bims-ginsta Biomed News
on Genome instability
Issue of 2025–11–09
43 papers selected by
Jinrong Hu, National University of Singapore
  1. Designing protein-based artificial kinetochores as decoys to prevent meiotic errors in oocytes.
  2. Repair of DNA double-strand breaks leaves heritable impairment to genome function.
  3. Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.
  4. Secretome translation shaped by lysosomes and lunapark-marked ER junctions.
  5. CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci.
  6. Spatiotemporal dynamics of the cardioimmune niche during lesion repair.
  7. Direct targeting and regulation of RNA polymerase II by cell signaling kinases.
  8. Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression.
  9. Spatial dynamics of brain development and neuroinflammation.
  10. Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses.
  11. Lineage-resolved atlas of the developing human cortex.
  12. Characterization of the mammalian prodefinitive angio-hematopoietic lineage.
  13. Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis.
  14. Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions.
  15. Poly-ubiquitylated transmembrane proteins outcompete other cargo for limited space inside clathrin-coated vesicles.
  16. Phosphorylation-dependent tuning of mRNA deadenylation rates.
  17. Lymph node environment drives FSP1 targetability in metastasizing melanoma.
  18. Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation.
  19. Notch signaling is a driver of glandular stem cell activity and regenerative migration after damage.
  20. Imaging the time course of DNA damage response at a nonrepetitive endogenous locus.
  21. Squidiff: predicting cellular development and responses to perturbations using a diffusion model.
  22. Functionally dominant hotspot mutations of mitochondrial ribosomal RNA genes in cancer.
  23. Pre-rRNAs control mitosis by maintaining chromosomal segregation through protecting SMC2 from AURKA-mediated phosphorylation.
  24. In vitro oogenesis breaks free of the ovary.
  25. A versatile cohesion manipulation system probes female reproductive age-related egg aneuploidy.
  26. Disparate leukemia mutations converge on nuclear phase-separated condensates.
  27. Membrane curvature at the ER-PM contact sites.
  28. Coordinated Remodeling of Ca2+ Signaling and Intracellular Organelles During Cell Division.
  29. Cell signaling meets gene transcription.
  30. Targeting FSP1 triggers ferroptosis in lung cancer.
  31. Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration.
  32. Fluorescence lifetime clocks quantify senescence and aging.
  33. Endoplasmic reticulum protein FAM134B acts as a regulator of mitochondrial morphology.
  34. Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1.
  35. Tunneling nanotube-mediated stem cell immunomodulation dysfunction promotes adipose inflammation and insulin resistance in GDM.
  36. A lipid flippase shapes the ciliary membrane and is essential for ciliogenesis.
  37. The origin of hepatocellular carcinoma depends on metabolic zonation.
  38. HIRA defines early replication initiation zones independently of their genome compartment.
  39. NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT.
  40. Tissue regeneration: Unraveling strategies for resolving pathological fibrosis.
  41. Imaging the cytoplasmic lives of single mRNAs.
  42. Site-specific DNA insertion into the human genome with engineered recombinases.
  43. Chemical compensation to mechanical loss in cell mechanosensation.
  1. Nat Cell Biol. 2025 Nov 04.
    Designing protein-based artificial kinetochores as decoys to prevent meiotic errors in oocytes.
    Yuanzhuo Zhou, Kohei Asai, Hirohisa Kyogoku, Tomoya S Kitajima.
      Chromosome mis-segregation during meiosis in oocytes causes miscarriages and congenital diseases. Ageing-associated premature chromosome separation is a major cause of mis-segregation. Effective prevention of premature chromosome separation has not yet been achieved. Here we design protein-based artificial kinetochores that act as decoys to prevent premature chromosome separation. Designed artificial kinetochore-like decoys are submicroscale clusters of NDC80-NUF2-tethered protein particles that can establish a biorientation-like state by competing with chromosomal kinetochores for HURP-decorated microtubules. This competition reduces excessive bipolar microtubule pulling forces exerted on chromosomes, thereby effectively preventing premature chromosome separation during meiosis I and II in aged mouse oocytes. These effects suppress egg aneuploidy. This study provides a decoy strategy with biocompatible artificial kinetochores to prevent ageing-associated meiotic errors in oocytes.
    DOI:  https://doi.org/10.1038/s41556-025-01792-w
  2. Science. 2025 Nov 06. 390(6773): eadk6662
    Repair of DNA double-strand breaks leaves heritable impairment to genome function.
    Susanne Bantele, Irene Mordini, Alva Biran, Nicolas Alcaraz, Gijs Zonderland, Alice Wenger, Nils Krietenstein, Anja Groth, Jiri Lukas.
      Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is unknown whether the surrounding chromatin is restored to its naïve state. We show that a single DNA double-strand break (DSB) within a topologically associated domain (TAD) harboring conformation-sensitive genes causes lasting chromatin alterations, which persist after completion of DNA repair and feature topological rearrangements and loss of local RNA species. These newly acquired features of postrepair chromatin are transmitted to daughter cells and manifest as heritable impairments of gene expression. These findings uncover a hitherto concealed dimension of DNA breakage, which we term postrepair chromatin fatigue and which confers heritable impairment of gene function beyond DNA repair.
    DOI:  https://doi.org/10.1126/science.adk6662
  3. EMBO J. 2025 Nov 03.
    Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.
    Yelena Y Bernadskaya, Ariel Kuan, Andreas Tjärnberg, Jonas Brandenburg, Ping Zhang, Keira Wiechecki, Nicole Kaplan, Margaux Failla, Maria Bikou, Oliver Madilian, Noah Bruderer, Wei Wang, Lionel Christiaen.
      During development, stem and progenitor cells divide and transition through multipotent states to generate the diverse cell types by undergoing defined changes in biomolecular composition, which underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, the cardiac and pharyngeal muscle programs are jointly primed in multipotent cardiopharyngeal progenitors, and segregate in distinct daughter cells only after cell division. Here, using the tunicate Ciona, we showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single-cell RNA-sequencing (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S, and G2 phases. We refer to this process as "transcriptome maturation", and identified candidate mature genes, including the Rho GAP-coding gene Depdc1b, which peaks in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and by enabling asymmetric cell division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". We show that both classic regulatory circuits and coupling with the G1-S transition drive transcriptome maturation, ensuring the timely deployment of lineage-specific programs.
    Keywords:  Cell Cycle; Gene Regulation; Heart; Multipotency; Oriented Cell Division
    DOI:  https://doi.org/10.1038/s44318-025-00613-y
  4. Nature. 2025 Nov 05.
    Secretome translation shaped by lysosomes and lunapark-marked ER junctions.
    Heejun Choi, Ya-Cheng Liao, Young J Yoon, Jonathan Grimm, Nan Wang, Luke D Lavis, Robert H Singer, Jennifer Lippincott-Schwartz.
      The endoplasmic reticulum (ER) is a highly interconnected membrane network that serves as a central site for protein synthesis and maturation1. A crucial subset of ER-associated transcripts, termed secretome mRNAs, encode secretory, lumenal and integral membrane proteins, representing nearly one-third of human protein-coding genes1. Unlike cytosolic mRNAs, secretome mRNAs undergo co-translational translocation, and thus require precise coordination between translation and protein insertion2,3. Disruption of this process, such as through altered elongation rates4, activates stress response pathways that impede cellular growth, raising the question of whether secretome translation is spatially organized to ensure fidelity. Here, using live-cell single-molecule imaging, we demonstrate that secretome mRNA translation is preferentially localized to ER junctions that are enriched with the structural protein lunapark and in close proximity to lysosomes. Lunapark depletion reduced ribosome density and translation efficiency of secretome mRNAs near lysosomes, an effect that was dependent on eIF2-mediated initiation and was reversed by the integrated stress response inhibitor ISRIB. Lysosome-associated translation was further modulated by nutrient status: amino acid deprivation enhanced lysosome-proximal translation, whereas lysosomal pH neutralization suppressed it. These findings identify a mechanism by which ER junctional proteins and lysosomal activity cooperatively pattern secretome mRNA translation, linking ER architecture and nutrient sensing to the production of secretory and membrane proteins.
    DOI:  https://doi.org/10.1038/s41586-025-09718-0
  5. Nat Biotechnol. 2025 Nov 06.
    CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci.
    Meishuo Liu, Keyun Huang, Jie Zhang, Qingyang Li, Xinming Wang, Buming Gu, Hao Tang, Zhenhai Du, Liangjun Hu, Shutao Qi, Yu Ma, Hongtao Yu, Wei Xie, Xianyang Fang, Haifeng Wang.
