bims-proteo Biomed News
on Proteostasis
Issue of 2026–04–19
sixty papers selected by
Eric Chevet, INSERM
  1. Structural plasticity of the membrane-bound protein degradation assembly supports bacterial adaptation to stress.
  2. SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis.
  3. TAX1BP1 targets STING1 via microautophagy and Golgiphagy to limit inflammatory signaling.
  4. Cutting edge: ESCRT-mediated phagophore closure in mammals.
  5. Dosage compensation of Caj1-induced cytotoxicity by Sis1 and Ydj1 reveals complex interactions among JDPs in the yeast cytosol.
  6. Nrf1 coordinates proteasome activity and autophagy to maintain cardiac proteostasis.
  7. Biophysical characterization of Cyclophilin B reveals membrane localization as its primary functional determinant as a prolyl isomerase.
  8. Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.
  9. 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
  10. A delayed translocation into the endoplasmic reticulum controls the post-translational modifications of PD-L1.
  11. Sorting out extracellular proteins: SORTACs harness sortilin for targeted protein degradation.
  12. PROTAC internalization and target degradation require clathrin-mediated endocytosis.
  13. GRASP55 maintains lysosome function by controlling sorting of lysosomal enzymes at the Golgi.
  14. Autophagy selectively clears ER in TNF-α-induced muscle atrophy.
  15. HECT-Type Ubiquitin Ligases: Emerging principles in the Era of Full-Length Structures.
  16. Graded activation of the CLEAR network through mTORC1 suppression on cargo-harboring lysosomes.
  17. Stress-induced proteome remodeling at the Golgi-endosome interface.
  18. The reticulon homology domain of Pex30 generates membrane curvature at ER subdomains for lipid droplet biogenesis.
  19. Turnover of missense mutant cytosolic proteins proceeds in the absence of major quality control E3 ligases.
  20. Unravelling chaperone-mediated microautophagy targeting KFERQ-like motif containing proteins in yeast.
  21. Template-driven scaffolding of SCFFBXO42 regulates PP2A degradation.
  22. Genetically encoded lockdown of SERCA in the endoplasmic reticulum membrane arrests Ca2+ signaling through proximity-covalent crosslinking.
  23. The endoplasmic reticulum protein Erg28 restrains Mto1-Mto2-γ-TuSC-mediated microtubule assembly.
  24. Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.
  25. Hijacking innate immunity to enhance mRNA therapeutics by blocking IFN-P-body-XRN1 axis-mediated degradation.
  26. SUMO E3 ligase SIZ1 promotes nuclear condensate-mediated immune activation in Arabidopsis.
  27. Large-scale endoplasmic reticulum membrane solidification spatially organizes proteins under thermal or metabolic stress.
  28. Proteolytic dissection of eIF4G reveals the closed-loop mRNP as an architecture for translation repression.
  29. LC3-linked Golgi-bypass exocytosis fortifies epithelial barrier defense.
  30. Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.
  31. Optogenetic Control of the Integrated Stress Response Limits Glioblastoma Invasion.
  32. Locally synthesized glycyl aminoacyl-tRNA synthetase is important for local translation in neurons.
  33. Hsp70 diversification and repurposing across the tree of life: Lessons from the evolutionary and mechanistic trajectory of the Hsp70-Hsp110 chaperone system.
  34. A covalent molecular glue hijacks the E3 ligase MKRN2 to degrade the ribosomal protein RPS7 and induce synthetic lethality in p53-deficient NSCLC cells.
  35. Ubiquitin-dependent degradation of MBD3 by TRIM59 promotes lung adenocarcinoma.
  36. CHK2-USP37 axis stabilizes FOXO4 to sustain senescence and evade apoptosis.
  37. RNA dicing promotes the expression of an oncogenic JAK1 isoform.
  38. A ULK1-MTFR1L feedback loop links mitochondrial fission, mitophagy and apoptosis.
  39. Ubiquitin ligase RCHY1 regulates autophagosome-lysosome fusion.
  40. DNA-Encoded Library (DEL) Selection Identifies a Distinct DDB1 Ligand Binding Site.
  41. ER-derived caveolin-coated vesicles transport newly synthesized cholesterol to the plasma membrane.
  42. From Initiation to Elongation: eIF3 as a Dual-Phase Guardian of Mitochondrial Integrity and Protein Homeostasis in Skeletal Muscle.
  43. Wntless degradation mediated by CaMKII inhibition drives endoplasmic reticulum stress and apoptosis.
  44. XPO1 inhibitor KPT-330 disrupts the core transcriptional regulatory circuitry of dedifferentiated liposarcoma by modulating the translation process.
  45. Ubiquitylation of DNA polymerase β via atypical K27 chains signals a DNA damage response.
  46. Mechanism of c-Cbl Transition from Autoinhibited to Partially Open State via Substrate Binding.
  47. Heat shock protein Gp96 (Grp94) in malaria: functional insights at the host-parasite interface and therapeutic perspectives.
  48. Golgi-derived phosphatidylinositol 4-phosphate is crucial for organization of the pre-autophagosomal structure.
  49. The E3 ubiquitin ligase UBR5 promotes ubiquitylation and degradation of the chromatin regulator ATAD2.
  50. Metabolite import by SLC33A1 is required for ATF6 activation during endoplasmic reticulum stress.
  51. Hsp70/Hsp90 Organizing Protein (HOP) Maintains CRAF Kinase Activity and Regulates MAPK Signaling by Enhancing Hsp90-CRAF Association.
  52. A Novel Role of the Ubiquitin Conjugating Enzyme, UBE2G2, in Regulation of Cell Shape and Movement.
  53. Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks.
  54. Proteomic Profiling Reveals How Physiological Media Reshape Cancer Cell Proteomes and Signaling Networks.
  55. Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
  56. Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition.
  57. A sequence knowledge-guided deep learning method for single-cell multi-omics translation.
  58. COPI-dependent intra-Golgi recycling at an intermediate stage of cisternal maturation.
  59. Septins associate with AP-3 to support trafficking to the vacuole/lysosome in yeast.
  60. Therapy-induced cholesterol biosynthesis drives lung cancer dormancy and drug resistance.
  1. Cell Rep. 2026 Apr 10. pii: S2211-1247(26)00309-8. [Epub ahead of print]45(4): 117231
    Structural plasticity of the membrane-bound protein degradation assembly supports bacterial adaptation to stress.
    Naseer Iqbal, Sandro Keller, Alireza Ghanbarpour.
      Protein degradation by ATPases associated with diverse cellular activities) (AAA+) proteases is essential for bacterial adaptation to stress. The membrane-bound protease FtsH forms an inner-membrane complex with the SPFH (stomatin, prohibitin, flotillin, and HflK/C) (SPFH) proteins HflK and HflC that promotes recovery from aminoglycoside antibiotics. Although open and closed HflK/C conformations have been described, their functional relevance has remained unclear. Here, we engineer a disulfide-crosslinked HflK/C variant to stabilize the closed state and determine its structure by high-resolution cryo-electron microscopy (cryo-EM). Cells expressing this variant, or an HflK/C mutant that disrupts FtsH binding, exhibit impaired growth under aminoglycoside stress, demonstrating that conformational dynamics and productive HflK/C-FtsH interactions are required for adaptation. Surprisingly, cryo-EM of the FtsH⋅HflK/C complex from tobramycin-treated cells reveals a distinct conformation with two openings that may facilitate substrate entry during proteotoxic stress. Together, these findings establish HflK/C conformational flexibility as a determinant of stress adaptation and provide a framework for understanding SPFH protein function.
    Keywords:  CP: molecular biology; FtsH AAA protease; HflK/C membrane assembly; SPFH family; aminoglycoside stress; bacterial stress response; cryo-electron microscopy; membrane protein quality control; proteostasis; stress-induced conformation
    DOI:  https://doi.org/10.1016/j.celrep.2026.117231
  2. Nat Cell Biol. 2026 Apr 17.
    SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis.
    Shanshan Liu, Mark Gad, Caifan Li, Kevin Cho, Yuyang Liu, Khando Wangdu, Viktor Belay, Alon Millet, Hiroyuki Kojima, Henry Sanford, Michele Wölk, Linas Urnavicius, Maria Fedorova, Gary J Patti, Ekaterina V Vinogradova, Richard K Hite, Kıvanç Birsoy.
      The endoplasmic reticulum (ER) requires an oxidative environment to support the efficient maturation of secretory and membrane proteins. This is in part established by glutathione, a redox-active metabolite present in reduced (GSH) and oxidized (GSSG) forms. The ER maintains a higher GSSG:GSH ratio than the cytosol; however, the mechanisms controlling ER redox balance remain poorly understood. To address this, we developed a method for the rapid immunopurification of the ER, enabling comprehensive profiling of its proteome and metabolome. Combining this approach with CRISPR screening, we identified SLC33A1 as the major ER GSSG exporter in mammalian cells. Loss of SLC33A1 led to GSSG accumulation in the ER and a liposome-based assay demonstrated that SLC33A1 directly transports GSSG. Cryogenic electron microscopy structures and molecular dynamics simulations revealed how SLC33A1 binds GSSG and identified residues critical for its transport. Finally, an imbalance in GSSG:GSH ratio induced ER stress and dependency on the ER-associated degradation pathway, driven by a shift in protein disulfide isomerases towards their oxidized forms. Together, our work establishes SLC33A1-mediated GSSG export as a key mechanism for ER redox homeostasis and protein maturation.
    DOI:  https://doi.org/10.1038/s41556-026-01922-y
  3. Autophagy. 2026 Apr 16. 1-3
    TAX1BP1 targets STING1 via microautophagy and Golgiphagy to limit inflammatory signaling.
    Sujit Suklabaidya, Suchitra Mohanty, Edward W Harhaj.
      The CGAS-STING1 pathway plays a key role in detecting cytosolic DNA and initiating immune responses. Excessive STING1 activation can lead to aberrant inflammation and autoinflammatory diseases; therefore, the STING1 degradation pathway is tightly regulated by several negative regulatory mechanisms. In our recent study, we show that the selective autophagy receptor TAX1BP1 functions as a negative regulator of STING1 signaling. TAX1BP1 promotes the degradation of activated STING1 through microautophagy by facilitating the interaction of STING1 with the ESCRT-0 protein HGS, and selective autophagy of the Golgi apparatus in a process known as Golgiphagy. In TAX1BP1-deficient macrophages, STING1 aggregates accumulate at the trans-Golgi network, leading to stronger antiviral and inflammatory responses. These findings support a novel mechanism linking organelle quality control and innate immune regulation, highlighting Golgiphagy as an important feedback mechanism that limits STING1 signaling.Abbreviations: cGAMP: cyclic guanosine monophosphate-adenosine monophosphate; CGAS: Cyclic GMP-AMP synthase; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; ECTV: ectromelia virus; HGS: hepatocyte growth factor-regulated tyrosine kinase substrate; IKK: IκB kinase; IRF3: interferon regulatory factor 3; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1; TAX1BP1: Tax1 binding protein 1.
    Keywords:  CGAS; Golgiphagy; SQSTM1/p62; STING1; TAX1BP1; microautophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2658230
  4. Biochem J. 2026 May 06. 483(5): 741-759
    Cutting edge: ESCRT-mediated phagophore closure in mammals.
    Yoshinori Takahashi, David M Opozda, Hong-Gang Wang.
      Autophagy delivers cytoplasmic materials to lysosomes, supporting protein and organelle quality control as well as nutrient recycling to maintain cellular homeostasis. A defining feature of macroautophagy, the major form of autophagy, is the formation of double-membrane autophagosomes that encapsulate cargo either non-selectively or through selective recognition mechanisms. Completion of autophagosome biogenesis requires closure of the phagophore, a step that ensures full cargo sequestration and enables efficient degradation following lysosomal fusion. Recent studies have uncovered a critical role for the endosomal sorting complex required for transport (ESCRT) machinery in mediating phagophore closure, revealing that this event contributes to cellular functions beyond cargo degradation. In the present review, we summarize current advances in defining the molecular mechanisms and physiological significance of phagophore closure in mammals and highlight emerging concepts and future directions for the field.
    Keywords:  autophagosome; autophagy; endosomal sorting; phagophore closure
    DOI:  https://doi.org/10.1042/BCJ20250148
  5. Genetics. 2026 Apr 17. pii: iyag100. [Epub ahead of print]
    Dosage compensation of Caj1-induced cytotoxicity by Sis1 and Ydj1 reveals complex interactions among JDPs in the yeast cytosol.
    Preeti Sagarika, Dharani Krishnadas Kurup, Anjitha Gireesh, Chandan Sahi.
