bims-proteo Biomed News
on Proteostasis
Issue of 2025–11–16
forty-six papers selected by
Eric Chevet, INSERM
  1. Termination of the integrated stress response.
  2. GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome.
  3. Degrons and degradation signals beyond short linear motifs.
  4. A retrograde, non-canonical integrated stress response cascade maintains synaptic strength under amino acid deprivation.
  5. Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B.
  6. MARK2 regulates C9orf72 repeat-associated non-AUG translation.
  7. Ca2+-driven PDIA6 biomolecular condensation ensures proinsulin folding.
  8. YTHDF2 regulates self non-coding RNA metabolism to control inflammation and tumorigenesis.
  9. Autophagy-dependent modulation of ER calcium release drives KCNMA1/BKCa signaling and seizure susceptibility.
  10. Biomolecular condensation of ERC1 recruits ATG8 and NBR1 to drive autophagosome formation for plant heat tolerance.
  11. Biomolecular Condensates in and Around the ER-Golgi Interface.
  12. Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response.
  13. Development of a targeted BioPROTAC degrader selective for misfolded SOD1.
  14. Stress changes the material state of a bacterial biomolecular condensate and shifts its function from mRNA decay to storage.
  15. Anle138b mitigates post-hypoxic cognitive impairment, α-Synuclein aggregation and UPR activation in Drosophila melanogaster.
  16. ERLIN1: A central regulator of protein quality control, lipid homeostasis, and cellular signaling at the endoplasmic reticulum.
  17. Monitoring the complexity and dynamics of mitochondrial translation.
  18. Branching beyond bifunctional linkers: synthesis of macrocyclic and trivalent PROTACs.
  19. Ist2 promotes lipid transfer by Osh6 via its membrane tethering and lipid scramblase activities.
  20. mTORC1 regulates autophagosomal components recycling through SNX16 phosphorylation.
  21. Investigating NFE2L1 activators for targeted protein aggregate clearance: a follow-up study.
  22. Non-catalytic UBL2 domain directs deubiquitinase USP11 toward K48-linked polyubiquitin chains.
  23. Molecular grammars of predicted intrinsically disordered regions that span the human proteome.
  24. Endoplasmic reticulum quality control and metal tolerance: reduced activity of glucosidase II enzyme affects positively cadmium tolerance in Arabidopsis thaliana.
  25. Alternative start codon selection shapes mitochondrial function and rare human diseases.
  26. UBQLN2 is necessary for UBE3A-mediated proteasomal degradation of the domesticated retroelement PEG10.
  27. Shotgun Approach for PROTAC Ternary Complex Modeling and Evaluation.
  28. Membrane-mimetic thermal proteome profiling (MM-TPP) toward mapping membrane protein-ligand dynamic interactions.
  29. Inducible tag-free degradation of endogenous proteins with AlissAID and development of a photoactivable inducer.
  30. How Feasible Is Docking of PROTACs to POI-E3L Complexes? Testing Physics-Based and ML-Based Docking Tools.
  31. Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons.
  32. Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome.
  33. LUBAC modulates CBM complex functions downstream of TRAF6 in T cells.
  34. Nonsense-mediated mRNA decay: a key regulatory system engaged in cancer.
  35. A cascade of structural rearrangements positions peptide release factor 2 for polypeptide hydrolysis on the ribosome.
  36. An engineered cysteine sensor optimized for high-throughput screening identifies regulators of intracellular thiol levels.
  37. Heat shock protein DNAJA2 controls insulin signaling and glucose homeostasis by preventing spontaneous insulin receptor endocytosis.
  38. Mechanistic insights into cargo sorting and export from the Golgi apparatus.
  39. Programmable DNA Nanospheres for Photothermal-Controlled Intracellular Protein Degradation.
  40. ER stress sensor PERK drives ferroptosis by disrupting MAMs-mediated mitochondrial homeostasis and promoting mtROS accumulation in acute myocardial infarction.
  41. An adversarial scheme for integrating multi-modal data on protein function.
  42. Palmitate impairs autophagic degradation via oxidative stress-perilysosomal Ca2+ overload-mTORC1 activation in pancreatic β-cells.
  43. Deep generative optimization of mRNA codon sequences for enhanced mRNA translation and therapeutic efficacy.
  44. StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models.
  45. The mechanism of pathogenic α1-antitrypsin aggregation in the human liver.
  46. Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease.
  1. Science. 2025 Nov 13. eadw5137
    Termination of the integrated stress response.
    Claudia De Miguel, Sigurdur R Thorkelsson, Agnieszka Fatalska, George Hodgson, Chao Wang, Anne Bertolotti.
      Stress responses enable cells to detect, adapt to, and survive challenges. The benefit of these signaling pathways depends on their reversibility. The integrated stress response (ISR) is elicited by phosphorylation of translation initiation factor eIF2, which traps and inhibits rate-limiting translation factor eIF2B thereby attenuating translation initiation. Termination of this pathway thus requires relieving eIF2B from P-eIF2 inhibition. Here, we found that eIF2 phosphatase subunits PPP1R15A and PPP1R15B (R15B) bound P-eIF2 in complex with eIF2B. Biochemical investigations guided by cryo-EM structures of native eIF2-eIF2B and P-eIF2-eIF2B complexes bound to R15B demonstrated that R15B enabled dephosphorylation of otherwise dephosphorylation-incompetent P-eIF2 on eIF2B. This sheds light on ISR termination, revealing that R15B rescues eIF2B from P-eIF2 inhibition, thereby safeguarding translation and cell fitness.
    DOI:  https://doi.org/10.1126/science.adw5137
  2. Nat Commun. 2025 Nov 13. 16(1): 9976
    GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome.
    Alžběta Roeselová, Sarah L Maslen, Jessica Zhiyun He, Gabija Jurkeviciute, Aleksandra Pajak, J Mark Skehel, Radoslav I Enchev, David Balchin.
      The bacterial chaperonin GroEL/ES promotes protein folding post-translation by transiently encapsulating client proteins within a central chamber. GroEL also binds translating ribosomes in vivo, implying an additional role in cotranslational folding. However, how GroEL/ES recognises and modulates ribosome-tethered nascent proteins is unclear. Here, we used biochemical reconstitution, structural proteomics and electron microscopy to study the mechanism by which GroEL/ES engages nascent polypeptides. We show that GroEL binds nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails, resulting in local structural destabilization of the client. Ribosome-tethered nascent domains are partially encapsulated upon GroES binding to GroEL, and recover their original conformation in the chaperonin cavity. Reconstitution of chaperone competition at the ribosome shows that both Trigger factor and GroEL can be accommodated on long nascent chains, but GroEL and DnaK are mutually antagonistic. Our findings extend the role of GroEL/ES in de novo protein folding, and reveal a plasticity of the chaperonin mechanism that allows cotranslational client encapsulation.
    DOI:  https://doi.org/10.1038/s41467-025-64968-w
  3. Nat Chem Biol. 2025 Nov 14.
    Degrons and degradation signals beyond short linear motifs.
    Baiyun Wang, Ning Zheng.
      Ubiquitin-dependent protein degradation regulates myriad fundamental cellular processes. At its core are degradation signals, or degrons, that initiate substrate engagement and ubiquitination by E3 ubiquitin ligases. Here we highlight how a variety of degradation signals promote substrate-E3 ligase interactions to orchestrate protein turnover with precision. While short linear motifs are frequently identified as degrons, an increasing number of degrons have recently been mapped to high-order protein structures, underscoring the architectural diversity and cryptic nature of degradation signals. Furthermore, nonproteinaceous signals beyond degrons often facilitate the precise control of protein ubiquitination. These additional signals can reside within substrates and E3 ligases or at their interfaces. Finally, we discuss how dysregulation of degrons and degradation signals is linked to human diseases. A deeper mechanistic understanding of degradation signals will guide new therapeutic strategies, whether by restoring defective protein ubiquitination or by harnessing targeted protein degradation.
    DOI:  https://doi.org/10.1038/s41589-025-02056-2
  4. Cell Rep. 2025 Nov 07. pii: S2211-1247(25)01293-8. [Epub ahead of print]44(11): 116522
    A retrograde, non-canonical integrated stress response cascade maintains synaptic strength under amino acid deprivation.
    Megumi Mori, Grant Kauwe, Ammar Aly, Edward H Liao, Gary Scott, A Pejmun Haghighi.
      Neuronal response to changes in nutrient availability is critical for maintaining metabolic homeostasis and organismal survival. Nevertheless, we know little about the molecular players that regulate and maintain neurotransmission under nutritional stress. We demonstrate that, under acute amino acid restriction, the maintenance of normal synaptic strength at the Drosophila larval neuromuscular junction critically depends on the integrated stress response (ISR) machinery. Our findings indicate that amino acid restriction triggers a non-canonical ISR cascade in muscle via GCN2 and eIF2α phosphorylation but independently of ATF4. We have identified Still life (Sif), an ortholog of human TIAM1, as a translational target of the ISR and show that it is required in muscle for mediating the action of the ISR. Our results reveal an intricate non-canonical ISR signaling cascade at the synapse and offer a new framework to separate the role of the ISR in proteostasis from its synaptic actions.