      Existing methods to visualize dynamic changes in the three-dimensional genome, promoter-enhancer interactions and the influence of epigenetic modifications in non-repetitive loci are limited. Here we introduce CRISPR PRO-LiveFISH (Pooled gRNAs with Orthogonal bases LiveFISH), which combines orthogonal bases from expanded genetic alphabet technology and rational single guide RNA (sgRNA) design to efficiently label multiple non-repetitive loci in living cells. The optimized method allows simultaneous imaging of up to six genomic loci and uses as few as 10 sgRNAs for non-repetitive loci imaging without signal amplification. We demonstrate the method in diverse cell types, including primary cells, and apply it to reveal enhancer-promoter dynamics and a correlation between genomic dynamics and epigenetic states. We also show that PCDHα-enhancer interactions may persist despite spatial mobility and that BRD4 maintains super-enhancer contacts regulating MYC oncogene expression in cancer cells. CRISPR PRO-LiveFISH can be applied to diverse studies of chromatin dynamics and genome organization in living cells.
    DOI:  https://doi.org/10.1038/s41587-025-02887-3
  6. Nat Cardiovasc Res. 2025 Nov 03.
    Spatiotemporal dynamics of the cardioimmune niche during lesion repair.
    Andy Shing-Fung Chan, Joachim Greiner, Lisa Marschhäuser, Tomás A Brennan, Stefanie Perez-Feliz, Ankit Agrawal, Helene Hemmer, Katrin Sinning, Jennifer Wing Lam Cheung, Zafar Iqbal, Alexander Klesen, Tamara Antonela Vico, Julieta Aprea, Ingo Hilgendorf, Thomas Seidel, Martin Vaeth, Eva A Rog-Zielinska, Peter Kohl, Franziska Schneider-Warme, Dominic Grün.
      The heart is one of the least regenerative organs in humans, and ischemic heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes that occur during cardiac wound healing is an essential prerequisite to reducing health burden and improving cardiac function after myocardial tissue damage. Here, by integrating single-cell RNA sequencing with high-resolution spatial transcriptomics, we reconstruct the spatiotemporal dynamics of the fibrotic niches after cardiac injury in adult mice. We reveal a complex multicellular network that regulates cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages to prevent excessive fibrosis. We further discovered a rare population of progenitor-like cardiomyocytes after lesion, promoted by myeloid and lymphoid niche signals. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatiotemporal atlas provides valuable insights into the heterocellular interactions that control cardiac repair.
    DOI:  https://doi.org/10.1038/s44161-025-00739-6
  7. Science. 2025 Nov 06. 390(6773): eads7152
    Direct targeting and regulation of RNA polymerase II by cell signaling kinases.
    Preeti Dabas, Meritxell B Cutrona, Wojciech Rosikiewicz, Ryan P Kempen, Patrick Rodrigues, John Bowling, Mollie S Prater, Walter H Lang, Adithi Danda, Zhi Yuan, Beisi Xu, Shondra M Pruett-Miller, Gang Wu, Taosheng Chen, Aseem Z Ansari.
      Distinct phosphorylation marks are placed on the carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) during different stages of gene transcription. These phospho-CTD marks function as a molecular recognition code for the recruitment of stage-specific effector proteins. Querying ~80% of the human kinome, we identified 117 kinases that phosphorylate the CTD with a high degree of positional selectivity. The unifying characteristic linking these diverse kinases is that they selectively regulate Pol II at signal-responsive genes. An example of such "direct-at-gene" Pol II regulation is displayed by epidermal growth factor receptor (EGFR), a cell surface receptor tyrosine kinase. More broadly, our atlas of CTD kinases implicates Pol II as a direct regulatory end point for signal-transducing kinases that govern cellular physiology and contribute to the etiology of numerous diseases.
    DOI:  https://doi.org/10.1126/science.ads7152
  8. Nat Aging. 2025 Nov 04.
    Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression.
    Emily G Shuldiner, Saswati Karmakar, Min K Tsai, Jess D Hebert, Yuning J Tang, Laura Andrejka, Maggie R Robertson, Minwei Wang, Colin R Detrick, Hongchen Cai, Rui Tang, Christian A Kunder, David M Feldser, Dmitri A Petrov, Monte M Winslow.
      Most cancers are diagnosed in people over 60 years of age, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation (widely understood to contribute to cancer risk) it is associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses oncogenic KRAS-driven tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K-AKT pathway, weakened disproportionately. Single-cell transcriptomic analysis revealed that neoplastic cells in aged mice retain age-related transcriptomic changes, showing that the impact of age persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings underscore the interconnectedness of the pathways involved in aging and tumorigenesis and document tumor-suppressive effects of aging that may contribute to the deceleration in cancer incidence with age.
    DOI:  https://doi.org/10.1038/s43587-025-00986-z
  9. Nature. 2025 Nov;647(8088): 213-227
    Spatial dynamics of brain development and neuroinflammation.
    Di Zhang, Leslie A Rubio Rodríguez-Kirby, Yingxin Lin, Wenqi Wang, Mengyi Song, Li Wang, Lijun Wang, Shigeaki Kanatani, Tony Jimenez-Beristain, Yonglong Dang, Mei Zhong, Petra Kukanja, Shuozhen Bao, Shaohui Wang, Xinyi Lisa Chen, Fu Gao, Dejiang Wang, Hang Xu, Cong Ma, Xing Lou, Yang Liu, Jinmiao Chen, Nenad Sestan, Per Uhlén, Arnold Kriegstein, Hongyu Zhao, Gonçalo Castelo-Branco, Rong Fan.
      The ability to spatially map multiple layers of omics information across developmental timepoints enables exploration of the mechanisms driving brain development1, differentiation, arealization and disease-related alterations. Here we used spatial tri-omic sequencing, including spatial ATAC-RNA-protein sequencing and spatial CUT&Tag-RNA-protein sequencing, alongside multiplexed immunofluorescence imaging (co-detection by indexinng (CODEX)) to map dynamic spatial remodelling during brain development and neuroinflammation. We generated a spatiotemporal tri-omic atlas of the mouse brain from postnatal day 0 (P0) to P21 and compared corresponding regions with the human developing brain. In the cortex, we identified temporal persistence and spatial spreading of chromatin accessibility for a subset of layer-defining transcription factors. In the corpus callosum, we observed dynamic chromatin priming of myelin genes across subregions and identified a role for layer-specific projection neurons in coordinating axonogenesis and myelination. In a lysolecithin neuroinflammation mouse model, we detected molecular programs shared with developmental processes. Microglia exhibited both conserved and distinct programs for inflammation and resolution, with transient activation observed not only at the lesion core but also at distal locations. Overall, this study reveals common and differential mechanisms underlying brain development and neuroinflammation, providing a rich resource for investigating brain development, function and disease.
    DOI:  https://doi.org/10.1038/s41586-025-09663-y
  10. Dev Cell. 2025 Nov 04. pii: S1534-5807(25)00636-7. [Epub ahead of print]
    Myosin II regulates cellular thermo-adaptability and the efficiency of immune responses.
    Iván Company-Garrido, Alberto Zurita Carpio, Mariona Colomer-Rosell, Bernard Ciraulo, Ronja Molkenbur, Peter Lanzerstorfer, Fabio Pezzano, Costanza Agazzi, Robert Hauschild, Saumey Jain, Jeroen M Jacques, Valeria Venturini, Christian Knapp, Yufei Xie, Jack Merrin, Julian Weghuber, Marcel Schaaf, Romain Quidant, Eva Kiermaier, Jaime Ortega Arroyo, Verena Ruprecht, Stefan Wieser.
      Effective immune responses rely on the efficient migration of leukocytes. Yet, how temperature regulates migration dynamics at the single-cell level has remained poorly understood. Using zebrafish embryos and mouse tissue explants, we found that temperature positively regulates leukocyte migration speed, exploration, and arrival frequencies to wounds and lymph vessels. Complementary 2D and 3D cultures revealed that this thermokinetic control of cell migration is conserved across immune cell types, independently of the 3D tissue environment. By applying precise (sub-)cellular temperature modulation, we identified a rapid and reversible thermo-response that depends on myosin II activity. Small physiological increases in temperature (1°C -2°C), as present during fever-like conditions, profoundly increased immune responses by accelerating arrival times at lymphatic vessels and tissue wounds. These findings identify myosin-II-dependent actomyosin contractility as a critical mechanical structure regulating single-cell thermo-adaptability, with physiological implications for tuning the speed of immune responses in vivo.
    Keywords:  cell migration; thermo-adaptability of immune cells; thermobiology
    DOI:  https://doi.org/10.1016/j.devcel.2025.10.006
  11. Nature. 2025 Nov;647(8088): 194-202
    Lineage-resolved atlas of the developing human cortex.
