bims-proteo Biomed News
on Proteostasis
Issue of 2026–04–12
fifty-five papers selected by
Eric Chevet, INSERM
  1. The Contribution of Native Protein Complexes to Targeted Protein Degradation.
  2. Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS).
  3. The integrated stress response suppresses PINK1-dependent mitophagy by preserving mitochondrial import efficiency.
  4. Beyond CRBN and VHL: Parkin driven lysine-based ternary complexes for selective β3-Tubulin degradation.
  5. The molecular glue CLEO4-88 inhibits the ACAA1 thiolase by induced binding to GID4.
  6. FAM134B isoform 2/RETREG1-2 defines a calnexin-TOLLIP-coupled ER-phagy pathway that restricts Ebola virus glycoprotein and is antagonized by VP40 through macro-autophagy.
  7. Harnessing FBXO31 with Terminal Amide-Functionalized Molecules for Targeted Protein Degradation.
  8. Charged molecular glue discovery enabled by targeted degron display.
  9. 5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions.
  10. Endoplasmic reticulum architecture in liver metabolic regulation.
  11. Genetic dissection of rapid proteolysis identifies TXNDC15 as a key factor of ERAD and lipid homeostasis.
  12. Autophagic extracellular vesicles: a distinct secretory route linking autophagy to extracellular communication.
  13. A structural code for assembly specificity in GID/CTLH-type E3 ligases.
  14. Ligand-driven modulation of chaperone-cochaperone networks shapes proteostasis outcomes.
  15. Cholesterol-dependent lysosomal docking of mTORC1 mediated by TM6SF1.
  16. mtHsp70 chaperone converts mitochondrial proteostasis stress into impaired protein import.
  17. Targeted degradation of c-Myc through the midnolin-proteasome pathway.
  18. Covalent Reprogramming of Kinase Binders to Modulate Protein Abundance.
  19. Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR.
  20. SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response.
  21. Integrative genomic and functional analyses reveal NINL as a modulator of tau aggregation.
  22. Multivalent weak contacts shape chaperone-nascent protein interactions.
  23. ATF4-dependent upregulation of Bruno 1 remodels P-bodies to selectively protect mRNAs during ER stress throughout Drosophila melanogaster oogenesis.
  24. Translation in proximity to forming autophagosomes during sustained autophagy.
  25. Where and how do mammalian cells shape autophagosomes?
  26. The molecular basis of tricalbin-mediated membrane contact site organization in cells.
  27. Alzheimer's disease risk protein SorLA regulates ER homeostasis and lipid metabolism in human microglia, with conserved effects in neurons.
  28. ER discontinuities are common in C. elegans neurons, revealing a genetically tractable model for ER network maintenance.
  29. African swine fever virus MGF_110-8L promotes host cell autophagy and suppresses interferon signaling by activating the unfolded protein response.
  30. CDK/mTOR-dependent phosphorylation of UBE2H restrains its charging with ubiquitin and regulates CTLH-dependent degradation.
  31. Proteasome dysfunction underlies HERC2-linked neurodevelopmental disorder with Angelman-like clinical features.
  32. Systematic profiling of cytosolic membraneless organelles reveals enrichment of oncogenic mRNA upon oxidative stress.
  33. The SWR1 complex prevents the vacuolar delivery of ATG proteins through a noncanonical pathway.
  34. Newcastle disease virus exploits Golgi stress and Golgiphagy to promote ferroptosis.
  35. Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.
  36. A C-degron regulates Chk1 kinase by allowing stability of inactive Chk1 and by making it short- lived upon activation.
  37. Selective degradation of TBK1 uncovers mechanistic insights into blocking ccRCC progression.
  38. PARP16 is a Druggable Regulator of Ribosome MARylation and Protein Homeostasis in Ovarian Cancer Cells.
  39. Bifunctional proximity-inducing strategies for targeted and programmable post-translational modifications.
  40. Disrupting E3 ubiquitin ligase protein-protein interactions in cancer: chemical modalities, mechanisms, and therapeutic opportunities.
  41. Vancomycin eliminates gut deoxycholic acid, restoring ER proteostasis in ILC2s and relieving colitis.
  42. Shifts in protein aggregate stability define proteostasis decline in the aging human brain.
  43. Mechanisms of human mitochondrial leaderless mRNA translation initiation.
  44. Chronic short sleep in early life accelerates cognitive decline via disrupted proteostasis.
  45. HSPA2 modulates antiviral immunity by inhibiting TBK1 activation.
  46. Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.
  47. Reciprocal regulation of TNF receptor 1-mediated signaling and inflammatory damages by MARCH2 and USP22.
  48. STUB1-VCP/p97 limits PINK1 overaccumulation to safeguard mitophagy and memory.
  49. Experimental assessment of AI-based interactome mapping.
  50. Excess cysteine drives conjugate formation and impairs proliferation of NRF2-activated cancer cells.
  51. Uncovering cancer dependencies in peptide-interacting protein pockets.
  52. The Roles of Alix and VPS4A in Autophagy and Endosomal Pathways and Their Relation to HBV Replication.
  53. A diffusion-based framework for designing molecules in flexible protein pockets.
  54. Global analysis of cancer cell responses to USP9X inhibition.
  55. Distinct autophagy impairment mechanisms of huntingtin aggregates with different polyQ lengths.
  1. ACS Chem Biol. 2026 Apr 09.
    The Contribution of Native Protein Complexes to Targeted Protein Degradation.
    Lorraine Glennie, Nicole M Curnutt, Gajanan Sathe, Brune Le Chatelier, Freya Goff, Jin-Feng Zhao, Tyrell Cartwright, Karen Dunbar, Nicola T Wood, Thomas J Macartney, Christina M Woo, Gopal P Sapkota.
      Targeted protein degradation (TPD) destroys proteins of interest (POIs) by hijacking the cellular proteolytic machinery. Most proteins in cells exist and function as part of multiprotein or macromolecular complexes, thereby allowing a single protein to control multiple biological processes. Therefore, when a small molecule degrader induces the proximity between an E3 ligase and the POI, the macromolecular context of the POI potentially influences the degradation outcomes of the POI and of the complex components. Here, we explore the degradation of the eight CK1α-SACK1 (formerly known as FAM83A-H) complexes initiated by molecular glue degraders primarily designed to target Ser/Thr kinase CK1α. We demonstrate that lenalidomide-derived degraders DEG-77 and SJ3149, which selectively target the CK1α isoform, codegrade multiple SACK1 proteins. We show that the degradation of SACK1 proteins by DEG-77 and SJ3149 requires CK1α, the CUL4ACRBN E3 ligase complex, and the proteasome. In cells derived from palmoplantar keratoderma patients harboring the CK1α-binding-deficient SACK1GR265P mutation, DEG-77 targets CK1α and mitotic SACK1D but not SACK1GR265P, highlighting the requirement for CK1α-SACK1 interaction to achieve codegradation. Our study underscores the importance of POI context in TPD and reinforces the potential for selectively targeting specific protein complexes for degradation.
    DOI:  https://doi.org/10.1021/acschembio.6c00098
  2. Commun Biol. 2026 Apr 09.
    Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS).
    Tanner M Tessier, Matthew E R Maitland, Maria Kutera, Joseph M Dybas, Jonathan St-Germain, Cheryl H Arrowsmith, Dalia Barsyte-Lovejoy, Wei Zhang, Brian Raught, Matthew D Weitzman.
      The ubiquitin system regulates virtually all cellular processes, yet the vast majority of ubiquitylation sites identified in the human proteome cannot be attributed to specific E3 ligases. This knowledge gap hampers our understanding of ubiquitin signaling and the development of therapeutics leveraging the ubiquitylation system. Here we present Proximity-based Identification of Ubiquitin Sites (PrIUS), a versatile mass spectrometry-based approach combining proximity-dependent biotinylation (BioID) with ubiquitin remnant (diGly) enrichment. PrIUS enables simultaneous identification of E3 ligase interactors and direct mapping of substrate ubiquitylation sites within a single workflow. Using the E3 ligase NEDD4L, we demonstrated that E3 interactomes are inherently rich for diGly-modified peptides that remain largely undetectable without PTM-specific enrichment. PrIUS identified hundreds of high-confidence ubiquitylation sites, successfully distinguished substrates from non-substrate interactors (including adapters and E2 enzymes), and identified non-degradative ubiquitylation events. We also demonstrate utility for characterizing targeted protein degrader mechanisms by precisely mapping PROTAC-induced ubiquitylation sites. PrIUS thus provides a useful approach for elucidating E3-substrate relationships and characterizing mechanisms for emerging degrader therapeutics at amino acid resolution.
    DOI:  https://doi.org/10.1038/s42003-026-09964-6
  3. Nat Commun. 2026 Apr 09.
    The integrated stress response suppresses PINK1-dependent mitophagy by preserving mitochondrial import efficiency.
    Mingchong Yang, Zengshuo Mo, Kelly Walsh, Wen Liu, Imane Nait Irahal, Damien Arnoult, Xiaoyan Guo.
      Mitophagy is crucial for maintaining mitochondrial health, but how its levels adjust to different stress conditions remains unclear. In this study, we investigated the role of the DELE1-HRI axis of the integrated stress response (ISR) in regulating mitophagy, a key mitochondrial quality control mechanism. Our findings show that the ISR suppresses PINK1-dependent mitophagy under many mitochondrial stress conditions by maintaining mitochondrial presequence protein import, independent of ATF4 activation. Mitochondrial presequence protein import efficiency is tightly linked to the rate of protein synthesis. Without the ISR, increased protein synthesis overwhelms the mitochondrial import machineries, reducing import efficiency. This impairment can be mitigated by pharmacological attenuation of protein synthesis, such as with mTOR or general translation inhibitors. Under severe depolarizing stress, mitochondrial import is heavily impaired even with an active ISR, leading to significant PINK1 accumulation. In contrast, mild mitochondrial stress allows more efficient protein import in the presence of the ISR, resulting in lower mitophagy. Without the ISR, mitochondrial protein import becomes significantly compromised, causing PINK1 accumulation to reach the threshold level necessary to trigger mitophagy. These findings reveal a link between ISR-regulated protein synthesis, mitochondrial protein import, and mitophagy, offering potential therapeutic targets for diseases associated with mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s41467-026-71630-6
  4. Comput Biol Med. 2026 Apr 03. pii: S0010-4825(26)00224-6. [Epub ahead of print]208 111660
    Beyond CRBN and VHL: Parkin driven lysine-based ternary complexes for selective β3-Tubulin degradation.
    Sonia Kumari, M Elizabeth Sobhia.
      Targeted protein degradation (TPD) is a rapidly emerging and potentially transformative therapeutic modality. However, PROTACs have primarily relied on only two E3 ligases, CRBN and VHL, leaving the vast majority of over 600 human ubiquitin ligases unexplored. In this study, we explored Parkin, an RBR-type E3 ligase, as a new recruiter for targeted protein degradation. Parkin is known to ubiquitinate several cytoskeletal and mitochondrial proteins in vivo. Since Parkin has not yet been structurally incorporated into PROTAC workflows, we examined all available human crystal structures to understand its mechanism of ubiquitin transfer and distinguish between its active and autoinhibited conformations. A full-length, catalytically competent Parkin model with all functional domains was built using AlphaFold 2. Using this active Parkin structure, we generated multiple ternary complex conformations with β3-tubulin employing PROTACs varying in linker length and composition. These ternary complexes were filtered through lysine proximity screening, dynamic conformational sampling, interface analysis, and tubulin-isoform-specific lysine accessibility. Selected ternary complexes were further subjected to comprehensive MD studies and analysed using BSA, PCA, Time-lagged independent component analysis (tICA), and Markov state modeling (MSM), revealing stable, degradation-competent conformations. This study paves the way for leveraging Parkin as a versatile E3 ligase in targeted protein degradation, offering new opportunities to modulate proteins implicated in critical cellular processes and complex pathophysiological conditions.
    Keywords:  Molecular dynamics; PCA; PROTACs; Parkin; Selectivity; β3-tubulin degradation
    DOI:  https://doi.org/10.1016/j.compbiomed.2026.111660
  5. Nat Chem Biol. 2026 Apr 09.
    The molecular glue CLEO4-88 inhibits the ACAA1 thiolase by induced binding to GID4.
    Chetan K Chana, Ines Ben Makhlouf, Jaeyoun Kim, April J Y Yu, Nathalie Moatti, Stephen Orlicky, Cassandra J Wong, Leon Baronijan, XiaoJing Tang, Daniel Mao, Brett Larsen, Laura McGary, Brendon Seale, Pavel Mader, Derek F Ceccarelli, Philip Barbulescu, Alberto Martin, Daniel Durocher, Laurence Pelletier, Anne-Claude Gingras, Frank Sicheri.
