Tor Erik Rusten

• Balaguera, Nathalia Chica; Andersen, Aram Nikolai; Munoz, Sara Orellana; Llorente, Ignacio Garcia; P, Aurélie Nguéa & Nakken, Sigve [Show all 14 contributors for this article] (2026). Time-resolved functional genomics using deep learning reveals global hierarchical control of autophagy. Nature Cell Biology. ISSN 1465-7392. 28(3), p. 465–479. doi: 10.1038/s41556-025-01837-0. Full text in Research Archive Show summary

  Recycling of cellular components through autophagy maintains homeostasis in changing nutrient environments. Although its core mechanisms are extensively studied, understanding of its systems-wide dynamic regulation remains limited, particularly regarding how autophagy is inactivated once nutrients are restored. Here we mapped the genetic network that controls activation and inactivation of autophagy during nitrogen changes by combining time-resolved high-content imaging, deep learning and latent feature analysis. This dataset, termed AutoDRY, categorizes 5,919 mutants based on nutrient response kinetics and their contributions to autophagosome formation and clearance. Integrating these profiles with functional and genetic network data uncovered hierarchical and multilayered control of autophagy and revealed multiple new regulatory pathways. Notably, we identified the retrograde pathway as a pivotal time-varying modulator that tunes the expression of core autophagy genes and plays a central role in autophagy inactivation. Together, this study establishes a systems-level resource to guide future investigations of autophagy.

• Dillard, Caroline Marie Claude; Reis, Jose Gerardo Belem Teles Roque Dos; Jain, Ashish; Antunes, Marina Manuel Goncalves; Duran, Paula Ruiz & Qi, Yanyan [Show all 9 contributors for this article] (2025). NF-κB signaling driven by oncogenic Ras contributes to tumorigenesis in a Drosophila carcinoma model. PLoS Biology. ISSN 1544-9173. 23(4), p. 1–24. doi: 10.1371/journal.pbio.3002663. Full text in Research Archive Show summary

  Cancer-driving mutations synergize with inflammatory stress signaling pathways during carcinogenesis. Drosophila melanogaster tumor models are increasingly recognized as models to inform conserved molecular mechanisms of tumorigenesis with both local and systemic effects of cancer. Although initial discoveries of the Toll-NFκB signaling pathway in development and immunity were pioneered in Drosophila , limited information is available for its role in cancer progression. Using a well-studied cooperative Ras V12 -driven epithelial-derived tumor model, we here describe functions of Toll-NF-κB signaling in malignant Ras V12 , scrib - tumors. The extracellular Toll pathway components ModSP and PGRP-SA and intracellular signaling Kinase, Pelle/IRAK, are rate-limiting for tumor growth. The Toll pathway NFκB protein Dorsal as well as cactus/I κΒ show elevated expression in tumors with highest expression in invasive cell populations. Oncogenic Ras V12 , and not loss of scribble, confers increased expression and heterogenous distribution of two Dorsal isoforms, DorsalA and DorsalB, in different tumor cell populations. Mechanistic analyses demonstrates that Dorsal, in concert with the BTB-transcription factor Chinmo, drives growth and malignancy by suppressing differentiation, counteracting apoptosis, and promoting invasion of Ras V12 , scrib - tumors.

• Reis, Jose Gerardo Belem Teles Roque Dos; Jain, Ashish; Liu, Dan; Khezri, Rojyar; Antunes, Marina Manuel Goncalves & Micheli, Sofia [Show all 9 contributors for this article] (2025). EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactions in Drosophila melanogaster. Cell Reports Methods. 5(11), p. 1–16. doi: 10.1016/j.crmeth.2025.101220. Full text in Research Archive Show summary

  Studying intercellular and interorgan interactions in animal models is key to understanding development, physiology, and disease. We introduce EyaHOST, a system for clonal combinatorial loss- and gain-of-function genetics in fluorescently labeled cells under QF2-QUAS eya promoter control. Distinct from mosaic analysis with a repressible cell marker (MARCM), it reserves the use of genome-wide GAL4-UAS tools to manipulate any host tissue. EyaHOST-driven RasV12 overexpression with scribble knockdown recapitulates key cancer features, including systemic catabolic switching and organ wasting. We demonstrate effective tissue-specific manipulation of host compartments, including homotypic epithelial neighbors, immune cells, fat body, and muscle. Organ-specific inhibition of autophagy or stimulation of growth signaling via PTEN knockdown in fat body or muscle prevents cachexia-like wasting. Additionally, tumors trigger caspase-driven apoptosis in the neighboring epithelium, and blocking apoptosis with p35 enhances tumor growth. EyaHOST provides a modular platform to dissect mechanisms of intercellular and interorgan communication under physiological or disease conditions.

• Rusten, Tor Erik (2025). Autophagy regulation by signaling. Current Opinion in Cell Biology. ISSN 0955-0674. 97. doi: 10.1016/j.ceb.2025.102595. Full text in Research Archive Show summary

  The first identified regulators of autophagy were the hormones Glucagon and Insulin, long before the recognition that they act through receptor-mediated cell signaling pathways. More than two decades since the identification of the autophagy molecular machinery, we appreciate that regulation of autophagy is complex, operates at several levels, and serves many functions to maintain cellular and organismal health. TORC1 remains the best-defined gatekeeper, serving to sense nutrient and energy sufficiency while also integrating systemic growth factor signaling to control cell growth and autophagy autonomously. This review summarizes the current understanding of autophagy regulation by signaling through TORC1-dependent and independent mechanisms and discusses the emerging understanding of control and coordinated response of autophagy at the organism level.

