bims-proteo Biomed News
on Proteostasis
Issue of 2026–01–25
48 papers selected by
Eric Chevet, INSERM
  1. Targeted recruitment of USP15 enhances CTLA4 surface levels and restricts its degradation.
  2. Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity.
  3. ER membrane receptors engage core autophagy machinery to initiate ER-phagy.
  4. Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling.
  5. Ubiquitination-Driven Reprogramming of Proteostasis in Metastasis.
  6. SIRT7 safeguards ERα proteostasis via deacetylation-dependent degradation of unliganded and misfolded receptors.
  7. Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry.
  8. Proteasome Cap Targeting Chimeras for Ubiquitination-Independent Targeted Protein Degradation.
  9. The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis.
  10. A cytokine receptor-targeting chimera toolbox for expanding extracellular targeted protein degradation.
  11. Calumenin prevents fibroblast senescence and lung aging by promoting vimentin proteostasis.
  12. In-vitro Reconstitution of Bacterial Ubiquitination and VCP/p97-mediated Elimination.
  13. Nanoscopy of Organelle Handoff Portals Reveals Direct Coupling between Endoplasmic Reticulum Remodeling and Microtubule-Based Transport.
  14. Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning.
  15. A small molecule VDAC ligand inhibits ERAD and induces selective cancer cell death via disruption of calcium homeostasis.
  16. Uncovering genetic interactions in the DNA repair network in response to endogenous damage and ionizing radiation.
  17. A stochastic mechanism drives fast substrate translocation in the AAA+ machine ClpB.
  18. The pivotal role of endoplasmic reticulum in cancer glucose metabolism.
  19. eIF3g binding to GUCG boxes located in mRNA coding regions enhances translation of mild heat shock response genes in the yeast Saccharomyces cerevisiae.
  20. Proteasome activator Blm10 maintains cellular proteostatic balance and gamete quality in budding yeast.
  21. Discovery of 2-Chloro-pyrrolo[2,3-d]pyrimidin-4-one Derivatives as Protein Disulfide Isomerase Inhibitors with a Novel Allosteric-Covalent Binding Mode and Anti-Glioblastoma Activity.
  22. Multi-omics analysis reveals ER stress as a main feature in two endothelial cell models of N-linked congenital disorders of glycosylation.
  23. Click. Screen. Degrade. A Miniaturized D2B Workflow for Rapid PROTAC Discovery.
  24. Molecular engineering of lysosome-based degraders unveils a rapidly expanding therapeutic strategy.
  25. Cholesterol depletion activates trafficking-coupled sphingolipid synthesis.
  26. The Atg2-Atg18 complex interacts with the Atg1 complex to localize to the pre-autophagosomal structure in Saccharomyces cerevisiae.
  27. Identification of an allosteric site on the E3 ligase adapter cereblon.
  28. Hierarchical mechanisms control the clearance of DNA lesion-stalled RNA polymerase II.
  29. GFP-free live neuron quantitative imaging reveals compartmentalization and growth dynamics of polyQ aggregates.
  30. An Engineered Nanovesicles-Based Lysosome-Targeting Protein Degradation Platform (NV-TACs) for Cancer Immunotherapy.
  31. Uridine analogs prevent stress granule formation, not by blocking PKR recognition, but by inhibiting the synthesis of T7 RNA Polymerase byproducts.
  32. Multi-stimuli activated PROTAC prodrug for controlled protein degradation with enhanced therapeutic effects.
  33. Degradation determinants are abundant in human noncanonical proteins and minor annotated isoforms.
  34. C3orf33/MISO regulates mitochondrial homeostasis via mitophagy.
  35. The UFL1-AKT positive feedback loop promotes breast cancer progression by enhancing lipid synthesis.
  36. Silencing lipid catabolism determines longevity in response to fasting.
  37. UFMylation at the Crossroads of Health and Cancer: A Blessing in Disguise.
  38. ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing.
  39. Predicting protein interfaces in the age of AlphaFold: Why dynamics and disorder remain a challenge.
  40. BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions.
  41. UBR4 Attenuates Cisplatin-Induced Acute Kidney Injury by Regulating the HRI-ISR Axis.
  42. The critical role of GRP78/BiP MARylation in ER stress of KRAS-mutant colorectal cancer.
  43. Multimodal supramolecular targeting chimeras enable spatiotemporally resolved protein degradation in vivo.
  44. Peripheral lysosome levels dictate mTORC1 inactivation even when catabolically impaired.
  45. ERLIN2-Ca2+-CREB signaling coordinates circadian timing via CRY1/CRY2 feedback.
  46. Proteolysis-targeting chimera (PROTAC): a promising senolytic strategy.
  47. Inhibition of RNase L enhances the expression efficiency of mRNA-LNPs.
  48. Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.
  1. Life Sci Alliance. 2026 Apr;pii: e202503563. [Epub ahead of print]9(4):
    Targeted recruitment of USP15 enhances CTLA4 surface levels and restricts its degradation.
    Francesca Querques, Victoria Ciampani, Pei Yee Tey, Victoria D Kutilek, Elma Kadic, Michael J Clague, Sylvie Urbé.
      Induced protein proximity offers powerful new routes to modulate protein fate. Whereas proteolysis-targeting chimeras (PROTACs) promote degradation through E3 ligase recruitment, the converse principle, targeted protein stabilisation or enhancement via deubiquitylase (DUB) recruitment, is only beginning to emerge. The immune checkpoint receptor CTLA4, whose deficiency causes severe autoimmunity, undergoes rapid ubiquitin-dependent lysosomal degradation, making it one of the most short-lived transmembrane proteins. Using an inducible "RapTag" system, which brings together tagged proteins through rapalog-mediated FKBP-FRB dimerisation, we show that enforced proximity to the broad-specificity DUB USP15 markedly increases total and cell surface CTLA4 levels. Controlled expression of WT or catalytically inactive USP15 in isogenic cell lines revealed a clear requirement for DUB activity. The elevation of CTLA4 at the plasma membrane exceeded that of the total cellular pool, consistent with a diversion from ubiquitin-driven lysosomal sorting towards recycling. This easily adaptable platform enables systematic testing of DUB-substrate combinations that informs rational Enhancement Targeting Chimera (ENTAC) design for downstream drug discovery efforts and targeted protein rescue in therapeutic contexts.
    DOI:  https://doi.org/10.26508/lsa.202503563
  2. Nat Commun. 2026 Jan 19.
    Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity.
    Irene Schwartz, Valentina Budroni, Mathilde Meyenberg, Zuzana Hodakova, Harald Hornegger, Kathrin Hacker, Siegfried Schwartz, Daniel B Grabarczyk, Julian F Ehrmann, Sara Scinicariello, David Haselbach, Jörg Menche, Tim Clausen, G Elif Karagöz, Gijs A Versteeg.
      APOBEC family members play crucial roles in antiviral restriction. However, certain APOBEC3 (A3) proteins drive harmful hypermutation in humans, contributing to cancer. The cancer-associated A3 proteins are capable of transiting from the cytosol to the nucleus, where they can cause genome mutations. Here, we uncover a specific set of cellular pathways that protect genomic DNA from the major cancer-associated A3 proteins. Through genetic and proteomic screening, we identify UBR4, UBR5, and HUWE1 as key ubiquitin E3 ligases marking cancer-associated A3B and A3H-I for degradation, thereby limiting A3-driven hypermutation. Mechanistically, UBR5 and HUWE1 recognize A3s in the absence of their RNA binding partner, thus promoting proteasomal degradation of APOBEC3 protein that is not engaged in its antiviral cellular function. Depletion or mutation of the E3 ligases in cells and human cancer samples increases A3-driven genome mutagenesis. Our findings reveal that UBR4, UBR5, and HUWE1 are crucial factors in a ubiquitination cascade that maintains human genome stability.
    DOI:  https://doi.org/10.1038/s41467-026-68420-5
  3. Proc Natl Acad Sci U S A. 2026 Jan 27. 123(4): e2523465123
    ER membrane receptors engage core autophagy machinery to initiate ER-phagy.
    Cha Wu, Haixia Yang, Chen Wang, Peiqi Huang, Ning Yan, Ruobing Ren, Wei Liu, Yi Lu, Chunmei Chang.
      Endoplasmic reticulum (ER) phagy is the form of selective autophagy that governs ER abundance and integrity by targeting dysfunctional ER fragments for degradation. How the recognition of ER fragments as autophagy substrates is coupled to engagement of the core autophagic machinery is largely unknown. Here, using a combination of in vitro reconstitution systems, structural modeling, and cell biology, we demonstrate that ER membrane receptors directly engage the core autophagy component ATG9A, as well as the PI3P-binding protein WIPI2, to initiate ER-associated autophagosome biogenesis. ER-phagy receptor-ATG9A association nucleates the recruitment of the other key autophagy proteins required to initiate ER-phagy. In parallel, ER-phagy receptor-WIPI2 engagement promotes rapid LC3 lipidation for autophagic membrane expansion. These data show how ER-phagy receptors trigger the cascade of events leading to ER autophagosome formation.
    Keywords:  ER-phagy; ER-phagy receptor; autophagosome biogenesis; autophagy machinery; in vitro reconstitution
    DOI:  https://doi.org/10.1073/pnas.2523465123
  4. bioRxiv. 2025 Dec 07. pii: 2025.12.06.692499. [Epub ahead of print]
    Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling.
    Johannes F Hevler, Mirat Sojitra, Tomislav Caval, Michael Schoof, André Mateus, Carolyn R Bertozzi.
      Protein glycosylation regulates essential cellular processes including protein folding, stability, and cell-cell interactions; however, how aberrant glycosylation impacts protein function and interaction networks remains poorly understood. Here we combine mass spectrometry-based proteomics, chemical glycobiology, and molecular dynamics simulations to systematically investigate glycosylation dependent protein stability and function. By perturbing the secretory pathway at defined steps, we generated proteins with distinct glycan structures and analyzed their functional consequences using thermal proteome profiling. This approach revealed that cells mount convergent stress responses to diverse glycosylation perturbations, characterized by coordinated trafficking reorganization. This reorganization effectively redirects protein flux from secretion toward degradation. We further identified that perturbing terminal glycan modifications, particularly sialylation and fucosylation, exerts the most profound effects on cell surface protein function. We studied in detail how loss of fucosylation restricts the conformational dynamics of key domains in integrin alpha 4, reducing VCAM-1 binding affinity and suggesting a potential therapeutic strategy for multiple sclerosis. Overall, our systematic approach uncovered extensive complexity in how glycosylation regulates protein function beyond simple glycoform identification and provides a resource for dissecting essential glycan-protein relationships.