      Molecular glues promote protein-protein interactions by enhancing the surface complementarity between proteins. Those that recruit an E3 ubiquitin ligase to a target can elicit ubiquitination and subsequent destruction of the target protein-a mechanism that underpins the field of targeted protein degradation (TPD). Here we explored whether small-molecule binders to the CTLH E3 ligase subunit GID4 could act as molecular glues. We discovered that CLEO4-88 functions as a molecular glue (EC50 = 12.5 nM) to promote the interaction of GID4 with the peroxisomal thiolase ACAA1 in vitro and in cellulo. An atomic structure of the ternary complex revealed an allosteric mechanism whereby CLEO4-88 binds solely to GID4 and induces a conformational change conducive to binding ACAA1. Biochemical analysis demonstrated that, while ACAA1 cannot be recruited by GID4 to a CTLH holoenzyme for ubiquitination, ternary complex formation inhibits ACAA1 thiolase activity, thus demonstrating potential utility beyond TPD.
    DOI:  https://doi.org/10.1038/s41589-026-02183-4
  6. bioRxiv. 2026 Apr 02. pii: 2026.04.01.715898. [Epub ahead of print]
    FAM134B isoform 2/RETREG1-2 defines a calnexin-TOLLIP-coupled ER-phagy pathway that restricts Ebola virus glycoprotein and is antagonized by VP40 through macro-autophagy.
    Jing Zhang, Tao Wang, Jiaxin Wen, Jing Lan, Sunan Li, Yong-Hui Zheng.
      Selective autophagy of the endoplasmic reticulum (ER-phagy) is critical for ER proteostasis and host defense, yet how ER quality-control pathways interface with ER-phagy to restrict viral glycoproteins remains poorly defined. Previously, the 1st known ER-phagy receptor gene RETREG1 (RETR1)/FAM134B gene was reported to restrict Ebola virus (EBOV) replication in vivo by inhibiting the viral glycoprotein (GP) and viral protein 40 kDa (VP40) expression, but this mechanism remains unknown. Here, we identify the truncated RETR1/FAM134B isoform 2 (RETR1-2), but not its full-length protein RETR1, as an ER-phagy receptor that targets EBOV-GP for degradation. RETR1-2 broadly triggers GP degradation across ebolavirus species but not Marburg virus and inhibits EBOV replication. Mechanistically, RETR1-2 recognizes EBOV-GP via its luminal domain, undergoes GP-induced oligomerization, and directs GP-containing ER membranes to lysosomes through canonical macro-autophagy. Using unbiased mass spectrometry, we identified TOLLIP as the key cytoplasm adaptor for RETR1-2, which also requires cooperation with the ER chaperone calnexin for EBOV-GP degradation. Notably, the PI3P-binding C2 domain of TOLLIP mediates its interaction with RETR1-2, and the EBOV-GP degradation occurs independently of ubiquitination, revealing an unexpected role for TOLLIP in ER-phagy. Furthermore, EBOV-VP40 antagonizes this pathway by selectively targeting RETR1-2 for macroautophagic degradation independently of TOLLIP, thereby restoring GP expression and viral infectivity. Nevertheless, RETR1-2 reciprocally degrades VP40 via a similar mechanism. Together, these findings define a calnexin-TOLLIP-RETR1-2 axis that links ER quality control to ER-phagy-mediated antiviral restriction and uncover a reciprocal host-virus arms race centered on selective macro-autophagy.
    DOI:  https://doi.org/10.64898/2026.04.01.715898
  7. J Am Chem Soc. 2026 Apr 10.
    Harnessing FBXO31 with Terminal Amide-Functionalized Molecules for Targeted Protein Degradation.
    Chenlu Zhang, Xiaokang Jin, Chen Zhou, M Jamal Jenkins, Isabella A Riha, Xiaoyu Zhang.
      Targeted protein degradation (TPD) is a powerful strategy for controlling protein abundance. Here, we establish FBXO31 as a TPD-competent E3 ligase by exploiting its recognition of C-terminal amide-bearing degrons. Using an amidated Ala-Phe motif as a chemical recruiter, multiple small-molecule binders can be transformed into FBXO31-dependent degraders that induce the rapid and potent degradation of FKBP12, multiple kinases, and BET proteins BRD2, BRD3, and BRD4. Mechanistic studies confirm FBXO31-mediated ternary complex formation and identify key residues in FBXO31 required for recruiter engagement and target degradation.
    DOI:  https://doi.org/10.1021/jacs.6c02580
  8. Nat Chem Biol. 2026 Apr 06.
    Charged molecular glue discovery enabled by targeted degron display.
    Zhe Zhuang, Woong Sub Byun, Jakub Chrustowicz, Zuzanna Kozicka, Veronica L Li, Dinah M Abeja, Katherine A Donovan, Sara Sepic, Inchul You, Mikołaj Słabicki, Eric S Fischer, Stephen M Hinshaw, Benjamin L Ebert, Brenda A Schulman, Nathanael S Gray.
      Small molecules that induce protein interactions hold tremendous potential as new medicines, probes for molecular pathways and tools for agriculture. Explosive growth of targeted protein degradation drug development has spurred renewed interest in proximity-inducing molecules, especially molecular glue degraders (MGDs). These compounds catalyze the destruction of disease-causing proteins by reshaping protein surfaces and promoting cooperative binding between ubiquitylating enzymes and target proteins. MGD discovery for predefined targets is a major challenge in contemporary drug discovery. Here, we solve this important chemical challenge through 'chemocentric' MGD discovery of ZZ1, a BET-family protein degrader and a prodrug of a negatively charged glue. ZZ1 activation unmasks a sulfinic acid that binds the modular CTLH ubiquitin ligase complex through a basic pocket in its YPEL5 subunit. These findings demonstrate a previously unrecognized capacity of YPEL5 to recruit CTLH substrates and enable the discovery of MGDs for exceedingly common acidic and basic degrons.
    DOI:  https://doi.org/10.1038/s41589-026-02182-5
  9. bioRxiv. 2026 Mar 31. pii: 2026.03.30.714548. [Epub ahead of print]
    5-Azacytidine incorporation into mRNAs disrupts translation and induces ribosome collisions.
    Alexis B Roberson, James Marks, Ruby Pitts, Bavavarshini Tamilselvam, Brian Grieb, William P Tansey, Sezen Meydan.
      5-Azacytidine (5-AzaC) is a cytidine analog and is widely used to treat myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Although its therapeutic activity is primarily attributed to hypomethylation resulting from DNA incorporation, the majority of 5-AzaC is incorporated into RNA. However, the functional consequences of 5-AzaC incorporation into RNA have been unknown. Here, we show that 5-AzaC treatment of cells leads to inhibition of protein synthesis. Ribo-seq, Disome-seq, and RNA-seq in cells treated with 5-AzaC exhibit a time-dependent C-to-G transversion signature in mRNAs within 2 h of treatment. These transversion events are enriched within footprint positions corresponding to the A-site of monosomes or leading stalled ribosome in a disome complex. Consistently, ribosome and disome footprints are accumulated at sites with C-rich codons in the A-site, specifically with the codons containing a C in the second position. 5-AzaC activates the integrated stress response (ISR) and the ribotoxic stress response (RSR) in a GCN2- and ZAK-dependent manner, consistent with disome-mediated signaling. Furthermore, loss of the Ribosome Quality Control (RQC) factor, ZNF598, sensitizes cells to 5-AzaC. Collectively, our results support a model where 5-AzaC is rapidly incorporated into mRNAs, disrupts decoding, and triggers disome-mediated signaling pathways, which contribute to its cytotoxicity. These findings suggest that translation disruption represents an additional layer of 5-AzaC's mechanism of action, alongside its known DNA-mediated effects.
    DOI:  https://doi.org/10.64898/2026.03.30.714548
  10. Trends Cell Biol. 2026 Apr 07. pii: S0962-8924(26)00035-8. [Epub ahead of print]
    Endoplasmic reticulum architecture in liver metabolic regulation.
    Leonardo Luis Artico, Sophia Hakam, Güneş Parlakgül, Ana Paula Arruda.
      The endoplasmic reticulum (ER) is a central hub for essential cellular processes, including lipid and glucose metabolism, protein folding, calcium homeostasis, and detoxification. The ER exhibits a complex architecture, comprising multiple subdomains such as the nuclear envelope and the peripheral ER, which is further organized into sheets, tubules, three-way junctions, and contact sites. Both ER form and function are highly adaptive, with a robust capacity to respond to changes in environmental cues such as nutritional states. Here, we discuss remodeling of ER shape - as a fundamental mechanism of metabolic regulation, which enables the diversification and fine-tuning of metabolic function in physiology, while also representing a potential point of vulnerability during metabolic stress. We focus on the liver, a central organ in systemic energy homeostasis, and examine how hepatic ER morphology and its dynamic interorganelle interactions are reorganized in response to nutritional fluctuations and how this remodeling reflects on metabolic function.
    Keywords:  endoplasmic reticulum; hepatocytes; lipids; liver; metabolism; organelle contacts
    DOI:  https://doi.org/10.1016/j.tcb.2026.03.004
  11. bioRxiv. 2026 Apr 02. pii: 2026.04.01.715723. [Epub ahead of print]
    Genetic dissection of rapid proteolysis identifies TXNDC15 as a key factor of ERAD and lipid homeostasis.
    Yuyang Liu, Michelle Yinfei Yaochai, Shanshan Liu, Hanan Alwaseem, Kivanc Birsoy.
      Biological systems face a constantly changing environment and must swiftly respond to stimuli, yet how cells sense and adapt to environmental and physiological cues is incompletely understood. Short-lived proteins can be rapidly induced upon perturbation, enabling swift activation of adaptive cellular responses. Leveraging genome-wide data on protein-transcript correlation, we systematically searched for rapid proteolysis substrates whose abundance reflects the activity of the underlying proteolytic machinery. Here, focusing on the candidate substrate ABHD2, we employed CRISPR-based functional screens to dissect its degradation and identified TXNDC15 as an essential factor in MARCHF6-mediated ER-associated protein degradation (ERAD). Unexpectedly, TXNDC15 supports substrate exit and degradation from the ER via a catalysis-independent mechanism. Loss of TXNDC15 remodels the ER proteome and lipid homeostasis. Together, our work defines a missing component of ERAD and provides a generalizable strategy to decode post-translational regulatory circuits.
    DOI:  https://doi.org/10.64898/2026.04.01.715723
  12. Autophagy. 2026 Apr 09.
    Autophagic extracellular vesicles: a distinct secretory route linking autophagy to extracellular communication.
    Hongqi Wei, Yuxuan Fu.
      Macroautophagy/autophagy is classically defined as a degradative pathway that delivers cytoplasmic material to lysosomes. However, accumulating evidence indicates that autophagy can also support unconventional secretion. A recent study identifies a previously unrecognized subtype of small extracellular vesicles termed autophagic extracellular vesicles (AEVs). These vesicles originate from amphisomes formed by the fusion of autophagosomes with multivesicular bodies and are characterized by a size below 100 nm together with the presence of autophagic cargos, ESCRT-III components and RAB13. Importantly, biogenesis of AEVs is distinct from that of classical exosomes, which requires specific components of the ESCRT III complex and the GTPase RAB27A. The further finding that enterovirus can exploit AEVs to infect receptor-negative cells, thereby expanding viral tropism, suggests that secretory autophagy serves as a pivotal mechanism driving pathogen dissemination. This work provides the conceptual framework of extracellular vesicle heterogeneity and positions secretory autophagy as an important contributor to intercellular communication.
    Keywords:  Amphisomes; ESCRT-III; RAB13; autophagic extracellular vesicles (AEVs); enterovirus; secretory autophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2658229
  13. Elife. 2026 Apr 08. pii: RP110152. [Epub ahead of print]15
    A structural code for assembly specificity in GID/CTLH-type E3 ligases.
    Pia Maria van Gen Hassend, Hermann Schindelin.
      GID/CTLH-type E3 ligases assemble into conserved ring-shaped architectures built from repeating LisH-CTLH-CRA modules, yet the molecular rules that enforce their highly specific subunit arrangement have remained unknown. Here, we decode the structural 'assembly specificity code' that governs CRA-CRA pairing. Using crystal structures of multiple CTLH-CRA domains, including the RanBP9-muskelin heterodimer, integrated with quantitative binding analyses, we show that several interfaces operate with exceptionally high affinity, reaching the picomolar range, and that conserved sequence and geometric features enable each subunit to only select cognate partners. Strikingly, targeted perturbations of these features are sufficient to reprogram pairing preferences, enabling engineered subunits such as RanBP10 or Twa1 to adopt non-native interaction partners. These findings reveal the molecular logic that preserves the architecture of GID/CTLH-type E3 ligases and demonstrate that their assembly code is both decipherable and engineerable, providing a conceptual foundation for reconfiguring these ring-shaped E3 ligases.
