bims-proteo Biomed News
on Proteostasis
Issue of 2025–01–05
27 papers selected by
Eric Chevet, INSERM
  1. ATG9A facilitates the closure of mammalian autophagosomes.
  2. Linear ubiquitination at damaged lysosomes induces local NFKB activation and controls cell survival.
  3. Stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) sequesters misfolded proteins during stress.
  4. Tsg101 mimicry of canonical E2 enzymes underlies its role in ubiquitin signaling.
  5. Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70.
  6. The known unknowns of the Hsp90 chaperone.
  7. Vimentin is a ubiquitination and degradation substrate of the ubiquitin ligase KPC1.
  8. Global organelle profiling reveals subcellular localization and remodeling at proteome scale.
  9. Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
  10. Sensory quiescence induces a cell-non-autonomous integrated stress response curbed by condensate formation of the ATF4 and XRP1 effectors.
  11. Liver-specific gene PGRMC1 blocks c-Myc-induced hepatocarcinogenesis through ER stress-independent PERK activation.
  12. mRNA decay pre-complex assembly drives timely cell-state transitions during differentiation.
  13. Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes in Escherichia coli.
  14. Assessment of SREBP Activation Using a Microsomal Vesicle Budding Assay.
  15. NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development.
  16. Ca2+/calmodulin-dependent protein kinase II β decodes ER Ca2+ transients to trigger autophagosome formation.
  17. PIM2 inhibition promotes MCL1 dependency in plasma cells involving integrated stress response-driven NOXA expression.
  18. Dengue and Zika virus NS4B proteins differ in topology and in determinants of ER membrane protein complex dependency.
  19. The human zinc-binding cysteine proteome.
  20. Discovery of a Natural Ent-Kaurene Diterpenoid Oridonin as an E3 Ligase Recruiter for PROTACs.
  21. Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics.
  22. Topological confinement by a membrane anchor suppresses phase separation into protein aggregates: Implications for prion diseases.
  23. Functional protein mining with conformal guarantees.
  24. Cell migration signaling through EGFR-VAV2-Rac1 pathway is sustained in endosomes.
  25. Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs.
  26. MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays.
  27. FBP1 controls liver cancer evolution from senescent MASH hepatocytes.
  1. J Cell Biol. 2025 Feb 03. pii: e202404047. [Epub ahead of print]224(2):
    ATG9A facilitates the closure of mammalian autophagosomes.
    Ruheena Javed, Muriel Mari, Einar Trosdal, Thabata Duque, Masroor Ahmad Paddar, Lee Allers, Michal H Mudd, Aurore Claude-Taupin, Prithvi Reddy Akepati, Emily Hendrix, Yi He, Michelle Salemi, Brett Phinney, Yasuo Uchiyama, Fulvio Reggiori, Vojo Deretic.
      Canonical autophagy captures within specialized double-membrane organelles, termed autophagosomes, an array of cytoplasmic components destined for lysosomal degradation. An autophagosome is completed when the growing phagophore undergoes ESCRT-dependent membrane closure, a prerequisite for its subsequent fusion with endolysosomal organelles and degradation of the sequestered cargo. ATG9A, a key integral membrane protein of the autophagy pathway, is best known for its role in the formation and expansion of phagophores. Here, we report a hitherto unappreciated function of mammalian ATG9A in directing autophagosome closure. ATG9A partners with IQGAP1 and key ESCRT-III component CHMP2A to facilitate this final stage in autophagosome formation. Thus, ATG9A is a central hub governing all major aspects of autophagosome membrane biogenesis, from phagophore formation to its closure, and is a unique ATG factor with progressive functionalities affecting the physiological outputs of autophagy.
    DOI:  https://doi.org/10.1083/jcb.202404047
  2. Autophagy. 2025 Jan 02. 1-21
    Linear ubiquitination at damaged lysosomes induces local NFKB activation and controls cell survival.
    Laura Zein, Marvin Dietrich, Denise Balta, Verian Bader, Christoph Scheuer, Suzanne Zellner, Nadine Weinelt, Julia Vandrey, Muriel C Mari, Christian Behrends, Friederike Zunke, Konstanze F Winklhofer, Sjoerd J L Van Wijk.
      Lysosomes are the major cellular organelles responsible for nutrient recycling and degradation of cellular material. Maintenance of lysosomal integrity is essential for cellular homeostasis and lysosomal membrane permeabilization (LMP) sensitizes toward cell death. Damaged lysosomes are repaired or degraded via lysophagy, during which glycans, exposed on ruptured lysosomal membranes, are recognized by galectins leading to K48- and K63-linked poly-ubiquitination (poly-Ub) of lysosomal proteins followed by recruitment of the macroautophagic/autophagic machinery and degradation. Linear (M1) poly-Ub, catalyzed by the linear ubiquitin chain assembly complex (LUBAC) E3 ligase and removed by OTULIN (OTU deubiquitinase with linear linkage specificity) exerts important functions in immune signaling and cell survival, but the role of M1 poly-Ub in lysosomal homeostasis remains unexplored. Here, we demonstrate that L-leucyl-leucine methyl ester (LLOMe)-damaged lysosomes accumulate M1 poly-Ub in an OTULIN- and K63 Ub-dependent manner. LMP-induced M1 poly-Ub at damaged lysosomes contributes to lysosome degradation, recruits the NFKB (nuclear factor kappa B) modulator IKBKG/NEMO and locally activates the inhibitor of NFKB kinase (IKK) complex to trigger NFKB activation. Inhibition of lysosomal degradation enhances LMP- and OTULIN-regulated cell death, indicating pro-survival functions of M1 poly-Ub during LMP and potentially lysophagy. Finally, we demonstrate that M1 poly-Ub also occurs at damaged lysosomes in primary mouse neurons and induced pluripotent stem cell-derived primary human dopaminergic neurons. Our results reveal novel functions of M1 poly-Ub during lysosomal homeostasis, LMP and degradation of damaged lysosomes, with important implications for NFKB