    Matthew G Keefe, Marilyn R Steyert, Tomasz J Nowakowski.
      The human neocortex is composed of diverse cell types1 that are generated during development according to spatially and temporally organized programmes initiated by neural stem cells2-5. Despite the growing number of studies that have captured snapshots of gene expression of single cells along the axis of differentiation and maturation, the underlying map of lineage relationships that link individual progenitor cells to specific subtypes of neurons and glia remains unknown, especially in humans. Here we applied prospective lineage tracing to map the manifold of human neural stem and progenitor cell differentiation across the developmental window encompassing neurogenesis and gliogenesis in human primary tissue. By profiling the clonal output of 6,402 progenitor cells, we created a lineage-resolved map of human cortical development. Here we show that cortical progenitors switch from glutamatergic to GABAergic (involving γ-aminobutyric acid) neurogenesis around midgestation, which coincides with an onset of oligodendrocyte generation. Additionally, we find that truncated radial glia maintain a glutamatergic neurogenic potential for a protracted period during human cortical development. Unexpectedly, we find that late-born glutamatergic neurons derived from truncated radial glia exhibit molecular features of deep cortical layer neurons and may contribute to the expansion of the subplate region during midgestation.
    DOI:  https://doi.org/10.1038/s41586-025-09033-8
  12. Sci Immunol. 2025 Nov 07. 10(113): eadt6616
    Characterization of the mammalian prodefinitive angio-hematopoietic lineage.
    Tomi Lazarov, Pierre-Louis Loyher, Hairu Yang, Zi-Ning Choo, Zihou Deng, Sonja Nowotschin, Ying-Yi Kuo, Ting Zhou, Araitz Alberdi-Gonzalez, Ralf Stumm, Elvira Mass, Elisa Gomez Perdiguero, Anna-Katerina Hadjantonakis, Frederic Geissmann.
      Mammalian hematopoietic cells arise from mesodermal progenitors in a close developmental relationship with endothelium and along three distinct cell lineages known as primitive, prodefinitive, and definitive hematopoiesis. However, the developmental hierarchies between early mesodermal progenitors, endothelium, and blood cell lineages are incompletely understood. Here, fate-mapping, cloning, and genetic experiments identified a population of KDR+CXCR4+ prodefinitive angio-hematopoietic progenitors (PDAPs) in murine primitive streak stage mesoderm and human induced pluripotent stem cell (hiPSC) cultures. PDAPs gave rise to yolk sac (YS) and rostral (cephalic) endothelial cells and RUNX1-dependent prodefinitive hematopoietic cells, including erythro-myeloid progenitors (EMPs) and tissue macrophages, via NOTCH1-independent hemogenic endothelial cells. Notably, PDAPs did not give rise to primitive erythropoiesis or to caudal endothelium and definitive hematopoiesis. These results identify a previously unrecognized layer of lineage segregation in early mammalian mesoderm that characterizes the prodefinitive angio-hematopoietic lineage and the origin of tissue macrophages and rostral blood vessels that may be of interest for pathophysiology and cell-based therapy efforts.
    DOI:  https://doi.org/10.1126/sciimmunol.adt6616
  13. Mol Cell. 2025 Nov 06. pii: S1097-2765(25)00853-6. [Epub ahead of print]
    Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis.
    Fan Zheng, Zanlin Yu, Junming Zhuang, Lingraj Vannur, William Nickols, YongQiang Wang, Liying Li, Sho Joseph Ozaki Tan, Seungmin Yoo, Yifan Cheng, Chuankai Zhou.
      Cytosolic translation activity is fine-tuned by environmental conditions primarily through signaling pathways that target translation initiation factors. Although mitochondria possess their own translation machinery, they lack an autonomous signaling network analogous to their cytosolic counterpart for regulating translation activity. Consequently, our understanding of how mitochondrial translation activity is adjusted under different metabolic environments remains very limited. Here, we report a noncanonical mechanism for regulating mitochondrial translation activity via metabolism-dependent changes in the mitochondrial ribosome (mitoribosome) in S. cerevisiae. These changes arise from a metabolism-modulated mitoribosome assembly pathway that regulates the composition and conformation of the mitoribosome, thereby adjusting its translation activity to meet metabolic demands. Moreover, the translation activity of the mitoribosome feeds back to regulate the biogenesis of nuclear-encoded mitochondrial proteins, influencing mitochondrial functions and aging. Such a ribosomal remodeling-based "gear-switching" mechanism represents an orthogonal mode of translation regulation, compensating for the absence of a translation-modulating signaling network within mitochondria.
    Keywords:  aging; metabolism; mitochondria; mitoribosome; translation activity
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.012
  14. Cell. 2025 Nov 05. pii: S0092-8674(25)01178-X. [Epub ahead of print]
    Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions.
    Hangpeng Li, James L T Dalgleish, George Lister, Maria Julia Maristany, Jan Huertas, Ana M Dopico-Fernandez, Joseph C Hamley, Nicholas Denny, Gianna Bloye, Weijiao Zhang, Lance Hentges, Roman Doll, Ye Wei, Michela Maresca, Emilia Dimitrova, Lior Pytowski, Edward A J Tunnacliffe, Mira Kassouf, Doug Higgs, Elzo de Wit, Robert J Klose, Lothar Schermelleh, Rosana Collepardo-Guevara, Thomas A Milne, James O J Davies.
      Chromatin structure is a key determinant of gene expression in eukaryotes, but it has not been possible to define the structure of cis-regulatory elements at the scale of the proteins that bind them. Here, we generate multidimensional chromosome conformation capture (3C) maps at base-pair resolution using Micro Capture-C ultra (MCCu). This can resolve contacts between individual transcription factor motifs within cis-regulatory elements. Using degron systems, we show that removal of Mediator complex components alters fine-scale promoter structure and that nucleosome depletion plays a key role in transcription factor-driven enhancer-promoter contacts. We observe that chromatin is partitioned into nanoscale domains by nucleosome-depleted regions. This structural conformation is reproduced by chemically specific coarse-grained molecular dynamics simulations of the physicochemical properties of chromatin. Combining MCCu with molecular dynamics simulations and super-resolution microscopy allows us to propose a unified model in which the biophysical properties of chromatin orchestrate contacts between cis-regulatory elements.
    Keywords:  chromatin structure; chromosome conformation capture; cis-regulatory elements; enhancer-promoter interactions; gene regulation; mediator complex; molecular dynamics simulations; nuclear organization; transcription factors
    DOI:  https://doi.org/10.1016/j.cell.2025.10.013
  15. Cell Rep. 2025 Oct 25. pii: S2211-1247(25)01243-4. [Epub ahead of print]44(11): 116472
    Poly-ubiquitylated transmembrane proteins outcompete other cargo for limited space inside clathrin-coated vesicles.
    Hao-Yang Liu, Susovan Sarkar, Feng Yuan, Grant Ashby, Carl C Hayden, Jon M Huibregtse, Jeanne C Stachowiak.
      Endocytic recycling of transmembrane proteins is essential to cellular function. The intracellular domains of transmembrane proteins are frequently ubiquitylated, a modification that is recognized by adaptor proteins during clathrin-mediated endocytosis. Recent work suggests that transmembrane proteins compete for space within highly crowded endocytic structures, suggesting that enhanced internalization of one group of transmembrane proteins may come at the expense of others. Here, we show that preferential internalization of poly-ubiquitylated transmembrane proteins can result in reduced endocytosis of mono-ubiquitylated and non-ubiquitylated proteins. Further, poly-ubiquitylated receptors significantly outcompeted their less ubiquitylated counterparts for uptake of extracellular ligands. These findings suggest that clathrin-coated vesicles may act as selective filters, prioritizing highly ubiquitylated transmembrane proteins for uptake while leaving others behind. Given that poly-ubiquitylation is thought to signal protein aging and damage, these findings suggest a mechanism for selective internalization of high priority cargo, with simultaneously exclusion and protection of functional proteins lacking poly-ubiquitylation.
    Keywords:  CP: Cell biology; clathrin; endocytosis; membrane traffic; transmembrane protein; ubiquitylation
    DOI:  https://doi.org/10.1016/j.celrep.2025.116472
  16. Nat Struct Mol Biol. 2025 Nov 03.
    Phosphorylation-dependent tuning of mRNA deadenylation rates.
    James A W Stowell, Conny W H Yu, Zhuo A Chen, Lily K DeBell, Giselle Lee, Tomos Morgan, Ludwig Sinn, Sylvie Agnello, Francis J O'Reilly, Juri Rappsilber, Stefan M V Freund, Lori A Passmore.