      Cellular proteostasis depends on tightly regulated Hsp70-J-domain protein (JDP) networks that coordinate protein folding and degradation. Here, we define a previously unrecognized role for the budding yeast JDP Caj1 in modulating nucleocytoplasmic protein quality control. We show that elevated Caj1 levels broadly disrupt proteostasis, stabilizing diverse misfolded substrates by impairing their degradation and triggering the accumulation of ubiquitinated proteins, along with constitutive activation of the heat shock response (HSR). Caj1-induced defects were associated with the accumulation of ubiquitinated proteins. They were genetically suppressed by loss of the E3 ubiquitin ligases and enhanced by loss of deubiquitinating enzymes, revealing functional coupling between Caj1 activity and ubiquitin-mediated protein turnover. Co-overexpression of the major nucleocytoplasmic JDPs Ydj1 and Sis1 suppressed Caj1 toxicity, with Sis1 acting through a J-domain-dependent, Hsp104-independent mechanism. Our findings uncover a dosage-sensitive regulatory interplay among JDPs and demonstrate that relative JDP abundance, rather than absolute levels, is a critical determinant of proteostasis capacity, revealing a previously unrecognized functional network linking Caj1, Sis1, and Ydj1 in shaping cellular protein quality control.
    Keywords:  Caj1; JDP; Protein quality control; Sis1; Ydj1
    DOI:  https://doi.org/10.1093/genetics/iyag100
  6. Commun Biol. 2026 Apr 17.
    Nrf1 coordinates proteasome activity and autophagy to maintain cardiac proteostasis.
    Lakindu P Kankanamge, Hyunji An, Qin Guo, Maksymillian Prondzynski, Soon Ho Kwon, Durgesh Anil Bonde, William T Pu, Eric N Olson, Miao Cui.
      Proteolytic stress frequently arises during disease and aging, particularly in long-lived, post-mitotic cells such as cardiomyocytes. To maintain proteostasis, cardiomyocytes depend on coordinated protein quality control pathways, including the ubiquitin-proteasome system and autophagy. Mechanisms that activate these pathways hold therapeutic potential for heart disease. Here, we demonstrate that transient activation of nuclear factor erythroid 2-like 1 (Nfe2l1, also known as Nrf1), a transcriptional regulator of proteasome activity, in cardiomyocytes during ischemia/reperfusion injury improves cardiac function. In addition to regulating the proteasome, we identify a critical role for Nrf1 in activating autophagy, which is essential for its cardioprotective effects. Through multi-omics analyses, we define both transcriptional and post-transcriptional functions of Nrf1 that underlie its cardioprotective activity. Loss-of-function studies in mice demonstrate that Nrf1, but not its homolog Nrf2, is required for autophagy and baseline cardiac function. Together, our findings establish a dual function of Nrf1 in promoting cardiac proteostasis by regulating both proteasomal and autophagic protein quality control pathways. Activating Nrf1 thus offers a therapeutic strategy for treating ischemic heart disease.
    DOI:  https://doi.org/10.1038/s42003-026-10067-5
  7. Protein Sci. 2026 May;35(5): e70579
    Biophysical characterization of Cyclophilin B reveals membrane localization as its primary functional determinant as a prolyl isomerase.
    Sarah C DeVoe, Thomas C Yost, Ashley J Newton, Gavin A Grever, Melissa Fernandez Ayala, Wendell P Griffith, Robert D Latvala, Philipp A M Schmidpeter.
      The endoplasmic reticulum (ER) provides a specialized environment for the folding of secreted and membrane proteins, a process supported by many different chaperones. Among these chaperones, peptidyl-prolyl cis/trans isomerases (PPIases) catalyze a rate-limiting conformational step in protein folding, yet the principles governing isoform-specific function of PPIases remain poorly defined. Cyclophilin B (CypB), an ER-resident PPIase, has been implicated in early folding events, but whether its activity reflects biochemical adaptation to the ER environment is unclear. Here, we report the biophysical characterization of human CypB and compare it with the cytosolic isoform Cyclophilin A. Spectroscopic and enzymatic analyses show that CypB adopts the canonical cyclophilin fold and displays catalytic activity toward multiple substrates under both cytosolic- and ER-mimicking conditions, indicating that its enzymatic properties are not uniquely tuned to the ER milieu. Confocal imaging confirms that full-length CypB is enriched in the ER, and that removal of its N-terminal segment disrupts this localization. Together, these results indicate that subcellular localization, mediated by an N-terminal membrane anchor, rather than catalytic specialization, may define the physiological role of CypB. Our findings underscore compartmentalization as a central organizing principle of proteostasis in the secretory pathway.
    Keywords:  Cyclophilin B; endoplasmic reticulum; peptidyl‐prolyl isomerase; protein folding; proteostasis; subcellular localization
    DOI:  https://doi.org/10.1002/pro.70579
  8. Elife. 2026 Apr 17. pii: RP107160. [Epub ahead of print]14
    Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.
    Irene Lamberti, Jeffrey A Chao, Cédric Gobet, Felix Naef.
      mRNA translation involves multiple regulatory steps, but how translation elongation influences protein output remains unclear. Using SunTag live-cell imaging and mathematical modeling, we quantified translation dynamics in single mRNAs across diverse coding sequences. Our Totally Asymmetric Exclusion Process (TASEP)-based Hidden Markov Model revealed a strong coordination between initiation and elongation rates, resulting in consistently low ribosome density (≤12% occupancy) across all reporters. This coupling persisted under pharmacological inhibition of the elongation factor eIF5A, where proportional decreases in both initiation and elongation rates maintained homeostatic ribosome density. In contrast, eIF5A knockout cells exhibited a significant decrease in ribosome density, suggesting altered coordination. Together, these results highlight a dynamical coupling of initiation and elongation rates at the single-mRNA level, preventing ribosome crowding and maintaining translational homeostasis in mammalian cells.
    Keywords:  SunTag; TASEP; computational biology; eIF5A; human; single-molecule imaging; systems biology; translation elongation
    DOI:  https://doi.org/10.7554/eLife.107160
  9. EMBO Rep. 2026 Apr 13.
    5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
    Jimmy Ly, Eric M Smith, Matteo Di Bernardo, Yi Fei Tao, Elizabeth M Black, Ekaterina Khalizeva, Iain M Cheeseman.
      The 5' untranslated region (5' UTR) of an mRNA is classically viewed as a regulatory region that controls the amount of protein production, but not the resulting protein sequence. Here, we demonstrate that 5' UTR length plays a direct role in alternative N-terminal protein isoform production by controlling start codon selection. We find that very short 5' UTRs enhance leaky ribosome scanning, thereby promoting the production of truncated alternative N-terminal protein isoforms. We also show that endogenous changes in 5' UTR length due to alternative transcription initiation can tune the relative abundance of alternative N-terminal isoforms from the same gene. In addition, we identify mutations in rare genetic diseases that alter 5' UTR length, including a deletion in the VHL 5' UTR in von Hippel-Lindau disease that shifts translation toward the shorter VHLp19 isoform. Together, our results implicate 5' UTR length as a determinant of alternative N-terminal isoform production and reveal an underappreciated mechanism by which noncoding changes can reshape the proteome.
    DOI:  https://doi.org/10.1038/s44319-026-00776-7
  10. Nat Commun. 2026 Apr 11.
    A delayed translocation into the endoplasmic reticulum controls the post-translational modifications of PD-L1.
    Magda Cannata Serio, Fulvia Vitale, Gianluca Scerra, Raffaella Bonavita, Patrick Poullet, Maria Gabriella Caporaso, Laura Marrone, Simona Romano, Maurizio Renna, Franck Perez, Massimo D'Agostino.
      N-terminal signal peptides (SPs) are traditionally considered as drivers of co-translational translocation of newly synthesised proteins into the endoplasmic reticulum (ER). However, growing evidences suggest that proteins with SPs can also undergo post-translational insertion into the ER membrane after synthesis is complete. Recently, an intermediate third mechanism has been uncovered where proteins with marginally hydrophobic or suboptimal SPs are translocated following an initial delay after translation initiation. Here, we show that this "delayed translocation" allows a temporary exposure of the nascent chain to the cytosolic environment, enabling exoplasmic domain modifications by cytosolic enzymes. We report that programmed death ligand-1 (PD-L1) follows this pathway, featuring a suboptimal SP that exposes its extracellular domain to the cytosol, enabling AMPK-dependent regulation of PD-L1 function. Importantly, optimising the SP of PD-L1 eliminates the cytosolic exposure, disrupting PD-L1's trafficking and maturation, highlighting the physiological importance of the delayed translocation mechanism.
    DOI:  https://doi.org/10.1038/s41467-026-71760-x
  11. Cell Chem Biol. 2026 Apr 16. pii: S2451-9456(26)00104-2. [Epub ahead of print]33(4): 428-429
    Sorting out extracellular proteins: SORTACs harness sortilin for targeted protein degradation.
    Chen Zhou, Xiaoyu Zhang.
      In this issue of Cell Chemical Biology, Gustafsen et al.1 develop sortilin-based lysosome targeting chimeras (SORTACs), which exploit sortilin-mediated endocytosis to degrade extracellular proteins. This strategy converts antibodies or small molecules into degraders and enables efficient elimination of cytokines and membrane proteins, illustrating new opportunities for extracellular targeted protein degradation.
    DOI:  https://doi.org/10.1016/j.chembiol.2026.03.012
  12. bioRxiv. 2026 Apr 08. pii: 2026.04.06.716751. [Epub ahead of print]
    PROTAC internalization and target degradation require clathrin-mediated endocytosis.
    Hao-Yang Liu, Zhengyu Wang, Rahul Sharma, Jessica Perez, Brandon W Kusaj, Hongfei Zhou, Minmin Wang, Jon M Huibregtse, Hong-Yu Li, Jeanne C Stachowiak.
      Proteolysis-targeting chimeras (PROTACs) are emerging as potent tools for targeted protein degradation that overcome many of the limitations of traditional small molecule inhibitors. Yet how these hetero-bifunctional therapeutics enter cells remains a mystery. While passive diffusion is conventionally assumed, the bulky structure of PROTACs suggests that active transport may be required. Recently, the fatty acid transporter CD36 was identified as a key receptor for PROTACs. However, because the uptake mechanism of CD36 is itself unknown, how PROTACs enter cells remains a mystery. Here we show that PROTAC uptake and function require clathrin-mediated endocytosis. We uncover previously unrecognized clathrin adaptor-binding motifs in the CD36 C-terminus and use live-cell imaging to visualize the recruitment of both CD36 and PROTACs to sites of clathrin-mediated endocytosis on the cellular plasma membrane. Strikingly, disruption of clathrin assembly through either genetic or pharmacological means abolishes all detectable PROTAC-induced protein degradation, demonstrating that the clathrin pathway is required for the function of PROTACs that utilize diverse E3 enzymes against multiple targets. These results elucidate the molecular mechanism of PROTAC entry into cells, providing critical information for optimizing cellular uptake and response to targeted degraders.
    DOI:  https://doi.org/10.64898/2026.04.06.716751
  13. EMBO Rep. 2026 Apr 16.
    GRASP55 maintains lysosome function by controlling sorting of lysosomal enzymes at the Golgi.
    Julian Nüchel, Maryam Omidi, Stephanie A Fernandes, Marina Tauber, Sandra Pohl, Markus Plomann, Constantinos Demetriades.
      Lysosomes are multifunctional organelles that play important roles in cellular recycling, signaling, and homeostasis, relying on precise trafficking and activation of lysosomal enzymes. While the Golgi apparatus plays a central role in lysosomal enzyme sorting, the mechanisms linking Golgi function to lysosomal activity remain incompletely understood. Here, we identify the Golgi-resident protein GRASP55, but not its paralog GRASP65, as necessary for lysosome function. Loss of GRASP55 expression leads to missorting and secretion of lysosomal enzymes, lysosomal dysfunction and bloating. GRASP55 deficiency also disrupts lysosomal mTORC1 signaling, reducing the phosphorylation of its lysosomal substrates TFEB/TFE3, while sparing its non-lysosomal targets. Mechanistically, GRASP55 binds and maintains the COPI adaptor GOLPH3 protein at the Golgi, thereby controlling the Golgi localization and stability of LYSET and GNPTAB that are required for mannose 6-phosphate (M6P) tagging of lysosomal enzymes. These findings reveal an essential role for GRASP55 in Golgi-lysosome communication and lysosomal enzyme trafficking and underscore the importance of Golgi-mediated protein sorting in lysosome function and lysosomal mTORC1 signaling.
    DOI:  https://doi.org/10.1038/s44319-026-00773-w
  14. Autophagy Rep. 2026 ;5(1): 2649064
    Autophagy selectively clears ER in TNF-α-induced muscle atrophy.
    Ursula K Dueren, Alan An Jung Wei, A Elisabeth Gressler, Simon Rapp, Oliver Popp, Robert Kerridge, Viviana Buonomo, Paolo Grumati, Philipp Mertins, Matthias Selbach, Anna Katharina Simon, Thomas Sommer.