signaling, inflammation and cell death.Abbreviation: ATG: autophagy related; BafA1: bafilomycin A1; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CRISPR: clustered regularly interspaced short palindromic repeats; CHUK/IKKA: component of inhibitor of nuclear factor kappa B kinase complex; CUL4A-DDB1-WDFY1: cullin 4A-damage specific DNA binding protein 1-WD repeat and FYVE domain containing 1; DGCs: degradative compartments; DIV: days in vitro; DUB: deubiquitinase/deubiquitinating enzyme; ELDR: endo-lysosomal damage response; ESCRT: endosomal sorting complex required for transport; FBXO27: F-box protein 27; GBM: glioblastoma multiforme; IKBKB/IKKB: inhibitor of nuclear factor kappa B kinase subunit beta; IKBKG/NEMO: inhibitor of nuclear factor kappa B kinase regulatory subunit gamma; IKK: inhibitor of NFKB kinase; iPSC: induced pluripotent stem cell; KBTBD7: kelch repeat and BTB domain containing 7; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LCD: lysosomal cell death; LGALS: galectin; LMP: lysosomal membrane permeabilization; LLOMe: L-leucyl-leucine methyl ester; LOP: loperamide; LUBAC: linear ubiquitin chain assembly complex; LRSAM1: leucine rich repeat and sterile alpha motif containing 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NBR1: NBR1 autophagy cargo receptor; NFKB/NF-κB: nuclear factor kappa B; NFKBIA/IĸBα: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; OPTN: optineurin; ORAS: OTULIN-related autoinflammatory syndrome; OTULIN: OTU deubiquitinase with linear linkage specificity; RING: really interesting new gene; RBR: RING-in-between-RING; PLAA: phospholipase A2 activating protein; RBCK1/HOIL-1: RANBP2-type and C3HC4-type zinc finger containing 1; RNF31/HOIP: ring finger protein 31; SHARPIN: SHANK associated RH domain interactor; SQSTM1/p62: sequestosome 1; SR-SIM: super-resolution-structured illumination microscopy; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TH: tyrosine hydroxylase; TNF/TNFα: tumor necrosis factor; TNFRSF1A/TNFR1-SC: TNF receptor superfamily member 1A signaling complex; TRIM16: tripartite motif containing 16; Ub: ubiquitin; UBE2QL1: ubiquitin conjugating enzyme E2 QL1; UBXN6/UBXD1: UBX domain protein 6; VCP/p97: valosin containing protein; WIPI2: WD repeat domain, phosphoinositide interacting 2; YOD1: YOD1 deubiquitinase.
    Keywords:  Cell death; LUBAC; NF-κB; OTULIN; linear ubiquitination; lysosomes
    DOI:  https://doi.org/10.1080/15548627.2024.2443945
  3. FEBS J. 2024 Dec 30.
    Stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) sequesters misfolded proteins during stress.
    Benjamin S Rutledge, Young J Kim, Donovan W McDonald, Juan C Jurado-Coronel, Marco A M Prado, Jill L Johnson, Wing-Yiu Choy, Martin L Duennwald.
      Co-chaperones are key elements of cellular protein quality control. They cooperate with the major heat shock proteins Hsp70 and Hsp90 in folding proteins and preventing the toxic accumulation of misfolded proteins upon exposure to stress. Hsp90 interacts with the co-chaperone stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) and activator of Hsp90 ATPase protein 1 (Aha1) among many others. Sti1 and Aha1 control the ATPase activity of Hsp90, but Sti1 also facilitates the transfer of client proteins from Hsp70 to Hsp90, thus connecting these two major branches of protein quality control. We find that misbalanced expression of Sti1 and Aha1 in yeast and mammalian cells causes severe growth defects. Also, deletion of STI1 causes an accumulation of soluble misfolded ubiquitinated proteins and a strong activation of the heat shock response. We discover that, during proteostatic stress, Sti1 forms cytoplasmic inclusions in yeast and mammalian cells that overlap with misfolded proteins. Our work indicates a key role of Sti1 in proteostasis independent of its Hsp90 ATPase regulatory functions by sequestering misfolded proteins during stress.
    Keywords:  Sti1; co‐chaperone; protein homeostasis; scaffolding; yeast
    DOI:  https://doi.org/10.1111/febs.17389
  4. Proc Natl Acad Sci U S A. 2025 Jan 07. 122(1): e2419542121
    Tsg101 mimicry of canonical E2 enzymes underlies its role in ubiquitin signaling.
    David A Nyenhuis, Susan M Watanabe, Nico Tjandra, Carol A Carter.
      Tsg101 is a highly conserved protein best known as an early-functioning component of cellular ESCRT machinery participating in recognition, sorting, and trafficking of cellular cargo to various intracellular destinations. It shares sequence and structural homology to canonical ubiquitin-conjugating (E2) enzymes and is linked to diverse events regulated by Ub signaling. How it might fulfill these roles is unclear. Here, we show that Tsg101 E2 mimicry permits interactions with diverse ubiquitin ligating (E3) enzymes and underlies its multifunctional capabilities. Coexpression of Tsg101 with the E3 ligase NNedd4-2s protected the enzyme from degradation and, remarkably, other widely divergent ligases as well. Structural alignment with UbcH5, a canonical E2 enzyme, revealed that recognition at the E2-E3 interface, a region broadly conserved despite sequence and structural differences in both E2 and E3 enzymes, was critical for protection. Nevertheless, UbcH5 failed to protect NNedd4-2s, indicating that the UEV chaperone function is unique to the variant. Studies using Cy5-Ub-VME showed that Tsg101-mediated protection reduced accessibility to Cys residues in the ligase. Access to Tsg101 Ub-binding sites was critical: Rabeprazole, which interferes with Tsg101 Ub-binding, diminished E3 ligase protection. Thus, E2 mimicry permitting control of E3 ligase ubiquitin signaling underlies Tsg101's broad ability to participate in multiple cellular functions. The study provides mechanistic insight into how Tsg101, by partnering with diverse E3 ligases, can contribute to a broad range of cellular activities.
    Keywords:  E3 ligase; ESCRT; HIV-1; Tsg101; ubiquitin
    DOI:  https://doi.org/10.1073/pnas.2419542121
  5. Nat Commun. 2024 Dec 30. 15(1): 10815
    Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70.
