bims-proteo Biomed News
on Proteostasis
Issue of 2026–07–19
53 papers selected by
Eric Chevet, INSERM
  1. Clearance and secretion of α-synuclein by RTN3L-mediated endoplasmic reticulum autophagy.
  2. The E3 ligase TRIM13 restrains LPS-induced inflammation by reducing STIM1 abundance and the IRE1α-dependent unfolded protein response.
  3. Structural basis of cotranslational protein N-terminal acetylation by NatB in human cells.
  4. Two Mechanisms One Molecule: Developing a 'Truly' Bifunctional Degrader Targeting Rpn13 and CRBN.
  5. Role of Pbr1, a putative oxidoreductase, in the ER quality control and folding of yeast Fks1 glucan synthase.
  6. COMPASS: A Computational Pipeline to Identify Linkers Predicting Ubiquitinable PROTAC-Induced Ternary Complexes.
  7. Large-scale quaternary structural transitions underlie gain of function of SPOP cancer mutations.
  8. Dissecting the functional divergence of DCAF11 isoforms in protein degradation.
  9. The Sigma1 ER membrane receptor promotes structural protein folding and genome packaging of dengue virus.
  10. Developmental priming of adult proteostasis and longevity by NuA4 complex activity in early life.
  11. ER quality control: how cells detoxify their own membrane from lipid stress.
  12. Induced ubiquitination of the partially disordered estrogen receptor alpha via a 14-3-3 directed molecular glue-PROTAC.
  13. Regulatory T cell immunosuppressive function requires chaperone-mediated autophagy.
  14. Distinct cell type-specific mechanisms underlie cognitive dysfunction during persistent integrated stress response activation.
  15. PERK deficiency amplifies molecular, structural, and network vulnerability to repetitive mild traumatic brain injury.
  16. A quantitative approach for defining the degradability landscape of protein degraders.
  17. De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging.
  18. FGF21 induced by endoplasmic reticulum stress maintains medullary thymic epithelial cell function and central immune tolerance.
  19. ZnF-UBP domains regulate deubiquitinase activity by relieving ubiquitin product inhibition.
  20. Structure-Guided Discovery of Novel Dual-Site FEM1B Ligands and Assessment of Their Use in Targeted Protein Degradation.
  21. Identification of Clofibric Acid as a Synoviolin (SYVN1) Ligand for Proteolysis-Targeting Chimera (PROTAC) Development.
  22. Spalt-related is an inhibitor of mTORC1-mediated growth activated by the integrated stress response.
  23. The regulation of protein phosphatase 4 by FBXO42 is required for cancer cell survival.
  24. Pan-Cancer Landscape of Spatial PTM and Mutation Clusters Reveals Allosteric Regulation of Protein-Protein Interactions.
  25. Dynamic global acetylation remodeling during the yeast heat shock response.
  26. Genome-wide CRISPR-Cas9-based screening revealed the role of ubiquitin ligase TRIM25 in ribosome degradation via ribophagy.
  27. Metabolite glues as a means of purine sensing and chemotherapeutic response.
  28. Damage control: new functions for the Arp2/3 complex and WHAMM in autophagy and lysosomal homeostasis.
  29. Combating ageing beyond the cell: Emerging roles of extracellular proteostasis.
  30. Ufl1-Mediated UFMylation Sustains Amelogenesis by Stabilizing RUNX2.
  31. Receptor-mediated Golgi retention of Fam20 kinases tunes secretome phosphorylation during lactation.
  32. TRiC-assisted folding of class I HDAC family proteins regulated by distinct co-chaperone and cofactor networks.
  33. Lysosomes and lysosomal dysfunction in ageing biology.
  34. Leucine rich repeat containing protein 8B (LRRC8B) - A novel modulator of endoplasmic reticulum (ER) stress response.
  35. The autoimmune regulator (AIRE) is a target of the E3-Ubiquitin ligase Seven-in-absentia homolog 1 (SIAH1).
  36. Novel CDK-independent function of CDC25 phosphatases in mRNA translation.
  37. Understanding protein ISGylation, a multifaceted posttranslational modification.
  38. ALR couples IMS redox and heme biosynthesis beyond the disulfide relay.
  39. Loss of E3 Ubiquitin Ligase RINES via CpG Methylation Relieves Suppression of STAT3 and MYC, Facilitating Multiple Tumorigeneses.
  40. Visual system function requires translational regulation of ATF4 by Hbs1-Pelo.
  41. Identification of substrates of the protein tyrosine phosphatase PTP1B using in situ site-specific photo-crosslinking.
  42. Thermo-sensing mechanisms of splicing control by nuclear stress bodies.
  43. Ubiquitin-elongating enzyme Ufd2 confers resistance to hygromycin B in Saccharomyces cerevisiae.
  44. Local translation of endosome-associated lc3b mRNA in axons contributes to endosomal clearance.
  45. Granular component sub-phases direct ribosome biogenesis in the nucleolus.
  46. Circular RNAs-Stress Granule Interplay Drives Aging-Related Proteostasis Loss.
  47. Nuclear PI3P produced by the Beclin-1/Vps34 complex regulates DNA mismatch repair.
  48. Autophagy maintains high endothelial venule identity and function during inflammation.
  49. Tissue-specific consequences of impaired RNA surveillance converge on mitochondrial homeostasis.
  50. Cell-type-specific ATF6α programs regulate epithelial mitochondrial homeostasis and pericyte remodeling during physiological and exposure-accelerated lung aging.
  51. The unfolded protein sensor IRE1 is essential for homeostatic dendritic cell maturation.
  52. Multidomain Relaxation Dispersion NMR Resolves an Intermediate-Gated Binding Pathway for Selective Recognition of Linear Diubiquitin by HOIL-1L.
  53. Convergent nuclear proteostasis alterations across 40S ribosomal protein deficiencies.
  1. Mol Biol Cell. 2026 Jul 15. mbcE26030138
    Clearance and secretion of α-synuclein by RTN3L-mediated endoplasmic reticulum autophagy.
    Yihong Ye, Kamal Kumar, Yue Xu, Fenfen Xu, Susan Ferro-Novick.
      The misfolding and aggregation of α-synuclein (α-syn), an abundant synaptic protein, leads to the pathogenesis of Parkinson's disease and related synucleinopathies. The cell-to-cell propagation of seeding-competent α-syn is initiated by unconventional protein secretion, yet the physiological pathway(s) underlying this process remain poorly defined. Here we show that α-syn secretion in human cells is mediated by Reticulon-3L (RTN3L)-dependent endoplasmic reticulum autophagy (ER-phagy), a conserved protein quality-control pathway that safeguards ER protein homeostasis. We also demonstrate that RTN3L cooperates with several autophagy regulators, including the ULK1 cofactor FIP200, to drive the delivery of α-syn into an acidic endolysosomal compartment. Increasing concentrations of α-syn disrupt ER-lysosome traffic and α-syn-containing vesicles appear to be rerouted to the cell surface. Consistent with this proposal, knockdown of vesicle associated SNAREs, that mediate fusion at the cell surface, disrupt α-syn secretion. These findings suggest that pathogenic α-syn secretion arises as a by-product of a physiological clearance mechanism, driven by the fusion of autophagosome-derived vesicles with the plasma membrane. Our results provide a conceptual framework for understanding how an intracellular proteostasis pathway, when mis-regulated, could contribute to the spread of neurodegenerative pathology.
    DOI:  https://doi.org/10.1091/mbc.E26-03-0138
  2. Sci Signal. 2026 Jul 14. 19(946): eaeb2470
    The E3 ligase TRIM13 restrains LPS-induced inflammation by reducing STIM1 abundance and the IRE1α-dependent unfolded protein response.
    Zheng Li, Xuelian Li, Zhou Yu, Qian Fang, Tong Xia, Jiaying Huang, Mingjin Yang, Taoyong Chen.
      Recognition of the bacterial product lipopolysaccharide (LPS) by Toll-like receptor 4 (TLR4) initiates inflammatory responses. The unfolded protein response (UPR) elicited by endoplasmic reticulum (ER) stress can strengthen TLR4-dependent inflammatory responses. Here, we report that the ER-localized E3 ubiquitin ligase TRIM13 restrained LPS-induced inflammatory responses in macrophages and in mice by protecting the cells from ER stress. TRIM13 mediated Lys33-linked polyubiquitylation of the ER-localized Ca2+ sensor STIM1, promoting its degradation. TRIM13 deficiency caused STIM1 accumulation and activated store-operated Ca2+ entry (SOCE) and the inositol-requiring enzyme 1 α (IRE1α) branch of the UPR. Suppressing SOCE, chelating extracellular Ca2+, relieving ER stress, or blocking IRE1α activation inhibited the amplification of inflammatory responses caused by the loss of TRIM13 in macrophages. Pharmacological inhibition of IRE1α ameliorated chemically induced colitis in TRIM13-deficient mice. Our study suggests that TRIM13 restrains inflammation by limiting LPS-induced activation of SOCE and the IRE1α branch of the UPR.
    DOI:  https://doi.org/10.1126/scisignal.aeb2470
  3. Nat Commun. 2026 07 11. pii: 6088. [Epub ahead of print]17(1):
    Structural basis of cotranslational protein N-terminal acetylation by NatB in human cells.
    Natalia Silva Alves, Pawel Knejski, Alain Scaiola, Marc Leibundgut, Martin Gamerdinger, Nenad Ban, Elke Deuerling.
      Cotranslational N-terminal acetylation is a widespread modification that shapes protein stability, localization, and function in eukaryotic cells. The essential human NatB complex (NAA25-NAA20) acetylates the initiator methionine of a substantial fraction of the proteome, yet how NatB engages translating ribosomes has remained unclear. Here we define the cotranslational mechanism underlying NatB function. NatB is recruited by the nascent polypeptide-associated complex (NAC) through a high-affinity interaction between the NACα UBA domain and the auxiliary subunit NAA25, while both NatB subunits form additional contacts with the ribosomal surface near the tunnel exit. Together, these interactions position the NatB active site directly adjacent to the emerging nascent chain, enabling efficient modification of newly synthesized proteins. Structural comparisons reveal a conserved ribosome-binding architecture shared with other N-acetyltransferases, including NatA/E and NatD, implying mutually exclusive ribosome occupancy. Together with prior work, these findings establish NAC as a central organizer of cotranslational N-terminal processing.
    DOI:  https://doi.org/10.1038/s41467-026-75207-1
  4. J Am Chem Soc. 2026 Jul 17.
    Two Mechanisms One Molecule: Developing a 'Truly' Bifunctional Degrader Targeting Rpn13 and CRBN.
    Cody A Loy, Shawn E Vinogradsky, Darci J Trader.
      Targeted protein degradation (TPD) has emerged as a powerful strategy to eliminate disease-relevant proteins, yet current approaches remain largely constrained to hijacking ubiquitin ligases. We previously introduced ByeTACs, bifunctional molecules that directly recruit proteins to the proteasome for E-ligase independent degradation. Here, we report "Truly" degraders, a new class of dual-mechanism molecules that combine a ligand for the proteasomal receptor Rpn13 with a ligand for cereblon (CRBN) to simultaneously engage both ubiquitin-independent and ubiquitin-dependent degradation pathways. Structure-guided design identified an optimal linker length that supports efficient substrate processing, with the PEG4 derivative (Truly-4) inducing robust depletion of both Rpn13 and CRBN in several cancer cell types. Remarkably, Truly-4 is the first noncovalent small molecule shown to degrade full-length Rpn13, a target previously approached using covalent or domain-restricted strategies. Mechanistic studies confirmed that degradation of Rpn13 proceeds via CRBN-dependent E3 ligase activity, whereas CRBN degradation occurs through an E-ligase independent process, consistent with a ByeTAC mechanism. Importantly, Truly-4 induces selective cytotoxicity in hematologic and solid cancer cell lines but not in healthy cells, despite comparable Rpn13 depletion, indicating that dual degradation can uncouple target engagement from toxicity. These findings establish a generalizable framework for engineering bifunctional degraders that program the proteasome to execute parallel degradation mechanisms and highlight proteasome receptors as druggable nodes for selective destruction of disease-relevant proteins.