• Kolapalli, Srinivasa P.; Beese, Carsten J.; Reid, Steven E.; Brynjólfsdóttir, Sólveig H.; Jørgensen, Maria H. & Jain, Ashish [Show all 17 contributors for this article] (2025). Pellino 3 E3 ligase promotes starvation-induced autophagy to prevent hepatic steatosis. Science Advances. 11(3). doi: 10.1126/sciadv.adr2450. Full text in Research Archive Show summary

  Nutrient deprivation is a major trigger of autophagy, a conserved quality control and recycling process essential for cellular and tissue homeostasis. In a high-content image-based screen of the human ubiquitome, we here identify the E3 ligase Pellino 3 (PELI3) as a crucial regulator of starvation-induced autophagy. Mechanistically, PELI3 localizes to autophagic membranes, where it interacts with the ATG8 proteins through an LC3-interacting region (LIR). This facilitates PELI3-mediated ubiquitination of ULK1, driving ULK1’s subsequent proteasomal degradation. PELI3 depletion leads to an aberrant accumulation and mislocalization of ULK1 and disrupts the early steps of autophagosome formation. Genetic deletion of Peli3 in mice impairs fasting-induced autophagy in the liver and enhances starvation-induced hepatic steatosis by reducing autophagy-mediated clearance of lipid droplets. Notably, PELI3 expression is decreased in the livers of patients with metabolic dysfunction–associated steatotic liver disease (MASLD), suggesting its role in hepatic steatosis development in humans. The findings suggest that PELI3-mediated control of autophagy plays a protective role in liver health.

• Migliano, Simona Maria; Schultz, Sebastian Wolfgang; Wenzel, Eva; Takats, Szabolcs; Liu, Dan & mørk, silje [Show all 10 contributors for this article] (2023). Removal of hypersignaling endosomes by simaphagy. Autophagy. ISSN 1554-8627. p. 1–23. doi: 10.1080/15548627.2023.2267958. Full text in Research Archive Show summary

  Activated transmembrane receptors continue to signal following endocytosis and are only silenced upon ESCRT-mediated internalization of the receptors into intralumenal vesicles (ILVs) of the endosomes. Accordingly, endosomes with dysfunctional receptor internalization into ILVs can cause sustained receptor signaling which has been implicated in cancer progression. Here, we describe a surveillance mechanism that allows cells to detect and clear physically intact endosomes with aberrant receptor accumulation and elevated signaling. Proximity biotinylation and proteomics analyses of ESCRT-0 defective endosomes revealed a strong enrichment of the ubiquitin-binding macroautophagy/autophagy receptors SQSTM1 and NBR1, a phenotype that was confirmed in cell culture and fly tissue. Live cell microscopy demonstrated that loss of the ESCRT-0 subunit HGS/HRS or the ESCRT-I subunit VPS37 led to high levels of ubiquitinated and phosphorylated receptors on endosomes. This was accompanied by dynamic recruitment of NBR1 and SQSTM1 as well as proteins involved in autophagy initiation and autophagosome biogenesis. Light microscopy and electron tomography revealed that endosomes with intact limiting membrane, but aberrant receptor downregulation were engulfed by phagophores. Inhibition of autophagy caused increased intra- and intercellular signaling and directed cell migration. We conclude that dysfunctional endosomes are surveyed and cleared by an autophagic process, simaphagy, which serves as a failsafe mechanism in signal termination.

• Javed, Ruheena; Jain, Ashish; Duque, Thabata; Hendrix, Emily; Paddar, Masroor Ahmad & Khan, Sajjad [Show all 19 contributors for this article] (2023). Mammalian ATG8 proteins maintain autophagosomal membrane integrity through ESCRTs. EMBO Journal. ISSN 0261-4189. p. 1–22. doi: 10.15252/embj.2022112845. Full text in Research Archive
• Mehto, Subhash; Jena, Kautilya Kumar; Yadav, Rina; Priyadarsini, Swatismita; Samal, Pallavi & Krishna, Sivaram [Show all 20 contributors for this article] (2022). Selective autophagy of RIPosomes maintains innate immune homeostasis during bacterial infection. EMBO Journal. ISSN 0261-4189. p. 1–23. doi: 10.15252/embj.2022111289. Full text in Research Archive Show summary

  The NOD1/2-RIPK2 is a key cytosolic signaling complex that activates NF-κB pro-inflammatory response against invading pathogens. However, uncontrolled NF-κB signaling can cause tissue damage leading to chronic diseases. The mechanisms by which the NODs-RIPK2-NF-κB innate immune axis is activated and resolved remain poorly understood. Here, we demonstrate that bacterial infection induces the formation of endogenous RIPK2 oligomers (RIPosomes) that are self-assembling entities that coat the bacteria to induce NF-κB response. Next, we show that autophagy proteins IRGM and p62/SQSTM1 physically interact with NOD1/2, RIPK2 and RIPosomes to promote their selective autophagy and limit NF-κB activation. IRGM suppresses RIPK2-dependent pro-inflammatory programs induced by Shigella and Salmonella. Consistently, the therapeutic inhibition of RIPK2 ameliorates Shigella infection- and DSS-induced gut inflammation in Irgm1 KO mice. This study identifies a unique mechanism where the innate immune proteins and autophagy machinery are recruited together to the bacteria for defense as well as for maintaining immune homeostasis.