    Keywords:  CP: metabolism; CP: neuroscience; GCN2; amino acid sensing; eIF2alpha; integrated stress response; presynaptic release; regulation of translation; retrograde signaling; synaptic set point
    DOI:  https://doi.org/10.1016/j.celrep.2025.116522
  5. Protein Sci. 2025 Dec;34(12): e70365
    Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B.
    Jade M Katinas, Kangsa Amporndanai, Ashley J Taylor, Kristie L Rose, Peter C Gareiss, Roberto A Crespo, Jason Phan, Alex G Waterson, Stephen W Fesik.
      Targeted protein degradation using PROTACs (PROteolysis TArgeting Chimeras) has emerged as a transformative therapeutic strategy, largely relying on a small number of E3 ubiquitin ligases such as CRBN and VHL. However, resistance, toxicity, and poor oral bioavailability limit the utility of PROTACs and highlight the need to expand the E3 ligase toolbox. Fem-1 homolog B (FEM1B) is a lesser-known E3 ligase that offers a promising alternative due to its broad expression and ability to recognize diverse degron motifs. Here, we describe the development of a stable construct of FEM1B, the results of a protein-observed NMR-based fragment screen using this construct, and the X-ray structures of some of the fragment hits when bound to the protein. From these results, new PROTACs utilizing FEM1B as the E3 ligase may be discovered, providing an alternative E3 ligase for targeted protein degradation.
    Keywords:  1H‐13C‐SOFAST HMQC; E3 ligase; Fem‐1 homolog B (FEM1B); NMR; X‐ray crystal structure; construct design; fragment screen
    DOI:  https://doi.org/10.1002/pro.70365
  6. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2514182122
    MARK2 regulates C9orf72 repeat-associated non-AUG translation.
    Yu-Ning Lu, Xiangning Li, Lindsey Hayes, Xiao-Feng Zhao, Jiou Wang.
      Protein homeostasis is exquisitely regulated through processes involving protein synthesis essential for cellular health and disease prevention. Repeat-associated non-AUG (RAN) translation at expanded GGGGCC repeats in the C9orf72 gene produces dipeptide repeat (DPR) proteins that are implicated in amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). However, the mechanisms promoting this noncanonical translation remain incompletely understood. Here, we identify microtubule affinity-regulating kinase 2 (MARK2) as a key eIF2α kinase that enhances RAN translation under proteotoxic stress. We show that MARK2-eIF2α signaling, activated by misfolded proteins including DPRs and TDP-43, is upregulated in C9-ALS patient tissues. Loss of MARK2 significantly suppresses RAN translation in reporter cells, patient-derived neurons, and a mouse model and confers neuroprotection under proteotoxic conditions. These findings position MARK2 as a critical stress-sensing cytosolic regulator that promotes repeat-associated noncanonical translation and associated toxicity.
    Keywords:  MARK2; eIF2α; integrated stress response
    DOI:  https://doi.org/10.1073/pnas.2514182122
  7. Nat Cell Biol. 2025 Nov;27(11): 1952-1964
    Ca2+-driven PDIA6 biomolecular condensation ensures proinsulin folding.
    Young-Ho Lee, Tomohide Saio, Mai Watabe, Motonori Matsusaki, Shingo Kanemura, Yuxi Lin, Taro Mannen, Tsubura Kuramochi, Yuka Kamada, Katsuya Iuchi, Michiko Tajiri, Kotono Suzuki, Yan Li, Yunseok Heo, Kotone Ishii, Kenta Arai, Kazunori Ban, Mayuko Hashimoto, Shuichiro Oshita, Satoshi Ninagawa, Yoshikazu Hattori, Hiroyuki Kumeta, Airu Takeuchi, Shinji Kajimoto, Hiroya Abe, Eiichiro Mori, Takahiro Muraoka, Takakazu Nakabayashi, Satoko Akashi, Tsukasa Okiyoneda, Michele Vendruscolo, Kenji Inaba, Masaki Okumura.
      The endoplasmic reticulum (ER) plays crucial roles in maintaining protein quality control and regulating dynamic Ca2+ storage in eukaryotic cells. However, the proteostasis system involved in ER-mediated protein quality control has not been fully characterized. Here we show that Ca2+ triggers the condensation of PDIA6, an ER-resident disulfide isomerase and molecular chaperone, into quality control granules. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the PDIA6 condensates recruit proinsulin, thereby accelerating the oxidative proinsulin folding and suppressing the proinsulin aggregation inside quality control granules, essential for secretion of insulin.
    DOI:  https://doi.org/10.1038/s41556-025-01794-8
  8. Nat Commun. 2025 Nov 12. 16(1): 9946
    YTHDF2 regulates self non-coding RNA metabolism to control inflammation and tumorigenesis.
    Seungwon Yang, Yan-Hong Cui, Haixia Li, Jiangbo Wei, Gayoung Park, Ming Sun, Michelle Verghese, Emma Wilkinson, Teresa Nam, Linnea Louise Lungstrom, Xiaolong Cui, Tae Young Ryu, Jing Chen, Marc Bissonnette, Chuan He, Yu-Ying He.
      The role of m6A RNA methylation of self non-coding RNA remains poorly understood. Here we show that m6A-methylated self U6 snRNA is recognized by YTHDF2 to reduce its stability and prevent its binding to Toll-like receptor 3 (TLR3), leading to decreased inflammatory responses in human and mouse cells and mouse models. At the molecular level, endosomal U6 snRNA binds to the LRR21 domain in TLR3, independent of m6A methylation, to activate inflammatory gene expression, a mechanism that is distinct from that of the best known synthetic TLR3 agonist poly I:C. Both U6 snRNA and YTHDF2 are localized to endosomes via the transmembrane protein SIDT2, where YTHDF2 functions to prevent the U6-TLR3 interaction. We further show that UVB exposure inhibits YTHDF2 by inducing its dephosphorylation and autophagic protein degradation in human keratinocytes and mouse skin. Skin-specific deletion of Ythdf2 in mice enhanced the UVB-induced skin inflammatory response and promoted tumor initiation. Taken together, our findings demonstrate that YTHDF2 plays a crucial role in controlling inflammation by inhibiting m6A U6-mediated TLR3 activation, suggesting that YTHDF2 and m6A U6 are potential therapeutic targets for preventing and treating inflammation and tumorigenesis.
    DOI:  https://doi.org/10.1038/s41467-025-64898-7
  9. Autophagy. 2025 Nov 10. 1-3
    Autophagy-dependent modulation of ER calcium release drives KCNMA1/BKCa signaling and seizure susceptibility.
    Gaga Kochlamazashvili, Marijn Kuijpers.
      Macroautophagy/autophagy is best known for its role in maintaining cellular homeostasis through degradation of damaged proteins and organelles. In neurons, autophagy also contributes to the regulation of activity by adjusting the availability of cellular components to physiological demand. In a recent study, we show that autophagy shapes neuronal excitability by restraining a calcium-dependent pathway that couples endoplasmic reticulum calcium release to KCNMA1/BKCa activity at the plasma membrane. When autophagy is lost, this pathway is enhanced, and seizure susceptibility increases.
    Keywords:  Autophagy; BKCa; ERphagy; axon; calcium; endoplasmic reticulum; epilepsy; excitability; neuron; ryanodine receptor
    DOI:  https://doi.org/10.1080/15548627.2025.2580436
  10. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2425689122
    Biomolecular condensation of ERC1 recruits ATG8 and NBR1 to drive autophagosome formation for plant heat tolerance.
    Ka Kit Chung, Kai Ching Law, Ziwei Zhao, Juncai Ma, Xiao-Tong Zhan, Cheuk Him Chiang, Kwan Ho Leung, Ruben Shrestha, Yixin Wu, Chaorui Li, Ka Ming Lee, Lei Feng, Xibao Li, Kam Bo Wong, Shou-Ling Xu, Caiji Gao, Xiaohong Zhuang.
      Macroautophagy (hereafter autophagy) is essential for cells to respond to nutrient deficiency by delivering cytosolic contents to vacuoles for degradation via the formation of a multilayer organelle named an autophagosome. A set of autophagy-related (ATG) regulators are recruited to the phagophore assembly site for phagophore initiation, including its expansion and closure, and subsequent delivery into the vacuole. However, it remains elusive how the phagophore assembly is regulated under different stress conditions. Here, we described an uncharacterized Arabidopsis (Arabidopsis thaliana) ERC (ELKS/Rab6-interacting/CAST) protein family as an interacting partner of ATG8. ERC1 proteins translocate to the phagophore membrane and develop into ring-like autophagosomes upon autophagic induction. Notably, we found that ERC1 proteins possess the ability to assemble into substantial droplets together with ATG8e proteins prior to ATG8 conjugation to the membrane. Through multiscale characterization, we demonstrated that the ERC1 membraneless droplet represents a distinct type of plant condensate. Additionally, ERC1 directly binds to NBR1 to promote NBR1 degradation. ERC1 dysfunction suppresses the turnover of ubiquitinated substrates and compromises plant tolerance to heat stress. Our study suggests a model for autophagic degradation in response to heat stress by the action of ERC1-mediated biomolecular condensation in Arabidopsis.
    Keywords:  ATG8; ERC protein family; NBR1; autophagosome formation; biomolecular condensation
    DOI:  https://doi.org/10.1073/pnas.2425689122
  11. Subcell Biochem. 2026 ;110 221-243
    Biomolecular Condensates in and Around the ER-Golgi Interface.
    Miguel Ruiz, Savannah M Bogus, Andreas M Ernst.
