bims-proteo Biomed News
on Proteostasis
Issue of 2026–02–08
sixty papers selected by
Eric Chevet, INSERM
  1. Structural basis for pseudokinase-mediated regulation of GCN2 in the integrated stress response.
  2. The ER membrane protein complex acts as a chaperone to promote the biogenesis of multi-bundle membrane proteins.
  3. Proteostasis of organelles in aging and disease.
  4. Spatial organization of ER-derived protein aggregates in the nucleus requires the Hsp70-family member BiP.
  5. Functional integrity of the SEL1L-HRD1 complex is critical for endoplasmic reticulum-associated degradation and organismal viability.
  6. Cullin-3 adaptor SHKBP1 inhibits SQSTM1/p62 oligomerization and Keap1 sequestration.
  7. Ribosome-associated quality control of aberrant protein production during amino acid limitation.
  8. A near-complete map of human cytosolic degrons and their relevance for disease.
  9. Molecular chaperones and proteostasis regulation during cytosolic translation.
  10. Emerging Biologic Modalities for Targeted Protein Degradation.
  11. ER remodelling is a feature of ageing and depends on ER-phagy.
  12. Machine learning, docking, or physics for structure prediction of ligand-induced ternary complexes.
  13. Decreased tRNA abundance contributes to decreased translation elongation rate in a prolonged mitosis.
  14. Inosine misincorporation into mRNA triggers the integrated stress response and activates an innate immune gene expression signature.
  15. Discovery of SKP2-Recruiting PROTACs for Target Protein Degradation.
  16. Protein C-terminal variations impact proteostasis.
  17. Single-molecule dynamics of the TRiC chaperonin system in vivo.
  18. Proteome-wide C-degron activity profiling connects conditional regulation of the CTLH E3 ligase complex to ribosome biogenesis.
  19. Re‑thinking translation quality control in bacteria: from trans‑translation to collided‑disome surveillance.
  20. Protein disulfide isomerases in amyotrophic lateral sclerosis: Endoplasmic reticulum proteostasis and neuromuscular function.
  21. The endoplasmic reticulum displays high polarity with low protein aggregation in human cells.
  22. HRD1 negatively regulates autolysosome formation by inhibiting liquid-liquid phase separation of SNAP29.
  23. Organelles harbour pH gradients.
  24. Embracing diversity: PTMs, the chaperone code, and the emergence of new chaperone entities.
  25. Proximity proteomics reveals OTUD6B regulation of stress granule dynamics through coalescence with VCP/p97.
  26. Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion.
  27. Bi-allelic loss-of-function variants in JKAMP cause a neurodevelopmental syndrome associated with dysregulation of GPR37 trafficking.
  28. Biomolecular Condensates Dictate the Folding Landscape of Proteins.
  29. Development of PolyHis-Targeting PROTAC Degraders.
  30. Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins.
  31. Benchmarking Deep Learning for PROTAC Ternary Complex Prediction.
  32. Increasing Proteasome Activity to Alter XBP1 Signaling of the UPR Pathway.
  33. A multivalent adaptor mechanism drives the nuclear import of proteasomes.
  34. Linear ubiquitination of the NMDA receptor GluN2A subunit facilitates the GluN2B-to-GluN2A switch and synaptic maturation.
  35. Photosensitizer proximity labeling captures the lipid and protein interactomes.
  36. PtdIns(3,5)P2 is an endogenous ligand of STING in innate immune signalling.
  37. Endothelial Cell Secretome Alterations Induced by Inflammatory Stress.
  38. Activated ATF6α is a hepatic tumour driver restricting immunosurveillance.
  39. 5' UTR length regulates alternative N-terminal protein isoform production in health and disease.
  40. The anticancer drug mitoxantrone triggers the formation of ribosome-enriched stress granules independently of the classical translational control pathways.
  41. TGFB-inducible VASN (vasorin) promotes lysosomal acidification.
  42. Activating GCN2 and subsequently the Unfolded Protein Response with the small oral molecule NXP800 delays tumor growth in osteosarcoma.
  43. The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD.
  44. Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling.
  45. Cancer cachexia in STK11/LKB1-mutated non-small cell lung cancer is dependent on tumor-secreted GDF15.
  46. eRNAs Modulate mRNA Stability and Translation Efficiency to Bridge Transcriptional and Post-transcriptional Gene Regulation.
  47. Transcriptional responses to proteotoxic stressors are profoundly diverse and tissue-specific.
  48. Cellular quiescence uncouples the proteome from the transcriptome in neural stem cells.
  49. Starvation-independent alarmone production inhibits translation through GTP depletion.
  50. An interpretable molecular framework for predicting cancer driver missense mutations.
  51. Reliable repurposing of the antibody interactome inside the cell.
  52. Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.
  53. Intersections between proteostasis and immunity: insights from Caenorhabditis elegans.
  54. UFMylation deficiency in hepatocytes activates the KEAP1-NRF2 pathway and contributes to hepatocarcinogenesis.
  55. Structure-Guided Synthetic Peptide Targeting Nucleolus and Neural Progenitor Protein Nuclear Import Impairs Ribosome Biogenesis and Cancer Cell Proliferation.
  56. Mannose metabolic pathway senses glucose supply and regulates cell fate decisions.
  57. Divergent roles of Hsp70 chaperones in orthoflavivirus protein secretion and virion formation.
  58. PRKN activation for mitophagy requires an NME3-regulated phosphatidic acid signal that separates mitochondria from endoplasmic reticulum tethering.
  59. A pharmacological modality to sequester homomeric proteins.
  60. N6-methyladenosine (m6A) modification of TXNIP in 3'UTR instigates abdominal aorta aneurysm in mice.
  1. Proc Natl Acad Sci U S A. 2026 Feb 03. 123(5): e2526598123
    Structural basis for pseudokinase-mediated regulation of GCN2 in the integrated stress response.
    Yixin Liu, Jagannath Misra, Debarshi Ryan Bhowmik, Brady O'Boyle, Kirk A Staschke, Natarajan Kannan, Ronald C Wek, Natalia Jura.
      The general control nonderepressible 2 (GCN2) is a conserved stress-responsive protein that plays a critical role in restoring cellular homeostasis in the integrated stress response (ISR). In response to amino acid starvation or ribosome stalling and collisions, GCN2 phosphorylates the translation initiation factor eIF2α, conferring translational control to alleviate stress. GCN2 is a multidomain protein, containing a tandem kinase domain (KD) and a catalytically inactive pseudokinase domain (ψKD). Stress-induced activation of the kinase domain requires allosteric regulation and dimerization mediated by its regulatory domains. While the pseudokinase domain is essential for GCN2 function in yeast, its mechanistic role remains unclear and underexplored in other organisms. Here, we present the first crystal structure of the human GCN2 ψKD, revealing its distinct structural features. The structure visualizes an insertion N-terminal to helix αC unique to the GCN2 ψKD that interacts with the pseudoactivation loop, stabilizing an inactive conformation. Further structural analysis shows that the ψKD forms a dimer in the crystal lattice via a network of hydrophobic and electrostatic interactions spanning both the N- and C-lobes. Mutations that disrupt the dimer interface reduced downstream ATF4 expression that is important for stress adaptation, underscoring the functional significance of the GCN2 ψKD dimer in regulating GCN2 activity. Complementary AI-guided structure predictions indicate that the dimeric GCN2 ψKD architecture is conserved across evolution. These results support the role of ψKD dimerization as a regulatory feature in GCN2-mediated ISR signaling.
    Keywords:  ATF4 translation; GCN2; dimerization; integrated stress response; pseudokinase
    DOI:  https://doi.org/10.1073/pnas.2526598123
  2. bioRxiv. 2026 Jan 15. pii: 2026.01.14.699575. [Epub ahead of print]
    The ER membrane protein complex acts as a chaperone to promote the biogenesis of multi-bundle membrane proteins.
    Marinda Stanton, Bharti Singal, Mahamaya Biswal, Megha Agarwal, Caroline Elizabeth Scheuing, Gerardo Dasaev Vargas, Alex Gao, Casey A Gifford, Tino Pleiner.
      Nearly half of the ∼5,000 human membrane proteins need to assemble into stoichiometric complexes as part of their biogenesis at the endoplasmic reticulum (ER) membrane. How ER resident biogenesis factors coordinate membrane insertion, folding and assembly is not well understood. Here, we demonstrate that the ER membrane protein complex (EMC) insertase additionally acts as a chaperone to facilitate the assembly of heterotrimeric voltage-gated calcium channels (Ca v ). Using function-separating mutations and inhibitory nanobodies we show that nascent Ca v channels are degraded prematurely when EMC's chaperone function is selectively perturbed. Blocking EMC's chaperone function strongly impaired Ca v -dependent cardiomyocyte contraction. EMC engagement of the pore-forming Ca v α-subunit occurred co-translationally and required Ca v α's first transmembrane domain bundle to protrude from the nascent ribosome•Sec61•multipass translocon complex. Our findings establish a chaperone function for the EMC and reveal that biogenesis of multi-bundle membrane proteins requires a highly orchestrated, co-translational interplay between ER biogenesis factors.
    DOI:  https://doi.org/10.64898/2026.01.14.699575
  3. FEBS J. 2026 Feb 04.
    Proteostasis of organelles in aging and disease.
    Yara Nabawi, Cansu Doğan, Dunja Petrović, Gülce Perçin, Seda Koyuncu, David Vilchez.
      To maintain proteome integrity within distinct subcellular compartments, cells rely on tightly regulated proteostasis mechanisms, including protein synthesis, folding, trafficking, and degradation. Disruption of these processes leads to the accumulation of damaged proteins and structural changes that progressively compromise organelle function, contributing to aging and age-associated disorders, such as neurodegeneration, cancer, and metabolic dysfunction. Here, we discuss recent insights into how proteostasis influences the integrity and function of specific organelles, including the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes, as well as membraneless organelles, such as stress granules, processing bodies, the nucleolus, and nuclear speckles. We further discuss how dysfunction in these systems contributes to different hallmarks of aging and disease progression, highlighting potential therapeutic strategies aimed at maintaining organelle homeostasis to promote healthy aging.
    Keywords:  aging; cellular stress responses; membraneless organelles; membrane‐bound organelles; neurodegenerative diseases; organelle dysfunction; protein aggregation; proteostasis; stress granules
    DOI:  https://doi.org/10.1111/febs.70439
  4. Biochem Biophys Res Commun. 2026 Feb 04. pii: S0006-291X(26)00170-1. [Epub ahead of print]805 153406
    Spatial organization of ER-derived protein aggregates in the nucleus requires the Hsp70-family member BiP.
    Shoukang Du, Yuhan Wang, Ting Gang Chew.
      Cells maintain proteostasis by sequestering misfolded proteins into deposition sites. Aggregation-prone endoplasmic reticulum (ER) proteins form membrane-bound nuclear compartments that are cleared during cell division, yet the mechanisms underlying their spatial organization remain unclear. Here, using transcriptomic and proteomic analyses, we identified the ER-localized Hsp70 chaperone BiP as a key player. Genetic depletion or chemical inhibition of BiP prevented nuclear aggregate formation, while manipulating BiP regulators perturbed the aggregate formation. BiP-driven aggregation precedes the inner nuclear membrane synthesis that encapsulated the aggregates. Under proteostatic stress, nuclear aggregates localized adjacent to ER-derived aggregates. Our findings demonstrate that BiP is essential for organizing ER-derived aggregates in the nucleus, which further regulate nuclear proteostasis through spatial interactions with nuclear aggregates.
    Keywords:  BiP; Endoplasmic reticulum; Nucleus; Protein aggregates; Proteostasis
    DOI:  https://doi.org/10.1016/j.bbrc.2026.153406
  5. Proc Natl Acad Sci U S A. 2026 Feb 10. 123(6): e2517927123
    Functional integrity of the SEL1L-HRD1 complex is critical for endoplasmic reticulum-associated degradation and organismal viability.
    Xiawei Zhang, Liangguang Leo Lin, Linxiu Pan, Xiaoqiong Wei, Huilun Helen Wang, Zexin Jason Li, Ling Qi.
      The SEL1L-HRD1 complex is the most conserved branch of endoplasmic reticulum-associated degradation (ERAD), yet whether SEL1L is strictly required for HRD1 function in mammals has remained unclear. Here, we show, using complementary in vivo and in vitro approaches, that direct SEL1L-HRD1 binding is essential for ERAD activity and neonatal survival. Three knock-in mouse models targeting this interface reveal a clear genotype-phenotype relationship: the L709P variant, which abolishes SEL1L-HRD1 association, causes complete neonatal lethality; the partially disruptive S658P variant results in partial lethality; and the P699T mutation preserves the interaction and yields normal viability. Mechanistically, our data show that the SEL1L-HRD1 interface is essential for ERAD complex formation and activity, enabling both substrate handoff and E2 enzyme recruitment, and that the L709P mutation effectively uncouples these core steps of the mammalian ERAD pathway. These findings establish SEL1L-HRD1 coupling as a core requirement for mammalian ERAD function and early postnatal viability.
