonzalo; Garcia, Judith & Polte, Christine [Show all 12 contributors for this article] (2019). CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression. Scientific Reports. 9(1). doi: 10.1038/s41598-019-50547-9. Full text in Research Archive Show summary

  CD98 heavy chain (CD98hc) forms heteromeric amino acid (AA) transporters by interacting with different light chains. Cancer cells overexpress CD98hc-transporters in order to meet their increased nutritional and antioxidant demands, since they provide branched-chain AA (BCAA) and aromatic AA (AAA) availability while protecting cells from oxidative stress. Here we show that BCAA and AAA shortage phenocopies the inhibition of mTORC1 signalling, protein synthesis and cell proliferation caused by CD98hc ablation. Furthermore, our data indicate that CD98hc sustains glucose uptake and glycolysis, and, as a consequence, the pentose phosphate pathway (PPP). Thus, loss of CD98hc triggers a dramatic reduction in the nucleotide pool, which leads to replicative stress in these cells, as evidenced by the enhanced DNA Damage Response (DDR), S-phase delay and diminished rate of mitosis, all recovered by nucleoside supplementation. In addition, proper BCAA and AAA availability sustains the expression of the enzyme ribonucleotide reductase. In this regard, BCAA and AAA shortage results in decreased content of deoxynucleotides that triggers replicative stress, also recovered by nucleoside supplementation. On the basis of our findings, we conclude that CD98hc plays a central role in AA and glucose cellular nutrition, redox homeostasis and nucleotide availability, all key for cell proliferation.

• Ballina, Laura Rodriguez de la; Munson, Michael Joseph & Simonsen, Anne (2019). Lipids and Lipid-Binding Proteins in Selective Autophagy. Journal of Molecular Biology (JMB). ISSN 0022-2836. p. 1–25. doi: 10.1016/j.jmb.2019.05.051. Full text in Research Archive Show summary

  Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, where cargo is broken down into basic building blocks that are released to the cytoplasm for the cell to reuse. Autophagic degradation can target either cytoplasmic material in bulk (non-selective autophagy) or particular cargo in what is called selective autophagy. Proper autophagic turnover requires the orchestrated participation of several players that need to be tightly and temporally coordinated. Whereas a large number of autophagy-related (ATG) proteins have been identified and their functions and regulation are starting to be understood, there is substantially less knowledge regarding the specific lipids constituting the autophagic membranes as well as their role in initiating, enabling or regulating the autophagic process. This review focuses on lipids and their corresponding binding proteins that are crucial in the process of selective autophagy.

View all works in NVA