      Skeletal muscle atrophy is a pathological condition characterized by the progressive loss of muscle mass and function, driven by factors such as disuse, inflammation, and aging. While the ubiquitin-proteasome system is established as the central mediator of myofibrillar protein degradation, the role of selective autophagy and the degradation of organelles remains underexplored in this context. To address this, we employed a quantitative, time-resolved in vitro analysis of protein synthesis and degradation in C2C12 myotubes undergoing TNF-α-induced atrophy, using dynamic Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) coupled with LC-MS/MS. Our data challenges the classical view of atrophy as a uniform, degradation-centric process. Instead, we reveal temporally distinct patterns of selective protein turnover, including differential degradation of myofibrillar, ribosomal, and endoplasmic reticulum (ER)-resident proteins. Early atrophy is characterized by suppressed short-term protein synthesis, increased ubiquitin-ligase expression, proteasomal activation, and ribosome turnover. In contrast, late atrophy features proteasome-dependent myofibrillar protein degradation, selective synthesis, and degradation of mitochondrial and cytoplasmic ribosomes, indicative of metabolic adaptation. Moreover, we identify a temporal shift in autophagic selectivity: from ER homeostasis to a stress-induced ER-degradation program. Notably, autophagy inhibition during atrophy leads to the accumulation of ER-phagy receptors Tex264 and Calcoco1, implicating ER-phagy as a key contributor to atrophic remodeling and highlighting receptor-mediated selective autophagy as a regulatory axis in muscle proteostasis. By elucidating the role of ER-phagy, this study opens avenues for therapeutic interventions targeting proteostasis in inflammation-induced muscle-wasting, contributing to a refined understanding of muscle atrophy beyond proteasomal degradation, particularly in acute inflammatory conditions such as sepsis.
    Keywords:  Dynamic SILAC; ER-phagy; TNF-α; autophagy; inflammation; muscle atrophy; proteostasis
    DOI:  https://doi.org/10.1080/27694127.2026.2649064
  15. J Biol Chem. 2026 Apr 09. pii: S0021-9258(26)00310-8. [Epub ahead of print] 111440
    HECT-Type Ubiquitin Ligases: Emerging principles in the Era of Full-Length Structures.
    Thornton Fokkens, Blanca Baños-Jaime, Sonja Lorenz.
      The ubiquitin system coordinates an increasingly intricate network of cellular pathways. Specificity in substrate recognition and ubiquitin modification is largely conferred by ubiquitin ligases, a highly diversified enzyme family comprising 672 members in human cells. Among these, 28 belong to the HECT (Homologous to E6AP C-terminus) family, whose distinctive structural features and functional specializations have remained incompletely understood. While the catalytic principles of the defining C-terminal HECT domain are well established, the manner in which this domain is embedded within, and regulated by, full-length enzymes long remained elusive. Over the past five years, a series of cryo-electron microscopy studies of full-length HECT-type ligases have yielded unprecedented insights into their overall architectures, regulatory mechanisms, and linkage and substrate specificities. Here, we synthesize these advances to provide an up-to-date structural framework for HECT-type ligase function and highlight key questions for future investigation, including implications for small-molecule discovery.
    Keywords:  E3; cryo electron microscopy; enzyme mechanism; posttranslational modification; substrate recognition; ubiquitination
    DOI:  https://doi.org/10.1016/j.jbc.2026.111440
  16. Cell Rep. 2026 Apr 09. pii: S2211-1247(26)00306-2. [Epub ahead of print]45(4): 117228
    Graded activation of the CLEAR network through mTORC1 suppression on cargo-harboring lysosomes.
    Cheng-Wei Hsieh, Guang-Chao Chen, Wei Yuan Yang.
      Cellular lysosomal capacity is tightly controlled to match catabolic demands and sustain lysosomal signaling pathways. Here, we report that cells can adjust their lysosomal capacity in response to varying autophagy loads. Manipulating the number of mitochondria targeted for mitophagy leads to a proportional upregulation of transcription factor EB (TFEB)-mediated lysosome adaptation programs. This quantitative control is exerted through Rag GTPase-driven mTORC1 suppression. GATOR1 is selectively recruited to lysosomes containing autophagic cargo, initiating local Rag GTPase-dependent suppression of mTORC1 activities. This mitophagy-induced mTORC1 suppression leads to TFEB activation and dephosphorylation of TOS-motif-containing substrates (S6K and 4EBP) under nutrient-rich conditions. This phenomenon similarly occurs during aggrephagy. These findings suggest that autophagic cargo-harboring lysosomes exhibit consistently low mTORC1 activity. Lysosomes can, therefore, sense the magnitude of autophagy loads and quantitatively translate this signal into TFEB activation to support self-regulated homeostasis.
    Keywords:  CP: molecular biology; GATOR1; TFEB; aggregate autophagy; folliculin; lysosome; mTORC1; mitophagy
    DOI:  https://doi.org/10.1016/j.celrep.2026.117228
  17. J Cell Sci. 2026 Apr 16. pii: jcs.264535. [Epub ahead of print]
    Stress-induced proteome remodeling at the Golgi-endosome interface.
    Gina Simon, Savina Abraham Pol, Melisa Dendusic, Nina Schulze, Simone Stupia, Michelle Koci, Lana Buzuk, Beatrice Thier, Philine Steinbach, Hai Trinh, Jasmin Schillinger, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Michael Ehrmann, Annette Paschen, Doris Hellerschmied.
      Cellular stress response pathways support cell survival under stress and are often leveraged by cancer cells to gain advantageous traits. How cells respond to Golgi apparatus (Golgi) stress is incompletely understood, limiting insights into the role of Golgi stress in cancer. Here, we combined small molecule stress models and proteomic analyses to elucidate stress-induced changes at the Golgi. Our data establish the depletion of Golgi transport proteins as a common response to different Golgi stressors, including ionophores and inhibitors of the Oxysterol binding protein (OSBP). Ionophores further induce de novo expression of the stress response protein FAM129A/NIBAN1, which localizes to the remodeled secretory pathway. In a group of melanoma cells, displaying a dedifferentiated epithelial-to-mesenchymal-transition (EMT)-like phenotype, FAM129A is constitutively expressed. In these cells, stress-induced localization of FAM129A to the secretory pathway is achieved by relocalization from the plasma membrane. Collectively, our data highlight the Golgi-endosome interface as a critical hub of the cellular response to Golgi stress and reveal cancer cell specific effects of this response.
    Keywords:  Chemical biology; FAM129A/NIBAN1; Golgi stress; Ionophores; Melanoma
    DOI:  https://doi.org/10.1242/jcs.264535
  18. bioRxiv. 2026 Apr 08. pii: 2026.04.08.717014. [Epub ahead of print]
    The reticulon homology domain of Pex30 generates membrane curvature at ER subdomains for lipid droplet biogenesis.
    Morgan House, Nikhil Nambiar, Steve M Abel, Amit S Joshi.
      Lipid droplets (LDs) are dynamic organelles that store neutral lipids and form in the endoplasmic reticulum (ER) membrane. Formation of new LDs is a controlled process and requires proteins with specific functions to form and grow from the ER membrane without any defect. In vitro studies have suggested a role for membrane curvature in LD emergence from the ER. Here, we use the membrane-shaping protein Pex30 to investigate the impact of ER membrane curvature on LD biogenesis and morphology. We modified the reticulon homology domain (RHD) of Pex30, which is responsible for tubulating the ER membrane, by extending the short hairpin transmembrane domains (TMD). The Pex30 (TMD) mutants cannot tubulate the ER membrane and generate less local membrane curvature that WT Pex30. Additionally, these mutants are unable to restore delayed LD biogenesis observed in cells devoid of Pex30. Our results indicate that Pex30 RHD generates local membrane curvature at ER subdomains that drives formation of new LDs.
    DOI:  https://doi.org/10.64898/2026.04.08.717014
  19. MicroPubl Biol. 2026 ;2026
    Turnover of missense mutant cytosolic proteins proceeds in the absence of major quality control E3 ligases.
    Heather A Baker, Claire Grall-Johnson, Paulina M Budzyńska, John Kim, Thibault Mayor.
      Protein quality control (QC) safeguards cellular proteostasis by directing misfolded proteins for degradation via the ubiquitin-proteasome system. QC is compartmentalized within cells, and the key proteins involved in the turnover of cytosolic proteins with mutations in mammalian cells are not well defined. Using a fluorescent reporter assay that provides a readout for protein stability, we examined the contributions of known QC E3 ligases (STUB1, UBE2O, UBR4, UBR5, and HUWE1) on the turnover of disease-associated missense variants. Loss of individual ligases did not consistently stabilize substrates, indicating that none of these E3s appear to broadly recognize missense mutant proteins.
    DOI:  https://doi.org/10.17912/micropub.biology.001990
  20. Autophagy. 2026 Apr 13. 1-22
    Unravelling chaperone-mediated microautophagy targeting KFERQ-like motif containing proteins in yeast.
    Krishna Upadhayay, Pushpender Bhardwaj, Namra Farooqi, Bhagyashree Rabha, Adarsh Mishra, Kamalesh Verma, Ramandeep Singh, Deepak Sharma.
      Under prolonged starvation, mammalian cells activate chaperone-mediated autophagy (CMA) that degrades cellular proteins containing KFERQ-like motifs via lysosomes. During CMA, the lysosomal membrane protein LAMP2A acts as an essential receptor for the HSPA8/HSC70-CMA substrate complex. Thus, the evidence of CMA in organisms lacking LAMP2A on lysosomes/vacuoles is still lacking. Here, we examined the fate of proteins containing such motifs in S. cerevisiae that lack the CMA receptor on vacuoles. Intriguingly, we found that even in the absence of LAMP2A, proteins containing such motifs translocate into vacuoles upon prolonged starvation. We report for the first time that phosphatidylserine acts as an Hsp70-family protein-substrate receptor on the vacuolar membrane to facilitate the substrate translocation into vacuoles. As the newly discovered degradation pathway is dependent upon cytosolic Hsp70 (as in CMA) as well as the ESCRT complex, and involves invagination of the vacuolar membrane, we refer to it as chaperone-mediated microautophagy. Taken together, this study has led to the identification of a novel cellular pathway in S. cerevisiae that facilitates the clearance of cellular proteins under chronic stress.Abbreviations: CMA: chaperone-mediated autophagy; CMA-tag: KFERQ motif; ESCRT: endosomal sorting complexes required for transport; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HSPA8: heat shock protein 8; LAMP2A: lysosomal-associated membrane protein type 2A; Lact-C2: lactadherin C2 domain; PAmCherry: photoactivatable mCherry; PBS: phosphate-buffered saline; PS: phosphatidylserine; PtdIns4P: phosphatidylinositol-4-phosphate; RFP: red fluorescent protein; TBST: Tris-buffered saline with Tween 20.
    Keywords:  CMA; Chaperones; KFERQ motifs; microautophagy; phosphatidylserine; protein degradation
    DOI:  https://doi.org/10.1080/15548627.2026.2654191
  21. Nature. 2026 Apr 15.
    Template-driven scaffolding of SCFFBXO42 regulates PP2A degradation.
    Sebastien Coassolo, Nairie Michaelian, Timurs Maculins, Caleigh M Azumaya, Tommy K Cheung, Jianping Yin, Inna Zilberleyb, Kanika Bajaj Pahuja, Thomas Garner, Ted Lau, Davis Mau, Matthew Grimmer, Jean-Philippe Fortin, Mike Costa, Yoana N Dimitrova, Christopher M Rose, Peter L Hsu, Robert L Yauch.
      Protein phosphatase 2A (PP2A) is a Ser/Thr phosphatase that regulates the phosphorylation of almost all cellular processes, including cell division and proliferation1,2. PP2A forms heterotrimeric holoenzyme complexes comprising a catalytic subunit (PP2Ac), a scaffolding subunit (PP2Aa) and variable B regulatory subunits that exert precise control over enzyme substrate specificity and prevent indiscriminate dephosphorylation of phosphoproteins3. However, the mechanisms that control the activity of uncomplexed catalytic subunits have remained relatively unclear. Here we find that the E3 ligase SKP1-CUL1-F-box (SCF) complex containing F-box other protein 42 (FBXO42, also known as JFK; hereafter, SCFFBXO42) degrades holoenzyme-free PP2Ac in a complex with the coiled-coil protein CCDC6 to maintain cancer cell fitness. The cryo-electron microscopy structure of the FBXO42-CCDC6-PP2Ac assembly reveals a pseudosymmetric architecture in which CCDC6 forms a central dimeric template that recruits multiple copies of PP2Ac and creates a substrate for FBXO42. Both the quaternary structure of this CCDC6-PP2Ac heterodimer and the post-translationally methylated tail of PP2Ac are recognized by FBXO42 for ubiquitination. The multivalent structure facilitated by CCDC6 enables the assembly of multiple degradation complexes along a single coiled coil, leading to the turnover of free phosphatases and downregulation of catalytic activity. Together, our findings define a mechanism for PP2A control through the ubiquitin-proteosome system and establish a paradigm for cullin-RING ligase-substrate interactions.
    DOI:  https://doi.org/10.1038/s41586-026-10368-z
  22. FEBS Lett. 2026 Apr 15.
    Genetically encoded lockdown of SERCA in the endoplasmic reticulum membrane arrests Ca2+ signaling through proximity-covalent crosslinking.
    Yiying Li, Kozo Hamada.