    DOI:  https://doi.org/10.64898/2025.12.06.692499
  5. Adv Sci (Weinh). 2026 Jan 20. e22165
    Ubiquitination-Driven Reprogramming of Proteostasis in Metastasis.
    Dongping Wei, Jiayan Chen, Yaping Xu.
      Metastasis, the leading cause of cancer-related mortality, poses a fundamental proteostatic challenge, requiring rapid and precise proteome remodeling in response to stress. While ubiquitination is linked to protein degradation, our recent work uncovered a non-canonical, metastasis-promoting mechanism centered on DCAF12, a substrate receptor of the Cullin 4-RING ubiquitin ligase complex. DCAF12 mediates non-degradative ubiquitination of TRiC/CCT chaperonin subunits, allosterically activating the chaperonin to enhance its assembly, stability, and folding capacity. This ubiquitination-dependent activation circuit enables metastatic cells to efficiently fold and stabilize diverse pro-metastatic proteins, thereby facilitating dynamic proteome reprogramming. Herein, we present the DCAF12-TRiC/CCT axis as a central regulatory component of this adaptive response, explore its evolutionary basis, and propose DCAF12 as a prototype for a broader class of "DCAFome" regulators of chaperone function. This mechanistic understanding establishes a direct rationale for therapeutically targeting this axis to disrupt adaptive proteostasis. Moreover, we outline a therapeutic paradigm termed "proteostatic stress creation." This framework encompasses a spectrum of strategies, from precision protein-protein interaction inhibitors to state-selective degraders of DCAF12 or its ubiquitinated chaperonin subunits. These approaches can potentially disrupt the DCAF12-TRiC/CCT axis, thereby undermining the proteostatic resilience that sustains advanced cancers.
    Keywords:  DCAF12; TRiC/CCT; metastasis; proteostasis; ubiquitination
    DOI:  https://doi.org/10.1002/advs.202522165
  6. J Biol Chem. 2026 Jan 20. pii: S0021-9258(26)00043-8. [Epub ahead of print] 111173
    SIRT7 safeguards ERα proteostasis via deacetylation-dependent degradation of unliganded and misfolded receptors.
    Mengdi Cao, Junfeng Zhang, Huixia Liu, Ronghui Fan, Faliang Wu, Yitong Meng, Tiansheng Li, Yalan Wu, Xiaolong Tang.
      SIRT7 has been implicated in diverse physiological and pathological processes, yet its role in sexual dimorphism and the underlying molecular mechanisms remain insufficiently explored. Given that ERα-mediated estrogen signaling is a central regulator of sexual dimorphism and that ERα undergoes stringent quality control to preserve signaling sensitivity, we investigated whether SIRT7 and ERα are mechanistically connected. Here, we identify SIRT7 as a molecular inspector that safeguards the quality of estrogen receptor α (ERα) to fine-tune estrogen signaling through the regulation of ERα proteostasis. Under estrogen-deprived conditions or in the presence of misfolded ERα, SIRT7 deacetylates ERα and promotes its degradation through the E3 ubiquitin ligase STUB1, thereby maintaining a functional receptor pool and preserving estrogen responsiveness. During this process, deacetylated ERα competes with SIRT7 for STUB1 binding, an E3 ligase that is also required for SIRT7 protein turnover, thus leading to SIRT7 stabilization. As a feedback mechanism, upon estrogen (E2) stimulation, E2-bound ERα activates non-genomic MAPK signaling to trigger SIRT7 degradation via another E3 ligase UBR5, which ensures the proper receptor signaling activation. Given the central role of ERα in aging and hormone-related cancers, our findings highlight SIRT7 as a key regulator linking age-associated disorders and hormone-driven tumorigenesis.
    Keywords:  ERα; Estrogen signaling; Protein degradation; Receptor quality control; SIRT7
    DOI:  https://doi.org/10.1016/j.jbc.2026.111173
  7. Nat Struct Mol Biol. 2026 Jan 20.
    Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry.
    Stefano Annunziato, Chao Quan, Etienne J Donckele, Ilaria Lamberto, Richard D Bunker, Mary Zlotosch, Laura Schwander, Anastasia Murthy, Lars Wiedmer, Camille Staehly, Michelle Matysik, Samuel Gilberto, Despina Kapsitidou, Daric Wible, Gian Marco De Donatis, Peter Trenh, Rohitha SriRamaratnam, Vaik Strande, Raphael Lieberherr, David Lyon, Danielle Steiner, Joao Silva, Reinaldo Almeida, Elena Dolgikh, Bradley DeMarco, Jennifer Tsai, Amine Sadok, Vladislav Zarayskiy, Magnus Walter, Ralph Tiedt, Kevin J Lumb, Debora Bonenfant, Bernhard Fasching, John C Castle, Sharon A Townson, Pablo Gainza, Georg Petzold.
      Molecular glue degraders (MGDs) are small-molecule compounds that divert E3 ligases to degrade nonnatural substrates called neosubstrates. Clinically effective MGDs bind cereblon (CRBN), a substrate receptor of the Cullin 4-RING E3 ubiquitin ligase (CRL4CRBN), and recruit neosubstrates to an MGD-induced neosurface on the CRBN CULT domain through molecular mimicry of a natural CRBN degron. Here, we identify G3BP2 (Ras-GAP SH3 domain-binding protein 2), a neosubstrate that bypasses canonical interactions with CRBN by engaging an unconventional binding site on the CRBN LON domain. The ternary complex interface does not resemble known interactions with CRBN. Instead, CRBN leverages a preexisting protein-protein interaction (PPI) hotspot on the target protein by mimicking an endogenous binding partner of G3BP2. Our findings suggest that composite neosurfaces that mimic and stabilize the footprint of natural PPIs (in short, 'glueprints') could become a viable strategy for the rational expansion of the MGD target repertoire.
    DOI:  https://doi.org/10.1038/s41594-025-01738-8
  8. Angew Chem Int Ed Engl. 2026 Jan 20. e20039
    Proteasome Cap Targeting Chimeras for Ubiquitination-Independent Targeted Protein Degradation.
    Chen Song, Qi Liu, Tingjian Wang, Yan Song, Logan H Sigua, Paul M Park, Scott Ficarro, Sunwoo Lee, Sarah Picaud, Panagis Filippakopoulos, Jarrod Marto, Milka Kostic, Adam D Durbin, Kenneth Anderson, Jun Qi.
      Selective degradation of a disease-associated protein of interest (POI) is a powerful therapeutic strategy. FDA-approved and investigational glue and degrader drugs function by recruiting a POI to an E3 ubiquitin ligase that mediates POI polyubiquitination and triggers proteasomal degradation. However, using E3 ligases as an intermediary and requiring POI polyubiquitination makes this mechanism of action complex and difficult to rationalize and optimize. These issues have led to interest in evaluating whether direct recruitment of non-ubiquitinated POIs to the proteasome might achieve the same pharmacological outcome. Here, we examined the potential of direct-to-proteasome non-ubiquitinated POI recruitment. Using a tag strategy, we first demonstrated that the proteasomal 19S cap region proteins, RPN13 and RPN1, can recruit non-ubiquitinated POI model proteins, such as BRD4, to the proteasome and induce degradation. Subsequently, we developed small molecule-based bifunctional recruiter molecules (Proteasome Cap Targeting Chimeras, CAP-TACs) and showed that they recruit several distinct POIs, including BRD4, PRMT5, and FKBP12, to specific subunits in the 19S cap region and induce their ubiquitination-independent, proteasome-dependent degradation. This study provides further evidence that bifunctional small molecules can re-localize POIs to the proteasome and induce their degradation in the absence of ubiquitination, which broadens the capabilities of targeted protein degradation.
    Keywords:  CAP‐TAC; Proteasome cap region protein induced degradation; RPN13 induced degradation; Small molecule recruiter to proteosome; Ubiquitination independent degradation
    DOI:  https://doi.org/10.1002/anie.202520039
  9. Mol Cell. 2026 Jan 19. pii: S1097-2765(25)01021-4. [Epub ahead of print]
    The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis.
    Alžběta Roeselová, Santosh Shivakumaraswamy, Gabija Jurkeviciute, Jessica Zhiyun He, Josef Auburger, Jaro L Schmitt, Günter Kramer, Bernd Bukau, Radoslav I Enchev, David Balchin.
      Natural proteins often form intricate multidomain, oligomeric architectures. This presents a prima facie challenge to cellular homeostasis, as topologically complex proteins seldom refold efficiently in vitro. Here, we show that the efficient folding and assembly of the five-domain homotetramer β-galactosidase is obligatorily coupled to its synthesis on the ribosome, and we define the underlying mechanisms. During refolding from a denaturant, maturation of the catalytic domain is frustrated. Assembly outpaces monomer folding, and non-native oligomers accumulate. Efficient de novo folding is characterized by segmental domain folding, shaped by the binding of a nascent amphipathic helix to a cryptic pocket on uL23 on the ribosome surface. Homomer assembly also initiates cotranslationally via recruitment of a full-length subunit to the nascent polypeptide, and the failure to do so results in misassembly. Our results reveal how the ribosome can dictate the timing of folding and assembly to enable efficient biogenesis of a topologically complex protein.
    Keywords:  cotranslational folding; protein assembly; protein folding; ribosome
    DOI:  https://doi.org/10.1016/j.molcel.2025.12.022
  10. Proc Natl Acad Sci U S A. 2026 Jan 27. 123(4): e2524129123
    A cytokine receptor-targeting chimera toolbox for expanding extracellular targeted protein degradation.
    Kaan Kumru, Zi Yao, Brandon B Holmes, Fangzhu Zhao, Yun Zhang, Emilio Ferrara, Trenton M Peters-Clarke, Kevin K Leung, James A Wells.
      Extracellular targeted protein degradation (eTPD) is an important new modality for manipulating the extracellular proteome. However, most eTPD receptors are expressed broadly or are restricted to the liver, limiting specific degradation in other tissues. Cytokine receptor-targeting chimeras (kineTACs) are genetically encoded bispecifics for eTPD that fuse a natural ligand like CXCL12 to an antibody, directing soluble or membrane proteins for lysosomal degradation using the widely expressed chemokine receptor CXCR7 (K. Pance et al., Nat. Biotechnol. 41, 273-281 (2023)]. Here, we dramatically expand the kineTAC toolbox by constructing 81 different kineTACs based on an unbiased list of cytokines, chemokines, and growth factors. Remarkably, 55 of these expressed at suitable levels for analysis without any optimization. Many of these kineTACs bind receptors that have unique cell-type expression profiles, allowing for eTPD in specific cells and tissues, and some were more potent than the original CXCL12-based kineTAC against specific targets. We further show the internalizing capability of a kineTAC can enhance the performance of antibody drug conjugates. We believe these simple, genetically encoded tools will be useful for expanding the applications for optimized or cell type-selective eTPD.