      Biomolecular condensates represent a new paradigm of cytoplasmic organization. In recent years, an increasing amount of evidence suggests that protein condensates can directly impact the morphology and function of membrane compartments. The early secretory pathway, which comprises the ER and Golgi compartments, is emerging as a hotspot for biomolecular condensates. In this chapter, we discuss recent reports suggesting diverse roles for condensates in cargo sorting, regulating membrane traffic, and shaping organelle morphology. This promotes a view in which biomolecular condensates may significantly contribute to defining the anatomy and specific functions of the Golgi and its surrounding membranes.
    Keywords:  Condensates; ER; ER exit sites (ERESs); ER-Golgi interface; Early secretory pathway; Golgi matrix; Liquid-liquid phase separation; Self-organization
    DOI:  https://doi.org/10.1007/978-3-032-06936-8_9
  12. Nucleic Acids Res. 2025 Oct 28. pii: gkaf1072. [Epub ahead of print]53(20):
    Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response.
    Lorenzo Lafranchi, Glancis Luzeena Raja, Alberto M Arenas, Anna Spinner, Kovi R Shrung, Maximilian Hornisch, Dörte Schlesinger, Carmen Navarro Luzon, Linus Brinkenstråhle, Rui Shao, Ilaria Piazza, Janne Lehtiö, Rui M M Branca, Simon J Elsӓsser.
      Microproteins encoded by short open reading frames (sORFs) of <100 codons have been predicted to constitute a substantial fraction of the eukaryotic proteome. However, the relevance and roles of a majority of microproteins remain undefined, as only a small fraction of these intriguing cellular players have been characterized in-depth so far. Here, we use pooled overexpression screens with a library of 11 338 sORFs to overcome the challenge of elucidating which of the thousands of putative translated sORFs are biologically functional. As a proof-of-concept, we performed a phenotypic screen to identify sORFs protecting cells from treatment with the nucleotide analogue 6-thioguanine. With this approach, we identified two cytoprotective microproteins: altDDIT3 and PIPPI. PIPPI is encoded within the LCR16a core duplicon of the Morpheus/NPIP gene cluster. We show that PIPPI modulates the cellular response to protein folding stress in the endoplasmic reticulum (ER) and interacts with proteins in the same pathway, including protein disulfide isomerase ERp44. PIPPI overexpression protects, while PIPPI knockdown sensitizes cells to ER stress. Besides providing mechanistic insights into a new microprotein, this study highlights the power of using pooled overexpression screens to identify functional microproteins.
    DOI:  https://doi.org/10.1093/nar/gkaf1072
  13. Nat Commun. 2025 Nov 10. 16(1): 9713
    Development of a targeted BioPROTAC degrader selective for misfolded SOD1.
    Christen G Chisholm, Rachael Bartlett, Mikayla L Brown, Emma-Jayne Proctor, Natalie E Farrawell, Jody Gorman, Fabien Delerue, Lars M Ittner, Kara L Vine-Perrow, Heath Ecroyd, Neil R Cashman, Darren N Saunders, Luke McAlary, Jeremy S Lum, Justin J Yerbury.
      The accumulation of misfolded proteins underlies a broad range of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Due to their dynamic nature, these misfolded proteins have proven challenging to target therapeutically. Here, we specifically target misfolded disease variants of the ALS-associated protein superoxide dismutase 1 (SOD1), using a biological proteolysis targeting chimera (BioPROTAC) composed of a SOD1-specific intrabody and an E3 ubiquitin ligase. Screening of intrabodies and E3 ligases for optimal BioPROTAC construction reveals a candidate capable of degrading multiple disease variants of SOD1, preventing their aggregation in cells. Using CRISPR/Cas9 technology to develop a BioPROTAC transgenic mouse line, we demonstrate that the presence of the BioPROTAC delays disease progression in the SOD1G93A mouse model of ALS. Delayed disease progression is associated with protection of motor neurons, a reduction of insoluble SOD1 accumulation and preservation of innervated neuromuscular junctions. These findings provide proof-of-concept evidence and a platform for developing BioPROTACs as a therapeutic strategy for the targeted degradation of neurotoxic misfolded species in the context of neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41467-025-65481-w
  14. Nat Commun. 2025 Nov 14. 16(1): 10019
    Stress changes the material state of a bacterial biomolecular condensate and shifts its function from mRNA decay to storage.
    Luis A Ortiz-Rodríguez, Hadi Yassine, Ali Hatami, Vidhyadhar Nandana, Christopher A Azaldegui, Jiayu Cheng, Yingxi Zhu, Jared M Schrader, Julie S Biteen.
      Bacterial ribonucleoprotein bodies (BR-bodies) are dynamic biomolecular condensates that play a pivotal role in RNA metabolism. We investigated how BR-bodies significantly influence mRNA fate by transitioning between liquid- and solid-like states in response to stress. With a combination of single-molecule and bulk fluorescence microscopy, biochemical assays, and quantitative analyses, we determine that BR-bodies promote efficient mRNA decay in a liquid-like condensate during exponential growth. On the other hand, BR-bodies are repurposed from sites of mRNA decay to reservoirs for mRNA storage under stress; a functional change that is enabled by their transition to a more rigid state, marked by reduced internal dynamics, increased molecular density, and prolonged residence time of Ribonuclease E. Furthermore, we manipulated ATP levels and translation rates, and we conclude that the accumulation of ribosome-depleted mRNA is a key factor driving BR-body rigification, and that condensate maturation further contributes to this process. Upon nutrient replenishment, stationary-phase BR-bodies disassemble, releasing stored mRNAs for rapid translation, demonstrating that BR-body function is governed by a reversible mechanism for resource management. These findings reveal adaptive strategies by which bacteria regulate RNA metabolism through condensate-mediated control of mRNA decay and storage.
    DOI:  https://doi.org/10.1038/s41467-025-65358-y
  15. Acta Neuropathol Commun. 2025 Nov 11. 13(1): 230
    Anle138b mitigates post-hypoxic cognitive impairment, α-Synuclein aggregation and UPR activation in Drosophila melanogaster.
    Aaron T Fehr, Jennifer Jung, Alma Kokott-Vuong, Sabri E M Sahnoun, Aya A Ezzat, Michael Huber, Tonya M Bliss, Aaron Voigt, Jörg B Schulz, Pardes Habib.
      Cerebral ischemia increases the risk of post-stroke cognitive impairment (PSCI), but the underlying molecular mechanisms remain unclear. Emerging evidence suggests that hypoxia/ischemia-induced oxidative and endoplasmic reticulum (ER) stress may contribute to protein misfolding and α-Synuclein (α-Syn) aggregation, potentially triggering the unfolded protein response (UPR) to alleviate ER stress. Using bimolecular fluorescence complementation in Drosophila melanogaster and HEK-293 cells, we investigated the effect of acute, repetitive and chronic hypoxia on α-Syn aggregation, UPR activation, mortality, longevity, locomotor function, sleep, and cognition. Furthermore, we evaluated the post-hypoxic in vivo biodistribution and therapeutic efficacy of the aggregation inhibitor anle138b. Acute severe hypoxia induced more α-Syn aggregation than chronic or repetitive hypoxia, resulting in higher mortality, reduced longevity, delayed motor recovery, cognitive impairment, and activation of the detrimental PERK branch of the UPR. Anle138b significantly reduced α-Syn aggregation, repressing post-hypoxic PERK activation and improving survival and decision-making. Our findings demonstrate the effectiveness of anle138b in mitigating hypoxia-induced α-Syn aggregation and cognitive impairment, paving the way for future studies on its potential as a therapeutic strategy for PSCI.
    Keywords:  ER stress; Hypoxia; Neurodegeneration; Neuroprotective therapy; Post-stroke cognitive impairment; Stroke
    DOI:  https://doi.org/10.1186/s40478-025-02099-5
  16. Cell Signal. 2025 Nov 06. pii: S0898-6568(25)00639-4. [Epub ahead of print] 112224
    ERLIN1: A central regulator of protein quality control, lipid homeostasis, and cellular signaling at the endoplasmic reticulum.
    Hyojeong Cho, Beomwoo Lee, Changgyu Son, Jaeseok Choi, Sunho Eom, Jongsun Park.
      Endoplasmic reticulum lipid raft-associated protein 1 (ERLIN1) is an endoplasmic reticulum (ER)-resident stomatin/prohibitin/flotillin/HflK/C (SPFH) family protein that assembles into oligomeric complexes within detergent-resistant membrane domains. ERLIN1 regulates multiple cellular functions, including protein quality control, calcium signaling, and lipid metabolism. Together with ERLIN2, it forms ER-associated degradation (ERAD) nanodomains through interactions with RING finger protein 170 (RNF170) and transmembrane and ubiquitin-like domain-containing 1 (TMUB1). These specialized domains facilitate the degradation of inositol 1,4,5-trisphosphate receptor type 1 (IP3R) via the ERAD pathway. ERLIN1 also controls cholesterol metabolism by inhibiting sterol regulatory element-binding protein (SREBP) activation and promoting 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) degradation. In addition, it blocks cholesterol esterification, thereby enhancing cholesterol transport to the Golgi apparatus. ERLIN1 further regulates cell fate by promoting autophagy and suppressing apoptosis; in complex with ERLIN2, it interacts with activating molecule in Beclin 1-regulated autophagy protein 1 (AMBRA1) at mitochondria-associated membranes to initiate autophagy and binds phosphatidylinositol 3-phosphate to stabilize autophagy signaling. Its overexpression enhances tumor progression, whereas silencing triggers apoptosis in colorectal cancer. Mutations in ERLIN1 are linked to neurodegenerative diseases such as hereditary spastic paraplegia type 62 and atypical amyotrophic lateral sclerosis. The ERLIN1/2 complex also influences immune responses and viral replication through cholesterol regulation. Collectively, these diverse and integrated functions highlight the potential of ERLIN1 as a therapeutic target in cancer, metabolic, neurodegenerative, and infectious diseases.