      Shortening of messenger RNA poly(A) tails by the Ccr4-Not complex initiates mRNA decay and is a major determinant of gene regulation. RNA adaptors modulate the specificity of deadenylation by binding to Ccr4-Not through their intrinsically disordered regions (IDRs). However, the determinants of specificity and their regulation are largely unclear. Here we use nuclear magnetic resonance spectroscopy, biochemical reconstitution and structural modeling to show that dispersed segments within the IDR of the fission yeast Puf3 RNA adaptor interact with Ccr4-Not, consistent with multivalency. Binding can be modulated by phosphorylation, altering the deadenylation rate in a continuously tunable manner. Regulation of deadenylation through multivalency and phosphorylation likely occurs in evolutionarily divergent IDRs from additional RNA adaptors, including human Pumilio and Tristetraprolin. Overall, our in vitro data suggest that mRNA decay can be regulated not only as a bistable on-off switch but also by a graded mechanism, rationalizing how post-transcriptional gene expression can be fine-tuned.
    DOI:  https://doi.org/10.1038/s41594-025-01688-1
  17. Nature. 2025 Nov 05.
    Lymph node environment drives FSP1 targetability in metastasizing melanoma.
    Mario Palma, Milena Chaufan, Cort B Breuer, Sebastian Müller, Marie Sabatier, Cameron S Fraser, Krystina J Szylo, Mahsa Yavari, Alanis Carmona, Mayher Kaur, Luiza Martins Nascentes Melo, Feyza Cansiz, June Monge-Lorenzo, Midori Flores, Eikan Mishima, Toshitaka Nakamura, Bettina Proneth, Marcos Labrado, Yanshan Liang, Nicole Cayting, Lan Zheng, Tatiana Cañeque, Ludovic Colombeau, Adam Wahida, José Pedro Friedmann Angeli, Alpaslan Tasdogan, Sheng Hui, Raphaël Rodriguez, Marcus Conrad, Nathan E Reticker-Flynn, Jessalyn M Ubellacker.
      Ferroptosis has emerged as an actionable target to eliminate therapy-resistant and metastatic cancers1. However, which ferroptosis surveillance systems may offer a therapeutic window to leverage redox maladaptation in cancer remains unclear. In melanoma, glutathione peroxidase 4 (GPX4) impedes ferroptosis during haematogenous metastasis, but is dispensable during lymphatic metastasis2. Here, using a metastatic mouse melanoma model selected for lymph node metastasis, we show that lymph-node-derived metastatic cells exhibit markedly diminished expression of glutamate-cysteine ligase (GCLC) and reduced glutathione (GSH) levels relative to their parental counterparts. This metabolic shift occurs within the hypoxic lymphatic niche. Under comparable low-oxygen conditions, GPX4 undergoes ubiquitination and proteasomal degradation. In response, lymph node metastatic cells acquire increased reliance on ferroptosis suppressor protein 1 (FSP1), which is localized with perinuclear lysosomes. These findings reveal that the reduced reliance on the GPX4 axis enables melanoma cells to shift toward FSP1 dependency. Notably, intratumoural monotherapy with selective FSP1 inhibitors (viFSP1 and FSEN1) effectively suppresses melanoma growth in lymph nodes, but not in subcutaneous tumours, emphasizing a microenvironment-specific dependency on FSP1. Thus, targeting FSP1 in the lymph nodes holds strong potential for blocking melanoma progression.
    DOI:  https://doi.org/10.1038/s41586-025-09709-1
  18. Cell Metab. 2025 Oct 31. pii: S1550-4131(25)00437-1. [Epub ahead of print]
    Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation.
    Maria-Kyriaki Drekolia, Janina Mettner, Daiyu Wang, Fredy Delgado Lagos, Christian Koch, Dennis Hecker, Jeanette Eresch, Yifang Mao, Marion Bähr, Dieter Weichenhan, Julio Cordero, Janina Wittig, Boran Zhang, Hanyu Cui, Xiaoming Li, James A Oo, Andreas Weigert, Mauro Siragusa, Stephan Klatt, Ingrid Fleming, Stefan Günther, Mario Looso, Ralf P Brandes, Harald F Langer, Andreas Papapetropoulos, Mahak Singhal, Marcel H Schulz, Christoph Plass, Joerg Heineke, Gergana Dobreva, Jiong Hu, Sofia-Iris Bibli.
      Endothelial metabolism underpins tissue regeneration, health, and longevity. We uncover a nuclear oxidative catabolic pathway linking cystine to gene regulation. Cells preparing to proliferate upregulate the SLC7A11 transporter to import cystine, which is oxidatively catabolized by cystathionine-γ-lyase (CSE) in the nucleus. This generates acetyl units via pyruvate dehydrogenase, driving site-specific histone H3 acetylation and chromatin remodeling that sustain endothelial transcription and proliferation. Combined loss of SLC7A11 and CSE abolishes cystine oxidative and reductive metabolism and causes embryonic lethality, whereas single deletions reveal distinct effects. SLC7A11 deficiency triggers compensatory cysteine de novo biosynthesis, partially maintaining angiogenesis, while CSE deletion disrupts nuclear cystine oxidative catabolism, transcription, and vessel formation. Therapeutically, cystine supplementation promotes vascular repair in retinopathy of prematurity, myocardial infarction, and injury in aging. These findings establish the role of cystine nuclear oxidative catabolism as a fundamental metabolic axis coupling nutrient utilization to gene regulation, with implications for vascular regeneration.
    Keywords:  CSE; SLC7A11; aging; cystine; epigenetics; vascular growth
    DOI:  https://doi.org/10.1016/j.cmet.2025.10.003
  19. EMBO J. 2025 Nov 05.
    Notch signaling is a driver of glandular stem cell activity and regenerative migration after damage.
    Davide Cinat, Rufina Maturi, Jeremy P Gunawan, Anne L Jellema-de Bruin, Laura Kracht, Paola Serrano Martinez, Yi Wu, Abel Soto-Gamez, Marc-Jan van Goethem, Inge R Holtman, Sarah Pringle, Lara Barazzuol, Rob P Coppes.
      Organoid models have significantly enhanced our understanding of adult stem cell function, however, uncovering regulatory mechanisms governing rare and often quiescent stem cells in glandular organs remains challenging. Here, we employ an integrative multi-omics approach, combining single-cell RNA sequencing, bulk ATAC and RNA sequencing, to profile the cellular populations and signaling pathways characterizing a mouse salivary gland organoid model across different temporal stages and after radiation-induced damage. Our findings identify Sox9- and Itgb1/Cd44-expressing cells as primitive adult stem/progenitor populations with a critical migratory role in tissue repair. Notch signaling is a key driver of self-renewal and migration in response to irradiation. Additionally, scRNA-seq analysis of irradiated salivary gland tissue confirms these findings in an in vivo setting. Extending these findings to murine and patient-derived salivary, mammary and thyroid gland organoids, we reveal the conserved role of Notch signaling in coordinating stem/progenitor cell-mediated regeneration across glandular tissues. These insights position Notch signaling as a central regulator of glandular stem cell-like populations and as a promising therapeutic target for enhancing glandular tissue regeneration following cancer therapies.
    Keywords:  Adult Stem Cells; Cell Migration; Glandular Organoids; Notch Signaling; Radiotherapy
    DOI:  https://doi.org/10.1038/s44318-025-00607-w
  20. Cell Rep Methods. 2025 Nov 03. pii: S2667-2375(25)00255-3. [Epub ahead of print] 101219
    Imaging the time course of DNA damage response at a nonrepetitive endogenous locus.
    Adam T Rybczynski, W Taylor Cottle, Po-Ta Chen, Jiwoong Kwon, Tiantian Shang, Yanbo Wang, Paul Meneses, Sushil Pangeni, Yeji Park, Momcilo Gavrilov, Taekjip Ha.
      DNA double-strand breaks (DSBs) are among the most genotoxic lesions. Investigating the cellular dynamics of repair factors during DSB repair requires methodologies that preserve both spatial and temporal information. Here, we describe a method for tracking repair progression over time at any desired genomic locus by combining DSB induction on the seconds timescale (very fast CRISPR) and genomic labeling using local genome denaturation (genome oligopaint via local denaturation fluorescence in situ hybridization [GOLDFISH]). Through protocol optimization to retain repair signatures such as γH2AX, p53-binding protein 1 (53BP1), and BRCA1, we show that the kinetics of DSB foci formation at nonrepetitive endogenous loci can be measured with minutes time resolution.