    Marc A Morizono, Kelly L McGuire, Natalie I Birouty, Mark A Herzik.
      Maintenance of protein homeostasis is necessary for cell viability and depends on a complex network of chaperones and co-chaperones, including the heat-shock protein 70 (Hsp70) system. In human mitochondria, mitochondrial Hsp70 (mortalin) and the nucleotide exchange factor (GrpEL1) work synergistically to stabilize proteins, assemble protein complexes, and facilitate protein import. However, our understanding of the molecular mechanisms guiding these processes is hampered by limited structural information. To elucidate these mechanistic details, we used cryoEM to determine structures of full-length human mortalin-GrpEL1 complexes in previously unobserved states. Our structures and molecular dynamics simulations allow us to delineate specific roles for mortalin-GrpEL1 interfaces and to identify steps in GrpEL1-mediated nucleotide and substrate release by mortalin. Subsequent analyses reveal conserved mechanisms across bacteria and mammals and facilitate a complete understanding of sequential nucleotide and substrate release for the Hsp70 chaperone system.
    DOI:  https://doi.org/10.1038/s41467-024-54499-1
  6. Elife. 2024 Dec 31. pii: e102666. [Epub ahead of print]13
    The known unknowns of the Hsp90 chaperone.
    Laura-Marie Silbermann, Benjamin Vermeer, Sonja Schmid, Katarzyna Tych.
      Molecular chaperones are vital proteins that maintain protein homeostasis by assisting in protein folding, activation, degradation, and stress protection. Among them, heat-shock protein 90 (Hsp90) stands out as an essential proteostasis hub in eukaryotes, chaperoning hundreds of 'clients' (substrates). After decades of research, several 'known unknowns' about the molecular function of Hsp90 remain unanswered, hampering rational drug design for the treatment of cancers, neurodegenerative, and other diseases. We highlight three fundamental open questions, reviewing the current state of the field for each, and discuss new opportunities, including single-molecule technologies, to answer the known unknowns of the Hsp90 chaperone.
    Keywords:  Hsp90; molecular biophysics; molecular chaperones; proteostasis; structural biology
    DOI:  https://doi.org/10.7554/eLife.102666
  7. Biochem Biophys Res Commun. 2024 Dec 20. pii: S0006-291X(24)01767-4. [Epub ahead of print]745 151231
    Vimentin is a ubiquitination and degradation substrate of the ubiquitin ligase KPC1.
    Yossi Gottfried, Chen Lulu-Shimron, Gilad Goldhirsh, Yael Fisher, Tamar Ziv, Dave S B Hoon, Yelena Kravtsova-Ivantsiv, Aaron Ciechanover.
      The ubiquitin proteasome system (UPS), driven by ubiquitin as a degradation signal, eliminates, in a highly specific manner, 'abnormal' proteins and proteins that completed their function. This process involves a hierarchical cascade of E1, E2, and E3 enzymes. The E3 ubiquitin ligases, act as specific receptors that bind their cognate substrates. We have previously shown that the ubiquitin ligase KPC1 possesses a strong tumor-suppressive characteristic caused by the p50 subunit of the NF-κB transcription factor, which is generated by limited, KPC1-mediated processing of its p105 precursor. In this study, we identified vimentin as a novel substrate of the KPC1. We demonstrated that the ligase forms a complex with vimentin and modifies it by ubiquitination. Overexpression of KPC1 in HEK293T cells downregulates vimentin expression. Conversely, deletion of KPC1 in HAP1 cells results in upregulation of vimentin. Importantly, we revealed both in vitro and in a tumor model in mice that at least part of this effect is mediated through the downregulation of vimentin. Furthermore, in human clear cell renal cell carcinoma (ccRCC) samples, we found a negative correlation between KPC1 and vimentin expression. Overall, we demonstrate that the KPC1 ubiquitin E3 ligase downregulates vimentin expression, thereby reducing migration and tumorigenicity of cancer cells.
    Keywords:  KPC1; Protein degradation; Tumor suppressor; Ubiquitin ligase; Vimentin
    DOI:  https://doi.org/10.1016/j.bbrc.2024.151231
  8. Cell. 2024 Dec 26. pii: S0092-8674(24)01344-8. [Epub ahead of print]
    Global organelle profiling reveals subcellular localization and remodeling at proteome scale.
    Marco Y Hein, Duo Peng, Verina Todorova, Frank McCarthy, Kibeom Kim, Chad Liu, Laura Savy, Camille Januel, Rodrigo Baltazar-Nunez, Madhurya Sekhar, Shivanshi Vaid, Sophie Bax, Madhuri Vangipuram, James Burgess, Leila Njoya, Eileen Wang, Ivan E Ivanov, Janie R Byrum, Soorya Pradeep, Carlos G Gonzalez, Yttria Aniseia, Joseph S Creery, Aidan H McMorrow, Sara Sunshine, Serena Yeung-Levy, Brian C DeFelice, Shalin B Mehta, Daniel N Itzhak, Joshua E Elias, Manuel D Leonetti.
      Defining the subcellular distribution of all human proteins and their remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immunocapture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membraneless compartments. A graph-based analysis assigns the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following HCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides key insights for elucidating cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org.
    Keywords:  CRISPR; HCoV-OC43 coronavirus; cell biology; ferroptosis; k-NN graph; mass spectrometry; native organelle IP; protein localization; spatial proteomics; subcellular remodeling; viral infection
    DOI:  https://doi.org/10.1016/j.cell.2024.11.028
  9. Nat Commun. 2024 Dec 30. 15(1): 10796
    Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
    Célia Alecki, Javeria Rizwan, Phuong Le, Suleima Jacob-Tomas, Mario Fernandez Comaduran, Morgane Verbrugghe, Jia Ming Stella Xu, Sandra Minotti, James Lynch, Jeetayu Biswas, Tad Wu, Heather D Durham, Gene W Yeo, Maria Vera.
      Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal cord motor neurons of mouse and human origin localize a subset of chaperone mRNAs to their dendrites and use microtubule-based transport to increase this asymmetric localization following proteotoxic stress. The most abundant dendritic chaperone mRNA encodes a constitutive heat shock protein 70 family member (HSPA8). Proteotoxic stress also enhances HSPA8 mRNA translation efficiency in dendrites. Stress-mediated HSPA8 mRNA localization to the dendrites is impaired by depleting fused in sarcoma-an amyotrophic lateral sclerosis-related protein-in cultured spinal cord mouse motor neurons or by expressing a pathogenic variant of heterogenous nuclear ribonucleoprotein A2/B1 in neurons derived from human induced pluripotent stem cells. These results reveal a neuronal stress response in which RNA-binding proteins increase the dendritic localization of HSPA8 mRNA to maintain proteostasis and prevent neurodegeneration.
    DOI:  https://doi.org/10.1038/s41467-024-55055-7
  10. Nat Commun. 2025 Jan 02. 16(1): 252
    Sensory quiescence induces a cell-non-autonomous integrated stress response curbed by condensate formation of the ATF4 and XRP1 effectors.
    Shashank Shekhar, Charles Tracy, Peter V Lidsky, Raul Andino, Katherine J Wert, Helmut Krämer.
      Sensory disabilities have been identified as significant risk factors for dementia but underlying molecular mechanisms are unknown. In different Drosophila models with loss of sensory input, we observe non-autonomous induction of the integrated stress response (ISR) deep in the brain, as indicated by eIF2αS50 phosphorylation-dependent elevated levels of the ISR effectors ATF4 and XRP1. Unlike during canonical ISR, however, the ATF4 and XRP1 transcription factors are enriched in cytosolic granules that are positive for RNA and the stress granule markers Caprin, FMR1, and p62, and are reversible upon restoration of vision for blind flies. Cytosolic restraint of the ATF4 and XRP1 transcription factors dampens expression of their downstream targets including genes of cell death pathways activated during chronic cellular stress and thus constitutes a chronic stress protective response (CSPR). Cytosolic granules containing both p62 and ATF4 are also evident in the thalamus and hippocampus of mouse models of congenital or degenerative blindness. These data indicate a conserved link between loss of sensory input and curbed stress responses critical for protein quality control in the brain.
    DOI:  https://doi.org/10.1038/s41467-024-55576-1
  11. Nat Commun. 2025 Jan 02. 16(1): 50
    Liver-specific gene PGRMC1 blocks c-Myc-induced hepatocarcinogenesis through ER stress-independent PERK activation.
    Fubo Ji, Jianjuan Zhang, Liping Mao, Yaqi Tan, Meihua Ye, Xianglei He, Yongzhi Zhao, Jiaxin Liu, Yan Zhang, Nachuan Zhang, Jiong Shi, Jianing Yan, Xiujun Cai, Bin Zhao, Jianping Jin, Pinglong Xu, Stephanie Roessler, Xin Zheng, Junfang Ji.
      Roles of liver-specific genes (LSGs) in tumor initiation and progression are rarely explored in hepatocellular carcinoma (HCC). Here we show that LSGs are generally downregulated in HCC tumor tissues compared to non-HCC liver tissues, and low-LSG HCCs show poor prognosis and the activated c-Myc pathway. Among the c-Myc- and patient prognosis-associated LSGs, PGRMC1 significantly blocks c-Myc-induced orthotopic HCC formation. The role of PGRMC1 depends on its localization to the endoplasmic reticulum (ER) membrane, where PGRMC1 interacts with PERK through their ER luminal domains. This interaction in turn activates PERK in an ER stress-independent manner, which phosphorylates eIF2α and consequently inhibits c-Myc protein translation. In HCC patients, PGRMC1 level is significantly reduced in tumor tissues and negatively associated with the c-Myc signature. Patients with low-PGRMC1 in their tumors have poor prognosis. Collectively, deregulated LSGs in HCC are associated with the c-Myc pathway activation and PGRMC1 blocks c-Myc-induced hepatic carcinogenesis through promoting ER stress-independent PERK activation.
    DOI:  https://doi.org/10.1038/s41467-024-55745-2
  12. Cell Rep. 2024 Dec 30. pii: S2211-1247(24)01489-X. [Epub ahead of print]44(1): 115138
    mRNA decay pre-complex assembly drives timely cell-state transitions during differentiation.
    Hideyuki Komori, Geeta Rastogi, John Paul Bugay, Hua Luo, Sichun Lin, Stephane Angers, Craig A Smibert, Howard D Lipshitz, Cheng-Yu Lee.
      Complexes that control mRNA stability and translation promote timely cell-state transitions during differentiation by ensuring appropriate expression patterns of key developmental regulators. The Drosophila RNA-binding protein brain tumor (Brat) promotes the degradation of target transcripts during the maternal-to-zygotic transition in syncytial embryos and uncommitted intermediate neural progenitors (immature INPs). We identify ubiquitin-specific protease 5 (Usp5) as a candidate Brat interactor essential for the degradation of Brat target mRNAs. Usp5 promotes the formation of the Brat-deadenylase pre-complex in mitotic neural stem cells (neuroblasts) by facilitating Brat interactions with the scaffolding components of deadenylase complexes. The adaptor protein Miranda binds the RNA-binding domain of Brat, limiting its ability to bind target mRNAs in mitotic neuroblasts. Cortical displacement of Miranda activates Brat-deadenylase complex activity in immature INPs. We propose that the assembly of an enzymatically inactive and RNA-binding-deficient pre-complex poises mRNA degradation machineries for rapid activation, driving timely developmental transitions.
    Keywords:  Brat; CP: Developmental biology; CP: Molecular biology; Drosophila; Usp5; cell state transitions; deadenylase complexes; differentiation; mRNA decay; maternal mRNAs; neuroblast
    DOI:  https://doi.org/10.1016/j.celrep.2024.115138
  13. Proc Natl Acad Sci U S A. 2025 Jan 07. 122(1): e2409536121
    Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes in Escherichia coli.
    Tora Hävermark, Mikhail Metelev, Erik Lundin, Ivan L Volkov, Magnus Johansson.
