Helene Knævelsrud

• Ullern, Halvor; Johannessen, Julie Aarmo; Kasikci, Feyza; Formica, Miriam; Melve, Naghmeh Karimi & Andresen, Siri [Show all 12 contributors for this article] (2026). FLCN loss is characterized by SQSTM1/p62 accumulation despite functional autophagy flux in Birt-Hogg-Dubé syndrome-associated kidney cancer. Autophagy Reports. 5(1). doi: 10.1080/27694127.2026.2705631. Full text in Research Archive
• Løchen, Arja Katrina Lea Arnesen; Søreng, Kristiane; Veroni, Chiara; Moncho, Laura Cristina Trachsel; Asp, Nagham Theres & Gaupset, Robin [Show all 10 contributors for this article] (2026). Interaction of HS1BP3 with cortactin modulates TKS5 localisation, cell secretion and cancer malignancy. Molecular Oncology. ISSN 1574-7891. doi: 10.1002/1878-0261.70248. Full text in Research Archive Show summary

  The HCLS1-Binding Protein 3 (HS1BP3) interacts with the SH3 domain of cortactin (CTTN), a protein that contributes to a malignant phenotype in cancers. Here, we demonstrate that high expression of HS1BP3 is associated with reduced survival for gastric adenocarcinoma and triple negative breast carcinoma patients and that HS1BP3 is specifically upregulated in these cancers. We mapped the HS1BP3-cortactin interaction site to the third proline-rich region (PRR3.1) of HS1BP3 and show that this interaction is important for cancer cell proliferation, extracellular matrix degradation and secretion. HS1BP3 expression was found to correlate with expression of the invadopodia scaffold protein TKS5 and we show that the localisation of TKS5 inside multivesicular endosomes is increased in cells expressing an HS1BP3 PRR3.1 mutant. Overall, our results highlight the importance of the direct interaction between HS1BP3 and cortactin in cancer development by regulating cell proliferation, secretion and invasion, which may provide an explanation for the negative correlation between HS1BP3 levels and the survival of gastric adenocarcinoma and triple negative breast cancer patients.

• Andresen, Siri; Outa, Amani al; Formica, Miriam; Enserink, Jorrit & Knævelsrud, Helene (2025). Improved detection of lipidated Atg8a by immunoblotting in Drosophila melanogaster cells and tissues enables precise investigation of Atg8a flux and its termination. Autophagy. ISSN 1554-8627. 21(11), p. 2497–2517. doi: 10.1080/15548627.2025.2508551. Full text in Research Archive Show summary

  Macroautophagy/autophagy is an essential intracellular catabolic process for maintaining cellularhomeostasis. In Drosophila melanogaster, Atg8a lipidation serves as a key marker for autophagy, yettraditional methods often fail to effectively detect its lipidated state. To overcome this limitation, wedeveloped a refined approach that employs N-ethylmaleimide (NEM) to inhibit Atg4, thereby pre-serving Atg8a lipidation during sample preparation both in vitro and in vivo. We determined theoptimal concentration of the autophagic inhibitors bafilomycin A1 (BafA1) and chloroquine (CQ)required for inhibition of autolysosomal degradation. Furthermore, we investigated the effects ofprolonged nutrient deprivation on autophagic flux and TORC1 signaling. Our findings not onlyvalidate the effectiveness of this new approach to monitor lipidation of Atg8a but also provideinsights into selection of autolysosomal inhibitors and nutrient-dependent regulatory roles of TORC1in Drosophila.

• Presacan, Oriana; Mesa, María Hernández; Aldea, Alexandru C.; Andresen, Siri; Outa, Amani al & Johannessen, Julie Aarmo [Show all 9 contributors for this article] (2025). Explainable AI to unveil cellular autophagy dynamics. PLOS ONE. 20(9). doi: 10.1371/journal.pone.0331045. Full text in Research Archive Show summary

  Autophagy is a fundamental intracellular renovation process vital for maintaining cellular homeostasis through the degradation and recycling of damaged components. It is implicated in numerous pathological conditions, including cancer and neurodegenerative diseases. However, its dynamic nature and complexity pose challenges for manual analysis. In this study, we present a computational pipeline that leverages advanced deep learning models to automate the analysis of autophagic processes in 6,240 fluorescence microscopy images from the CELLULAR dataset. Our framework integrates object detection, cell segmentation, classification by autophagic state, cellular tracking, and explainability methods for interpretability. We achieved optimal results using YOLOv8 for object detection with a mAP50 of 0.80, U-Net++ for segmentation with an IoU of 0.82, and a vision transformer for classification with an accuracy of 0.86. To track cells, we developed a custom algorithm capable of handling complex scenarios such as cell division and morphological changes, all without requiring annotated tracking data. To enhance transparency, we employed explainability techniques based on class activation mappings to analyze model decision-making processes and validate classification outcomes, complemented by t-SNE visualizations for deeper insights into the data. Collaboration with biology experts validated our findings, highlighting the pipeline’s potential to advance autophagy research. This study demonstrates the potential of deep learning and explainable AI to streamline biomedical research, reduce manual effort, and uncover key autophagy dynamics.