    Keywords:  CTLH-CRA domain; GID/CTLH complex; Maea; RanBP9/10; Twa1; homo sapiens; molecular biophysics; mouse; muskelin; protein engineering; rat; structural biology; ubiquitin E3 ligase
    DOI:  https://doi.org/10.7554/eLife.110152
  14. Protein Sci. 2026 May;35(5): e70543
    Ligand-driven modulation of chaperone-cochaperone networks shapes proteostasis outcomes.
    Andrea Magni, Giorgio Bonollo, Gauthier Trèves, Francesco Frigerio, Fabrizio Cinquini, Silvia Pavoni, A Sofia F Oliveira, Adrian J Mulholland, Stefano A Serapian, Giorgio Colombo.
      Protein homeostasis depends on a delicate interplay between folding and degradation, orchestrated by molecular chaperones. Among them, Hsp90 is a central hub, regulating nearly 10% of the proteome through ATP-driven conformational cycles and selective interactions with cochaperones. The glucocorticoid receptor (GR) represents a paradigmatic Hsp90 client, whose maturation requires sequential remodeling steps involving multi-protein assemblies. While cryo-EM provided snapshots of these complexes, the dynamic determinants of GR activation and the antagonistic roles of cochaperones FKBP51 and FKBP52 remain poorly understood. Here, we integrate unbiased equilibrium atomistic molecular dynamics with nonequilibrium simulations of four different Hsp90-cochaperone-client assemblies that oversee distinct steps of GR maturation to elucidate how finely tuned dynamics and coordination/communication mechanisms determine functional emergence. Perturbations encoded by ligand insertion or removal reveal steroid binding as critical for both structural stability and inter-component communication. Ligand engagement not only stabilizes GR's active conformation but also feeds back to reshape chaperone and cochaperone dynamics, thereby modulating progression through the folding pathway. Steroid binding reinforces the interface in the Hsp90-p23-GR assembly, positioning cochaperone p23 as a molecular sensor for ligand occupancy. Comparative analyses of post-maturation complexes further uncover how immunophilins FKBP51 and FKBP52, despite structural similarity, elicit divergent allosteric effects on GR conformation and Hsp90-ATPase, determining opposing client fates. Our results establish ligand binding as an active modulator of chaperone-mediated folding, linking metabolic cues (ligand presence and levels) to client maturation. More broadly, they highlight cochaperones as dynamic checkpoints that selectively bias client outcomes, revealing generalizable principles of proteostasis regulation and opportunities for therapeutic intervention.
    Keywords:  Hsp90; allostery; chaperones; internal dynamics; ligand recognition; ligand regulation of function; molecular dynamics; protein folding
    DOI:  https://doi.org/10.1002/pro.70543
  15. bioRxiv. 2026 Apr 03. pii: 2026.04.01.715928. [Epub ahead of print]
    Cholesterol-dependent lysosomal docking of mTORC1 mediated by TM6SF1.
    Sen Hong, Liangjie Jia, Rong Wang, Nadia Elghobashi-Meinhardt, Helen H Hobbs, Xiaochun Li.
      The Transmembrane 6 Superfamily (TM6SF) comprises two members: TM6SF1, a ubiquitously expressed lysosomal membrane protein of unknown function, and TM6SF2, an endoplasmic reticulum protein required for lipidation of Apolipoprotein B-containing lipoproteins. Here, we identify TM6SF1 as a cholesterol-bound lysosomal docking factor for mTORC1. Loss of TM6SF1 disrupts spatial organization of the lysosomal mTORC1 machinery and results in constitutive activation of Transcription Factor EB (TFEB) without altering lysosomal pH or interfering with cholesterol trafficking. Using cryo-electron microscopy, we determined the structure of human TM6SF1 at 2.9-Å resolution, revealing a cholesterol-bound polytopic homodimer. Biochemical analyses show that TM6SF1 directly engages LAMTOR1 to stabilize the Ragulator complex, and that disruption of cholesterol binding to TM6SF1 impairs this interaction, leading to mTORC1 mislocalization and sustained TFEB activation. These findings establish cholesterol-bound TM6SF1 as a structural determinant of mTORC1 docking, uncovering a direct mechanistic link between lysosomal cholesterol and growth control.
    DOI:  https://doi.org/10.64898/2026.04.01.715928
  16. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2526136123
    mtHsp70 chaperone converts mitochondrial proteostasis stress into impaired protein import.
    Rupa Banerjee, Vanessa Trauschke, Nils Bertram, Ina Aretz, Christof Osman, Don C Lamb, Dejana Mokranjac.
      Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a variety of cellular processes. The conformational cycles of several Hsp70 chaperones, driven by ATP binding and hydrolysis, and regulated by cochaperones and substrate proteins, were analyzed in vitro in great detail. In contrast, little is known about the conformation Hsp70s adopt in their natural environments. In mitochondria, mtHsp70 is distributed between the TIM23 complex at the inner membrane, where it is involved in import of proteins from the cytosol, and a matrix-pool that is primarily involved in folding of proteins and prevention of their aggregation. Here, we used fluorescence microscopy to analyze the conformation of mtHsp70 at the single molecule level within physiologically active mitochondria. Our results revealed that the majority of mtHsp70 molecules are present in a substrate-bound state, suggesting that the mtHsp70 network functions at the limits of its capacity. To understand the biological significance of this finding, we modulated the levels of unfolded proteins in the matrix. Unfolded proteins reduced the association of mtHsp70 with the TIM23 complex and specifically impaired mtHsp70-dependent import of proteins. Our data show that unfolded proteins lead to a redistribution of mtHsp70 within mitochondria revealing how mitochondrial proteostasis stress is signaled to the cell-unfolded proteins remove mtHsp70 from the import sites, reducing the efficiency of protein import and initiating cellular programs to rescue or remove dysfunctional mitochondria. Thus, mtHsp70 acts as a mitochondrial quality control sensor that converts proteostasis stress into impaired protein import.
    Keywords:  Hsp70 chaperones; mitochondria; protein homeostasis; protein import; single molecule FRET
    DOI:  https://doi.org/10.1073/pnas.2526136123
  17. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2520128123
    Targeted degradation of c-Myc through the midnolin-proteasome pathway.
    Jingyuan Zhao, Huanhuan Wu, Han Yu, Chenyu Li, Yuling Mao, Hong Yuan, Shuai Li.
      Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy; however, most TPD technologies employ either the ubiquitin-proteasome system or the lysosomal degradation system. Here, we report the development of midnolin-based targeting chimeras (MbTACs), a ubiquitin-independent TPD that degrades target proteins. We designed and synthesized peptide-based MbTACs, which are multifunctional molecules containing c-Myc-recognition moieties and midnolin binding moieties. MbTACs promote the formation of a ternary complex consisting of the target protein, MbTACs, and midnolin via chemically induced proximity; subsequently, midnolin recruits the proteasome to degrade the target protein. Biological evaluations demonstrated that the MbTACs could degrade c-Myc effectively through the midnolin-proteasome pathway. The antitumor effects of MbTACs were further validated in vitro and in vivo. Collectively, our results provide a ubiquitin-independent TPD tool. MbTACs represent a conveniently developed modular peptide degradation chimera and have the potential to be widely used in disease therapy. We expect the MbTACs to provide a dimension for TPD design.
    Keywords:  MbTACs; c-Myc; midnolin; targeted protein degradation (TPD)
    DOI:  https://doi.org/10.1073/pnas.2520128123
  18. Adv Sci (Weinh). 2026 Apr 09. e75153
    Covalent Reprogramming of Kinase Binders to Modulate Protein Abundance.
    Chen Mozes, Xiaokang Jin, Miguel A Campos, Chen Zhou, Xiaoyu Zhang.
      Small molecules that modulate protein abundance through induced proximity expand the landscape beyond traditional inhibition. Here, we explore how introducing covalent or latent electrophilic groups into a multi-kinase binder scaffold reprograms protein abundance within the kinase family. Using the broad-spectrum kinase ligand TL13-87 as a template, we synthesize analogs bearing α-chloroacetamide, acrylamide, or terminal amine groups. Quantitative proteomics reveals that while most analogs have minimal global impact, MKI-AA, a multi-kinase inhibitor bearing an acrylamide warhead, uniquely stabilizes Aurora kinase A (AURKA). Mechanistic studies show that MKI-AA acts post-translationally to suppress AURKA ubiquitination and proteasomal degradation. Proteomic mapping of MKI-AA-induced AURKA interactors reveals changes in protein associations upon treatment, providing mechanistic insights into how MKI-AA influences AURKA stability. Intriguingly, adding a short linker to MKI-AA converts it from a stabilizer into a degrader, highlighting how subtle structural variations can invert functional outcomes.
    Keywords:  enzymes; kinases; protein degraders; protein stabilizers; proteomics
    DOI:  https://doi.org/10.1002/advs.75153
  19. bioRxiv. 2026 Mar 13. pii: 2026.03.12.711310. [Epub ahead of print]
    Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR.
    Avijit Mallick, Yunguang Du, Cole Haynes.
      Mitochondrial dysfunction and extracellular protein aggregation occur in neurodegenerative diseases such as Alzheimer's disease (AD). However, it remains unclear if these processes are functionally linked. Here, we identify a signaling pathway that is activated upon accumulation of aggregation-prone proteins in the extracellular space. We find that the transcription factor ATFS-1, which regulates the mitochondrial unfolded protein response, also regulates transcripts required for endosomal recycling, multiple plasma membrane-localized signaling receptors, and secreted proteins that bind aggregation-prone proteins in the extracellular space, including transthyretin and Aβ, and promote their degradation. Interestingly, Aβ(1-42) aggregation induces atfs-1 -dependent transcription by promoting degradation of the bZIP protein ZIP-3, which antagonizes ATFS-1. ZIP-3 accumulates in the cytosol when it is phosphorylated by kinases that function downstream of plasma membrane-localized signaling receptors, including the WNT and glutamate receptors. Upon ligand binding, the signaling receptors stimulate the cognate kinase, many of which we found phosphorylate ZIP-3, impeding ZIP-3 degradation, allowing it to antagonize atfs-1 -dependent transcription. However, accumulation of aggregation-prone proteins such as Aβ(1-42) causes endosomal swelling, which impairs endosomal recycling, instead diverting signaling receptors to lysosomes for degradation. In turn, the depletion of signaling receptors reduces the level of ZIP-3 phosphorylation, resulting in ZIP-3 degradation and activation of atfs-1 -dependent transcription, which promotes extracellular proteostasis. Our findings uncover an unexpected coupling between endocytic quality control and mitochondrial signaling, revealing a circuit that preserves extracellular proteostasis and promotes organismal resilience.
    DOI:  https://doi.org/10.64898/2026.03.12.711310
  20. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2536296123
    SARS-CoV-2 and MERS-CoV disrupt host protein synthesis via nsp1 with differential effects on the integrated stress response.
    Nicholas A Parenti, Renee Cusic, David M Renner, Nathaniel Jackson, Chengjin Ye, Li Hui Tan, Jessica J Pfannenstiel, Anthony R Fehr, Noam A Cohen, Luis Martinez-Sobrido, James M Burke, Susan R Weiss.
      Coronaviruses pose a serious threat to public health, driving the need for antiviral therapeutics and vaccines. Therefore, it is paramount to understand how this family of viruses evades cellular antiviral responses and establishes productive infection. The conserved coronavirus nonstructural protein 1 (nsp1) has been shown to inhibit host protein synthesis and, in some coronaviruses, promote host messenger RNA (mRNA) degradation while viral mRNAs are protected. We showed previously that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) induces activation of host integrated stress response (ISR) kinases protein kinase R (PKR) and PKR-like endoplasmic reticulum kinase (PERK), which promote phosphorylation of eukaryotic initiation factor 2 (eIF2α) and consequent inhibition of host protein synthesis. In contrast, eIF2α remains unphosphorylated during Middle East respiratory syndrome coronavirus (MERS-CoV) infection. To investigate the interactions of nsp1 and the ISR kinases, we utilized recombinant SARS-CoV-2 and MERS-CoV expressing nsp1 with mutations in each of two conserved domains. Upon infection with SARS-CoV-2 nsp1 mutants, translation was shut down in wildtype (WT) and PKR knockout (KO) cells but rescued in PERK KO cells, likely due to reduced p-eIF2α. In contrast, translation was rescued during infection with the analogous MERS-CoV nsp1 mutants even in WT cells. Moreover, SARS-CoV-2 WT suppressed expression of GADD34, a negative regulator of eIF2α phosphorylation, while SARS-CoV-2 nsp1 mutants induced GADD34. In contrast, MERS-CoV WT induced GADD34. Utilizing single-molecule fluorescence in situ hybridization, we found that SARS-CoV-2 and MERS-CoV nsp1 promote host mRNA degradation during WT, but not nsp1 mutant, infection. Thus, SARS-CoV-2 and MERS-CoV differ in interactions with the ISR and nsp1 control of host protein synthesis.