    Keywords:  Autophagy; Cellular signaling; Cholesterol metabolism; ERLIN1; Endoplasmic reticulum–associated degradation (ERAD)
    DOI:  https://doi.org/10.1016/j.cellsig.2025.112224
  17. Mol Cell. 2025 Nov 12. pii: S1097-2765(25)00863-9. [Epub ahead of print]
    Monitoring the complexity and dynamics of mitochondrial translation.
    Taisei Wakigawa, Mari Mito, Yushin Ando, Haruna Yamashiro, Kotaro Tomuro, Haruna Tani, Kazuhito Tomizawa, Takeshi Chujo, Asuteka Nagao, Takeo Suzuki, Osamu Nureki, Fan-Yan Wei, Yuichi Shichino, Yuzuru Itoh, Tsutomu Suzuki, Shintaro Iwasaki.
      Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.
    Keywords:  MELAS; Ribo-Seq; disome; kinetics; mitochondria; mitoribosomes; mtIF3; ribosome profiling; tRNA modification; translation
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.022
  18. Nat Protoc. 2025 Nov 11.
    Branching beyond bifunctional linkers: synthesis of macrocyclic and trivalent PROTACs.
    Yuting Cao, Alexandra L Harris, Alessio Ciulli.
      Proteolysis-targeting chimeras (PROTACs) are traditionally conceptualized and synthesized by connecting two ligands, one for a target protein and one for an E3 ligase, via a bifunctional linker. Chemical creativity has recently explored the development of more elaborate and unusual linkers beyond conventional bifunctionals, allowing the development of macrocyclic and trivalent PROTACs. In two distinct proof-of-concept studies guided by the co-crystal structure of bivalent PROTAC MZ1 in complex with the E3 ubiquitin ligase von Hippel-Lindau and the second bromodomain of Brd4, we designed macrocyclic macroPROTAC-1 and trivalent PROTAC SIM1. These designs aimed to enhance protein degradation by constraining the PROTAC in its bioactive conformation or increasing avidity and cooperativity within the PROTAC ternary complex by augmenting the binding valency to the target protein, respectively. Here we describe the step-by-step synthesis of the macrocyclic macroPROTAC-1 and trivalent PROTAC SIM1, detailing the generation of the macrocyclic and trivalent cores and their subsequent conjugation to the respective ligands. This two-part procedure is expected to take ~14 d for the synthesis of macroPROTAC-1 and 10 d for the synthesis of SIM1. In this protocol, we also provide a brief introduction into the biophysical and cellular evaluation of these unusual molecules, representative structures of key negative control compounds and their utility, and highlight recent developments and expansion beyond pioneering exemplars.
    DOI:  https://doi.org/10.1038/s41596-025-01283-0
  19. Sci Adv. 2025 Nov 14. 11(46): eadz2217
    Ist2 promotes lipid transfer by Osh6 via its membrane tethering and lipid scramblase activities.
    Alicia Fabbre, Camille Syska, Heitor Gobbi Sebinelli, Anna Cardinal, Maud Magdeleine, Noha Al-Qatabi, Juan Martín D'Ambrosio, Cédric Montigny, Guillaume Lenoir, Alenka Čopič, Guillaume Drin.
      Lipid transfer proteins unevenly distribute lipids within the cell, which is crucial for its functioning. In yeast, Osh6 transfers phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM) by exchange with phosphatidylinositol 4-phosphate. We investigated why its activity depends on Ist2, an ER-resident lipid scramblase that connects the ER to the PM via an intrinsically disordered region (IDR). We found that Osh6, in a lipid-loaded state, binds the Ist2 IDR with micromolar affinity and functions at ER-PM contact sites only if its binding site within the IDR is sufficiently distant from the ER membrane. We determined, in reconstituted contact sites, that the association of Osh6 with the Ist2 IDR enables rapid, directed PS transfer. We identified the Ist2-binding site in Osh6 by molecular modeling and functional analyses. Last, we established that Ist2's scramblase activity sustains Osh6-mediated PS transfer between membranes. Identifying these functional partnerships highlights why lipid transport processes are organized in membrane contact sites.
    DOI:  https://doi.org/10.1126/sciadv.adz2217
  20. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2511069122
    mTORC1 regulates autophagosomal components recycling through SNX16 phosphorylation.
    Huilin Que, Fengping Liu, Yang Chen, Wenmin Tian, Shuaixin Gao, Catherine C L Wong, Yan Li, Shixuan Wang, Xianbin Meng, Yueguang Rong.
      During autophagy, the contents enclosed within autophagosomes are degraded, while the outer membrane components are recycled from autolysosomes by the recycler complex through the recently discovered autophagosomal components recycling (ACR) process. This recycling is essential for maintaining autophagic activity. However, the molecular machinery and upstream regulatory mechanisms driving this recycling process remain poorly understood. Here, we identify SNX16 as a key component of the recycler complex, which localizes to autolysosomes and is required for ACR. SNX16 functions in ACR by regulating recycler complex formation, facilitating cargo recognition, and mediating the connection between STX17-SNX4-SNX5 and dynein-dynactin complexes. In addition, SNX16-cargo interactions are regulated by two ACR-related small GTPases, Rab32 and Rab38. Importantly, mTORC1 phosphorylates SNX16 to regulate ACR by inhibiting its interactions with STX17 and other recycler components, thus preventing recycler complex formation. Taken together, our findings identify SNX16 as a recycler component and establish a link between mTORC1 and ACR.
    Keywords:  SNX16; autophagosomal components recycling; autophagy
    DOI:  https://doi.org/10.1073/pnas.2511069122
  21. RSC Med Chem. 2025 Oct 22.
    Investigating NFE2L1 activators for targeted protein aggregate clearance: a follow-up study.
    Zuzana Smahelova, Lucie Svobodova, Jindrich Sedlacek, Michael Adamek, Marketa Pimkova Polidarova, Pavel Majer, Ales Machara, Klara Grantz Saskova.
      Disruption of protein homeostasis (proteostasis), whether by acute proteotoxic stress or chronic expression of mutant proteins, can lead to the accumulation of toxic protein aggregates. Such aggregation is a hallmark of numerous diseases and is often associated with impaired protein clearance mechanisms. The transcription factor nuclear factor erythroid 2-related factor 1 (encoded by NFE2L1, also known as Nrf1) plays a central role in restoring proteostasis by increasing proteasome synthesis. Therefore, pharmacological activation of NFE2L1 under non-stress conditions represents a promising therapeutic strategy for neurodegenerative and other proteostasis-related diseases. In our previous study, we identified bis(phenylmethylene)cycloalkanone derivatives as NFE2L1 activators capable of inducing proteasome subunit expression, increasing heat shock protein levels, and stimulating autophagy. Building upon these findings, we have now developed a new library of structurally related compounds to identify novel more potent NFE2L1 activators. By systematically examining how specific chemical substitutions affect NFE2L1 activation, this work advances our understanding of the structure-activity relationships within this pathway.
    DOI:  https://doi.org/10.1039/d5md00584a
  22. J Biol Chem. 2025 Nov 07. pii: S0021-9258(25)02776-0. [Epub ahead of print] 110924
    Non-catalytic UBL2 domain directs deubiquitinase USP11 toward K48-linked polyubiquitin chains.
    Sin-Rong Lee, Han-Hsiun Chen, Ruey-Hwa Chen, Kuen-Phon Wu.
      Ubiquitin-specific proteases (USPs), comprising the largest deubiquitinase family, are generally thought to have poor discrimination of ubiquitin (Ub) linkage types, but a number of USPs show preference toward certain linkages. USP11, a USP-family member implicated in cancer and neurodegeneration, carries an atypical catalytic domain which is split into two segments through the insertion of a UBL2 domain and an intrinsically disordered region (IDR). In addition, the chain-type selectivity of USP11 remains unclear based on the conflicting data from in vitro and in vivo studies. Here, we identify an important role of the UBL2-IDR in altering the ability of USP11 to cleave K29, K33, and K48 chains, with K48 chain showing the most significant effect. Using in vitro studies with Ub-tetramer and ubiquitinated proteins as well as cell-based analyses, we demonstrate that UBL2 domain endows USP11 with a selectivity towards the K48-linked Ub chains. Importantly, this function of UBL2 is not observed in its paralogs USP4 and USP15, which display broad activities towards most chain types. By leveraging AI-based virtual screening, we have identified selective USP11 inhibitors, including the FDA-approved drugs Fenoldopam and Olanzapine and their analogs, which act through a unique chemical scaffold and display significant efficacy both in vitro and in cells. Our findings not only uncover a previously unrecognized mechanism of linkage selectivity within the USP family but also provide a robust platform for the rational design of USP11-targeted therapeutics, underscoring the critical role of non-catalytic domains in deubiquitinase regulation and offering promising avenues for therapeutic intervention.