    Keywords:  ER quality control; ERAD; SEL1L variants; SEL1L–HRD1 interaction; neonatal lethality
    DOI:  https://doi.org/10.1073/pnas.2517927123
  6. J Cell Biol. 2026 Apr 06. pii: e202501207. [Epub ahead of print]225(4):
    Cullin-3 adaptor SHKBP1 inhibits SQSTM1/p62 oligomerization and Keap1 sequestration.
    Lin Luan, Xiaofu Cao, Zijun Xia, Shivanshi Vaid, Manuel D Leonetti, Jeremy M Baskin.
      SQSTM1/p62 is a master regulator of the autophagic and ubiquitination pathways of protein degradation and the antioxidant response. p62 functions in these pathways via reversible assembly and sequestration of additional factors into cytoplasmic phase-separated structures termed p62 bodies. The physiological roles of p62 in these various pathways depend on numerous mechanisms for regulating p62 body formation and dynamics that are incompletely understood. Here, we identify a new mechanism for regulation of p62 oligomerization and incorporation into p62 bodies by SHKBP1, a cullin-3 E3 ubiquitin ligase adaptor, that is independent of its potential functions in ubiquitination. We map an SHKBP1-p62 protein-protein interaction outside of p62 bodies that limits p62 assembly into p62 bodies and affects the antioxidant response involving sequestration of Keap1 and nuclear translocation of Nrf2. These studies provide a non-ubiquitination-based mechanism for an E3 ligase adaptor in regulating p62 body formation and cellular responses to oxidative stress.
    DOI:  https://doi.org/10.1083/jcb.202501207
  7. bioRxiv. 2026 Jan 15. pii: 2026.01.14.699605. [Epub ahead of print]
    Ribosome-associated quality control of aberrant protein production during amino acid limitation.
    Alicia M Darnell, Christopher Chidley, Victoria Paradise, Danica S Cui, Kristian Davidsen, Sarah C Lincoln, Keene L Abbott, Ryan Elbashir, Campbell P Vander Heiden, Peter K Sorger, Lucas B Sullivan, Joseph H Davis, Matthew G Vander Heiden.
      Amino acids can become limiting for protein synthesis through depletion of charged tRNAs, leading to ribosome stalling and disruption of translation elongation at specific codons. To assess whether this is a mechanism by which amino acid availability can directly influence gene expression, we designed a reporter library to measure translation disruption across all sense codons in the context of amino acid limitations. We found that arginine limitation consistently impairs translation at the arginine codon AGA, resulting in synthesis of proteins from endogenous transcripts. In contrast, GCN2 pathway activation suppresses translation disruption following depletion of most other amino acids. Genome-wide screens revealed that the ribosome quality control trigger (RQC-T) and RQC pathways, which resolve ribosome collisions on defective mRNAs, catalyze ribosome splitting and premature fall-off in response to arginine depletion. Additionally, the E3 ubiquitin ligase RNF14, recently shown to clear ribosome A-site obstructions, promotes translation disruption through both ribosome fall-off and frameshifting during arginine limitation. Together, these data show that the RQC machinery is engaged by tRNA-limited ribosomes and identify a new role for RNF14 as a regulator of translation upon arginine limitation.
    DOI:  https://doi.org/10.64898/2026.01.14.699605
  8. Sci Adv. 2026 Feb 06. 12(6): eadz3483
    A near-complete map of human cytosolic degrons and their relevance for disease.
    Vasileios Voutsinos, Kristoffer E Johansson, Fia B Larsen, Martin Grønbæk-Thygesen, Nicolas Jonsson, Emma Holm-Olesen, Giulio Tesei, Amelie Stein, Douglas M Fowler, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen.
      Degrons are short protein segments that direct proteins for degradation via the ubiquitin-proteasome system, ensuring the removal of signaling proteins and clearance of misfolded proteins. We have performed a large-scale screen of more than 200,000 30-residue peptides from more than 5000 human cytosolic proteins, achieving 99.7% coverage. We find that 19% of peptides act as strong degrons, 30% as intermediate, and 51% as non-degrons. We identify both known and previously unidentified degradation signals and show that most depend on the E1 ubiquitin-activating enzyme and the proteasome. Structural mapping shows that many degrons are buried and likely become active upon protein unfolding. Training of a machine learning model allowed us to describe the degron properties and predict the cellular abundance of missense variants that operate by forming degrons in exposed and disordered protein regions, thus providing a mechanism of pathogenicity for germline coding variants at such positions.
    DOI:  https://doi.org/10.1126/sciadv.adz3483
  9. FEBS J. 2026 Jan 30.
    Molecular chaperones and proteostasis regulation during cytosolic translation.
    Ulrike Topf.
      Molecular chaperones ensure that proteins attain their mature state by assisting in proper folding, preventing aggregation, refolding misfolded proteins, and targeting irreparably misfolded proteins for degradation. This comprehensive role is vital for maintaining cellular homeostasis and responding to stress conditions. In this review, I focus on the multifaceted roles of chaperones in regulating protein production, spanning from ribosome biogenesis to controlling translation rate and translation fidelity through the folding of essential translation factors in eukaryotes. I discuss the function of ribosome- and nascent chain-bound molecular chaperones for the translation machinery and protein synthesis. Finally, I highlight findings on the interdependence of the two pillars of protein homeostasis when cells experience cellular stress and organisms face pathophysiological conditions.
    Keywords:  chaperones; folding; proteostasis; ribosome biogenesis; translation
    DOI:  https://doi.org/10.1111/febs.70419
  10. J Biol Chem. 2026 Feb 04. pii: S0021-9258(26)00118-3. [Epub ahead of print] 111248
    Emerging Biologic Modalities for Targeted Protein Degradation.
    Alana G Caldwell, Harshil Parmar, Xiaoyu Zhang.
      Targeted protein degradation (TPD) has emerged as a powerful approach for eliminating disease-associated proteins by harnessing the ubiquitin-proteasome system. Biologic degraders are modular protein chimeras that recruit ubiquitin machinery to target proteins. They offer high specificity, modular design, and the ability to access targets traditionally considered challenging for small molecule ligands. This review surveys the expanding landscape of biologic TPD modalities, highlighting E3 ligase- and E2 enzyme-based degraders, TRIM-Away and TRIMbody-Away systems, and diverse biologics-based ligands that serve as target-binding components. We also discuss emerging peptide-based strategies, which bridge biologic and synthetic approaches. Finally, we highlight future opportunities to improve biologic degraders and their potential to expand the scope of targeted protein degradation.
    DOI:  https://doi.org/10.1016/j.jbc.2026.111248
  11. Nat Cell Biol. 2026 Feb 02.
    ER remodelling is a feature of ageing and depends on ER-phagy.
    Eric K F Donahue, Nathaniel L Hepowit, Elizabeth M Ruark, Alexandra G Mulligan, Brennen Keuchel, Nicholas D Urban, Li Peng, Stedman Stephens, Derek J Johnson, Natalie S Wallace, Lauren P Jackson, Mark H Ellisman, Rafael Arrojo E Drigo, Andrew W Folkmann, Matthias C Truttmann, Jason A MacGurn, Kristopher Burkewitz.
      The endoplasmic reticulum (ER) comprises an array of subdomains, each defined by a characteristic structure and function. Although altered ER processes are linked to age-onset pathogenesis, it is unclear whether shifts in ER structure or dynamics underlie these functional changes. Here we establish ER structural and functional remodelling as a conserved feature of ageing across yeast, Caenorhabditis elegans and mammals. Focusing on C. elegans as the exemplar of metazoan ageing, we reveal striking age-related reductions in ER volume across diverse tissues and a morphological shift from rough sheets to tubular ER. This morphological transition corresponds with large-scale shifts in ER proteome composition from protein synthesis to lipid metabolism, a phenomenon conserved in mammalian tissues. We show that Atg8 and ULK1-dependent ER-phagy drives age-associated ER remodelling through tissue-specific factors, including the previously uncharacterized ER-phagy regulator TMEM-131 and the IRE-1-XBP-1 branch of the unfolded protein response. Providing support for a model where ER remodelling is adaptive, diverse lifespan-extending paradigms downscale and remodel ER morphology throughout life. Furthermore, mTOR-dependent lifespan extension in yeast and worms requires ER-phagy, indicating that ER remodelling is a proactive and protective response during ageing. These results reveal ER-phagy and ER dynamics as pronounced, underappreciated mechanisms of both normal ageing and age-delaying interventions.
    DOI:  https://doi.org/10.1038/s41556-025-01860-1
  12. Curr Opin Struct Biol. 2026 Jan 30. pii: S0959-440X(25)00235-0. [Epub ahead of print]97 103217
    Machine learning, docking, or physics for structure prediction of ligand-induced ternary complexes.
    Riccardo Solazzo, Shu-Yu Chen, Sereina Riniker.
      Proteolysis-targeting chimeras (PROTACs) and molecular glues promote targeted protein degradation by recruiting an E3 ligase to proteins of interest (POIs). An accurate 3D structure of the ternary complex formed by E3 ligase, ligand, and POI is central to the rational design of degraders. Elucidating this structure with crystallography or cryo-EM can be challenging due to conformational flexibility, dynamic protein-protein interactions, and high-dimensional binding landscapes. To facilitate structure-based design in the absence of an experimental structure, computational approaches have been proposed: (i) multistep methods involving traditional docking pipelines, and (ii) single-step methods with deep learning models to directly predict the complex structure. Multistep methods are limited by sampling complexity, accurate input structures, scoring accuracy, and computational cost, while single-step methods are faster but are constrained by training-data scarcity. Here, we examine recent advances and emerging tools in modeling ternary complexes, critically discuss their predictive power and limitations, and highlight remaining challenges.
    DOI:  https://doi.org/10.1016/j.sbi.2025.103217
  13. bioRxiv. 2026 Jan 14. pii: 2026.01.13.699274. [Epub ahead of print]
    Decreased tRNA abundance contributes to decreased translation elongation rate in a prolonged mitosis.
    Emily Sparago, Ryan Johnston, Shawn M Lyons, Michael D Blower.
      Cells undergo dramatic structural rearrangements upon entering mitosis. In addition, the biochemistry of mitotic cells is dramatically altered, including a significant decrease in protein synthesis. The majority of studies of mitotic translation have used cells synchronized by cell cycle altering drugs in transformed cells and much less is known about mitotic translation in primary cells under native conditions. Previous work has found that mitosis activates the integrated stress response (ISR) to trigger eIF2α phosphorylation, but little is known about the input for this response. In this study, we focus on mitotic translational regulation in an immortalized, non-transformed cell line. We confirm decreased mitotic protein synthesis in primary cells and under native conditions. Additionally, we confirm activation of the ISR by phosphorylation of eIF2α during both normal and prolonged mitosis. Interestingly, we also find that decreased translational elongation during mitosis, as evidenced by increased eEF2 phosphorylation and a slower elongation rate. Analysis of mitotic ribosome profiling data revealed an increase in pausing at Alanine-GCG codons during mitosis and a decreased abundance of its cognate tRNA-Ala CGC by northern blotting. Decreased tRNA-Ala CGC is likely sustained by the inability to synthesize additional tRNA due to RNAPol III inhibition in mitosis, yielding an stronger effect with an increased time in mitosis. These results suggest that decreased translation elongation in mitosis triggers inhibition of initiation to decrease global protein synthesis.
    DOI:  https://doi.org/10.64898/2026.01.13.699274
  14. bioRxiv. 2026 Jan 17. pii: 2026.01.16.699979. [Epub ahead of print]
    Inosine misincorporation into mRNA triggers the integrated stress response and activates an innate immune gene expression signature.
    Jacob H Schroader, Naa N Adade, Emmanuel E Adade, Mark A Bratslavsky, Hannah K Shorrock, Bradley R Smith, Ting Zhou, Steven Lotz, Taylor Bertucci, Sally Temple, Alex M Valm, Cara T Pager, J Andrew Berglund, Mark T Handley, Gabriele Fuchs, Kaalak Reddy.
      The inosine triphosphate pyrophosphatase (ITPase) enzyme restricts levels of the non-canonical nucleotides (deoxy)inosine triphosphate (dITP/ITP) and prevents their aberrant misincorporation into nucleic acids. ITPase deficiency is associated with dilated cardiomyopathy and epileptic encephalopathy in humans and is usually fatal in infancy. It leads to pronounced inosine misincorporation into RNA but the cellular consequences of this misincorporation are not well understood and the pathogenic basis of ITPase deficiency remains unknown. Here we show that cellular transfection of mRNA with inosine misincorporation activates the integrated stress response (ISR) with an innate immune gene expression signature. This stress response triggers stress granule formation and is modulated by the double stranded RNA sensor protein Kinase R (PKR). Inosine nucleoside treatment of ITPase-deficient cells leads to endogenous inosine misincorporation into mRNA and activation of the ISR. Further, differentiation of human ITPase-deficient induced pluripotent stem cells into neurons results in a low-level stress response. Thus, our study establishes inosine misincorporation into mRNA as an unappreciated form of cellular stress. This is normally prevented by the ITPase enzyme, with implications for the pathogenesis of ITPase deficiency.
    DOI:  https://doi.org/10.64898/2026.01.16.699979
  15. Adv Sci (Weinh). 2026 Feb 04. e15159
    Discovery of SKP2-Recruiting PROTACs for Target Protein Degradation.