• Lobert, Viola; Skardal, Maren; Malerød, Lene; Simensen, Julie Elisabeth; Algra, Hermine Arida & Andersen, Aram Nikolai [Show all 12 contributors for this article] (2022). PHLPP1 regulates CFTR activity and lumen expansion through AMPK. Development. ISSN 0950-1991. 149(20), p. 1–10. doi: 10.1242/dev.200955. Full text in Research Archive Show summary

  Complex organ development depends on single lumen formation and its expansion during tubulogenesis. This can be achieved by correct mitotic spindle orientation during cell division, combined with luminal fluid filling that generates hydrostatic pressure. Using a human 3D cell culture model, we have identified two regulators of these processes. We find that pleckstrin homology leucine-rich repeat protein phosphatase (PHLPP) 2 regulates mitotic spindle orientation, and thereby midbody positioning and maintenance of a single lumen. Silencing the sole PHLPP family phosphatase in Drosophila melanogaster, phlpp, resulted in defective spindle orientation in Drosophila neuroblasts. Importantly, cystic fibrosis transmembrane conductance regulator (CFTR) is the main channel regulating fluid transport in this system, stimulated by phosphorylation by protein kinase A and inhibited by the AMP-activated protein kinase AMPK. During lumen expansion, CFTR remains open through the action of PHLPP1, which stops activated AMPK from inhibiting ion transport through CFTR. In the absence of PHLPP1, the restraint on AMPK activity is lost and this tips the balance in the favour of channel closing, resulting in the lack of lumen expansion and accumulation of mucus.

• Rusten, Tor Erik & Khezri, Rojyar (2022). Autophagy power expands: fuse those cells! EMBO Journal. ISSN 0261-4189. doi: 10.15252/embj.2022111424. Full text in Research Archive Show summary

  The lysosomal degradation pathway of autophagy depends on a set of evolutionarily conserved autophagy‐related molecules (ATGs) bestowed with the power to direct membrane trafficking and biology. In this issue of EMBO Journal, Kakanj P et al reveal a surprising role for the autophagy machinery in cell fusion (Kakanj et al, 2022). Autophagy is physiologically required for cell syncytium formation through dismantling the lateral plasma membrane during wound healing, and unchecked autophagy can drive cell fusion in epithelial tissues without compromising epithelial integrity.

• Holland, Petter; Quintana, Eduardo Martin; Khezri, Rojyar; Schoborg, Todd Andrew & Rusten, Tor Erik (2022). Computed tomography with segmentation and quantification of individual organs in a D. melanogaster tumor model. Scientific Reports. 12(1). doi: 10.1038/s41598-022-05991-5. Full text in Research Archive Show summary

  Abstract Drosophila melanogaster tumor models are growing in popularity, driven by the high degree of genetic as well as functional conservation to humans. The most common method to measure the effects of a tumor on distant organs of a human cancer patient is to use computed tomography (CT), often used in diagnosing cachexia, a debilitating cancer-induced syndrome most visibly characterized by loss of muscle mass. Successful application of high resolution micro-CT scanning of D. melanogaster was recently reported and we here present the segmentation of all visible larval organs at several stages of tumor development. We previously showed the strong expected reduction in muscle mass as the tumor develops, and we here report a surprisingly strong reduction also in gut and Malpighian tubules (kidney) volume. Time-point of tumor development was found to have a stronger correlation to cachectic organ volume loss than tumor volume, giving support to the previously proposed idea that tumor size does not directly determine degree of cachexia.

• Khezri, Rojyar; Holland, Petter; Schoborg, Todd Andrew; Abramovich, Ifat; Takats, Szabolcs & Dillard, Caroline Marie Claude [Show all 21 contributors for this article] (2021). Host autophagy mediates organ wasting and nutrient mobilization for tumor growth. EMBO Journal. ISSN 0261-4189. 40(18). doi: 10.15252/embj.2020107336. Full text in Research Archive Show summary

  During tumor growth—when nutrient and anabolic demands are high—autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12; scrib−/− tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding, and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.

• Dillard, Caroline Marie Claude; José, Gerardo Teles Reis, & Rusten, Tor Erik (2021). RasV12 scrib−/− tumors: A cooperative oncogenesis model fueled by tumor/host interactions. International Journal of Molecular Sciences. ISSN 1661-6596. 22:8873, p. 1–27. doi: 10.3390/ijms22168873. Full text in Research Archive Show summary

  The phenomenon of how oncogenes and tumor-suppressor mutations can synergize to promote tumor fitness and cancer progression can be studied in relatively simple animal model systems such as Drosophila melanogaster. Almost two decades after the landmark discovery of cooperative oncogenesis between oncogenic RasV12 and the loss of the tumor suppressor scribble in flies, this and other tumor models have provided new concepts and findings in cancer biology that has remarkable parallels and relevance to human cancer. Here we review findings using the RasV12; scrib−/− tumor model and how it has contributed to our understanding of how these initial simple genetic insults cooperate within the tumor cell to set in motion the malignant transformation program leading to tumor growth through cell growth, cell survival and proliferation, dismantling of cell–cell interactions, degradation of basement membrane and spreading to other organs. Recent findings have demonstrated that cooperativity goes beyond cell intrinsic mechanisms as the tumor interacts with the immediate cells of the microenvironment, the immune system and systemic organs to eventually facilitate malignant progression.