    DOI:  https://doi.org/10.1021/jacs.6c02914
  5. Proc Natl Acad Sci U S A. 2026 Jul 21. 123(29): e2612792123
    Role of Pbr1, a putative oxidoreductase, in the ER quality control and folding of yeast Fks1 glucan synthase.
    Keisuke Obara, Hiroki Okada, Guihong Tan, Shinsuke Ohnuki, Godai Suzuki, Haruka Ohtake, Karen Kubo, Farzan Ghanegolmohammadi, Shunsuke Ishizaka, Yoko Yashiroda, Aoi Okita, Emi Mishiro-Sato, Kuninori Suzuki, Yasushi Tamura, Rei Ashine, Yoshiki Ikeda, Takumi Kamura, Jolanda van Leeuwen, Brenda Andrews, Erfei Bi, Nobuo N Noda, Charles Boone, Yoshikazu Ohya.
      The biogenesis of multipass membrane proteins challenges the endoplasmic reticulum (ER) quality control, particularly when transmembrane segments contain polar or charged residues required for function. Fks1, the catalytic subunit of yeast β-(1,3)-glucan synthase, exemplifies this challenge because its large multipass transmembrane architecture must support glucan synthesis at the plasma membrane while also undergoing efficient biogenesis in the ER. Here, we investigate the cellular role of PBR1 (YNL181W), an essential gene whose role remains uncharacterized even though its predicted product has similarity to oxidoreductases. By integrating quantitative morphological profiling with global genetic interaction analysis, we found that PBR1 function converges on cell-wall biosynthesis and closely parallels that of FKS1. Partial loss of Pbr1 function caused temperature-sensitive growth defects but also impaired β-(1,3)-glucan synthesis, and weakened cell-wall integrity. Under these conditions, Fks1 failed to accumulate at the cell surface and, instead, accumulated in ER-associated compartments, where it exhibited reduced stability. Biochemical analyses revealed the accumulation of immature Fks1 species, including forms defective in glycosylation, consistent with compromised ER quality control. A spontaneous missense suppressor allele of FKS1 partially restored Fks1 stability and growth, supporting a functional relationship between the two proteins. Pbr1 is a cytosol-facing ER membrane protein that physically associates with Fks1, and structural modeling suggests that it adopts a Rossmann-like fold capable of binding pyridine nucleotides despite divergence from canonical catalytic motifs. Together, these findings identify Pbr1 as an ER-associated, chaperone-like factor required for the folding and maturation of Fks1.
    Keywords:  ER quality control; glucan synthase; yeast
    DOI:  https://doi.org/10.1073/pnas.2612792123
  6. ChemMedChem. 2026 Jul 29. 21(14): e70385
    COMPASS: A Computational Pipeline to Identify Linkers Predicting Ubiquitinable PROTAC-Induced Ternary Complexes.
    Sébastien Sueron, Sayyed Jalil Mahdizadeh, Eric Chevet, Xavier Guillory, François-Hugues Porée, Leif A Eriksson.
      PROteolysis TArgeting Chimeras (PROTACs) are bifunctional molecules designed to induce targeted protein degradation by forming a transient ternary complex between an E3 ubiquitin ligase and a protein of interest (POI), leading to the E3-mediated ubiquitination of the POI and its subsequent proteasomal degradation. Although PROTACs have emerged as highly promising therapeutic tools, rational design remains challenging due to limited structural understanding of the resulting assemblies, the dynamic nature of the ternary interface, and the critical role of the linker. Herein, we present COMPASS (COmputational Modeling of PROTAC Assembly with Structure-based Screening), a computational pipeline that allows the screening of linker libraries by assessing both ternary complex formation and ubiquitination potential. COMPASS functions as a high-sensitivity negative filter, identifying linkers that cannot form productive complexes and enabling their elimination before synthesis. Benchmarking against 20 crystallographic structures yielded <6 Å Cα-RMSD across all systems, outperforming existing methods. Retrospective validation across 8 distinct E3/POI systems (112 PROTACs) yielded 93% recall against degradation endpoints. Discriminative power is strongest when linker geometry is rate-limiting, a regime complementary to the stability and cooperativity effects that static structural modeling cannot capture.
    Keywords:  PROTAC; degradation; medicinal chemistry; molecular modeling; ternary complex; ubiquitination
    DOI:  https://doi.org/10.1002/cmdc.70385
  7. Mol Cell. 2026 Jul 13. pii: S1097-2765(26)00419-3. [Epub ahead of print]
    Large-scale quaternary structural transitions underlie gain of function of SPOP cancer mutations.
    Matthew J Cuneo, Ömer Güllülü, Mohamed-Raafet Ammar, Xinrui Gui, Kelly Churion, Martin Turk, Brian G O'Flynn, Nafiseh Sabri, Tanja Mittag.
      Speckle-type POZ protein (SPOP), a substrate receptor for the Cullin-3-RING (CRL3) ubiquitin ligase, is mutated in different cancers. Both activating and inactivating mutations in SPOP drive oncogenesis, underscoring the need for precise regulation. Among substrate receptors, SPOP uniquely assembles into filaments that are multivalent for substrate binding. Conversely, many substrates contain multiple SPOP-binding motifs. How this unusual reciprocal multivalent architecture regulates ubiquitination and how mutations activate SPOP are unclear. Gain-of-function mechanisms are also generally poorly understood. Here, we reveal that SPOP assemblies exist in an equilibrium between an active filament and a large, autoinhibited, circular "double-donut" state. Activating mutations shift the equilibrium, resulting in aberrant substrate turnover. Combinations of activating and inactivating mutations can produce intermediate activities, thus uncovering a tunable regulatory axis with implications for targeted cancer therapies. Therefore, SPOP's ability to assemble into long filaments is required for its regulation in human cells and underlies a gain-of-function mechanism.
    Keywords:  Cullin ring ligase; SPOP; cryo-EM; endometrial cancer; filament; gain of function; higher-order oligomer; prostate cancer; proteostasis; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.030
  8. RSC Chem Biol. 2026 Jul 10.
    Dissecting the functional divergence of DCAF11 isoforms in protein degradation.
    Xiaokang Jin, Xiaoyu Zhang.
      DCAF11 is a substrate receptor of the Cullin-RING ligase 4 (CRL4) ubiquitin ligase complex and an emerging effector supporting targeted protein degradation. DCAF11 exists as two major isoforms, but their functional differences remain incompletely understood. Here, we show that DCAF11 isoforms 1 and 2 assemble into CRL4 complexes with similar efficiency and exhibit largely overlapping endogenous substrate profiles, including proteins implicated in electrophile detoxification. In contrast, they differ in their compatibility with small-molecule degraders: covalent PROTACs engage both isoforms, whereas a non-covalent molecular glue selectively utilizes isoform 1. These findings reveal isoform-dependent control of protein degradation and highlight opportunities for isoform-selective targeting.
    DOI:  https://doi.org/10.1039/d6cb00119j
  9. PLoS Pathog. 2026 Jul;22(7): e1014347
    The Sigma1 ER membrane receptor promotes structural protein folding and genome packaging of dengue virus.
    Riya Sarkar, Whitney Reid, Renaldo Sutanto, Andrew W Tai, Billy Tsai.
      Dengue virus (DENV) exploits the host endoplasmic reticulum (ER) to support viral protein translation and folding, replication, and assembly, although the identity of ER factors that promote these distinct steps during infection remain unclear. Here we demonstrate that the ER-resident Sigma1 ER membrane receptor (S1R) promotes virus structural protein folding and genome packaging of DENV during infection. Under S1R knockdown (KD), DENV infection is impaired without compromising virus translation or replication. Strikingly, EM analysis revealed that DENV particles in and secreted from S1R-depleted cells are smaller, likely because they are empty particles devoid of the vRNA genome. Biochemical experiments demonstrated that S1R binds to the prM structural protein and under S1R KD, the prM, E and C structural proteins became detergent-insoluble. Thus, without S1R, all three virus structural proteins misfold, impairing efficient genome packaging. Together, these findings identify a novel ER chaperone that supports a critical DENV infection step.
    DOI:  https://doi.org/10.1371/journal.ppat.1014347
  10. EMBO J. 2026 Jul 16.
    Developmental priming of adult proteostasis and longevity by NuA4 complex activity in early life.
    Yihan Wang, Xiong Xiong, Runshuai Zhang, Long Xiao, Xinyu Ruan, Tianyi Ni, Zicheng Liu, Jie Chen, Shenlu Qin, Zhuo Du, Yanxiao Zhang, Lianfeng Wu.
      Proteostasis collapse, a hallmark of aging and neurodegeneration like Alzheimer's disease (AD), causes irreversible damage in late life. Whether late-life proteostasis capacity is developmentally programmed remains unclear, as mechanistic studies requiring lifelong tracking and molecular manipulation are challenging or impossible in long-lived species. Using C. elegans as a lifelong, genetically tractable AD model, we uncover a critical early-life window during which reducing TIP60/NuA4 acetyltransferase complex activity enduringly enhances proteostasis and extends lifespan. Mechanistically, NuA4 reduction depletes H4K16ac, triggering a compensatory, early-life-biased, XBP-1-mediated unfolded protein response (UPRER). This UPRER activation remodels endoplasmic reticulum (ER) morphology and reprograms lipid metabolism, driving selective oleic acid (OA) accumulation. Crucially, this developmentally-installed OA reservoir confers lasting resilience against proteotoxic stress, an effect mimicked by OA supplementation. Together, these findings establish a chromatin-ER-lipid axis that developmentally primes adult proteostasis and suggest early-life interventions as a strategy to promote healthy aging and resilience to proteotoxic stress.
    DOI:  https://doi.org/10.1038/s44318-026-00851-8
  11. Biochimie. 2026 Jul 17. pii: S0300-9084(26)00167-7. [Epub ahead of print]
    ER quality control: how cells detoxify their own membrane from lipid stress.
    Helin Elhan, Abdou Rachid Thiam.
      The endoplasmic reticulum (ER) is the principal site of glycerolipid synthesis in eukaryotic cells. The continuous production of lipid intermediates, including phosphatidic acid (PA), diacylglycerol (DAG), and triacylglycerol (TAG), destabilizes the ER membrane when they accumulate. To maintain bilayer integrity, cells deploy two sequential strategies: enzymatic conversion of these intermediates into membrane-compatible phospholipids, and their physical sequestration into lipid droplets (LDs), ER-derived organelles whose biogenesis is actively regulated by the seipin complex. LD growth is further sustained by the relocalization of TAG-synthesizing enzymes to the LD surface and by bridge-like lipid transfer proteins at ER-LD contact sites. When these mechanisms are overwhelmed, the accumulation of non-bilayer lipids drives ER stress and lipotoxicity, thereby contributing to the development of metabolic diseases. Here, we review the molecular logic of ER lipid quality control, from intermediate-driven membrane stress to the regulated responses that neutralize it.
