bims-ginsta Biomed News
on Genome instability
Issue of 2025–11–23
forty papers selected by
Jinrong Hu, National University of Singapore
  1. Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
  2. Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine.
  3. Reprogramming the GRHL2-CDK19 axis by gene therapy alleviates prostate aging.
  4. Genetic elements promote retention of extrachromosomal DNA in cancer cells.
  5. Cadherins modulate the self-organizing potential of pseudo-embryos.
  6. Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
  7. Capturing aberrant cell behaviors producing defects in human embryos via live imaging.
  8. Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants.
  9. Retinal calcium waves coordinate uniform tissue patterning of the Drosophila eye.
  10. Hepatic zonation determines tumorigenic potential of mutant β-catenin.
  11. Organ-specific rewiring of mitochondrial integrity through COX7A dictates cellular ploidy control.
  12. A mechanical origin for implantation defects in embryos from aged females.
  13. ZAK activation at the collided ribosome.
  14. IFN-I signaling enhances salivary gland stem and progenitor cell activity after irradiation.
  15. Novel Tissue Mechanics-Guided Cellular Flows Enable the Evolution of Feather Follicles.
  16. Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation.
  17. Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.
  18. Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells.
  19. Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulation.
  20. Engineering Inducible Cell Fate Transitions by Harnessing Epigenetic Silencing.
  21. Mechanochemical mechanism underlying intercellular Ca2+ wave propagation and its crucial role in apoptotic cell extrusion.
  22. Endothelial senescent-cell-specific clearance alleviates metabolic dysfunction in obese mice.
  23. Chromosome duplication causes premature aging via defects in ribosome quality control.
  24. CD4+ Tregs Regulate Heart Growth and Regeneration Through MRG15/TIP60-Mediated Epigenomic Remodeling in Proliferating Cardiomyocytes.
  25. Tripotent Lgr5 stem cells in the posterior tongue generate lingual, taste, and salivary gland lineages.
  26. Deubiquitinases cleave ubiquitin-fused ribosomal proteins and physically counteract their targeting to the UFD pathway.
  27. TRPM-mediated mechanoreception regulates myosin oscillation during tissue elongation.
  28. Proteome-wide profiling of S-nitrosylated proteins using the SNOTRAP probe and mass spectrometry-based detection.
  29. Programmable initiation of mRNA translation by trans-RNA.
  30. Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase.
  31. DNA fragmentation factor B suppresses interferon to enable cancer persister cell regrowth.
  32. Deletion of an enhancer that controls Wnt gene expression following tissue injury produces increased adipogenesis in regenerated muscle.
  33. Homeostatic control of energy metabolism by monocyte-derived macrophages.
  34. Spatial Transcriptomic Characteristics of the Aging Human Ovary.
  35. Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy.
  36. Structural basis of regulated N-glycosylation at the secretory translocon.
  37. Epithelial-derived basement membranes help orchestrate crypt-villus patterning in vitro.
  38. Computational design of pH-sensitive binders.
  39. Improved T cell surfaceomics by depleting intracellularly labelled dead cells.
  40. Non-Muscle α-Actinin-4 Couples Sarcomere Function to Cardiac Remodeling.
  1. Nat Metab. 2025 Nov 20.
    Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
    Sarmistha Mukherjee, Ricardo A Velázquez Aponte, Caroline E Perry, Won Dong Lee, Kevin A Janssen, Marc Niere, Gabriel K Adzika, Mu-Jie Lu, Hsin-Ru Chan, Xiangyu Zou, Beishan Chen, Nicole Bye, Teresa Xiao, Jin-Seon Yook, Oniel Salik, David W Frederick, Ryan B Gaspar, Khanh V Doan, James G Davis, Joshua D Rabinowitz, Douglas C Wallace, Nathaniel W Snyder, Shingo Kajimura, Xiaolu A Cambronne, Mathias Ziegler, Joseph A Baur.