    Keywords:  antibodies; cytokines; receptor recycling; targeted protein degradation
    DOI:  https://doi.org/10.1073/pnas.2524129123
  11. Proc Natl Acad Sci U S A. 2026 Jan 27. 123(4): e2426723123
    Calumenin prevents fibroblast senescence and lung aging by promoting vimentin proteostasis.
    Ting Dong, Xue Jiao, Huirui Wang, Yinghui Gao, Yuliang Xu, Hui Li, Senbiao Fang, Xinyi Chen, Mengmeng Wang, Hanbing Zhu, Nianyu Li, Bo Han, Mei Qi, Kaige Lyu, Kaicheng Ma, Ke Li, Haigen Fu, Bowen Gu, Wenfei Li, Yingying Qin, Zi-Jiang Chen, Xiaohui Liu, Hongxiang Lou.
      Progressive lung fibrosis is linked to aging-related dysfunction in fibroblasts, which remains poorly understood. To investigate the alterations in fibroblasts, particularly the molecular programs driving this profibrotic evolution in the aging lung, we isolated senescent lung fibroblasts from aged mice. We observed aberrant vimentin aggregates, which correlate with accelerated fibroblast senescence. CRISPR-based screening identified calumenin as a chaperone protein essential for vimentin proteostasis. A fibroblast-specific knockout of calumenin promotes the accumulation of vimentin aggregates and profibrotic factors migracytosis, exacerbating fibroblast senescence and lung aging. Mechanistically, calumenin collaborates with the TRiC complex to facilitate proper vimentin folding and recruits the chaperonin subunit Chaperonin Containing TCP1 Subunit 2 (CCT2) to degrade misfolded vimentin aggregates. Pathologically, external profibrotic stimuli trigger calcium transients and induce calumenin degradation, resulting in fibroblast senescence and the initiation of fibrosis. The natural product 9-85, derived from high-content screening, specifically targets and disrupts vimentin aggregates upon stimulation, alleviating aging-related lung fibrosis. Our findings reveal that calumenin coordinates vimentin quality control to shape cell structure and suppress the secretome of senescent fibroblasts, providing a promising therapeutic strategy for aging-related organ fibrosis.
    Keywords:  aging-related fibrosis; calumenin; fibroblast senescence; vimentin proteostasis
    DOI:  https://doi.org/10.1073/pnas.2426723123
  12. J Vis Exp. 2026 Jan 02.
    In-vitro Reconstitution of Bacterial Ubiquitination and VCP/p97-mediated Elimination.
    Sourav Ghosh, Udit Kumar Das, Sumit Rakshit, Anirban Banerjee.
      Ubiquitination is a versatile post-translational modification that plays a critical role in cytosolic immunity. Upon invasion of the host cells, pathogenic bacteria are initially enclosed within an endosome, from which they break free and escape into the cytosol to avoid lysosomal degradation. Once in the cytosol, bacteria are rapidly tagged with ubiquitin chains by host E3 ligases, marking them for clearance via multiple effector pathways, including autophagy and the proteasome. To delineate the contribution of individual pathways in bacterial elimination, in-vitro reconstitution offers a controlled and unambiguous approach. Here, using Streptococcus pneumoniae (SPN) as a model bacterial pathogen, we present a detailed protocol for its ubiquitination using mammalian cell lysates or pure ubiquitin enzyme complex, followed by treatment with purified VCP/p97-UFD1-NPLOC4 complex to assess its bacteriolytic activity independent of other cellular factors. Overall, this procedure holds the potential to illuminate the function of immunity-linked ubiquitin ligases and effectors in a cell-free context, where dissecting such mechanisms can be challenging in intact cells.
    DOI:  https://doi.org/10.3791/69454
  13. ACS Nano. 2026 Jan 20.
    Nanoscopy of Organelle Handoff Portals Reveals Direct Coupling between Endoplasmic Reticulum Remodeling and Microtubule-Based Transport.
    Jin-Sung Park, Il-Buem Lee, Hyeon-Min Moon, Hyeonjun Jeon, MinHyeong Lee, Chungho Kim, Seok-Cheol Hong, Minhaeng Cho.
      How biosynthetic organelles leave the endoplasmic reticulum (ER) and engage with microtubule tracks remains a central question. Combining interferometric scattering with fluorescence nanoscopy, we tracked nanometer-scale handoff events in living cells. ER-derived organelles undergo biased diffusion along ER tubules toward nearby microtubules. ER three-way junctions function as nanoscopic hubs where a cargo pauses, contacts multiple microtubules, and then launches onto a track for long-range travel. During this process, the ER maintains a membrane tether to the departing cargo, extending its tubules and forming new junctions, thereby coupling internetwork transfer with membrane morphogenesis. These observations reveal an integrated mechanism that links organelle biogenesis, directional trafficking, and continual ER and cellular remodeling, underscoring the ER's active role in steering transport and repurposing its own output. More broadly, this single-label, dual-mode nanoscopy provides a minimally perturbative, high-speed, and broadly applicable platform for probing the nanoscale dynamics of diverse organelles and cytoskeletal processes in the crowded intracellular environment.
    Keywords:  ER remodeling; ER-microtubule junction; autophagosome; interferometric scattering microscopy; nanoscopy; organelle transfer
    DOI:  https://doi.org/10.1021/acsnano.5c15844
  14. Mol Syst Biol. 2026 Jan 22.
    Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning.
    Erik Marcel Heller, Karen Barthel, Markus Räschle, Klaske M Schukken, Jason M Sheltzer, Zuzana Storchová.
      Aneuploidy, a hallmark of cancer, alters chromosome copy numbers and with that the abundance of hundreds of proteins. Evidence suggests that levels of proteins encoded on affected chromosomes are often buffered toward their abundances observed in diploids. Despite its prevalence, the molecular mechanisms driving this protein dosage compensation remain largely unknown. It is unclear whether all proteins are buffered similarly, what factors determine buffering, and whether dosage compensation varies across different cell lines or tumor types. Moreover, its potential adaptive advantage and therapeutic relevance remain unexplored. We established a novel approach to quantify protein dosage buffering in a gene copy number-dependent manner, showing that dosage compensation is widespread but variable in cancer samples. By developing multifactorial machine learning models, we identify gene dependency, protein complex participation, haploinsufficiency, and mRNA decay as key predictors of buffering. We show that dosage compensation affects oncogenic potential and that higher buffering correlates with reduced proteotoxic stress and increased drug resistance. These findings highlight protein dosage compensation as a crucial regulatory mechanism with therapeutic potential in aneuploid cancers.
    Keywords:  Aneuploidy; Buffering; Cancer; Dosage Compensation; Machine Learning
    DOI:  https://doi.org/10.1038/s44320-026-00187-9
  15. Nat Commun. 2026 Jan 17.
    A small molecule VDAC ligand inhibits ERAD and induces selective cancer cell death via disruption of calcium homeostasis.
    Wenjing Yan, Daniel C Talley, Antara Syam, Carina Danchik, Yongwang Zhong, Xianzheng Zhang, Xiaoying Liu, Bolormaa Baljinnyam, Stephen C Kales, Matthew G Cyr, Yuhong Fang, Alexey V Zakharov, Xin Hu, Taylor Niehoff, Tuan Xu, Yanyan Qu, Allison Yang, Valentine V Courouble, Qin Yao, Anton Simeonov, Ruili Huang, Tatiana K Rostovtseva, Sergey M Bezrukov, Christopher A LeClair, Josephine M Egan, Hua Wang, Dingyin Tao, Ganesha Rai, Mark J Henderson, Shengyun Fang.
      Endoplasmic reticulum-associated degradation (ERAD) is a critical protein quality control mechanism that also regulates lipid metabolism and calcium homeostasis. Dysregulation of ERAD and unfolded protein response underlies diseases including cancer, neurodegenerative disorders, and metabolic syndromes. Small molecule modulators of ERAD could enable mechanistic discovery and therapeutic intervention, but few have been identified. Using a high-content screening, we discovered several ERAD-modulating compounds, including NCATS-SM0225, an ERAD inhibitor that unexpectedly binds all three isoforms of VDAC, outer mitochondrial membrane proteins enriched at mitochondria-associated membranes. This led us to discover an essential role for VDACs in ERAD and ER-phagy. NCATS-SM0225 elevates cytosolic, ER, and mitochondrial calcium through calcium influx and IP3R-MCU activity. This calcium imbalance strengthens VDAC1-IP3R coupling and activates PERK, which phosphorylates STIM1 and drives degradation of key ERAD regulators. Loss of these components amplifies PERK signaling and selectively kills cancer cells while sparing normal cells. These findings uncover a cancer-specific role of VDACs in ERAD regulation and calcium signaling, highlighting a therapeutically actionable vulnerability.
    DOI:  https://doi.org/10.1038/s41467-025-67816-z
  16. Cell Rep. 2026 Jan 16. pii: S2211-1247(25)01622-5. [Epub ahead of print]45(1): 116850
    Uncovering genetic interactions in the DNA repair network in response to endogenous damage and ionizing radiation.
    Benjamin Nebenfuehr, Lynn Sanford, Erin R Taylor, Kerri Ball, Catherine E Woods-Killam, Hannah I Ghasemi, Bruce Proctor, Raquel Ortega, Colin Sempeck, Robin D Dowell, Nausica Arnoult.
      Genomic integrity relies on a complex network of DNA damage response (DDR) pathways that repair endogenous and exogenous lesions, yet how individual factors operate within this broader landscape remains unclear. We performed a large-scale combinatorial CRISPR-Cas9 knockout screen targeting 461 DNA repair genes, disrupting over 100,000 gene combinations under basal conditions and after ionizing radiation (IR). This approach uncovered thousands of genetic interactions spanning pathways that respond to endogenous damage and those specific to double-strand break repair. From this dataset, we validated both positive and negative interactions under basal and irradiated conditions, including a synthetic lethal relationship between MRE11A and the E3 ligase UBR5, a role for Ku70/80 in preventing unscheduled nuclease activity at telomeres, an IR-specific vulnerability upon co-disruption of CYREN and PARG, and a link between CYREN-mediated radioresistance and innate immunity. This resource enables mechanistic insight and reveals therapeutic vulnerabilities in DNA-repair-deficient cancers.
    Keywords:  CP: molecular biology; CRISPR; CYREN; DNA damage; DNA repair; Ku; MRE11; UBR5; combinatorial screen; telomeres
    DOI:  https://doi.org/10.1016/j.celrep.2025.116850
  17. Nat Commun. 2026 Jan 21.
    A stochastic mechanism drives fast substrate translocation in the AAA+ machine ClpB.