• 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?

• Johannessen, Julie Aarmo; Formica, Miriam; Haukeland, Aina Louise C.; Bråthen, Nora Rojahn; Outa, Amani al & Larsen, Miriam Aarsund [Show all 9 contributors for this article] (2023). The human leukemic oncogene MLL-AF4 promotes hyperplastic growth of hematopoietic tissues in Drosophila larvae. iScience. 26(10). doi: 10.1016/j.isci.2023.107726. Full text in Research Archive Show summary

  MLL-rearranged (MLL-r) leukemias are among the leukemic subtypes with poorest survival, and treatment options have barely improved over the last decades. Despite increasing molecular understanding of the mechanisms behind these hematopoietic malignancies, this knowledge has had poor translation into the clinic. Here, we report a Drosophila melanogaster model system to explore the pathways affected in MLL-r leukemia. We show that expression of the human leukemic oncogene MLL-AF4 in the Drosophila hematopoietic system resulted in increased levels of circulating hemocytes and an enlargement of the larval hematopoietic organ, the lymph gland. Strikingly, depletion of Drosophila orthologs of known interactors of MLL-AF4, such as DOT1L, rescued the leukemic phenotype. In agreement, treatment with small-molecule inhibitors of DOT1L also prevented the MLL-AF4-induced leukemia-like phenotype. Taken together, this model provides an in vivo system to unravel the genetic interactors involved in leukemogenesis and offers a system for improved biological understanding of MLL-r leukemia.

• Outa, Amani al; Hicks, Steven; Thambawita, Vajira L B; Andresen, Siri; Enserink, Jorrit Martijn & Halvorsen, Pål [Show all 8 contributors for this article] (2023). CELLULAR, A Cell Autophagy Imaging Dataset. Scientific Data. doi: 10.1038/s41597-023-02687-x. Full text in Research Archive Show summary

  Cells in living organisms are dynamic compartments that continuously respond to changes in their environment to maintain physiological homeostasis. While basal autophagy exists in cells to aid in the regular turnover of intracellular material, autophagy is also a critical cellular response to stress, such as nutritional depletion. Conversely, the deregulation of autophagy is linked to several diseases, such as cancer, and hence, autophagy constitutes a potential therapeutic target. Image analysis to follow autophagy in cells, especially on high-content screens, has proven to be a bottleneck. Machine learning (ML) algorithms have recently emerged as crucial in analyzing images to efficiently extract information, thus contributing to a better understanding of the questions at hand. This paper presents CELLULAR, an open dataset consisting of images of cells expressing the autophagy reporter mRFP-EGFP-Atg8a with cell-specific segmentation masks. Each cell is annotated into either basal autophagy, activated autophagy, or unknown. Furthermore, we introduce some preliminary experiments using the dataset that can be used as a baseline for future research.

• Knævelsrud, Helene; Tjønndal, Anne Beret & Hansen, Kai Arne (2022). #sommerkroppen2022: Hva bør jeg gjøre? Morgenbladet. ISSN 0805-3847. Full text in Research Archive
• Formica, Miriam; Storaci, Alessandra Maria; Bertolini, Irene; Carminati, Francesca; Knævelsrud, Helene & Vaira, Valentina [Show all 7 contributors for this article] (2021). V-ATPase controls tumor growth and autophagy in a Drosophila model of gliomagenesis. Autophagy. ISSN 1554-8627. 17(12), p. 4442–4452. doi: 10.1080/15548627.2021.1918915. Full text in Research Archive Show summary