    Keywords:  coronavirus; integrated stress response; mRNA degradation; mRNA translation; nonstructural protein 1
    DOI:  https://doi.org/10.1073/pnas.2536296123
  21. Alzheimers Dement. 2026 Apr;22(4): e71352
    Integrative genomic and functional analyses reveal NINL as a modulator of tau aggregation.
    Samantha K Swift, Guangming Huang, J Nicholas Cochran, Ricardo D'Oliveira Albanus, Miguel A Minaya, Patricia A Castruita, Rui Zhang, Katherine J Miller, Emma Starr, Grant Galasso, Jacob A Marsh, Aimee W Kao, Oscar Harari, Jennifer S Yokoyama, Celeste M Karch.
       INTRODUCTION: Proteostasis dysfunction is a hallmark of frontotemporal dementia (FTD) and Alzheimer's disease (AD), yet the genetic and molecular pathways that disrupt protein homeostasis remain poorly understood.
    METHODS: We integrated human genetics, transcriptomics, and functional studies to identify proteostasis network components involved in tauopathy.
    RESULTS: We identified 18 proteostasis network genes harboring 75 rare, damaging variants enriched in FTD and/or AD. These genes, spanning multiple proteostasis pathways, were differentially expressed in microtubule associated protein tau (MAPT) mutant neurons and dysregulated in FTD and AD brains. NINL, which encodes Nlp, emerged as the only gene consistently upregulated across all datasets. NINL overexpression reduced tau seeding and enhanced lysosomal proteolytic activity, whereas two FTD-enriched NINL frame shift variants impaired Nlp expression and abolished these protective effects.
    DISCUSSION: We identified a set of proteostasis genes with genetic and transcriptional links to neurodegeneration and revealed NINL as a novel regulator of tau aggregation.
    Keywords:  Alzheimer's disease; NINL; autophagy lysosomal pathway; brain tissue; frontotemporal dementia; functional genomics; human genetics; proteostasis; stem cell models; tau; tau aggregation; tauopathy
    DOI:  https://doi.org/10.1002/alz.71352
  22. bioRxiv. 2026 Mar 10. pii: 2026.03.09.709851. [Epub ahead of print]
    Multivalent weak contacts shape chaperone-nascent protein interactions.
    Nandakumar Rajasekaran, Dmitri Toptygin, Ting-Wei Liao, Vincent J Hilser, Taekjip Ha, Christian M Kaiser.
      Molecular chaperones interact with non-native proteins, playing crucial roles in preventing misfolding and enable efficient folding in the cellular environment. Trigger factor is a bacterial chaperone that binds to ribosomes, interacting with nascent polypeptides emerging from the ribosome and guiding their early folding steps. In contrast to the central role of the chaperone in promoting folding of newly synthesized proteins, its dynamic interactions with nascent chains emerging from the ribosome remain poorly understood. Here, we use single-molecule fluorescence and optical tweezers approaches to directly observe and characterize trigger factor interactions with a ribosome-bound client protein at increasing chain lengths. We find that trigger factor binding to nascent proteins is best described by a combination of multiple weak, dynamic interactions that are established after the chaperone docks onto the ribosome and evolve during polypeptide elongation. Application of mechanical force perturbs trigger factor binding, supporting a multivalent interaction model. This binding mode may help to stabilize nascent proteins against misfolding while allowing them to dynamically sample conformational space in search of their native structures.
    DOI:  https://doi.org/10.64898/2026.03.09.709851
  23. bioRxiv. 2026 Apr 05. pii: 2026.04.01.715972. [Epub ahead of print]
    ATF4-dependent upregulation of Bruno 1 remodels P-bodies to selectively protect mRNAs during ER stress throughout Drosophila melanogaster oogenesis.
    Samantha N Milano, Livia V Bayer, Julie J Ko, Gwendolyn S Posner, Albina H Granovsky, Diana P Bratu.
      P-bodies are cytoplasmic membraneless organelles involved in mRNA storage, yet their role in cellular stress responses remains poorly understood. Here, we demonstrate that P-bodies are rapidly and selectively remodeled during the early response to endoplasmic reticulum (ER) stress in D. melanogaster oogenesis, positioning them as key early stress responders. Notably, this remodeling occurs within minutes of stress induction and precedes stress granule formation. This early remodeling is characterized by changes in P-body morphology and internal organization and promotes selective mRNA regulation. Specifically, ER stress leads to the recruitment and stabilization of maternal mRNAs and those encoding P-body components, while transcripts not associated with P-bodies are degraded. These observations indicate that P-body remodeling is not merely structural but functionally linked to the selective preservation of mRNA populations during stress. Mechanistically, we find that this process is driven by transcriptional upregulation of the RNA-binding protein, Bruno 1, downstream of ATF4-dependent stress signaling, thereby establishing a direct connection between the unfolded protein response and condensate regulation. Consistent with this model, loss of Bruno 1 abolishes, whereas its overexpression enhances P-body remodeling, demonstrating that stress-induced changes in RNA binding protein levels can actively reprogram condensate properties. Together, our findings reveal that P-bodies function as dynamic, stress-responsive hubs that integrate transcriptional signaling with post-transcriptional control, enabling the selective preservation of essential mRNAs during ER stress. More broadly, this work uncovers a previously unrecognized mechanism by which stress signaling pathways reorganize cytoplasmic architecture to shape mRNA fate.
    DOI:  https://doi.org/10.64898/2026.04.01.715972
  24. Nat Commun. 2026 Apr 10.
    Translation in proximity to forming autophagosomes during sustained autophagy.
    Yunping Xue, Kaela O'Connor, Karsten Nalbach, Alexandre Savard, Karyn E King, Ryan C Russell, Christian Behrends, Derrick Gibbings.
      Autophagy is an evolutionarily conserved catabolic process. In a process requiring a cascade of over 35 autophagy-related genes (Atg), a cupped phagophore membrane expands to surround cytoplasmic material, and seals itself to form an autophagosome, which finally fuses with lysosomes. Large numbers of autophagosomes form during stress responses, while simultaneously cells drastically reduce translation to conserve energy. Here, using proximity-labeling and Fluorescence in situ Hybridization we demonstrate that multiple mRNAs encoding proteins required for autophagy preferentially localize in proximity to forming autophagosomes. Polysome fractionation and proteomics of nascent proteins in proximity to forming autophagosomes provides evidence for the local translation of these mRNAs. Translation and the ribosome-binding protein RACK1 were required for the localization of these mRNAs to forming autophagosomes. Inhibition of translation or knockdown of RACK1 caused depletion of several proteins required for autophagy and a reduction in the number of autophagosomes. Local translation may enable a rapid, energy-efficient supply of proteins for autophagy to enable cells to massively induce autophagy while conserving energy during cell stress.
    DOI:  https://doi.org/10.1038/s41467-026-71551-4
  25. J Biol Chem. 2026 Apr 07. pii: S0021-9258(26)00298-X. [Epub ahead of print] 111428
    Where and how do mammalian cells shape autophagosomes?
    Claudia Puri, David C Rubinsztein.
      Autophagy is a fundamental cellular process responsible for degrading and recycling cytoplasmic components and regulates homeostasis, development, and survival under stress. Autophagy plays critical roles in diseases including neurodegeneration, cancers, and various infectious and inflammatory conditions. While the molecular machinery of autophagy has been well studied, increasing evidence highlights a complex interplay between autophagy and endocytosis. Traditionally, mammalian autophagosomes were believed to originate from compartments closely associated with the endoplasmic reticulum (ER), or the ER itself. However, more recent research has demonstrated that the recycling endosome serves as the main platform for autophagosome formation. The recruitment of WIPI2, an essential autophagy protein, to autophagosome initiation sites depends on its coincident detection of phosphatidylinositol 3-phosphate (PI(3)P) and RAB11A, a recycling endosome marker. This enables conjugation of LC3 (microtubule-associated protein light-chain 3) family members to the recycling endosome membranes to become nascent autophagosomes. These findings underscore the critical role of RAB11- compartment in autophagosome biogenesis. Contrary to the conventional model that has inferred that autophagosomes derive from spherical precursors with single apertures, structured illumination microscopy reveals these precursors are finger-like structures - much like a hand grasping an object. We will describe the experimental path that led to an understanding of how autophagosomes form from outgrowths of the recycling endosomes, then close after engulfing their contents. This step is a prerequisite for the final step of autophagosome formation, the release of autophagosomes from the recycling endosome membranes, a process that is perturbed by a major Alzheimer's disease gene.
    DOI:  https://doi.org/10.1016/j.jbc.2026.111428
  26. J Cell Sci. 2026 Apr 08. pii: jcs.264421. [Epub ahead of print]
    The molecular basis of tricalbin-mediated membrane contact site organization in cells.
    Lazar Ivanović, Anne-Laure Boinet, Andrea Picco, Eliane Zinn, Daniela Ross-Kaschitza, Marko Kaksonen, Wanda Kukulski.
      Membrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate contacts between endoplasmic reticulum (ER) and plasma membrane in yeast. Tricalbins are integral to the ER, have a cytosolic lipid binding domain and bind the plasma membrane through C2 domains. Here, we combine fluorescence recovery after photobleaching with correlative light and 3D electron microscopy to dissect how tricalbins control their localization, dynamic distribution and contact site organization. We find that heteromerization via lipid binding domains is a prerequisite for tricalbin accumulation at contact sites, membrane curvature sensing and restrained mobility in the ER. By altering tricalbin protein domains, we show that intermembrane distances and intrinsically disordered regions interdependently control distribution and dynamics of contact site tethers. Our study reveals principles of contact site architecture that are fine-tuned by tricalbin domain organization.
    Keywords:  Correlative light and electron microscopy; FRAP; Live imaging; Membrane contact sites; Tricalbins; Yeast
    DOI:  https://doi.org/10.1242/jcs.264421
  27. Acta Neuropathol. 2026 Apr 06. pii: 37. [Epub ahead of print]151(1):
    Alzheimer's disease risk protein SorLA regulates ER homeostasis and lipid metabolism in human microglia, with conserved effects in neurons.
    Imdadul Haq, Jason C Ngo, Nainika Roy, Emily Lee, Muniyat A Choudhury, Rajesh K Soni, Andrew F Teich, Richard P Mayeux, Philip L De Jager, Ye He, Xuebing Wu, David A Bennett, Marta Olah, Falak Sher.
      Microglial dysfunction is a hallmark of Alzheimer's disease (AD), yet the molecular mechanisms driving these impairments remain poorly defined. Genetic studies implicate several AD-associated genes in regulating microglial activity, including SORL1, which encodes the sorting receptor SorLA. Although SorLA is highly expressed in microglia, its functional role in cellular homeostasis has remained unclear. Here, we investigated SorLA function using human brain tissue, primary microglia from rapid autopsies, and CRISPR-engineered human iPSC-derived microglia and neurons. Integrated multi-omics analyses, including single-cell RNA sequencing, lipidomics, and proteomics, together with biochemical and functional assays, revealed that SorLA deficiency induces endoplasmic reticulum (ER) stress and interferon signaling, promotes lipid droplet accumulation, and impairs phagocytic and immune functions. Protein co-complex mapping and structural modeling identified ER-associated proteins co-enriched with SorLA, including SUN2, calnexin (CANX), and multiple COPI complex components (COPA, COPB1, COPG1, ARCN1), implicating SorLA in ER proteostasis and intracellular trafficking. Notably, SORL1 deletion in iPSC-derived neurons recapitulated key phenotypes observed in microglia, including lipid droplet accumulation and SorLA-SUN2 co-immunoprecipitation, indicating that this ER-associated pathway operates across distinct brain cell types. Together, these findings identify an ER-related role for SorLA that extends beyond its established function in endocytic trafficking. Loss of SorLA triggers maladaptive stress responses, perturbs lipid handling, and compromises cellular resilience, thereby contributing to AD-relevant cellular dysfunction.
    Keywords:   SORL1/SorLA; Alzheimer’s disease; Endoplasmic reticulum stress (ER); Lipid metabolism; Microglia
    DOI:  https://doi.org/10.1007/s00401-026-03002-9
  28. bioRxiv. 2026 Apr 02. pii: 2026.03.31.715740. [Epub ahead of print]
    ER discontinuities are common in C. elegans neurons, revealing a genetically tractable model for ER network maintenance.