    Keywords:  DiffDock; K48-linkage; UBL2; USP1; deubiquitinase; polyubiquitin chain
    DOI:  https://doi.org/10.1016/j.jbc.2025.110924
  23. Cell. 2025 Nov 12. pii: S0092-8674(25)01191-2. [Epub ahead of print]
    Molecular grammars of predicted intrinsically disordered regions that span the human proteome.
    Kiersten M Ruff, Matthew R King, Alexander W Ying, Vicky Liu, Avnika Pant, Whitney E Lieberman, Min Kyung Shinn, Xiaolei Su, Cigall Kadoch, Rohit V Pappu.
      Intrinsically disordered regions (IDRs) of proteins are defined by molecular grammars. This refers to IDR-specific non-random amino acid compositions and non-random patterning of distinct pairs of amino acid types. Here, we introduce grammars inferred using NARDINI+ (GIN) as a resource that uncovers IDR-specific and IDRome-spanning grammars. Using GIN-enabled analyses, we find that specific IDR features and GIN clusters are associated with distinct biological processes, intra-cellular localization preferences, specialized molecular functions, and functionalization as assessed by cellular fitness correlations. IDRs with exceptional grammars, defined as sequences with high-scoring non-random features, are harbored in proteins and complexes that enable spatial and temporal sorting of biochemical activities within the nucleus. Overall, GIN can be used to extract sequence-function relationships of individual IDRs or clusters of IDRs, to redesign extant IDRs or design de novo IDRs, to perform evolutionary analyses through the lens of molecular grammars and GIN clusters, and to make sense of IDR-specific disease-associated mutations.
    Keywords:  RNA polymerase; biomolecular condensates; cancer; intrinsically disordered regions; molecular grammars; subcellular localization; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.cell.2025.10.019
  24. Plant Physiol Biochem. 2025 Nov 04. pii: S0981-9428(25)01265-3. [Epub ahead of print]229(Pt D): 110737
    Endoplasmic reticulum quality control and metal tolerance: reduced activity of glucosidase II enzyme affects positively cadmium tolerance in Arabidopsis thaliana.
    Maria De Benedictis, Antonia Gallo, Danilo Migoni, Paride Papadia, Francesco Paolo Fanizzi, Gian Pietro Di Sansebastiano, Pietro Roversi, Angelo Santino.
      The Endoplasmic Reticulum Quality Control (ERQC) machinery is highly conserved among eukaryotes and assists the newly synthetized proteins in the folding process. Previous works have reported the involvement of ERQC in plant immunity and biotic stress response. However, the interaction between ERQC pathway and heavy metals exposure has been poorly investigated in plants. In the present study, we showed that the Arabidopsis thaliana rsw3 mutant, characterised by a reduced activity of the ER Glucosidase II enzyme, exhibits an increased tolerance to cadmium (Cd) stress. Under standard conditions, rsw3 seedlings exhibit shorter primary roots compared to Wild-type (Wt) plantlets, because of a constitutive ER stress and a consequent upregulation of both ERQC and Unfolded Protein Response (UPR) stress markers in root or shoot tissues. Interestingly, differently from Wt seedlings, these markers remain unchanged in rsw3 under Cd stress. Biochemical data here provided linked the enhanced Cd tolerance of rsw3 to the brassinosteroid receptor 1, BRI1, as the partial impairment of GII activity positively affects the accumulation of the active form of BRI1 receptor on the plasma membrane under Cd stress.
    Keywords:  Abiotic stress; BRI1; Cadmium; ER glucosidase II; Endoplasmic reticulum quality control
    DOI:  https://doi.org/10.1016/j.plaphy.2025.110737
  25. Mol Cell. 2025 Nov 07. pii: S1097-2765(25)00854-8. [Epub ahead of print]
    Alternative start codon selection shapes mitochondrial function and rare human diseases.
    Jimmy Ly, Matteo Di Bernardo, Yi Fei Tao, Ekaterina Khalizeva, Christopher J Giuliano, Sebastian Lourido, Mark D Fleming, Iain M Cheeseman.
      Rare genetic diseases collectively affect millions of individuals. A common target of many rare diseases is the mitochondria, intracellular organelles that originated through endosymbiosis. Eukaryotic cells require related proteins to function both within the mitochondria and in the host cell. By analyzing N-terminal protein isoforms generated through alternative start codon selection, we identify hundreds of differentially localized isoform pairs, including dual-localized isoforms that are essential for both mitochondrial and host cell function. Subsets of dual mitochondria-localized isoforms emerged during early eukaryotic evolution, coinciding with mitochondrial endosymbiosis. Importantly, we identify dozens of rare disease alleles that affect these alternative protein variants with unique molecular and clinical consequences. Alternative start codon selection can bypass pathogenic nonsense and frameshift mutations, thereby selectively eliminating specific isoforms, which we term isoform-selective alleles (ISAs). Together, our findings illuminate the evolutionary and pathological relevance of alternative translation, offering insights into the molecular basis of rare human diseases.
    Keywords:  TRNT1; alternative N-terminal isoforms; alternative translation; mitochondria; proteomic diversity; rare diseases; start codon selection; translation initiation
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.013
  26. J Cell Sci. 2025 Nov 14. pii: jcs.264105. [Epub ahead of print]
    UBQLN2 is necessary for UBE3A-mediated proteasomal degradation of the domesticated retroelement PEG10.
    Julia E Roberts, Phuoc T Huynh, Luis O Carale, Alexandra M Whiteley.
      Ubiquilins are a family of extrinsic ubiquitin receptors that are thought to facilitate protein degradation by shuttling proteins to the proteasome. However, the defining characteristics of Ubiquilin clients, and the steps of Ubiquilin-mediated degradation, have been elusive. Previously, we showed Ubiquilin 2 (UBQLN2) regulates the proteasomal degradation of PEG10, a unique virus-like protein which comes in two forms: a gag protein which is not regulated by UBQLN2, and a gag-pol protein which is dependent on UBQLN2. Here, we refine the model of Ubiquilin activity through further investigation of the UBQLN2-mediated degradation of PEG10. Gag-pol and gag proteins undergo distinct degradation processes; while both forms bind to UBQLN2 independent of their ubiquitination status, only gag-pol protein is degraded in a UBQLN2, ubiquitin, and proteasome-dependent fashion. Cellular gag-pol is ubiquitinated, and mutation of key lysine residues in the pol region rendered gag-pol insensitive to UBQLN2. Degradation of gag-pol was also dependent on the E3 ubiquitin ligase UBE3A, which requires UBQLN2 to regulate gag-pol levels. Together, these data clarify our understanding of UBQLN2-mediated degradation and highlight the importance of UBE3A in regulating PEG10.
    Keywords:  E6AP; PEG10; UBE3A; UBQLN2; Ubiquilin; proteasome
    DOI:  https://doi.org/10.1242/jcs.264105
  27. J Chem Inf Model. 2025 Nov 14.
    Shotgun Approach for PROTAC Ternary Complex Modeling and Evaluation.
    Tanfeng Zhao, Yi Qin Gao.
      Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce protein degradation by forming ternary complexes with the target protein (protein of interest, POI) and the E3 ubiquitin ligase. Most commonly used degrader design strategies start with known POI and E3 binders, followed by the replacement of different linkers. Structure-based linker design is promising, yet successful cases using ternary complex structures to guide linker design remain scarce, primarily due to the inherent flexibility and conformational diversity of the complexes. This challenge is compounded by two key limitations: first, obtaining high-quality POI-egrader-E3 ternary complex crystal structures faces major technical hurdles; second, existing crystal structures in the PDB only capture static snapshots of these dynamically changing systems, with some even biased by crystal packing. Although many computational tools for ternary complex modeling have been developed so far, their accuracy still needs improvement. Currently, the commonly used methods for evaluating ternary complex modeling all rely on comparison with crystal structures while ignoring potential issues that may exist. Therefore, it is necessary to develop new modeling and evaluation methods to guide degrader design. In this study, the conformation distribution extracted from multiple parallel MD trajectories for a ternary complex is used as a reference, and we propose a framework consisting of a new modeling protocol and a scoring to generate and evaluate a ternary complex ensemble. The results of 5 tested cases demonstrate that our protocol generates complexes that can cover or are at least close to the high-density regions of the MD trajectory. This framework is particularly suitable for the POI-degrader-E3 system, which has multiple possible stable conformations and PPIs.
    DOI:  https://doi.org/10.1021/acs.jcim.5c02037
  28. Elife. 2025 Nov 12. pii: RP104549. [Epub ahead of print]14
    Membrane-mimetic thermal proteome profiling (MM-TPP) toward mapping membrane protein-ligand dynamic interactions.
    Rupinder Singh Jandu, Ashim Bhattacharya, Frank Antony, Mohammed Al-Seragi, Hiroyuki Aoki, Mohan Babu, Franck Duong van Hoa.