    Keywords:  Diacylglycerol; Kennedy pathway; endoplasmic reticulum; ferroptosis; lipid droplets; lipid quality control; lipotoxicity
    DOI:  https://doi.org/10.1016/j.biochi.2026.07.007
  12. Nat Commun. 2026 Jul 15.
    Induced ubiquitination of the partially disordered estrogen receptor alpha via a 14-3-3 directed molecular glue-PROTAC.
    Carlo J A Verhoef, Charlotte Crowe, Mark A Nakasone, Aitana DeLaCuadra-Basté, Tessa Harzing, Naomi A S Span, Gajanan Sathe, Laura C Demmers, Kentaro Iso, Christian Ottmann, Luc Brunsveld, Alessio Ciulli, Peter J Cossar.
      Proteins lacking defined ligandable pockets remain challenging drug targets. Here, we develop a molecular glue-based PROTAC (MGPROTAC) approach that chemically conjugates a molecular glue stabilizer to a VHL-recruiting ligand to capture and ubiquitinate the 14-3-3/Estrogen receptor α (ERα) complex. Our designed MGPROTACs engage a composite interface between 14-3-3 and the disordered F-domain of ERα, promoting cooperative complex formation and targeted ubiquitination. Biophysical characterization revealed distinct linker-dependent cooperativities across the MGPROTAC series, which influenced both cellular permeability and ubiquitination efficiency. Cryo-EM of the most cooperative MGPROTAC uncovered de novo VHL-14-3-3ζ contacts, while molecular dynamics simulations rationalize the stabilizing interactions underlying cooperativity. Strikingly, fine-tuning linker design enables selective ubiquitination of distinct complex subunits. These findings establish a structural and mechanistic framework for integrating molecular glue and PROTAC principles, expanding the scope of drug discovery to previously intractable protein complexes.
    DOI:  https://doi.org/10.1038/s41467-026-75333-w
  13. Autophagy. 2026 Jul 16. 1-3
    Regulatory T cell immunosuppressive function requires chaperone-mediated autophagy.
    Ranee Harrison, Floralba Gjergjova, Susmita Kaushik, Yair Botbol, Ana Maria Cuervo, Fernando Macian.
      Regulatory T cells (Tregs) are essential for maintaining immune tolerance. We recently identified chaperone-mediated autophagy (CMA), a selective lysosomal degradation pathway, as a critical regulator of Treg function. Treg activation induces CMA, but this response is markedly diminished with aging. Mice lacking CMA specifically in Tregs develop systemic inflammation, impaired immune tolerance and reduced lifespan. We confirm that CMA is a fundamental mechanism supporting Treg suppressive function as CMA-deficient Tregs are unable to suppress intestinal inflammation in a model of inflammatory bowel disease and fail to block the anti-oncogenic immune response activated in a syngeneic tumor model. Mechanistically, CMA supports metabolic fitness, remodels immune-related protein networks, and promotes degradation of the m6A RNA demethylase FTO, linking lysosomal proteostasis to epitranscriptomic control of IL-2 responsiveness. Restoration of CMA in aged mice improves Treg function, highlighting CMA as a promising therapeutic target for both inflammatory diseases and cancer immunotherapy.
    Keywords:  Anti-oncogenic immune response; Immunotolerance; inflammatory bowel disease; proteostasis; regulatory T cells; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2700476
  14. Proc Natl Acad Sci U S A. 2026 Jul 21. 123(29): e2537017123
    Distinct cell type-specific mechanisms underlie cognitive dysfunction during persistent integrated stress response activation.
    Kristof Torkenczy, Lucas C Reineke, Sean W Dooling, Benjamin W Henderson, Benjamin Yang, Dongze He, Richard M Myers, Peter Walter, Stefka Tyanova, Mauro Costa-Mattioli.
      Persistent activation of the integrated stress response (ISR) is a central driver of cognitive decline in both neurodevelopmental and neurodegenerative disorders. However, the cell type-specific mechanisms underlying these deficits remain poorly understood. By integrating single-cell RNA-seq and single-cell assay for transposase-accessible chromatin sequencing, we generated a brain ISR atlas using Ppp1r15bR658C mice, a clinically relevant model of intellectual disability characterized by selective and persistent ISR activation. We find that distinct brain cell types differentially engage transcriptional and chromatin remodeling programs. Notably, selective deletion of the major ISR downstream effector ATF4 in GABAergic neurons, but not in glutamatergic neurons, exacerbates ISR-mediated cognitive decline in Ppp1r15bR658C mice, demonstrating that different neuronal subtypes rely on distinct ISR effectors. We define a molecular single-cell signature of persistent ISR activation that serves as a metric of ISR-mediated cellular vulnerability and as a biomarker for cognitive dysfunction across human cognitive disorders. These findings demonstrate that cell type-specific responses drive cognitive dysfunction during persistent ISR activation.
    Keywords:  cellular homoeostasis; cognitive decline; single-cell ATAC-sequencing; single-cell RNA-sequencing
    DOI:  https://doi.org/10.1073/pnas.2537017123
  15. Neurobiol Dis. 2026 Jul 11. pii: S0969-9961(26)00271-8. [Epub ahead of print] 107526
    PERK deficiency amplifies molecular, structural, and network vulnerability to repetitive mild traumatic brain injury.
    Marangelie Criado-Marrero, Sakthivel Ravi, Daylin Barroso, Tristyn N Garza, Diana M Cuestas Torres, Christian Lessard, Juan Pablo Castano, MacKenzie L Bolen, Uriel Rubinovich, Stefan Prokop, Paramita Chakrabarty, Laura P W Ranum, Marcelo Febo, Jose Francisco Abisambra.
      Repetitive mild traumatic brain injury (rmTBI) produces cumulative cellular stress that can lead to progressive brain dysfunction, yet the mechanisms governing vulnerability to repeated injury remain unclear. Protein kinase RNA-like endoplasmic reticulum kinase (PERK) regulates cellular proteostasis through the unfolded protein response and is implicated in neurodegeneration and acute brain injury. Here, we directly tested the role of PERK deficiency in shaping the brain's response to rmTBI. Using a mouse model of neuronal PERK deficiency, we combined spatial protein profiling and tissue analyses with resting-state functional MRI and diffusion tensor imaging to assess molecular, functional, and structural outcomes after rmTBI. PERK deficiency increased susceptibility to rmTBI-induced disruption of protein homeostasis, altered large-scale functional connectivity, and exacerbated white matter microstructural changes consistent with axonal and myelin damage. Molecular alterations were spatially aligned with imaging-defined network and white matter abnormalities. These findings identify PERK signaling as a key determinant of brain resilience to repetitive mild injury and link ER stress dysregulation to network-level dysfunction following rmTBI.
    Keywords:  CHIMERA; Diffusion tensor imaging; Microglia; PERK; Repetitive mild TBI; Resting state functional MRI; Stress
    DOI:  https://doi.org/10.1016/j.nbd.2026.107526
  16. Nat Commun. 2026 Jul 13.
    A quantitative approach for defining the degradability landscape of protein degraders.
    Wei Du, Lamberto De Boni, Benjamin David Hopkins, Olivier Elemento.
      Targeted protein degradation (TPD) is an emerging therapeutic modality, but how multiple factors jointly determine degradation efficacy remains poorly understood. Here we present a quantitative framework for modeling the cellular mechanism of action of TPD, allowing for prediction of cellular efficacy with practically obtainable parameters. Applying this model to published data on 41 targets reveals a common range of degradation rate between 0.1 and 10 min-1, reflecting a characteristic efficiency of the TPD process. We define the degradability landscape, which provides a holistic characterization of the degradation propensity of a target of interest and serves as a roadmap for degrader optimization. We show how degradability is influenced by key factors such as target half-life and E3 level. We further quantify functional inhibition for kinase targets, enabling direct comparison between degrader and small molecule inhibitors. Finally, we uncover degrader discovery opportunities by systematically identifying targets with the potential to achieve superior degradation to facilitate TPD translational development.
    DOI:  https://doi.org/10.1038/s41467-026-75591-8
  17. Science. 2026 Jul 16. eaeb0822
    De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging.
    Long Tran, Steffen Klein, David Juergens, Shajesh Sharma, Justin Decarreau, Gyu Rie Lee, Yujia Wang, Wei Chen, Asim K Bera, Alex Kang, Jon Woods, Emily Joyce, Dionne K Vafeados, Nicole Roullier, Xinting Li, Bingxu Liu, Yang Bo, Edin Muratspahić, Tim A Brown, Jonathan B Grimm, Ronak Patel, Luke D Lavis, Julia Mahamid, Linna An, David Baker.
      Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostability. To combine these strengths, we used de novo protein design to generate small, nanomolar-affinity, high-selectivity binders (NovoTags) for three cell-permeable dyes spanning the visible spectrum. We show that the NovoTag fluorescent lifetimes can be tuned and demonstrate their application in lifetime and wavelength-based multiplexed fluorescence imaging. We further design a two-chain NovoTag that functions as a chemically induced dimerization system with fluorescent readout in living cells, or as a minimally perturbing proximity probe in fixed cells. Our approach combines the advantages of fluorescent proteins and small-molecule dyes, expanding the toolkit for cellular imaging.
    DOI:  https://doi.org/10.1126/science.aeb0822
  18. Sci Adv. 2026 Jul 17. 12(29): eaee9999
    FGF21 induced by endoplasmic reticulum stress maintains medullary thymic epithelial cell function and central immune tolerance.
    Yuki Masuda, Yoshiaki Nakayama, Ryohei Shimizu, Hiroshi Hasegawa, Morichika Konishi.
      Medullary thymic epithelial cells (mTECs) establish central immune tolerance by expressing diverse tissue-restricted antigens and eliminating self-reactive thymocytes. Here, we show that fibroblast growth factor 21 (FGF21), although predominantly produced in the liver, is also expressed locally by mature mTECs and contributes to central tolerance. Fgf21-deficient mice exhibited exacerbated peripheral autoimmune responses. FGF21 supported the number and function of mTECs and promoted clonal deletion in cooperation with thymic dendritic cells. In mature mTECs, endoplasmic reticulum stress induced FGF21 expression through unfolded protein response pathways, with FGF21 acting preferentially within the mature mTEC compartment as a stress-responsive metabolic regulator downstream of the integrated stress response. By limiting sustained stress and preserving protein homeostasis, FGF21 maintained mTEC integrity and central tolerance. These findings identify FGF21 as a key regulator of thymic immune homeostasis and as a potential therapeutic target for autoimmune disease.
    DOI:  https://doi.org/10.1126/sciadv.aee9999
  19. Nat Commun. 2026 Jul 17.
    ZnF-UBP domains regulate deubiquitinase activity by relieving ubiquitin product inhibition.
    Jack A Alexandrovics, Rashmi Agrata, Jan André Hane, Philipp Schenk, Anthony Cerra, Ueli Nachbur, Malte Gersch, Jeffrey J Babon, David Komander.
      Most ubiquitin specific protease (USP) deubiquitinases (DUBs) combine non-selective catalytic domains with one or multiple 'exo'-domains that contribute substrate specificity and localisation, but are generally poorly characterised. Zinc-Finger UBP (ZnF-UBP) domains exist in 12 USP DUBs, yet their function is unclear. We here comprehensively analyse human ZnF-UBP domains, and reveal that 8 of 14 bind ubiquitin (Ub) via an unattached Ub C-terminal GlyGly motif. We focus on USP16, a nucleosome DUB with activity for Ub and Ub-like modifiers, and show that its ZnF-UBP domain can bind substrates, but is also a crucial contributor to enzyme kinetics. Slow Ub release from the catalytic domain after cleavage causes product inhibition, which is overcome in cis by ZnF-UBP-mediated product release. Interestingly, supplying a high affinity product-capturing ZnF-UBP domain in trans, activates USP16 and other USP enzymes. Our data shows the importance of product inhibition as a regulatory mechanism in DUBs, and exemplifies the unappreciated role of exo-domains in regulating DUB function beyond substrate binding.