    Kelsey N Mabry, Eric K F Donahue, Aaron D Orgel, Brennen Keuchel, Max G Kushner, Kristopher Burkewitz.
      The neuronal endoplasmic reticulum (ER) extends from the soma into axons and dendrites to coordinate protein trafficking, lipid metabolism, inter-organelle organization, and calcium homeostasis. Conserved genes involved in shaping the tubular ER are implicated in neurodevelopment and neurodegeneration, suggesting that ER structure and dynamics influence neuronal health and drive pathogenesis. However, the links between ER morphology and neuronal function and resilience remain incompletely understood. While models typically depict the neuronal ER as a fully continuous network, here we show that micron-scale ER discontinuities in neurites are unexpectedly common in young, unstressed C. elegans . These discontinuities occur in both axonal and dendritic compartments with a consistent frequency that varies between motor and mechanosensory neuron types. Using live imaging and photokinetic assays of endogenously tagged markers of the ER, we confirm that these gaps reflect true loss of ultrastructural continuity. Subpopulations of ER tubule tips are highly motile, and the majority of ER discontinuities are resolved in less than an hour. Suggesting the formation of discontinuities is linked to cellular damage, their frequency increases with both age and environmental stress. Finally, in agreement with prior observations across models, discontinuities are exacerbated by impairment of certain ER shaping factors involved in hereditary spastic paraplegia, such as reticulon. These findings reveal a model where ER discontinuities are not uncommon in healthy animals, and provide a tractable system in C. elegans to dissect the molecular mechanisms maintaining ER structural homeostasis in vivo.
    DOI:  https://doi.org/10.64898/2026.03.31.715740
  29. Vet Microbiol. 2026 Apr 06. pii: S0378-1135(26)00145-8. [Epub ahead of print]317 111013
    African swine fever virus MGF_110-8L promotes host cell autophagy and suppresses interferon signaling by activating the unfolded protein response.
    Yuan-Pan Hou, Jin-Ke Yang, Yue Wang, Tian Xia, Xin Wu.
      African swine fever virus (ASFV) infection induces cellular stress that activates the unfolded protein response (UPR), a key pathway for restoring endoplasmic reticulum (ER) homeostasis. However, the mechanisms by which ASFV modulates the UPR remain incompletely understood. Here, we identify the ASFV protein MGF_110-8L as a key regulator of the UPR, leading to the dissociation and activation of the UPR sensors PERK, IRE1α, and ATF6, which subsequently restore ER homeostasis. Moreover, MGF_110-8L triggers UPR-dependent autophagy, which in turn contributes to the suppression of type I interferon-mediated immune responses. Deletion of MGF_110-8L (ASFV-Δ8 L) markedly reduced the activation of both UPR and autophagy pathways and led to enhanced type I interferon responses. Together, our findings reveal a novel mechanism by which an ASFV protein activates the host UPR-autophagy axis to restore cellular homeostasis and modulate host innate immunity, highlighting MGF_110-8L as a potential target for therapeutic development.
    Keywords:  African swine fever virus (ASFV); Autophagy; BiP; MGF_110–8 L; Unfolded protein response (UPR)
    DOI:  https://doi.org/10.1016/j.vetmic.2026.111013
  30. bioRxiv. 2026 Mar 09. pii: 2026.03.07.710281. [Epub ahead of print]
    CDK/mTOR-dependent phosphorylation of UBE2H restrains its charging with ubiquitin and regulates CTLH-dependent degradation.
    Yingqian Chen, Valentina Rossio, Joao A Paulo, Menuka Karki, Sandhya Manohar, Noelle Ozimek, Laura Frizzi, Steven P Gygi, Randall W King.
      The C-terminal to LisH (CTLH) complex is a modular multi-subunit E3 ligase with diverse biological functions, yet how its overall ubiquitylation activity is tuned remains unclear. Here, we identify CDK- and mTOR-dependent phosphorylation of the cognate E2 enzyme UBE2H as a key regulator of CTLH E3 catalytic capacity. Phosphorylation of two N-terminal serine residues (S3/S5) reduces UBE2H charging with ubiquitin, thereby limiting the pool of active E2 available to CTLH. Mitotic CDK activity inactivates UBE2H during mitosis, whereas mTOR restrains UBE2H charging in interphase to couple CTLH-dependent ubiquitylation to nutrient status. Preventing this phosphorylation maintains UBE2H charging, enhances CTLH-mediated substrate degradation, promotes CTLH subunit turnover, and causes proliferation and mitotic defects. Using hyperactive UBE2H, we identify two additional CTLH substrates, the mitotic kinase NEK9 and Angio-associated migratory cell protein (AAMP) and define a DR-like C-degron recognized by the CTLH subunit MKLN1. These findings reveal how regulation of an E2 enzyme by cell cycle and nutrient signaling pathways dynamically shape CTLH activity.
    DOI:  https://doi.org/10.64898/2026.03.07.710281
  31. Cell Death Discov. 2026 Apr 08.
    Proteasome dysfunction underlies HERC2-linked neurodevelopmental disorder with Angelman-like clinical features.
    Joan Sala-Gaston, Laura Costa-Sastre, Manel Garcia-Diez, Tania López-Hernández, Juanma Ramírez, Nerea Osinalde, Jose Antonio Valer, Claudia Arnedo-Pac, Bernat Crosas, Emma L Baple, Andrew H Crosby, Ugo Mayor, Francesc Ventura, Jose Luis Rosa.
      Biallelic hypomorphic variants in the E3 ubiquitin ligase HERC2 cause a neurodevelopmental disorder clinically resembling Angelman syndrome, characterized by global developmental delay, intellectual disability, autism spectrum features, and movement abnormalities. Defining the target substrates of HERC2 is essential for understanding its biological role and the mechanisms underlying its pathological variants. To this end, we performed a quantitative proteomic analysis using biotinylated ubiquitin to identify HERC2 targets and assess their regulation in cells expressing HERC2 with or without ubiquitin‑ligase activity. This approach revealed extensive sets of subunits from major multimeric complexes, including the proteasome, the tRNA-biosynthesis machinery, microtubule‑associated assemblies, vesicle‑coat complexes, centrosomes, and the Ski and GATOR2 complexes, as substrates of HERC2-dependent ubiquitylation. Among these, the proteasome emerged as the most prominently affected complex. We identified up to eleven proteins required for assembly of the 19S regulatory particle whose ubiquitylation depends on HERC2. Mechanistically, we show that HERC2 recognizes unassembled subunits via chaperone-mediated interactions and targets them for proteasomal degradation. Loss of this mechanism in HERC2‑deficient cells alters proteasomal activity. It is noteworthy that fibroblasts derived from patients carrying the common pathogenic variant c.1781 C > T (p.Pro594Leu) exhibit impaired processing of 19S subunits and an aberrant increase in proteasome activity. Our findings establish a link between HERC2-related neurodevelopmental disorder and impaired proteasome activity, elucidate the molecular mechanisms through which HERC2 regulates proteostasis and how its disruption contributes to human pathology, and underscore potential therapeutic strategies for affected individuals.
    DOI:  https://doi.org/10.1038/s41420-026-03095-x
  32. Cell Rep. 2026 Apr 04. pii: S2211-1247(26)00281-0. [Epub ahead of print]45(4): 117203
    Systematic profiling of cytosolic membraneless organelles reveals enrichment of oncogenic mRNA upon oxidative stress.
    Savannah O'Connell, Helen E King, Peter Kjer-Hansen, Karina Pazaky, Gabriela Santos Rodriguez, Daisy Kavanagh, Helaine Graziele S Vieira, Javier Fernandez-Chamorro, Robert J Weatheritt.
      Cytosolic mRNA regulation during and after stress is driven by distinct membraneless organelles. However, their compositional and functional dynamics throughout the stress response remain unclear. We combine APEX2-mediated proximity labeling, RNA sequencing, and high-content imaging to map the human P-body and stress granule transcriptomes during oxidative stress and recovery. Our findings reveal that P-bodies undergo extensive compositional remodeling during stress and that these changes persist during stress recovery. P-body-associated mRNAs during stress exhibit increased AU-rich elements and oncogenic content relative to the cytosol. In contrast, stress granule-associated mRNAs closely resemble the cytosol. These results uncover critical differences between P-bodies and stress granules, shedding light on their functional specialization. Our study provides a valuable resource of cytosolic membraneless organelle-associated transcripts and suggests a specialized role for P-bodies in stress adaptation and recovery.
    Keywords:  APEX-sequencing; CP: cell biology; CP: molecular biology; P-bodies; bioinformatics; membraneless organelles; stress granules; stress response
    DOI:  https://doi.org/10.1016/j.celrep.2026.117203
  33. J Cell Biol. 2026 Jun 01. pii: e202511133. [Epub ahead of print]225(6):
    The SWR1 complex prevents the vacuolar delivery of ATG proteins through a noncanonical pathway.
    Siyu Fan, Huan Yang, Jianting Lei, Xinyue Gong, Yiyu Lin, Yuan Zhou, Yuhang Cui, Yuanyuan Ding, Mingzhu Fan, Shan Feng, Weijing Yao, Dong Fang, Kunrong Mei, Hongguang Xia, Cong Yi.
      Autophagy is a conserved catabolic process that relies on vacuoles or lysosomes. While autophagosome formation is well characterized, the mechanisms that prevent autophagy-related proteins form being enclosed by the autophagosome and degraded in the vacuole remain unclear in yeast. Here, we show that the SWR1 chromatin remodeling complex plays an essential, noncanonical role in this process. Genome-wide screening identified the SWR1 complex as a critical regulator that prevents the vacuolar delivery of multiple autophagy proteins. This process depends on the structural integrity and ATPase activity of the SWR1 complex. Mechanistically, the SWR1 subunit Rvb1 interacts directly with Atg21, and this interaction is important for SWR1 localization to the phagophore assembly site and efficient protein retrieval. Disruption of the Atg21-Rvb1 interaction results in the vacuolar accumulation of autophagy proteins. These findings uncover an unexpected link between a chromatin remodeling complex and the autophagy machinery, highlighting the Atg21-Rvb1 module as a key regulator of autophagy dynamics in yeast.
    DOI:  https://doi.org/10.1083/jcb.202511133
  34. Autophagy. 2026 Apr 10. 1-17
    Newcastle disease virus exploits Golgi stress and Golgiphagy to promote ferroptosis.
    Xianjin Kan, Mengqing Yang, Guanglei Xie, Yuncong Yin, Hui Jiang, Yanmei Yuan, Yingjie Sun, Chan Ding.
      Ferroptosis, characterized by iron-dependent lipid peroxidation, has emerged as a pivotal cell death pathway in various diseases, yet its regulation during viral infection remains elusive. Here, we reveal that Newcastle disease virus (NDV) exploits the Golgi apparatus as a central hub to orchestrate ferroptotic cell death in tumor cells. NDV infection provokes robust Golgi stress and Golgiphagy, leading to the selective degradation of ARF1 (ARF GTPase 1), a GA-resident regulator of redox homeostasis, which in turn triggers a cascade of reactive oxygen species accumulation, lipid peroxidation, and ferroptosis. Mechanistically, we show that this process is dependent on the activation of the Golgi stress response and macroautophagy/autophagy-lysosome pathway. Importantly, inhibition of Golgi stress by exogenous spermine not only alleviates NDV-induced ferroptosis, but also demonstrates antiviral and cytoprotective effects, underscoring the translational potential of targeting the Golgi stress axis. Our findings uncover a previously unappreciated axis of virus-host interaction centering on Golgi stress and ferroptosis and suggest that modulation of organelle-specific stress responses represents a promising therapeutic strategy in both antiviral and cancer contexts.Abbreviations: AMPK: AMP-activated protein kinase; ARF1: ARF GTPase 1; ARF4: ARF GTPase 4; ATG7: autophagy related 7; BFA: brefeldin A; CGAS: cyclic GMP-AMP synthase; CHX: cycloheximide; CQ: chloroquine; CREB3: cAMP responsive element binding protein 3; DFO: deferoxamine; ER: endoplasmic reticulum; Fe2+: ferrous ions, GA: Golgi apparatus; GOLGA2/GM130: golgin A2; GPX4: glutathione peroxidase 4; GSH: glutathione; GSR: Golgi stress response; HCMV: human cytomegalovirus; HSV-1: herpes simplex virus 1; Lip-1: Liproxstatin-1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MDA: malondialdehyde; mtDNA: mitochondrial DNA; MTOR: mechanistic target of rapamycin kinase; NDV: Newcastle disease virus; NCOA4: nuclear receptor coactivator 4; PUFA: polyunsaturated fatty acid; ROS: reactive oxygen species; Rot: rotenone; SLC7A11: solute carrier family 7 member 11; SERPINH1/HSP47: serpin family H member 1; TFE3: transcription factor binding to IGHM enhancer 3; WT: wild-type.