• Kolapalli, Srinivasa P.; Sahu, Rinku; Chauhan, Nishant R.; Jena, Kautilya K.; Mehto, Subhash & Das, Saroj K. [Show all 14 contributors for this article] (2021). RNA-Binding RING E3-Ligase DZIP3/hRUL138 Stabilizes Cyclin D1 to Drive Cell-Cycle and Cancer Progression. Cancer Research. ISSN 0008-5472. p. 315–331. doi: 10.1158/0008-5472.CAN-20-1871. Full text in Research Archive
• Holland, Petter; Hagopian, William Martin; Jahren, Anne Hope Florine & Rusten, Tor Erik (2021). Natural abundance isotope ratios to differentiate sources of carbon used during tumor growth in vivo. BMC Biology. 19(1), p. 1–10. doi: 10.1186/s12915-021-01012-5. Full text in Research Archive Show summary

  Background Radioactive or stable isotopic labeling of metabolites is a strategy that is routinely used to map the cellular fate of a selected labeled metabolite after it is added to cell culture or to the circulation of an animal. However, a labeled metabolite can be enzymatically changed in cellular metabolism, complicating the use of this experimental strategy to understand how a labeled metabolite moves between organs. These methods are also technically demanding, expensive and potentially toxic. To allow quantification of the bulk movement of metabolites between organs, we have developed a novel application of stable isotope ratio mass spectrometry (IRMS). Results We exploit natural differences in 13C/12C ratios of plant nutrients for a low-cost and non-toxic carbon labeling, allowing a measurement of bulk carbon transfer between organs in vivo. IRMS measurements were found to be sufficiently sensitive to measure organs from individual Drosophila melanogaster larvae, giving robust measurements down to 2.5 μg per sample. We apply the method to determine if carbon incorporated into a growing solid tumor is ultimately derived from food or host tissues. Conclusion Measuring tumor growth in a D. melanogaster larvae tumor model reveals that these tumors derive a majority of carbon from host sources. We believe the low cost and non-toxic nature of this methodology gives it broad applicability to study carbon flows between organs also in other animals and for a range of other biological questions.

• Kumar, Suresh; Javed, Ruheena; Mudd, Michal H.; Pallikkuth, Sandeep; Lidke, Keith A. & Jain, Ashish [Show all 22 contributors for this article] (2021). Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes. Cell. ISSN 0092-8674. 184(24), p. 5950–5969. doi: 10.1016/j.cell.2021.10.017. Full text in Research Archive Show summary

  The biogenesis of mammalian autophagosomes remains to be fully defined. Here, we used cellular and in vitro membrane fusion analyses to show that autophagosomes are formed from a hitherto unappreciated hybrid membrane compartment. The autophagic precursors emerge through fusion of FIP200 vesicles, derived from the cis-Golgi, with endosomally derived ATG16L1 membranes to generate a hybrid pre-autophagosomal structure, HyPAS. A previously unrecognized apparatus defined here controls HyPAS biogenesis and mammalian autophagosomal precursor membranes. HyPAS can be modulated by pharmacological agents whereas its formation is inhibited upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or by expression of SARS-CoV-2 nsp6. These findings reveal the origin of mammalian autophagosomal membranes, which emerge via convergence of secretory and endosomal pathways, and show that this process is targeted by microbial factors such as coronaviral membrane-modulating proteins

• Jena, Kautilya Kumar; Mehto, Subhash; Nath, Parej; Chauhan, Nishant Ranjan; Sahu, Rinku & Dhar, Kollori [Show all 17 contributors for this article] (2020). Autoimmunity gene IRGM suppresses cGAS-STING and RIG-I-MAVS signaling to control interferon response. EMBO Reports. ISSN 1469-221X. 21:e50051(9), p. 1–24. doi: 10.15252/embr.202050051. Full text in Research Archive Show summary

  Activation of the type 1 interferon response is extensively connected to the pathogenesis of autoimmune diseases. Loss of function of Immunity Related GTPase M (IRGM) has also been associated to several autoimmune diseases, but its mechanism of action is unknown. Here, we found that IRGM is a master negative regulator of the interferon response. Several nucleic acid‐sensing pathways leading to interferon‐stimulated gene expression are highly activated in IRGM knockout mice and human cells. Mechanistically, we show that IRGM interacts with nucleic acid sensor proteins, including cGAS and RIG‐I, and mediates their p62‐dependent autophagic degradation to restrain interferon signaling. Further, IRGM deficiency results in defective mitophagy leading to the accumulation of defunct leaky mitochondria that release cytosolic DAMPs and mtROS. Hence, IRGM deficiency increases not only the levels of the sensors, but also those of the stimuli that trigger the activation of the cGAS‐STING and RIG‐I‐MAVS signaling axes, leading to robust induction of IFN responses. Taken together, this study defines the molecular mechanisms by which IRGM maintains interferon homeostasis and protects from autoimmune diseases.