    Guanjun Dong, Aima Huang, Ziqing Zhao, Bikai Lai, Xin Pan, Huiyu Yang, Xiaohan Xu, Tianwei Wang, Fangchen Zhao, Zhimin Zhang, Yongbo Xue, Guanjun Deng, Wenbin Deng, Jianwei Chen.
      Proteolysis targeting chimeras (PROTACs) have emerged as an intriguing therapeutic strategy for targeted protein degradation (TPD), functioning as heterobifunctional compounds that induce the redirection of E3 ligases to ubiquitinate neo-substrates for proteasomal degradation. Despite the presence of over 600 E3 ligases, only a limited subset has been successfully harnessed for TPD. This study demonstrates that S-phase kinase-associated protein 2 (SKP2), the substrate receptor of the Cullin RING ligase 1 (CRL1) subfamily, can be employed for TPD using a selective, non-covalent SKP2 recruiter, SL1. We designed and synthesized SKP2-recruiting degraders by linking SL1 to the BRD4 inhibitor JQ1. These compounds effectively induce BRD4 degradation in MV-4-11 cells, with the most potent compound 2-1 exhibiting a half-maximal degradation (DC50) of 298 nM, validating their potential as PROTACs. Mechanistic investigations show that 2-1 promotes BRD4 ubiquitination and subsequent degradation in a proteasome- and neddylation-dependent manner, which can be rescued by SKP2 knockdown and knockout. We further demonstrate that SKP2-directed PROTACs effectively degrade Androgen receptor (AR) in 22RV1 cells. These findings emphasize that SKP2, frequently overexpressed in various tumor cells, can be successfully exploited for TPD through non-covalent PROTACs, expanding the pool of E3 ligases available for potential therapeutic applications.
    Keywords:  BRD4; E3 ligase; PROTAC; SKP2; targeted protein degradation
    DOI:  https://doi.org/10.1002/advs.202515159
  16. Nat Commun. 2026 Feb 03.
    Protein C-terminal variations impact proteostasis.
    Ching-Yu Chu, Shu-Yu Hsu, Chi-Wei Yeh, Kun-Hai Yeh, Li-Chin Wang, Lo-Tung Lee, Shu-Chuan Chen, Chen-Hsin Yu, Hsueh-Chi S Yen.
      Protein C-termini can vary due to errors or programmed regulation, contributing to proteome diversity, yet their impact on the proteome remains poorly understood. Although aberrant C-termini are often linked to protein degradation, it is unclear if this holds true universally. In this study, we examine how C-terminal variations-arising from disease-associated nonstop mutations, alternative splicing, and translational readthrough-affect protein half-lives. Our findings indicate that, contrary to previous studies, erroneous C-termini can either stabilize or destabilize proteins. We have identified multiple oncoproteins and tumor suppressors whose protein stability is altered by disease-relevant nonstop mutations. Notably, we have found that C-terminal variations commonly influence the stability of canonical proteins, extending beyond their role in protein quality control. Furthermore, we have uncovered C-terminal features that distinguish erroneous from wild-type proteins and reveal that hydrophobic C-termini are targeted by a complex ubiquitin ligase network. Overall, our work broadens the understanding of C-terminal-dependent protein degradation and supports that C-terminal variation is a widespread strategy for generating protein forms with distinct half-lives to exert diverse biological functions.
    DOI:  https://doi.org/10.1038/s41467-026-68979-z
  17. Nature. 2026 Feb 04.
    Single-molecule dynamics of the TRiC chaperonin system in vivo.
    Rongqin Li, Niko Dalheimer, Martin B D Müller, F Ulrich Hartl.
      The essential chaperonin T-complex protein ring complex (TRiC) (also known as chaperonin containing TCP-1 (CCT)) mediates protein folding in cooperation with the co-chaperone prefoldin (PFD)1-5. In vitro experiments have shown that the cylindrical TRiC complex facilitates folding through ATP-regulated client protein encapsulation6-9. However, the functional dynamics of the chaperonin system in vivo remain unexplored. Here we developed single-particle tracking in human cells to monitor the interactions of TRiC-PFD with newly synthesized proteins. Both chaperones engaged nascent polypeptides repeatedly in brief probing events typically lasting around one second, with PFD recruiting TRiC. As shown with the chaperonin client actin8, the co-translational interactions of PFD and TRiC increased in frequency and lifetime during chain elongation. Close to translation termination, PFD bound for several seconds, facilitating TRiC recruitment for post-translational folding involving multiple reaction cycles of around 2.5 s. Notably, the lifetimes of TRiC interactions with a folding-defective actin mutant were markedly prolonged, indicating that client conformational properties modulate TRiC function. Mutant actin continued cycling on TRiC until it was targeted for degradation. TRiC often remained confined near its client protein between successive binding cycles, suggesting that the chaperonin machinery operates within a localized 'protective zone' in which free diffusion is restricted. Together, these findings offer detailed insight into the single-molecule dynamics and supramolecular organization of the chaperonin system in the cellular environment.
    DOI:  https://doi.org/10.1038/s41586-025-10073-3
  18. bioRxiv. 2026 Jan 14. pii: 2026.01.14.698769. [Epub ahead of print]
    Proteome-wide C-degron activity profiling connects conditional regulation of the CTLH E3 ligase complex to ribosome biogenesis.
    Drew W Grant, Shengjiang Tan, Dylan E Ramage, Mamie Z Li, Ying Di, Iva A Tchasovnikarova, Michael P Weekes, Stephen J Elledge, Alan J Warren, Richard T Timms.
      Many E3 ubiquitin ligases recognize cognate degron motifs located at protein termini, but the paucity of bona fide substrates of N-degron and C-degron pathways hampers our understanding of their physiological significance. Here, by devising an expression screening approach to assess the effect of C-terminal "capping" on the stability of thousands of human proteins, we systematically identify a suite of full-length substrates harboring C-terminal degrons. Interrogating one leading candidate, ZMYND19, we characterize a C-degron pathway governed by the Muskelin substrate adaptor of the CTLH E3 ligase complex. Cell-to-cell variability in ZMYND19 stability uncovered conditional regulation, with CTLH-mediated degradation impaired by TNF-α stimulation but enhanced by mTOR inhibition. Parallel genetic and proteomic screens identified two poorly characterized proteins, AAMP and AEN, as additional substrates of the CTLH Muskelin C-degron pathway, leading us to define an essential role for AAMP in ribosome maturation through chaperone activity towards ribosomal protein uL16. Altogether, these data define a C-degron pathway through which the Muskelin substrate adaptor connects conditional regulation of the CTLH E3 ligase complex to control of ribosome biogenesis.
    DOI:  https://doi.org/10.64898/2026.01.14.698769
  19. Biosci Biotechnol Biochem. 2026 Feb 04. pii: zbag015. [Epub ahead of print]
    Re‑thinking translation quality control in bacteria: from trans‑translation to collided‑disome surveillance.
    Hiraku Takada.
      Cells must recycle stalled ribosomes while preventing the accumulation of aberrant nascent chains. In bacteria, this is achieved by overlapping pathways with distinct substrates: ribosome-rescue systems act mainly on non-stop mRNAs, whereas ribosome-associated quality control (RQC) targets mid-ORF arrests. Work in Gram-positive bacteria defined an RQC mechanism that appends C-terminal degrons to stalled peptides, yet the full set of bacterial substrates and splitting factors remains unresolved, and enteric bacteria notably lack a canonical RQC elongation factor. This review traces the field from the discovery of tmRNA (also known as 10Sa RNA or SsrA RNA) through alternative rescue pathways to the current bacterial RQC framework. I summarize mechanisms across three layers-processing of 50S-peptidyl-tRNA, collision sensing and splitting, and downstream proteolysis-and compare species-level strategies and conservation patterns. I highlight how rescue and quality control intersect during phage infection, and outline key mechanistic uncertainties and experiments needed to resolve them.
    Keywords:  RQC; Ribosome; tmRNA; translation quality control
    DOI:  https://doi.org/10.1093/bbb/zbag015
  20. Neural Regen Res. 2026 Jan 27.
    Protein disulfide isomerases in amyotrophic lateral sclerosis: Endoplasmic reticulum proteostasis and neuromuscular function.
    Guillermo Diaz, Claudio Hetz.
      
    DOI:  https://doi.org/10.4103/NRR.NRR-D-25-01874
  21. Commun Biol. 2026 Feb 03.
    The endoplasmic reticulum displays high polarity with low protein aggregation in human cells.
    Xinwei Hu, Junlin Chen, Ping Liu, Huaiyue Zhang, Yu Liu, Xin Zhang, Lei Wang.
      Many physicochemical properties in the cellular milieu are important for cell function and survival. However, the polarity of different subcellular compartments and its role in protein condensate and aggregate formation within cells are less characterized. Here, we develop a method to compare the polarity in different subcellular compartments using the same polarity-sensitive solvatochromic fluorescent probe. Unexpectedly, the endoplasmic reticulum (ER) lumen displays a higher polarity and a more crowded environment than the cytosol in human cells. Polarity-decreasing and crowding-increasing hypertonic conditions induce condensate or aggregate formation of two intrinsically disordered proteins, with-no-lysine kinase 1 and Huntingtin gene (Htt) exon1 with an expanded polyQ stretch (Htt-polyQ), in the cytosol. However, targeting Htt-polyQ to the ER prevents its aggregation, suggesting that polarity but not crowding is more relevant to protein aggregation. Our results reveal the heterogeneity in subcellular polarity and crowding, and uncover previously unrecognized high-polarity in the ER lumen, which provides a unique environment for maintaining robust proteostasis.
    DOI:  https://doi.org/10.1038/s42003-025-09491-w
  22. Cell Rep. 2026 Jan 29. pii: S2211-1247(25)01686-9. [Epub ahead of print]45(2): 116914
    HRD1 negatively regulates autolysosome formation by inhibiting liquid-liquid phase separation of SNAP29.
    Wenyan Qu, Di Chen, Hongyu Zhao, Qiang Sheng, Juan Wang, Yujun Shen, Yuxian Shen.
      Autophagy is a highly conserved cellular process in which cytoplasmic contents are sequestrated by autophagosomes and delivered to lysosomes for degradation. Generation of degradative autolysosomes mediated by SNARE proteins is essential; however, the regulatory mechanisms governing this process remain underexplored. This study aimed to demonstrate that E3 ubiquitin ligase HRD1 regulates liquid-liquid phase separation (LLPS) of SNAP29, thereby modulating SNARE assembly. We found that HRD1 deficiency enhances autophagy activity and promotes autolysosome formation in a SNAP29-dependent manner. We also determined that SNAP29 forms highly dynamic condensates in in vivo and in vitro, which are crucial for the assembly of the SNARE complex. Mechanistically, HRD1 interacts with SNAP29 to suppress its condensation, whereas HRD1 depletion accelerates both SNAP29 condensate formation and SNARE complex assembly. Our findings reveal that HRD1 acts as a negative regulator in autolysosome formation by interacting with SNAP29, inhibiting its LLPS process, thereby modulating the binding affinity among SNARE components.
    Keywords:  CP: Cell biology; HRD1; SNAP29; SNARE assembly; autolysosome; liquid-liquid phase separation
    DOI:  https://doi.org/10.1016/j.celrep.2025.116914
  23. Res Sq. 2026 Jan 20. pii: rs.3.rs-8395568. [Epub ahead of print]
    Organelles harbour pH gradients.
    Yamuna Krishnan, Sangyoon Lee, Sandip Chakraborty, Soyoung Kim, Asif Ali, Koushambi Mitra, Matthew Zajac, Anastasia Brown, David Pincus.
      Organelle pH is critical to organelle identity and function. Resident proteins that define each organelle modify transiting cargo proteins, with both retention and trafficking between organelles governed by pH-dependent mechanisms. For example, lysosomal enzymes bind mannose-6-phosphate receptors at the higher pH (~6.5) of the Golgi and dissociate at the lower pH (~5.5) of late endosomes. Proteins that stray from the endoplasmic reticulum (ER) are captured by KDEL receptors in the acidic Golgi and returned into the neutral ER. This pH-tuned trafficking system compartmentalizes organelle function and prevents mis-localization of critical enzymes. Dysregulated organelle pH disrupts their function and leads to various diseases. Because protons move rapidly in water, the pH within a single organelle is currently assumed to be spatially uniform. Here, using a reporter sensitive from pH 5.5 - 10.5 to map a spectrum of organelles at high resolution, we discovered that pH gradients exist within single, large or long organelles such as the ER and mitochondria, and in membrane-less organelles without ion-transporting proteins such as the nucleolus. These new findings upend our understanding of organellar pH, prompting new questions about proton diffusion within the cell, and its potential consequences on organelle function.
    DOI:  https://doi.org/10.21203/rs.3.rs-8395568/v1
  24. Cell Stress Chaperones. 2026 Feb 03. pii: S1355-8145(26)00004-0. [Epub ahead of print] 100148
    Embracing diversity: PTMs, the chaperone code, and the emergence of new chaperone entities.
    Chander S Digwal, Shujuan Wang, Gabriela Chiosis.