    Keywords:  ARF1; Golgi stress; Golgiphagy; Newcastle disease virus; ferroptosis; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2026.2653010
  35. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2527957123
    Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.
    Aakash Saha, Christopher L Tang, Diana Murray, Barry Honig.
      Many protein-protein interactions (PPIs) are mediated by the binding of short linear motifs (SLiMs) to peptide recognition domains (PRDs). Here, we describe PrePPI-SLiM, a proteome-scale computational pipeline that leverages data from the Eukaryotic Linear Motif (ELM) database to predict whether two proteins will form a peptide-mediated complex. The ELM database defines classes of protein-peptide interactions with SLiMs represented by sequence motifs and PRDs represented by Pfam domains. PrePPI-SLiM systematically evaluates all pairwise combinations of proteins within a proteome and identifies PRD-SLiM pairs that occur in the same ELM class. This evidence together with disorder prediction and sequence conservation of the motif are integrated in a naïve Bayes framework to assign a likelihood for complex formation. To obtain potential PDB templates for atomistic models of PrePPI-SLiM interactions, we associate individual PPI predictions with homologous PDB complexes involving the same PRD Pfam domain and SLIM, and obtain PDB templates for 92% of our high-confidence predictions. Moreover, studies with AF3Complex suggest that prior knowledge of the interacting PRD and SLiM, as provided here, is a critical starting point for creating a 3D model of the specific sequences of the PRD and SLiM query proteins. Finally, we demonstrate that clustering of the high-confidence PrePPI-SLiM interactome yields functionally coherent PPI networks that reveal mechanistic insights into cellular processes. The PrePPI webserver provides convenient access to high-confidence PrePPI-SLiM predictions, PDB templates for modeling, and functional networks.
    Keywords:  Pfam domain; interactome; protein recognition domain (PRD); protein-protein interactions (PPIs); short linear motifs (SLiMs)
    DOI:  https://doi.org/10.1073/pnas.2527957123
  36. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2605594123
    A C-degron regulates Chk1 kinase by allowing stability of inactive Chk1 and by making it short- lived upon activation.
    Jang-Hyun Oh, Ju-Yeon Hyun, Shun-Jia Chen, Alexander Varshavsky.
      The Arg/N-degron pathway of Saccharomyces cerevisiae is mediated by two interacting E3 ubiquitin ligases, Ubr1 and Ufd4. We show here that the mitotic checkpoint kinase Chk1 bears a C-degron that can be recognized by both Ubr1 and Ufd4. Ubr1 is an E3 that can target both N-degrons and C-degrons. Deleting 4 residues from the C terminus of full-length Chk11-527 abrogates the bulk of Ubr1/Ufd4 affinity for the resulting Chk11-523, inhibits its polyubiquitylation and degradation, and arrests cell growth. Toxicity of the 4-residue C-terminally (Ct)-deleted Chk11-523 was traced to its kinase activity, since the kinase-inactive [Formula: see text] was nontoxic. The L506R mutation is known to activate Chk1 kinase in a way that bypasses other Chk1 activation pathways. Both kinase-active and kinase-inactive Chk1 proteins that contained the L506R mutation ([Formula: see text] and [Formula: see text]) were short-lived in vivo, in contrast to wildtype Chk11-527. Furthermore, the catalytic N-terminal (Nt) domain of Chk1 physically interacted with its Ct-domain. These and other results strongly suggested the following mechanism of Chk1 regulation. Ct-residues of Chk11-527 are a part of its C-degron, targeted by Ubr1/Ufd4 E3s. But the Ct-domain of Chk11-527 (including its C-degron) can also bind to the catalytic Nt-domain. The resulting conformation of Chk11-527 is inactive as a kinase and relatively long-lived, since the catalytic Nt-domain sterically sequesters C-degron. An induced (e.g., through a regulatory phosphorylation) dissociation of Ct-domain from Nt-domain activates the catalytic Nt-domain and also exposes the C-degron of Chk1. Thus, activation of Chk1 kinase would make it, simultaneously, a short-lived protein.
    Keywords:  Chk1; Ubr1; Ufd4; degron
    DOI:  https://doi.org/10.1073/pnas.2605594123
  37. Cell Chem Biol. 2026 Apr 07. pii: S2451-9456(26)00105-4. [Epub ahead of print]
    Selective degradation of TBK1 uncovers mechanistic insights into blocking ccRCC progression.
    Chengheng Liao, Siying Lyu, Rebecca L Johnson, Tiantian Shang, Xiaoyu Wang, Nina Gildor, Shina Li, Noelle S Williams, Lindsey I James, Lianxin Hu, Qing Zhang.
      Clear cell renal cell carcinoma (ccRCC), the most common kidney cancer subtype, often features the inactivation of the von Hippel-Lindau (VHL) tumor suppressor, creating therapeutic vulnerabilities. Although HIF2α inhibitors have shown clinical promise, many VHL-deficient tumors remain resistant. -binding kinase 1 (TBK1) has emerged as a synthetic lethal target in this context. Here, we report UNC8209, an optimized cereblon(CRBN)-recruiting proteolysis-targeting chimera (PROTAC) that selectively and potently degrades TBK1. Compared with earlier TBK1 degraders, UNC8209 exhibits enhanced degradation efficiency and improved selectivity over off-target kinases, including IKKε. TBK1 degradation by UNC8209 suppresses proliferation in VHL-deficient ccRCC models and impairs tumor growth in vivo with minimal toxicity within a defined therapeutic window. In addition, the anti-proliferative effects of UNC8209 extend to multiple tumor types addicted to elevated TBK1 activity. Together, these findings establish UNC8209 as a selective chemical probe and support TBK1 degradation as a therapeutic strategy in TBK1-dependent cancers.
    Keywords:  PROTAC; TBK1; VHL; cancer therapeutics; ccRCC; cereblon; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.chembiol.2026.03.013
  38. bioRxiv. 2026 Apr 02. pii: 2026.04.01.715986. [Epub ahead of print]
    PARP16 is a Druggable Regulator of Ribosome MARylation and Protein Homeostasis in Ovarian Cancer Cells.
    Sridevi Challa, Morgan Dasovich, Jonathan C Abshier, Komal Pekhale, Lu Yang, Cristel V Camacho, W Lee Kraus.
      Cytosolic NAD□ synthesis supports ovarian cancer growth by enabling PARP16-dependent mono(ADP-ribosyl)ation (MARylation) of ribosomal proteins, thereby fine-tuning translation and maintaining protein homeostasis. While genetic depletion of PARP16 disrupts ribosome MARylation and impairs tumor cell growth, the therapeutic potential of pharmacologic PARP16 inhibition in this pathway remains unexplored. Here, we characterized the effects of DB008, a tool compound that functions as a selective inhibitor of PARP16, in ovarian cancer cells. Biochemical analyses demonstrated that PARP16 undergoes NAD□-dependent auto-MARylation and that NMNAT-2 supplies NAD□ to support this activity. DB008 potently inhibited PARP16 auto-MARylation in vitro. In ovarian cancer cells, DB008 engaged PARP16, reduced its MARylation, and decreased ribosome-associated MARylation. Consistent with PARP16 depletion, DB008 enhanced global protein synthesis, increased protein aggregation, and suppressed cell growth and anchorage-independent colony formation. CRISPR-mediated deletion of the PARP16 gene in ovarian cancer cells abolished the effects of DB008 on translation, protein aggregation, and proliferation, demonstrating on-target activity. Moreover, cells expressing a PARP16 mutant resistant to DB008 were unaffected by inhibitor treatment, further confirming that the cellular effects of DB008 require on-target inhibition. Finally, DB008 significantly inhibited tumor growth in OVCAR3 xenografts, with on-target engagement of PARP16 in the xenograft tumors. Collectively, these findings establish PARP16 as a druggable regulator of ribosome MARylation and protein homeostasis in ovarian cancer and provide pharmacologic proof-of-concept that disrupting ribosomal MARylation impairs tumor growth.
    DOI:  https://doi.org/10.64898/2026.04.01.715986
  39. Adv Drug Deliv Rev. 2026 Apr 07. pii: S0169-409X(26)00108-0. [Epub ahead of print] 115874
    Bifunctional proximity-inducing strategies for targeted and programmable post-translational modifications.
    Sadiya Tanga, Pallabi Das, Tuhin Baran Samoi, Arpita Hota, Arkadeep Karmakar, Basudeb Maji.
      The development of proteolysis-targeting chimeras (PROTACs) from their initial idea to their rise as a more comprehensive platform for proximity-driven regulation of protein function is traced in this review. We describe the design principles and mechanistic underpinnings of classical PROTAC architectures, and we talk about how these systems have evolved to include lysosomal, autophagic, and organelle-directed clearance pathways in addition to ubiquitin-proteasome-mediated degradation. Acknowledging the constraints imposed by existing degrader technologies-specifically, limited E3 ligase diversity and context-dependent efficacy- we highlight recent developments intended to address these issues. These include investigating novel E3 ligase repertoires, combining computational and AI-guided design approaches, and creating degradation platforms that can target biomolecules that were previously unreachable, like membrane proteins and RNA-associated complexes. The review also examines the development of biomolecular chimeras (BI-TACs), which extend targeted degradation across various cellular compartments, and next-generation proximity-based modalities, such as LYTACs, AUTACs, and RIBOTACs. Crucially, we address the concurrent emergence of functional modulation techniques mediated by engineered post-translational modifications and proximity-induced stabilization. Induced proximity can be used for protein rewiring and functional control in addition to degradation, as demonstrated by platforms like DUBTACs, PHICS, PHORCs, DEPTACs, ACETACs, RIPTACs, and TCIPs. Lastly, With the emergence of bacterial PROTACs (BacPROTACs), which show the versatility of proximity pharmacology across biological domains, we examine how targeted protein degradation has spread beyond mammalian systems. All of these developments point to a shift away from degradation-centric methods and toward a more comprehensive proximity pharmacology framework that can reshape protein fate, function, and therapeutic tractability.
    Keywords:  AI-driven PROTAC; Bifunctional molecules; Deubiquitination; Induced proximity targeted protein degradation; PROTAC; Post-translational modification; Proximity-induced PTM; Ubiquitin-proteasome system
    DOI:  https://doi.org/10.1016/j.addr.2026.115874
  40. Biochem Pharmacol. 2026 Apr 06. pii: S0006-2952(26)00284-4. [Epub ahead of print]250(Pt 1): 117951
    Disrupting E3 ubiquitin ligase protein-protein interactions in cancer: chemical modalities, mechanisms, and therapeutic opportunities.
    Emadeldin M Kamel, Sally Mostafa Khadrawy, Mohamed A M Ali, Noha A Ahmed, Nour Y S Yassin, Saleh Alkhedhairi, Faris F Aba Alkhayl, Al Mokhtar Lamsabhi.
      The ubiquitin-proteasome system (UPS) governs protein turnover through an enzymatic cascade (E1, E2 and E3) that attaches ubiquitin to substrates, marking them for proteasomal degradation. E3 ubiquitin ligases confer substrate specificity, placing them at the center of many disease pathways and making them attractive drug targets in cancer and beyond. Inhibiting E3-associated protein-protein interactions-for example, blocking an E3 from binding its substrate-can stabilize critical proteins, including tumor suppressors, and offers a route to "drugging the undruggable" by targeting interfaces rather than catalytic sites. However, E3 PPIs are challenging because their interfaces are often large and relatively flat, with few deep pockets, and conventional drug-like libraries may yield few hits. Despite this, recent progress includes clinical-stage small-molecule inhibitors of specific E3-substrate interactions (notably MDM2-p53), fragment-based discovery of novel E3 ligands, and the emergence of "molecular glue" degraders that recruit neosubstrates to E3s. This review surveys E3 biology (classes and mechanisms), maps key interfaces amenable to disruption, and summarizes screening and structure-guided design strategies for PPI inhibitors. We also emphasize common pitfalls (including assay artifacts) and the need for orthogonal biophysical and cellular target-engagement validation. We highlight case studies targeting E3-substrate pairs such as MDM2-p53, VHL-HIF1α and Keap1-Nrf2, and discuss efforts aimed at E2-E3 interfaces, E3 dimerization/oligomerization, and pathogen-driven hijacking of E3 machinery. Finally, we address translational considerations-including selectivity, pharmacology, biomarkers and safety-and outline outlooks for assessing and expanding the druggability of E3 interfaces. Collectively, these advances show how previously intractable E3 ligase interactions are becoming tractable targets for therapeutic modulation.