• Kumar, Suresh; Jain, Ashish; Choi, Seong Won; Silva, Gustavo Peixoto Duarte da; Allers, Lee & Mudd, Michal H. [Show all 11 contributors for this article] (2020). Mammalian Atg8-family proteins are upstream regulators of the lysosomalsystem by controlling MTOR and TFEB. Autophagy. ISSN 1554-8627. 16(12), p. 2305–2306. doi: 10.1080/15548627.2020.1837423. Full text in Research Archive
• Kumar, Suresh; Jain, Ashish; Choi, Seong Won; Silva, Gustavo Peixoto Duarte da; Allers, Lee & Mudd, Michal H. [Show all 11 contributors for this article] (2020). Mammalian Atg8 proteins and the autophagy factor IRGM control mTOR and TFEB at a regulatory node critical for responses to pathogens. Nature Cell Biology. ISSN 1465-7392. 22(8), p. 973–985. doi: 10.1038/s41556-020-0549-1. Full text in Research Archive
• Kumar, Suresh; Gu, Yuexi; Abudu, Yakubu Princely; Bruun, Jack-Ansgar; Jain, Ashish & Farzam, Farzin [Show all 14 contributors for this article] (2019). Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation. Developmental Cell. ISSN 1534-5807. 49(1), p. 130–144.e6. doi: 10.1016/j.devcel.2019.01.027. Full text in Research Archive Show summary

  Syntaxin 17 (Stx17) has been implicated in autophagosome-lysosome fusion. Here, we report that Stx17 functions in assembly of protein complexes during autophagy initiation. Stx17 is phosphorylated by TBK1 whereby phospho-Stx17 controls the formation of the ATG13⁺FIP200⁺ mammalian pre-autophagosomal structure (mPAS) in response to induction of autophagy. TBK1 phosphorylates Stx17 at S202. During autophagy induction, Stx17^pS202 transfers from the Golgi, where its steady-state pools localize, to the ATG13⁺FIP200⁺ mPAS. Stx17^pS202 was in complexes with ATG13 and FIP200, whereas its non-phosphorylatable mutant Stx17^S202A was not. Stx17 or TBK1 knockouts blocked ATG13 and FIP200 puncta formation. Stx17 or TBK1 knockouts reduced the formation of ATG13 protein complexes with FIP200 and ULK1. Endogenous Stx17^pS202 colocalized with LC3B following induction of autophagy. Stx17 knockout diminished LC3 response and reduced sequestration of the prototypical bulk autophagy cargo lactate dehydrogenase. We conclude that Stx17 is a TBK1 substrate and that together they orchestrate assembly of mPAS.

• Fang, Evandro Fei; Hou, Yujun; Lautrup, Sofie Hindkjær; Jensen, Martin Borch; Yang, Beimeng & Sengupta, Tanima [Show all 29 contributors for this article] (2019). NAD+ augmentation restores mitophagy and limits accelerated aging in Werner syndrome. Nature Communications. 10:5284, p. 1–18. doi: 10.1038/s41467-019-13172-8. Full text in Research Archive Show summary

  Metabolic dysfunction is a primary feature of Werner syndrome (WS), a human premature aging disease caused by mutations in the gene encoding the Werner (WRN) DNA helicase. WS patients exhibit severe metabolic phenotypes, but the underlying mechanisms are not understood, and whether the metabolic deficit can be targeted for therapeutic intervention has not been determined. Here we report impaired mitophagy and depletion of NAD+, a fundamental ubiquitous molecule, in WS patient samples and WS invertebrate models. WRN regulates transcription of a key NAD+ biosynthetic enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1). NAD+ repletion restores NAD+ metabolic profiles and improves mitochondrial quality through DCT-1 and ULK-1-dependent mitophagy. At the organismal level, NAD+ repletion remarkably extends lifespan and delays accelerated aging, including stem cell dysfunction, in Caenorhabditis elegans and Drosophila melanogaster models of WS. Our findings suggest that accelerated aging in WS is mediated by impaired mitochondrial function and mitophagy, and that bolstering cellular NAD+ levels counteracts WS phenotypes.

• Dillard-Eple, Caroline Marie Claude & Rusten, Tor Erik (2019). Cell Competition Triggers Suicide by Autophagy. Developmental Cell. ISSN 1534-5807. doi: 10.1016/j.devcel.2019.09.014. Full text in Research Archive Show summary

  Cell competition eradicates weaker cells from an epithelium and is important for organ homeostasis. In this issue of Developmental Cell, Nagata et al. (2019) uncover that eradication of loser cells depends on autophagy-mediated cell death.

• Khezri, Rojyar & Rusten, Tor Erik (2019). Autophagy and tumorigenesis in drosophila. Advances in Experimental Medicine and Biology. ISSN 0065-2598. 1167, p. 113–127. doi: 10.1007/978-3-030-23629-8_7. Full text in Research Archive
• Kumar, Suresh; Jain, Ashish; Farzam, Farzin; Jia, Jingyue; Gu, Yuexi & Choi, Seong Won [Show all 12 contributors for this article] (2018). Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins. Journal of Cell Biology. ISSN 0021-9525. 217(3), p. 997–1013. doi: 10.1083/jcb.201708039. Full text in Research Archive Show summary

  Autophagy is a conserved eukaryotic process with metabolic, immune, and general homeostatic functions in mammalian cells. Mammalian autophagosomes fuse with lysosomes in a SNARE-driven process that includes syntaxin 17 (Stx17). How Stx17 translocates to autophagosomes is unknown. In this study, we show that the mechanism of Stx17 recruitment to autophagosomes in human cells entails the small guanosine triphosphatase IRGM. Stx17 directly interacts with IRGM, and efficient Stx17 recruitment to autophagosomes requires IRGM. Both IRGM and Stx17 directly interact with mammalian Atg8 proteins, thus being guided to autophagosomes. We also show that Stx17 is significant in defense against infectious agents and that Stx17–IRGM interaction is targeted by an HIV virulence factor Nef.