      Dr. Len Neckers played a pioneering role in establishing that HSP90 is regulated by post-translational modifications (PTMs), fundamentally reshaping how molecular chaperones are understood. This insight laid the foundation for what has become known as the "chaperone code", the concept that coordinated PTM patterns act as regulatory signals governing chaperone function, interactions, and stress responsiveness. In this short perspective, I reflect on how Len's early work seeded this conceptual shift and how subsequent advances have revealed that PTMs not only fine-tune canonical chaperone activities but can also enable chaperones to adopt non-canonical functional states under specific stress conditions. These developments have expanded the landscape of chaperone biology, illustrating how chemical encoding can diversify chaperone behavior and reconfigure protein networks. Together, they highlight the enduring impact of Len's contributions and the importance of embracing complexity in understanding chaperone function.
    Keywords:  Chaperone code; Epichaperomes; HSP90; Non-canonical chaperone functions; Post-translational modification (PTM); Stress biology
    DOI:  https://doi.org/10.1016/j.cstres.2026.100148
  25. Cell Death Dis. 2026 Feb 06.
    Proximity proteomics reveals OTUD6B regulation of stress granule dynamics through coalescence with VCP/p97.
    Dian Yang, Yichao Liu, Yueshun Hong, Enming Miao, Peng Wang, Yuming Sun, Lina Zhou, Shuyan Liu, Yingqiu Zhang, Hongqiang Qin, Mingliang Ye, Han Liu.
      Stress granules (SGs) are membrane-less organelles formed through liquid-liquid phase separation of proteins and RNAs, serving as temporary repositories for biomacromolecules to protect cells under stress conditions. Impaired SG disassembly is closely implicated in neurodegenerative diseases and aging, yet the mechanisms regulating SG dynamics are incompletely investigated. The constituents of heterogenous SGs are complicated and broadly categorized as core and shell components. In contrary to the relatively stable core components, our understanding of the diverse SG shell is deficient. By combining interactomic and proximity proteomic approaches, we reveal that the deubiquitinating enzyme OTUD6B is associated with SG-related functions. Immunofluorescence assays showed that OTUD6B localized to SGs, as well as regulated their early assembly and clearance, partially dependent on its enzymatic activity. Further proximity proteomics and interactomics results uncover the ATPase VCP/p97, a key SG disassembly factor, as an OTUD6B-associated protein. OTUD6B and VCP association is governed through their disordered regions normally participated in biomolecular condensation. VCP knockdown or pharmacological inhibition phenocopied OTUD6B silencing by leading to defects in SG dynamics. Mechanistically, SG coalescence of VCP incurred by OTUD6B in a partially enzymatic activity-dependent manner functions to accelerate not only the early assembly, but also SG clearance following stress removal. Therefore, our findings establish OTUD6B as a critical modulator of SG dynamics, linking its function to stress responses and potential disease mechanisms.
    DOI:  https://doi.org/10.1038/s41419-026-08451-4
  26. Nat Metab. 2026 Feb 05.
    Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion.
    Meltem Weger, Daniel Mauvoisin, Dominic Hoyle, Jingkui Wang, Eva Martin, James Rae, Charles Ferguson, Glynis Klinke, Michelle Cielesh, Kyle L Macauslane, Mark Larance, Manfredo Quadroni, Iain Templeman, Jean-Philippe Walhin, Leonidas G Karagounis, James A Betts, Jonathan D Johnston, Fanny Durussel, Dmitri Firsov, Stephane Fournier, Olivier Müller, Benjamin L Schulz, Robert G Parton, Benjamin D Weger, Frédéric Gachon.
      The liver has a key role in inter-organ communication by secreting most circulating plasma proteins. However, the mechanisms governing hepatic protein secretion remain unclear. Here we show that hepatic protein secretion follows a diurnal rhythm regulated by food intake in humans and mice. Using liver microsomal proteomics, we find that proteins implicated in the early secretory pathway, such as protein glycosylation and folding in the endoplasmic reticulum (ER) and Golgi apparatus, exhibit a rhythmic expression profile, which is abolished in Bmal1-knockout mice. Mechanistically, we show that hepatic glycogenolysis provides substrates for protein N-glycosylation. In mice, perturbing hepatic glycogenolysis with pharmacological or nutritional interventions leads to ER stress and attenuates diurnal protein secretion. We confirm these results in humans, as genetic variants associated with glycogen storage disease and congenital disorders of glycosylation also alter hepatic protein secretion. Overall, our work uncovers hepatic glycogen metabolism as a circadian regulator of protein secretion.
    DOI:  https://doi.org/10.1038/s42255-026-01453-8
  27. Am J Hum Genet. 2026 Feb 04. pii: S0002-9297(26)00030-3. [Epub ahead of print]
    Bi-allelic loss-of-function variants in JKAMP cause a neurodevelopmental syndrome associated with dysregulation of GPR37 trafficking.
    Telethon Undiagnosed Diseases Program
      The endoplasmic reticulum (ER) serves as a key hub for protein homeostasis, maintaining a strict quality-control system that ensures only properly folded proteins reach their destinations, while misfolded proteins are degraded via ER-associated degradation (ERAD) or selective ER-phagy. JKAMP, which encodes an ER-resident transmembrane protein involved in ERAD, has not previously been associated with human disease. Here, we report bi-allelic loss-of-function variants in JKAMP in 14 affected individuals from 10 unrelated families presenting with a neurodevelopmental syndrome characterized by intellectual disability, developmental delay, seizures, hypotonia, microcephaly, and dysmorphic features. An in vivo zebrafish model lacking jkamp recapitulated key aspects of the human disorder, including developmental abnormalities and impaired myelin production, further corroborating its pathogenic role. Mechanistic studies identified GPR37, a brain-enriched orphan G protein-coupled receptor (GPCR) and known JKAMP interactor, as a critical downstream effector. GPR37 plays essential roles in dopaminergic signaling, inflammatory pain regulation, neuroprotection, and myelination. Loss of JKAMP resulted in defective folding and degradation of GPR37, leading to its accumulation within the ER and impaired trafficking to the plasma membrane, likely due to impaired ER quality control. These findings establish JKAMP as a previously unrecognized contributor to human neurodevelopment and uncover a pathogenic mechanism linking ER protein quality control to GPCR regulation and neurological disease.
    Keywords:  GPR37; JKAMP; bi-allelic loss-of-function variants; developmental delay; endoplasmic reticulum; intellectual disability; zebrafish model
    DOI:  https://doi.org/10.1016/j.ajhg.2026.01.008
  28. bioRxiv. 2026 Jan 20. pii: 2026.01.12.699095. [Epub ahead of print]
    Biomolecular Condensates Dictate the Folding Landscape of Proteins.
    Nathaniel Hess, Jerelle A Joseph.
      Protein structure is exquisitely sensitive to the surrounding chemical environment, and many proteins encounter complex environments within cells. Importantly, numerous proteins organize into biomolecular condensates-dense macromolecular assemblies with distinct physicochemical properties. This raises a fundamental question: how does condensation reshape protein structure and dynamics? Here, we investigate how protein folding landscapes are altered inside condensates, using the protein α-helix as a model folded domain. Atomistic simulations show that free energy surfaces within condensates differ markedly from those in dilute solution or in the presence of inert crowders. We then use Bayesian optimization to develop a chemically specific, near-atomistic model for quantification of α-helical folding and apply it to characterize diverse helices, including α-helical domains from the disease-associated proteins TDP43, Annexin A11, and the Androgen Receptor, within condensates of varying physicochemical properties. Our results support a framework in which multivalent interactions drive unfolding while crowding promotes folding, and protein conformational ensembles inside condensates emerge from this balance. Additionally, we show that folding transitions are kinetically frustrated inside condensates because they are coupled to the timescale of contact rearrangement with co-condensate proteins. As such, folding landscapes within condensates are dually sequence-dependent, informed by both the sequence of the folded domain and co-condensate proteins. Together, our work has implications for understanding condensate-mediated proteinopathies, targeting aberrant condensates, and designing condensates to program protein function across scales.
    DOI:  https://doi.org/10.64898/2026.01.12.699095
  29. Angew Chem Int Ed Engl. 2026 Feb 02. e22845
    Development of PolyHis-Targeting PROTAC Degraders.
    Hui Chen, Dong Zhu, Monica Billitti, Annan Sun, Lingtao Jin, Emily Moser, Nahid F Mivechi, Guangrong Zheng, Dongwen Lv.
      Targeted protein degradation (TPD) via proteolysis targeting chimeras (PROTACs) enables selective removal of proteins of interest (POIs) by hijacking the ubiquitin-proteasome system (UPS). However, broad application is constrained by the availability of high-quality target ligands, which remain scarce for much of the human proteome, limiting assessment of POIs for UPS-mediated degradation. To address this challenge, we developed polyhistidine-targeting PROTACs (polyHisTACs) by conjugating a nickel-nitrilotriacetic acid (Ni2 +-NTA) headgroup to ligands of VHL or CRBN, thereby recruiting these E3 ligase complexes to polyHis-tagged POIs. As expected, polyHisTACs effectively degraded CRISPR-engineered, endogenously polyHis-tagged BRD4 and also induced robust degradation of an exogenously expressed polyHis-tagged RNA-binding protein, PSPC1, a target that is typically considered undruggable. In summary, polyHisTACs overcome key limitations of existing tag-based degrader systems by leveraging a minimal, easily implemented polyHis tag. This platform provides a versatile, reliable way to evaluate UPS-mediated degradability in the absence of target-specific ligands and serves as a practical tool for acute POI depletion in basic research.
    Keywords:  HiBiT; PROTAC; polyhistidine; targeted protein degradation
    DOI:  https://doi.org/10.1002/anie.202522845
  30. J Am Chem Soc. 2026 Feb 05.
    Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins.
    Lu-Yi Chen, Wei-Lin Lu, Tanvi Pathania, I-Hsuan Chu, Meng-Ru Ho, Wei-Chen Chuang, Yuan-Chao Lou, Ta I Hung, Yohei Miyanoiri, Chia-En A Chang, Kuen-Phon Wu.
      AI-designed protein variants have demonstrated remarkable resistance to heat and chemical stress, yet the molecular mechanisms underlying this stability remain unclear. Here, we present a comprehensive biophysical and nuclear magnetic resonance (NMR) analysis of thermally stable ubiquitin and its ProteinMPNN-designed variants, R4 and R10, together with a second system based on the less stable ISG15 C-terminal domain (ISG15-CTD). Both R4/R10 and ProteinMPNN-designed ISG15-CTD variants (ICVs) exhibit extraordinary thermostability beyond 120 °C, and resist extreme denaturation at pH 3.0 in 8 M urea. NMR relaxation and hydrogen-deuterium exchange, and molecular-dynamics simulations reveal a protective mesostructured hydration shell that strengthens the hydrogen bonding network between protein-bound and bulk water, thereby suppressing unfolding. Sequence and electrostatic analyses indicate that this hydration arises from charge enrichment and clustering on the protein surface. These findings identify mesostructured hydration as a general, sequence-encoded mechanism of ProteinMPNN-driven stability and provide a physical framework for designing highly resilient biomolecules.
    DOI:  https://doi.org/10.1021/jacs.5c19875
  31. Proteins. 2026 Feb 03.
    Benchmarking Deep Learning for PROTAC Ternary Complex Prediction.
    Haoyu Chen, Fengjiao Wei, Jiajie Li, Zhuobin Shi, Shanshan Chen, Yu Fang, Shuxin Li, Xinru Gao, Lin Ju, Senbiao Fang, Ximing Xu.
      Proteolysis Targeting Chimeras (PROTACs) represent a transformative approach to drug development by leveraging the intracellular ubiquitin-proteasome system (UPS) for the selective degradation of target proteins. A PROTAC molecule comprises three essential components: a ligand that binds to the E3 ubiquitin ligase, a ligand that targets the protein of interest, and a flexible linker that connects the two. This distinctive structure enables the PROTAC to simultaneously engage with both the target protein and the E3 ligase, facilitating their interaction. Such proximity initiates the ubiquitination of the target protein, marking it for recognition and subsequent degradation. In this study, we benchmark ternary complexes based on PROTACs using four recently employed predictive tools: Chai-1, AlphaFold2, AlphaFold3, and Protenix. Comparative analysis indicated that the ternary complexes predicted by the four prediction tools demonstrated satisfactory accuracy (Cα-RMSD < 10 Å). Among the evaluated tools, three-Chai-1, AlphaFold3, and Protenix-demonstrated superior performance in over half of the tests, while AlphaFold2 exhibited comparatively lower performance. However, significant challenges remained in accurately predicting the orientation of POI and the E3 ligase (Cα-RMSD < 10 Å when POI or E3 ligase were used as reference), as well as the position of the small molecule PROTAC (RMSD < 5 Å). By benchmarking these tools, we underscore recent advancements in protein structure prediction, enhance our understanding of the mechanisms underpinning PROTAC complexes, and provide a valuable reference for evaluating the binding conformations of other ternary complexes, as well as for the development of future predictive tools.
    Keywords:  AlphaFold3; PROTAC; deep learning; structure prediction benchmarking; ternary complex prediction
    DOI:  https://doi.org/10.1002/prot.70117
  32. Chembiochem. 2026 Jan;27(2): e202500854
    Increasing Proteasome Activity to Alter XBP1 Signaling of the UPR Pathway.