  Glioblastoma (GBM), a very aggressive and incurable tumor, often results from constitutive activation of EGFR (epidermal growth factor receptor) and of phosphoinositide 3-kinase (PI3K). To understand the role of autophagy in the pathogenesis of glial tumors in vivo, we used an established Drosophila melanogaster model of glioma based on overexpression in larval glial cells of an active human EGFR and of the PI3K homolog Pi3K92E/Dp110. Interestingly, the resulting hyperplastic glia express high levels of key components of the lysosomal-autophagic compartment, including vacuolar-type H+-ATPase (V-ATPase) subunits and ref(2)P (refractory to Sigma P), the Drosophila homolog of SQSTM1/p62. However, cellular clearance of autophagic cargoes appears inhibited upstream of autophagosome formation. Remarkably, downregulation of subunits of V-ATPase, of Pdk1, or of the Tor (Target of rapamycin) complex 1 (TORC1) component raptor prevents overgrowth and normalize ref(2)P levels. In addition, downregulation of the V-ATPase subunit VhaPPA1-1 reduces Akt and Tor-dependent signaling and restores clearance. Consistent with evidence in flies, neurospheres from patients with high V-ATPase subunit expression show inhibition of autophagy. Altogether, our data suggest that autophagy is repressed during glial tumorigenesis and that V-ATPase and MTORC1 components acting at lysosomes could represent therapeutic targets against GBM.

• Klionsky, Daniel J.; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud Khaled; Abdoli, Asghar & Abudu, Yakubu Princely [Show all 50 contributors for this article] (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. ISSN 1554-8627. 17(1), p. 1–382. doi: https:/www.tandfonline.com/doi/full/10.1080/15548627.2020.1797280. Full text in Research Archive
• Korsvoll, Nils Hallvard; Tjønndal, Anne & Knævelsrud, Helene (2020). Hvorfor er vi så besatt av alt som er julete? Morgenbladet. ISSN 0805-3847. Full text in Research Archive
• Søreng, Kristiane; Knævelsrud, Helene; Holland, Petter & Simonsen, Anne (2017). HS1BP3 inhibits autophagy by regulation of PLD1. Autophagy. ISSN 1554-8627. 13(5), p. 985–986. doi: 10.1080/15548627.2017.1291483. Full text in Research Archive Show summary

  Macroautophagy/autophagy is a membrane trafficking and intracellular degradation process involving the formation of double-membrane autophagosomes and their ultimate fusion with lysosomes. Much is yet to be learned about the regulation of this process, especially at the level of the membranes and lipids involved. We have recently found that the PX domain protein HS1BP3 (HCLS1 binding protein 3) is a negative regulator of autophagosome formation. HS1BP3 depletion increases the formation of LC3-positive autophagosomes both in human cells and zebrafish. HS1BP3 localizes to ATG16L1- and ATG9-positive autophagosome precursors deriving from recycling endosomes, which appear to fuse with LC3-positive phagophores. The HS1BP3 PX domain interacts with phosphatidic acid (PA) and 3’-phosphorylated phosphoinositides. When HS1BP3 is depleted, the total cellular PA content is upregulated stemming from increased activity of the PA-producing enzyme PLD (phospholipase D) and increased localization of PLD1 to ATG16L1-positive membranes. We propose that HS1BP3 negatively regulates autophagy by decreasing the PA content of the ATG16L1-positive autophagosome precursor membranes through inhibition of PLD1 activity and localization. This is an Accepted Manuscript of an article published by Taylor & Francis Group in Autophagy on 20 Mar 2017, available online: http://www.tandfonline.com/10.1080/12345678.1234.123456.

• Holland, Petter; Knævelsrud, Helene; Søreng, Kristiane; Mathai, Benan John; Lystad, Alf Håkon & Pankiv, Serhiy [Show all 16 contributors for this article] (2016). HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels. Nature Communications. 7. doi: 10.1038/ncomms13889. Full text in Research Archive Show summary

  A fundamental question is how autophagosome formation is regulated. Here we show that the PX domain protein HS1BP3 is a negative regulator of autophagosome formation. HS1BP3 depletion increased the formation of LC3-positive autophagosomes and degradation of cargo both in human cell culture and in zebrafish. HS1BP3 is localized to ATG16L1- and ATG9-positive autophagosome precursors and we show that HS1BP3 binds phosphatidic acid (PA) through its PX domain. Furthermore, we find the total PA content of cells to be significantly upregulated in the absence of HS1BP3, as a result of increased activity of the PA-producing enzyme phospholipase D (PLD) and increased localization of PLD1 to ATG16L1-positive membranes. We propose that HS1BP3 regulates autophagy by modulating the PA content of the ATG16L1-positive autophagosome precursor membranes through PLD1 activity and localization. Our findings provide key insights into how autophagosome formation is regulated by a novel negative-feedback mechanism on membrane lipids.