    Remi Casier, Dorit Levy, Inbal Riven, Yoav Barak, Gilad Haran.
      How biological machines harness ATP to drive mechanical work remains a crucial question. Structural studies of protein-translocating AAA+ machines proposed a coupled and sequential translocation process, whereby ATP hydrolysis events lead to short threading steps. Yet, direct real-time observation of these events remains elusive. Here, we employ single-molecule FRET spectroscopy to track substrate translocation through ClpB, a quality control AAA+ machine. We isolate ClpB and its substrate within lipid vesicles and find that translocation events, while dependent on ATP, take milliseconds, much faster than ATP hydrolysis times. Surprisingly, the translocation rate depends weakly on temperature and ATP concentration. Using three-color FRET experiments, we find that translocation events can occur bidirectionally but are not always complete. Replacing ATP with the slowly hydrolysable analog ATPγS abolishes both rapid translocation and directionality. These results indicate a fast, stochastic Brownian-motor-like mechanism, redefining how ATP is coupled with mechanical action in AAA+ machines.
    DOI:  https://doi.org/10.1038/s41467-026-68478-1
  18. iScience. 2026 Jan 16. 29(1): 114503
    The pivotal role of endoplasmic reticulum in cancer glucose metabolism.
    Cecilia Marini, Maddalena Ghelardoni, Sonia Carta, Tiziana Bachetti, Silvia Bruno, Isotta Cainero, Silvia Ravera, Roberto Benelli, Marco Scotto, Francesca Vitale, Santina Bruzzone, Serena Losacco, Sabrina Chiesa, Matteo Bauckneht, Gabriele Tancreda, Matteo Raineri, Anna Maria Orengo, Andrea Benzi, Gianmario Sambuceti.
      The endoplasmic reticulum (ER) supports essential biosynthetic and quality control functions. These processes rely on sustained energy supply and precise redox control within the ER lumen. While ATP can be imported from mitochondria, pyridine nucleotides are impermeable to the ER membrane, necessitating compartment-specific mechanisms to regulate NAD(H) and NADP(H) pools. Here, we demonstrate that the ER-confined pentose phosphate pathway (ER-PPP), driven by hexose-6-phosphate dehydrogenase (H6PD), processes large amounts of glucose equivalents to preserve the local redox homeostasis in triple-negative breast cancer (TNBC) cells. H6PD silencing decreases the NADPH regeneration within the ER lumen. The consequent impairment of protein folding machinery accelerates lysosomes generation, up to disrupt the equivalence between the cell release of lactate and H+. Finally, the simultaneous impairment of glucose-6P (G6P) degradation (by H6PD silencing) and hydrolysis (by silencing glucose-6-phosphatase) eventually results in a measurable ER collapse documenting the high-rate nature of G6P flux across the reticular membrane.
    Keywords:  Cancer; Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2025.114503
  19. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1533. [Epub ahead of print]54(2):
    eIF3g binding to GUCG boxes located in mRNA coding regions enhances translation of mild heat shock response genes in the yeast Saccharomyces cerevisiae.
    Hiroaki Kato, Akihiro Oguro, Yuanhui Mao, Kinsley Ochsner, Hailey Casey, Grace Sakai, Ji Wan, Shingo Usuki, Leiming Tang, Mizuki Asano, Nirmala Bardiya, Kade Kaufman, Susumu Ishiguro, Naoki Tani, Kazuyuki Kumagai, Akira Nakamura, Chingakham Ranjit Singh, Taiichi Sakamoto, Eiji Obayashi, Shu-Bing Qian, Katsura Asano.
      Eukaryotic translation initiation factor 3 (eIF3) is a multi-subunit complex that promotes ribosome recruitment and messenger RNA (mRNA) selection. Here, we show that its eIF3g subunit, along with the binding partner eIF3i, mediates transcript-specific translation under mild heat stress through direct RNA binding. First, SELEX experiments identified a short GUCG-centered motif preferentially recognized by eIF3g, suggesting a sequence-specific binding preference. Next, ribosome profiling of yeast eIF3i mutant revealed that mRNAs containing GUCG motifs in their 5' coding regions exhibit elevated ribosome occupancy in a manner dependent on eIF3g/eIF3i module. A subset of SELEX-identified motifs, collectively termed the GUCG box, was found enriched in the 5'-terminal coding region of the regulated mRNAs. Reporter assays confirmed that these 5'-terminal coding regions are sufficient to drive heat-induced translation. Mutational analyses and biolayer interferometry demonstrated that disruption of the GUCG motif impairs eIF3g binding and diminishes translational induction. Moreover, GUCG motifs are periodically distributed across coding sequences and enriched near start codons, consistent with their role in stabilizing initiating ribosomes. Overall, this study establishes the GUCG box as a bona fide eIF3g-binding motif and validates its functional importance in vivo. These findings provide new insight into how eIF3 mediates stress-adaptive translation through sequence-specific RNA recognition.
    DOI:  https://doi.org/10.1093/nar/gkaf1533
  20. bioRxiv. 2025 Dec 11. pii: 2025.12.08.693079. [Epub ahead of print]
    Proteasome activator Blm10 maintains cellular proteostatic balance and gamete quality in budding yeast.
    Maia C Reyes, Diego R Ramos-Ortiz, Jiarong A Cheng, Silvan Spiri, Ella Doron-Mandel, Jenny Kim Kim, Yanzhe Ma, Marko Jovanovic, Andreas Martin, Gloria Ann Brar.
      The proteasome is the central macromolecular complex that is responsible for regulated protein degradation in eukaryotic cells. Its best characterized substrates are ubiquitinated proteins that are targeted to the 26S proteasome complex, consisting of a 19S regulatory particle (RP) capping the barrel-shaped 20S core peptidase (CP). The CP can interact with other caps that modulate its function, including Blm10/PA200, a large monomeric protein whose biological function is not well understood. Blm10 is highly upregulated during gametogenesis in budding yeast, suggestive of a natural stage-specific modulation of proteasome composition. Here, we investigate the function Blm10 during yeast gametogenesis, identifying it as a weak activator of the proteasome that can displace the 19S RP from the CP. Due to this competition for the CP, overexpression of Blm10 can lead to attenuation of ubiquitin-dependent degradation and consequent proteostatic defects. Cells lacking Blm10 also display markers of proteostatic stress, including Hsp104 foci and heat sensitivity, suggesting that Blm10 safeguards normal proteostatic balance. We find that Blm10 is important for maintaining gamete fitness and ensuring normal rejuvenation of aged cells following gametogenesis. Overall, our data suggest a role for Blm10-proteasomes in maintaining gamete proteostasis through fine-tuning of proteasome activity and prevention of protein aggregation.
    DOI:  https://doi.org/10.64898/2025.12.08.693079
  21. J Med Chem. 2026 Jan 23.
    Discovery of 2-Chloro-pyrrolo[2,3-d]pyrimidin-4-one Derivatives as Protein Disulfide Isomerase Inhibitors with a Novel Allosteric-Covalent Binding Mode and Anti-Glioblastoma Activity.
    Qiulin Zhang, Haiwen Lin, Jiafan Yuan, Shi-Peng Zhang, Haotian Wang, Hanjie Hu, Jingyi Wang, Xiaofei Wang, Zhaofa Wu, Shi-Chao Lu, Youwei Ai, Bo Yan.
      Protein disulfide isomerase (PDI) is an endoplasmic reticulum oxidoreductase/chaperone, and its dysregulation contributes to cancer progression, particularly glioblastoma. A high-throughput screen identified TC8026 as a PDI-active hit, and further optimization afforded a pyrrolo[2,3-d]pyrimidin-4-one series with up to 20-fold improved potency. Representative analogues (30w, 30z, 30aa, and 30ab) potently inhibited PDI, induced endoplasmic reticulum stress-mediated apoptosis in glioblastoma cells, and 30z significantly suppressed tumor growth in a U251 xenograft model. Mechanistic studies revealed a previously unrecognized allosteric-covalent binding mode. The inhibitors initially engage an allosteric pocket within the b' domain involving residues H256 and F304, thereby perturbing the substrate-binding interface and inducing conformational changes that expose the noncatalytic cysteine C312 for covalent capture. This b'-directed allosteric covalency, distinct from conventional catalytic cysteine modification, confers enhanced selectivity within the PDI family. These findings define a novel allosteric-covalent chemotype of PDI inhibitors with a unique binding mechanism and promising antiglioblastoma potential.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c03058
  22. Mol Genet Metab. 2026 Jan 19. pii: S1096-7192(26)00020-X. [Epub ahead of print]147(3): 109737
    Multi-omics analysis reveals ER stress as a main feature in two endothelial cell models of N-linked congenital disorders of glycosylation.
    Karen Driesen, Veronika Holubová, Pedro Magalhães, Shauni Loopmans, Mainak Guharoy, Isabelle Meyts, Eva Morava, Bart Ghesquière, Peter Witters.
      Glycosylation is one of the most important posttranslational modifications. When the glycosylation machinery is affected, this leads to a congenital disorder of glycosylation (CDG). CDG are a class of rare multisystemic diseases that often affect the endoplasmic reticulum (ER). Although vascular complications have been reported in CDG, the contribution of endothelial dysfunction to these phenotypes remains incompletely understood. Here, we evaluated the effect of glycosylation deficiency on endothelial dysfunction by generating two endothelial cell models using pharmacological inhibitors: tunicamycin (a well-known glycosylation inhibitor at the level of DPAGT1), and 2-deoxy-2-fluoro-D-mannose (FMan). This is a novel inhibitor that inhibits mannose and related sugar-phosphate metabolism. These cell models were subjected to transcriptomics, proteomics, and tracer metabolomics to pinpoint the pathways that are most affected across these different levels. Both transcriptomics and proteomics revealed ER stress as the top upregulated feature. This was functionally characterized by decreased cell growth, induced apoptosis, decreased cell migration, and induced an immune response. The barrier function of the cells was not affected. Here, we demonstrate that N-glycosylation deficiency triggers an ER stress response, contributing to endothelial dysfunction, and investigated ER stress mitigation as a potential therapeutic strategy for CDG.
    Keywords:  Congenital disorders of glycosylation; ER stress; Endothelial dysfunction; Omics
    DOI:  https://doi.org/10.1016/j.ymgme.2026.109737
  23. J Med Chem. 2026 Jan 23.
    Click. Screen. Degrade. A Miniaturized D2B Workflow for Rapid PROTAC Discovery.