    Keywords:  E3 ubiquitin ligases; Protein–protein interactions; Small-molecule inhibitors; Targeted cancer therapy; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1016/j.bcp.2026.117951
  41. JCI Insight. 2026 Apr 08. pii: e197470. [Epub ahead of print]11(7):
    Vancomycin eliminates gut deoxycholic acid, restoring ER proteostasis in ILC2s and relieving colitis.
    Qiuheng Tian, Han Liu, Xiang Gu, Jing Shen, Xi Yuan, Mengqi Zheng, Yunjiao Zhai, Yatai Chen, Penghu Han, Yangchun Ma, Wei Xin, Hongyue Ma, Yu Li, Sihan Wang, Lei Guo, Detian Yuan, Yanbo Yu, Shiyang Li.
      Ulcerative colitis (UC) remission is marked by gut microbiota restructuring, but how microbial metabolites influence immune-mediated tissue repair is unclear. Here, we demonstrate that oral vancomycin alleviates colitis symptoms in murine models, mirroring its clinical efficacy in inducing remission in patients with UC. Mechanistically, vancomycin's therapeutic effect is achieved by reducing deoxycholic acid (DCA). We reveal that DCA impairs mucosal repair driven by group 2 innate lymphoid cells (ILC2s) by inducing ER stress through direct binding to thioredoxin-related transmembrane protein 2 (TMX2). This interaction disrupts TMX2's role in protein folding, triggering unresolved unfolded protein response via hyperactivation of PERK/eIF2α signaling, which suppresses the production of pro-healing molecules by ILC2s. Pharmacological inhibition of PERK phosphorylation restores ILC2 function and accelerates colitis resolution. Our work uncovers a pathogenic microbiota/DCA/ILC2 axis that obstructs mucosal healing and positions vancomycin as a targeted strategy to eliminate DCA, thereby promoting UC remission.
    Keywords:  Gastroenterology; Immunology; Inflammatory bowel disease; Innate immunity; Protein misfolding
    DOI:  https://doi.org/10.1172/jci.insight.197470
  42. bioRxiv. 2026 Mar 30. pii: 2026.03.27.714902. [Epub ahead of print]
    Shifts in protein aggregate stability define proteostasis decline in the aging human brain.
    Edward Anderton, Jordan B Burton, Christina D King, Anna C Foulger, Dipa Bhaumik, Daria Timonina, Zachary Mayeri, Manish Chamoli, Julie K Andersen, Birgit Schilling, Gordon J Lithgow.
      Loss of proteostasis and the accumulation of insoluble protein aggregates are features of aging across model organisms and occur in all major age-related neurodegenerative diseases; yet how aggregation proceeds during normal human brain aging remains unknown. Here, using detergent-fractionation proteomics, we show that brain aging does not involve uniform aggregate accumulation; rather, the insoluble proteome undergoes asymmetric remodeling beginning in midlife, with maximum-stability aggregates declining sharply by old age and intermediate-stability aggregates accumulating progressively before accelerating after age 80. Intermediate-stability aggregates are prone to liquid-liquid phase separation and are enriched among Alzheimer's disease plaque and tangle constituents. Proteasome and cytosolic chaperone capacity predict individual differences in aggregate burden as strongly as chronological age, offering human-level evidence in support of therapies targeting these pathways. These findings establish aggregate remodeling as a feature of normal brain aging and position intermediate-stability aggregate accumulation as a molecular event on the path to neurodegenerative disease.
    DOI:  https://doi.org/10.64898/2026.03.27.714902
  43. Nat Commun. 2026 Apr 04.
    Mechanisms of human mitochondrial leaderless mRNA translation initiation.
    Shuangjie Shen, Yinghua Xu, Daniel L Kober, Jinfan Wang.
      Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ribosomes initiate translation remain poorly understood, particularly because mitochondrial mRNAs generally lack the 5' untranslated regions that guide translation initiation in bacterial and cytoplasmic systems. Using real-time single-molecule fluorescence measurements, biochemical assays, and cryo-EM analysis, we show that human mitochondrial translation initiation occurs through two parallel pathways. In one pathway, leaderless mRNA first loads onto the 28S small subunit, followed by recruitment of the 39S large subunit to form the 55S initiation complex. In the second pathway, a preassembled 55S monosome directly loads onto leaderless mRNA. Both pathways require recruitment of mtIF2 and fMet-tRNAMet before mRNA binding. However, the monosome-loading pathway tolerates non-formylated Met-tRNAMet and is suppressed by mtIF3. Together, these findings define the heterogeneous pathways of human mitochondrial translation initiation on leaderless mRNAs.
    DOI:  https://doi.org/10.1038/s41467-026-71535-4
  44. bioRxiv. 2026 Mar 30. pii: 2026.03.26.714554. [Epub ahead of print]
    Chronic short sleep in early life accelerates cognitive decline via disrupted proteostasis.
    Robert Komlo, Kamalini Sengupta, Ewa Strus, Nirinjini Naidoo.
      Chronic short sleep (CSS) is an emerging public health issue that frequently begins in adolescence and is common among healthcare professionals and others engaged in shift work. Epidemiological studies associate CSS and sleep disruption with metabolic disorders, cardiovascular disease, cognitive decline, and heightened Alzheimer's disease risk. Building on our prior findings that sleep deprivation perturbs proteostasis and activates endoplasmic reticulum (ER) stress pathways, we investigated the long-term consequences of CSS in young adult wild-type mice over the course of one year. Mice exposed to CSS displayed impaired cognition in hippocampal dependent tasks by 28 weeks of age, indicating emerging memory deficits. At the molecular level, CSS disrupted hippocampal proteostasis-particularly protein folding processes-and triggered ER stress and activation of the unfolded protein response (UPR). Importantly, disrupted proteostasis preceded the behavioral decline, with diminution of the key chaperone and UPR regulator BiP occurring at 20-22 weeks of age. CSS also increased markers of cellular stress and neuroinflammation while reducing the expression of proteins associated with memory function. Age also seemed to be a cellular stressor, causing a longitudinal increase in UPR, ISR, and neuroinflammation markers. Together, these results indicate that both chronic short sleep and age compromise proteostasis and promote neuroinflammation, contributing to progressive cognitive dysfunction.
    DOI:  https://doi.org/10.64898/2026.03.26.714554
  45. Cell Rep. 2026 Apr 03. pii: S2211-1247(26)00300-1. [Epub ahead of print]45(4): 117222
    HSPA2 modulates antiviral immunity by inhibiting TBK1 activation.
    Chenglong Li, Sirui Li, Yihua Zhang, Manman Li, Xiaowu Hong, Dapeng Yan.
      The production of type I interferons (IFN-I) induced by viruses is critical for the host to resist viral infection. While emerging studies have implicated heat shock protein A2 (HSPA2) in various diseases, its specific role in antiviral immunity remains elusive. Here, using Hspa2-deficient mice and cellular models, we demonstrate that HSPA2 negatively regulates IFN-I production by targeting TANK-binding kinase 1 (TBK1). Mechanistically, HSPA2 binds to TBK1 and competes with the HECT and RLD domains containing E3 ubiquitin protein ligase 5 (HERC5) for TBK1 binding, thereby abrogating HERC5-dependent K63-linked ubiquitination of TBK1 at lysine 608 (K608), which disrupts the formation of TBK1-associated complexes and suppresses the subsequent dimerization and nuclear translocation of interferon regulatory factor 3 (IRF3), ultimately blocking IFN-I production. This study provides insights into the regulatory network governing innate immune homeostasis and identifies HSPA2 as a potential target for antiviral therapy.
    Keywords:  CP: microbiology; CP: molecular biology; HERC5; HSPA2; TBK1; antiviral innate immunity; type I interferon; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2026.117222
  46. Cell Death Dis. 2026 Apr 10.
    Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.
    Lili Li, Taekyu Ha, Jing-Xin Feng, Michael DiPrima, Dunrui Wang, Parthav Jailwala, Thomas Meyer, Justin Lack, Hidetaka Ohnuki, Giovanna Tosato.
      Despite therapeutic advances, metastatic colorectal cancer remains a therapeutic challenge as most patients will develop resistance to therapy and will progress. Epigenetic mechanisms are implicated in enabling the acquisition of new phenotypic traits as drivers of colorectal cancer progression, rather than new genetic mutations or expansion of existing mutant clones. It remains unclear, however, which epigenetic mechanisms sustain colorectal cancer plasticity, how they are induced, and how this plasticity generates subclonal diversity that drives the aggressive cancer phenotype. Here we identify the integrated stress response as an inducer of colorectal cancer cell plasticity, subclonal diversity, and tumor progression in the stress-surviving cells. Combined analysis of chromatin accessibility and gene transcription profiling in these cells found the emergence of an endogenous interferon response as a key phenotypic trait associated with subclonal colorectal cancer cell diversity, treatment resistance and heightened aggressiveness. We unveil a new experimental approach to successfully prevent treatment-resistant colorectal cancer progression by combining epigenetic modulators with a cereblon-dependent degrader of GSPT1, a regulator of protein synthesis, to normalize chromatin accessibility and induce colorectal cancer cell death. Collectively, our study identifies the integrated stress response as an inducer of epigenetic and transcriptional plasticity in colorectal cancer cells and highlights a successful approach to therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41419-026-08720-2
  47. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2531389123
    Reciprocal regulation of TNF receptor 1-mediated signaling and inflammatory damages by MARCH2 and USP22.
    Hui-Fang Li, Rui Liu, Peng Ren, Hong-Bing Shu, Shu Li.
      The tumor necrosis factor (TNF) receptor 1 (TNF-R1) plays critical roles in inflammatory response and autoimmune diseases. The underlying mechanisms on posttranslational regulation of TNF-R1 and its functional significance remain enigmatic. In this study, we identified the deubiquitinase USP22 as a positive regulator of TNF-R1. USP22 is minimally associated with TNF-R1, which is markedly increased following TNF stimulation. USP22 deconjugates K27-linked polyubiquitination of TNF-R1 at K340, which reverses its proteasomal degradation. USP22 deficiency reduces TNF-triggered signaling and transcriptional induction of proinflammatory genes in human cell lines and primary mouse immune cells. Conversely, the membrane-associated E3 ligase MARCH2 is constitutively associated with TNF-R1, resulting in K27-linked polyubiquitination of TNF-R1 at K340 and its proteasomal degradation. MARCH2 deficiency promotes TNF-triggered signaling in various cell types. In mice, USP22 deficiency alleviates imiquimod (IMQ)-induced psoriasis-like dermatitis with reduced inflammatory cell infiltration and splenomegaly. In an acute liver injury model, USP22 deficiency reduces TNF/D-gal-induced inflammatory cytokine expression, liver damage, and inflammatory death, whereas MARCH2 deficiency increases TNF/D-gal-induced inflammatory cytokine expression and exacerbates pathological features of acute liver injury. These findings demonstrate that MARCH2 and USP22 reciprocally regulate K27-linked polyubiquitination and stability of TNF-R1, revealing regulatory mechanisms on TNF-R1-mediated inflammatory response.
    Keywords:  TNF-R1; USP22; inflammatory response; polyubiquitination; psoriasis
    DOI:  https://doi.org/10.1073/pnas.2531389123
  48. Autophagy. 2026 Apr 11.
    STUB1-VCP/p97 limits PINK1 overaccumulation to safeguard mitophagy and memory.
    Jin-Yi Lin, Ze-Bo Huang, Evandro F Fang, Guang Lu.
      PINK1 serves as the central regulator of PINK1-PRKN-mediated mitophagy, and its precise regulation is critical for efficient mitochondrial clearance. Although the cleavage of PINK1 and its subsequent degradation via the N-end rule pathway under basal conditions are well understood, how full-length PINK1 stability is regulated following mitochondrial damage has remained elusive. In our recent study, we identified the STUB1-VCP/p97 axis as a mechanism that fine-tunes full-length PINK1 levels during mitophagy. We demonstrate that STUB1 functions as an E3 ubiquitin ligase that catalyzes K48-linked polyubiquitination of full-length PINK1, which is subsequently recognized and extracted by VCP/p97 for proteasomal degradation. Disruption of this axis results in excessive accumulation of full-length PINK1, accelerated turnover of PRKN, and impaired mitophagy. Moreover, we find that this regulatory mechanism is compromised in the brains of patients with Alzheimer disease (AD), and its disruption leads to neuronal mitophagy defects and impaired associated learning capability in C. elegans. These findings demonstrate that the STUB1-VCP/p97 complex fine-tunes PINK1 levels to ensure efficient mitophagy and preserve mitochondrial homeostasis.Abbreviations: AD, Alzheimer disease; CALCOCO2/NDP52, calcium binding and coiled-coil domain 2; MPP, mitochondrial processing peptidase; MQC, mitochondrial quality control; OMM, outer mitochondrial membrane; OPTN, optineurin; PARL, presenilin associated rhomboid like; PINK1, PTEN induced kinase 1; PRKN, parkin RBR E3 ubiquitin protein ligase; SILAC, stable isotope labeling by amino acids in cell culture; STUB1, STIP1 homology and U-box containing protein 1; TPR, tetratricopeptide repeat; VCP/p97, valosin containing protein; WIPI2, WD repeat domain, phosphoinositide interacting 2.