    DOI:  https://doi.org/10.1038/s41467-026-75469-9
  20. J Med Chem. 2026 Jul 15.
    Structure-Guided Discovery of Novel Dual-Site FEM1B Ligands and Assessment of Their Use in Targeted Protein Degradation.
    Lingbo Xu, Ruyi Huang, Yuying Ma, Li Yang, Yueying Li, Chengping He, Zhenhao Zhang, Yang Teng, Wei Li, Zan Chen, Yue Wei, Zufeng Guo, Linfeng Li.
      Targeted protein degradation (TPD) represents a promising approach for eliminating disease-causing proteins beyond traditional inhibition. However, the reliance on a limited number of E3 ligases remains a major bottleneck. FEM1B, an E3 ligase substrate receptor with multiple substrate-recognition modes, represents an attractive but underexplored TPD platform. In this study, through a structure-guided approach exploiting the spatial proximity between a druggable C-degron-binding pocket and a second binding site containing a reactive cysteine, we developed FL47, a dual-site ligand that combines extensive noncovalent interactions with targeted covalent engagement. FL47 exhibits submicromolar affinity, robust cellular target engagement, and markedly reduced cytotoxicity relative to previously reported covalent recruiters. We further applied FL47 in the development of FEM1B-based PROTACs and incorporated a chemical endocytic prodrug strategy that markedly enhanced degradation activity. This work introduces a novel dual-site binding strategy for E3 ligase ligand discovery and broadens the potential toolbox for TPD applications.
    DOI:  https://doi.org/10.1021/acs.jmedchem.6c00968
  21. ACS Med Chem Lett. 2026 Jul 09. 17(7): 1430-1439
    Identification of Clofibric Acid as a Synoviolin (SYVN1) Ligand for Proteolysis-Targeting Chimera (PROTAC) Development.
    Julia Warren, Anandarao Munakala, Keith D Zientek, Kilsun Kim, Phillip A Wilmarth, Ashok P Reddy, Bingbing X Li, Xiangshu Xiao.
      Targeted protein degradation (TPD) via proteolysis-targeting chimeras (PROTACs) is a powerful therapeutic strategy, yet only a small fraction of the >600 human E3 ligases have been harnessed. To expand this repertoire, we developed clickable photoaffinity probes based on clinically used drugs and metabolites to identify potential E3 ligases as targets. Here, we report the discovery of clofibric acid with a molecular weight of only 214 Da as a ligand for synoviolin (SYVN1). We demonstrate its utility by developing clofibric acid-based BRD4 PROTACs. The linker length and architecture play a critical role in the target degradation efficiency. The clofibric acid-derived BRD4 PROTACs achieve selective BRD4 degradation in an SYVN1-dependent manner. Our findings establish clofibric acid as a robust addition to the TPD toolbox, offering a novel E3 ligase recruitment strategy for the development of next-generation degraders.
    Keywords:  E3 ligase; PROTAC; SYVN1; chemoproteomics, degradation; clofibric acid
    DOI:  https://doi.org/10.1021/acsmedchemlett.6c00223
  22. EMBO J. 2026 Jul 11.
    Spalt-related is an inhibitor of mTORC1-mediated growth activated by the integrated stress response.
    Onur Deniz, Ying Liu, Tuuli Kirkinen, Krista Kokki, Kateryna Gaertner, Pau Clavell-Revelles, Jaakko Mattila, Ville Hietakangas.
      Anabolic and catabolic processes are coordinated by a conserved regulatory network, which includes the nutrient-sensing protein kinase mTOR complex 1 (mTORC1) and the insulin- and stress-responsive transcription factor FoxO. In a physiological setting, these regulators align growth, storage, reproduction, and aging with nutrient availability. Here, we identify transcription factor Spalt-related (Salr), previously implicated in organogenesis, as a negative regulator of growth and lipid storage in Drosophila melanogaster. Salr activates catabolic gene expression and restricts mTORC1-mediated cell growth in the Drosophila fat body. The genomic binding of Salr overlaps extensively with that of FoxO, and a similar convergence is observed for their mammalian homologs, SALL1 and FOXO1. Both Salr and FoxO are activated upon fasting, but respond to distinct cues: while FoxO displays transient activation and is responsive to AKT inhibition, Salr is activated in a slow and sustained manner through the integrated stress response. Once activated, Salr counters nuclear localization of FoxO. Taken together, we show that Salr and FoxO are growth-inhibitory transcription factors that act in a convergent manner to respond to nutrient stress through distinct cues.
    DOI:  https://doi.org/10.1038/s44318-026-00858-1
  23. EMBO Rep. 2026 Jul 14.
    The regulation of protein phosphatase 4 by FBXO42 is required for cancer cell survival.
    Stephan H Spangenberg, Nicholas Garaffo, Enya Marie Catherine Alcindor, Benjamin Lusk, Vijaya Pandey, Adam D Longhurst, Emma Bolech, Becky Xu Hua Fu, Luke A Gilbert, James A Wohlschlegel, David P Toczyski.
      FBXO42 is a poorly characterized F-box protein essential in 15% of cancer cell lines from diverse lineages. High-throughput approaches indicate that FBXO42 function correlates with that of coiled-coil protein CCDC6, and that the two proteins interact physically, but the relationship between them is not understood. We show that FBXO42 ubiquitinates PPP4C (protein phosphatase 4 catalytic subunit) and negatively regulates its expression. FBXO42 binds PPP4C independently of CCDC6. Similarly, we show that CCDC6 physically interacts with PPP4C independently of FBXO42, and identify a PPP4C binding site within CCDC6. However, mutation of CCDC6 does not reduce PPP4C ubiquitination, suggesting that FBXO42 and CCDC6 bind and regulate PPP4C through separate mechanisms. Viability of an FBXO42- and CCDC6-dependent glioblastoma cell line is rescued when PPP4C is knocked down along with FBXO42 or CCDC6, suggesting that aberrant activation of PPP4C is a driver of cell death when FBXO42 or CCDC6 activity is compromised. These findings tie together previous data suggesting that FBXO42 functions with CCDC6 by providing mechanistic insight into their independent regulation of PP4.
    DOI:  https://doi.org/10.1038/s44319-026-00828-y
  24. J Chem Inf Model. 2026 Jul 17.
    Pan-Cancer Landscape of Spatial PTM and Mutation Clusters Reveals Allosteric Regulation of Protein-Protein Interactions.
    Dongfang Luo, Jiani Zheng, Xikun Du, Danni Xia, Meng Zhang, Zhongjie Liang.
      Post-translational modifications (PTMs) and somatic mutations are pervasive in cancer, yet their three-dimensional organization and coordinated regulatory mechanisms within protein-protein interactions (PPIs) remain poorly understood. Here we develop ClusTar, a structural framework that systematically identifies spatial clusters of PTMs and mutations within PPIs and links them to protein dynamics and functional regulation. Integrating TCGA genomics, CPTAC proteomics, and structural PPI data across ten cancer types, we identify 3,966 high-confidence PTM-mutation clusters that are enriched in functional residues and frequently overlap with ligand-binding pockets. Dynamics analyses reveal that many clusters are mechanically coupled to PPI interfaces and mediate long-range allosteric communications. In RhoA complexes, glutamine substitutions at acetylated lysine sites (K7Q, K18Q, K104Q and K118Q/K162Q) have been observed to redistribute key network hubs and rewire allosteric communication pathways among clustered residues. Experimental validation demonstrates that these mutations strengthen protein interactions and promote breast cancer cell migration, highlighting their potential as allosteric hotspots. Together, our results establish a pan-cancer structural atlas of PTM-mutation clusters and highlight allosteric hotspots as potential targets for modulating PPIs.
    DOI:  https://doi.org/10.1021/acs.jcim.6c01767
  25. Genome Biol. 2026 Jul 17. pii: 229. [Epub ahead of print]27(1):
    Dynamic global acetylation remodeling during the yeast heat shock response.
    Rebecca E Hardman-Kavanaugh, Aaron J Storey, Tara N Stuecker, Stephanie E Hood, Gregory A Barrett-Wilt, Venkata R Krishnamurthi, Yong Wang, Stephanie D Byrum, Samuel G Mackintosh, Rick D Edmondson, Wayne P Wahls, Alan J Tackett, Jeffrey A Lewis.
       BACKGROUND: All organisms experience stress and must rapidly respond to changing conditions. Thus, cells have evolved sophisticated rapid-response mechanisms such as post-translational protein modification to rapidly and reversibly modulate protein activity. One such post-translational modification is reversible lysine acetylation, where proteomic studies have identified thousands of acetylated proteins across diverse organisms. While the sheer size of the 'acetylome' is striking, the function of acetylation for the vast majority of proteins remains largely obscure.
    RESULTS: Here, we find that global acetylation plays a previously unappreciated role in the heat shock response of Saccharomyces cerevisiae. Dysregulated acetylation renders cells heat sensitive, and the acetylome is globally remodeled during heat shock over time, with ~ 400 high-confidence acetyl marks across ~ 200 proteins significantly changing. Proteins with significant acetylome changes strongly overlap with genes induced or repressed by heat shock. Intriguingly, we find nearly 40 proteins with at least two acetyl marks that significantly change in the opposite directions. These proteins are strongly enriched for chaperones and ribosomal proteins, suggesting that these two key processes are coordinately regulated by protein acetylation during heat shock.
    CONCLUSIONS: Our results suggest that protein acetylation helps activate induced proteins and inactivate repressed proteins during heat shock. We hypothesize that the same type of activating and inactivating marks that exist on histones may be a general feature of proteins regulated by acetylation. Overall, this work has identified a new layer of post-translational regulation that likely augments the classic heat shock response.
    DOI:  https://doi.org/10.1186/s13059-026-04194-9
  26. Autophagy. 2026 Jul 13.
    Genome-wide CRISPR-Cas9-based screening revealed the role of ubiquitin ligase TRIM25 in ribosome degradation via ribophagy.
    Julia Golubeva, Alexey Mikhailov, Nikita Shepelev, Elizaveta Pleshko, Ekaterina Guseva, Vera Sidorova, Elena Shagimardanova, Nadezda Andrianova, Egor Plotnikov, Dmitry Karpov, Svetlana Novikova, Victor Zgoda, Maria Rubtsova, Olga Dontsova, Petr Sergiev.
      Ribophagy is a crucial mechanism that maintains ribosome homeostasis in the cell by directing nonfunctional ribosomes to degradation via macroautophagy/autophagy. Impaired ribophagy may lead to ribosome quality control disorders and may consequently be associated with various diseases known as ribosomopathies. This topic has been actively studied over the past decade, but the complete mechanism of ribophagy is not fully understood. To study the mechanism of ribophagy, we performed a genome-wide CRISPR-Cas9-based screening using a fluorescent ribophagy reporter, which is a cell line with ribosomes carrying RPL29 fused with mCherry and GFP fluorescent proteins. Using the genome-wide Brunello library of guide RNAs, we identified the most promising targets for further study, including the ubiquitin ligase TRIM25, for which we have shown specific binding to the ribosome during ribophagy induction, leading to ubiquitination of the ribosome on the nascent peptide chain and degradation of the whole ribosome. Our findings also demonstrated that poly(I:C) treatment, which mimics viral infection, activates ribophagy in a TRIM25-dependent manner, suggesting the ribophagy pathway could be an antiviral defense mechanism. Taken together, we discovered a novel regulator of ribophagy, TRIM25, which provides new insights into the regulation of selective autophagy in the context of ribosomopathies.