    Marko Mitrović, Francesco Aleksy Greco, Yiliam Cruz García, Aleksandar Lučić, Lasse Hoffmann, Rohit Chander, Julia Schönfeld, Nick Liebisch, Saran Aswathaman Sivashanmugam, Martin Peter Schwalm, Markus Egner, Max Lewandowski, Daniel Merk, Viktoria Morasch, Elmar Wolf, Susanne Müller, Thomas Hanke, Ewgenij Proschak, Kerstin Hiesinger, Stefan Knapp.
      Targeted protein degradation is one of the fastest developing fields in medicinal chemistry and chemical biology. Despite significant development in assay technologies and inhibitor discovery, the development of PROTACs remains a challenging endeavor since rational design approaches remain widely elusive. Our workflow eliminates the rate-limiting step of classic synthesis, namely compound purification, and pairs it with high-throughput, semi-automated plate-based synthesis, and direct cellular assay evaluation. We applied this direct-to-biology approach to four diverse targets, demonstrating the general applicability of this technology. PROTAC synthesis was realized by using the highly efficient copper-catalyzed azide-alkyne cycloaddition reaction. This simplified reaction setup enabled synthesis in the nanomole scale with reaction volumes as low as 5 μL. The high-throughput strategy allows hundreds of PROTACs to be synthesized and evaluated within a few days, facilitating comprehensive assessment of target degradability, rapid hit identification, and selection of the most suitable E3 ligase for degrader development.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c02543
  24. Autophagy. 2026 Jan 21.
    Molecular engineering of lysosome-based degraders unveils a rapidly expanding therapeutic strategy.
    Adele Rivault, Jade Dussart-Gautheret, Rachid Benhida, Anthony R Martin, Patrick Auberger, Arnaud Jacquel, Guillaume Robert.
      The targeted degradation of oncogenic or misfolded proteins has emerged as a promising therapeutic strategy. While proteolysistargeting chimeras (PROTACs) and related technologies have successfully hijacked the ubiquitin-proteasome system to eliminate disease-driving proteins, recent advances highlight the lysosome as a powerful alternative degradation route. Lysosome-based degradation strategies offer broader substrate scope, subcellular targeting flexibility, and the ability to degrade proteins beyond the reach of the proteasome. In this review, we provide a comprehensive overview of synthetic molecules and engineered systems designed to traffic target proteins to the lysosome. These include lysosome targeting chimeras (LYTACs), autophagytargeting chimeras (AUTACs), autophagytethering compounds (ATTECs), and other modalities that exploit endogenous trafficking pathways for selective protein clearance. By mapping the current landscape of lysosome-targeting degraders, this article underscores the therapeutic potential of lysosomal proteolysis and outlines future directions for molecular engineering in this rapidly evolving field.
    Keywords:  Biodegraders; chimera compounds; drug design; lysosome; targeted degradation
    DOI:  https://doi.org/10.1080/15548627.2026.2618626
  25. J Cell Biol. 2026 Apr 06. pii: e202502083. [Epub ahead of print]225(4):
    Cholesterol depletion activates trafficking-coupled sphingolipid synthesis.
    Yeongho Kim, Jan Parolek, Christopher G Burd.
      Homeostatic pathways maintain the lipid composition of organelle membranes, and mechanistic links between lipid sensing, synthesis, and trafficking are lacking. Acute depletion of cell cholesterol elicits an increase in the rate of very-long-chain (VLC) sphingomyelin synthesis in the Golgi apparatus, thereby promoting cholesterol retention in the plasma membrane. Stable isotope metabolic analyses and lipid trafficking assays showed that the increase in VLC-sphingomyelin results from an increase in the rate of coatomer II-dependent trafficking of VLC-ceramide from the endoplasmic reticulum to the Golgi apparatus. An integral membrane protein of the coatomer II network, cTAGE5, is required for endoplasmic reticulum-to-Golgi trafficking of ceramide and cTAGE5 overexpression caused herniations of the endoplasmic reticulum network that entrapped a synthetic ceramide analog to which cTAGE5 could be photochemically cross-linked. We propose that cTAGE5 is a ceramide sensor for export of VLC-ceramide from the endoplasmic reticulum exit site.
    DOI:  https://doi.org/10.1083/jcb.202502083
  26. Mol Biol Cell. 2026 Jan 21. mbcE25060273
    The Atg2-Atg18 complex interacts with the Atg1 complex to localize to the pre-autophagosomal structure in Saccharomyces cerevisiae.
    Yuri Yasuda, Kanae Hitomi, Nobuo N Noda, Tetsuya Kotani, Hitoshi Nakatogawa.
      During autophagy induction in Saccharomyces cerevisiae, over twenty autophagy-related (Atg) proteins localize to the site of autophagosome formation to generate the pre-autophagosomal structure (PAS), where phase-separated condensates of the Atg1 kinase complex serve as a scaffold for recruiting other Atg proteins. The lipid transfer protein Atg2 forms a complex with the phosphatidylinositol 3-phosphate (PI3P)-binding protein Atg18 and mediates lipid influx from the endoplasmic reticulum to the PAS for membrane expansion. In this study, we discover that the Atg2-Atg18 complex interacts with the Atg1 complex. This interaction involves the C-terminal regions of Atg2 and the Atg1 complex subunit Atg29, and is enhanced by Atg1-dependent phosphorylation of Atg29. This interaction, together with Atg18 binding to PI3P, promotes PAS localization of the Atg2-Atg18 complex. These findings provide new insight into PAS organization and highlight the Atg1 complex as a central hub coordinating Atg protein assembly during autophagosome formation.
    DOI:  https://doi.org/10.1091/mbc.E25-06-0273
  27. Nature. 2026 Jan 21.
    Identification of an allosteric site on the E3 ligase adapter cereblon.
    Vanessa N Dippon, Zeba Rizvi, Anthony E Choudhry, Chun-Wa Chung, Ibrahim F Alkuraya, Wenqing Xu, Xavier B Tao, Anthony J Jurewicz, Jessica L Schneck, Wenqian Chen, Nicole M Curnutt, Farah Kabir, Kwok-Ho Chan, Markus A Queisser, Caterina Musetti, Han Dai, Gabriel C Lander, Andrew B Benowitz, Christina M Woo.
      Cereblon (CRBN) is the target of thalidomide derivatives1 that achieve therapeutic efficacy against some haematologic neoplasias2-4 by recruiting neosubstrates for degradation5-7. Despite the intense investigation of orthosteric thalidomide derivatives, little is known about alternate binding sites on CRBN. Here we report an evolutionarily conserved cryptic allosteric binding site on CRBN. Small-molecule SB-405483 binds the allosteric site to cooperatively enhance the binding of orthosteric ligands and alter their neosubstrate degradation profiles. A survey of over 100 orthosteric ligands and their degradation targets reveals trends in the classes of compounds and neosubstrates in which degradation outcomes are enhanced or inhibited by SB-405483. Structural investigations provide a mechanistic basis for the effects of the allosteric ligand by shifting the conformational distribution of CRBNopen to a novel CRBNint and increasing the CRBNclosed state. The discovery of a cryptic allosteric binding site on CRBN that alters the functional effects of orthosteric ligands opens new directions with broad implications for improving the selectivity and efficacy of CRBN therapeutics.
    DOI:  https://doi.org/10.1038/s41586-025-09994-w
  28. Nat Commun. 2026 Jan 19.
    Hierarchical mechanisms control the clearance of DNA lesion-stalled RNA polymerase II.
    Paula J van der Meer, George Yakoub, Kotaro Tsukada, Yuka Nakazawa, Tomoo Ogi, Martijn S Luijsterburg.
      Stalling of elongating RNA polymerase II (RNAPII) at DNA lesions blocks transcription and triggers transcription-coupled repair (TCR). However, the mechanisms determining the fate of stalled RNAPII remain incompletely understood. Here, we develop a time-resolved assay to track RNAPII clearance and degradation at UV-induced lesions. We show that RNAPII ubiquitylation by CSB and the CRL4CSA ubiquitin ligase is essential, as loss of these proteins causes persistent RNAPII accumulation at damage sites. Downstream of CSB/CRL4CSA-mediated ubiquitylation, two distinct pathways mediate RNAPII removal. The primary rapid route relies on TFIIH, with its XPD helicase activity driving RNAPII dissociation after proper recruitment and positioning by ELOF1, UVSSA, and STK19. A secondary slow pathway is mediated by the ubiquitin-dependent segregase VCP, which compensates for impaired TFIIH function. While VCP contributes only minimally in TCR-proficient cells, inhibition of VCP in TFIIH-deficient contexts completely abrogates RNAPII clearance. Together, these findings establish a hierarchical program in which CSB/CRL4CSA-mediated ubiquitylation initiates RNAPII processing, TFIIH/XPD helicase activity provides the main clearance mechanism, and VCP-dependent extraction acts as a backup when TFIIH fails. This mechanistic framework explains how cells resolve DNA lesion-stalled RNAPII during normal and compromised TCR.
    DOI:  https://doi.org/10.1038/s41467-026-68413-4
  29. Proc Natl Acad Sci U S A. 2026 Jan 27. 123(4): e2505321123
    GFP-free live neuron quantitative imaging reveals compartmentalization and growth dynamics of polyQ aggregates.
    Xiaotian Bi, Berea Suen, Li-En Lin, Kun Miao, Lu Wei.
      Huntington's Disease (HD), the most prevalent polyglutamine (polyQ) neurodegenerative disorder, features brain aggregates induced by mutant huntingtin (mHtt) proteins harboring expanded polyQ tracts. Despite extensive efforts, molecular mechanisms of polyQ aggregates remain elusive. Here, we establish quantitative stimulated Raman scattering imaging of polyQ aggregates (q-aggSRS) for noninvasive investigations in live neuronal cocultures using deuterated glutamine labeling. Q-aggSRS allows for specific visualization by targeting the distinct Raman peak from carbon-deuterium bonds, eliminating the need for bulky fluorescent protein tagging (e.g., EGFP). Coupled with analysis from aggregate-tailored expansion microscopy, newly designed two-color imaging, and pulse-chase visualization, we comprehensively quantified the mHtt and non-mHtt proteins within the same aggregates across varying sizes, cell types, mHtt constructs, and subcellular locations. Our findings demonstrate a two-phase aggregate model with a distinct core-shell spatial organization, reveal significant heterogeneity in nucleus/cytoplasm compartmentalization specific to neurons, and identify previously unrecognized loosely packed aggregates specifically in neuronal nuclei. These insights should advance our understanding of native polyQ aggregates, and our proposed interaction coefficients may offer quantitative parameters for developing effective HD therapies.
    Keywords:  live-neuronal imaging; protein aggregation; stimulated Raman scattering microscopy
    DOI:  https://doi.org/10.1073/pnas.2505321123
  30. J Am Chem Soc. 2026 Jan 21.
    An Engineered Nanovesicles-Based Lysosome-Targeting Protein Degradation Platform (NV-TACs) for Cancer Immunotherapy.