      Reversible conformational dynamics of membrane proteins are essential for intracellular signaling, but no method enables their irreversible arrest in living cells. Here, we developed a genetically encoded proximity-based lockdown enzyme derived from an engineered transglutaminase catalytic core (TGC) that covalently crosslinks membrane proteins. By fusing TGC to the endoplasmic reticulum (ER)-resident microprotein ALN encoded by a short open reading frame (sORF), we created an organelle-specific module that selectively catalyzes covalent crosslinking within the SERCA Ca2+ pump, strongly suppressing its ATP-dependent pump activity and arresting ER Ca2+ signaling. This engineered lockdown enzyme remodels ER membrane protein architecture and restricts conformational dynamics, providing a versatile platform for long-term covalent control of intracellular signaling and a foundation for future therapeutic cellular applications. Impact statement Our proximity-based lockdown enzyme, engineered from microbial transglutaminase, provides a new strategy to covalently arrest the conformational states of organelle-resident membrane proteins in living cells, enabling long-term control of intracellular signaling and establishing a foundation for next-generation cellular therapeutics.
    Keywords:  calcium ATPase; calcium homeostasis; calcium signaling; endoplasmic reticulum; microprotein; transglutaminase
    DOI:  https://doi.org/10.1002/1873-3468.70342
  23. Cell Rep. 2026 Apr 15. pii: S2211-1247(26)00338-4. [Epub ahead of print]45(4): 117260
    The endoplasmic reticulum protein Erg28 restrains Mto1-Mto2-γ-TuSC-mediated microtubule assembly.
    Shengnan Zheng, Zhikai Chen, Lingyun Nie, Wenyue Liu, Yaqian Zhang, Kai Jiang, Xing Liu, Chao Xu, Xuebiao Yao, Chuanhai Fu.
      Interphase microtubule arrays play critical roles in a variety of cellular functions, including the spatial organization and distribution of the endoplasmic reticulum (ER). However, the role of the ER in regulation of microtubule assembly remains poorly characterized. Here, we identify Erg28, a conserved transmembrane protein localized to the ER, as a key factor that inhibits microtubule assembly. Biochemical analyses demonstrate that Erg28 physically interacts with the microtubule assembly-promoting factors-the Mto1-Mto2 complex and the γ-tubulin small complex (γ-TuSC)-and significantly attenuates the binding of γ-TuSC to the Mto1-Mto2 complex. Additionally, microscopic analyses show that Erg28 inhibits microtubule assembly mediated by Mto1-Mto2 complex and γ-TuSC in vitro. The cytosolic N-terminal region of Erg28 is indispensable for its inhibitory activity. Moreover, erg28 deletion leads to excessive microtubule assembly, causing nuclear shape deformation. These findings provide insights into the regulatory mechanism by which the ER influences microtubule cytoskeleton organization.
    Keywords:  CP: Cell biology; Erg28; Mto1; endoplasmic reticulum; microtubule; γ-tubulin complex
    DOI:  https://doi.org/10.1016/j.celrep.2026.117260
  24. Nat Commun. 2026 Apr 17.
    Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.
    Toni Gouhier, Cosmin Saveanu, Gwenael Badis.
      Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway known to degrade mRNAs containing premature termination codons (PTCs). mRNA recognition by the Upf1, Upf2 and Upf3 NMD factors is favoured by long distances between the stop codon and the poly(A)-binding protein (Pab1) binding site. Using Nanopore direct RNA sequencing, we now show that PTC-containing NMD targets account for only 6% of Upf1-associated RNA and have long poly(A) tails, indicating that Upf1-binding occurs prior to their deadenylation. Conversely, most Upf1-associated mRNAs have short poly(A) tails, lack a PTC and correspond to highly expressed genes. A short poly(A) tail is thus an important feature of a new class of Upf1 targets, redefining the scope of the NMD RNA degradation pathway. Recognition of short poly(A)-tailed mRNAs by Upf1, Upf2 and Upf3 (the NMD machinery) triggers their decapping, uncovering a hitherto unknown role of the NMD machinery in the degradation of these transcripts.
    DOI:  https://doi.org/10.1038/s41467-026-72132-1
  25. Nat Commun. 2026 Apr 17.
    Hijacking innate immunity to enhance mRNA therapeutics by blocking IFN-P-body-XRN1 axis-mediated degradation.
    Tinghong Zhang, Xing Peng, Jinling Qin, Binqiang Zhu, Shuaihua Zhang, Shijie Deng, Zhimin Song, Yulong Han, Hui Zheng, Jingjing Chen, Yun Zhang, Yaofeng Wang, Jingyuan Zhang, Yumin Zhou, Pixin Ran, Ningyi Shao, Bin Zhu, Yunshen Chan, Shu Meng.
      Innate immune activation is a major driver of unmodified in vitro-transcribed (IVT) mRNA degradation; however, how modified IVT mRNAs are degraded, and the related regulation mechanisms, remain poorly understood. Through a focused screen of viral- and host-derived immune suppressors, we identify 13 factors that enhance mRNA performance, with SOCS1 and the coronaviral membrane protein (M) emerging as the most potent. Multi-omics analyses reveal that pseudouridine-modified IVT mRNA undergoes rapid deadenylation and predominant 3'-5' decay, followed by bidirectional degradation, closely resembling endogenous mRNA decay kinetics, and is extensively associated with canonical mRNA decay machineries. Mechanistically, IVT mRNA activates IFN-β signaling, which promotes processing body (P-body) formation and XRN1-mediated 5'-3' degradation. Suppression of IFN signaling by SOCS1 or M markedly enhances mRNA expression across diverse cell types, organoid systems, and murine disease models. Together, these findings define a type I interferon-P-body-XRN1 axis that constrains modified IVT mRNA stability and provides a framework for enhancing mRNA therapeutics.
    DOI:  https://doi.org/10.1038/s41467-026-72025-3
  26. Nat Commun. 2026 Apr 15.
    SUMO E3 ligase SIZ1 promotes nuclear condensate-mediated immune activation in Arabidopsis.
    Min Jia, Enrico Calvanese, Rachel Bai, Yiling Fang, Yangnan Gu.
      SIZ1, a major plant SUMO E3 ligase, has diverse roles in development and immunity. Although loss-of-function phenotypes have categorized SIZ1 as a negative immune regulator, its broad substrate range complicates interpretation of its core function. Here we show that SIZ1 overaccumulation unexpectedly activates robust immune responses and cell death, dependent on its E3 ligase activity. Proximity-labeling proteomics revealed that SIZ1 function converges on the MOS4-Associated Complex (MAC), a critical immune signaling module that forms pro-immune nuclear condensates during pathogen attack. Both SIZ1 and the immune receptor SNC1 are recruited to MAC-dependent nuclear condensates (MDNCs) upon pathogen challenge, where they synergistically potentiate immune responses and cell death. SIZ1 SUMOylates and stabilizes MAC components, reinforcing MDNC formation and sustaining immune signaling. This mechanism counteracts the previously identified MDNC-inhibitory mechanism mediated by karyopherin KA120, establishing a regulatory system that balances immune-promoting condensate assembly with disassembly to prevent autoimmunity while maintaining rapid defense capacity.
    DOI:  https://doi.org/10.1038/s41467-026-72063-x
  27. bioRxiv. 2026 Apr 12. pii: 2026.04.09.717431. [Epub ahead of print]
    Large-scale endoplasmic reticulum membrane solidification spatially organizes proteins under thermal or metabolic stress.
    Paul M Mueller, Melissa R Mikolaj, Elmehdi Belbaraka, Finn Hartstein, Sophia Altinoluk, Bjoern Perder, Philipp Trnka, Robert-William Welke, Heike Naumann, Nina Taudien, Michele Solimena, Severine Kunz, Ilya Levental, Kandice R Levental, Andreas Mueller, Helge Ewers, Kedar Narayan, Oliver Rocks.
      Organelle homeostasis is a key determinant of cellular fitness, yet how cells remodel their membranes in response to environmental change remains unclear. Here, we identify a temperature- and lipid saturation-dependent transformation of endoplasmic reticulum membranes into giant, rigid, multilamellar tubes in cells and in vivo. These "rods" emerge from demixing of saturated lipids into solid-like domains - a previously unrecognised, large-scale endomembrane phase behaviour, fundamentally distinct from the transient liquid-ordered nanodomains of the plasma membrane. ER-tubulating reticulon-homology proteins are excluded from rods; their segregation drives progressive membrane flattening and ultimately multilayered wrapping. Surfactant-producing alveolar type-II lung cells, enriched in saturated lipids, form rods even at 37degC, demonstrating that native lipid metabolism can induce this transformation. This spatially organizing lipid-protein domain interplay may tune the ER tubule/sheet balance and provide a homeoviscous mechanism to preserve fluidity in the cholesterol-poor ER under thermal or metabolic stress.
    DOI:  https://doi.org/10.64898/2026.04.09.717431
  28. bioRxiv. 2026 Apr 07. pii: 2026.04.06.716749. [Epub ahead of print]
    Proteolytic dissection of eIF4G reveals the closed-loop mRNP as an architecture for translation repression.
    Ryan Johnston, Mollie A Brekker, Noelle Khalil, Monty E Goldstein, Anne Aldrich, Autumn O Grimins, Sami Gritli, Assen Marintchev, Michael D Blower, Mohsan Saeed, Shawn M Lyons.
      Formation of a "closed-loop" mRNP, in which the 5' cap and 3' poly(A) tail are bridged by eIF4E-eIF4G-PABP interactions, has long been proposed to drive efficient translation initiation. Direct tests of this model in mammalian cells have remained elusive. Using auxin-inducible degron (AID) technology to acutely deplete eIF4G1, we find that global translation is only partially reduced and recovers without restoration of eIF4G1 levels. We identify eIF4G3 as an underappreciated contributor to basal translation that buffers translational output upon eIF4G1 loss without increased protein expression, explaining the modest defects observed in prior RNAi-based studies. Systematic replacement of eIF4G1 with defined cleavage products and interaction mutants reveals that PABP binding by eIF4G1 is dispensable for bulk translation initiation: the central caspase-3 cleavage fragment of eIF4G1 (casp3-cp M ), which lacks the PABP-interaction domain, fully rescues global protein synthesis, and acute depletion of both major cytoplasmic PABP paralogs primarily destabilizes mRNAs rather than impairing initiation. In contrast, the N-terminal enteroviral 2A cleavage product (2A-cp N ) is a potent, dominant translational repressor that requires simultaneous eIF4E and PABP engagement to form a dead-end closed-loop mRNP that sequesters initiation factors without enabling 43S recruitment. These findings reveal that the eIF4G-PABP closed-loop architecture is not required for productive initiation but can be actively co-opted for translational silencing. This explains why viral eIF4G cleavage, but not factor depletion, produces near-complete translational shutoff. The modular architecture of eIF4G enables diametrically opposing translational outcomes through selective proteolytic processing.
    DOI:  https://doi.org/10.64898/2026.04.06.716749
  29. Autophagy. 2026 Apr 12.
    LC3-linked Golgi-bypass exocytosis fortifies epithelial barrier defense.
    Jiabin Wang, Junkai Wang, Xinyu Xiao, Lingling Zheng, Xia Lu, Li Wang, Xin Bian, Long Lin.
      Cells dynamically regulate membrane protein delivery to meet physiological demands, yet how external cues rapidly mobilize unconventional Golgi-bypass exocytic routes in vivo remains unclear. Here we define LC3/Atg8-associated carrier exocytosis (LACES), a conserved program that couples microbial cues to accelerated surface delivery. In the Caenorhabditis elegans intestine, phenazine-1-carboxamide (PCN) triggers VPS-34-dependent PtdIns3P generation at ILE-1/ERGIC-53 subdomains, enabling Atg8ylation on preexisting single-membrane RAB-8 carriers. This route accelerates delivery of the ABC transporter PGP-1 and improves host survival during infection, while operating independently of the unfolded protein response, canonical macroautophagy/autophagy initiation modules, and LC3-associated phagocytosis regulators. The pathway is engaged by multiple extracellular bacteria and also functions in mammalian epithelia, where PCN increases apical ΔF508-CFTR delivery in polarized Caco-2 cysts with measurable functional improvement and enhances LC3-RAB8 interactions in mouse intestinal epithelium. These findings establish a conserved LC3-linked Golgi-bypass route and illustrate how microbial cues can rapidly rewire epithelial membrane trafficking to fortify barrier defense.
    Keywords:  Atg8ylation; LC3-linked Golgi-bypass secretion; RAB8 carriers; epithelial barrier defense; phenazine-1-carboxamide; unconventional protein secretion
    DOI:  https://doi.org/10.1080/15548627.2026.2659291
  30. Nature. 2026 Apr 15.
    Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.
    Zeynep Ilgın Kılıç, Joyce van Loenhout, Marten Chaillet, Robert M van Es, Paula Sobrevals Alcaraz, Harmjan R Vos, Willem E M Noteborn, Miguel Ricardo Leung.