      The bacterial chaperone Trigger factor (TF) binds to ribosome-nascent chain complexes (RNCs) and cotranslationally aids the folding of proteins in bacteria. Decades of studies have given a broad, but often conflicting, description of the substrate specificity of TF, its RNC-binding dynamics, and competition with other RNC-binding factors, such as the Signal Recognition Particle (SRP). Previous RNC-binding kinetics experiments were commonly conducted on stalled RNCs in reconstituted systems, and consequently, may not be representative of the interaction of TF with ribosomes translating mRNA in the cytoplasm of the cell. Here, we used single-particle tracking (SPT) to measure TF binding to actively translating ribosomes inside living Escherichia coli. In cells, TF displays distinct binding modes-longer (ca 1 s) and shorter (ca 50 ms) RNC bindings. Consequently, we conclude that TF, on average, stays bound to the RNC for only a fraction of the translation cycle. Further, binding events are interrupted only by transient excursions to a freely diffusing state (ca 40 ms), suggesting a highly dynamic binding and unbinding cycle of TF in vivo. We also show that TF competes with SRP for RNC binding, and in doing so, tunes the binding selectivity of SRP.
    Keywords:  co-translational processing; protein folding; single-particle tracking; super-resolution microscopy
    DOI:  https://doi.org/10.1073/pnas.2409536121
  14. Bio Protoc. 2024 Dec 20. 14(24): e5139
    Assessment of SREBP Activation Using a Microsomal Vesicle Budding Assay.
    Mingfeng Xia, Tessa Edwards, Shunxing Rong.
      Sterol regulatory element binding proteins (SREBPs) are transcription factors that reside in the endoplasmic reticulum (ER) membrane as inactive precursors. To be active, SREBPs are translocated to the Golgi where the transcriptionally active N-terminus is cleaved and released to the nucleus to regulate gene expression. Nuclear SREBP levels can be determined by immunoblot analysis; however, this method can only determine the steady-state levels of nuclear SREBPs and does not capture the actual status of activation. The vesicle budding assay provides an alternative way to quantify the activation of SREBPs by monitoring the initiation of SREBP translocation from the ER to the Golgi through vesicles. Microsomal membranes isolated from the liver are incubated in a reaction buffer containing the necessary components to facilitate vesicle formation. Microsomal membranes and vesicles are isolated and SREBPs are quantified in each by immunoblot analysis. The amount of SREBPs found in the budded vesicles provides an assessment of the SREBP activation in the liver. Key features • This protocol describes a method to isolate budding vesicles from liver ER membranes. • The in vitro budding assay can be applied to investigate the movement of proteins from the ER to the Golgi. • This protocol was developed based on the procedures described previously with cultured cells [1-3].
    Keywords:  Budding assay, Sterol regulatory element binding protein (SREBP); Cytosol preparation; Endoplasmic reticulum (ER); Golgi complex (Golgi); Microsomal isolation
    DOI:  https://doi.org/10.21769/BioProtoc.5139
  15. Nat Commun. 2024 Dec 30. 15(1): 10898
    NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development.
    Ethan C Strayer, Srikar Krishna, Haejeong Lee, Charles Vejnar, Nils Neuenkirchen, Amit Gupta, Jean-Denis Beaudoin, Antonio J Giraldez.
      The cis-regulatory elements encoded in an mRNA determine its stability and translational output. While there has been a considerable effort to understand the factors driving mRNA stability, the regulatory frameworks governing translational control remain more elusive. We have developed a novel massively parallel reporter assay (MPRA) to measure mRNA translation, named Nascent Peptide Translating Ribosome Affinity Purification (NaP-TRAP). NaP-TRAP measures translation in a frame-specific manner through the immunocapture of epitope tagged nascent peptides of reporter mRNAs. We benchmark NaP-TRAP to polysome profiling and use it to quantify Kozak strength and the regulatory landscapes of 5' UTRs in the developing zebrafish embryo and in human cells. Through this approach we identified general and developmentally dynamic cis-regulatory elements, as well as potential trans-acting proteins. We find that U-rich motifs are general enhancers, and upstream ORFs and GC-rich motifs are global repressors of translation. We also observe a translational switch during the maternal-to-zygotic transition, where C-rich motifs shift from repressors to prominent activators of translation. Conversely, we show that microRNA sites in the 5' UTR repress translation following the zygotic expression of miR-430. Together these results demonstrate that NaP-TRAP is a versatile, accessible, and powerful method to decode the regulatory functions of UTRs across different systems.
    DOI:  https://doi.org/10.1038/s41467-024-55274-y
  16. Mol Cell. 2024 Dec 26. pii: S1097-2765(24)01000-1. [Epub ahead of print]
    Ca2+/calmodulin-dependent protein kinase II β decodes ER Ca2+ transients to trigger autophagosome formation.
    Qiaoxia Zheng, Huan Zhang, Hongyu Zhao, Yong Chen, Hongzhining Yang, Tingting Li, Qixu Cai, Yingyu Chen, Youjun Wang, Mingjie Zhang, Hong Zhang.
      In multicellular organisms, very little is known about how Ca2+ transients on the ER outer surface elicited by autophagy stimuli are sustained and decoded to trigger autophagosome formation. Here, we show that Ca2+/calmodulin-dependent protein kinase II β (CaMKIIβ) integrates ER Ca2+ transients to trigger liquid-liquid phase separation (LLPS) of the autophagosome-initiating FIP200 complex. In response to ER Ca2+ transients, CaMKIIβ is recruited from actin filaments and forms condensates, which serve as sites for the emergence of or interaction with FIP200 puncta. CaMKIIβ phosphorylates FIP200 at Thr269, Thr1127, and Ser1484 to modulate LLPS and properties of the FIP200 complex, thereby controlling its function in autophagosome formation. CaMKIIβ also controls the amplitude, duration, and propagation of ER Ca2+ transients during autophagy induction. CaMKIIβ mutations identified in the neurodevelopmental disorder MRD54 affect the function of CaMKIIβ in autophagy. Our study reveals that CaMKIIβ is essential for sustaining and decoding ER Ca2+ transients to specify autophagosome formation in mammalian cells.