    Youmei Xiao, Xiuman Zhou, Xiaoshuang Niu, Xiaoyun Ye, Danhong Chen, Qingyu Dong, Zhuoying He, Xin Yang, Mengfan Wang, Wenxuan Zeng, Ye Su, Feiyu Luo, Juan Liu, Yanfeng Gao.
      Lysosome-Targeting Chimeras (LYTAC) technology offers a revolutionary approach for specifically degrading extracellular and membrane proteins. However, current LYTAC platforms face multiple technical challenges, including ligand screening, linker optimization, and the need to balance the characteristics between the protein of interest (POI) and lysosome-targeting receptor (LTR). To overcome these challenges, we engineered NV-TACs (Nanovesicle-based TArgeting Chimeras)─a linker-free LYTAC platform that integrates native nanovesicles displaying the endogenous ligands of POI and LTRs as bioinspired membrane protein degradation modules. As a proof-of-concept, PD-1 (as the binder of PD-L1) and transferrin (as the binder of transferrin receptor, TFRC) were engineered into biocompatible fibroblast-derived nanovesicles. This platform demonstrates significant scalability, allowing flexible module integration and functional assembly. NV-TACs efficiently degrade PD-L1 on tumor and immune cells through the TFRC-mediated specific lysosomal endocytosis pathway, and it has been expanded to the degradation of other membrane proteins. Notably, by incorporation of a therapeutic payload (ML210), NV-TACs simultaneously exhibited targeted protein degradation and ML210-mediated ferroptosis through payload delivery capacity. Both in anti-PD-1-responsive and -resistant tumor models, NV-TACs demonstrated significant therapeutic efficacy without obvious systemic toxicity. The platform of NV-TACs paves new avenues for developing linker-free, modular, and bioinspired targeted protein degradation platforms.
    DOI:  https://doi.org/10.1021/jacs.5c17801
  31. RNA. 2026 Jan 22. pii: rna.080481.125. [Epub ahead of print]
    Uridine analogs prevent stress granule formation, not by blocking PKR recognition, but by inhibiting the synthesis of T7 RNA Polymerase byproducts.
    Sean J Ihn, Emily Jiang, Nevraj S KeJiou, Yifan E Wang, Laura Farlam-Williams, Alexander F Palazzo, Hyun O Lee.
      mRNA-based therapeutics are commonly produced through T7 RNA Polymerase-mediated in vitro transcription. Introducing these exogenous RNAs into human cells activates an RNA sensor Protein Kinase R (PKR), which suppresses translation initiation and reduces their therapeutic effectiveness. Incorporating uridine analogs into these transcripts prevents PKR activation and translation shutdown, but the underlying mechanism remains unclear. Here, we demonstrate that treating T7 RNA Polymerase-produced transcripts with RNase III, which selectively degrades double-stranded RNA (dsRNA), blocks PKR activation and downstream translation-inhibition events, including eIF2α phosphorylation and stress granule formation in human cells. Interestingly, dsRNAs generated with uridine analogs robustly induce eIF2α phosphorylation and stress granules to the same extent as dsRNA containing uridine. These findings indicate that uridine analogs do not prevent PKR from detecting dsRNA. Instead, we show that uridine analogs decrease the production of T7 RNA Polymerase byproducts, including antisense RNA and dsRNA, which activate PKR and downstream stress responses. Finally, we demonstrate that higher amounts of exogenous RNA, lacking T7 RNA Polymerase byproducts, can induce stress granules independently of PKR and phospho-eIF2α, but dependent on stress granule scaffold proteins G3BP1 and G3BP2. Together, our findings show that uridine analogs mitigate PKR signaling not by blocking mRNA-PKR interactions, but by minimizing dsRNA byproducts from T7 Polymerase transcription. Furthermore, stress granule formation in response to high levels of exogenous RNA can occur through a mechanism that does not depend on PKR but relies on G3BP1 and G3BP2. These insights clarify the role of uridine analogs in PKR activation and may inform future therapeutic RNA design.
    Keywords:  PKR; T7 RNA Polymerase; biomolecular condensates; stress granules; uridine analogs
    DOI:  https://doi.org/10.1261/rna.080481.125
  32. Eur J Med Chem. 2026 Jan 09. pii: S0223-5234(26)00016-4. [Epub ahead of print]306 118571
    Multi-stimuli activated PROTAC prodrug for controlled protein degradation with enhanced therapeutic effects.
    Tianyang Zhou, Yibo Gao, Bohan Ma, Chi Wang, Shan Xu, Xiaoyu Feng, Bin Wang, Yanlin Jian, Lei Li.
      Proteolysis-targeting chimeras (PROTACs) have emerged as a transformative strategy for targeted protein degradation, yet their clinical translation is hindered by systemic toxicity and poor tumor selectivity, leading to dose-limiting side effects. To overcome these limitations, we designed a multi-stimuli-responsive prodrug that enables tumor-selective activation of PROTACs in response to elevated reactive oxygen species (ROS) and glutathione (GSH) in the tumor microenvironment. By masking the hydroxyl group of the VHL ligand with a ROS/GSH-cleavable thioether-urea linker, we developed a PROTAC prodrug that responds to 1O2, HOCl, H2O2, and GSH-key mediators of oxidative stress in tumors. This proof-of-concept was verified by caging BRD4 and AR PROTAC with a methylene blue fluorophore to yield NZ-BRD and NZ-AR. Upon encountering tumor-associated stimuli, these prodrugs underwent efficient activation, releasing functional PROTACs that selectively degraded BRD4 and AR in prostate cancer cells. Intriguingly, the methylene blue liberated during activation served as a self-amplifying photosensitizer, creating a positive feedback loop that boosted 1O2 generation and further enhanced prodrug cleavage. The synergistic effect between PROTAC-mediated protein degradation and photodynamic therapy led to superior antitumor efficacy of PROTAC prodrugs in vitro and in vivo. Our work establishes a spatiotemporally controlled drug activation paradigm that combines precision protein degradation with ROS-amplified activation, presenting a promising approach to mitigate the systemic toxicity associated with conventional PROTAC therapy.
    Keywords:  PROTAC; Photodynamic therapy; Prodrug; Reactive oxygen species (ROS)
    DOI:  https://doi.org/10.1016/j.ejmech.2026.118571
  33. Genome Biol Evol. 2026 Jan 19. pii: evag009. [Epub ahead of print]
    Degradation determinants are abundant in human noncanonical proteins and minor annotated isoforms.
    Claudio Casola, Adekola Owoyemi, Nikolaos Vakirlis.
      The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of thousands of potential novel proteins through ribosome profiling and proteomics. Determining the physiological activity of these noncanonical proteins has proven difficult, because they are encoded by different types of coding regions and tend to share no sequence similarity with canonical polypeptides. Evidence from immunopeptidomic assays combined with a better understanding of the quality control of protein synthesis suggest that many noncanonical proteins may possess low stability in the cellular environment. Here, we tested this hypothesis by analyzing the frequency of multiple sequence features eliciting either proteasomal degradation or autophagy across 91,003 canonical (annotated) protein isoforms and 11,499 noncanonical proteins. Overall, noncanonical proteins were enriched for degradation-related features compared to all canonical proteins. Notably, degradation determinants were also enriched in canonical protein isoforms starting with a non-methionine amino acid. Analyses of original and shuffled sequences showed evidence of selective pressure either against or towards the accumulation of specific degradation signatures only in major isoforms of canonical proteins. However, stability was significantly higher in noncanonical proteins with evidence of phenotypic effects upon knock-out in cell lines. Notably, we found that the C-terminal tail hydrophobicity represents a reliable proxy for degradation propensity with potential applications in identifying functional noncanonical proteins. These findings underscore the critical role of degradation processes in regulating the half-life of noncanonical proteins and demonstrate the power of degradation-associated signatures in discriminating noncanonical genes likely to encode biologically functional molecules.
    Keywords:  cryptic proteins; microproteins; noncanonical ORFs; proteasome; protein degradation
    DOI:  https://doi.org/10.1093/gbe/evag009
  34. Autophagy. 2026 Jan 22.
    C3orf33/MISO regulates mitochondrial homeostasis via mitophagy.
    Jianshuang Li, Wenjun Wang, Li He, Qinghua Zhou.
      Mitochondria maintain homeostasis through dynamic remodeling and stress-responsive pathways, including the formation of specialized subdomains. Peripheral mitochondrial fission generates small MTFP1-enriched mitochondria (SMEM), which encapsulate damaged mtDNA and facilitate its macroautophagic/autophagic degradation. However, the underlying mechanism governing SMEM biogenesis remains unclear. In our recent study, we identified C3orf33/CG30159/MISO as a conserved regulator of mitochondrial dynamics and stress-induced subdomain formation in Drosophila and mammalian cells. C3orf33/MISO is an integral inner mitochondrial membrane (IMM) protein that assembles into discrete subdomains, which we confirm as small MTFP1-enriched mitochondria (SMEM). Mechanistically, C3orf33/MISO promotes mitochondrial fission by recruiting MTFP1 to activate the FIS1-DNM1L pathway while suppressing fusion via OPA1 exclusion. Under basal conditions, MISO is rapidly turned over and contributes to mitochondrial morphology maintenance. Upon specific IMM stresses (e.g. mtDNA damage, OXPHOS dysfunction, cristae disruption), C3orf33/MISO is stabilized, thereby initiating SMEM assembly. These SMEM compartments function as stress-responsive hubs that spatially coordinate IMM reorganization and target damaged mtDNA to the periphery for lysosome-mediated clearance via mitophagy. Together, we address these fundamental gaps by identifying C3orf33/MISO as the key protein that controls SMEM formation to preserve mitochondrial homeostasis under stress.
    Keywords:  Homeostasis; MISO; SMEM; mitochondrial subdomains; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2621110
  35. Nat Commun. 2026 Jan 20. 17(1): 614
    The UFL1-AKT positive feedback loop promotes breast cancer progression by enhancing lipid synthesis.
    Fei Meng, Yating Du, Junjie Liang, Huiyan Li, Jingjing Wang, Kexin Tang, Ruixue Kong, Huanran Sun, Tingting Yin, Junru Qin, Xiaomeng Yang, Changliang Shan, Min Liu, Guiwen Yang, Jichun Zhang, Yijie Wang, Jun Zhou, Yan Chen.