      Mammalian oocytes store proteins for embryonic development on abundant structures known as cytoplasmic lattices (CPLs)1; however, the mechanisms by which they achieve this are unclear, largely because the molecular composition of the lattices themselves is unknown. Here, we use cryo-electron microscopy and artificial intelligence-based modeling to elucidate the molecular architecture and protein composition of native CPLs from mouse oocytes. We find that CPLs are formed by at least 13 different proteins assembling into a megadalton-scale complex, including multiple copies of maternal effect factors such as PADI6 and the subcortical maternal complex (SCMC). We show that proteins essential for early embryonic development are in fact structural components of the CPLs, including the cytoskeletal proteins α- and β-tubulin, which are incorporated into CPLs as unpolymerized dimers; and an array of ubiquitination factors such as the epigenetic regulator and E3 ligase UHRF1, ubiquitin-conjugating E2 enzymes, and ubiquitin ligase substrate adaptors. This represents an elegant molecular mechanism by which oocytes stockpile vital proteins through direct incorporation into highly stable supramolecular assemblies. Our structures solve the decades-long mystery of the CPLs, thereby providing a structural framework for understanding how disrupting stored maternal factors leads to infertility and developmental defects.
    DOI:  https://doi.org/10.1038/s41586-026-10513-8
  31. Cell Biochem Funct. 2026 Apr;44(4): e70212
    Optogenetic Control of the Integrated Stress Response Limits Glioblastoma Invasion.
    Lisa K Månsson, Ethan Dickson, Lun Hao, Angela A Pitenis, Maxwell Z Wilson.
      The integrated stress response (ISR) is a highly conserved signaling network, allowing cells to adapt and respond to various stressors. With its aggressive spread and high recurrence rates, glioblastoma multiforme (GBM) is one of the toughest cancers to date, yet the role of the ISR is still to be well understood, whether activation may suppress or promote this disease, and drug-treatment of GBM has thus far shown inconclusive results. In this work, we use an optogenetic tool, opto-PKR, to specifically trigger ISR activation via light-induced oligomerizing PKR-kinases, offering high spatiotemporal and reversible control, while avoiding potential upstream damage or side effects from drugs. Using immunofluorescence and RNA-sequencing, we show that targeted ISR activation reaching levels where both adaptive (ATF4) and terminal responses (CHOP) are activated results in subsequent downregulation of genes associated with the extracellular environment and glial cell migration, further supported by ECM-stain and scratch assays. Next, we show inhibition of aggressive spread for ISR-activated GBM spheroids in collagen 3D culture. Photopatterning of ISR activation in spheroids demonstrates a cell-intrinsic effect at the tissue scale, and recovery studies indicate a tunable, non-ablative intervention space. These findings suggest a route to containment and motivate ISR-activating small molecule screening in GBM models.
    Keywords:  3D Culture; Opto‐PKR; cancer; cell migration; therapeutics
    DOI:  https://doi.org/10.1002/cbf.70212
  32. Life Sci Alliance. 2026 Jun;pii: e202603630. [Epub ahead of print]9(6):
    Locally synthesized glycyl aminoacyl-tRNA synthetase is important for local translation in neurons.
    Tyler Brent de Leon, Adi Golani-Armon, Bar Cohen, Yoav S Arava.
      Regulation of gene expression is essential for neuronal development and function. A prominent regulatory mechanism involves synthesis of proteins at their activity site. Such local protein synthesis enables neurons to respond rapidly and tightly to stimuli. Key components of the translation machinery, including mRNA and ribosomes, were identified in subcellular regions of neurons. Yet, the role of tRNAs and their charging enzymes, aminoacyl-tRNA synthetases (ARS), in this process remains largely unclear. Here, we demonstrate that glycyl-tRNA synthetase (Gars1) mRNA is abundant in neurites and undergoes local translation, producing GARS1 protein. Notably, Gars1 mRNA colocalizes with mitochondria in a translation-dependent manner, with its coding sequence (CDS) sufficient to direct this association. The localized GARS1 protein is in close proximity to tRNAGly, and disrupting their proximity impairs local protein synthesis in neurites. These findings establish the functional importance of GARS1 and tRNAGly in neuritic translation and highlight mitochondria as hubs for mRNA transport and translation.
    DOI:  https://doi.org/10.26508/lsa.202603630
  33. FEBS J. 2026 Apr 14.
    Hsp70 diversification and repurposing across the tree of life: Lessons from the evolutionary and mechanistic trajectory of the Hsp70-Hsp110 chaperone system.
    Pierre Goloubinoff, Paolo De Los Rios, Mathieu E Rebeaud.
      The 70 kDa Heat Shock Proteins (Hsp70s) are molecular chaperones ubiquitous in most free-living bacteria and archaea, and in the cytosol and ATP-containing organelles of eukaryotic cells, where they act as ATP-fueled nanomachines that unfold, remodel, and translocate polypeptides. In bacteria, Hsp70 (DnaK) operates with the J-domain cochaperone DnaJ and the nucleotide exchange factor (NEF) GrpE, which accelerates ADP release and ATP rebinding. Many simple prokaryotes encode a single canonical DnaK, but more complex bacteria often harbor additional DnaK-derived paralogues with modified, truncated, or missing domains required for substrate and DnaJ binding, raising questions about their functions and possible roles in proteostasis. A suggestive parallel comes from eukaryogenesis, when a gene duplication of an ancestral Hsp70 gave rise to Hsp110. Hsp110s have largely abandoned direct DnaJ, GrpE, and substrate binding; yet, through the reversible formation of NBD-mediated Hsp70-Hsp110 heterodimers, they act as potent NEFs that enhance Hsp70-driven disaggregation of compact protein aggregates. By analogy, we propose that NBD-containing DnaK paralogues in prokaryotes may likewise function as dedicated DnaK cochaperones, tuned to boost protein disaggregation and repair and specialized for the specific lifestyles and associated stressors of these organisms.
    Keywords:  Hsp110; Hsp70; NEF; evolution; structure–function
    DOI:  https://doi.org/10.1111/febs.70535
  34. Br J Pharmacol. 2026 Apr 16.
    A covalent molecular glue hijacks the E3 ligase MKRN2 to degrade the ribosomal protein RPS7 and induce synthetic lethality in p53-deficient NSCLC cells.
    Yuqi Pan, Shengjie Hua, Ruolan Yang, Qinman He, Yan Xu, Zeyu Jiang, Xiaoyang Gong, Shurui Zhang, Xiao Wang, Hongli Yu, Hao Wu, Hongmei Wen, Pin Wang, Bo Hang, Xinzhi Wang.
       BACKGROUND AND PURPOSE: Functional inactivation of the tumour suppressor p53 drives therapeutic resistance in non-small cell lung cancer (NSCLC). While targeted protein degradation offers a potential solution, the repertoire of ligandable E3 ligases remains limited. This study aimed to identify and characterise 2,6-didehydroxyspeperomin B (DPB) as a novel covalent molecular glue that targets p53-deficient NSCLC and to elucidate its mechanism of action involving the E3 ligase MKRN2.
    EXPERIMENTAL APPROACH: Cytotoxicity of DPB was assessed in p53 wild-type and p53-deficient NSCLC cells and orthotopic mouse models. Direct cellular targets were identified using quantitative thiol-reactivity proteomics (QTRP) and validated via biophysical assays and site-directed mutagenesis. The molecular glue mechanism was mapped using co-immunoprecipitation-mass spectrometry and genetic knockout/rescue studies. Downstream effects on ribosome biogenesis and protein synthesis were quantified.
    KEY RESULTS: DPB exhibited potent, selective cytotoxicity against p53-deficient NSCLC cells and suppressed tumour growth in vivo, outperforming standard chemotherapy. The E3 ubiquitin ligase MKRN2 was the direct target, with DPB covalently modifying the Cys335 residue. Mechanistically, DPB acted as a molecular glue, creating a neo-interface recruiting the ribosomal protein RPS7 to MKRN2. This induced ubiquitination and proteasomal degradation of RPS7, triggering acute nucleolar stress and apoptosis. The synthetic lethal effect was entirely dependent on a functional MKRN2-RPS7 axis.
    CONCLUSION AND IMPLICATIONS: Our findings identify DPB as a covalent molecular glue that harnesses the previously unexploited E3 ligase MKRN2 to eliminate p53-deficient cancer cells. This work validates the MKRN2-RPS7 axis as a synthetic lethal vulnerability and expands the E3 ligase toolbox for targeted protein degradation, providing a novel therapeutic strategy for drug-resistant NSCLC.
    Keywords:  MKRN2; NSCLC; RPS7; covalent inhibitor; molecular glue; p53‐deficient; synthetic lethality
    DOI:  https://doi.org/10.1111/bph.70434
  35. Acta Biochim Biophys Sin (Shanghai). 2026 Jan 25.
    Ubiquitin-dependent degradation of MBD3 by TRIM59 promotes lung adenocarcinoma.
    Wenhui Yang, Jin Ren, Yufang Wang, Jiahe Shi, Ziwan Cai, Cuihong Cai, Jing Zheng, Jingjing Qu, Jianya Zhou.
      Methyl-CpG binding domain protein 3 (MBD3) functions as a critical tumor suppressor in lung adenocarcinoma (LUAD), yet the ubiquitin-dependent mechanisms orchestrating its proteasomal turnover remain elusive. Here, we demonstrate that MBD3 undergoes ubiquitination and identify tripartite motif-containing protein 59 (TRIM59) as the cognate E3 ligase. TRIM59 physically associates with the N-terminal MBD domain of MBD3 and catalyzes its polyubiquitination and degradation, and mass spectrometry mapping reveals that this process occurs primarily at lysine residues K41, K90, and K92. Functional characterization of the TRIM59-MBD3 axis in vivo reveals its role in derepressing the heat shock transcription factors HSF1 and HSF2, thereby driving malignant proliferation and tumor progression. Tissue microarray immunohistochemistry reveals that TRIM59 is upregulated, whereas MBD3 is downregulated in LUAD tissues, establishing an inverse expression pattern that supports oncogenesis. Our findings unveil an unappreciated layer of MBD3 regulation and identify the TRIM59-MBD3 ubiquitination cascade as a potential therapeutic vulnerability in LUAD.
    Keywords:  HSF1/2; MBD3; TRIM59; lung adenocarcinoma; ubiquitination
    DOI:  https://doi.org/10.3724/abbs.2026044
  36. Proc Natl Acad Sci U S A. 2026 Apr 21. 123(16): e2526252123
    CHK2-USP37 axis stabilizes FOXO4 to sustain senescence and evade apoptosis.
    Jiahui Sun, Anke Geng, Zhiwei Song, Lingjiang Chen, Zhen-Ning Zhang, Ying Jiang, Zhiyong Mao.
      Cellular senescence, a state of permanent cell cycle arrest, contributes to tissue dysfunction and aging through the accumulation of apoptosis-resistant senescent cells. Although the transcription factor FOXO4 is known to enhance senescent cell survival, the mechanisms regulating its stability have remained unclear. Here, we identify a DNA damage response (DDR)-driven CHK2-USP37-FOXO4 axis essential for maintaining the apoptotic resistance of senescent cells. We demonstrate that FOXO4 protein stability is elevated in stress-induced senescent cells, resulting from reduced ubiquitin-proteasomal degradation. A deubiquitinase screen identified USP37 as the key enzyme stabilizing FOXO4 through direct interaction and removal of K48-linked polyubiquitin chains. Depletion of USP37 destabilizes FOXO4 and sensitizes senescent cells to apoptosis. Mechanistically, persistent DDR signaling during senescence activates CHK2, which phosphorylates USP37 at Thr589, thereby enhancing its binding to FOXO4. Importantly, ablation of USP37 in senescent cells increases the rate of apoptosis, a phenotype that is rescued by FOXO4 reexpression. Together, our work unveils USP37 as a CHK2-regulated stabilizer of FOXO4 that maintains the apoptotic resistance of senescent cells, suggesting the CHK2-USP37-FOXO4 axis as a therapeutic target for age-related pathologies.
    Keywords:  DNA damage response (DDR); FOXO4; USP37; apoptosis; cellular senescence
    DOI:  https://doi.org/10.1073/pnas.2526252123
  37. Cell Rep. 2026 Apr 13. pii: S2211-1247(26)00336-0. [Epub ahead of print]45(4): 117258
    RNA dicing promotes the expression of an oncogenic JAK1 isoform.
    Rob van der Kammen, Or Yakov, Shinyeong Ju, Ferhat Alkan, Onno B Bleijerveld, Cheolju Lee, William James Faller, Yuval Malka.
      The translation of an mRNA transcript is traditionally thought to be limited to its open reading frames (ORFs). However, recent findings reveal a more complex reality in which the proteome vastly exceeds transcriptome limits. Here, we demonstrate that JAK1 mRNA can be cleaved into a truncated, uncapped form with a shorter ORF, leading to the translation of the JH1 kinase domain independently of other domains, a process we term "RNA dicing." Canonical and diced JAK1 variants differently impact cell proliferation and tumorigenesis, with the balance of these isoforms altered in tumorigenesis and in response to IFN-γ. Analyzing JAK1 nonsense mutations in endometrial tumors reveals that mutations inhibit the tumor-suppressive functions of canonical JAK1 while enhancing the oncogenic diced JH1 domain. This results in a better response to the JAK1 inhibitor momelotinib, highlighting RNA dicing's role in patient stratification. Our findings show that RNA dicing diversifies mRNA products, significantly impacting biological functions.