    Keywords:  Antiviral defense; E3 ubiquitin ligase; RPL29; innate immunity; poly(I:C); ribosomopathies; selective autophagy; ubiquitination
    DOI:  https://doi.org/10.1080/15548627.2026.2702255
  27. Nature. 2026 Jul 15.
    Metabolite glues as a means of purine sensing and chemotherapeutic response.
    Samuel R Witus, Megan M Kober, Heegwang Roh, Zhi Yang, Fouad Choueiry, Avani S Ghate, Denis V Titov, Michael Rapé.
      Molecular glues stabilize weak interactions to impart new functionalities to complexes1-3. Although molecular glues have been described in plant signalling and as human therapeutics4,5, it is unclear whether this modality provides endogenous regulation in human cells. Here we show that purine nucleotides are molecular glues that tether the rate-limiting enzyme in purine biosynthesis-phosphoribosyl pyrophosphate amidotransferase (PPAT)-to its inhibitor NUDT5. This mechanism allows cells to sense the levels of purines and to establish essential feedback control of their synthesis. We refer to such molecules as metabolite glues. Thiopurine chemotherapeutics6, which have been in clinical use since the 1950s, glue the same complex but adopt distinct orientations for enhanced function. Unlike most known glues, the PPAT-NUDT5 metabolite-glue pocket can adjust its conformation to notable compound alterations, enabling increased glue potency and improved on-target activity. We therefore identify endogenous metabolite glues as a mode of nutrient sensing that can be exploited for therapeutic benefit.
    DOI:  https://doi.org/10.1038/s41586-026-10790-3
  28. Autophagy Rep. 2026 ;5(1): 2698348
    Damage control: new functions for the Arp2/3 complex and WHAMM in autophagy and lysosomal homeostasis.
    Lianna H Wagner, Kenneth G Campellone.
      Macroautophagy is an intracellular degradation process that relies on autophagosomes and lysosomes to maintain cellular and organismal homeostasis. Actin cytoskeletal rearrangements driven by the Arp2/3 (actin-related protein 2/3) complex, an essential actin nucleator, impact multiple steps of this pathway, but where and when Arp2/3-mediated actin assembly is most influential has remained unclear. Recent work now shows that the Arp2/3 complex is crucial in the later stages of autophagy due to its function in maintaining lysosomal integrity. WHAMM (WASP homolog associated with actin, membranes, and microtubules) is the key nucleation-promoting factor that activates Arp2/3 at permeabilized lysosomes, uncovering new roles for actin, the Arp2/3 complex, and WHAMM in lysosomal damage responses.
    Keywords:  ATG8; Actin; Arp2/3 complex; JMY; LC3; WASP; WHAMM; autophagy; cytoskeleton; lysosome
    DOI:  https://doi.org/10.1080/27694127.2026.2698348
  29. FEBS J. 2026 Jul 12.
    Combating ageing beyond the cell: Emerging roles of extracellular proteostasis.
    Siddharth R Venkatesh, Ivan Gallotta, Bolanle F Olabiyi, Yoon Hee Choi, Sarah Inglesfield, Janet R Kumita, Collin Y Ewald, Della C David.
      Proteostasis, the maintenance of a healthy proteome, is a fundamental pillar of cellular and organismal health that declines with age. While the intracellular proteostasis network (PN) is well-characterised, proteostasis mechanisms acting in the extracellular space remain understudied. Yet, these mechanisms face unique challenges and are critical for ensuring functional systemic signalling, immune surveillance and structural integrity. In contrast to the cytosol, extracellular environments lack ATP-activated chaperones and a comprehensive ubiquitin-proteasome system and instead rely on specialised secreted chaperones, extracellular proteases and receptor-mediated clearance mechanisms. This review examines the emerging landscape of the extracellular proteostasis network (exPN) and its challenges with age. We discuss how age-related remodelling of the extracellular proteome, shifts in extracellular physicochemical properties and disrupted fluid dynamics collectively create a permissive environment for protein misfolding and aggregation. We evaluate current experimental models of extracellular protein damage and examine how exPN factors target specific stages of the aggregation process to cooperatively safeguard extracellular proteome integrity. Analysis of recent human proteomic data spanning the life course uncovers an unexpected upregulation of exPN components with age. We further explore the role of extracellular proteostasis in inflammageing, a defining hallmark of ageing. Finally, we highlight strategies that bolster extracellular proteostasis as a promising frontier for extending healthspan, limiting age-associated protein aggregation and restoring extracellular matrix homeostasis. By adopting an ageing-centred perspective, we move beyond the disease context to present a holistic overview of extracellular proteostasis in organismal health, thereby positioning the exPN as a critical yet under-exploited target for biomedical intervention.
    Keywords:  ageing; extracellular chaperones; extracellular matrix; extracellular proteases; extracellular proteostasis network; immunity; protein aggregation
    DOI:  https://doi.org/10.1111/febs.70647
  30. FASEB J. 2026 Jul 31. 40(14): e72127
    Ufl1-Mediated UFMylation Sustains Amelogenesis by Stabilizing RUNX2.
    Da Liu, Lin Chen, Huning Xu, Xueqin Yang, Ke Wang, Miao Wang, Xiao-Jing Zhu.
      UFMylation is a conserved ubiquitin-like post-translational modification that controls protein stability and tissue homeostasis, while its role in amelogenesis remains largely uncharacterized. Here, we investigated the function of UFL1, the sole E3 ligase of the UFMylation pathway, in mammalian enamel development using K14-Cre-mediated epithelial-specific Ufl1 knockout mice. Ufl1 ablation caused severe amelogenesis imperfecta, with impaired enamel deposition, hypomineralization, and progressive tooth damage, accompanied by abnormal cervical loop development. Transcriptomic profiling revealed elevated endoplasmic reticulum stress and dysregulated expression of enamel mineralization genes, including significant downregulation of downstream targets of RUNX2, a master regulator of amelogenesis. We further demonstrated that UFL1 and DDRGK1 directly interacted with RUNX2, and UFL1-mediated UFMylation stabilized RUNX2 protein at the post-translational level. Taken together, this study identifies a novel UFMylation-RUNX2 regulatory axis essential for amelogenesis, providing new mechanistic insights into amelogenesis imperfecta and potential therapeutic targets for dental enamel defects.
    Keywords:  Ameloblasts; Amelogenesis Imperfecta; dental enamel; gene deletion; protein stability; tooth development
    DOI:  https://doi.org/10.1096/fj.202601306R
  31. J Cell Biol. 2026 Aug 03. pii: e202507107. [Epub ahead of print]225(8):
    Receptor-mediated Golgi retention of Fam20 kinases tunes secretome phosphorylation during lactation.
    Xiaotong Yang, Jueyin He, Xiulan Chen, Xi'e Wang, Chenyun Hu, Xuqian Zhao, Xinxin Chen, Jiaojiao Yu, Ping Liu, Jifeng Wang, Xi Wang, Junjie Hu, Mei Ding, Fuquan Yang, Chih-Chen Wang, Lei Wang.
      Fam20C, the first protein kinase identified in the secretory pathway, governs the majority phosphorylation of the secretome. Although Fam20C has a high propensity for secretion, its kinase activity occurs intracellularly. How Fam20C clients are phosphorylated inside cells remains elusive. Here, we demonstrate that the pseudokinase Fam20A forms a heterocomplex with Fam20C on the Golgi membrane, anchoring the cleaved, mature form of Fam20C within the Golgi. Their Golgi localization is promoted by a set of cargo receptors ERGIC2 and ERGIC3, which drive the ER-to-Golgi transport of Fam20A-Fam20C. Importantly, both ERGIC2 and ERGIC3 are upregulated in the mammary gland during lactation, and Ergic2 or Ergic3 knockout mice display global changes in secretome phosphorylation, less phosphorylated β-casein in milk, and deficiency in offspring growth. Our findings uncover a previously unrecognized mechanism for the spatiotemporal regulation of Fam20 kinases, crucial for efficient phosphorylation of secretory proteins during lactation.
    DOI:  https://doi.org/10.1083/jcb.202507107
  32. Sci Adv. 2026 Jul 17. 12(29): eaef3048
    TRiC-assisted folding of class I HDAC family proteins regulated by distinct co-chaperone and cofactor networks.
    Zuyang Li, Qiaoyu Zhao, Wanying Jiang, Qianqian Song, Xuehai Zhou, Xiangyi Shi, Qing Zhang, Yanxing Wang, Yinghong Lin, Yue Yin, Chen Pan, Yao Cong.
      Class I histone deacetylases (HDAC1, HDAC2, HDAC3, and HDAC8) are key chromatin regulators, but how they are activated by chaperonin TRiC remains elusive. Using cryo-electron microscopy, cross-linking mass spectrometry, and biochemistry analyses of tagged HDACs overexpressed in HEK293F cells, we identify class I HDACs as TRiC substrates and elucidate the TRiC-assisted folding pathways of HDAC1 and HDAC3 across ATPase cycle, orchestrated by distinct co-chaperone/cofactor networks. In closed TRiC chamber, both clients adopt near-native conformations and engage similar binding interfaces. In the open state, however, their pathways diverge: HDAC3 involves Hsp70 atop TRiC and PDCD5 within the chamber, whereas HDAC1 involves prefoldin atop TRiC, revealing distinct mechanisms of substrate delivery and folding modulation. We also identify an unexpected bent conformation of CCT4 in TRiC-HDAC1 complex that may relate to co-chaperone release. By contrast, HDAC8 folds independently of TRiC. Together, these findings reveal client-specific co-chaperone/cofactor networks governing TRiC-assisted folding of class I HDACs, shedding light on the sophisticated regulatory landscape of TRiC.
    DOI:  https://doi.org/10.1126/sciadv.aef3048
  33. Nat Cell Biol. 2026 Jul 15.
    Lysosomes and lysosomal dysfunction in ageing biology.
    Matthew L Steinhauser, Yuan Liu, Stacey J Sukoff Rizzo, Bill B Chen, Toren Finkel, Jay Xiaojun Tan.
      Lysosomes are essential regulators of cellular homeostasis. Emerging evidence positions lysosomes as both vulnerable targets and active drivers of ageing biology. During ageing, lysosomes exhibit impaired biogenesis, defective acidification, reduced hydrolytic activity and compromised membrane integrity. These defects impair the clearance of damaged organelles and macromolecules and promote cellular stress responses, inflammageing and senescence, causing age-dependent functional decline across tissues. Lysosomal dysfunction has been increasingly linked to age-related diseases, including neurodegeneration, cardiometabolic disorders and increased susceptibility to infection, among others. Thus, lysosomal dysfunction is a hallmark of ageing that drives age-related pathology. Here we review recent progress in lysosomal biogenesis and quality control, discuss how lysosomes intersect with fundamental ageing mechanisms and evaluate emerging therapeutic strategies that target lysosomes to promote healthy ageing and potentially ameliorate age-associated pathologies.
    DOI:  https://doi.org/10.1038/s41556-026-02007-6
  34. Biochim Biophys Acta Mol Cell Res. 2026 Jul 17. pii: S0167-4889(26)00094-7. [Epub ahead of print] 120195
    Leucine rich repeat containing protein 8B (LRRC8B) - A novel modulator of endoplasmic reticulum (ER) stress response.
    N Raja Mathanki, Olivia Neibel Isaac Newton, Amal Kanti Bera.