      UFMylation, a ubiquitin-like modification, is crucial for cellular processes and is linked to human diseases, including cancer. However, its role in cancer remains unclear. Here, we report that UFL1 promotes breast tumor growth by remodeling lipid metabolism. Mechanistically, UFL1 interacts with and UFMylates AKT, enhancing its localization at the endoplasmic reticulum and phosphorylation by PDK1 and mTORC2, thereby increasing AKT-mediated lipid synthesis. Moreover, AKT phosphorylates UFL1, boosting its activity. Thus, UFL1 and AKT form a positive feedback loop, accelerating lipid synthesis and breast tumor growth. Clinically, UFL1 levels are increased in human breast tumors and are associated with poor clinical outcomes in breast cancer patients. Importantly, UFMylation inhibitors sensitize breast cancer cells to AKT inhibitors and anticancer drugs. Our findings reveal a critical role for UFMylation in lipid metabolism and identify the UFL1-AKT axis as a potential therapeutic target in breast cancer.
    DOI:  https://doi.org/10.1038/s41467-026-68492-3
  36. Nat Commun. 2026 Jan 22.
    Silencing lipid catabolism determines longevity in response to fasting.
    Lexus Tatge, Juhee Kim, Rene Solano Fonseca, Kyle Feola, Jordan M Wall, Gupse Otuzoglu, Ann C Johnson, Kielen R Zuurbier, Jaeyoung Oh, Shaghayegh T Beheshti, Victor A Lopez, Anthony J Daley, Emma G Werner, Patrick Metang, Sonja L B Arneaud, Abigail Watterson, Jeffrey G McDonald, Vincent S Tagliabracci, Michael E French, Peter M Douglas.
      Oscillations between lipid anabolism and catabolism are essential for maintaining cellular health during metabolic fluctuations. Fasting, a conserved determinant of aging, improves disease outcomes and extends lifespan, yet the relative contributions of lipid catabolism versus its attenuation to fasting-induced longevity remain unresolved. The metabolic flexibility of C. elegans under variable nutrient availability provides a powerful system to address this question. We show that lifespan extension from fasting depends not on sustained activation of lipid catabolism, but on its silencing upon nutrient replenishment. The fasting-responsive nuclear hormone receptor NHR-49 activates β-oxidation; however, unlike classical ligand-regulated receptors, NHR-49 is regulated through ligand-independent mechanisms involving cofactor-mediated transcriptional attenuation and protein turnover. We identify casein kinase 1 alpha 1 (KIN-19) as a key regulator of metabolic plasticity and fasting-induced longevity that silences β-oxidation via primed phosphorylation of NHR-49. Thus, cooperative ligand-independent silencing of this conserved nuclear hormone receptor promotes fasting-associated longevity.
    DOI:  https://doi.org/10.1038/s41467-026-68764-y
  37. FASEB J. 2026 Jan 31. 40(2): e71336
    UFMylation at the Crossroads of Health and Cancer: A Blessing in Disguise.
    Congcong Li, Daixing Zhong, Yuqian Ma, Ruiqi Sun, Jia Chen, Qinhao Wang, Lintao Jia, Xia Li, Yi Ru.
      Despite its similarity in structural basis with ubiquitin system, UFMylation, an emerging ubiquitin-like (UBL) posttranslational modification, is characterized by covalent conjugation of Ubiquitin-fold modifier 1 (UFM1) to the target proteins, which can regulate diverse cellular processes to maintain cellular homeostasis. Growing evidence has revealed that UFMylation is associated with developmental disorders, tumorigenesis, heart failure and inflammation. Here, we highlight a comprehensive advance in the components and the biochemical peculiarities of UFMylation system, as well as its pathophysiological roles in cancer. Then the potential of chemicals targeting UFMylation for cancer therapy is discussed.
    Keywords:  UFMylation; targeted drug; tumorigenesis; ubiquitin‐like protein
    DOI:  https://doi.org/10.1096/fj.202501039R
  38. Nucleic Acids Res. 2026 Jan 22. pii: gkag022. [Epub ahead of print]54(3):
    ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing.
    Rodrigo Alarcon, Daniel Köster, Stine Behrmann, Zoya Ignatova.
      Transfer RNAs (tRNAs) play an essential role in protein synthesis and cellular homeostasis, and their dysregulation is associated with various human pathologies. Recent advances in direct RNA sequencing by the Nanopore platform have enabled simultaneous profiling of tRNA abundance, modifications, and aminoacylation status. However, the high sequence similarity among tRNAs and the lack of robust demultiplexing strategies reduce the accuracy and limit the scalability of current approaches. Here, we developed ADAM-tRNA-seq, a framework that addresses two key limitations of the Nanopore-based direct tRNA sequencing. First, we develop an RNA-based barcode demultiplexing method, that employs a barcode embedded in the sequencing adapter, recognized by the Dorado basecaller. Second, we designed a hierarchy-based mapping strategy that mitigates read loss due to multimapping by classifying reads at the isodecoder, isoacceptor, or isotype levels, thereby enhancing quantification accuracy. We validated ADAM-tRNA-seq using both synthetic tRNAs and a complex human tRNA pool, and systematically optimized it to achieve up to 99% classification precision. Together, these developments enable more accurate, scalable, and comprehensive characterization of tRNA pools across diverse sample types.
    DOI:  https://doi.org/10.1093/nar/gkag022
  39. Cell Syst. 2026 Jan 21. pii: S2405-4712(25)00341-2. [Epub ahead of print]17(1): 101508
    Predicting protein interfaces in the age of AlphaFold: Why dynamics and disorder remain a challenge.
    Alireza Omidi, Jennifer M Bui, Jörg Gsponer.
      Two recent studies in Cell Systems show why protein dynamics matter for prediction. By moving beyond static structures and embracing the dynamic "jigglings and wigglings" that Richard Feynman famously described, these approaches improve accuracy in binding site predictions for flexible systems despite challenges such as sparse training data. Together, they signal a shift toward models that try to capture the full energy landscape, paving the way for deeper insights into protein function.
    DOI:  https://doi.org/10.1016/j.cels.2025.101508
  40. Proc Natl Acad Sci U S A. 2026 Jan 27. 123(4): e2515691123
    BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions.
    Mariana E G de Araujo, Sascha J Amann, Taras Stasyk, Alexander Schleiffer, Eva Rauch, Paula Flümann, Isabel I Singer, Leopold Kremser, Vojtech Dostal, Thanida Laopanupong, Nikolaus Obojes, Moritz H Wallnöfer, Flora S Gradl, Robert Kurzbauer, Caroline Krebiehl, Samuel Kofler, Irina Grishkovskaya, Georg F Vogel, Michael W Hess, Bettina Sarg, Tim Clausen, David Haselbach, Lukas A Huber.
      BORC and BLOC-1 are multisubunit complexes that regulate endolysosomal trafficking. Although they are presumed to be distinct, their paralogous origins and shared subunits suggest the potential for higher-order assembly. Here, we reveal the conserved octameric architecture of BORC formed by two intertwined tetramers and present the structure of C. elegans BORC. Through cross-linking mass spectrometry of endogenous complexes, we validate this model for human BORC and demonstrate that the integrity of the complex, which is essential for lysosomal transport, relies on specific interfacial residues. We also clarify the disruptive nature of disease-causing mutations and propose that the formation and function of BORC are likely regulated by specific cues. These cues might include the phosphorylation of Snapin and a pH-sensitive histidine residue in BORCS5. Additionally, we present direct biochemical and structural evidence of BORC-BLOC-1 hybrid complexes. Finally, we link a specific hybrid complex to the regulation of transferrin receptor recycling via interaction with the EARP complex. Our work challenges the paradigm of BORC and BLOC-1 as separate entities, establishing a model of dynamic complex formation wherein modular assembly creates functional specialization to meet diverse cellular demands.
    Keywords:  BLOC-1; BORC; EARP; lysosome; recycling endosome
    DOI:  https://doi.org/10.1073/pnas.2515691123
  41. Free Radic Biol Med. 2026 Jan 16. pii: S0891-5849(26)00033-X. [Epub ahead of print]
    UBR4 Attenuates Cisplatin-Induced Acute Kidney Injury by Regulating the HRI-ISR Axis.
    Zeyu Tang, Chen Li, Cheng Yang, Xinghua Chen, Maoqing Tian, Liwen Qiao, Jiefei Zeng, Wenjing Zhen, Wei Liang, Lunzhi Liu, Huiming Wang, Xiangyou Li, Lu Zhang.
      Cisplatin is widely used in treating solid tumors, but its dose-limiting nephrotoxicity, which manifests as acute kidney injury (AKI), remains a major clinical challenge. The molecular pathways determining proximal tubular epithelial cell (PTEC) susceptibility during cisplatin-induced injury are not fully elucidated. Here, we identify ubiquitin protein ligase E3 component n-recognin 4 (UBR4) as a key regulator of the integrated stress response (ISR), which plays an important role in regulating reactive oxygen species (ROS) accumulation and mitophagy in the kidney. UBR4 expression was markedly upregulated in PTECs of mice with cisplatin-induced AKI. Tubule-specific Ubr4 deficiency exacerbated kidney dysfunction, tubular damage, and cell death. Mechanistically, UBR4 promoted ubiquitination and degradation of the kinase HRI, thereby constraining ISR overactivation and alleviating its inhibitory effect on mitophagy. Consistent with this mechanism, both genetic enhancement of UBR4 and pharmacological inhibition of the ISR with ISRIB significantly mitigated cisplatin-induced nephrotoxicity. Together, our findings uncover a previously unrecognized UBR4-HRI-ISR regulatory axis that serves as an intrinsic protective mechanism in the kidney and highlight UBR4 as a promising therapeutic target for preventing cisplatin-induced tubular injury.
    Keywords:  HRI; UBR4; acute kidney injury; integrated stress response; mitophagy
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.01.025
  42. JCI Insight. 2026 Jan 23. pii: e182809. [Epub ahead of print]11(2):
    The critical role of GRP78/BiP MARylation in ER stress of KRAS-mutant colorectal cancer.
    Shuxian Zhang, Xiaodan Chen, Qian Gong, Jing Huang, Yi Tang, Ming Xiao, Ming Li, Qingshu Li, Yalan Wang.
      Nearly 50% of patients with KRAS-mutant colorectal cancer (CRC) currently lack effective targeted therapy. The accumulation of KRAS-mutant proteins can trigger a sustained high level of endoplasmic reticulum (ER) stress, and the UPR-based long-term protective regulatory pathway inhibits the aggregation of unfolded proteins, thereby maintaining the stability of the ER and enabling the continued survival of KRAS-mutant tumors. However, the critical factors that affect the regulation of ER homeostasis in KRAS-mutant CRC are still unclear. Mono-ADP ribosylation (MARylation) catalyzed by ART1 is the most important modification of GRP78/BiP and stabilizes the internal environment of the ER. In this study, KRAS mutation increased the levels of ART1, ER stress, and MARylated GRP78/BiP in CRC cells. Inhibiting MARylated GRP78/BiP can impede the downstream IRE1α/XBP1/TFAF2/JNK and PERK/eIF2α/ATF4 cascades by affecting the binding and dissociation of GRP78/BiP with receptors to hinder the growth of KRAS-mutant CRC cells and accelerate their apoptosis. We propose that KRAS-mutant CRC cells are more sensitive to intervention with MARylated GRP78/BiP because more modifications are needed to maintain ER stability. We also conducted a preliminary study on the specific site of function. Clarifying this molecular mechanism can provide a experimental basis for identifying effective targets for the intervention of KRAS-mutant CRC.