    Keywords:  CP: imaging; CP: molecular biology; DNA DSB; DNA FISH; DNA damage response; DNA damage response kinetics; DNA double-strand breaks; DNA repair; GOLDFISH; vfCRISPR
    DOI:  https://doi.org/10.1016/j.crmeth.2025.101219
  21. Nat Methods. 2025 Nov 03.
    Squidiff: predicting cellular development and responses to perturbations using a diffusion model.
    Siyu He, Yuefei Zhu, Daniel Naveed Tavakol, Haotian Ye, Yeh-Hsing Lao, Zixian Zhu, Cong Xu, Shradha Chauhan, Guy Garty, Raju Tomer, Gordana Vunjak-Novakovic, James Zou, Elham Azizi, Kam W Leong.
      Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying disease mechanisms remains challenging. Here we present Squidiff, a diffusion model-based generative framework that predicts transcriptomic changes across diverse cell types in response to environmental changes. We demonstrate the robustness of Squidiff across cell differentiation, gene perturbation and drug response prediction. Through continuous denoising and semantic feature integration, Squidiff learns transient cell states and predicts high-resolution transcriptomic landscapes over time and conditions. Furthermore, we applied Squidiff to model blood vessel organoid development and cellular responses to neutron irradiation and growth factors. Our results demonstrate that Squidiff enables in silico screening of molecular landscapes and cellular state transitions, facilitating rapid hypothesis generation and providing valuable insights into the regulatory principles of cell fate decisions.
    DOI:  https://doi.org/10.1038/s41592-025-02877-y
  22. Nat Genet. 2025 Nov 03.
    Functionally dominant hotspot mutations of mitochondrial ribosomal RNA genes in cancer.
    Sonia Boscenco, Jacqueline Tait-Mulder, Minsoo Kim, Cerise Tang, Tricia Park, Flora McNulty, Sergio Lilla, Sara Zanivan, Alejandro Huerta-Uribe, Benan Nalbant, Mark Zucker, David Sumpton, Geoffray Monteuuis, Christopher B Jackson, Wei Wei, Patrick F Chinnery, Ronan Chaligne, Caleb A Lareau, Ed Reznik, Payam A Gammage.
      The vast majority of recurrent somatic mutations arising in tumors affect protein-coding genes in the nuclear genome. Here, through population-scale analysis of 14,106 whole tumor genomes, we report the discovery of highly recurrent mutations affecting both the small (12S, MT-RNR1) and large (16S, MT-RNR2) mitochondrial RNA subunits of the mitochondrial ribosome encoded within mitochondrial DNA (mtDNA). Compared to non-hotspot positions, mitochondrial rRNA hotspots preferentially affected positions under purifying selection in the germline and demonstrated structural clustering within the mitoribosome at mRNA and tRNA interacting positions. Using precision mtDNA base editing, we engineered models of an exemplar MT-RNR1 hotspot mutation, m.1227G>A. Multimodal profiling revealed a heteroplasmy-dependent decrease in mitochondrial function and loss of respiratory chain subunits from a heteroplasmic dosage of ~10%. Mutation of conserved positions in ribosomal RNA that disrupt mitochondrial translation therefore represent a class of functionally dominant, pathogenic mtDNA mutations that are under positive selection in cancer genomes.
    DOI:  https://doi.org/10.1038/s41588-025-02374-0
  23. Cell Death Dis. 2025 Nov 07. 16(1): 812
    Pre-rRNAs control mitosis by maintaining chromosomal segregation through protecting SMC2 from AURKA-mediated phosphorylation.
    Shiqi Sun, Kunqi Su, Yang Jiang, Yuying Wang, Yang Hu, Chang Wang, Zhuochen Zhao, Chunfeng Zhang, Baocai Xing, Xiaojuan Du.
      In interphase, 47S pre-rRNA is transcribed by RNA polymerase I (Pol I) and processed to form intermediate pre-rRNAs and finally produce mature rRNAs in the nucleolus. During mitosis, nucleolus disassembles and pre-rRNAs including 45S, 30S and 32S pre-rRNAs relocate in the peri-chromosomal region (PR). Inhibition of pre-rRNA transcription impairs chromosome dispersion in prometaphase. However, how pre-rRNAs regulate mitosis remains elusive. Here, we unravel a novel mechanism for pre-rRNAs to control mitosis. Inhibition of Pol I prolongs the mitotic process and induces defective chromosomal segregation, resulting in mitotic catastrophe. We isolated chromosome and determined the chromosome-binding proteins by mass-spectrometry. Using quantitative proteomics analysis, immunoprecipitation and immunofluorescent staining, we found that AURKA approaches chromosome when Pol I is inhibited. The AURKA-binding proteins on the chromosome were determined by immunoprecipitation and mass-spectrometry after cells were treated with Act D, BMH-21 or CX5461, respectively, and the chromosomal segregation controlling proteins were selected. When Pol I was inhibited, the binding of AURKA with SMC2, the crucial component of Condensin, is significantly enhanced. Importantly, SMC2 is phosphorylated by AURKA only when Pol I was inhibited. Alignment of SMC2 amino acid sequence with substrates of AURKA shows that SMC2 possesses the consensus R/K/N-R-X-S/T-B, and T574 is the only potential AURKA-catalyzed phosphorylation site. Indeed, SMC2 T574 is phosphorylated by AURKA in cell and in vitro. Thereafter, we generated SMC2 T574-P specific antibody, and confirmed that endogenous SMC2 T574 is phosphorylated by AURKA in mitosis in the absence of pre-rRNAs. Consequently, phosphorylation of SMC2 T574 disrupts the SMC2/SMC4 binding and the binding of SMC2 and SMC4 to chromosomal DNA, leading to chromosomal segregation defect. The phosphorylation deficient Flag-SMC2 T574A reverses the mitotic catastrophe caused by Pol I inhibition. Collectively, we demonstrate that pre-rRNAs protect SMC2 from the AURKA-mediated phosphorylation to maintain normal mitosis.
    DOI:  https://doi.org/10.1038/s41419-025-08169-9
  24. Dev Cell. 2025 Nov 03. pii: S1534-5807(25)00605-7. [Epub ahead of print]60(21): 2843-2845
    In vitro oogenesis breaks free of the ovary.
    Jay W Zussman, Diana J Laird.
      In this issue of Developmental Cell, Nosaka et al. differentiate mouse pluripotent stem cells to large germinal vesicle-stage oocyte-like cells in the absence of ovarian somatic cells. Their paradigm advances the field toward clinical translation and offers insights into oogonial cyst breakdown, X chromosome dynamics, and requirements for oocyte growth and meiotic resumption.
    DOI:  https://doi.org/10.1016/j.devcel.2025.09.020
  25. Nat Aging. 2025 Nov 03.
    A versatile cohesion manipulation system probes female reproductive age-related egg aneuploidy.
    Jiyeon Leem, Tom Lemonnier, Ani Khutsaidze, Lei Tian, Xiaojun Xing, Suxia Bai, Timothy Nottoli, Binyam Mogessie.
      Female reproductive aging is accompanied by a sharp increase in egg aneuploidy rates. Premature loss of chromosome cohesion proteins and early separation of chromosomes are thought to cause high aneuploidy rates during maternal aging. However, because cohesion loss occurs gradually throughout a woman's reproductive lifespan, and because cytoskeletal defects alone can lead to chromosomal abnormalities, the main causes of the rapid rise in aneuploidy at older reproductive ages are still unclear. In this study, we created a versatile and tunable cohesion manipulation system that enables rapid, dose-dependent degradation of the meiotic cohesin REC8 in live mouse oocytes. By coupling this system with quantitative high-resolution live imaging, we directly observed cohesion protein behavior during meiosis and tested the longstanding threshold model of aneuploidy development. Our results show that premature sister chromatid separation sharply increases only when REC8 levels drop below a critical threshold, supporting the idea of a nonlinear, vulnerability-triggering cohesion limit. We also used our system to examine how other age-related issues, such as cytoskeletal disruption and partial centromere dysfunction, can exacerbate chromatid separation in the context of weakened cohesion. This work provides a tractable oocyte platform for modeling and dissecting the multifactorial mechanisms driving female reproductive age-related egg aneuploidy.
    DOI:  https://doi.org/10.1038/s43587-025-00997-w
  26. Cell. 2025 Nov 04. pii: S0092-8674(25)01149-3. [Epub ahead of print]
    Disparate leukemia mutations converge on nuclear phase-separated condensates.