      The endoplasmic reticulum (ER), a major calcium ion (Ca2+) reservoir, plays a pivotal role in lipid synthesis, protein synthesis, and secretion. Disruption of ER function leads to the accumulation of misfolded proteins, resulting in ER stress. To restore cellular homeostasis, the unfolded protein response (UPR) is activated. However, prolonged or irreversible ER stress can trigger apoptosis and cell death. Cellular dysfunction and apoptosis arising from disrupted ER Ca2+ homeostasis are often implicated in neurodegenerative and metabolic disorders. We investigated the role of LRRC8B, an ER-resident protein previously linked to ER Ca2+ homeostasis, in the ER stress response. LRRC8B expression was upregulated in response to chemically induced ER stress. Overexpression of LRRC8B enhanced the viability of HEK293T cells exposed to the ER stressor tunicamycin, whereas LRRC8B knockdown increased their susceptibility to apoptosis. Furthermore, LRRC8B overexpression reduced protein aggregation during ER stress by upregulating cytoprotective genes associated with the adaptive UPR, including BiP, calnexin, and PDI. Conversely, LRRC8B knockdown decreased BiP expression and elevated the levels of ER stress-induced apoptotic proteins such as CHOP, Bax, and cleaved caspase-3. Co-treatment with the chemical chaperone, 4-PBA, partially rescued the LRRC8B knockdown cells undergoing apoptosis. In Neuro 2a (N2a) cells, LRRC8B overexpression diminished the aggregation of mutant huntingtin protein (HTT-83Q), associated with Huntington's disease, whereas its knockdown exacerbated HTT-83Q aggregation. Taken together, these findings suggest that LRRC8B is a key modulator of the ER stress response and plays a cytoprotective role.
    Keywords:  ER stress; LRRC8B; Protein aggregation; Tunicamycin; UPR
    DOI:  https://doi.org/10.1016/j.bbamcr.2026.120195
  35. Apoptosis. 2026 07 14. pii: 193. [Epub ahead of print]31(8):
    The autoimmune regulator (AIRE) is a target of the E3-Ubiquitin ligase Seven-in-absentia homolog 1 (SIAH1).
    Adrián Tirado-Herranz, Alba Pastor-Moreno, María Area-Navarro, Jacqueline Noboa-Velástegui, Oscar Conchillo, José Ramón Palacio, Xavier Daura, Iñaki Alvarez.
      The autoimmune regulator (AIRE) is expressed in medullary thymic epithelial cells (mTECs) and is crucial for generating an immunocompetent T cell repertoire during central tolerance. Loss of AIRE function causes autoimmune polyglandular syndrome type 1 (APS-1), also known as autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Intracellular proteins are regulated by ubiquitination pathways. E3 ubiquitin ligases are specific proteins that confer selectivity to polyubiquitination, tagging proteins for proteasomal degradation while also performing other functions. In mTECs, peptides generated via the class I antigen-processing pathway are presented by HLA-I molecules to CD8 thymocytes to eliminate self-reactive T-cell precursors. AIRE induces promiscuous gene expression in mTECs, but little is known about the regulatory mechanisms of AIRE. Previously, we and others demonstrated that AIRE is an apoptosis inductor. Here, we demonstrate that AIRE increases the intracellular levels of SIAH-interacting protein (SIP), an adaptor protein of the SIAH E3 ubiquitin ligase family. We also show that AIRE interacts with SIAH1 in the human thymus. While AIRE contains two putative SIAH-interacting motifs, it interacts with SIAH proteins only through the sequence spanning residues 119-125. AlphaFold modeling indicated that the interaction between AIRE and SIAH1 is highly analogous to that observed between SIP and SIAH1, suggesting that both proteins compete for SIAH1 binding. The CARD domain and the SIAH-interacting motif is required to AIRE-mediated apoptosis. AIRE co-localized with SIAH proteins in the cytoplasm of HEK-293 cells. Finally, SIAH1 ubiquitinated AIRE, targeting it for proteasomal degradation. Collectively, these findings reveal a novel pathway for the degradation and regulation of AIRE.
    Keywords:  Antigen processing; Apoptosis ; Autoimmune regulator (AIRE); Central tolerance; E3-ubiquitin ligase SIAH; Thymus
    DOI:  https://doi.org/10.1007/s10495-026-02398-9
  36. EMBO Rep. 2026 Jul 14.
    Novel CDK-independent function of CDC25 phosphatases in mRNA translation.
    Sauyeun Shin, Marie Cargnello, Lisa Pinchedé, Claire Medale Giamarchi, Cléa Villette, Alexandre Gay, Virginie Salnot, Emilie-Fleur Gautier, Erik Dassi, Stefania Millevoi, Anne Cammas, Stéphane Manenti.
      Molecular and functional networks driving coordination between cell cycle and mRNA translation remain to be explored. Here, we use mass spectrometry-based proteomics to comprehensively investigate the interactome and phosphoproteome of the cell cycle regulator CDC25A. We identify actors of mRNA regulation, such as RNA-binding proteins and translation factors, as interacting partners of CDC25A. CDC25A overexpression increases global translation, whereas catalytic inactivation or pharmacological inhibition decreases protein synthesis. A Cyclin-Dependent Kinase (CDK) interaction-deficient mutant of CDC25A also enhances translation, indicating a CDK-independent role. Our results further reveal an interplay between CDC25A and CDC25B whereby downregulation of CDC25A leads to compensatory overexpression of CDC25B. The roles of CDC25A and CDC25B in mRNA translation are independent of their roles in the cell cycle, with CDC25A possibly regulating translation elongation and CDC25B rather involved in initiation. In acute myeloid leukemia cells, CDC25A depletion also inhibits translation, suggesting its potential relevance as a therapeutic target. We propose that CDC25 phosphatases might be signaling platforms coordinating cell cycle progression with protein synthesis.
    DOI:  https://doi.org/10.1038/s44319-026-00852-y
  37. Cell Chem Biol. 2026 Jul 13. pii: S2451-9456(26)00230-8. [Epub ahead of print]
    Understanding protein ISGylation, a multifaceted posttranslational modification.
    David Joseph Shirley, Euna Yoo.
      ISG15 represents a key ubiquitin-like modifier induced primarily by interferon signaling. ISG15 is synthesized as a precursor, processed to a mature form, and covalently conjugated to substrates through a dedicated E1-E2-E3 enzymatic cascade involving UBE1L, UBE2L6, and E3 ligases such as HERC5, TRIM25, and ARIH1. This modification is reversed by deISGylases, particularly the highly specific protease USP18, which also negatively regulates interferon signaling. ISGylation impacts diverse molecular and cellular processes, including protein stability and function, protein-protein interaction, autophagy, transcription/translation, DNA damage response, and innate immunity. Advances in chemical biology and mass spectrometry-based proteomics have enabled the characterization of enzymes involved in (de)ISGylation and mapping of ISGylated proteins and sites. Dysregulated ISGylation is implicated in cancer, infection, neurodegenerative disorders, and inflammatory diseases, underscoring its broad pathophysiological relevance.
    Keywords:  ISG15; USP18; interferon; ubiquitin-like protein
    DOI:  https://doi.org/10.1016/j.chembiol.2026.06.006
  38. Sci Adv. 2026 Jul 17. 12(29): eaed2430
    ALR couples IMS redox and heme biosynthesis beyond the disulfide relay.
    Julia Racho, Dylan Stobbe, Jan Jirschitzka, Marijana Croon, Carmelina Petrungaro, Muna Ali, Dario Wernet, Markus Habich, Nele Sophie Gawellek, Julian Strippel, Finn Dicke, Jörn Dengjel, Stephanie Kath-Schorr, Bent Brachvogel, Thomas Langer, Aleksandra Trifunovic, Ines Neundorf, Jan Riemer.
      Proteins in the mitochondrial intermembrane space (IMS) play essential roles in respiratory chain assembly, metabolism, signaling, and organelle dynamics. Their stability and functionality often depend on structural disulfide bonds introduced by the mitochondrial disulfide relay, mediated by MIA40 and ALR. In this system, the sulfhydryl oxidase ALR reoxidizes MIA40, which in turn oxidizes incoming substrate proteins. Although evidence has suggested that ALR can also act independently of MIA40, its endogenous substrates have remained unknown. In this study, we captured proteins directly oxidized by ALR. Among these, we found coproporphyrinogen III oxidase (CPOX), a key enzyme in heme biosynthesis. We show that ALR-mediated disulfide bond formation is crucial for maintaining CPOX stability in the IMS, thereby ensuring effective heme biosynthesis and mitochondrial functionality. Notably, while disulfide-deficient CPOX failed to rescue CPOX loss when localized to the IMS, it retained functionality when redirected to the cytosol. However, this bypass compromised pathway efficiency, leading to the accumulation of protoporphyrinogen IX, a highly hydrophobic and redox-active intermediate that sensitized cells to cell death. Together, our findings reveal that ALR has functions beyond the MIA pathway and highlight that oxidative protein folding in the IMS relies not only on a relay mechanism but also on a broader disulfide-introducing network of enzymes.
    DOI:  https://doi.org/10.1126/sciadv.aed2430
  39. Adv Sci (Weinh). 2026 Jul 14. e23684
    Loss of E3 Ubiquitin Ligase RINES via CpG Methylation Relieves Suppression of STAT3 and MYC, Facilitating Multiple Tumorigeneses.
    Lili Li, Ka Man Ng, Xingsheng Shu, Xiaoxue Chai, Kai Yau Wong, Gopesh Srivastava, Anthony T C Chan, Wai Yee Chan, Qian Tao.
      Dysregulated protein modifications alter the stability and activation status of key regulatory proteins and contribute to tumorigenesis. RING finger (RNF) proteins as E3 ubiquitin ligases, play fundamental roles in diverse biological processes, including cancer cell stemness. Through cancer epigenomic profiling, we identify tumor-specific promoter CpG methylation of the E3 ligase RINES across multiple common cancer types (esophageal, nasopharyngeal, colorectal, breast, lung, kidney, cervical, and liver), in addition to previously reported gastric cancer, which correlates with poor patient survival. We further find that RINES inhibits tumor cell growth in vivo and in vitro. Mechanistically, RINES physically interacts with STAT3 and MYC to promote their protein degradation via its E3 ubiquitin ligase activity. RING domain-dependent ubiquitin-proteasome degradation of STAT3 and MYC is essential for RINES-mediated suppression of cancer stemness. Consistently, RINES knockdown diminishes the ubiquitination of STAT3 and MYC and elevates their protein stability, which enhances cancer stem cell properties and promotes tumorigenesis. Thus, our study establishes RINES as a bona fide tumor suppressor that directly modulates STAT3 and MYC stability to restrict cancer cell stemness. RINES promoter methylation may serve as a promising epigenetic biomarker for multiple common cancers.
    Keywords:  E3 ligase; RINES; methylation; stemness; tumor suppressor; ubiquitination
    DOI:  https://doi.org/10.1002/advs.202523684
  40. EMBO Rep. 2026 Jul 17.
    Visual system function requires translational regulation of ATF4 by Hbs1-Pelo.
    Katherine Tempro, Inês Lago-Baldaia, Narayanan Nampoothiri V P, Christopher Garbark, Abby J Carney, Vilaiwan M Fernandes, Deepika Vasudevan.