• O'Farrell, Fergal; Lobert, Viola; Sneeggen, Marte; Jain, Ashish; Katheder, Nadja Sandra & Wenzel, Eva [Show all 11 contributors for this article] (2017). Class III phosphatidylinositol-3-OH kinase controls epithelial integrity through endosomal LKB1 regulation. Nature Cell Biology. ISSN 1465-7392. 19(12), p. 1412–1423. doi: 10.1038/ncb3631. Full text in Research Archive
• Katheder, Nadja Sandra; Khezri, Rojyar; O'Farrell, Fergal; Schultz, Sebastian; Jain, Ashish & Rahman, Mohammed Mahidur [Show all 14 contributors for this article] (2017). Microenvironmental autophagy promotes tumour growth. Nature. ISSN 0028-0836. 541(7637), p. 417–420. doi: 10.1038/nature20815. Full text in Research Archive
• Katheder, Nadja Sandra & Rusten, Tor Erik (2017). Microenvironment and tumors-nurturing relationship. Autophagy. ISSN 1554-8627. 3(13), p. 1241–1243. doi: 10.1080/15548627.2017.1310361. Full text in Research Archive Show summary

  When exposed to adverse environmental conditions, cells degrade their own content to recycle cellular building blocks through a process called autophagy. A large body of literature has connected autophagy to cancer, but most studies up until now focused on its function in transformed cells. In her thesis, Nadja Katheder dissected the role of autophagy in a well-characterized neoplastic in vivo tumor model in Drosophila and demonstrates a novel non-cell-autonomous requirement of this process for tumor growth. Neighboring epithelial cells and distal tissues increase autophagy in the presence of a malignant tumor. Pharmacological autophagy inhibition reduces tumor growth and genetic ablation of autophagy in the microenvironment reveals a tumor-supportive role of this process in this specific cell population. Tumor cells are metabolically stressed and induce autophagy in their neighbors through a TNFα-JNK-IL-6 signaling cascade. Moreover, they are dependent on amino acid import to sustain their proliferation, which indicates a coupling of metabolism between these two cell populations. Finally, allografted growth-impaired tumors from autophagy-deficient donor animals resume growth in an autophagy-competent host. Together, the results described in this thesis highlight the tumor-promoting role of autophagy the microenvironment and show that cancer cells engage their epithelial neighbors as essential contributors aiding their own growth.

• O'Farrell, Fergal; Lobert, Viola; Sneeggen, Marte; Jain, Ashish; Katheder, Nadja Sandra & Wenzel, Eva [Show all 11 contributors for this article] (2017). Class III phosphatidylinositol-3-OH kinase controls epithelial integrity through endosomal LKB1 regulation. Nature Cell Biology. ISSN 1465-7392. 19, p. 1412–1423. doi: 10.1038/ncb3631. Full text in Research Archive
• Schmid, Martin R.; Anderl, Ines; Vo, Hoa T.M.; Valanne, Susanna; Yang, Hairu & Kronhamn, Jesper [Show all 9 contributors for this article] (2016). Genetic screen in drosophila larvae links ird1 function to toll signaling in the fat body and hemocyte motility. PLOS ONE. 11:e0159473(7). doi: 10.1371/journal.pone.0159473. Full text in Research Archive
• Jain, Ashish; Rusten, Tor Erik; Katheder, Nadja Sandra; Elvenes, Julianne; Bruun, Jack-Ansgar & Sjøttem, Eva [Show all 8 contributors for this article] (2015). P62/sequestosome-1, autophagy-related gene 8, and autophagy in Drosophila are regulated by nuclear factor erythroid 2-related factor 2(NRF2), independent of transcription factor TFEB. Journal of Biological Chemistry. ISSN 0021-9258. 290(24), p. 14945–14962. doi: 10.1074/jbc.M115.656116. Full text in Research Archive Show summary

  The selective autophagy receptor p62/sequestosome 1 (SQSTM1) interacts directly with LC3 and is involved in oxidative stress signaling in two ways in mammals. First, p62 is transcriptionally induced upon oxidative stress by the NF-E2-related factor 2 (NRF2) by direct binding to an antioxidant response element in the p62 promoter. Second, p62 accumulation, occurring when autophagy is impaired, leads to increased p62 binding to the NRF2 inhibitor KEAP1, resulting in reduced proteasomal turnover of NRF2. This gives chronic oxidative stress signaling through a feed forward loop. Here, we show that the Drosophila p62/SQSTM1 orthologue, Ref(2)P, interacts directly with DmAtg8a via an LC3-interacting region motif, supporting a role for Ref(2)P in selective autophagy. The ref(2)P promoter also contains a functional antioxidant response element that is directly bound by the NRF2 orthologue, CncC, which can induce ref(2)P expression along with the oxidative stress-associated gene gstD1. However, distinct from the situation in mammals, Ref(2)P does not interact directly with DmKeap1 via a KEAP1-interacting region motif; nor does ectopically expressed Ref(2)P or autophagy deficiency activate the oxidative stress response. Instead, DmAtg8a interacts directly with DmKeap1, and DmKeap1 is removed upon programmed autophagy in Drosophila gut cells. Strikingly, CncC induced increased Atg8a levels and autophagy independent of TFEB/MitF in fat body and larval gut tissues. Thus, these results extend the intimate relationship between oxidative stress-sensing NRF2/CncC transcription factors and autophagy and suggest that NRF2/CncC may regulate autophagic activity in other organisms too.