    Keywords:  Ca(2+) transient; CaMKIIβ; FIP200; autophagosome; liquid-liquid phase separation
    DOI:  https://doi.org/10.1016/j.molcel.2024.12.005
  17. Nat Commun. 2025 Jan 02. 16(1): 256
    PIM2 inhibition promotes MCL1 dependency in plasma cells involving integrated stress response-driven NOXA expression.
    Marion Haas, Sabrina Cherfa, Léa Nguyen, Maxence Bourgoin, Gersende Caron, Elise Dessauge, Tony Marchand, Laurent Delpy, Patrick Auberger, Jérôme Moreaux, Arnaud Jacquel, Thierry Fest.
      Our study explores the complex dynamics of the integrated stress response (ISR) axis, highlighting PIM2 kinase's critical role and its interaction with the BCL2 protein family, uncovering key mechanisms of cell survival and tumor progression. Elevated PIM2 expression, a marker of various cancers, often correlates with disease aggressiveness. Using a model of normal and malignant plasma cells, we show that inhibiting PIM2 kinase inhibits phosphorylated BAD production and activates ISR-mediated NOXA expression. This shift towards MCL1 dependence underscores the synergy achieved through combined PIM/MCL1 inhibition, driven largely by ISR-mediated NOXA expression. In mouse xenograft models, dual targeting of PIM2 and MCL1 effectively controls tumor growth-a response reversed by ISR-specific inhibition and upregulation of genes linked to tumor cell dissemination. This work elucidates the molecular intricacies of PIM2 inhibition and its implications for cancer therapy, especially in tumors with elevated PIM2 expression.
    DOI:  https://doi.org/10.1038/s41467-024-55572-5
  18. J Virol. 2024 Dec 31. e0144324
    Dengue and Zika virus NS4B proteins differ in topology and in determinants of ER membrane protein complex dependency.
    Samuel S Porter, Talon M Gilchrist, Samantha Schrodel, Andrew W Tai.
      Flaviviruses utilize the cellular endoplasmic reticulum (ER) for all aspects of their lifecycle. Genome replication and other viral activities take place in structures called replication organelles (ROs), which are invaginations induced in the ER membrane. Among the required elements for RO formation is the biogenesis of viral nonstructural proteins NS4A and NS4B. We have previously shown that NS4A and NS4B from Dengue virus (DENV) and Zika virus (ZIKV) depend on the cellular ER membrane protein complex (EMC) for biogenesis. Here, we find that this dependency extends to the NS4A and NS4B proteins of Yellow Fever virus (YFV) and West Nile virus (WNV), which share similar computationally predicted membrane topologies. However, we demonstrate that ZIKV NS4B has different determinants of its dependency on the EMC than those for DENV NS4B, as well as a different membrane topology. Furthermore, we characterize mutant isolates of DENV and ZIKV that were serially passaged in EMC knockout cells and find that none are completely independent of the EMC for infection, and that mutant NS4B proteins remain sensitive to EMC depletion, suggesting a high genetic barrier to EMC depletion. Collectively, our findings are consistent with a model in which the EMC recognizes multiple determinants in the NS4B protein to support infection in several flaviviruses of critical public health importance.IMPORTANCEThe NS4A and NS4B proteins of flaviviruses are critically important to replication, but little is known about their function. It has been previously reported that the cellular EMC supports the biogenesis of NS4A and NS4B from Dengue and Zika virus. In this work, we demonstrate that this dependency on the EMC for NS4A and NS4B biogenesis extends to the West Nile and Yellow Fever viruses. Furthermore, we examine the features of ZIKV NS4B and find that its membrane topology of ZIKV NS4B and its determinants of dependency on the EMC are different from those previously described in DENV NS4B. Finally, we present evidence that there is a high genetic barrier for Dengue and Zika viruses to overcome EMC depletion.
    Keywords:  Dengue fever; Zika; flavivirus; virology
    DOI:  https://doi.org/10.1128/jvi.01443-24
  19. Cell. 2024 Dec 26. pii: S0092-8674(24)01341-2. [Epub ahead of print]
    The human zinc-binding cysteine proteome.
    Nils Burger, Melanie J Mittenbühler, Haopeng Xiao, Sanghee Shin, Shelley M Wei, Erik K Henze, Sebastian Schindler, Sepideh Mehravar, David M Wood, Jonathan J Petrocelli, Yizhi Sun, Hans-Georg Sprenger, Pedro Latorre-Muro, Amanda L Smythers, Luiz H M Bozi, Narek Darabedian, Yingde Zhu, Hyuk-Soo Seo, Sirano Dhe-Paganon, Jianwei Che, Edward T Chouchani.
      Zinc is an essential micronutrient that regulates a wide range of physiological processes, most often through zinc binding to protein cysteine residues. Despite being critical for modulation of protein function, the cysteine sites in the majority of the human proteome that are subject to zinc binding remain undefined. Here, we develop ZnCPT, a deep and quantitative mapping of the zinc-binding cysteine proteome. We define 6,173 zinc-binding cysteines, uncovering protein families across major domains of biology that are subject to constitutive or inducible zinc binding. ZnCPT enables systematic discovery of zinc-regulated structural, enzymatic, and allosteric functional domains. On this basis, we identify 52 cancer genetic dependencies subject to zinc binding and nominate malignancies sensitive to zinc-induced cytotoxicity. We discover a mechanism of zinc regulation over glutathione reductase (GSR), which drives cell death in GSR-dependent lung cancers. We provide ZnCPT as a resource for understanding mechanisms of zinc regulation of protein function.
    Keywords:  GSR; cancer; cysteine proteomics; glutathione reductase; zinc; zinc-binding proteome
    DOI:  https://doi.org/10.1016/j.cell.2024.11.025
  20. J Am Chem Soc. 2024 Dec 30.
    Discovery of a Natural Ent-Kaurene Diterpenoid Oridonin as an E3 Ligase Recruiter for PROTACs.
    Jie Huang, Xuekun Fu, Fang Qiu, Zhijian Liang, Chunhao Cao, Zhuqian Wang, Hongzhen Chen, Siran Yue, Duoli Xie, Yiying Liang, Aiping Lu, Chao Liang.