      Integral membrane proteins (IMPs) are central targets for small-molecule therapeutics, yet robust, unbiased, and detergent-free approaches to assess their on- and off-target interactions remain limited. Previously, we introduced the Peptidisc membrane mimetic (MM) for water-soluble stabilization of the membrane proteome and interactome (Carlson et al., eLife, 2019). In this work, we combine the Peptidisc with thermal proteome profiling (TPP) to establish membrane-mimetic thermal proteome profiling (MM-TPP), a method that enables proteome-wide mapping of membrane protein-ligand interactions. Using a membrane protein library derived from mouse liver tissue, we detected the specific effects of ATP and orthovanadate on the thermal stability of ATP-binding cassette (ABC) transporters, as well as stability shifts driven by the hydrotropic effect of ATP and its by-products on G protein-coupled receptors (GPCRs). In contrast, detergent-based TPP (DB-TPP) with ATP-VO4 failed to yield specific enrichment of ATP-binding proteins, underscoring the unique capacity of MM-TPP. To further validate the approach, we demonstrated the ability of MM-TPP to detect specific ligand-induced stabilization of cognate targets, exemplified by the selective thermal stabilization of the P2RY12 receptor by 2-methylthio-ADP. Together, these findings position MM-TPP as a robust platform for uncovering both on- and off-target effects of small molecules, providing insights into the druggable membrane proteome and its stability in consequence of changing dynamic ligands.
    Keywords:  biochemistry; chemical biology; drug screening; ligand; liver; membrane proteins; mouse; proteome; receptors
    DOI:  https://doi.org/10.7554/eLife.104549
  29. Commun Biol. 2025 Nov 10. 8(1): 1546
    Inducible tag-free degradation of endogenous proteins with AlissAID and development of a photoactivable inducer.
    Yoshitaka Ogawa, Kohei Nishimura, Masakazu Nambo, Yuichiro Tsuchiya, Sanae Oka, Toshihiko Fujimori, Kazuya Ichihara, Akinobu Matsumoto, Keisuke Obara, Takumi Kamura.
      Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target proteins remains a common challenge. Here, we demonstrated the efficiency of an affinity linker-based super-sensitive AID system for the conditional knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with a small protein binder, enabling the control of green fluorescent protein and mCherry fusion proteins. Additionally, this system can be used to degrade tag-free targets, such as Ras proteins. We also developed caged 5-adamantyl-indole-3-acetic acid that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.
    DOI:  https://doi.org/10.1038/s42003-025-08912-0
  30. J Chem Inf Model. 2025 Nov 12.
    How Feasible Is Docking of PROTACs to POI-E3L Complexes? Testing Physics-Based and ML-Based Docking Tools.
    Roberto Jiménez-Boi, Raúl Miñán, Chiara Pallara, Estrella Lozoya, Victor Guallar, Alexis Molina, Robert Soliva.
      Targeted protein degradation (TPD) is an innovative drug discovery approach that leverages small molecules to induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase (E3L) for selective degradation. Among TPD modalities, proteolysis-targeting chimeras (PROTACs) present unique challenges for computational modeling due to their size, flexibility, and complex binding interactions. This study evaluates the performance of physics-based and machine learning (ML)-based docking tools for modeling PROTAC-mediated ternary complexes in self-docking and cross-docking scenarios. A benchmark of 43 POI-PROTAC-E3L experimentally resolved structures was analyzed using GLIDE, MOE, rDock, DiffDock, and GeoDirDock. Docking strategies took into account van der Waals scaling, hydrogen bond constraints, receptor flexibility via normal mode analysis (NMA), and AlphaFold2 structures. Results show rDock with high sampling outperforming other physics-based tools, while ML-based tools achieved competitive root-mean-square deviation values but gave good results for systems close to those in their training sets and often generated unrealistic poses, emphasizing the need for postprocessing refinement. Receptor flexibility introduced through NMA significantly enhanced docking results. This work establishes performance benchmarks for PROTAC docking and offers guidelines for leveraging docking tools in PROTAC discovery workflows.
    DOI:  https://doi.org/10.1021/acs.jcim.5c01581
  31. Sci Adv. 2025 Nov 14. 11(46): eady4521
    Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons.
    Veronica Costiniti, Wyatt C Tran, Nandhini Rajesh Babu, Evgeny Kanshin, Beatrix Ueberheide, Alec C Kimmelman, Robert S Banh.
      Differential mRNA translation efficiency (mTE) of codons is important in regulating protein synthesis and cellular states and can change in response to amino acid availability. While the mTE of codons is canonically associated with their corresponding transfer RNA (tRNA) isoacceptors, its regulation by amino acids in mammalian cells remains unexplored. We found that ELAC2, a 3' tRNA maturation endonuclease, decreases the mTE of UC[C/U] serine (Ser) codons in response to Ser limitation. Ablation of ELAC2 restored UC[C/U] mTE but reduced the mTE of AG[U/C] Ser codons. Among the tRNASer isoacceptors, tRNASer(GCU) decreased the most in ELAC2-deficient cells. Unexpectedly, tRNASer(GCU) delivery restored AG[U/C] mTE and reduced UC[C/U] mTE in ELAC2-deficient cells. Last, we deciphered the effects of Ser-sensitive codons on mRNA translation and the human proteome. Our study revealed that in response to Ser limitation, regulation of tRNASer(GCU) levels fine-tune the mTE of UC[C/U] or AG[U/C] Ser-sensitive codons and shapes the proteome.
    DOI:  https://doi.org/10.1126/sciadv.ady4521
  32. PLoS Comput Biol. 2025 Nov;21(11): e1012929
    Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome.
    Ami G Sangster, Cameron Dufault, Haoning Qu, Denise Le, Julie D Forman-Kay, Alan M Moses.
      The biological function of a protein is often determined by its distinct functional units, such as folded domains and intrinsically disordered regions. Identifying and categorizing these protein segments from sequence has been a major focus in computational biology which has enabled the automatic annotation of folded protein domains. Here we show that embeddings from the unsupervised protein language model ProtT5 can be used to identify and categorize protein segments without relying on conserved patterns in primary amino acid sequence. We present Zero-shot Protein Segmentation (ZPS), where we use embeddings from ProtT5 to predict the boundaries of protein segments without training or fine-tuning any parameters. We find that ZPS boundary predictions for the human proteome are better at reproducing reviewed annotations from UniProt than established bioinformatics tools and ProtT5 embeddings of ZPS segments can categorize over 200 of the most common UniProt annotations in the human proteome, including folded domains, sub-domains, and intrinsically disordered regions. To explore ZPS predictions, we introduce a new way to visualize protein embeddings that closely resembles diagrams of distinct functional units in protein biology. Since ZPS and segment embeddings can be used without training or fine-tuning, the approach is not biased towards known annotations and can be used to identify and categorize unannotated protein segments. We used the segment embeddings to identify unannotated mitochondrion targeting signals and SYGQ-rich prion-like domains, which are functional regions within intrinsically disordered regions. We expect that the analysis of protein segment embedding similarity can lead to valuable information about protein function, including about intrinsically disordered regions and poorly understood protein regions.
    DOI:  https://doi.org/10.1371/journal.pcbi.1012929
  33. Nat Commun. 2025 Nov 10. 16(1): 9899
    LUBAC modulates CBM complex functions downstream of TRAF6 in T cells.
    Carina Graß, Franziska Ober, Constanze Sixt, Bahareh Nemati Moud, Irina Antoshkina, Frederick Eberstadt, Alisa Puhach, Göksu Avar, Antonia Keßler, Thomas J O'Neill, Thomas Seeholzer, Jan Kranich, Thomas Brocker, Katja Lammens, Michael P Menden, Christina E Zielinski, Daniel Krappmann.
      The CARD11-BCL10-MALT1 (CBM) complex drives NF-κB signaling and MALT1 protease activation after T cell receptor (TCR) stimulation, forming a central signaling hub in adaptive immunity. Both linear ubiquitin chain assembly complex (LUBAC), consisting of HOIP, HOIL-1 and SHARPIN, and TRAF6 interact with the CBM complex. Still, the coordinated activity of these E3 ligases in controlling CBM activity remains elusive. Here we demonstrate that LUBAC, unlike TRAF6, is largely dispensable for TCR-induced NF-κB activation in human CD4+ T cells. However, HOIP contributes to NF-κB target gene expression and, with TRAF6, modulates MALT1 substrate recognition, influencing T cell responses. Further, LUBAC-mediated conjugation of Met1-linked ubiquitin chains to BCL10 strictly depends on TRAF6, but putative Met1-ubiquitin acceptor lysines in BCL10 serve essential structural roles that limit accessibility within BCL10-MALT1 filaments. Thus, LUBAC acts downstream of TRAF6 to modulate MALT1 substrate recognition and to catalyze BCL10 ubiquitination, which is incompatible with BCL10-MALT1 filament formation.
    DOI:  https://doi.org/10.1038/s41467-025-65879-6
  34. Cell Commun Signal. 2025 Nov 11. 23(1): 489
    Nonsense-mediated mRNA decay: a key regulatory system engaged in cancer.
    Hongyu Pan, Xinyu Wu, Bingshuang Hu, Huihua Xiong, Yao Luo, Jian-Kang Zhou.
      Nonsense-mediated mRNA decay (NMD) is a critical cellular surveillance mechanism that prevents the translation of defective or deleterious proteins. The regulation of NMD, including both its activation and the evasion of its target mRNA, is intricately linked to tumorigenesis. When NMD becomes overactivated, it can downregulate tumor suppressor transcripts, or eliminate immunogenic peptides, thereby promoting tumor growth and immune evasion. In contrast, reduced or defective NMD can stabilize mutated oncogene transcripts and drive tumor progression. This review provides a comprehensive overview of the physiological mechanisms of NMD, its diverse substrate features, and its regulatory dynamics. We further focus on recent advances in clarifying the interplay between NMD and tumor biology. By integrating the current findings, we aim to provide an insightful understanding of how NMD contributes to tumor initiation, tumor progression, and immune modulation.