    Gandhar K Datar, Elmira Khabusheva, Archish Anand, Joshua Beale, Marwa Sadek, Chun-Wei Chen, Evdokiia Potolitsyna, Nayara Alcantara-Contessoto, Guangyuan Liu, Josephine De La Fuente, Christina Dollinger, Anna Guzman, Alejandra Martell, Katharina Wohlan, Abhishek Maiti, Nicholas J Short, S Stephen Yi, Vibeke Andresen, Bjørn Tore Gjertsen, Brunangelo Falini, Rachel E Rau, Lorenzo Brunetti, Nidhi Sahni, Margaret A Goodell, Joshua A Riback.
      During cancer development, mutations promote changes in gene expression that cause transformation. Leukemia associated with aberrant HOXA expression is driven by translocations of nucleoporin genes or KMT2A as well as mutations in NPM1. The mechanistic convergence of these disparate mutations remains elusive. Here, we demonstrate that mutant nucleophosmin 1 (NPM1c) forms nuclear condensates in human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to recruit NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo leukemic expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate that we term the coordinating body (C-body) and establish C-bodies as a therapeutic vulnerability in leukemia.
    Keywords:  AML; HOX; KMT2A; MENIN; NPM1; NUP98; XPO1; acute myeloid leukemia; condensate; phase separation
    DOI:  https://doi.org/10.1016/j.cell.2025.10.010
  27. Trends Cell Biol. 2025 Nov 06. pii: S0962-8924(25)00225-9. [Epub ahead of print]
    Membrane curvature at the ER-PM contact sites.
    Yang Yang, Luis A Valencia, Bianxiao Cui.
      Membrane contact sites between the endoplasmic reticulum (ER) and plasma membrane (PM) are essential for lipid transfer, calcium signaling, and membrane organization. While the formation and function of ER-PM contacts are increasingly well-characterized, the spatiotemporal regulation of their localization remains elusive. Emerging evidence using nanopatterned substrates, ultrastructural imaging, and protein localization analyses indicates that membrane curvature can act as a spatial cue for the recruitment of specific tethering proteins, influencing where contact sites form. This opinion article synthesizes recent advances linking membrane topography ER-PM contact organization and highlights systems where curvature actively orchestrates contact position through curvature-sensing proteins. It also outlines key unanswered questions about how membrane curvature integrates into broader signaling networks that govern organelle contact communication.
    Keywords:  ER–PM contact; RyR2; calcium signaling; junctophilin; membrane curvature
    DOI:  https://doi.org/10.1016/j.tcb.2025.10.002
  28. Annu Rev Physiol. 2025 Nov 07.
    Coordinated Remodeling of Ca2+ Signaling and Intracellular Organelles During Cell Division.
    Fang Yu, Lama Assaf, Khaled Machaca.
      Cell division is essential for organismal growth and development and is associated with changes in signaling dynamics, including Ca2+ signaling, to meet structural, functional, and energetic needs. The process of cell division must ensure equal separation of both the genetic material and cellular organelles. Organelle segregation to the daughter cells is in most cases associated with their remodeling to support equal distribution. Here, we review the concurrent remodeling of organelles and Ca2+ signaling during cell division. Interesting patterns emerge, showing that organelle dynamics, specifically the plasma membrane, endoplasmic reticulum, and mitochondria, underlie Ca2+ signaling remodeling during cell division.
    DOI:  https://doi.org/10.1146/annurev-physiol-061324-091825
  29. Science. 2025 Nov 06. 390(6773): 568-569
    Cell signaling meets gene transcription.
    Richard Young.
      Receptor tyrosine kinases directly regulate RNA polymerase II in the nucleus.
    DOI:  https://doi.org/10.1126/science.aec1434
  30. Nature. 2025 Nov 05.
    Targeting FSP1 triggers ferroptosis in lung cancer.
    Katherine Wu, Alec J Vaughan, Jozef P Bossowski, Yuan Hao, Aikaterini Ziogou, Seon Min Kim, Tae Ha Kim, Mari N Nakamura, Ray Pillai, Mariana Mancini, Sahith Rajalingam, Mingqi Han, Toshitaka Nakamura, Lidong Wang, Suckwoo Chung, Diane Simeone, David Shackelford, Yun Pyo Kang, Marcus Conrad, Thales Papagiannakopoulos.
      Emerging evidence indicates that cancer cells are susceptible to ferroptosis, a form of cell death that is triggered by uncontrolled lipid peroxidation1-3. Despite broad enthusiasm about harnessing ferroptosis as a novel anti-cancer strategy, whether ferroptosis is a barrier to tumorigenesis and can be leveraged therapeutically remains unknown4,5. Here, using genetically engineered mouse models of lung adenocarcinoma, we performed tumour-specific loss-of-function studies of two key ferroptosis suppressors, GPX46,7 and ferroptosis suppressor protein 1 (FSP1)8,9, and observed increased lipid peroxidation and robust suppression of tumorigenesis, suggesting that lung tumours are highly sensitive to ferroptosis. Furthermore, across multiple pre-clinical models, we found that FSP1 was required for ferroptosis protection in vivo, but not in vitro, underscoring a heightened need to buffer lipid peroxidation under physiological conditions. Lipidomic analyses revealed that Fsp1-knockout tumours had an accumulation of lipid peroxides, and inhibition of ferroptosis with genetic, dietary or pharmacological approaches effectively restored the growth of Fsp1-knockout tumours in vivo. Unlike GPX4, expression of FSP1 (also known as AIFM2) was prognostic for disease progression and poorer survival in patients with lung adenocarcinoma, highlighting its potential as a viable therapeutic target. To this end, we demonstrated that pharmacologic inhibition of FSP1 had significant therapeutic benefit in pre-clinical lung cancer models. Our studies highlight the importance of ferroptosis suppression in vivo and pave the way for FSP1 inhibition as a therapeutic strategy for patients with lung cancer.
    DOI:  https://doi.org/10.1038/s41586-025-09710-8
  31. Nat Cancer. 2025 Nov 06.
    Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration.
    Jing Han, Xiaoman Lu, Mengmeng Guo, Ruizhe He, Meilian Zhuo, Saisai Wang, Yong Li, Xiangzheng Liu, Di Zou, Jiacheng Wang, Jiangjiao Mao, Qian Chen, Xia Wang, Junya Peng, Wei Xie, Charles J David, Mo Chen.
      Acute pancreatitis-induced acinar-to-ductal metaplasia involves global chromatin remodeling and contributes to normal tissue regeneration. Oncogenic KRAS hijacks this process to promote PDAC formation. Here we show that regeneration and KRASG12D-driven oncogenesis can be decoupled from tissue regeneration through a chromatin remodeler, SMARCA5. We show that SMARCA5 maintains KRASG12D-dependent chromatin accessibility at regions specifically required for malignancy, without affecting chromatin opening that occurs during normal regeneration. Without SMARCA5, regeneration can be restored in the presence of KRASG12D. Mechanistically, regeneration-related or malignancy-related chromatin remodeling activities occur in a time-sensitive manner. The activity of SMARCA5 is controlled spatiotemporally by transcription factor RUNX1, which only accumulates at sufficient levels with sustained MAPK signals. We further show that inhibition of the SMARCA5-containing NoRC complex specifically inhibits the growth of PDAC organoid but not that of normal tissue derived from patients.
    DOI:  https://doi.org/10.1038/s43018-025-01065-3
  32. Nat Aging. 2025 Nov 06.
    Fluorescence lifetime clocks quantify senescence and aging.
    Chenxu Yan, Caiqi Liu, Bofang Liu, Qiaoqiao Zheng, Xingyuan Zhao, Sirui Lu, Xiaoqing Fu, Wennan Li, Juan Li, Dan Li, Yongkang Yao, Yutao Zhang, Huanhu Zhu, Ping Shi, Wei-Hong Zhu, Zhiqian Guo.
      Epigenetic and omics-based clocks have provided invaluable tools to quantify aging, yet these clocks do not provide direct readouts of aging in real-time in living systems. As methylation changes in nucleolar ribosomal DNA are reliably associated with aging and cellular senescence, we hypothesized that shifts in rRNA species could be leveraged to generate image-based clocks using selective dyes. Here we engineer sensitive and photostable hybrid polymethine dyes selective for rRNA. We present a fluorescence lifetime imaging strategy to visually quantify age- and cellular senescence-dependent nucleolar RNA changes that bypasses requirements for extensive sample preparation such as DNA isolation and enables in vivo, real-time age quantification. We demonstrate resolution through cellular to organismal scales and demonstrate translatability by generating clocks from cells and tissues, as well as Caenorhabditis elegans, mice and human samples. Our fluorescence lifetime imaging strategy thus enables in vivo measurements of aging and senescence and expands the toolbox for aging biology research and translation.
    DOI:  https://doi.org/10.1038/s43587-025-01001-1
  33. J Cell Sci. 2025 Nov 03. pii: jcs.263920. [Epub ahead of print]
    Endoplasmic reticulum protein FAM134B acts as a regulator of mitochondrial morphology.