    Keywords:  CP: molecular biology; JAK1; RNA dicing; alternative polyadenylation; cap-independent translation; endometrial cancer; m6A modification; oncogenic signaling
    DOI:  https://doi.org/10.1016/j.celrep.2026.117258
  38. J Cell Sci. 2026 Apr 13. pii: jcs.264577. [Epub ahead of print]
    A ULK1-MTFR1L feedback loop links mitochondrial fission, mitophagy and apoptosis.
    Riccardo Babic, Leon Lucya, Christoph Reiter, Franziska Kriegenburg, Ramón Castellanos-Martínez, David M Hollenstein, Florian Becker, Carola Hunte, Claudine Kraft.
      Mitophagy, the selective degradation of damaged mitochondria, preserves mitochondrial quality, yet how mitochondrial fission is coordinated with autophagy initiation remains unclear. Here we identify the mitochondrial outer membrane protein MTFR1L as a key component of mitophagy initiation hubs after using a synthetic FKBP-FRB system to tether ULK1 kinase to mitochondria independently of damage. We find that MTFR1L is enriched at ULK1 foci together with additional fission factors and constitutive mitochondrial targeting of MTFR1L shifts mitochondrial morphology towards fragmentation. MTFR1L depletion decreases respiratory capacity, elevates apoptosis, and impairs mitophagy flux. Upon mitophagy induction, MTFR1L is phosphorylated in a ULK1 kinase-dependent manner, and reciprocally modulates ULK1 activity, establishing a feedback loop. Moreover, MTFR1L is required for proper ATG13 stability. These findings position MTFR1L as a critical link between mitochondrial fission and the autophagy machinery, coordinating mitophagy initiation and cell survival.
    Keywords:  ATG13; Autophagy; MTFR1L; Mitophagy; ULK1
    DOI:  https://doi.org/10.1242/jcs.264577
  39. Cell Death Discov. 2026 Apr 15.
    Ubiquitin ligase RCHY1 regulates autophagosome-lysosome fusion.
    Ruchi Umargamwala, Jantina Manning, Julian M Carosi, Donna Denton, Sharad Kumar.
      Autophagy is a fundamental cellular recycling process that maintains homeostasis during animal development and under nutrient-limiting conditions. In our previous work, we employed autophagy-dependent cell death (ADCD) in the obsolete Drosophila larval midgut as a model to identify the enzymes involved in protein modification via ubiquitination with potential roles in autophagy regulation. From a genetic screen we identified RING E3 ligase RCHY1 as a candidate regulator. Here, we demonstrate that RCHY1 is essential for autophagy regulation during larval midgut ADCD in Drosophila and promotes autophagic flux in HeLa cells. Loss of Rchy1 impaired autophagosome-lysosome fusion and led to the accumulation of amphisomes in larval midgut cells. Similarly, depletion of RCHY1 in HeLa cells disrupted autophagic flux and reduced autolysosome formation, indicating evolutionary conservation of its function. Collectively, our findings identify RCHY1 as a putative regulator of autophagy that facilitates autophagosome-lysosome fusion.
    DOI:  https://doi.org/10.1038/s41420-026-03088-w
  40. ACS Med Chem Lett. 2026 Apr 09. 17(4): 757-767
    DNA-Encoded Library (DEL) Selection Identifies a Distinct DDB1 Ligand Binding Site.
    Shiva Krishna Reddy Guduru, John P Caldwell, Katherine M Digianantonio, Sarah M Prophet, Song Yang, Peter Gareiss, Christine Jones, Alicia Harbin, Brittany Driscoll, Md Fazlul Karim, Alexander Scott, Avani Patel, Amanda E Chapman, Marci Crandall, Gabriella Miklossy, Nicholas T Barczak, Antonella P Stroppa, John P Corradi, Jordan J Clark, Mee-Kyung Chung, Natalie Rg Reinhardt, William E Butcher, Rashaun Wilson, Cory Stiff, Arman Fathizadeh, Lin Yuan, Gan Wang, Hanqing Dong, Brett R Beno, Kurt Zimmermann, David R Langley, Angela M Cacace, Miklós Békés.
      Heterobifunctional proteolysis targeting chimeras (PROTACs) are proven to degrade disease-causing proteins, and many PROTACs have already entered into clinical trials. The majority of these PROTACs recruit cereblon (CRBN) or von Hippel-Lindau (VHL) substrate receptors of cullin RING E3 ubiquitin ligases, but there remains a need for alternative E3 ligase ligands. In this study, we enable DDB1 as an E3 ligase adapter protein for PROTAC drug discovery, describe a DNA-encoded library (DEL) ligand discovery campaign, and report the identification of a novel DDB1 ligand. Structure-guided modifications allowed DDB1 ligands to be developed from the initial DEL hit with nanomolar potency. Biochemical assays, cellular target engagement, and X-ray crystallography analysis demonstrated binding of the ligand to a unique pocket within DDB1. This chemical series furthers our understanding of ligand binding pockets within DDB1 and expands the repertoire of small molecules that may be suitable for the incorporation into PROTACs.
    Keywords:  DNA damage-binding protein 1 (DDB1); DNA-encoded library (DEL); E3 ubiquitin ligase; X-ray crystallography; ligand discovery; structure-based drug design
    DOI:  https://doi.org/10.1021/acsmedchemlett.6c00003
  41. J Cell Biol. 2026 Jun 01. pii: e202502001. [Epub ahead of print]225(6):
    ER-derived caveolin-coated vesicles transport newly synthesized cholesterol to the plasma membrane.
    Ming Sun, Yuan-Bin Liu, Pu-Yu Sun, Zhao-Chen Sheng, Jia-Wen Liu, Pei-Xin Yuan, Wen-Zhuo Zhu, Gang Deng, Xing-Yan Wen, Xiaolu Zhao, Jie Luo, Bao-Liang Song.
      Cholesterol must be precisely partitioned within cells, with the plasma membrane (PM) holding the highest levels. In contrast, the endoplasmic reticulum (ER)-the site of cholesterol synthesis-contains very little cholesterol. How newly synthesized cholesterol moves from the ER to the PM remains poorly defined. Here, we identify a COPII-independent trafficking route in which nascent cholesterol is exported via specialized cholesterol transport vesicles (CTVs). A genome-wide screen reveals that DEGS1-derived ceramide is essential for CTV formation at the ER. Biochemical purification shows that caveolins serve as the vesicle coat, and loss of caveolins eliminates CTV production. Silencing PACSINs or dynamins leads to intracellular accumulation of CTVs, suggesting impaired vesicle scission. CTV delivery to the PM depends on actin filaments and the motors MYO1C and MYO1E. In vitro reconstitution with giant unilamellar vesicles demonstrates that ceramide promotes inward budding, whereas CAV1 drives outward budding. This work identifies a previously unrecognized class of ER-derived, caveolin-coated vesicles that transport cholesterol to the PM.
    DOI:  https://doi.org/10.1083/jcb.202502001
  42. FASEB J. 2026 Apr 30. 40(8): e71808
    From Initiation to Elongation: eIF3 as a Dual-Phase Guardian of Mitochondrial Integrity and Protein Homeostasis in Skeletal Muscle.
    Jianing Xia, Kexin Liao, Jiahuan Wang, Minghao Lu, Yonghao Mu, Yingying Lin.
      Skeletal muscle is the largest organ by mass in the human body, and its functional capacity depends on the precise coordination of protein synthesis, mitochondrial bioenergetics, and regenerative potential. Eukaryotic translation initiation factor 3 (eIF3), a 13-subunit complex (~800 kDa) best known for its multifaceted roles in cancer, is now emerging as a key translational regulator in skeletal muscle physiology and disease. Here, we present a perspective that synthesizes recent advances into a unifying "dual-phase guardian" model. In the first phase, eIF3f acts at the level of translation initiation as a scaffold bridging mTORC1 and S6K1, integrating anabolic and catabolic signals, particularly the MAFbx/Atrogin-1 ubiquitin-proteasome axis, to govern net protein synthesis and muscle mass. In the second phase, eIF3e remains bound to 80S ribosomes during early translation elongation (codons 1-60) of approximately 2700 mRNAs encoding mitochondrial and membrane-associated proteins, facilitating co-translational quality control through chaperone recruitment (e.g., CCT/TRiC). Haploinsufficiency of eIF3e in mice produces mitochondrial hyperfusion, diminished respiratory complex I activity, sarcomeric degeneration, and progressive loss of grip strength, a phenotype recapitulating features of mitochondrial myopathy. Complementing these findings, eIF3b supports satellite cell-mediated muscle regeneration by resolving RNA G-quadruplex structures in the 5'-UTR of Anp32e mRNA, while eIF3a modulates fibrotic remodeling through TGF-β/Smad3 signaling. We situate these subunit-level findings within the broader landscape of translational regulators in muscle (eIF2α/ISR, eIF5A, eEF2) and critically evaluate the translational potential and therapeutic challenges, including the absence of human clinical data, tissue-selectivity concerns, and species-specific limitations, that must be addressed before these mechanistic insights can inform treatment of sarcopenia, disuse atrophy, and mitochondrial myopathy.
    Keywords:  co‐translational quality control; eIF3; mTORC1; mitochondrial homeostasis; muscle atrophy; protein synthesis; skeletal muscle; translation elongation
    DOI:  https://doi.org/10.1096/fj.202600039R
  43. Cell Rep. 2026 Apr 11. pii: S2211-1247(26)00334-7. [Epub ahead of print]45(4): 117256
    Wntless degradation mediated by CaMKII inhibition drives endoplasmic reticulum stress and apoptosis.
    Zhongkai Gu, Jude Owiredu, Betul Ersoy-Fazlioglu, Bailin Wu, Michael Lu, Steven P Balk, Xin Yuan.
      Noncanonical Wnt signaling stimulates calcium release and subsequent activation of calcium/calmodulin-dependent protein kinase 2 (CaMKII). We find that CaMKII inhibition decreases Wnt synthesis and identify the downregulation of Wntless (WLS) as the basis for this decrease. WLS transports palmitoylated Wnts to the cell surface, and in the absence of Wnts, it undergoes endoplasmic reticulum (ER)-associated degradation (ERAD). CaMKII inhibition increases proteasome-dependent WLS degradation, which can be suppressed by Wnt overexpression, indicating that CaMKII contributes to ER handling of unliganded WLS and prevention of ERAD. CaMKII inhibition also causes a loss of calnexin, an ER stress response through the activation of PERK, and apoptosis in cells expressing high levels of WLS. Moreover, these effects can be prevented by WLS knockdown. The findings reveal a previously unidentified role for CaMKII in supporting ER chaperone functions. They further show that high levels of unliganded WLS could be a potent driver of ER stress in the presence of CaMKII inhibitors, which may have efficacy in tumors expressing high levels of WLS.
    Keywords:  CP: cell biology; ER stress response; PERK; UPR; Wnt/β-catenin; Wnt5A; Wntless; apoptosis; calcium/calmodulin-dependent protein kinase 2; calnexin; ruxolitinib
    DOI:  https://doi.org/10.1016/j.celrep.2026.117256
  44. Oncogene. 2026 Apr 16.
    XPO1 inhibitor KPT-330 disrupts the core transcriptional regulatory circuitry of dedifferentiated liposarcoma by modulating the translation process.
    Xiaorui Fan, Ying Zhang, Zhengming Yang, Tuan Zea Tan, Xingze Huang, Suya Zheng, Jiyang Liu, Long Xie, Ting Tao, Victor Kwanmin Lee, Chao Yu, H Phillip Koeffler, Ye Chen, Liang Xu.
      Dedifferentiated liposarcoma (DDLPS) is a rare and aggressive subtype of liposarcoma, driven by a core transcriptional regulatory circuitry (CRC) that sustains tumor proliferation. This malignancy poses considerable clinical challenges, marked by high postoperative recurrence and metastatic potential, alongside a lack of effective targeted therapies. In this study, we establish that KPT-330 (Selinexor), a selective inhibitor of exportin 1 (XPO1), effectively compromises DDLPS cell viability by perturbing CRC homeostasis. Mechanistically, we demonstrate that KPT-330 attenuates the cellular translation machinery in a biphasic manner: initially, it disrupts translation initiation by suppressing eukaryotic translation initiation factor 4E phosphorylation and eukaryotic translation initiation factor 4 F complex assembly; subsequently, it impedes translation elongation by inhibiting the nuclear export of ribosomal large subunit proteins. Furthermore, we identify a synergistic antitumor effect between KPT-330 and translation inhibitors, including everolimus and homoharringtonine. Notably, the disruptive impact of KPT-330 on CRC homeostasis extends to other cancer cell lineages, underscoring its broad mechanistic relevance. Collectively, our findings elucidate a novel mechanism through which KPT-330 destabilizes CRC via translational dysregulation and highlight its potential therapeutic utility in combination regimens for DDLPS.
    DOI:  https://doi.org/10.1038/s41388-026-03794-w
  45. Nucleic Acids Res. 2026 Apr 13. pii: gkag344. [Epub ahead of print]54(7):
    Ubiquitylation of DNA polymerase β via atypical K27 chains signals a DNA damage response.
    Qingming Fang, Christopher A Koczor, Wynand P Roos, Steve McClellan, Joel F Andrews, Robert W Sobol.