      Deletion mutations in the translation termination factor HBS1L result in progressive loss of vision in human patients, amongst other developmental anomalies. The etiology of vision defects seen with HBS1L deletion remains unknown. Here, we use the Drosophila visual system to demonstrate that the HBS1L ortholog, Hbs1, and its interaction partner, Pelo, are required for proper phototransduction. Hbs1 mutants showed 'vacuolization' of the lamina layer, indicative of defective synapse transmission between photoreceptors and lamina neurons. Depleting Hbs1 in lamina neurons replicated the phototransduction defects seen in Hbs1 mutants, suggesting that Hbs1-Pelo is required for proper lamina neuron function. Mechanistically, we found that loss of HBS1L in both Drosophila and cultured human cells results in reduced levels of the stress responsive Activating Transcription Factor 4 (ATF4). Strikingly, restoring ATF4 expression in the lamina partially rescues ERG defects in Hbs1 mutants, indicating that ATF4 is likely a relevant mRNA target regulated by Hbs1-Pelo in these cells. Together, we propose a model wherein Hbs1-Pelo-mediated translation regulation of ATF4 in lamina neurons underlies the inherited retinal disease caused by HBS1L deletion.
    DOI:  https://doi.org/10.1038/s44319-026-00882-6
  41. bioRxiv. 2026 Jul 10. pii: 2026.07.06.736850. [Epub ahead of print]
    Identification of substrates of the protein tyrosine phosphatase PTP1B using in situ site-specific photo-crosslinking.
    Andrew C Johns, Yethmie S Goonatilleke, David C Cabanero, Yanzhe Ma, Minhee Lee, Anne E van Vlimmeren, Marko Jovanovic, Neel H Shah.
      Protein tyrosine phosphorylation is critical for cellular function, and aberrant phosphorylation is tied to a wide range of human diseases. Identifying the substrates of protein tyrosine phosphatases, the enzymes that erase this modification, is critical to understanding human biology and disease states. The state-of-the-art method for tyrosine phosphatase substrate identification requires the use of mutations that modestly increase the lifetime of enzyme-substrate complexes by kill catalytic activity. While these "substrate-trapping" mutants are useful tools, they work best for high-affinity or abundant substrates that remain phosphatase-bound through cell lysis and enrichment. Here, we use site-specific photo-crosslinking to covalently capture the substrates of tyrosine phosphatases in situ . We identify eight different positions around the active site of the phosphatase PTP1B where photo-crosslinker amino acids can be incorporated via amber codon suppression without dramatically disrupting catalytic activity. We then conduct photo-crosslinking experiments in mammalian cells and identify crosslinked proteins by mass spectrometry proteomics, revealing that our approach can capture known PTP1B interactors and substrates. We then show that PTP1B photo-crosslinking in situ is sensitive to enzyme localization and identify new PTP1B substrates that regulate contacts between the endoplasmic reticulum and plasma membrane. We also demonstrate that photo-crosslinking can capture signal-dependent interactions. For example, we observe PTP1B crosslinking to the epidermal growth factor (EGF) receptor, a known substrate, in an EGF-dependent manner, and we identify other potential EGF-dependent substrates. Overall, our approach reveals previously unknown roles of PTP1B in signaling systems and could be readily extended to other tyrosine phosphatases in the same family.
    DOI:  https://doi.org/10.64898/2026.07.06.736850
  42. Mol Cell. 2026 Jul 16. pii: S1097-2765(26)00423-5. [Epub ahead of print]
    Thermo-sensing mechanisms of splicing control by nuclear stress bodies.
    Tsuyoshi Ueno, Shungo Adachi, Ichiro Taniguchi, Nobuo N Noda, Kensuke Ninomiya, Tetsuro Hirose.
      Nuclear stress bodies (nSBs) are stress-inducible membraneless organelles formed on HSATIII long noncoding RNAs (lncRNAs) that regulate pre-mRNA splicing during thermal stress recovery. During stress, dephosphorylated serine/arginine-rich splicing factors (SRSFs) accumulate in nSBs, whereas upon stress removal, their kinase CLK1 is recruited to rephosphorylate SRSFs, thereby promoting target intron detention. However, the mechanism underlying CLK1 localization to nSBs has remained unclear. Using HeLa cells and cell-free reconstitution, we identify CLK1 Ser341 phosphorylation as a critical determinant of its nSB localization and define its regulatory mechanism. Ser341 is phosphorylated under normal conditions, dephosphorylated by protein phosphatase 1(PP1) during stress, and rephosphorylated by RIOK2 during recovery, thus enabling CLK1 localization to nSBs specifically during recovery. We further identify PPP1R2, an entirely intrinsically disordered PP1 inhibitory subunit, as a reversible thermosensor that dissociates under stress to activate PP1. Together, our findings reveal multilayered thermosensing mechanisms that coordinate the staged localization of SRSFs and CLK1 to nSBs, thereby regulating temperature-dependent pre-mRNA splicing.
    Keywords:  intrinsically disordered protein; nuclear stress body; protein kinase; protein localization; protein phosphatase; splicing regulation; thermosensor
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.034
  43. MicroPubl Biol. 2026 ;2026
    Ubiquitin-elongating enzyme Ufd2 confers resistance to hygromycin B in Saccharomyces cerevisiae.
    Kaikeyi M Paxton, James A Avaala, Chance S Creviston, Joseph Gumina, Jason D True, Eric M Rubenstein.
      Aberrant proteins are targeted for proteasomal degradation by polyubiquitylation catalyzed by sequential action of ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). A subset of proteasomal substrates require ubiquitin chain extension by ubiquitin-elongating enzymes (E4s) prior to proteolysis. We tested the requirement of Ufd2, the founding member of the E4 enzyme family, in resisting proteotoxic stress caused by the aminoglycoside hygromycin B in Saccharomyces cerevisiae . The human homolog, UBE4B, is a potential therapeutic target for neurological disease and cancer. UFD2 deletion sensitized yeast to hygromycin B, consistent with a role for the E4 in protein quality control.
    DOI:  https://doi.org/10.17912/micropub.biology.002152
  44. EMBO Rep. 2026 Jul 17.
    Local translation of endosome-associated lc3b mRNA in axons contributes to endosomal clearance.
    Francesca Pappacena, Cinzia Caterino, Stefano De Pretis, Cristina Sironi, Alessandro Esposito, Giuliana Cesare, Michela Bruni, Jean-Michel Cioni.
      RNA localization to organelles is emerging as a key mechanism for regulating protein expression at the subcellular level in neurons. Although certain transcripts associate with endosomes, the functional significance remains poorly understood. Using APEX-seq, we identify a broad set of mRNAs localized to endosomes. We focus on the autophagy-related lc3b mRNA and confirm its endosomal association in cultured cells and Xenopus neuronal axons. In axons, lc3b mRNA is translated at endosomes, where the resulting LC3B protein also colocalizes, suggesting a tight spatial coupling between transcript localization and protein function. Impairment of LC3B membrane insertion via expression of a mutant ATG7 leads to the accumulation of enlarged axonal endosomes. Moreover, RAB5 overactivation promotes the formation of dysfunctional endosomes in axons that are targeted and cleared by LC3B-mediated autophagy. Finally, chloroquine-induced damage to axonal endosomes triggers their targeting by LC3B in a translation-dependent manner. Collectively, our findings expand the catalog of endosome-associated transcripts and reveal a functional link between autophagy and endosomal turnover in axons.
    DOI:  https://doi.org/10.1038/s44319-026-00867-5
  45. Mol Cell. 2026 Jul 15. pii: S1097-2765(26)00424-7. [Epub ahead of print]
    Granular component sub-phases direct ribosome biogenesis in the nucleolus.
    Priyanka Dogra, Mylene C Ferrolino, Suparna Khatun, Qi Miao, Michele Tolbert, Aaron Pitre, Shondra M Pruett-Miller, Swarnendu Tripathi, David W Baggett, Jaison John, George E Campbell, Katelyn Jackson, Richa Bajpai, Toler Freyaldenhoven, Eric Gibbs, Cheon-Gil Park, Richard W Kriwacki.
      The hierarchical, multiphase organization of the nucleolus underlies ribosome biogenesis. Ribonucleoprotein particles that regulate ribosomal subunit assembly are heterogeneously distributed in the nucleolar granular component (GC). However, the molecular origins of the GC's spatial heterogeneity and their link to ribosome subunit assembly remain poorly understood. Here, using super-resolution microscopy in DLD-1 cells, we uncover that key GC biomolecules-NPM1, SURF6, and ribosomal RNA (rRNA)-are heterogeneously localized within GC sub-phases. In vitro reconstitution with E. coli- and human-derived rRNA revealed that these GC biomolecules form multiphase condensates with a SURF6/rRNA-rich core and NPM1-rich shell, providing a mechanistic basis for this heterogeneity. SURF6's association with rRNA weakens upon ribosome subunit assembly, enabling NPM1 to extract assembled subunits from condensates, suggesting an assembly-line-like mechanism of subunit efflux from the GC. Our results establish a framework for understanding the GC's heterogeneous structure and reveal how its distinct sub-phases facilitate ribosome subunit assembly.
    Keywords:  assembly factor; granular component; intrinsically disordered region; multiphase condensate; nucleolus; phase separation; ribonucleoprotein assembly; ribosome biogenesis; spatial heterogeneity; structured illumination microscopy
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.035
  46. Aging Cell. 2026 Jul;25(7): e70641
    Circular RNAs-Stress Granule Interplay Drives Aging-Related Proteostasis Loss.
    José M Izquierdo.
      Aging involves a gradual loss of cellular balance, leading to reduced function and increased disease risk. While impaired proteostasis is a key hallmark of aging, more evidence shows the importance of RNA homeostasis (ribostasis), particularly the regulation of circular RNAs (circRNAs). CircRNAs are stable RNA molecules that build up over time and are linked to age-related cellular dysfunctions. In this regard, Kim et al. 2026 provide new insights into the impact of circRNA turnover on aging and lifespan. Their findings indicate that the accumulation of circRNAs is partly due to a decline in ribonuclease K (RNASEK), an enzyme that breaks down circRNAs. Using models such as worms, mice, and human cells, they show that RNASEK is crucial for healthy aging and longevity, suggesting its role is conserved across species. The research also shows that circRNAs gather in stress granules (SGs), which are ribonucleoprotein complexes formed during cell stress. RNASEK collaborates with heat shock protein 90 to prevent harmful RNA-rich aggregates, maintaining cellular dynamics in balance. These findings suggest a link between ribostasis and proteostasis, identifying circRNA clearance as a potential factor in longevity. The study also points to RNASEK as a promising target for treating age-related diseases. However, key questions remain, such as how RNASEK specifically degrades circRNAs, whether specific circRNAs or overall circRNA levels drive aging traits, and whether circRNA buildup is a cause or result of cell aging. Further research is needed to evaluate the conservation, safety, and therapeutic potential of this proteostasis-ribostasis axis in human biology.
    Keywords:  CircRNAs; RNASEK; aging; longevity; proteostasis; ribostasis; stress granules
    DOI:  https://doi.org/10.1111/acel.70641
  47. Nucleic Acids Res. 2026 Jul 03. pii: gkag696. [Epub ahead of print]54(13):
    Nuclear PI3P produced by the Beclin-1/Vps34 complex regulates DNA mismatch repair.
    Xinyi Li, Mariella Vicinanza, Ana Lopez, Beatrice Paola Festa, Lars Schlotawa, Antonio Daniel Barbosa, Michael Takla, Gabriel Balmus, Angeleen Fleming, David C Rubinsztein.