      PROTACs have emerged as a therapeutic modality for the targeted degradation of proteins of interest (POIs). Central to PROTAC technology are the E3 ligase recruiters, yet only a few of them have been identified due to the lack of ligandable pockets in ligases, especially among single-subunit ligases. We propose that binders of partner proteins of single-subunit ligases could be repurposed as new ligase recruiters. MDM2 is a single-subunit ligase overexpressed in tumors. Nucleolin (NCL) is an MDM2 partner protein that displays a similar tumor-specific overexpression pattern and nuclear-cytoplasmic shuttling role to MDM2. Furthermore, NCL is selectively translocated on the tumor cell surface, where it acts as an internalization receptor for its binders. We reveal that the NCL-binding Oridonin (Ori), a natural ent-kaurene diterpenoid, is capable of recruiting MDM2 by employing NCL as a molecular bridge. We design Ori-based PROTACs for modulating oncogenic POIs, including BRD4 and EGFR. These PROTACs direct the assembly of MDM2-NCL-PROTAC-POI complexes to induce proteasomal degradation of POIs and tumor shrinkage. In addition to its role as a ligase engaged by PROTACs, MDM2, along with its homologue MDMX, plays a nonredundant function in inhibiting p53 activity. Dual inhibition of MDM2/X is proposed as a promising antitumor strategy. We demonstrate that Ori also recruits MDMX in an NCL-dependent manner. Ori-based homo-PROTACs induce MDM2/X dual degradation and attenuate tumor progression. Our findings prove the feasibility of repurposing the binders of ligase partner proteins as new ligase recruiters in PROTACs and highlight the potential of Ori as an MDM2/X recruiter.
    DOI:  https://doi.org/10.1021/jacs.4c14650
  21. Nat Commun. 2025 Jan 02. 16(1): 73
    Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics.
    George S Biggs, Emma E Cawood, Aini Vuorinen, William J McCarthy, Harry Wilders, Ioannis G Riziotis, Antonie J van der Zouwen, Jonathan Pettinger, Luke Nightingale, Peiling Chen, Andrew J Powell, David House, Simon J Boulton, J Mark Skehel, Katrin Rittinger, Jacob T Bush.
      Identifying pharmacological probes for human proteins represents a key opportunity to accelerate the discovery of new therapeutics. High-content screening approaches to expand the ligandable proteome offer the potential to expedite the discovery of novel chemical probes to study protein function. Screening libraries of reactive fragments by chemoproteomics offers a compelling approach to ligand discovery, however, optimising sample throughput, proteomic depth, and data reproducibility remains a key challenge. We report a versatile, label-free quantification proteomics platform for competitive profiling of cysteine-reactive fragments against the native proteome. This high-throughput platform combines SP4 plate-based sample preparation with rapid chromatographic gradients. Data-independent acquisition performed on a Bruker timsTOF Pro 2 consistently identified ~23,000 cysteine sites per run, with a total of ~32,000 cysteine sites profiled in HEK293T and Jurkat lysate. Crucially, this depth in cysteinome coverage is met with high data completeness, enabling robust identification of liganded proteins. In this study, 80 reactive fragments were screened in two cell lines identifying >400 ligand-protein interactions. Hits were validated through concentration-response experiments and the platform was utilised for hit expansion and live cell experiments. This label-free platform represents a significant step forward in high-throughput proteomics to evaluate ligandability of cysteines across the human proteome.
    DOI:  https://doi.org/10.1038/s41467-024-55057-5
  22. Proc Natl Acad Sci U S A. 2025 Jan 07. 122(1): e2415250121
    Topological confinement by a membrane anchor suppresses phase separation into protein aggregates: Implications for prion diseases.
    Kalpshree Gogte, Fatemeh Mamashli, Maria Georgina Herrera, Simon Kriegler, Verian Bader, Janine Kamps, Prerna Grover, Roland Winter, Konstanze F Winklhofer, Jörg Tatzelt.
      Protein misfolding and aggregation are a hallmark of various neurodegenerative disorders. However, the underlying mechanisms driving protein misfolding in the cellular context are incompletely understood. Here, we show that the two-dimensional confinement imposed by a membrane anchor stabilizes the native protein conformation and suppresses liquid-liquid phase separation (LLPS) and protein aggregation. Inherited prion diseases in humans and neurodegeneration in transgenic mice are linked to the expression of anchorless prion protein (PrP), suggesting that the C-terminal glycosylphosphatidylinositol (GPI) anchor of native PrP impedes spontaneous formation of neurotoxic and infectious PrP species. Combining unique in vitro and in vivo approaches, we demonstrate that anchoring to membranes prevents LLPS and spontaneous aggregation of PrP. Upon release from the membrane, PrP undergoes a conformational transition to detergent-insoluble aggregates. Our study demonstrates an essential role of the GPI anchor in preventing spontaneous misfolding of PrPC and provides a mechanistic basis for inherited prion diseases associated with anchorless PrP.
    Keywords:  liquid-liquid phase separation; membrane; neurodegenerative diseases; prion; protein aggregation
    DOI:  https://doi.org/10.1073/pnas.2415250121
  23. Nat Commun. 2025 Jan 02. 16(1): 85
    Functional protein mining with conformal guarantees.
    Ron S Boger, Seyone Chithrananda, Anastasios N Angelopoulos, Peter H Yoon, Michael I Jordan, Jennifer A Doudna.
      Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model. Our method (1) lets users select many biologically-relevant loss metrics (i.e. false discovery rate) and assigns reliable functional probabilities for annotating genes of unknown function; (2) achieves state-of-the-art performance in enzyme classification without training new models; and (3) robustly and rapidly pre-filters proteins for computationally intensive structural alignment algorithms. Our framework enhances the reliability of protein homology detection and enables the discovery of uncharacterized proteins with likely desirable functional properties.
    DOI:  https://doi.org/10.1038/s41467-024-55676-y
  24. J Cell Sci. 2025 Jan 02. pii: jcs.263541. [Epub ahead of print]
    Cell migration signaling through EGFR-VAV2-Rac1 pathway is sustained in endosomes.