• Knævelsrud, Helene; Søreng, Kristiane; Raiborg, Camilla; Håberg, Karin; Rasmuson, Fredrik & Brech, Andreas [Show all 12 contributors for this article] (2013). Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. Journal of Cell Biology. ISSN 0021-9525. 202(2), p. 331–349. doi: 10.1083/jcb.201205129. Full text in Research Archive
• Knævelsrud, Helene; Carlsson, Sven R & Simonsen, Anne (2013). SNX18 tubulates recycling endosomes for autophagosome biogenesis. Autophagy. ISSN 1554-8627. 9(10), p. 1639–1641. doi: 10.4161/auto.26124. Full text in Research Archive
• Knævelsrud, Helene & Simonsen, Anne (2012). Lipids in autophagy: Constituents, signaling molecules and cargo with relevance to disease. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. ISSN 1388-1981. 1821(8), p. 1133–1145. doi: 10.1016/j.bbalip.2012.01.001. Full text in Research Archive
• Knævelsrud, Helene; Ahlquist, Terje Cruickshank; Merok, Marianne Aarstad; Nesbakken, Arild; Stenmark, Harald Alfred & Lothe, Ragnhild A [Show all 7 contributors for this article] (2010). UVRAG mutations associated with microsatellite unstable colon cancer do not affect autophagy. Autophagy. ISSN 1554-8627. 6(7), p. 863–870. doi: 10.4161/auto.6.7.13033. Full text in Research Archive
• Knævelsrud, Helene & Simonsen, Anne (2010). Fighting disease by selective autophagy of aggregate-prone proteins. FEBS Letters. ISSN 0014-5793. 584(12), p. 2635–2645. doi: 10.1016/j.febslet.2010.04.041. Full text in Research Archive

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• Knævelsrud, Helene (2026). Cell scientist to watch – Helene Knævelsrud. Journal of Cell Science. ISSN 0021-9533. 139(6). doi: 10.1242/jcs.264800. Full text in Research Archive
• Knævelsrud, Helene & Tooze, Sharon A. (2025). Autophagy Across Scales – From Molecules to Physiology. Journal of Molecular Biology (JMB). ISSN 0022-2836. 437(18), p. 169300–169300. doi: 10.1016/j.jmb.2025.169300. Full text in Research Archive
• Knævelsrud, Helene; Tjønndal, Anne & Hansen, Kai Arne (2022). #sommerkroppen2022: Hva bør jeg gjøre? Full text in Research Archive
• Bustad, Helene J.; Flydal, Marte Innselset; Knævelsrud, Helene; Langaker, Ann Helen; Boye, Erik & Kristensen, Tom (2022). Slik utvikler vi norske fagtermer i celle-og molekylærbiologi. Tidsskrift for Den norske legeforening (Tidsskriftet). ISSN 0029-2001. 142(2). doi: 10.4045/tidsskr.21.0465. Full text in Research Archive
• Outa, Amani al; Knævelsrud, Helene; Laczko, Balint & Jensenius, Alexander Refsum (2022). Winner of RRI-inspired transdisciplinary side quest call. [Internet]. Centre for Digital Life Norway. Full text in Research Archive Show summary

  Centre for Digital Life Norway (DLN) is excited to congratulate the team behind the project “The autophagic symphony – Unveiling the final rhythm” as winner of DLN’s RRI-inspired transdisciplinary side quest call.

• Bratland-Sanda, Solfrid; Knævelsrud, Helene & Eriksen, Stefka Georgieva (2021). Hvorfor er folk glade i sol og varme? Morgenbladet. ISSN 0805-3847. Full text in Research Archive
• Bustad, Helene J.; Flydal, Marte Innselset; Knævelsrud, Helene; Boye, Erik & Kristensen, Tom Arne (2021). Et kappløp for norsk fagspråk. Michael. ISSN 1893-9651. 18(26), p. 81–91. Full text in Research Archive
• Hem, Erlend; Knævelsrud, Helene & Johannessen, Helene Bustad (2020). Norsk fagspråk må styrkes. Full text in Research Archive
• Eikenes, Åsmund Husabø; Bratland-Sanda, Solfrid; Midtbøen, Arnfinn Haagensen; Bøhn, Einar Duenger; Snipstad, Sofie & Høgestøl, Sofie A.E. [Show all 7 contributors for this article] (2019). Forsker Grand Prix vil forandre forskningen din. Full text in Research Archive
• Knævelsrud, Helene; Snipstad, Sofie & Eikenes, Åsmund Husabø (2018). Nullfunn gir gullfunn. Full text in Research Archive
• Knævelsrud, Helene; Snipstad, Sofie & Eikenes, Åsmund Husabø (2018). Nullfunn gir gullfunn. Full text in Research Archive

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