      DNA polymerase β (Polβ) stability is tightly regulated by specific binding partners that prevent its degradation by the proteasome. Ubiquitin (Ub) chains, differing in their structural arrangements (topology), contribute to distinct cellular functions. To investigate Polβ ubiquitylation, we utilized CRISPR/Cas9-modified cell lines expressing endogenous, mClover-tagged Polβ. Our results reveal that Polβ is primarily modified with ubiquitin chains linked through lysine residues 27 [Ub(K27)] and 29 [Ub(K29)]. We further observed that Ub(K27) and Ub(K29) chains impact the utilization of ubiquitin chains linked through lysine residues 6 [Ub(K6)] and 48 [Ub(K48)] upon Polβ ubiquitylation. The ubiquitin ligase TRIP12 preferentially attaches Ub(K27) and Ub(K29) chains to Polβ. While Polβ ubiquitylation with Ub(K27) appears to have a non-degradative role, mixed ubiquitin chains and Ub(K48) chains trigger Polβ degradation. Following DNA damage, Polβ and XRCC1 translocate from the cytosol to the nucleus, while ubiquitylated Polβ relocates from the chromatin to the cytosol. This translocation of Polβ, modified with Ub(K27) chains, promotes the dissociation of the Polβ/XRCC1 complex within chromatin, and oxidative stress enhances their association in the cytosol. These findings demonstrate that atypical ubiquitin chain modifications play crucial roles in DNA repair and the DNA damage response, underscoring the unexpected importance of these chain topologies in maintaining genome integrity.
    DOI:  https://doi.org/10.1093/nar/gkag344
  46. J Chem Inf Model. 2026 Apr 15.
    Mechanism of c-Cbl Transition from Autoinhibited to Partially Open State via Substrate Binding.
    Yijing Zhang, Yuxuan Wang, Kaiyuan Song, Guanyi Li, Lin-Tai Da, Yaxue Zhao.
      Cellular Casitas B-lineage lymphoma (c-Cbl), a RING-type E3 ligase, regulates the degradation of diverse proteins, whose dysregulation is implicated in solid tumors and hematological malignancies. The conformational change of c-Cbl with substrate binding plays a critical role in the activation of c-Cbl, which facilitates the opening of the RING domain and exposes c-Cbl's ubiquitin-conjugating enzyme (E2) recognition sites to promote E2 binding and following ubiquitin transfer. However, the molecular mechanism of this conformational transition that is essential for c-Cbl-targeted drug discovery remains unclear. Here, by performing NEB (nudged elastic band) calculations, molecular dynamics (MD) simulations, and Markov state model (MSM), we revealed the molecular mechanism of c-Cbl transformation from autoinhibited to partially open conformation upon substrate binding at the molecular level and identified the key metastable states of c-Cbl during this process, which are beneficial for discovery and development of small molecules targeting c-Cbl.
    DOI:  https://doi.org/10.1021/acs.jcim.5c03086
  47. Front Cell Dev Biol. 2026 ;14 1760166
    Heat shock protein Gp96 (Grp94) in malaria: functional insights at the host-parasite interface and therapeutic perspectives.
    Djibaba Djoumoi, Abou Abdallah Malick Diouara, Mamadou Diop, Cheikh Momar Nguer, Babacar Mbengue, Fatou Thiam.
      Heat shock protein Gp96 (also known as Grp94 or endoplasmin) is the endoplasmic reticulum (ER)-resident paralog of the Hsp90 family and a central regulator of ER proteostasis and immune receptor biogenesis in mammalian cells. By controlling the folding, quality control, and trafficking of a restricted yet functionally critical set of client proteins, including Toll-like receptors, integrins, and immunoglobulins, Gp96 plays an essential role in innate immunity and inflammatory signaling. In the context of malaria, accumulating evidence suggests that host-derived Gp96 is involved in immune activation and disease severity, notably through its extracellular release under conditions of cellular stress, where it functions as a danger-associated molecular pattern (DAMP). Elevated circulating Gp96 levels have been associated with severe malaria phenotypes, supporting its potential value as a biomarker of host stress and immune dysregulation. In parallel, Plasmodium falciparum expresses its own ER-resident Hsp90 homolog, PfGp96, which retains the conserved domain architecture of Hsp90 while exhibiting parasite-specific adaptations, including divergence in ER retention motifs. However, the biological functions, client repertoire, and essentiality of PfGp96 remain poorly defined, and direct evidence supporting its validation as a drug target is currently limited. This review critically synthesizes current knowledge on Gp96 and PfGp96, emphasizing experimentally validated functions, host-parasite interface dynamics, and unresolved knowledge gaps. We discuss the opportunities and challenges of targeting Gp96-related pathways for biomarker development and therapeutic intervention in malaria, while outlining key priorities for future functional and translational research.
    Keywords:  Gp96; Grp94; PfGp96; Plasmodium falciparum; heat shock proteins; malaria; therapeutic targeting
    DOI:  https://doi.org/10.3389/fcell.2026.1760166
  48. J Biol Chem. 2026 Apr 09. pii: S0021-9258(26)00315-7. [Epub ahead of print] 111445
    Golgi-derived phosphatidylinositol 4-phosphate is crucial for organization of the pre-autophagosomal structure.
    Huichao Lang, Kuninori Suzuki.
      Macroautophagy (hereafter autophagy) is a conserved intracellular degradation pathway that is essential for maintaining cellular homeostasis. Autophagosome (AP) formation involves pre-autophagosomal structure (PAS) organization and expansion of the isolation membrane (IM). Although phosphatidylinositol 4-phosphate (PtdIns4P) localizes to the IM and is required for autophagy, the specific functional role it plays in AP formation remains unclear. Pik1, a PtdIns 4-kinase localized to the Golgi, plays a critical role in this process. We used temperature-sensitive pik1 mutant cells and found that PAS localization of Atg9, Atg17, Atg1 and Atg13 remained normal at the restrictive temperature, indicating that PAS scaffold formation was unaffected. In contrast, the recruitment of downstream Atg proteins, the PtdIns 3-kinase complex I including Atg14, the Atg2-Atg18 complex, and Atg8, was impaired under the same condition. These findings demonstrate that Pik1-generated PtdIns4P is essential for PAS organization. Since Atg9 vesicles are derived from the Golgi, we hypothesized that PtdIns4P is transported to the PAS on Atg9 vesicles to mediate recruitment of downstream Atg proteins. To test this, we performed immunoprecipitation analysis using a PtdIns4P-binding protein and found that Atg9 was co-immunoprecipitated at the permissive temperature, but not at the restrictive temperature. This result indicates that PtdIns4P is enriched on Atg9 vesicles through Pik1 activity. Moreover, our assessment in pik1 mutant cells showed that IM expansion is impaired at the restrictive temperature. Collectively, these results identify PtdIns4P as a key component of PAS organization.
    Keywords:  Atg9; Pik1; Saccharomyces cerevisiae; autophagosome biogenesis; isolation membrane; lipid transfer; phosphatidylinositol 4-phosphate
    DOI:  https://doi.org/10.1016/j.jbc.2026.111445
  49. FEBS Lett. 2026 Apr 13.
    The E3 ubiquitin ligase UBR5 promotes ubiquitylation and degradation of the chromatin regulator ATAD2.
    Rikuto Honda, Miyu Takao, Yoshino Akizuki, Fumiaki Ohtake.
      UBR5 is a HECT-type E3 ubiquitin ligase that assembles K48-linked ubiquitin chains and generates K48-linked branched chains. UBR4 is another E3 that forms K48-linked chains through an atypical hemi-RING-like domain. To define substrates specific to each ligase, we analyzed tandem mass tag proteomics data and identified candidates that accumulated after UBR5 or UBR4 knockdown, respectively. UBR5 depletion caused a marked delay in turnover of the chromatin regulator ATAD2. We found that ATAD2 associated with UBR5 in co-immunoprecipitation assays, and UBR5 promoted ubiquitylation of ATAD2 in vitro and in cells. RNA-sequencing further showed that the expression of cell cycle-related genes was antagonistically regulated by ATAD2 and UBR5. These findings identify ATAD2 as a UBR5 substrate and reveal a regulatory module controlling gene expression.
    Keywords:  ATAD2; HECT domain; Proteolysis; UBR5; Ubiquitin
    DOI:  https://doi.org/10.1002/1873-3468.70339
  50. Life Sci Alliance. 2026 Jun;pii: e202603679. [Epub ahead of print]9(6):
    Metabolite import by SLC33A1 is required for ATF6 activation during endoplasmic reticulum stress.
    Ginto George, Heather P Harding, Richard Kay, David Ron, Adriana Ordoñez.
      The transcription factor ATF6α has a central role in adapting mammalian cells to ER stress via the unfolded protein response (UPR), prompting efforts to identify ATF6α modulators. Here, an unbiased genome-wide CRISPR-Cas9 screen performed in Chinese Hamster Ovary cells revealed that proteolytic processing of the ATF6α precursor to its active form was impaired in cells lacking the ER-resident solute carrier SLC33A1, a transporter previously implicated in acetyl-CoA import, sialylation, and Nε-lysine protein acetylation. Cells lacking SLC33A1 constitutively trafficked the ATF6α to the Golgi but exhibited impaired Golgi processing and activating proteolysis. IRE1α signalling was derepressed by SLC33A1 deficiency consistent with selective loss of ATF6α-mediated negative feedback in the UPR. Slc33a1-deleted cells accumulated unmodified sialylated N-glycans, precursors to acetylated glycans, likely reflecting impaired glycan processing. Deletion of ER-localised acetyltransferases NAT8 and NAT8B, which catalyse protein Nε-lysine acetylation in the secretory pathway, did not replicate the ATF6α processing defects observed in Slc33a1-deficient cells. Together, our findings highlight a role of SLC33A1-mediated metabolite transport in the post-ER ATF6α maturation, linking small-molecule metabolism to branch-specific signalling in the UPR.
    DOI:  https://doi.org/10.26508/lsa.202603679
  51. Mol Cell Biol. 2026 Apr 14. 1-20
    Hsp70/Hsp90 Organizing Protein (HOP) Maintains CRAF Kinase Activity and Regulates MAPK Signaling by Enhancing Hsp90-CRAF Association.
    Nilanjan Gayen, Sahana Mitra, Somesh Roy, Atin K Mandal.
      The stability and activity of CRAF/Raf1 kinase are stringently regulated by heat shock protein 90 (Hsp90). Hsp90-mediated client folding and maturation are governed by its co-chaperones, but their functionality in chaperoning CRAF kinase to support signaling under physiological conditions remains poorly understood. Here, we show that Hsp70/Hsp90 organizing protein (HOP) associates with CRAF kinase tomaintain its activity and facilitates MAPK pathway activation. This activation is mediated by TPR2A-2B-DP2 domain of HOP and requires efficient binding to Hsp90. Although Cdc37 recruits Hsp90, it cannot compensate for HOP function. Downregulation of HOP/Sti1 in yeast and mammalian cell culture significantly reduces the CRAF signaling. Our data suggest that Hsp90 is recruited to CRAF in two distinct steps: first during folding/maturation via HOP and Cdc37, and later during activation mediated by HOP. Therefore, HOP is a regulator of CRAF kinase during activation of MAPK pathway and serves as a modulator of growth signaling beyond its client folding and maturation function.
    Keywords:  HOP; Hsp70/Hsp90 organizing protein; Hsp90; MAPK signaling; RAF kinase; chaperone; heat shock protein 90; mitogen‐activated protein kinase signaling
    DOI:  https://doi.org/10.1080/10985549.2026.2647809
  52. FASEB J. 2026 Apr 30. 40(8): e71798
    A Novel Role of the Ubiquitin Conjugating Enzyme, UBE2G2, in Regulation of Cell Shape and Movement.
    Angela Lalnunthangi, Preeti Rai, Swati Tiwari.
      We report a novel function of the ubiquitin conjugating enzyme, UBE2G2, beyond its well-established role in endoplasmic reticulum (ER)-associated degradation (ERAD). We demonstrate UBE2G2 profoundly influences cell shape and motility. Inactive UBE2G2 induces significant cell elongation, independent of matrix stiffness, composition, or charge. Mutant cells showed reduced total actin stress fibers, with dominant cortical ventral stress fibers aligned along the long axis. Vinculin redistributed to ventral stress fibers, likely altering the actin-adhesion dynamics. Absence of prominent lamellipodia and polarized distribution of filopodia at cell extremities demonstrates a reduced capacity for isotropic spreading and shape change. This was supported by slow wound closure in mutant cells that displayed low persistence and displacement despite similar pathlength and speed as wildtype cells. Sequestration of wildtype UBE2G2 by AUP1 to the membrane fraction mimicked the elongated phenotype in control cells showing that the cytosolic pool of the enzyme is responsible for the observed phenotype. Our results that UBE2G2 inactivating mutations can lock cells into a polarized, high-tension state have direct implications for diseases with aberrant cell shape and mechano-transduction.
    Keywords:  actin; cell shape; focal adhesions; stress fibers; ubiquitin conjugating enzyme
    DOI:  https://doi.org/10.1096/fj.202504696R
  53. Nat Commun. 2026 Apr 11.
    Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks.