• Morelli, Elena; Ginefra, Pierpaolo; Mastrodonato, Valeria; Beznoussenko, Galina; Rusten, Tor Erik & Bilder, David [Show all 9 contributors for this article] (2014). Multiple functions of the SNARE protein Snap29 in autophagy, endocytic, and exocytic trafficking during epithelial formation in Drosophila. Autophagy. ISSN 1554-8627. 10(12), p. 2251–2268. doi: 10.4161/15548627.2014.981913. Full text in Research Archive
• Oppelt, Angela; Lobert, Viola Helene; Haglund, Kaisa; Mackey, Ashley M.; Rameh, Lucia E. & Liestøl, Knut [Show all 14 contributors for this article] (2013). Production of phosphatidylinositol 5-phosphate via PIKfyve and MTMR3 regulates cell migration. EMBO Reports. ISSN 1469-221X. 14(1), p. 57–64. doi: 10.1038/embor.2012.183. Full text in Research Archive
• 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
• O'Farell, Fergal; Rusten, Tor Erik & Stenmark, Harald Alfred (2013). Phosphoinositide 3-kinases as accelerators and brakes of autophagy. The FEBS Journal. ISSN 1742-464X. 280(24), p. 6322–6337. doi: 10.1111/febs.12486. Full text in Research Archive
• O'Farell, Fergal; Wang, Shenqiu; Katheder, Nadja Sandra; Rusten, Tor Erik & Samakovlis, Christos (2013). Two-Tiered Control of Epithelial Growth and Autophagy by the Insulin Receptor and the Ret-Like Receptor, Stitcher. PLoS Biology. ISSN 1544-9173. 11(7). doi: 10.1371/journal.pbio.1001612. Full text in Research Archive
• Klionsky, Daniel J.; Abdalla, FC; Abeliovich, H; Abraham, RT; Acevedo-Arozena, A & Adeli, K [Show all 1,261 contributors for this article] (2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy. ISSN 1554-8627. 8(4), p. 445–544. doi: 10.4161/auto.19496. Full text in Research Archive
• Rusten, Tor Erik; Vaccari, Thomas & Stenmark, Harald Alfred (2012). Shaping development with ESCRTs. Nature Cell Biology. ISSN 1465-7392. 14(1), p. 38–45. doi: 10.1038/ncb2381. Full text in Research Archive
• Sagona, Antonia; Nezis, Jonnis P; Pedersen, Nina Marie; Liestøl, Knut; Poulton, J & Rusten, Tor Erik [Show all 9 contributors for this article] (2010). PtdIns(3)P controls cytokinesis through KIF13A-mediated recruitment of FYVE-CENT to the midbody. Nature Cell Biology. ISSN 1465-7392. 12(4), p. 362–U140. doi: 10.1038/ncb2036. Full text in Research Archive
• Nezis, Ioannis; Shravage, Bhupendra V; Sagona, Antonia; Lamark, Trond; Bjørkøy, Geir & Johansen, Terje [Show all 10 contributors for this article] (2010). Autophagic degradation of dBruce controls DNA fragmentation in nurse cells during late Drosophila melanogaster oogenesis. Journal of Cell Biology. ISSN 0021-9525. 190(4), p. 523–531. doi: 10.1083/jcb.201002035. Full text in Research Archive Show summary

  Autophagy is an evolutionarily conserved pathway responsible for degradation of cytoplasmic material via the lysosome. Although autophagy has been reported to contribute to cell death, the underlying mechanisms remain largely unknown. In this study, we show that autophagy controls DNA fragmentation during late oogenesis in Drosophila melanogaster. Inhibition of autophagy by genetically removing the function of the autophagy genes atg1, atg13, and vps34 resulted in late stage egg chambers that contained persisting nurse cell nuclei without fragmented DNA and attenuation of caspase-3 cleavage. The Drosophila inhibitor of apoptosis (IAP) dBruce was found to colocalize with the autophagic marker GFP-Atg8a and accumulated in autophagy mutants. Nurse cells lacking Atg1 or Vps34 in addition to dBruce contained persisting nurse cell nuclei with fragmented DNA. This indicates that autophagic degradation of dBruce controls DNA fragmentation in nurse cells. Our results reveal autophagic degradation of an IAP as a novel mechanism of triggering cell death and thereby provide a mechanistic link between autophagy and cell death.