    Keywords:  Alzheimer disease; PINK1; PRKN; STUB1; VCP/p97; memory; mitochondrial homeostasis; mitophagy; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/15548627.2026.2658848
  49. Nat Commun. 2026 Apr 04.
    Experimental assessment of AI-based interactome mapping.
    Luke Lambourne, Anupama Yadav, Yang Wang, Alice Desbuleux, Dae-Kyum Kim, Florent Laval, Kerstin Spirohn-Fitzgerald, Tiziana Cafarelli, Carles Pons, István A Kovács, Noor Jailkhani, Sadie Schlabach, David De Ridder, Katja Luck, Vladimir V Botchkarev, Olivia Debnath, Wenting Bian, Yun Shen, Zhipeng Yang, Miles W Mee, Mohamed Helmy, Yves Jacob, Irma Lemmens, Thomas Rolland, Gregory G McClain, Atina G Coté, Marinella Gebbia, Nishka Kishore, Jennifer J Knapp, Joseph C Mellor, Gonen Memisoglu, Jüri Reimand, Jan Tavernier, Michael E Cusick, Quan Zhong, Patrick Aloy, Tong Hao, Benoit Charloteaux, Frederick P Roth, Javier De Las Rivas, Pascal Falter-Braun, David E Hill, Michael A Calderwood, Jean-Claude Twizere, Marc Vidal.
      Genotype-phenotype relationships are mediated through intricate networks of physical and functional interactions among macromolecules. Knowledge of the interactome is vital to understand and model genetics and cellular biology. Recent advances in accurately predicting tertiary protein structures using artificial intelligence (AI) approaches such as AlphaFold1 have revived the vision that the protein-protein interactome might be fully predictable through computational modeling of quaternary structures. Here we present a comprehensive experimental framework to systematically assess the impact of AI-driven interactome predictions for yeast2 and human3. We find that the quality of high-confidence predictions is on par with established experimental approaches. However, in proteome-wide screening, the tested AI approaches underperform in the discovery of strictly novel protein-protein interactions (PPIs) compared to experimental reference interactome maps. In particular, the yeast interactome map described here identifies >40-fold more novel PPIs than its AI counterpart. Strikingly, AlphaFold provides structural models for a substantial number of experimentally identified PPIs missed by the virtual screens. Our results suggest that, at this stage, the main contribution of AI predictions is to provide quaternary structure models for experimentally identified PPIs.
    DOI:  https://doi.org/10.1038/s41467-026-70942-x
  50. Nat Metab. 2026 Apr 07.
    Excess cysteine drives conjugate formation and impairs proliferation of NRF2-activated cancer cells.
    Jennifer A Brain, Anna-Lena B G Vigil, Kristian Davidsen, Ayaha Itokawa, Abby C Jurasin, Hannah J Kerbyson, Maximilian Kobiesa, Madeleine L Hart, Sang Jun Yoon, Peter Bellotti, Juan Pablo Maianti, Gina M DeNicola, Lucas B Sullivan.
      Cancer cells with constitutive NRF2 activation take up excess cystine beyond the cysteine demands of conventional pathways, implying unknown metabolic fates. Here, we develop an unbiased approach for the identification of cysteine metabolic fates and find that both known and previously uncharacterized cysteine-derived metabolites accumulate in NRF2-activated cancer cells. We identify many of these unknown metabolites as conjugates formed between cysteine and endogenous sugar metabolites, which can also be generated in vitro. We confirm the presence of these cysteine-derived conjugates in murine lung cancer models and primary human lung cancer samples, and their enrichment in NRF2-activated tumours in each context. Mechanistically, NRF2 promotes cystine uptake by driving SLC7A11 expression, which increases intracellular cysteine levels to promote these cysteine fates in a panel of cancer cell lines. Finally, we show that NRF2 activation creates a sensitivity to high environmental cystine, which impairs cell proliferation through excess free cysteine, and can be mitigated by sequestration into cysteine-derived conjugates. Overall, these findings reveal a cancer-associated metabolic vulnerability to excess cysteine stress, and reveal unrecognized routes of cysteine metabolism.
    DOI:  https://doi.org/10.1038/s42255-026-01499-8
  51. bioRxiv. 2026 Mar 15. pii: 2026.03.13.711608. [Epub ahead of print]
    Uncovering cancer dependencies in peptide-interacting protein pockets.
    Mihkel Örd, Liz Kogan, Devin Bradburn, Michelle Leiser, Mardo Kõivomägi, Norman E Davey, Pau Creixell.
      Cancer cells often become dependent on specific molecular functions. As many proteins perform multiple functions mediated by different pockets and interfaces, we hypothesized that we could identify distinct cancer dependencies and therapeutic vulnerabilities by disrupting peptide-binding pockets. To test this hypothesis, we screened a proteome-wide library of 7152 genetically encoded peptides across nine cancer cell lines. We identify common and selective dependencies on peptide-binding pockets and find that gene knockout and peptide-mediated inhibition of pockets often drive divergent phenotypes. For the common-essential gene HCF1, we identify a therapeutic window by using inhibitory peptides with varying affinity. Moreover, peptides targeting TLE1-4 reveal a dependency hidden in genetic screens by homolog redundancy. We also uncover that peptides inhibiting cyclin D drive specific suppression of leukemia cell proliferation and demonstrate that these peptides improve the potency of CDK4/6 inhibitors. Overall, our screening platform facilitates data-driven prioritization of molecular pockets for subsequent therapeutic translation.
    DOI:  https://doi.org/10.64898/2026.03.13.711608
  52. FASEB J. 2026 Apr 15. 40(7): e71771
    The Roles of Alix and VPS4A in Autophagy and Endosomal Pathways and Their Relation to HBV Replication.
    Jia Li, Thekla Kemper, Shuping Tong, Xueyue Wang, Yong Lin, Mengji Lu.
      Autophagic and endosomal pathways coordinately contribute to hepatitis B virus (HBV) production, with the endosomal sorting complex required for transport (ESCRT) components ALG-2-interacting protein X (Alix) and the vacuolar protein sorting 4A (VPS4A) playing important but mechanistically elusive roles. This study investigates the roles of Alix and VPS4A in HBV biogenesis within the context of endosomal trafficking and autophagy. Using gene silencing and overexpression of wild-type (WT) or dominant-negative (DN) mutants of Alix and VPS4A in HBV replication cell models, we found that Alix silencing increased intracellular HBV DNA and HBV surface antigen (HBsAg), extracellular HBsAg, and virions, while decreasing secreted naked capsids. It promoted HBsAg secretion along the early endosomes but reduced its transport to late endosomes and autophagosomes. Furthermore, Alix silencing impaired autophagosome formation by activating the AKT/MTOR pathway. In contrast, VPS4A silencing had minimal effects, whereas DN VPS4A significantly blocked HBV secretion by disrupting endosomal trafficking, promoting autophagosome formation and lysosome activity, ultimately leading to HBV degradation. Our findings demonstrate that the endosomal pathway is critical for HBV secretion when lysosomal activity is suppressed. Conversely, increased lysosomal function drives HBV degradation through the autophagosome-lysosome pathway.
    Keywords:  Alix; HBV; VPS4A; autophagosome; degradation; endosomal trafficking
    DOI:  https://doi.org/10.1096/fj.202504742R
  53. Sci Adv. 2026 Apr 10. 12(15): eaeb7045
    A diffusion-based framework for designing molecules in flexible protein pockets.
    Jian Wang, Dong Yan Zhang, Shreshty Budakoti, Nikolay V Dokholyan.
      Designing molecules for flexible protein pockets poses a substantial challenge in structure-based drug discovery, as proteins often undergo conformational changes upon ligand binding. While deep learning-based methods have shown promise in molecular generation, they typically treat protein pockets as rigid structures, limiting their ability to capture the dynamic nature of protein-ligand interactions. Here, we present YuelDesign, a diffusion-based framework that jointly models the pocket structures and ligand conformations of protein-ligand complexes. YuelDesign uses E3former to maintain rotational and translational equivariance. The framework incorporates dual diffusion processes, an elucidated diffusion model (EDM) for coordinates and a discrete denoising diffusion probabilistic model (D3PM) for ligand atom types, enabling iterative refinement of both geometry and chemical identity. Our results demonstrate that YuelDesign generates molecules with favorable drug-likeness, low synthetic complexity, diverse chemical functional groups, and docking energies comparable to native ligands. YuelDesign presents a versatile framework for designing drugs in flexible protein pockets, with promising implications for drug discovery applications.
    DOI:  https://doi.org/10.1126/sciadv.aeb7045
  54. EMBO J. 2026 Apr 07.
    Global analysis of cancer cell responses to USP9X inhibition.
    Philipp Schenk, Shane M Devine, Simon A Cobbold, Niall D Geoghegan, Elizabeth L Kyran, Ching-Seng Ang, Jack A Alexandrovics, Dale J Calleja, Dylan H Multari, Vineet Vaibhav, Bernadine G C Lu, Theresa A Klemm, Laura F Dagley, Kym N Lowes, Nicholas A Williamson, Pieter J A Eichhorn, Ashley P Ng, Rebecca Feltham, David Komander.
      The ubiquitin-specific protease (USP) USP9X is a human deubiquitinase (DUB) with a large number of described targets and cellular roles. In cancer, USP9X is found as an oncogene or as a tumour suppressor depending on context, and its utility as a target for cancer therapy remains unclear. We here describe WEHI-092, a piperazine-based USP9X-specific small-molecule inhibitor, which binds to a unique region in the USP9X Fingers-subdomain, distinct from known DUB-inhibitor binding sites. Using proteomics and ubiquitinomics, we show that USP9X targets distinct substrates compared to USP7, yet the substrate profile of USP9X varies significantly across cancer cell lines. We reveal a core set of 17 proteins commonly regulated by USP9X in most cell lines, which we consider as proximal biomarkers for USP9X inhibition. Consistent with proteomics, we show in unrelated cell lines that WEHI-092 treatment arrests the cell cycle in metaphase without inducing cell death. This explains growth suppression in long-term clonogenic assays in most cancer cell lines, and positions USP9X inhibitors as a new class of selective mitotic poisons.
    Keywords:  Cancer; DUB Inhibitor; Substrate Identification; USP9X; Ubiquitinomics
    DOI:  https://doi.org/10.1038/s44318-026-00742-y
  55. Cell Chem Biol. 2026 Apr 06. pii: S2451-9456(26)00102-9. [Epub ahead of print]
    Distinct autophagy impairment mechanisms of huntingtin aggregates with different polyQ lengths.
    Heejung Kim, Hae Nim Lee, Suhyun Kim, Seung Jae Hyeon, Hyunmin Jo, Kyung-Soo Inn, Hoon Ryu, Jihye Seong.
      Huntington's disease (HD) is characterized by the aggregation of mutant huntingtin (mHTT) containing elongated polyglutamine (polyQ) tracts. mHTT aggregates that fail to be cleared by autophagy cause neurotoxicity. While the polyQ length in patients with HD ranges from 40 to over 90 repeats, how these varying polyQ lengths affect autophagy impairment remains unclear. Using polyQ aggregation sensors based on bimolecular fluorescence complementation (BiFC), we uncovered distinct autophagy impairment mechanisms: PolyQ103 aggregates evade recognition by autophagy receptor SQSTM1/p62, whereas polyQ43 condensates are recognized by SQSTM1/p62, but their bulky association prevents complete autophagosome formation. Interestingly, overexpression of optineurin (Optn), another autophagy receptor, preferentially binds to polyQ103 aggregates but not polyQ43 condensates, improving cell survival. K63-ubiquitination on polyQ103 aggregates serves as a critical determinant for Optn recruitment via its UBAN domain. These findings reveal polyQ length-dependent pathological mechanisms underlying autophagy impairment of mHTT aggregates, suggesting potential therapeutic strategies for patients with longer polyQ sequences.
    Keywords:  BiFC; Huntington’s disease; SQSTM1/p62; autophagy; optineurin; polyQ lengths
    DOI:  https://doi.org/10.1016/j.chembiol.2026.03.010
This page is being maintained by Thomas Krichel. It was last updated on 2026‒04‒12 at 1:29.