    H Zhao, C Velez, A Naravane, A Saha, J Feldman, J Skolnick, D Murray, B Honig.
      We report on the integration of three methods that predict, on a proteome-wide scale, whether two proteins are likely to form a binary complex. The methods include PrePPI, which uses three-dimensional structure information as a basis for predictions, Topsy-Turvy, which uses a protein language model, and ZEPPI, which uses evolutionary information to evaluate protein-protein interfaces. Testing on the high-quality HINT database of binary PPIs reveals that the integrated method has better performance and identifies more high-confidence interactions than any of the component methods. The AF3Complex algorithm is used to predict the structures of 374 PPIs with a large fraction having at least partially overlapping interfaces with PrePPI models of the same complex. Clustering of the high-confidence E. coli interactome yields 385 subnetworks which have high functional coherence. Biological insights derived from the subnetworks, including the annotation of proteins of unknown function, are discussed in detail.
    DOI:  https://doi.org/10.1038/s41467-026-71166-9
  54. Mol Cell Proteomics. 2026 Apr 15. pii: S1535-9476(26)00065-4. [Epub ahead of print] 101569
    Proteomic Profiling Reveals How Physiological Media Reshape Cancer Cell Proteomes and Signaling Networks.
    Colin Zenge, Brittany Q Pham, Kihong Nam, Elana Apfelbaum, Heeseon An, Alban Ordureau.
      Altered metabolism is a hallmark of cancer, making metabolic enzymes attractive therapeutic targets. However, metabolic inhibitors have shown limited clinical success, partly due to differences between standard culture media and physiological nutrient conditions. Human plasma-like medium (HPLM) better recapitulates in vivo metabolite concentrations, yet its effects on cellular proteomes remain poorly characterized. We performed comprehensive TMTpro-based quantitative proteomics and phosphoproteomics across nine cancer cell lines cultured in DMEM or HPLM, consistently quantifying over 10,000 proteins and 24,000 phosphorylation sites across all three biological replicates with high reproducibility. Physiological media induced profound cell-type-specific remodeling of metabolic networks, mitochondrial proteomes, and signaling pathways. While decreased mTORC1 and CDK activity represented universal responses across all cell lines, metabolic enzyme expression exhibited striking heterogeneity. Enzymes in folate metabolism and pyrimidine salvage pathways showed consistent reductions across all cell types, indicating that drug responses may vary with media choice. Mitochondrial proteome composition and morphology displayed cell-type-specific adaptations. Phosphoproteomic analysis revealed kinase signaling networks underlying these metabolic changes. This dataset, accessible via an interactive web application, provides a resource for metabolic research using physiological media, highlighting substantial cell-type-specific variability in how media affect proteomes and signaling pathways.
    Keywords:  CDK activity; Cancer cell metabolism; Physiological Media; Proteomics; mTORC1 signaling
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101569
  55. EMBO J. 2026 Apr 13.
    Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
    Siqi Zheng, Ruifang Tian, Marsudi Siburian, Anna Haider Rubio, Yuanyuan Liu, Rene Wardenaar, Marjan Shirzai, Laura Kempe, Emma Dijkstra, Eliza Warszawik, Maria Suarez Peredo Rodriguez, Klaas Sjollema, Petra L Bakker, Patrick van Rijn, Michaela Borghesan, Judith Tml Paridaen, Stefano Santaguida, Floris Foijer.
      Triple-negative breast cancer (TNBC) is characterised by high rates of chromosomal instability (CIN) and rewired intercellular communication driven by both soluble factors and extracellular vesicles (EVs). To assess how CIN might affect EV-mediated signalling in TNBC, we studied the EV landscape of TNBC cell lines with induced CIN. We find that CIN leads to increased secretion of EVs and that these EVs promote cell migration of recipient cells. EVs are enriched for extracellular matrix (ECM) proteins, including EFEMP1. Indeed, modulation of EFEMP1 levels in EVs significantly alters migration behaviour of EV-treated cells. We show that EFEMP1 expression is regulated by STAT1, that EVs from STAT1-deficient cells no longer promote migration, and that this can be rescued by overexpression of EFEMP1 in STAT1-null cells. Xenografting TNBC cells with EFEMP1-enriched cells promotes migration in zebrafish embryos, suggesting that EFEMP1 expression is a factor that promotes metastasis. Together, our results identify a CIN-associated EV program in triple-negative breast cancer and highlight EFEMP1 as a potential therapeutic target to impair EV-driven tumour cell migration.
    DOI:  https://doi.org/10.1038/s44318-026-00766-4
  56. Cell. 2026 Apr 15. pii: S0092-8674(26)00333-8. [Epub ahead of print]
    Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition.
    José Reyes, Isabella Del Priore, Andrea C Chaikovsky, Nikhita Pasnuri, Ahmed M Elhossiny, Jin Park, Philipp Weiler, Tobias Krause, Andrew Moorman, Catherine Snopkowski, Meril Takizawa, Cassandra Burdziak, Nalin Ratnayeke, Ignas Masilionis, Yu-Jui Ho, Ronan Chaligné, Paul B Romesser, Aveline Filliol, Tal Nawy, John P Morris, Zhen Zhao, Marina Pasca Di Magliano, Direna Alonso-Curbelo, Dana Pe'er, Scott W Lowe.
      The benign-to-malignant transition is a defining step in cancer progression. To investigate when and how malignancy initiation occurs and tissue reorganization proceeds, we combine single-cell and spatial transcriptomic profiling in mouse models of pancreatic ductal adenocarcinoma (PDAC) that capture spontaneous p53 loss. Among Kras-mutant cells, we find that oncogenic and tumor-suppressive programs, including those controlled by p53, CDKN2A, and SMAD4, are co-activated in a discrete progenitor-like population, engaging senescence-like responses. Using a framework we developed for spatial analysis, we show that a niche centered on these cells undergoes stepwise remodeling during tumor progression, mirroring invasive PDAC. Transient KRAS inhibition depletes progenitor-like cells and dismantles their niche, delaying malignancy initiation. Conversely, p53 suppression enables progenitor cell expansion, epithelial-mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state at the convergence of cancer-driving mutations, plasticity, and tissue remodeling, revealing a critical window for intercepting malignancy.
    Keywords:  KRAS inhibitors; benign-to-malignant transition; niche dynamics; p53; pancreatic cancer; single-cell biology; spatial transcriptomics; tumor initiation; tumor suppression
    DOI:  https://doi.org/10.1016/j.cell.2026.03.032
  57. Genome Biol. 2026 Apr 14.
    A sequence knowledge-guided deep learning method for single-cell multi-omics translation.
    Mengyuan Zhao, Jiawei Li, Yanlin Jiang, Jiahui Yan, Xinyue Tang, Cheng Liang, Jijun Tang, Fei Guo.
       BACKGROUND: Analysis of proteins is key to understanding biological processes, disease pathogenesis, and advancing therapeutic development. However, proteome profiling remains significantly limited when compared to the exponential growth of single-cell RNA sequencing data, owing to technical challenges and prohibitive costs associated with large-scale protein detection. Recent advancements in multi-omics technologies have established essential connections between transcriptome and proteome layers, facilitating innovative computational approaches for predicting protein abundance based on transcriptome data.
    RESULTS: Here, we present scProTrans, an interpretable deep learning framework that synergizes sequence knowledge and multi-omics integration to achieve cross-omics translation in single-cell resolution. Our framework deciphers gene-protein associations through three innovative components: Firstly, a hierarchical attention mechanism that aligns gene/protein sequences with cellular contexts using CITE-seq training data; secondly a bidirectional encoder architecture implementing sequence-to-embedding-to-profile learning for modality translation; finally cell-specific associations capturing dynamic gene-protein interplay across heterogeneous cell populations. Extensive evaluations across 17 multi-omics datasets demonstrate that scProTrans surpasses state-of-the-art methods in single-cell protein abundance translation and enhances downstream analyses, including cell clustering, subtype identification, and biomarker discovery. scProTrans improves protein prediction accuracy and preserves low-abundance protein signals, two significant aspects of single-cell protein abundance translation. Additionally, scProTrans is extended to tri-omics scenarios (ATAC-RNA-protein) via modular encoder refactoring, achieving cross-modal prediction concordance comparable to experimental replication.
    CONCLUSIONS: This work advances multi-omics integration by establishing a sequence-aware paradigm for cross-modal translation, overcoming key limitations in proteome data acquisition. This modular architecture and its zero-shot capability make it a versatile platform for emerging multi-modal single-cell technologies.
    Keywords:  Multi-omics; Proteome profiling; Single-cell sequencing; Zero-shot translation
    DOI:  https://doi.org/10.1186/s13059-026-04070-6
  58. J Cell Biol. 2026 Jun 01. pii: e202509174. [Epub ahead of print]225(6):
    COPI-dependent intra-Golgi recycling at an intermediate stage of cisternal maturation.
    Adam H Krahn, Areti Pantazopoulou, Jotham Austin, Natalie Johnson, Conor F Lee-Smith, Benjamin S Glick.
      The traffic pathways that recycle resident Golgi proteins during cisternal maturation are not completely defined. We addressed this challenge using the yeast Saccharomyces cerevisiae, in which maturation of individual cisternae can be visualized directly. A new assay captures a specific population of Golgi-derived vesicles at the bud neck, thereby revealing which resident Golgi proteins are carried as cargo in those vesicles. This method supplies evidence for at least three classes of intra-Golgi vesicles with different cargo compositions. Consistent with our previously published data, one class of vesicles mediates a late pathway of intra-Golgi recycling with the aid of the AP-1 and Ent5 clathrin adaptors, and a second class of vesicles mediates an early pathway of intra-Golgi recycling with the aid of the COPI vesicle coat. Here, we identify another COPI-dependent pathway of intra-Golgi recycling and show that it operates kinetically between the two previously known pathways. Thus, intra-Golgi recycling is mediated by multiple COPI-dependent pathways followed by a clathrin-dependent pathway.
    DOI:  https://doi.org/10.1083/jcb.202509174
  59. Mol Biol Cell. 2026 Apr 15. mbcE26010055
    Septins associate with AP-3 to support trafficking to the vacuole/lysosome in yeast.
    Mitchell Leih, Michaela McCright, Cortney Angers, Michael Davey, Elizabeth Conibear, Alex Merz, Greg Odorizzi.
      Adaptor protein complex 3 (AP-3) mediates clathrin-independent transport to lysosomes, yet accessory factors supporting this pathway remain incompletely defined. In Saccharomyces cerevisiae, the C-terminal intrinsically disordered regions (IDRs) of both AP-3 large subunits (δ and β3) serve as platforms for association with accessory factors. Through proteomic analysis of proteins associated with these IDRs, we identify the septin cytoskeleton as a candidate AP-3-associated factor. Bimolecular fluorescence complementation (BiFC) reveals a hierarchical pattern of association: AP-3 shows preferential proximity to core septin subunits (Cdc10, Cdc3, Cdc12) over terminal subunits (Cdc11 and Shs1). These terminal subunits serve as alternative caps of septin octamers, generating structurally distinct assemblies. Significantly, dysfunction of Cdc11 but not Shs1 selectively impairs AP-3-dependent cargo sorting without affecting the parallel vacuolar protein sorting (VPS) pathway to the vacuole (lysosome in yeast), providing genetic evidence for a specific functional connection between Cdc11-containing septin assemblies and AP-3-mediated transport.
    DOI:  https://doi.org/10.1091/mbc.E26-01-0055
  60. J Clin Invest. 2026 Apr 15. pii: e191735. [Epub ahead of print]136(8):
    Therapy-induced cholesterol biosynthesis drives lung cancer dormancy and drug resistance.
    Yikai Zhao, Yijia Zhou, Linnuo Pan, Geng G Tian, Hsin-Yi Huang, Shijie Tang, Ming Lu, Zhangsen Zhou, Peng Zhang, Luonan Chen, Lele Zhang, Liang Hu, Hongbin Ji.
      Complete response is rarely observed in lung cancer molecular targeted therapy, despite great clinical success. Here, we found that molecular therapy targeted toward EGFR mutant, KRAS mutant, or ALK fusion lung cancer induced cholesterol biosynthesis, which promoted cancer cells to enter dormancy and thus escape drug killing. Combined statin treatments effectively blocked cholesterol biosynthesis, prevented cancer cells from entering dormancy, and thus resulted in dramatic tumor regression. We further identified a subpopulation of cycling cancer cells that persisted during molecular targeted therapy and remained sensitive to aurora kinase inhibitors. Triple-targeting cholesterol biosynthesis, aurora kinase, and individual oncogenic drivers almost eradicated all the cancer cells. Therapy-induced cancer dormancy was mainly attributed to activation of unfolded protein response, specifically the PERK-eIF2α axis, which triggers cholesterol biosynthesis and AKT signaling. Collectively, this work uncovers an unexpected role of a therapy-induced prosurvival program in promoting cancer dormancy and provides a potentially effective strategy to prevent drug resistance.
    Keywords:  Cancer; Cell biology; Drug therapy; Lung cancer; Metabolism
    DOI:  https://doi.org/10.1172/JCI191735
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