    Sebabrata Maity, Anwesha Dutta Gupta, Izaz Monir Kamal, Rajdeep Das, Rupsha Mondal, Arpit Tyagi, Deepak Sharma, Joy Chakraborty, Saikat Chakrabarti, Oishee Chakrabarti.
      The endoplasmic reticulum (ER) and mitochondria are known to affect myriad cellular mechanisms. More recently, dynamic association between them has been identified in different eukaryotes; these interactions vary in their composition and involvement in regulation of intracellular machineries. FAM134B or RETREG1, originally identified as an oncogene, regulates ER membrane shape and curvature. It is a key ER-phagy or reticulophagy receptor, which promotes autophagy of not only the ER but also simultaneous dual autophagy of ER and mitochondria. While it is known that FAM134B can potentiate contact with mitochondria, its direct involvement in affecting mitochondrial dynamics remains unexplored. Here we show that FAM134B can interact with the canonical fission-promoting protein, DRP1. Functional depletion of FAM134B leads to local Actin rearrangement and reduced DRP1 recruitment onto mitochondria, resulting in hyperfusion. A decrease in FAM134B levels is observed with aging in rat brains, cell and mouse models of Parkinson's disease and patient-derived samples. Our study establishes FAM134B as the ER partner that helps in maintaining mitochondrial morphology and dynamics.
    Keywords:  DRP1; FAM134B; Fission; Mitochondrial hyperfusion
    DOI:  https://doi.org/10.1242/jcs.263920
  34. Nat Struct Mol Biol. 2025 Nov 06.
    Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1.
    Connor Arkinson, Christine L Gee, Zeyuan Zhang, Ken C Dong, Andreas Martin.
      The 26S proteasome targets many cellular proteins for degradation during homeostasis and quality control. Proteasome-interacting cofactors modulate these functions and aid in substrate degradation. Here we solve high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and substoichiometric concentrations by time-resolved cryo-electron microscopy (cryo-EM). We identify distinct binding modes of TXNL1 that depend on the proteasome conformation and ATPase motor states. Together with biophysical and biochemical experiments, we show that the resting-state proteasome binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, in the actively degrading proteasome, TXNL1 uses additional interactions for high-affinity binding, whereby its C-terminal tail covers the catalytic groove of Rpn11 and coordinates the active-site Zn2+. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in several spiral-staircase arrangements that indicate temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the β-barrel mEos3.2 substrate while the ATPase hexamer is in a particular staircase register. Our findings advance current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct conformational states to coordinate cofactor binding and substrate processing.
    DOI:  https://doi.org/10.1038/s41594-025-01695-2
  35. Cell Rep. 2025 Nov 03. pii: S2211-1247(25)01276-8. [Epub ahead of print]44(11): 116505
    Tunneling nanotube-mediated stem cell immunomodulation dysfunction promotes adipose inflammation and insulin resistance in GDM.
    Bingnan Chen, Xuyang Chen, Jianxin Li, Ruohan Hu, Lijun Yang, Hongli Li, Xinmi Liu, Richard D Cannon, Richard Saffery, Boris Novakovic, Hongbo Qi, Hua Zhang, Xiaobo Zhou.
      Adipose-derived stem cells (ADSCs) represent a promising therapeutic resource, yet their immunometabolic regulation remains poorly defined. Here, we reveal a tunneling nanotube (TNT)-mediated communication mechanism between ADSCs and adipose tissue macrophages (ATMs) that maintains metabolic homeostasis during pregnancy. Using gestational diabetes mellitus (GDM) mouse models combined with live-cell imaging, scanning electron microscope, and multi-omics approaches, we demonstrate that mitochondrial transfer from ADSCs to ATMs via TNTs sustains ATM metabolic fitness. This process is governed by the WNT5A-RhoA-ROCK1 axis and becomes impaired under metabolic stress, driving ATMs inflammatory polarization and insulin resistance. Importantly, in situ ADSC administration restores mitochondrial transfer and improves metabolic parameters in GDM mice. Collectively, our work establishes TNT-mediated organelle sharing as a fundamental mechanism of stem cell-immune interaction and demonstrates that ADSC-based therapy represents a promising strategy for GDM by reprogramming the metabolism of immune cells.
    Keywords:  CP: Metabolism; CP: Stem cell research; adipose tissue macrophages; adipose-derived stem cells; gestational diabetes mellitus; mitochondria; tunneling nanotubes
    DOI:  https://doi.org/10.1016/j.celrep.2025.116505
  36. Curr Biol. 2025 Nov 05. pii: S0960-9822(25)01322-3. [Epub ahead of print]
    A lipid flippase shapes the ciliary membrane and is essential for ciliogenesis.
    Zhengmao Wang, Ruida He, Qingqing Liu, William J Snell, Muqing Cao, Junmin Pan.
      Ciliary motility and signaling are essential for human development and homeostasis.1,2 Although assembly of the microtubule-based core of the cilium, the axoneme, is well studied, we know little about formation of the cylindrically shaped ciliary membrane.2,3 During ciliogenesis, and in seamless coordination with the assembly of the axoneme, this membrane is built from the lipid bilayers of pre-ciliary membrane vesicles delivered near the base of the organelle.3,4 Upon vesicle exocytosis, their membrane curvature must be reversed as they become incorporated into the oppositely curved ciliary membrane. Here, we report that aminophospholipid flippases regulate the lipid composition of the outer leaflet of the ciliary membrane and are critical determinants of ciliary membrane shape and ciliogenesis. In mammalian cells, depletion of flippases results in fewer and shorter cilia. Upon initiation of ciliogenesis in Chlamydomonas, aminophospholipid flippase 2 (ALA2) is rapidly recruited laterally from the plasma membrane to the nascent ciliary membrane, where it appears as a C-terminally truncated form. Phosphatidylethanolamine (PE) is aberrantly enriched in the outer leaflet of the ciliary membrane of ala2 and ala1;ala2 mutants. Absence of ALA2 alone leads to diminished ciliary length, ciliary swelling, and frequent organelle detachment. In the double mutants, all newly formed cilia detach soon after ciliogenesis begins. This work reveals that the flippase-regulated lipid composition of the outer leaflet of the ciliary membrane determines the membrane curvature of this essential organelle, with implications for membrane remodeling in health and disease.
    Keywords:  Chlamydomonas; PE; cilia and flagella; ciliary membrane; ciliogenesis; lipid asymmetry; membrane curvature; phosphatidylethanolamine; phospholipid flippases
    DOI:  https://doi.org/10.1016/j.cub.2025.10.014
  37. Science. 2025 Nov 06. eadv7129
    The origin of hepatocellular carcinoma depends on metabolic zonation.
    Jason Guo, Roger Liang, Andrew Chung, Zhijie Li, Boyuan Li, Eric Chen, Lin Li, Jingjing Wang, Meng-Hsiung Hsieh, Ivy Xiangyi Fang, Benjamin Kroger, Yunguan Wang, Min Zhu, Xiongzhao Ren, Greg Mannino, Yuemeng Jia, Yonglong Wei, Stephen Moore, Daniel J Siegwart, Stephen S Chung, Zixi Wang, Tripti Sharma, Suman Komjeti, Yi Han, Purva Gopal, Guanghua Xiao, Tao Wang, Hao Zhu.
      The origin of cancer is poorly understood because premalignant cells are rarely followed in their native environments. While the spatial compartmentalization of metabolic functions is critical for proper liver function, it is unknown if cancers arise from some zones but not others, and if there are metabolic determinants of cancer risk. Zone-specific, mosaic introduction of Ctnnb1 and Arid2 mutations, commonly co-mutated genes in hepatocellular carcinoma (HCC), showed that position and metabolic context determine clone fates. Ctnnb1/Arid2-driven cancers were much more likely to arise in zone 3. The zone 3 genes Gstm2 and Gstm3 were required for efficient HCC initiation, in part through inhibition of ferroptosis. In the liver, the zonal determinants of HCC development can reveal metabolic vulnerabilities of cancer.
    DOI:  https://doi.org/10.1126/science.adv7129
  38. Nat Commun. 2025 Nov 06. 16(1): 9715
    HIRA defines early replication initiation zones independently of their genome compartment.
    Tina Karagyozova, Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Rocío Nunez-Vazquez, Marc A Martí-Renom, Leonid A Mirny, Geneviève Almouzni.