    Keywords:  Alternative splicing; Cancer progression; Nonsense-Mediated mRNA decay (NMD); Premature termination codon (PTC); Therapeutic targeting; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s12964-025-02503-6
  35. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2509408122
    A cascade of structural rearrangements positions peptide release factor 2 for polypeptide hydrolysis on the ribosome.
    Nina Michael, Bridget Y Huang, Korak Kumar Ray, Colin D Kinz-Thompson, Ruben L Gonzalez.
      Peptide release factor 2 (RF2) catalyzes the release of the nascent polypeptide chain from the bacterial ribosomal complex during translation termination and a subset of ribosome rescue pathways. Despite its critical role, the mechanisms that govern RF2 function and regulation remain elusive. Here, using single-molecule fluorescence resonance energy transfer, we characterize the conformational landscape that RF2 explores on the ribosomal complex and show that RF2 binding and dissociation from the ribosome follows a series of conformational rearrangements which depend on its ribosomal binding platform. We also show how further interactions with the ribosomal complex are necessary to properly position RF2 for polypeptide release. This work investigates not only the dynamics RF2 undergoes while in complex with the ribosome, but also identifies a potential mechanism by which the regulation of these dynamics may be disrupted, which may be exploited for future development of broad-spectrum antibiotics.
    Keywords:  ArfA; RF2; ribosome rescue; single-molecule kinetics; translation termination
    DOI:  https://doi.org/10.1073/pnas.2509408122
  36. Cell Chem Biol. 2025 Nov 10. pii: S2451-9456(25)00343-5. [Epub ahead of print]
    An engineered cysteine sensor optimized for high-throughput screening identifies regulators of intracellular thiol levels.
    Rachel P M Abrams, Rebecca G Donahue, Jessica Ma, Ying Mao, Morgan E Diolaiti, Alan Ashworth.
      Dysregulation of cysteine-dependent processes is implicated in many diseases, including cancer. Despite the importance of cysteine in crucial cellular functions, including protein synthesis, redox balance, and glutathione production, a lack of efficient assays to measure cellular cysteine has limited efforts to identify agents that affect physiological cysteine levels. We employed circular permutation to engineer a fluorescent sensor that changes conformation upon cysteine binding. Biochemical experiments showed that this sensor is selective for cysteine, operating in the 10 μM-10 mM range. To demonstrate the sensor's applicability, we performed high-throughput screens for compounds that reduce cellular cysteine. Liquid chromatography of cell extracts validated the effect of two hit compounds, and mechanistic investigations showed that one was dependent on the anticancer target, xCT. Future application of this sensor in cell biology and drug discovery will advance understanding of cysteine metabolism and drive the development of therapeutics that restore cysteine homeostasis.
    Keywords:  cellular sensor; cysteine; drug discovery; ferroptosis; high-throughput screening; oxidative stress; protein engineering
    DOI:  https://doi.org/10.1016/j.chembiol.2025.10.006
  37. Nat Commun. 2025 Nov 13. 16(1): 9973
    Heat shock protein DNAJA2 controls insulin signaling and glucose homeostasis by preventing spontaneous insulin receptor endocytosis.
    Yuanhua Qin, Wenjun Wu, Kequan Lin, Anthony J Davis, Yaping Huang.
      Dysregulation of heat shock protein DNAJA2 induces genomic instability and was consequently hypothesized to promote tumorigenesis. However, DNAJA2 knockout mice do not develop cancer but exhibit neonatal lethality and the underlying mechanism remains unknown. Here, we demonstrate that DNAJA2 maintains homeostatic glucose metabolism by regulating insulin signaling. Mechanistically, DNAJA2 binds to the insulin receptor (IR) and prevents adaptor protein 2 (AP2)-mediated spontaneous IR endocytosis by inhibiting the IR-AP2 interaction. Thus, DNAJA2 defects lead to reduced IR localization on the plasma membrane and suppression of the insulin-stimulated signaling cascade, thereby inhibiting glycogen synthesis and storage in the liver during embryogenesis, further resulting in neonatal lethality of DNAJA2-deficient mice. Analysis of public datasets reveals a strong association between DNAJA2 and metabolic phenotypes, including type 2 diabetes mellitus (T2DM) and obesity, in both humans and mice. In conclusion, our study elucidates the mechanism by which DNAJA2 regulates IR endocytosis, insulin signaling and glucose metabolism, shedding light on the pathogenesis of metabolic disorders.
    DOI:  https://doi.org/10.1038/s41467-025-64948-0
  38. Nat Rev Mol Cell Biol. 2025 Nov 10.
    Mechanistic insights into cargo sorting and export from the Golgi apparatus.
    Emma T Watson, William R Wegeng, Stamatina Aravani, Andreas M Ernst, Julia von Blume.
      The Golgi apparatus has a central role in the formation and trafficking of glycoproteins and lipids. It is organized into a series of flattened, membrane-bound compartments called cisternae, each housing a unique set of resident proteins that sequentially modify newly synthesized proteins and lipids as they move through the Golgi stack. In the final compartments, known as the trans-Golgi network (TGN), the processed cargoes are sorted and packaged into transport carriers. Despite substantial progress, key questions remain about how proteins and lipids are selectively sorted within the Golgi for delivery to specific destinations. In this Review we highlight recent insights on the biogenesis of membrane carriers at the TGN that enable transport of macromolecules along the secretory pathway and discuss how dysfunction of the molecular machinery gives rise to Golgi-related diseases.
    DOI:  https://doi.org/10.1038/s41580-025-00907-3
  39. Angew Chem Int Ed Engl. 2025 Nov 10. e17452
    Programmable DNA Nanospheres for Photothermal-Controlled Intracellular Protein Degradation.
    Yu Chen, Zongkang Guo, Hang Xiao, Wei Cai, Ziyue Peng, Kemin Wang, Wende Xiao, Jin Huang.
      Photothermal-controlled protein degradation has recently emerged as a promising ubiquitin proteasome-independent strategy for intracellular protein elimination by inducing localized heating to destroy target protein structures. However, current photothermal systems often suffer from low bioavailability and nonspecific distribution, which severely limit their therapeutic efficacy. Here, we report a programmable, photothermal-responsive DNA nanosphere (NS) for targeted and spatiotemporally controlled intracellular protein degradation. The modular NS integrates a tumor-targeting aptamer, a glutathione (GSH)-responsive disulfide linker, and a degradation unit composed of a photosensitizer and a protein-binding aptamer. After selective accumulation in tumor cells, the NS disassembles in the GSH-rich cytoplasm, releasing degradation modules that bind target proteins. Subsequent laser irradiation induces localized heating to disrupt protein conformation and activate autophagy-lysosomal clearance. This strategy enabled efficient programmed death-ligand 1 (PD-L1) degradation across multiple cancer cell models and demonstrated adaptability to other targets such as vascular endothelial growth factor (VEGF), thereby achieving synergistic antitumor effects with mild phototherapy. With improved tumor selectivity, cellular permeability, in vivo stability, and a highly modular design, this platform offers a multifunctional and translatable solution for intracellular protein degradation-based cancer therapy.
    Keywords:  DNA nanospheres; Intracellular protein degradation; Photothermal control; Synergistic cancer therapy
    DOI:  https://doi.org/10.1002/anie.202517452
  40. Pharmacol Res. 2025 Nov 07. pii: S1043-6618(25)00454-2. [Epub ahead of print]222 108029
    ER stress sensor PERK drives ferroptosis by disrupting MAMs-mediated mitochondrial homeostasis and promoting mtROS accumulation in acute myocardial infarction.
    Xueshu Tao, Yunxiang Zhang, Jiao Pang, Zihan Liao, Gaohan Chen, Xue Zhong, Xingrui Cao, Ying Lin, Dawei Guan, Yuan Tian, Liang Hao, Rui Zhao, Zhipeng Cao.
      Acute myocardial infarction (AMI) is a life-threatening condition in which ferroptosis represents an important form of regulated cardiomyocyte death, yet its upstream regulatory mechanisms remain incompletely understood. In this study, we investigated the role of the endoplasmic reticulum (ER) stress sensor PERK in the control of ferroptosis during ischemic injury. Using cardiac-specific PERK knockout mice, oxygen-glucose-deprived cardiomyocytes, and myocardial tissues from patients with AMI, we examined cardiac injury responses, mitochondrial function, ferroptosis-related protein expression, and the interaction between PERK and the mitochondrial fusion protein MFN2. We found that PERK expression and activation were markedly elevated in both murine and human AMI hearts. PERK activation disrupted mitochondria-ER contacts (MAMs), caused mitochondrial depolarization and excessive oxidative stress, and suppressed key antioxidant proteins, including xCT, GPX4, and FTH1, thereby promoting ferroptotic cell death. Conversely, genetic deletion or pharmacological inhibition of PERK preserved mitochondrial integrity, restored redox homeostasis, reduced infarct size, and improved cardiac function. Mechanistically, PERK interacted with MFN2 to modulate MAM stability, and transcriptomic analysis together with human validation supported a central role for the PERK-MAM-mtROS axis in ischemic injury. These findings demonstrate that PERK drives cardiomyocyte ferroptosis by destabilizing MAMs and enhancing mitochondrial oxidative stress, and they identify PERK as a promising therapeutic target for AMI.