    Keywords:  Cell biology; Cell stress; Colorectal cancer; Gastroenterology; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.182809
  43. Cell. 2026 Jan 16. pii: S0092-8674(25)01420-5. [Epub ahead of print]
    Multimodal supramolecular targeting chimeras enable spatiotemporally resolved protein degradation in vivo.
    Ji Liu, Tianyu Ma, Rui Yao, Lijuan Li, Qizhen Zheng, Ming Wang.
      Targeted protein degradation (TPD) has transformed strategies for modulating protein function in both basic biology and therapeutic development. However, current strategies often lack the spatial and temporal precision required for in vivo applications. Herein, we report supramolecular targeting chimeras (SupTACs), a modular and programmable platform that enables tissue-specific and temporally controlled protein degradation in vivo. SupTACs self-assemble into supramolecular nanoparticles (SNPs) that co-localize target-binding ligands and E3 ligase recruiters, thereby facilitating proteasomal degradation through multivalent supramolecular proximity. This strategy achieves robust and tissue-specific degradation, including liver and lung specificity, in multiple species up to non-human primates. As a proof of concept, lung-specific degradation of acyl-coenzyme A (CoA) synthetase long-chain family member 4 (ACSL4) using SupTACs effectively mitigates ferroptosis and pulmonary inflammation in a murine model of acute lung injury. By integrating modularity, tissue specificity, and temporal regulation, SupTACs establish a versatile platform for precise control of protein degradation for interrogating dynamic signaling networks and developing targeted therapeutics.
    Keywords:  PROTAC; bio-orthogonal activation; delivery; ferroptosis; in vivo protein degradation; lung inflammation; spatiotemporal; supramolecular nanoparticles; targeted protein degradation; tissue specific
    DOI:  https://doi.org/10.1016/j.cell.2025.12.007
  44. Cell Commun Signal. 2026 Jan 20.
    Peripheral lysosome levels dictate mTORC1 inactivation even when catabolically impaired.
    Huy Quang Dang, Therése Forssén, Spyridon Pantelios, Aisegkioul Nteli Chatzioglou, Ewa Kurzejamska, C Theresa Vincent, Yasir Ibrahim, Anders P Mutvei.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a central driver of cell growth that is frequently hyperactivated in cancer. While mTORC1 is activated at the lysosomal surface in response to growth factors and amino acids, the processes governing its inactivation are not fully understood. Here, we report that sustained mTORC1 suppression during leucine or arginine starvation requires the translocation of peripheral lysosomes to the perinuclear region. Our data suggest that a pool of mTOR remains active at peripheral lysosomes during starvation, and that increased spatial separation between lysosomes and the plasma membrane attenuates PI3K/Akt signaling-thereby reducing inputs that otherwise maintain mTORC1 activity. Consequently, preventing lysosome translocation and increasing peripheral lysosome levels sustains mTORC1 signaling during prolonged starvation in a PI3K/Akt-dependent manner independently of autophagy. Under these conditions, mTORC1 signaling persists even when lysosomal catabolism is perturbed by chloroquine or concanamycin A. Collectively, these data indicate that the peripheral lysosome pool, even when catabolically impaired, can sustain mTORC1 signaling under nutrient scarcity, by modulating PI3K/Akt signaling input to the pathway. These observations identify peripheral lysosome levels as a critical determinant of mTORC1 inactivation during nutrient stress and may have implications for diseases with aberrant mTORC1 signaling, including cancer.
    Keywords:  Amino acid deprivation; Catabolically impaired lysosomes; Lysosome positioning; MTORC1; PI3K-Akt signaling; Rab7; Rap1
    DOI:  https://doi.org/10.1186/s12964-026-02659-9
  45. FEBS Lett. 2026 Jan 23.
    ERLIN2-Ca2+-CREB signaling coordinates circadian timing via CRY1/CRY2 feedback.
    Yuwen Chen, Jiaxin Lin, Zongyou Zou, Zuo-Qin Yan, Ruizhe Qian, Chao Lu, Bingxuan Hua.
      Circadian regulation in peripheral cells depends on calcium dynamics, but the upstream mechanisms remain unclear. We identify endoplasmic reticulum lipid raft-associated protein 2 (ERLIN2) as a regulator of the peripheral clock. Knockdown and overexpression of ERLIN2 in C2C12 skeletal muscle cells show that ERLIN2 positively regulates cryptochrome circadian regulator 1/2 (CRY1/2) transcription and maintains rhythmicity. ERLIN2 regulates inositol 1,4,5-trisphosphate receptor (IP3R)-mediated Ca2+ release and activates the calcium/calmodulin-dependent protein kinase II (CaMKII)-mitogen-activated protein kinase (MAPK)-cAMP response element-binding protein (CREB) pathway. ATP induced IP3R-dependent Ca2+ transients, CREB phosphorylation, and Per1 expression, reshaping circadian rhythm, effects blocked by IP3R, Ca2+, or CaMKII inhibition. CRY1 enhances and CRY2 suppresses CREB signaling, establishing a feedback loop with ERLIN2. This ERLIN2-Ca2+-CREB-CRY1/2 axis couples membrane contact sites to circadian regulation. Impact statement This study reveals ERLIN2 as a key regulator linking calcium signaling to circadian rhythms, establishing an ERLIN2-Ca2+-CREB-CRY1/2 axis that advances understanding of cellular clock control.
    Keywords:  CREB pathway; CRY1/CRY2 feedback; ERLIN2; calcium signaling; circadian rhythm
    DOI:  https://doi.org/10.1002/1873-3468.70291
  46. Ageing Res Rev. 2026 Jan 18. pii: S1568-1637(26)00019-X. [Epub ahead of print] 103027
    Proteolysis-targeting chimera (PROTAC): a promising senolytic strategy.
    Gang Fan, Qingping Zhang, Weiming Guo, Miao Liu, Dong Tan, Zhihan Tang, Jing Yang.
      Senescent cells (SCs) accumulate with aging and contribute to the development of age-related pathologies. These cells evade apoptosis through upregulation of senescent cell anti-apoptotic pathways (SCAPs), making their selective elimination, a strategy termed senolysis, a promising therapeutic avenue. Proteolysis-targeting chimeras (PROTACs) represent an emerging class of bifunctional molecules that exploit the ubiquitin-proteasome system to degrade specific target proteins. By concurrently binding a protein of interest and an E3 ubiquitin ligase, PROTACs catalyze the degradation of SCAP components, offering a novel pharmacological approach to clear SCs. This review summarizes the principles and recent advances in PROTAC technology, with a focus on its application as a senolytic strategy. We highlight how PROTACs can overcome limitations of conventional inhibitors, such as targeting "undruggable" SCAP proteins, and provide a comparative analysis of major PROTAC classes targeting BCL-2 family members, p53, BRD4, SA-β-gal, and other emerging senescence regulators. Furthermore, we also discuss the aging-specific biological and translational challenges, including altered proteasomal activity, pharmacokinetics, tissue microenvironment, and immune clearance, that must be addressed to advance PROTAC senolytics toward clinical use in age-related diseases.
    Keywords:  Senescent cells; Senolysis，PROTAC; Targeted protein degradation
    DOI:  https://doi.org/10.1016/j.arr.2026.103027
  47. Mol Immunol. 2026 Jan 20. pii: S0161-5890(26)00009-X. [Epub ahead of print]190 101-109
    Inhibition of RNase L enhances the expression efficiency of mRNA-LNPs.
    Hong-My Nguyen, Britteny Cassaidy, Mark Collinge, James C Hickey, Jin Li, Amir Arellano-Saab, Steven W Kumpf, Mitchell Thorn.
      mRNA-LNPs offer a promising platform for therapeutic protein expression, however, achieving efficient and sustained translation remains a significant challenge. One of the major barriers to mRNA-LNP efficacy is the activation of innate immune responses that recognize foreign RNA and suppress subsequent protein synthesis. Among these, the OAS-RNase L pathway, involved in degradation of cytoplasmic mRNA, plays a key role. This study examined the impact of RNase L and RNase L blockade on mRNA-LNP expression efficiency. In THP-1 cells, which express high endogenous levels of RNase L, both genetic ablation and pharmacological inhibition of RNase L led to a marked increase in protein expression. In contrast, HeLa cells, which exhibit low RNase L expression, showed minimal response to RNase L inhibition. In human peripheral blood mononuclear cells (PBMCs), RNase L inhibition also enhanced mRNA expression, while blocking other RNA sensors such as TLR7/8, RIG-I, TLR3, or MAVS, did not. Activation of the OAS-RNase L pathway may be driven by double-stranded secondary structure formed by therapeutic mRNA, resulting in mRNA recognition and degradation. RNase L acts as a key post-transcriptional regulator of mRNA stability and translation. Targeting this pathway offers a strategy to improve the performance of mRNA-based therapeutics.
    Keywords:  2-5 A; DsRNA; Innate immunity; Lipid nanoparticles (LNPs); MRNA-LNPs; OAS-RNase L pathway; Protein translation; RNA degradation; RNA medicine; RNase L
    DOI:  https://doi.org/10.1016/j.molimm.2026.01.003
  48. Nat Commun. 2026 Jan 21.
    Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.
    Aaron Wacholder, Eric W Deutsch, Leron W Kok, Jip T van Dinter, Jiwon Lee, James C Wright, Sebastien Leblanc, Ayodya H Jayatissa, Kevin Jiang, Ihor Arefiev, Kevin Cao, Francis Bourassa, Felix-Antoine Trifiro, Michal Bassani-Sternberg, Pavel V Baranov, Annelies Bogaert, Sonia Chothani, Ivo Fierro-Monti, Daria Fijalkowska, Kris Gevaert, Norbert Hubner, Jonathan M Mudge, Jorge Ruiz-Orera, Jana Schulz, Juan Antonio Vizcaíno, John R Prensner, Marie A Brunet, Thomas F Martinez, Sarah A Slavoff, Xavier Roucou, Jyoti S Choudhary, Sebastiaan van Heesch, Robert L Moritz, Anne-Ruxandra Carvunis.
      Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist.
    DOI:  https://doi.org/10.1038/s41467-025-68002-x
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