    Kate A Kragness, Darci J Trader.
      Enhanced proteasome activity is known to confer resistance to cellular stress in vitro and in vivo, but such effects have largely been achieved through genetic upregulation of proteasome subunits and assembly factors. Here, we investigate whether small-molecule 20S proteasome activators can modulate XBP1 signaling during IRE1-driven unfolded protein response (UPR) activation. We show that pre-treatment with a 20S activator prior to IRE1 induction significantly attenuates XBP1 signaling, whereas treatment after chemical induction of IRE1 produces no detectable effect. These findings indicate that proteasome activators can bolster proteasome activity under endoplasmic reticulum (ER) stress, but their ability to modulate an ongoing UPR is limited. This work highlights a potential temporal window in which proteasome activation may influence stress-adaptive signaling.
    Keywords:  20S; proteasome; small molecule; stimulation
    DOI:  https://doi.org/10.1002/cbic.202500854
  33. Nat Commun. 2026 Feb 04.
    A multivalent adaptor mechanism drives the nuclear import of proteasomes.
    Hanna L Brunner, Robert W Kalis, Lorenz Grundmann, Zuzana Hodáková, Zuzana Koskova, Irina Grishkovskaya, Melanie de Almeida, Matthias Hinterndorfer, Hannah Knaudt, Simon Höfflin, Florian Andersch, Harald Kotisch, Achim Dickmanns, Sara Cuylen-Haering, Johannes Zuber, David Haselbach.
      Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a small unstructured protein whose mechanistic role has remained elusive despite its essential function. Using an integrated approach combining protein-wide saturation mutagenesis screens, cryo-EM, and biochemical reconstitution, we characterize AKIRIN2 as a scaffold protein that coordinates the assembly of an importin cluster around the proteasome. AKIRIN2 binds in multiple copies to the 20S proteasome and simultaneously interacts with importin IPO9 and the KPNA2/KPNB1 heterodimer. In the nucleus, RanGTP triggers importin dissociation, releasing the proteasome, while AKIRIN2 undergoes ubiquitin-independent degradation. Our findings reveal how AKIRIN2's multivalency facilitates the recruitment of multiple importins to the proteasome, a critical adaptation for transporting this large macromolecular complex into the nucleus and maintaining the nuclear proteome.
    DOI:  https://doi.org/10.1038/s41467-026-69162-0
  34. Proc Natl Acad Sci U S A. 2026 Feb 10. 123(6): e2515389123
    Linear ubiquitination of the NMDA receptor GluN2A subunit facilitates the GluN2B-to-GluN2A switch and synaptic maturation.
    Yuanyuan Chu, Yiwen Xu, Maoqing Huang, Xueying Fang, Xinying Huang, Zhengwei Yao, Jian Wu, Ning Zhou, Kaiwen He, Yanfen Liu, Tong Wang.
      N-methyl-D-aspartate-type glutamate receptors (NMDARs) initiate the synaptic plasticity underlying learning and memory. In forebrain excitatory neurons, NMDARs are heteromeric tetramers composed of two GluN1 subunits and two glutamate ionotropic receptor NMDA type subunit 2A (GluN2A) or GluN2B subunits. At birth, NMDARs contain primarily GluN2B, but within weeks, GluN2A-containing receptors predominate the forebrain, comprising over 65% of total NMDARs in adulthood. This rapid subunit switch is essential for neonatal cognitive development, yet mechanisms driving it remain unclear. Particularly, while GluN2B levels remain relatively constant, GluN2A increases several 100-fold, despite its mRNA rising by only ~10-fold, strongly suggesting involvement of unknown posttranslational regulation. Here, we show that in the neonatal mouse forebrain, the linear ubiquitination axis, composed of the E3 ligase complex LUBAC and the deubiquitinase OTULIN, shifts transiently toward higher activity, with HOIP upregulated and OTULIN downregulated. In neonatal mice, experimentally reducing the axis activity by OTULIN overexpression causes persistent synaptic immaturity and adult cognitive deficits. Using proteomic and biochemical assays, we identified GluN2A as a key substrate: Linear ubiquitination at six lysines in the GluN2A C-terminus stabilizes the subunit and promotes its synaptic expression, whereas disrupting this modification destabilizes GluN2A by promoting lysosomal degradation. Consistently, overexpression of wild-type GluN2A rescues OTULIN-induced synaptic immaturity, whereas the ubiquitination-deficient GluN2A-6KR mutant fails to rescue and further exacerbates this defect. OTULIN overexpression selectively promotes GluN2A degradation, thereby delaying the GluN2B-to-GluN2A switch and synaptic maturation. These findings reveal a role for the linear ubiquitination axis in selectively stabilizing GluN2A, supporting rapid synaptic and cognitive development.
    Keywords:  GluN2A; NMDA receptor; linear ubiquitination axis; subunit switch; synaptic development
    DOI:  https://doi.org/10.1073/pnas.2515389123
  35. Nat Chem Biol. 2026 Feb 06.
    Photosensitizer proximity labeling captures the lipid and protein interactomes.
    Andrew P Becker, Elijah Biletch, John Paul Kennelly, Soon-Gook Hong, Ashley R Julio, Miranda Villanueva, Rohith T Nagari, Daniel W Turner, Nikolas R Burton, Tomoyuki Fukuta, Liujuan Cui, Xu Xiao, Zaid Vellani, Alexander Nguyen, Julia J Mack, Peter Tontonoz, Keriann M Backus.
      The physical properties of cellular membranes are influenced by protein and lipid interactions. In situ proximity labeling interactomic methods are well suited to characterize these dynamic and often fleeting interactions. Yet, available methods require distinct chemistries for proteins and lipids. Here we establish a singlet oxygen-based photocatalytic proximity labeling platform (POCA) that reports intracellular interactomes for both proteins and lipids using cell-penetrant photosensitizer reagents. Cholesterol-directed POCA captured known and unprecedented cholesterol-binding proteins, including protein complexes sensitive to intracellular cholesterol levels and proteins uniquely captured by physiologically relevant lipoprotein uptake. Protein-directed POCA accurately mapped intracellular membrane complexes, defined sterol-dependent changes to the interactome of the cholesterol transport protein Aster-B and revealed singlet oxygen-mediated domain-specific Aster crosslinking. More broadly, we find that POCA is a versatile interactomics platform that is straightforward to implement, using the readily available HaloTag system, fulfilling unmet needs in intracellular singlet oxygen-based proximity labeling proteomics.
    DOI:  https://doi.org/10.1038/s41589-026-02140-1
  36. Nature. 2026 Feb 04.
    PtdIns(3,5)P2 is an endogenous ligand of STING in innate immune signalling.
    Jay Xiaojun Tan, Bo Lv, Jie Li, Tuo Li, Fenghe Du, Xiang Chen, Xuewu Zhang, Xiao-Chen Bai, Zhijian J Chen.
      Exposure to cytosolic DNA triggers innate immune responses through cyclic GMP-AMP (cGAMP) synthase (cGAS)1,2,3. After binding to DNA, cGAS produces cGAMP as a second messenger that binds to stimulator of interferon genes (STING), a signalling adaptor protein anchored to the endoplasmic reticulum (ER)3-5. STING then traffics from the ER through the Golgi to perinuclear vesicle clusters, which leads to activation of the kinases TBK1 and IKK and subsequent induction of interferons and other cytokines6-9. Here we show that phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2; also known as PI(3,5)P2) is an endogenous ligand of STING that functions together with cGAMP to induce STING activation. Proteomic analyses identified a constitutive interaction between STING and PIKFYVE, an enzyme that produces PtdIns(3,5)P2 in mammalian cells. Deletion of PIKFYVE blocked STING trafficking from the ER and TBK1 activation. In vitro reconstitution uncovered a strong and selective effect of PtdIns(3,5)P2 on STING activation by cGAMP. PtdIns(3,5)P2 bound directly to STING in fluorescence resonance energy transfer assays. Consistently, cryo-electron microscopy revealed that PtdIns(3,5)P2 promotes cGAMP-induced STING oligomerization10, functioning as a molecular glue. Similar to PIKFYVE depletion, mutation of the PtdIns(3,5)P2-binding residues in STING largely blocked its trafficking and downstream signalling. These findings reveal that PtdIns(3,5)P2 is a lipid ligand of STING with essential roles in innate immunity.
    DOI:  https://doi.org/10.1038/s41586-025-10084-0
  37. bioRxiv. 2026 Jan 15. pii: 2026.01.15.695726. [Epub ahead of print]
    Endothelial Cell Secretome Alterations Induced by Inflammatory Stress.
    Vi T Tang, Srishti Baid, Alejandra Castellanos, Venkatesha Basrur, Colin A Kretz, Alexey I Nesvizhskii, Xiang Gao, Qunfeng Dong, Mitchell J Weiss, Prabhodh S Abbineni.
      Endothelial cells detect pathogens through pattern recognition receptors, such as Toll-like receptor 4 (TLR4), which triggers the synthesis and secretion of molecules that initiate the innate immune response. Proteins bearing signal peptides are secreted through the classical endoplasmic reticulum (ER)-Golgi-dependent route, whereas select signal-peptide-lacking cytoplasmic proteins are secreted via less well-characterized ER-Golgi-independent mechanisms, collectively termed unconventional cytoplasmic protein secretion (UCPS). To systematically characterize the secretome of human umbilical vein-derived endothelial cells (HUVECs) and delineate the contribution of UCPS, we performed deep quantitative proteomics on HUVEC cell lysates and conditioned medium before and after TLR4 stimulation with lipopolysaccharide (LPS). Of 5205 proteins detected in either fraction, 381 were enriched in the conditioned medium and therefore classified as secreted. Of these, 333 proteins (87.4%) were secreted via the conventional pathway, and 48 (12.6%) were secreted via UCPS, 43 of which were not previously associated with this process. Predicted functions of UCPS-secreted proteins include redox regulation, proteostasis, cytoskeletal remodeling, and innate immune signaling. We confirmed that α-globin (HBA1), which functions as a redox sensor and regulator of nitric oxide in endothelial cells, is secreted constitutively by UCPS and at higher levels following inflammatory activation. Notably, UCPS cargo identity showed poor concordance with current computational predictors, underscoring the need for empirical datasets. Overall, our findings suggest that the HUVEC secretome includes both conventionally and unconventionally secreted proteins that regulate coagulation, angiogenesis, and immune function. Our findings establish a high-quality secretome dataset for HUVECs, providing a novel resource for future efforts to define the molecular determinants governing UCPS cargo selection and trafficking related to endothelial cell function.
    DOI:  https://doi.org/10.64898/2026.01.15.695726
  38. Nature. 2026 Feb 04.
    Activated ATF6α is a hepatic tumour driver restricting immunosurveillance.
    Xin Li, Cynthia Lebeaupin, Aikaterini Kadianaki, Clementine Druelle-Cedano, Niklas Vesper, Charlotte Rennert, Júlia Huguet-Pradell, Borja Gomez Ramos, Chaofan Fan, Robert Stefan Piecyk, Laimdota Zizmare, Pierluigi Ramadori, Luqing Li, Lukas Frick, Menjie Qiu, Cangang Zhang, Luiza Martins Nascentes Melo, Vikas Prakash Ranvir, Peng Shen, Johannes Hanselmann, Jan Kosla, Mirian Fernández-Vaquero, Mihael Vucur, Praveen Baskaran, Xuanwen Bao, Olivia I Coleman, Yingyue Tang, Miray Cetin, Zhouji Chen, Insook Jang, Stefania Del Prete, Mohammad Rahbari, Peng Zhang, Timothy V Pham, Yushan Hou, Aihua Sun, Li Gu, Laura C Kim, Ulrike Rothermel, Danijela Heide, Adnan Ali, Suchira Gallage, Nana Talvard-Balland, Marta Piqué-Gili, Albert Gris-Oliver, Alessio Bevilacqua, Lisa Schlicker, Alec Duffey, Kristian Unger, Marta Szydlowska, Jenny Hetzer, Duncan T Odom, Tim Machauer, Daniele Bucci, Pooja Sant, Jun-Hoe Lee, Jonas Rösler, Sven W Meckelmann, Johannes Schreck, Sue Murray, M Celeste Simon, Sven Nahnsen, Almut Schulze, Ping-Chih Ho, Manfred Jugold, Kai Breuhahn, Jan-Philipp Mallm, Peter Schirmacher, Susanne Roth, Nuh Rahbari, Darjus F Tschaharganeh, Stephanie Roessler, Benjamin Goeppert, Bertram Bengsch, Geoffroy Andrieux, Melanie Boerries, Nisar P Malek, Marco Prinz, Achim Weber, Robert Zeiser, Pablo Tamayo, Peter Bronsert, Konrad Kurowski, Robert Thimme, Detian Yuan, Rafael Carretero, Tom Luedde, Roser Pinyol, Felix J Hartmann, Michael Karin, Alpaslan Tasdogan, Christoph Trautwein, Moritz Mall, Maike Hofmann, Josep M Llovet, Dirk Haller, Randal J Kaufman, Mathias Heikenwälder.
      Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality and there are limited therapies1. Although endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR transducer ATF6α remains unclear2. Here we demonstrate the function of ATF6α as an ER-stress-inducing tumour driver and metabolic master regulator restricting cancer immunosurveillance for HCC, in contrast to its well-characterized role as an adaptive response to ER stress3. ATF6α activation in human HCC is significantly correlated with an aggressive tumour phenotype, characterized by reduced patient survival, enhanced tumour progression and local immunosuppression. Hepatocyte-specific ATF6α activation in mice induced progressive hepatitis with ER stress, immunosuppression and hepatocyte proliferation. Concomitantly, activated ATF6α increased glycolysis and directly repressed the gluconeogenic enzyme FBP1 by binding to gene regulatory elements. Restoring FBP1 expression limited ATF6α-activation-related pathologies. Prolonged ATF6α activation in hepatocytes triggered hepatocarcinogenesis, intratumoural T cell infiltration and nutrient-deprived immune exhaustion. Immune checkpoint blockade (ICB)4 restored immunosurveillance and reduced HCC. Consistently, patients with HCC who achieved a complete response to immunotherapy displayed significantly increased ATF6α activation compared with those with a weaker response. Targeting Atf6 through germline ablation, hepatocyte-specific ablation or therapeutic hepatocyte delivery of antisense oligonucleotides dampened HCC in preclinical liver cancer models. Thus, prolonged ATF6α activation drives ER stress, leading to glycolysis-dependent immunosuppression in liver cancer and sensitizing to ICB. Our findings suggest that persistently activated ATF6α is a tumour driver, a potential stratification marker for ICB response and a therapeutic target for HCC.
    DOI:  https://doi.org/10.1038/s41586-025-10036-8
  39. bioRxiv. 2026 Jan 20. pii: 2026.01.20.700518. [Epub ahead of print]
    5' UTR length regulates alternative N-terminal protein isoform production in health and disease.
    Jimmy Ly, Eric M Smith, Matteo Di Bernardo, Yi Fei Tao, Elizabeth M Black, Ekaterina Khalizeva, Iain M Cheeseman.
      The 5' untranslated region (5' UTR) of an mRNA is classically viewed as a regulatory region that controls the amount of protein production, but not the resulting protein sequence. Here, we demonstrate that 5' UTR length plays a direct role in alternative N-terminal protein isoform production by controlling start codon selection. We find that very short 5' UTRs enhance leaky ribosome scanning, thereby promoting the production of truncated alternative N-terminal protein isoforms. We also show that endogenous changes in 5' UTR length due to alternative transcription initiation can tune the relative abundance of alternative N-terminal isoforms from the same gene. In addition, we identify mutations in rare genetic diseases that alter 5' UTR length, including a deletion in the VHL 5' UTR in von Hippel-Lindau disease that shifts translation toward the shorter VHLp19 isoform. Together, our results implicate 5' UTR length as a determinant of alternative N-terminal isoform production and reveal an underappreciated mechanism by which noncoding changes can reshape the proteome.
    Highlights: 5' UTR length affects the landscape of endogenous alternative N-terminal protein isoformsGeneration of an alternative truncated AKR7A2 isoform is mediated by short 5' UTR lengthAlternative transcription initiation modulates 5' UTR length to tune N-terminal isoform ratiosPathogenic VHL 5' UTR variants perturb N-terminal isoform ratios by altering 5' UTR length.
    DOI:  https://doi.org/10.64898/2026.01.20.700518
  40. J Mol Biol. 2026 Feb 02. pii: S0022-2836(26)00044-6. [Epub ahead of print] 169671
    The anticancer drug mitoxantrone triggers the formation of ribosome-enriched stress granules independently of the classical translational control pathways.
    Marta Leśniczak-Staszak, Paulina Pietras, Agnieszka Fedoruk-Wyszomirska, Martino Morici, Mateusz Sowiński, Szymon Krawczyk, Małgorzata Andrzejewska, Eliza Wyszko, Michał Nowicki, Paul J Anderson, Ewelina Gowin, Pavel Ivanov, Daniel N Wilson, Witold Szaflarski.
      Mitoxantrone (MIT) is a chemotherapeutic drug widely used for its DNA intercalation and inhibition of topoisomerase. In this work, we show that MIT also affects cytoplasmic RNA-ribosome organization. In human cancer cells, MIT induced stress granules (SGs) that contained large ribosomal subunit proteins, including eL8, together with polyadenylated mRNA. These MIT-induced SGs were different from arsenite-induced SGs: they formed without eIF2α phosphorylation, mTOR inhibition, or 4E-BP1 activity, and they remained stable in the presence of cycloheximide and after drug withdrawal. In vitro assays further demonstrated that MIT promotes ribosome aggregation in a concentration- and salt-dependent manner. Taken together, our results identify a distinct type of ribosome-enriched SGs that form through RNA-ribosome condensation rather than classical translational stress pathways. This mechanism provides a direct example of how a clinically used drug can reorganize cytoplasmic RNA-protein complexes, with possible consequences for mRNA regulation, cancer therapy, and neurodegenerative disease.
    Keywords:  anticancer drugs; mitoxantrone; ribosome; stress granules
    DOI:  https://doi.org/10.1016/j.jmb.2026.169671
  41. Autophagy. 2026 Feb 02.
    TGFB-inducible VASN (vasorin) promotes lysosomal acidification.
    Jiong Yan, Yan Zhang, Swati Choksi, Melissa R Mikolaj, Adam Harned, Kedar Narayan, Zheng-Gang Liu.
      The lysosome is not only a degradative organelle but also an essential platform for signal transduction, such as with MTOR signaling. The reciprocal regulation between the lysosome and MTOR is central to macroautophagy/autophagy and metabolism. MTOR-mediated suppression of lysosomal acidification is important for lysosomal activity, autophagic flux, and cell survival. VASN is a transmembrane glycoprotein whose function is not fully understood. In the present study, we report that VASN is a TGFB-inducible protein and plays a crucial role in positively regulating lysosomal acidification. As a potential mechanism, we demonstrated that VASN localizes to the lysosome, interacts with lysosomal MTOR and STK11IP, and disrupts the binding of STK11IP to MTOR and the V-ATPase, which was recently reported to suppress lysosomal acidification. We found that VASN's function in modulating lysosomal activity is essential for optimal mitophagy induced by TGFB and terminal erythroid differentiation and is critical for the progression of mutant KRAS-driven lung cancer. Overall, our study identified VASN as a novel TGFB-inducible regulator of lysosomal function.
    Keywords:  Lysosome; MTOR; STK11IP; TGFB; V-ATPase; VASN; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2626397
  42. Cell Death Discov. 2026 Feb 05.
    Activating GCN2 and subsequently the Unfolded Protein Response with the small oral molecule NXP800 delays tumor growth in osteosarcoma.
    Emma Racineau, Morgane Lallier, Anaïs Postec, Jérôme Amiaud, Rose-Anne Thépault, Régis Brion, Séverine Battaglia, Céline Charrier, Marie-Anne Colle, Bénédicte Brounais-Le Royer, Marc Baud'huin, Franck Verrecchia, Benjamin Ory, Steven Georges, François Lamoureux.
      Osteosarcoma (OS) is the most common primary malignant bone tumor mainly affecting children and young adults. Despite current treatments combining polychemotherapy and surgery, survival rates have remained unchanged for decades, highlighting the need to identify novel therapeutic approaches. NXP800, a newly developed orally available molecule, represents a promising therapeutic option. The therapeutic efficacy of NXP800 was evaluated in vitro and in a preclinical murine xenograft model of OS. RNA-seq analysis and functional assays were conducted to investigate the mechanisms of action and molecular target of NXP800. NXP800 decreases the viability of OS cell lines by blocking proliferation and inducing apoptosis. Mechanistically, NXP800 activates the Unfolded Protein Response (UPR), as demonstrated by eIF2α phosphorylation and ATF4 upregulation. This effect is mediated through the engagement of the Integrated Stress Response (ISR) via the activation of GCN2 kinase. Inhibition of GCN2, either through molecular or pharmacological approaches, abolishes NXP800-induced eIF2α phosphorylation and partially restores OS cell viability. Furthermore, NXP800 activates the IRE1α/JNK/c-Jun pathway while increasing the expression of the pro-apoptotic protein Puma. Finally, NXP800 delays tumor growth in preclinical OS model by promoting apoptosis. This study is a preclinical proof-of-principle of therapeutic efficacy of NXP800 both in vitro and in vivo, highlighting the relevance of targeting GCN2, and consequently activating the ISR and UPR, to induce apoptosis and inhibit tumor progression in OS.
    DOI:  https://doi.org/10.1038/s41420-026-02941-2
  43. RNA. 2026 Feb 04. pii: rna.080653.125. [Epub ahead of print]
    The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD.
    Matthew S Modena, Chloe M Wohlenberg, Marcus J Viscardi, Christian R Dunn, Ben L Haag, Joshua A Arribere.
      Nonsense-Mediated mRNA Decay (NMD) is a translational-dependent mRNA decay pathway that regulates mRNAs and protects cells from the deleterious, truncated protein products of mRNAs with early stop codons. Despite substantial effort, the central biochemical reactions that comprise mRNA decay during NMD remain elusive. Research by our lab and others centers around the observation that NMD target mRNA cleavage by the endonuclease SMG-6 requires the presence of another NMD factor SMG-5, although the molecular basis of SMG-6's requirement for SMG-5 remained elusive. Here we present work to explain the requirement of SMG-5 in SMG-6-mediated mRNA cleavage. We revisit previous observations that SMG-5 contains a catalytically inactive PIN nuclease domain, and we show that although SMG-5 lacks conventional active site residues, the PIN domain of SMG-5 nevertheless contains highly conserved residues that are essential to NMD. We show that Alphafold predicts an interaction between SMG-5 and SMG-6 PIN domains, an interaction that we substantiate via in vitro pulldowns. We use the in silico models to design point mutations that perturb-and restore-NMD function in C. elegans via a compensatory salt bridge flip. Altogether, our data support the idea that SMG-5 and SMG-6 interact to form a functional complex, and we suggest molecular roles for the overlooked SMG-5 PIN domain in SMG-6-mediated mRNA cleavage.
    Keywords:  Alphafold; Nonsense-Mediated mRNA Decay; PIN domain; SMG-5; SMG-6
    DOI:  https://doi.org/10.1261/rna.080653.125
  44. bioRxiv. 2026 Jan 12. pii: 2026.01.11.698831. [Epub ahead of print]
    Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling.
    Kaja Plucińska, Charlotte R Wayne, Henry Sanford, Boby Mathew, Nathalie Ropek, Stephanie M Adaniya, Corey Model, Nicolás Gómez-Banoy, Ksenia Morozova, Xiongwen Cao, Jeffrey M Friedman, Ken H Loh, Paul Cohen, Ekaterina V Vinogradova.
      Intercellular communication is critical for maintaining organismal metabolic homeostasis. Here, we present a new method enabling temporally controlled, cell type-specific labeling of secreted and membrane proteins in key metabolic tissues. The method employs a genetically encoded proximity-labeling strategy by targeting a Cre-dependent TurboID ligase to the endoplasmic reticulum (ER) in ES cell-derived mice. Expression of TurboID in liver, adipose tissue, and spleen enabled the characterization of organ-specific ER proteomes at baseline and in response to fasting, inflammation, and dietary obesity, revealing tissue-and perturbation-specific changes and augmenting our understanding of how the proteomes of individual tissues change to regulate systemic energy balance. This comprehensive resource represents an important advance toward understanding both how cell-to-cell communication changes in response to energy homeostasis and how it contributes to these alterations. This method is broadly applicable and provides a means for identifying biomarkers and therapeutic targets across a wide range of tissues.
    DOI:  https://doi.org/10.64898/2026.01.11.698831
  45. Nat Commun. 2026 Jan 30.
    Cancer cachexia in STK11/LKB1-mutated non-small cell lung cancer is dependent on tumor-secreted GDF15.
    Jinhai Yu, Tong Guo, Arun Gupta, Ernesto M Llano, Thomas Salisbury, Naureen Wajahat, Dianne Zhao, Sean Slater, Qing Deng, Esra A Akbay, Beverly A Rothermel, John M Shelton, Bret M Evers, Zhidan Wu, Iphigenia Tzameli, Evanthia Pashos, James Kim, John D Minna, Puneeth Iyengar, Rodney E Infante.
      Cachexia is a wasting syndrome involving adipose, muscle, and body weight loss in cancer patients. Tumor loss-of-function mutations in STK11/LKB1, a regulator of AMP-activated protein kinase, induce cancer cachexia (CC) in preclinical models and are linked to weight loss in non-small cell lung cancer (NSCLC) patients. This study examines the role of the integrated stress response (ISR) cytokine growth differentiation factor 15 (GDF15) in regulating cachexia using patient-derived and engineered STK11/LKB1-mutant NSCLC lines. Tumor cell-derived serum GDF15 levels are elevated in mice bearing these tumors. Treatment with a GDF15-neutralizing antibody or silencing GDF15 from tumor cells prevents adipose/muscle loss, strength decline, and weight reduction, identifying tumors cells as the GDF15 source. Restoring wild-type STK11/LKB1 in NSCLC lines with endogenous STK11/LKB1 loss reverses the ISR and reduces GDF15 expression rescuing the cachexia phenotype. Collectively, these findings implicate tumor-derived GDF15 as a key mediator and therapeutic target in STK11/LKB1-mutant NSCLC-associated cachexia.