    Keywords:  Acute myocardial infarction; Ferroptosis; MAMs; Mitochondrial dysfunction; PERK; mtROS
    DOI:  https://doi.org/10.1016/j.phrs.2025.108029
  41. Cell Syst. 2025 Nov 10. pii: S2405-4712(25)00277-7. [Epub ahead of print] 101444
    An adversarial scheme for integrating multi-modal data on protein function.
    Rami Nasser, Leah V Schaffer, Trey Ideker, Roded Sharan.
      To begin deciphering the hierarchical structure of the cell, we need to integrate multiple types of data of different scales on subcellular organization. To this end, we developed MIRAGE, a multi-modal generative model for integrating protein sequence, protein-protein interaction, and protein localization data. Our adversarial approach successfully learns a joint embedding space that captures the complex relationships among these diverse modalities and allows us to generate missing modalities. We evaluate our model's performance against existing methods, obtaining superior performance in protein function prediction and protein complex detection. We apply MIRAGE to construct a hierarchical map of subcellular organization in HEK293T cells, recovering known protein assemblies across multiple scales.
    DOI:  https://doi.org/10.1016/j.cels.2025.101444
  42. JCI Insight. 2025 Nov 11. pii: e192827. [Epub ahead of print]
    Palmitate impairs autophagic degradation via oxidative stress-perilysosomal Ca2+ overload-mTORC1 activation in pancreatic β-cells.
    Ha Thu Nguyen, Luong Dai Ly, Thuy Thi Thanh Ngo, Soo Kyung Lee, Carlos Noriega Polo, Subo Lee, Taesic Lee, Seung-Kuy Cha, Xaviera Riani Yasasilka, Kae Won Cho, Myung-Shik Lee, Andreas Wiederkehr, Claes B Wollheim, Kyu-Sang Park.
      Saturated fatty acids impose lipotoxic stress on pancreatic β-cells, leading to β-cell failure and diabetes. In this study, we investigate the critical role of organellar Ca2+ disturbance on defective autophagy and β-cell lipotoxicity. Palmitate, a saturated fatty acid, induced perilysosomal Ca2+ elevation, sustained mTORC1 activation on the lysosomal membrane, suppression of the lysosomal transient receptor potential mucolipin 1 (TRPML1) channel, and accumulation of undigested autophagosomes in β-cells. These Ca2+ aberrations with autophagy defects by palmitate were prevented by an mTORC1 inhibitor or a mitochondrial superoxide scavenger. To alleviate perilysosomal Ca2+ overload, strategies such as lowering extracellular Ca2+, employing voltage-gated Ca2+ channel blocker or ATP-sensitive K+ channel opener effectively abrogated mTORC1 activation and preserved autophagy. Furthermore, redirecting perilysosomal Ca2+ into the endoplasmic reticulum (ER) with an ER Ca2+ ATPase activator, restores TRPML1 activity, promotes autophagic flux, and improves survival of β-cells exposed to palmitate-induced lipotoxicity. Our findings suggest oxidative stress-Ca2+ overload-mTORC1 pathway involvement in TRPML1 suppression and defective autophagy during β-cell lipotoxicity. Restoring perilysosomal Ca2+ homeostasis emerges as a promising therapeutic strategy for metabolic diseases.
    Keywords:  Aging; Autophagy; Calcium signaling; Diabetes; Endocrinology
    DOI:  https://doi.org/10.1172/jci.insight.192827
  43. Nat Commun. 2025 Nov 12. 16(1): 9957
    Deep generative optimization of mRNA codon sequences for enhanced mRNA translation and therapeutic efficacy.
    Yupeng Li, Fan Wang, Jiaqi Yang, Zirong Han, Linfeng Chen, Wenbing Jiang, Hao Zhou, Tong Li, Zehua Tang, Jianxiang Deng, Xin He, Gaofeng Zha, Zhaoyu Hu, Yong Hu, Linping Wu, Changyou Zhan, Caijun Sun, Yao He, Zhi Xie.
      Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDecode introduces several advances, including direct learning from large-scale ribosome profiling data and generative exploration of a large sequence space. In silico analysis demonstrates RiboDecode's robust predictive accuracy for unseen genes and cellular environments. In vitro experiments showed substantial improvements in protein expression, significantly outperforming past methods. In addition, RiboDecode enables mRNA design with consideration of cellular context and demonstrates robust performance across different mRNA formats, including m1Ψ-modified and circular mRNAs, an important feature for mRNA therapeutics. In vivo mouse studies showed that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboDecode represents a paradigm shift from rule-based to a data-driven, context-aware approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.
    DOI:  https://doi.org/10.1038/s41467-025-64894-x
  44. Cell. 2025 Nov 07. pii: S0092-8674(25)01136-5. [Epub ahead of print]
    StealTHY: An immunogen-free CRISPR platform to expose concealed metastasis regulators in immunocompetent models.
    Massimo Saini, Francesc Castro-Giner, Adriana Hotz, Magdalena K Sznurkowska, Manuel Nüesch, François M Cuenot, Selina Budinjas, Gilles Bilfeld, Ece Su Ildız, Karin Strittmatter, Ilona Krol, Zoi Diamantopoulou, Aino Paasinen-Sohns, Maria Waldmeier, Rafaela Cássio, Susanne Kreutzer, Zacharias Kontarakis, Ana Gvozdenovic, Nicola Aceto.
      CRISPR screens have become standard gene discovery platforms in various contexts, including cancer. Yet commonly available CRISPR-Cas9 tools are increasingly recognized as unfit for in vivo investigations in immunocompetent contexts, due to broad immunogenicity of bacterial nucleases and reporters. Here, we show how conventional CRISPR screens in tumor grafts are systematically jeopardized by immunoediting in syngeneic and humanized immunocompetent hosts, resulting in iatrogenic clonal dropouts and ultimately compromising target identification. To resolve this, we present StealTHY, an immunogen-free CRISPR platform compatible with virtually all immunocompetent designs, enabling preservation of clonal architecture and exposing previously concealed cancer vulnerabilities. Among these, we identify the AMH-AMHR2 axis as a formerly unappreciated metastasis target. Thus, with StealTHY, we provide a new resource to expand the applicability of CRISPR screens to immunocompetent models, including humanized tumor grafts, revealing metastasis regulators of therapeutic relevance.
    Keywords:  CRISPR; Cas9; anti-tumor immunity; cancer; cancer immunogenicity; humanized mice; metastasis; patient-derived xenografts; preclinical models of cancer
    DOI:  https://doi.org/10.1016/j.cell.2025.10.007
  45. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2507535122
    The mechanism of pathogenic α1-antitrypsin aggregation in the human liver.
    Ibrahim Aldobiyan, Emma L K Elliston, Narinder Heyer-Chauhan, Stefan T Arold, Lingyun Zhao, Brandon Huntington, Sarah M Lowen, Elena V Orlova, James A Irving, David A Lomas.
      Originating 2 to 3 millennia ago in a Scandinavian population, the SERPINA1 Z allele (Glu342Lys) is present in up to 2.5% of populations of Northern European descent and accounts for 95% of severe α1-antitrypsin deficiency. The α1-antitrypsin Z variant self-assembles into polymer chains that deposit within hepatocytes, predisposing to liver disease. Here, the 4.0Å subunit structure of polymers isolated directly from human liver tissue has been determined using cryoelectron microscopy. Challenges of flexibility, small subunit size, heterogeneous length, and preferred orientations were mitigated using antibody Fab domains and sample preparation strategies. This structure demonstrates that the formation of polymers in vivo involves self-incorporation of an exposed structural element (the reactive center loop) as an additional β-strand into the central β-sheet of α1-antitrypsin and displacement of a C-terminal region from one subunit with incorporation into the next. Unlike amyloid aggregation, this well-folded structure partially recapitulates a conformation adopted during normal function of the protein. These perturbations to the constituent α1-antitrypsin subunits of human tissue-derived polymers are consistent with a pronounced stability, their tendency toward long-chain forms, the ability of a subset to undergo canonical secretion, and the action of a class of small molecules that block polymerization in vivo.
    Keywords:  conformational pathology; domain swap; ex vivo structural biology; nonamyloid; serpin
    DOI:  https://doi.org/10.1073/pnas.2507535122
  46. Sci Adv. 2025 Nov 14. 11(46): eads7973
    Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease.
    Zechuan Shi, Sudeshna Das, Samuel Morabito, Jennifer Stocksdale, Emily Miyoshi, Shushrruth Sai Srinivasan, Nora Emerson, Arshi Shahin, Negin Rahimzadeh, Zhenkun Cao, Justine Silva, Andres A Castaneda, Elizabeth Head, Leslie Thompson, Vivek Swarup.
      The study of transcriptomic and epigenomic variations in neurodegenerative diseases, particularly tauopathies like Pick's disease (PiD) and Alzheimer's disease (AD), offers insights into their underlying regulatory mechanisms. Here, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched noncoding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database, scROAD, to visualize predicted single-cell TF occupancy and regulatory networks.
    DOI:  https://doi.org/10.1126/sciadv.ads7973
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