      Chromatin states and 3D architecture have been used as proxy to identify replication initiation zones (IZs) in mammalian cells, yet their functional interconnections remain a puzzle. Here, to dissect these relationships, we focus on the histone H3.3 chaperone HIRA recently implicated in early initiation zone (IZ) definition. We monitor 3D organisation, chromatin accessibility and histone post-translational modifications (PTMs) in wild-type and HIRA knock-out cells in parallel with early replication initiation. In the absence of HIRA, compartment A loses H3.3 enrichment and gains accessibility without changes in associated histone post-translational modifications (PTMs). Furthermore, impaired early firing at HIRA-dependent IZs does not correspond to changes in chromatin accessibility or patterns of histone H3 PTMs. Additionally, a small subset of early IZs initially in compartment A switch to B and lose early initiation in the absence of HIRA. Critically, HIRA complementation restores these early IZ, and H3.3 variant enrichment, without substantial compartment reversal. Thus, while HIRA contributes to compartment A features, its role in regulating early replication initiation can be uncoupled from accessibility, histone marks and compartment organisation.
    DOI:  https://doi.org/10.1038/s41467-025-65130-2
  39. Science. 2025 Nov 06. eadx9717
    NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT.
    Zheng Wu, Phong T Nguyen, Varun Sondhi, Run-Wen Yao, Zhifang Lu, Tao Dai, Jui-Chung Chiang, Feng Cai, Imani M Williams, Eliot B Blatt, Zengfu Shang, Ling Cai, Jing Zhang, Mya D Moore, Islam Alshamleh, Xiangyi Li, Tamaratare Ogu, Lauren G Zacharias, Rainah Winston, Joao S Patricio, Xandria Johnson, Wei-Min Chen, Qian Cong, Thomas P Mathews, Yuanyuan Zhang, Limei Zhang, Ralph J DeBerardinis.
      Cells generate purine nucleotides through de novo purine biosynthesis (DNPB) and purine salvage. Purine salvage represses DNPB to prevent excessive purine nucleotide synthesis through mechanisms that are incompletely understood. We identified Nudix hydrolase 5 (NUDT5) as a DNPB regulator. During purine salvage, NUDT5 suppresses DNPB independently of its catalytic function but through interaction with phosphoribosyl pyrophosphate amidotransferase (PPAT), the rate-limiting enzyme in the DNPB pathway. The NUDT5-PPAT interaction promoted PPAT oligomerization, suppressed PPAT's enzymatic activity, and facilitated disassembly of the purinosome, a metabolon that functions in DNPB. Disrupting the NUDT5-PPAT interaction overcame DNPB suppression during purine salvage, permitting excessive DNPB and inducing thiopurine resistance. Therefore, NUDT5 governs the balance between DNPB and salvage to maintain appropriate cellular purine nucleotide concentrations.
    DOI:  https://doi.org/10.1126/science.adx9717
  40. Cell Stem Cell. 2025 Nov 06. pii: S1934-5909(25)00370-4. [Epub ahead of print]32(11): 1639-1658
    Tissue regeneration: Unraveling strategies for resolving pathological fibrosis.
    Jiao Li, Shuyong Wang, Jie Yuan, Xiaoxu Mao, Xuan Wang, Lincheng Zhang, Qiulin Dong, Ziye Chen, Yunfang Wang, Nan Tang.
      Tissues are constantly exposed to stresses that cause both cellular and structural damage. In response, a coordinated healing process restores tissue integrity and functionality. When these stresses persist or the healing process becomes dysregulated, progressive tissue fibrosis can emerge. This condition is characterized by excessive scarring, disrupted tissue architecture, and loss of organ function. In this review, we explore the relationship between regeneration and fibrosis, with a focus on the lung and liver. We dissect cellular contributions and interplay among fibroblasts, epithelial progenitors, immune components, and vasculature in both regenerative and fibrotic responses to tissue injury. We also examine therapeutic strategies under development that navigate the complexities of immune mediators, fibrogenic myofibroblasts, and excess extracellular matrix (ECM) with small-molecule targeting and various cell-based approaches. By elucidating regulatory networks controlling regeneration and fibrosis, we aim to inform the development of targeted strategies to alleviate or reverse fibrosis, ultimately supporting long-term tissue health.
    Keywords:  fibrosis; fibrosis resolution; liver; lung; myofibroblast; regeneration
    DOI:  https://doi.org/10.1016/j.stem.2025.10.002
  41. J Mol Biol. 2025 Nov 01. pii: S0022-2836(25)00579-0. [Epub ahead of print] 169513
    Imaging the cytoplasmic lives of single mRNAs.
    Agata D Misiaszek, Jeffrey A Chao.
      Once an mRNA is exported to the cytoplasm, a transcript's fate is determined by the combinatorial interaction of a myriad of RNA-binding proteins that will determine its localization, translation and, eventual, degradation. To understand how these processes are regulated temporally and spatially in cells, a host of single-molecule fluorescent microscopy methodologies have been developed to interrogate different steps in the gene expression pathway. Here, we have highlighted the recent contributions of single-molecule measurements towards understanding the cytoplasmic lives of mRNAs and provide an outlook for future challenges and developments in the field.
    Keywords:  localization; mRNA degradation; single-molecule imaging; translation
    DOI:  https://doi.org/10.1016/j.jmb.2025.169513
  42. Nat Biotechnol. 2025 Nov 06.
    Site-specific DNA insertion into the human genome with engineered recombinases.
    Alison Fanton, Liam J Bartie, Juliana Q Martins, Vincent Q Tran, Laine Goudy, Courtney Kernick, Matthew G Durrant, Jingyi Wei, Zev Armour-Garb, April Pawluk, Silvana Konermann, Alexander Marson, Luke A Gilbert, Theodore L Roth, Patrick D Hsu.
      Insertions of large DNA sequences into the genome are broadly enabling for research and therapeutic applications. Large serine recombinases (LSRs) can mediate direct, site-specific genomic integration of multi-kilobase DNA sequences without a pre-installed landing pad, albeit with low insertion rates and high off-target activity. Here we present an engineering roadmap for jointly optimizing their DNA recombination efficiency and specificity. We combine directed evolution, structural analysis and computational models to rapidly identify additive mutational combinations. We further enhance performance through donor DNA optimization and dCas9 fusions, enabling simultaneous target and donor recruitment. Our top engineered LSR variants, superDn29-dCas9, goldDn29-dCas9 and hifiDn29-dCas9, achieve up to 53% integration efficiency and 97% genome-wide specificity at an endogenous human locus and effectively integrate large DNA cargoes up to 12 kb for stable expression in non-dividing cells, stem cells and primary human T cells. Rational engineering of DNA recombinases enables precise and efficient single-step genome insertion for diverse applications across gene and cell therapies.
    DOI:  https://doi.org/10.1038/s41587-025-02895-3
  43. Proc Natl Acad Sci U S A. 2025 Nov 11. 122(45): e2507935122
    Chemical compensation to mechanical loss in cell mechanosensation.
    Qin Ni, Zhuoxu Ge, Anindya Sen, Yufei Wu, Jinyu Fu, Alice Amitrano, Nitish Srivastava, Konstantinos Konstantopoulos, Sean X Sun.
      Mammalian cells sense and respond to environmental changes using a complex and intelligent system that integrates chemical and mechanical signals. The transduction of mechanical cues into chemical changes modulates cell physiology, allowing a cell to adapt to its microenvironment. Understanding how the chemical and mechanical regulatory modules interact is crucial for elucidating mechanisms of mechanosensation and cellular homeostasis. In this study, we find that cells exhibit nonmonotonic changes in cell volume and intracellular pH when subjected to physical stimuli and varying degrees of actomyosin cytoskeleton disruption. We find that these nonmonotonic responses are mediated by a chemical compensation mechanism, where the attenuation of actomyosin activity stimulates the activity of PI3K/Akt pathway. This, in turn, activates sodium-hydrogen exchanger 1 (NHE1), resulting in elevated intracellular pH and increased cell volume. Furthermore, we identify a competitive interaction between the PI3K/Akt and MAPK/ERK pathways-two major regulators of cell proliferation and motility. This competition modulates the chemical compensation based on the relative activities of these pathways. Our mathematical modeling reveals the network structure that is essential for establishing the nonmonotonic response. Interestingly, this regulatory system is altered in HT1080 fibrosarcoma, highlighting a potential mechanistic divergence in cancer cells in contrast to their normal-like counterpart, such as NIH 3T3 and HFF-1 fibroblasts. Overall, our work reveals a compensatory mechanism between chemical and mechanical signals, providing an infrastructure to elucidate the integrated mechanochemical response to environmental stimuli.
    Keywords:  PI3K signaling; biophysical modeling; cell volume; cytoskeleton; mechanosensation
    DOI:  https://doi.org/10.1073/pnas.2507935122
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