    DOI:  https://doi.org/10.1038/s41467-026-68702-y
  46. RNA. 2026 Feb 03. pii: rna.080681.125. [Epub ahead of print]
    eRNAs Modulate mRNA Stability and Translation Efficiency to Bridge Transcriptional and Post-transcriptional Gene Regulation.
    Rene Kuklinkova, Natalia Benova, Chinedu Anthony Anene.
      Enhancer RNAs (eRNAs) are best known for their role in transcriptional regulation, where they facilitate enhancer-promoter communication and chromatin remodelling. Yet growing evidence suggests that their function may extend beyond the nucleus. Here, we systematically characterise the decay kinetics of eRNAs across human cell types using time-resolved transcriptomics and kinetic modelling. While most eRNAs undergo canonical exponential decay, a subset displays non-linear dynamics, suggesting context-dependent degradation mechanisms. Perturbation of core decay regulators, including components of the m⁶A and CCR4-NOT pathways, reveals that eRNA stability is modulated by a patchwork of pathways governing mRNA turnover. Integrating transcriptome-wide ribosome profiling, RNA-Seq, and half-life data, we identify eRNAs associated with changes in mRNA stability and translation efficiency of their target protein-coding transcripts. Functional validation of one such eRNA, en4528, shows it regulates CDKN2C mRNA independently of transcription and impacts cell migration. These findings redefine the regulatory scope of eRNAs, positioning them as active participants in post-transcriptional gene control and cellular behaviour. The resulting decay profiles and regulatory annotations have been incorporated into the eRNAkit database, available at https://github.com/AneneLab/eRNAkit, enhancing its capacity for integrative systems-level analysis of eRNA function.
    Keywords:  Enhancer RNA; Post-transcriptional regulation; RNA–RNA interaction; eRNAs; mRNA stability
    DOI:  https://doi.org/10.1261/rna.080681.125
  47. Cell Stress Chaperones. 2026 Jan 29. pii: S1355-8145(26)00002-7. [Epub ahead of print] 100146
    Transcriptional responses to proteotoxic stressors are profoundly diverse and tissue-specific.
    Adelina Rabenius, Intisar Salim, Hilmar Lindström, Anastasiya Pak, Serhat Aktay, Anniina Vihervaara.
      Cells counteract proteotoxic conditions by launching transcriptional stress responses. While synthesis of Heat shock proteins (HSPs) upon acute stress is well-characterized, how distinct proteotoxic conditions reshape the transcriptome remains poorly understood. Here, we analyse polyA+ RNA expression under heat shock, HSP90 inhibition, and polyglutamine (polyQ) aggregation. We find fundamentally distinct transcriptional responses to proteotoxic stressors, and a systemic deficiency of mice under chronic stress to launch acute responses. While heat shock and HSP90 inhibition induce chaperones, polyQ aggregation increases expression of RNAs linked to transcription repression, chromatin remodeling, and autophagy. Analysing wildtype and Huntington's Disease (HD) mice reveals tissue-specific transcriptional adaptations to polyQ, including repressed cell-type specific functions and altered energy metabolism. Despite profound reprogramming, remarkably few genes exhibit consistently increased (Acy3, Abhd1, Tmc3) or decreased (Fos) RNA levels across HD brain regions. These results emphasize cellular background in disease manifestation, and support energy metabolism and detoxifying enzymes as therapeutic targets in late-stage HD. Moreover, the systemic deficiency of chronically stressed mice to launch responses challenges strategies that rely on induced transcription. Altogether, we characterize transcription signatures to proteotoxic stresses, identify key trans-activators driving proteotoxic stress responses, provide an interactive gene-by-gene viewer of global changes, and delineate tissue-specific transcription programs in HD mice.
    Keywords:  Acute response; HSP90 inhibition; Hsf1-/-; Huntington's Disease; Q175; R6/2; chronic stress; heat shock; polyQ
    DOI:  https://doi.org/10.1016/j.cstres.2026.100146
  48. EMBO J. 2026 Feb 05.
    Cellular quiescence uncouples the proteome from the transcriptome in neural stem cells.
    Alice Rossi, Antoine Coum, Manon Madelenat, Lachlan Harris, Stephanie Strohbuecker, Andrea Chai, Hania Fiaz, Rita Chaouni, Peter Faull, Neve Costello Heaven, William Grey, Dominique Bonnet, Fursham Hamid, Eugene V Makeyev, Ambrosius P Snijders, Gavin Kelly, François Guillemot, Rita Sousa-Nunes.
      Quiescence is a cellular state defined by reversible cell-cycle arrest and diminished biosynthesis, particularly of nucleic acids and proteins. These features protect stem cells from proliferation-induced mutations, self-renewal exhaustion, and environmental insults. Despite relevance to development, tissue homeostasis and cancer, we lack understanding about many aspects of quiescence regulation and unique molecular markers for this state. Here, we employ Drosophila and mammalian neural stem cells to reveal that a mechanism for inhibiting translation in quiescence is selective nuclear enrichment of transcripts from more than 2000 genes, resulting in uncoupling between transcriptome and proteome. Three-quarters of these transcripts become increasingly nuclear as quiescence deepens, and nuclear bias predicts protein downregulation for the large majority of targets. We find that a large fraction of nuclear-biased transcripts present GA-rich multivalency and relocalise to nuclear speckles with increased SR-protein enrichment, which we propose promotes their nuclear retention. Finally, our evidence for differing degrees of transcript processing in steady-state quiescence suggests regulated sequential deployment of factors towards cell-cycle reentry. In brief, we present a previously unappreciated layer of post-transcriptional control of quiescence.
    Keywords:  Neural Stem Cells; Nucleocytoplasmic Partitioning; Nucleoporins; Quiescence; RNA Localisation
    DOI:  https://doi.org/10.1038/s44318-026-00693-4
  49. bioRxiv. 2026 Jan 12. pii: 2026.01.12.699007. [Epub ahead of print]
    Starvation-independent alarmone production inhibits translation through GTP depletion.
    Kevin A England, Aude Trinquier, Leah K McKinney, Jue D Wang, Heather A Feaga.
      Bacteria produce the alarmone nucleotides (p)ppGpp during stress to affect replication, transcription, translation, and metabolism. Recently, pGpp was identified as a third alarmone that is produced from the hydrolysis of (p)ppGpp. Although pGpp is a major component of bacterial stress responses, its precise role in mediating these responses is poorly understood. ppGpp and pppGpp bind translation GTPases and therefore directly affect translation to conserve resources during periods of stress. Here, we show that while pGpp is a weaker inhibitor of protein synthesis than ppGpp and pppGpp in vitro , pGpp production in the model Gram-positive bacterium Bacillus subtilis leads to faster translation inhibition in vivo . Faster translation inhibition is accompanied by greater levels of disengaged ribosomal subunits and hibernating ribosome dimers, suggesting that translation initiation is strongly inhibited. We show that alarmone production in vivo causes a severe depletion of GTP, which is sufficient for translation inhibition. Finally, we find that pGpp production also causes more robust transcriptome remodeling than (p)ppGpp production. This work supports a model that implicates all three alarmones in translation inhibition via GTP depletion.
    DOI:  https://doi.org/10.64898/2026.01.12.699007
  50. Proc Natl Acad Sci U S A. 2026 Feb 10. 123(6): e2524289123
    An interpretable molecular framework for predicting cancer driver missense mutations.
    Yan Yang, Weikang Sun, Yang Liu, Jian Zhang, Minghui Li.
      Missense mutations play a critical role in human disease, contributing to both inherited disorders and cancer. However, accurately predicting their functional impact-particularly for cancer driver mutations-remains a major challenge due to limited validated labels and the complex molecular basis of oncogenesis. Here, we systematically characterized over 120,000 missense variants across pathogenic, benign, driver, passenger, recurrent somatic, and common population classes, using a comprehensive set of mechanistically grounded molecular features. By assessing the statistical burden of variations, we demonstrated that these features effectively discriminate among diverse variant classes and reveal a consistent enrichment of functional sites, structural integrity, and biophysical changes in pathogenic and driver mutations. Building on these insights, we developed MutaPheno, an interpretable framework for predicting the functional consequences of missense mutations. The model integrates 34 molecular-level features, encompassing structural, functional, physicochemical, and contextual descriptors, using a random forest algorithm. Trained exclusively on pathogenic and benign variants, MutaPheno achieved strong accuracy in predicting cancer driver mutations, outperforming both cancer-specific and general pathogenicity tools, while also demonstrating superior robustness when tested on unseen proteins. Our findings highlight the shared mechanisms between pathogenic and driver mutations and emphasize the role of molecular features in improving variant interpretation. MutaPheno provides a transparent and generalizable tool that can facilitate driver discovery and the development of targeted therapies.
    DOI:  https://doi.org/10.1073/pnas.2524289123
  51. Nat Commun. 2026 Jan 31.
    Reliable repurposing of the antibody interactome inside the cell.
    Caitlin M O'Shea, Rushba Shahzad, Kimia Aghasoleimani, Stuart Newman, Jiraporn Panmanee, Leonard C Schalkwyk, Greg N Brooke, Fiona E Benson, James S Trimmer, Daryl A Bosco, Takao Fujisawa, Hidenori Ichijo, Neil R Cashman, Stanislav Engel, Gareth S A Wright.
      Eighty-five percent of the human proteome has at least one interacting monoclonal antibody. These molecules penetrate the cytoplasm poorly and are very often non-functional within the cell. Analysis of antibody variable domains and characterisation of forty-five single-chain variable fragment (scFv) intrabodies expressed in human cells indicated charge to have the greatest impact on solubility. We created new interdomain linkers, optimised scFv domain orientation and found an optimisable charge discrepancy between variable heavy framework and CDR sites. When applied to reduce the search space and rank the products of AI-led inverse folding this creates a single highly soluble, abundant and stable intrabody with parent antibody epitope recognition. Over six hundred intrabody sequences are presented targeting sixty cytoplasmic proteins with linear, conformational, post-translational modification or oligomer specificity. Interactions were validated for p53, α-synuclein, SOD1, polyQ, FUS/TLS, UCHL1 and GFP. Here we show reliable repurposing of the sequenced antibody interactome inside the cell.
    DOI:  https://doi.org/10.1038/s41467-026-69057-0
  52. Nat Commun. 2026 Feb 05.
    Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.
    Vincent Schnapka, Tatiana I Morozova, Samiran Sen, Massimiliano Bonomi.
      Intrinsically disordered proteins are ubiquitous in biological systems and play essential roles in a wide range of biological processes and diseases. Despite recent advances in high-resolution structural biology techniques and breakthroughs in deep learning-based protein structure prediction, accurately determining structural ensembles of IDPs at atomic resolution remains a major challenge. Here, we introduce bAIes, a Bayesian framework that integrates AlphaFold2 predictions with physico-chemical molecular mechanics force fields to generate accurate atomic-resolution ensembles of IDPs. We show that bAIes produces structural ensembles that match a wide range of high- and low-resolution experimental data across diverse systems, achieving accuracy comparable to atomistic molecular dynamics simulations but at a fraction of their computational cost. Furthermore, bAIes outperforms state-of-the-art IDP models based on coarse-grained potentials as well as deep-learning approaches. Our findings pave the way for integrating structural information from modern deep-learning approaches with molecular simulations, advancing ensemble-based understanding of disordered proteins.
    DOI:  https://doi.org/10.1038/s41467-026-69172-y
  53. Dis Model Mech. 2026 Jan 01. pii: dmm052534. [Epub ahead of print]19(1):
    Intersections between proteostasis and immunity: insights from Caenorhabditis elegans.
    Emily R Troemel, Patricija van Oosten-Hawle, Michalis Barkoulas.
      Cells must properly synthesize, fold and degrade proteins to maintain protein homeostasis, or proteostasis. Studies in the model nematode host Caenorhabditis elegans have illuminated different ways in which proteostasis intersects with immune responses against pathogen infection, which is the focus of this Review. For example, pathogens often interfere with host proteostasis pathways to survive and replicate. Hosts, in turn, can sense these perturbations and then trigger immune responses, creating additional burdens on proteostasis. This Review is organized by the cellular compartments in which proteostasis pathways are activated, starting with the cytosolic processes of protein synthesis, folding, degradation and the ubiquitin-proteasome system. Next, we cover autophagy and lysosome-related processes, followed by pathways triggered in the endoplasmic reticulum and mitochondria. We discuss infections in C. elegans by bacteria, viruses, microsporidia and oomycetes; all of these pathogen types infect humans. We provide examples of how findings in C. elegans relate to mammals, noting how the coordination of proteostasis and immunity can be conserved across species. We emphasize a recurring theme in C. elegans that impairment of one proteostasis pathway can lead to compensatory activation of another pathway, ultimately providing a health benefit to the host, highlighting organismal resilience.
    Keywords:   C. elegans ; Infection; Innate immunity; Pathogen; Proteostasis
    DOI:  https://doi.org/10.1242/dmm.052534
  54. Redox Biol. 2026 Jan 25. pii: S2213-2317(26)00044-3. [Epub ahead of print]90 104046
    UFMylation deficiency in hepatocytes activates the KEAP1-NRF2 pathway and contributes to hepatocarcinogenesis.