    Itziar Pinilla-Macua, Sachin Surve, Alexander Sorkin.
      Ligand binding to EGFR activates Rho family GTPases, triggering actin cytoskeleton reorganization, cell migration and invasion. Activated EGFR is also rapidly endocytosed but the role of EGFR endocytosis in cell motility is poorly understood. Hence, we used live-cell microscopy imaging to demonstrate that endogenous fluorescently labeled VAV2, a guanine nucleotide exchange factor for Rho GTPases, is co-endocytosed with EGFR in genome-edited human oral squamous cell carcinoma (HSC3) cells, an in vitro model for head-and-neck cancer where VAV2 is known to promote metastasis and associates with poor prognosis. Chemotactic migration of HSC3 cells toward an EGF gradient is found to require both VAV2 and clathrin-mediated endocytosis. Moreover, sustained activation of Rac1, a Rho family GTPase promoting cell migration and a major substrate of VAV2, also depends on clathrin. Endogenous fluorescently labeled Rac1 localizes to EGFR-containing endosomes. Altogether, our findings suggest that signaling through the EGFR-VAV2-Rac1 pathway persists in endosomes and that this endosomal signaling is required for EGFR-driven cell migration.
    Keywords:  Cell motility; EGFR; Endocytosis; Rac1; VAV2
    DOI:  https://doi.org/10.1242/jcs.263541
  25. JACS Au. 2024 Dec 23. 4(12): 4866-4882
    Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs.
    Chungen Li, Yihan Chen, Weixue Huang, Yudi Qiu, Shengjie Huang, Yang Zhou, Fengtao Zhou, Jian Xu, Xiaomei Ren, Jinwei Zhang, Zhen Wang, Ming Ding, Ke Ding.
      Macrocyclization is a compelling strategy for conventional drug design for improving biological activity, target specificity, and metabolic stability, but it was rarely applied to the design of PROTACs possibly due to the mechanism and structural complexity. Herein, we report the rational design of the first series of "Head-to-Tail" macrocyclic PROTACs. The resulting molecule SHD913 exhibited pronounced Brd4 protein degradation with low nM DC50 values while almost totally dismissing the "hook effect", which is a general character and common concern of a PROTAC, in multiple cancer cell lines. Further biological evaluation revealed that the compound exhibited positive cooperativity and induced de novo protein-protein interactions (PPIs) in both biophysical and cellular NanoBRET assays and outperformed macroPROTAC-1 that is the first reported macrocyclic Brd4 PROTAC, in cellular assays. In vitro liver microsomal stability evaluation suggested that SHD913 demonstrated improved metabolic stability in different species compared with the linear counterpart. The co-crystal structure of Brd4BD2: SHD913: VCB (VHL, Elongin C and Elongin B) complex determination and molecular dynamics (MD) simulation also elucidated details of the chemical-induced PPIs and highlighted the crucial contribution of restricted conformation of SHD913 to the ternary complex formation. These results collectively support that macrocyclization could be an attractive and feasible strategy for a new PROTAC design.
    DOI:  https://doi.org/10.1021/jacsau.4c00831
  26. EMBO J. 2025 Jan 02.
    MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays.
    Romane Meurs, Mara De Matos, Adrian Bothe, Nicolas Guex, Tobias Weber, Aurelio A Teleman, Nenad Ban, David Gatfield.
      Ribosomes scanning from the mRNA 5' cap to the start codon may initiate at upstream open reading frames (uORFs), decreasing protein biosynthesis. Termination at a uORF can lead to re-initiation, where 40S subunits resume scanning and initiate another translation event downstream. The noncanonical translation factors MCTS1-DENR participate in re-initiation at specific uORFs, but knowledge of other trans-acting factors or uORF features influencing re-initiation is limited. Here, we establish a cell-free re-initiation assay using HeLa lysates to address this question. Comparing in vivo and in vitro re-initiation on uORF-containing reporters, we validate MCTS1-DENR-dependent re-initiation in vitro. Using this system and ribosome profiling in cells, we found that knockdown of the MCTS1-DENR homolog eIF2D causes widespread gene deregulation unrelated to uORF translation, and thus distinct to MCTS1-DENR-dependent re-initiation regulation. Additionally, we identified MCTS2, encoded by an Mcts1 retrogene, as a DENR partner promoting re-initiation in vitro, providing a plausible explanation for clinical differences associated with DENR vs. MCTS1 mutations in humans.
    Keywords:  DENR-MCTS1; In Vitro Translation; Re-Initiation; eIF2D; uORF
    DOI:  https://doi.org/10.1038/s44318-024-00347-3
  27. Nature. 2025 Jan 01.
    FBP1 controls liver cancer evolution from senescent MASH hepatocytes.
    Liver Cancer Collaborative
      Hepatocellular carcinoma (HCC) originates from differentiated hepatocytes undergoing compensatory proliferation in livers damaged by viruses or metabolic-dysfunction-associated steatohepatitis (MASH)1. While increasing HCC risk2, MASH triggers p53-dependent hepatocyte senescence3, which we found to parallel hypernutrition-induced DNA breaks. How this tumour-suppressive response is bypassed to license oncogenic mutagenesis and enable HCC evolution was previously unclear. Here we identified the gluconeogenic enzyme fructose-1,6-bisphosphatase 1 (FBP1) as a p53 target that is elevated in senescent-like MASH hepatocytes but suppressed through promoter hypermethylation and proteasomal degradation in most human HCCs. FBP1 first declines in metabolically stressed premalignant disease-associated hepatocytes and HCC progenitor cells4,5, paralleling the protumorigenic activation of AKT and NRF2. By accelerating FBP1 and p53 degradation, AKT and NRF2 enhance the proliferation and metabolic activity of previously senescent HCC progenitors. The senescence-reversing and proliferation-supportive NRF2-FBP1-AKT-p53 metabolic switch, operative in mice and humans, also enhances the accumulation of DNA-damage-induced somatic mutations needed for MASH-to-HCC progression.
    DOI:  https://doi.org/10.1038/s41586-024-08317-9
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