• Vaccari, T; Rusten, Tor Erik; Menut, L; Nezis, Ioannis P; Brech, Andreas & Stenmark, Harald Alfred [Show all 7 contributors for this article] (2009). Comparative analysis of ESCRT-I, ESCRT-II and ESCRT-III function in Drosophila by efficient isolation of ESCRT mutants. Journal of Cell Science. ISSN 0021-9533. 122(14), p. 2413–2423. doi: 10.1242/jcs.046391. Full text in Research Archive
• Rusten, Tor Erik & Stenmark, Harald Alfred (2009). How do ESCRT proteins control autophagy? Journal of Cell Science. ISSN 0021-9533. 122(13), p. 2179–2183. doi: 10.1242/jcs.050021. Full text in Research Archive
• Nezis, Ioannis P; Lamark, Trond; Velentzas, Athanassios D; Rusten, Tor Erik; Bjørkøy, Geir & Johansen, Terje [Show all 11 contributors for this article] (2009). Cell death during Drosophila melanogaster early oogenesis is mediated through autophagy. Autophagy. ISSN 1554-8627. 5(3), p. 298–302. Full text in Research Archive
• Nezis, Jonnis P; Lamark, T; Velentzas, AD; Rusten, Tor Erik; Bjørkøy, G & Johansen, Terje [Show all 11 contributors for this article] (2009). Cell death during Drosophila melanogaster early oogenesis is mediated through autophagy. Autophagy. ISSN 1554-8627. 5(3), p. 298–302. doi: 10.4161/auto.5.3.7454. Full text in Research Archive
• Rusten, Tor Erik & Simonsen, Anne (2008). ESCRT functions in autophagy and associated disease. Cell Cycle. ISSN 1538-4101. 7(9), p. 1166–1172. Full text in Research Archive
• Nezis, Jonnis P; Simonsen, Anne; Sagona, Antonia; Finley, K; Gaumer, S & Contamine, D [Show all 9 contributors for this article] (2008). Ref(2) P, the Drosophila melanogaster homologue of mammalian p62, is required for the formation of protein aggregates in adult brain. Journal of Cell Biology. ISSN 0021-9525. 180(6), p. 1065–1071. Full text in Research Archive
• Rusten, Tor Erik; Filimonenko, Maria; Rodahl, Lina Malin Westerberg; Stenmark, Harald Alfred & Simonsen, Anne (2008). ESCRTing autophagic clearance of aggregating proteins. Autophagy. ISSN 1554-8627. 4(2), p. 233–236. Full text in Research Archive
• Morrison, HA; Dionne, H; Rusten, Tor Erik; Brech, Andreas; Fisher, WW & Pfeiffer, BD [Show all 9 contributors for this article] (2008). Regulation of Early Endosomal Entry by the Drosophila Tumor Suppressors Rabenosyn and Vps45. Molecular Biology of the Cell. ISSN 1059-1524. 19(10), p. 4167–4176. doi: 10.1091/mbc.E08-07-0716. Full text in Research Archive
• Lindmo, Karine; Brech, Andreas; Finley, KD; Gaumer, S; Contamine, D & Rusten, Tor Erik [Show all 7 contributors for this article] (2008). The PI 3-kinase regulator Vps15 is required for autophagic clearance of protein aggregates. Autophagy. ISSN 1554-8627. 4(4), p. 500–506. Full text in Research Archive
• Haglund, Kaisa; Rusten, Tor Erik & Stenmark, Harald Alfred (2007). Aberrant receptor signaling and trafficking as mechanisms in oncogenesis. Critical reviews in oncogenesis. ISSN 0893-9675. 13(1). Full text in Research Archive
• Rusten, Tor Erik; Vaccart, T; Lindmo, Karine; Rodahl, Lina Malin Westerberg; Nezis, Ioannis P & Sem-Jacobsen, Catherine E [Show all 11 contributors for this article] (2007). ESCRTs and Fab1 regulate distinct steps of autophagy. Current Biology. ISSN 0960-9822. 17(20), p. 1817–1825. doi: 10.1016/j.cub.2007.09.032. Full text in Research Archive
• Rusten, Tor Erik; Stenmark, H & Stenmark, Harald (2006). Analyzing phosphoinositides and their interacting proteins. Nature Methods. ISSN 1548-7091. 3, p. 251–258. Full text in Research Archive
• Lindmo, Karine; Simonsen, Anne; Brech, Andreas; Finley, K; Rusten, Tor Erik & Stenmark, Harald Alfred (2006). A dual function for Deep orange in programmed autophagy in the Drosophila melanogaster fat body. Experimental Cell Research. ISSN 0014-4827. 312, p. 2018–2027. Full text in Research Archive
• Rusten, Tor Erik; Rodahl, Lina Malin Westerberg; Pattni, Krupa; Englund, C; Samakovlis, C & Dove, S [Show all 8 contributors for this article] (2006). Fab1 phosphatidylinositol 3-phosphate 5-kinase controls trafficking but not silencing of endocytosed receptors. Molecular Biology of the Cell. ISSN 1059-1524. 17, p. 3989–4001. Full text in Research Archive

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• Kumar, Suresh; Jain, Ashish; Choi, Seong Won; Silva, Gustavo Peixoto Duarte da; Allers, Lee & Mudd, Michal H. [Show all 11 contributors for this article] (2020). Author Correction: Mammalian Atg8 proteins and the autophagy factor IRGM control mTOR and TFEB at a regulatory node critical for responses to pathogens (Nature Cell Biology, (2020), 22, 8, (973-985), 10.1038/s41556-020-0549-1). Nature Cell Biology. ISSN 1465-7392. 22(10), p. 1286–1286. doi: 10.1038/s41556-020-0574-0. Full text in Research Archive
• Khezri, Rojyar & Rusten, Tor Erik (2019). Erratum: Correction to: Autophagy and Tumorigenesis in Drosophila (Advances in experimental medicine and biology). Advances in Experimental Medicine and Biology. ISSN 0065-2598. 1167, p. C1–C1. doi: 10.1007/978-3-030-23629-8_15. Full text in Research Archive
• Martens, Sascha; Rusten, Tor Erik & Kraft, Claudine (2013). Autophagy at sea. Autophagy. ISSN 1554-8627. 9(9), p. 1286–1291. doi: 10.4161/auto.25838. Full text in Research Archive
• Rusten, Tor Erik & Stenmark, Harald Alfred (2010). p62, an autophagy hero or culprit? Nature Cell Biology. ISSN 1465-7392. 12(3), p. 207–209. Full text in Research Archive
• Rusten, Tor Erik & Stenmark, Harald Alfred (2007). Developmental biology: Moonlighting at the pole. Nature. ISSN 0028-0836. 445, p. 497–499. doi: 10.1038/445497a. Full text in Research Archive

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