    Qian Liang, Shiwen Xu, Yaoyao Fang, Xue Wang, Yang Xiao, Yiwen Wang, Shujuan Li, Qifan Guo, Yu Cao, Ying Cao, Chao Liu, Yuqin Zhao, Yan Luo, Anqi Wu, Miao Wang, Junping Shi, Guoqing Li, Yu-Sheng Cong.
      The Kelch-like ECH-associated protein 1 (KEAP1) - Nuclear factor erythroid 2-related factor 2 (NRF2) pathway plays a central role in maintaining cellular redox balance, aberrant activation of the KEAP1-NRF2 pathway is involved in a variety of human malignant tumors including hepatocellular carcinoma. However, the underlying mechanisms remain unclear. UFMylation is a type of ubiquitin-like modifications with important biological functions, its deficiency is implicated in several pathogenesis. In this study, we show that hepatocyte specific Ufl1 knockout in mice results in several hepatic pathological alterations and promotes the development of diethylnitrosamine (DEN)-induced hepatocarcinogenesis. Furthermore, we identified KEAP1 as an UFMylation substrate, and deficiency in UFMylation modification resulted in ubiquitin-mediated degradation of KEAP1, and subsequent nuclear accumulation of NRF2, and activation of the KEAP1-NRF2 pathway. Consistently, we found that UFL1 expression is decreased and positively correlated with the level of KEAP1 in liver cancer samples. Our results suggest that UFL1 plays an important role in liver pathophysiology, in part by regulating the KEAP1-NRF2 pathway, thus provides novel insights into the molecular basis of hepatocarcinogenesis.
    Keywords:  Hepatocellular carcinoma; Hepatocytes; KEAP1-NRF2 pathway; UFL1; UFMylation
    DOI:  https://doi.org/10.1016/j.redox.2026.104046
  55. Chembiochem. 2026 Feb 12. 27(3): e202500799
    Structure-Guided Synthetic Peptide Targeting Nucleolus and Neural Progenitor Protein Nuclear Import Impairs Ribosome Biogenesis and Cancer Cell Proliferation.
    Abhishek Kumar, Suvam Saha, Yogendra Pratap Mathuria, Mukesh Kumar, Shailesh Kumar Gupta, Debasish Kumar Ghosh.
      Nucleolus and neural progenitor protein (NEPRO) is a nucleolar factor required for 40S ribosomal subunit maturation and is therefore essential for the high translational demand of proliferating cancer cells. Here, we identify a bipartite nuclear localization signal (NLS; aa 74-96) in NEPRO and show that residues in both basic clusters are required for nuclear targeting. A disease-associated mutation within the C-terminal cluster, R94C, abolished NEPRO nuclear localization and markedly reduced binding to importin-α1 in vitro and in cells. Importin-α1-NLS complexes revealed that R94 forms persistent hydrogen bonds, salt bridges, and hydrophobic contacts with importin-α1 residues (A269, W273, P308, T311, P312, N350), explaining its central role in NLS recognition. Guided by these insights, we designed a rational synthetic hexapeptide inhibitor (H2N-AWPTPD-COOH) that is soluble, monodisperse, shows intrinsic fluorescence and is non-amyloidogenic. AWPTPD peptide binds wild-type NEPRO but not the R94C variant, and ab initio modeling shows peptide engagement of the R94 surface. Cellular delivery of the synthetic peptide significantly mislocalized NEPRO to the cytoplasm, reduced polysome abundance, decreased collagen secretion/deposition and clonogenicity, and induced cell-cycle arrest with upregulation of senescence markers: p16INK4A and p21WAF1/CIP1. These results validate R94 as a targetable hotspot in NEPRO's NLS and demonstrate a peptide-based approach to perturb ribosome biogenesis and suppress cancer cell growth.
    Keywords:  cancer cell growth inhibition; nuclear localization signal; nucleolus and neural progenitor protein; peptide inhibitor; ribosome biogenesis
    DOI:  https://doi.org/10.1002/cbic.202500799
  56. J Biol Chem. 2026 Jan 28. pii: S0021-9258(26)00083-9. [Epub ahead of print] 111213
    Mannose metabolic pathway senses glucose supply and regulates cell fate decisions.
    Ziwei Wang, Yasuhide Miyamoto, Takehiro Suzuki, Miki Tanaka-Okamoto, Yu Mizote, Naoshi Dohmae, Hideaki Tahara, Naoyuki Taniguchi, Yoichiro Harada.
      Mammalian cells exploit diverse metabolic pathways to regulate cell fates during glucose deprivation. We previously reported that glucose deprivation lowers the metabolic activity of mannose pathway that is interconnected with glycolysis, leading to biosynthetic arrest and degradation of the glycan precursors for asparagine-linked glycosylation (N-glycosylation) in the endoplasmic reticulum (ER). However, the cellular role of this sequential metabolic response remains unknown, largely due to metabolic complications caused by glucose deprivation. Here, we genetically engineered cells to separate mannose pathway from glycolysis, allowing precise control of mannose pathway activity by adjusting mannose supply levels instead of changing glucose supply. Moderate decrease in mannose supply severely suppressed N-glycosylation, leading to activation of pro-survival PERK-eIF2 signals. Although further decrease in mannose supply to the minimal levels did not compromise cell survival, it depleted luminal protective glycocalyx of lysosomes and increased a risk of cell death by impairing lysosome integrity. These results indicate that low metabolic flux of glucose into mannose pathway initiates alterations in homeostasis of the ER and lysosomes, at least in part through N-glycosylation defects, leading to cell fate decisions.
    Keywords:  Cell fate decision; N-glycosylation; endoplasmic reticulum; glucose deprivation; lysosomes
    DOI:  https://doi.org/10.1016/j.jbc.2026.111213
  57. Npj Viruses. 2026 Feb 02. 4(1): 8
    Divergent roles of Hsp70 chaperones in orthoflavivirus protein secretion and virion formation.
    Lea Blank, Christin Lorenz, Imke Steffen.
      Orthoflaviviruses, such as tick-borne encephalitis virus (TBEV) and West Nile virus (WNV), can cause severe neurological disease and remain without specific antiviral treatments. We found that orthoflavivirus envelope (E) and non-structural protein 1 (NS1) interact with heat shock protein 70 (Hsp70) chaperones, key regulators of protein homeostasis and existing cancer drug targets. We examined how Hsp70 and endoplasmic reticulum-resident BiP contribute to viral protein secretion and infectivity of tick and mosquito-borne orthoflaviviruses. Targeting the Hsp70 nucleotide-binding domain with small-molecule inhibitor YM-1 significantly reduced infectivity of multiple orthoflaviviruses, while substrate-binding domain inhibitor PES-Cl specifically impaired NS1 secretion of tick-borne orthoflaviviruses. Protein degradation inhibitors restored NS1 expression in BiP-deficient cells but failed to rescue NS1 secretion. These data indicate that while BiP is essential for secretion of tick-borne orthoflavivirus NS1, it is not required for infectivity. The antiviral effect of YM-1 likely reflects inhibition of other chaperones or additional cellular targets.
    DOI:  https://doi.org/10.1038/s44298-026-00175-8
  58. Autophagy. 2026 Feb 04. 1-19
    PRKN activation for mitophagy requires an NME3-regulated phosphatidic acid signal that separates mitochondria from endoplasmic reticulum tethering.
    Chih-Wei Chen, Ying-Jung Chen, Xiaojing Cuili, Yi-Han Chen, Zee-Fen Chang.
      PINK1-dependent activation of PRKN/parkin on depolarized mitochondria causes mitophagy. The deficiency of NME3, a nucleoside diphosphate kinase/NDPK on the outer mitochondria membrane (OMM), is associated with a fatal neurodegenerative disorder. Here, we report that NME3 deficiency impairs p-S65-ubiquitin (Ub)-dependent PRKN binding on depolarized mitochondria without involving the loss of Ub phosphorylation by PINK1. Our mechanistic investigation revealed that NME3 interacts with PLD6/MitoPLD to generate phosphatidic acid (PA) from cardiolipin on the OMM of damaged mitochondria after depolarization. This lipid signal is essential for positioning MFN2 nearby PINK1 for phosphorylation of Ub conjugates on MFN2, thus enabling the subsequent amplification of PRKN binding to mitochondria. We provide further evidence that mitochondria-endoplasmic reticulum (Mito-ER) tethering prohibits the proximity of MFN2 with PINK1 and PRKN amplification on mitochondria. Importantly, the loss of NME3-regulated PA signal causes Mito-ER tethering. Overall, our findings suggest that NME3 cooperates with PLD6 to generate PA as a critical step in Mito-ER untethering, allowing MFN2 access to PINK1 for p-S65-poly-Ub-dependent feedforward activation of PRKN.Abbreviation ACTB: actin beta; BDNF brain derived neurotrophic factor; CL: cardiolipin; CRISPR: clustered regularly interspaced short palindromic repeats; DAG: diacylglycerol; ER: endoplasmic reticulum; FCCP: carbonyl cyanide p-(trifluoromethoxy) phenylhydrazone; FRET: Förster resonance energy transfer; IF: immunofluorescence; KO: knockout; KD: knockdown; LPIN1: lipin 1; MERCS: mitochondria-endoplasmic reticulum contact sites; MFN2: mitofusin 2; Mito: mitochondria; OMM: outer mitochondrial membrane; p-Ub: phosphorylated ubiquitin; PA: phosphatidic acid; PD: Parkinson disease; PINK1: PTEN induced kinase 1; PLA: proximity ligation assay; PLD6/MitoPLD: phospholipase D family member 6; PRKN: parkin RBR E3 ubiquitin protein ligase; RA: retinoic acid; RT-qPCR: reverse transcription-quantitative polymerase chain reaction; TEM: transmission electron microscopy; TN-NME3: TOMM20-NΔ-NME3; TOMM20: translocase of outer mitochondrial membrane 20; TUBB: tubulin beta class I; Ub: ubiquitin; VDAC: voltage dependent anion channel; WB: western blot.
    Keywords:  MFN2; NME3; PINK1; PRKN; mitophagy; phosphatidic acid
    DOI:  https://doi.org/10.1080/15548627.2026.2623981
  59. Nat Chem Biol. 2026 Feb 05.
    A pharmacological modality to sequester homomeric proteins.
    Ella Livnah, Ohad Suss, Adi Rogel, Atar Gilat, Yuval Abdan, José A Villegas, Ronen Gabizon, Almog Nadir, Yoav Shamir, Noam Y Steinman, Barr Tivon, Shira Albeck, Tamar Unger, Ofra Golani, Inna Goliand, Nadav Elad, Silvia Carvalho, Khriesto Shurrush, Haim Barr, David Margulies, Emmanuel D Levy, Nir London.
      Molecules that facilitate protein-protein interactions are immensely impactful. However, such compounds typically rely on accessory proteins to function, such as E3 ligases for targeted degradation, which may restrict their scope or lead to resistance. We alleviate the need for accessory proteins with a strategy that exploits protein symmetry as a selective vulnerability and is widely applicable because of the ubiquitous nature of homomeric proteins. We target homomeric proteins with PINCHs (polymerization-inducing chimeras)-bifunctional molecules composed of two linked ligands that bridge homomers and trigger their supramolecular assembly into insoluble polymers. We design PINCHs that achieve efficient polymerization of four targets. In cells, we observed that a PINCH targeting Keap1 exhibited a longer duration of action and a PINCH targeting BCL6 displayed selective lowering of B cell viability compared to their monomeric parents. Our results highlight PINCHs as a novel and general strategy to modulate and knock out protein function.
    DOI:  https://doi.org/10.1038/s41589-026-02141-0
  60. iScience. 2026 Feb 20. 29(2): 114630
    N6-methyladenosine (m6A) modification of TXNIP in 3'UTR instigates abdominal aorta aneurysm in mice.
    Fransky Hantelys, Wenfeng Yin, Ming Hui Zou.
      The thioredoxin-interacting protein (TXNIP) pathway is a central regulator of oxidative stress and contributes to vascular pathology. Here, we define how stress-responsive mRNA methylation controls TXNIP expression and drives abdominal aortic aneurysm (AAA). In angiotensin II (AngII)-infused ApoE -/- mice, TXNIP was markedly elevated in vascular smooth muscle cells (VSMCs), as confirmed by histological, protein, and transcript analyses. VSMC-specific TXNIP deletion (ApoE -/- TXNIP SM-/- ) significantly reduced AAA incidence, aortic remodeling, and elastic fiber degradation, establishing its essential role in disease progression. Mechanistic studies revealed that elevated m6A methylation, catalyzed by METTL3, promoted TXNIP translation via YTHDF1 binding to m6A sites within the 3' untranslated region (UTR), whereas YTHDF2 downregulation in AAA stabilized TXNIP transcripts. TXNIP translation also proceeded through a cap-independent process enhanced by mTOR inhibition. These findings identify an integrated m6A-dependent regulatory program governing TXNIP expression and highlight therapeutic opportunities for targeting AAA progression.
    Keywords:  Biochemistry; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2026.114630
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