      Genome integrity relies on DNA mismatch repair (MMR) to correct replication errors, yet whether non-protein cofactors regulate this pathway remains unexplored. Here, we identify nuclear phosphatidylinositol-3-phosphate (PI3P) as a lipid regulator of MMR. Using biosensors, lipid pulldown, and proximity ligation assays, we show that PI3P forms discrete nuclear puncta in close proximity to the MutSα (MSH2:MSH6) and MutSβ (MSH2:MSH3) MMR recognition complexes. Pharmacological or genetic depletion of the class III PI3-kinase Vps34 impaired MutSα and MutSβ heterodimer assembly without altering MMR protein nuclear abundance, compromised DNA substrate association of MMR components in nuclear extracts, and elevated microsatellite instability at mononucleotide repeats. Exogenous PI3P enhanced MMR recognition complex assembly and DNA association in PI3P-deficient nuclear extracts, supporting a role for PI3P in promoting MMR. We further show that a nuclear Beclin-1/Vps34 complex produces this PI3P pool through an autophagy-independent mechanism. Functionally, loss of nuclear PI3P blunts MMR-dependent DNA damage signaling and confers 6-thioguanine resistance in cultured cells and in Beclin-1-deficient zebrafish in vivo. These findings reveal an autophagy-independent nuclear function for the Beclin-1/Vps34 complex in genome maintenance and identify PI3P as a lipid mediator of MMR, thereby expanding the functional repertoire of nuclear phosphoinositide signaling.
    DOI:  https://doi.org/10.1093/nar/gkag696
  48. Immunity. 2026 Jul 17. pii: S1074-7613(26)00271-2. [Epub ahead of print]
    Autophagy maintains high endothelial venule identity and function during inflammation.
    Kathryn A Jacobs, Yichao Hua, Apostolos Panagiotis Nikolakopoulos, Swati Gupta, Gerlanda Vella, Ana Filipa Domingues Laranjeiro, Julie Bonnereau, Mélanie Guyot, Maria Livia Sassano, Larissa Mourao, Feyza Cansiz, Gabriele Allies, Nicolas Van Baren, Sophie Lucas, Hiroto Kawashima, Wiebke Sondermann, Florian Rambow, Alpaslan Tasdogan, Colinda Scheele, Patrizia Agostinis, Gabriele Bergers.
      High endothelial venules (HEVs) play a crucial role in adaptive immune responses in secondary lymphoid organs (SLOs). They are equipped with high amounts of peripheral node addressin (PNAd), harboring carbohydrate structures that serve as L-selectin ligands to efficiently facilitate lymphocyte homing. During inflammation, the HEV network expands in SLOs, increasing lymphocyte infiltration, but the underlying mechanisms that maintain HEVs remain underexplored. Here, we report that autophagy is essential for HEV function and expansion. Using single-cell transcriptomics, unbiased proteomics, intravital imaging, and an inducible HEV tracer system in mice, we demonstrate that autophagy deficiency compromises lymphotoxin beta receptor (LTβR) signaling and the unfolded protein response in HEVs, leading to disrupted PNAd production, dedifferentiation, and reduced lymphocyte homing. Autophagy deficiency and LTβR blockade impair HEV function and reduce skin inflammation in psoriasis-affected mice by limiting immune infiltration and cytokine release. Our work reveals that autophagy safeguards HEV identity and function during inflammation.
    Keywords:  HEV; UPR; autophagy; high endothelial venules; inflammation; lymph node; lymphotoxin-beta receptor; peripheral node addressin; psoriasis; unfolded protein response
    DOI:  https://doi.org/10.1016/j.immuni.2026.06.020
  49. bioRxiv. 2026 Jul 09. pii: 2026.07.08.737379. [Epub ahead of print]
    Tissue-specific consequences of impaired RNA surveillance converge on mitochondrial homeostasis.
    Lauryn A Higginson, Xingjun Wang, Derrick J Morton.
      RNA surveillance pathways maintain transcriptome integrity by eliminating aberrant, excess, and non-functional RNAs, yet it remains unclear whether distinct tissues exhibit equivalent requirements for RNA quality control. Here, we investigated the tissue-specific consequences of impaired RNA surveillance using a Drosophila allelic series of the RNA exosome subunit Rrp40. Comparative transcriptomic analyses revealed that neuronal-enriched head tissue and muscle-enriched thorax tissue exhibit largely distinct molecular programs following reduced RNA exosome activity despite disruption of the same RNA surveillance machinery. Antisense RNAs emerged as particularly sensitive targets of RNA exosome dysfunction, accumulating preferentially in neuronal tissue and largely independent of changes in overlapping sense host transcripts, indicating enhanced requirements for RNA-level quality control within the nervous system. Although tissue-specific transcriptomic alterations diverged substantially, multiple analyses converged on mitochondrial homeostasis as a shared vulnerability. Reduced RNA exosome activity was associated with widespread dysregulation of nuclear-encoded mitochondrial genes, mitochondrial dynamics pathways, and mitochondrial RNA regulatory programs, accompanied by progressive defects in mitochondrial organization, membrane potential, and ATP production. Mitochondrial dysfunction was further associated with activation of proteostatic stress pathways, including p62 accumulation and increased ubiquitination. Together, these findings demonstrate that tissue context shapes the molecular consequences of impaired RNA surveillance while revealing mitochondrial homeostasis as a convergent vulnerability arising from transcriptome instability. More broadly, our findings suggest that distinct tissue-specific defects in RNA regulation converge on common cellular vulnerabilities that ultimately govern tissue homeostasis.
    DOI:  https://doi.org/10.64898/2026.07.08.737379
  50. bioRxiv. 2026 Jul 10. pii: 2026.07.09.737329. [Epub ahead of print]
    Cell-type-specific ATF6α programs regulate epithelial mitochondrial homeostasis and pericyte remodeling during physiological and exposure-accelerated lung aging.
    Xuejian Huang, Jonathan E Bard, Bat-Ider Tumenbayar, Kokilavani Vedagiri, Caryn E Nelson, Harshavardhan Kenche, Celia E Reynolds, Adriana S Leme, Stephen J Moore, Noa A Perry, Steven D Shapiro, Yaron Perry, Yongho Bae, Anna Blumental-Perry.
      Proteostasis declines with lung aging, while the role of the Unfolded Protein Response (UPR) in lung aging and age-associated pulmonary diseases remains understudied. We investigated how deficiency in the UPR sensor ATF6α affects physiological and smoke exposure-accelerated lung aging. ATF6α -deficient mice exhibited accelerated alveolar simplification, a sign of lung parenchymal aging, which was exacerbated by smoking. Nevertheless, small airway vascular fibrotic remodeling, a prominent smoking induced pathology, was not evident in smoke-exposed ATF6α -deficient mice. Mechanistically, these divergent phenotypes arose from cell-type-specific ATF6α programs. In alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of the lung parenchyma, ATF6α maintained mitochondrial bioenergetics and sustained efficient re-differentiation into alveolar epithelial type 1 cells (AEC1s). In lung pericytes, ATF6α promoted extravasation, re-differentiation into myofibroblast-like cells, and production of collagens 1 and 3. These findings identify ATF6α as a cell-type-specific regulator of differentiation programs during lung aging and highlight the need to study ATF6α under defined physiological and pathological contexts before therapeutically targeting this pathway.
    DOI:  https://doi.org/10.64898/2026.07.09.737329
  51. Nat Commun. 2026 Jul 16.
    The unfolded protein sensor IRE1 is essential for homeostatic dendritic cell maturation.
    Victor Bosteels, Sandra Maréchal, Eva Cloots, Farzaneh Fayazpour, Clint De Nolf, Laurien Van Heddegem, Simon J Tavernier, Sofie Rennen, Seraja Amstelveen, Liesbet Martens, Evelien Van De Velde, Delphine De Sutter, Annick Verhee, Kim Deswarte, Wouter Saelens, Louis Boon, Julie Van Duyse, Gert Van Isterdael, Isabelle Guillas, Yvan Saeys, Bruno De Geest, Sven Eyckerman, Pieter Mestdagh, Bart N Lambrecht, Wilfried Le Goff, Sophie Janssens.
      Conventional type I dendritic cells (cDC1s) undergo homeostatic maturation upon apoptotic cell engulfment, hallmarked by the activation of the transcription factor LXRβ, which mediates cholesterol efflux and dampens interferon-stimulated gene expression. Here, we identify the unfolded protein response sensor IRE1 as an essential regulator of this process. Loss of IRE1 impairs cDC1, but not cDC2, homeostatic maturation and survival. IRE1 activation depends on apoptotic cell uptake and cholesterol influx, explaining its high basal activity in cDC1s. Rather than inducing a canonical unfolded protein response, IRE1 triggers a steady-state regulated IRE1-dependent decay program that degrades miR-92a-1, a microRNA targeting the cholesterol-efflux transporter Abcg1. Consequently, IRE1-deficient cDC1s show impaired cholesterol efflux and increased death, which can be rescued by blocking miRNA synthesis or treatment with reconstituted high-density lipoprotein. These findings establish IRE1 as a cholesterol sensor in cDC1s and reveal a parallel pathway to LXR that coordinates cholesterol homeostasis during DC maturation.
    DOI:  https://doi.org/10.1038/s41467-026-75716-z
  52. J Am Chem Soc. 2026 Jul 16.
    Multidomain Relaxation Dispersion NMR Resolves an Intermediate-Gated Binding Pathway for Selective Recognition of Linear Diubiquitin by HOIL-1L.
    Erik Walinda, Naoki Ishii, Daichi Morimoto, Kenji Sugase.
      Molecular recognition is governed not only by the structural complementarity of the final complex, but by the kinetic pathway through which it forms. Polyubiquitin chains, in which sequence-identical domains are covalently linked yet must be discriminated by dedicated receptors to encode distinct cellular signals, exemplify this challenge. For NMR relaxation dispersion studies of such systems, spectral overlap between identical domains prevents conventional uniform isotope labeling from resolving the per-domain exchange contributions. Here we show, using domain-selective 15N labeling combined with R2 relaxation dispersion, that the binding of linear (Met1-linked) diubiquitin to HOIL-1L NZF proceeds through an apparent three-state pathway as detected by relaxation dispersion, in which rapid ligand-dependent pre-equilibration populates a conformationally preorganized intermediate that is selectively captured by NZF in a slower, chain-type-selective step. This kinetic hierarchy offers a mechanistic basis for understanding the discrimination between linear and Lys63-linked ubiquitin chains that static structures alone cannot reveal. This strategy should be broadly applicable to multidomain recognition systems─including epigenetic reader complexes and multivalent signaling adaptors─where the pathway between known structural end points remains hidden.
    DOI:  https://doi.org/10.1021/jacs.6c09447
  53. Nat Commun. 2026 Jul 17.
    Convergent nuclear proteostasis alterations across 40S ribosomal protein deficiencies.
    Sonia G Gaspar, Miguel Sánchez-Álvarez, Rosa M Ramírez-Cota, Blanca Nieto, Marta Flujas, Miguel Á Del Pozo, Xosé R Bustelo, Mercedes Dosil.
      Defects in ribosome biogenesis cause ribosomopathies, but the pathogenic role of malformed preribosomes remains unclear. Using preribosome fractionation, live-cell and confocal microscopy, and automated imaging screens, we tracked abortive preribosomes following depletion of the 33 small-subunit ribosomal proteins (RPSs). We found that all RPS deficiencies lead to accumulation of nucleolar preribosome materials in the nucleoplasm, regardless of the affected 40S subunit maturation stage. These aberrant particles appear as dispersed complexes or persistent aggregates arising during nucleolar reassembly in late mitosis. Although nucleolar morphology remains largely intact, their accumulation impairs recycling of nucleolar factors and disrupts nucleolar-nucleoplasmic proteostasis. Distinct RPS deficiencies produce different preribosome behaviors, indicating maturation-specific properties. Notably, depletion of RPS19, the protein encoded by the most frequently mutated gene in Diamond-Blackfan anemia, causes particularly severe defects. Our findings identify nucleoplasmic preribosome aggregation and dispersion as common consequences of RPS deficits and potential contributors to 40S ribosomopathy pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-026-75682-6
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