      Nicotinamide adenine dinucleotide (NAD+) precursor supplementation shows metabolic and functional benefits in rodent models of disease and is being explored as potential therapeutic strategy in humans. However, the wide range of processes that involve NAD+ in every cell and subcellular compartment make it difficult to narrow down the mechanisms of action. Here we show that the rate of liver regeneration is closely associated with the concentration of NAD+ in hepatocyte mitochondria. We find that the mitochondrial NAD+ concentration in hepatocytes of male mice is determined by the expression of the transporter SLC25A51 (MCART1). The heterozygous loss of SLC25A51 modestly decreases mitochondrial NAD+ content in multiple tissues and impairs liver regeneration, whereas the hepatocyte-specific overexpression of SLC25A51 is sufficient to enhance liver regeneration comparably to the effect of systemic NAD+ precursor supplements. This benefit is observed even though NAD+ levels are increased only in mitochondria. Thus, the hepatocyte mitochondrial NAD+ pool is a key determinant of the rate of liver regeneration.
    DOI:  https://doi.org/10.1038/s42255-025-01408-5
  2. Genome Res. 2025 Nov 17. pii: gr.281058.125. [Epub ahead of print]
    Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine.
    Sarah Leichter, Kami Ahmad, Steve Henikoff.
      Aging compromises intestinal integrity, yet the chromatin changes driving this decline remain unclear. Polycomb-mediated repression is essential for silencing developmental genes, but this regulatory mechanism becomes dysregulated with age. Although shifts in Polycomb regulation within intestinal stem cells have been linked to gut aging, the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type-specific chromatin landscape changes during aging. We find that old enterocytes aberrantly repress genes essential for transmembrane transport and chitin metabolism, contributing to intestinal barrier decline - an example of antagonistic pleiotropy in a regenerative tissue. Barrier decline leads to derepression of JAK/STAT ligands in all cell types and increased proliferation of aging stem cells, with elevated RNA Polymerase II (RNAPII) at S-phase-dependent histone genes. Specific upregulation of histone genes during aging stem cell proliferation resembles RNAPII hypertranscription of histone genes in aggressive human cancers. Our work reveals that misregulation of the Polycomb-mediated H3K27me3 histone modification in differentiated cells during aging not only underlies tissue decline but also mirrors transcriptional changes in cancer, suggesting a common mechanism linking aging and cancer progression.
    DOI:  https://doi.org/10.1101/gr.281058.125
  3. Nat Aging. 2025 Nov 20.
    Reprogramming the GRHL2-CDK19 axis by gene therapy alleviates prostate aging.
    Guoqiang Sun, Zan He, Dongliang Lv, Qiaoran Wang, Gang Xu, Feifei Liu, Peiyu Wang, Bilan Luo, Yandong Zheng, Jinghao Hu, Shuhui Sun, Shuai Ma, Concepcion Rodriguez Esteban, Jiayin Yang, Xiaobing Fu, Juan Carlos Izpisua Belmonte, Weiqi Zhang, Jing Qu, Si Wang, Guang-Hui Liu.
      The prostate is a multifunctional organ of the male reproductive system whose aging process impairs sexual and urinary function and fertility and increases disease susceptibility, thereby compromising quality of life. However, the mechanisms underlying human prostate aging remain poorly understood. Here we integrated single-nucleus transcriptomics and histological analyses to elucidate the aging mechanisms of the primate prostate. We identified epithelial cell senescence, chronic inflammation and fibrosis as key hallmarks of prostate aging. In young epithelial cells, GRHL2 promotes CDK19 transcription, which sequesters p53, leading to the suppression of p21Waf1/Cip1. Aging-related downregulation of GRHL2 releases p53 from the CDK19-p53 complex, activating p21Waf1/Cip1 transcription and inducing cell senescence. Accordingly, a single injection of a GRHL2-based gene therapy strategy delayed prostate aging and alleviated age-related urinary dysfunction in vivo. Our findings elucidate key mechanisms of primate prostate aging and provide a foundation for developing therapies targeting prostate aging and associated pathologies.
    DOI:  https://doi.org/10.1038/s43587-025-01020-y
  4. Nature. 2025 Nov 19.
    Genetic elements promote retention of extrachromosomal DNA in cancer cells.
    Venkat Sankar, King L Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi, Katerina Kraft, Matthew G Jones, Britney Jiayu He, Xiaowei Yan, Julia A Belk, Kevin J Liu, Sangya Agarwal, Sean K Wang, Anton G Henssen, Paul S Mischel, Howard Y Chang.
      Extrachromosomal DNA (ecDNA) is a prevalent and devastating form of oncogene amplification in cancer1,2. Circular megabase-sized ecDNAs lack centromeres, stochastically segregate during cell division3-6 and persist over many generations. It has been more than 40 years since ecDNAs were first observed to hitchhike on mitotic chromosomes into daughter cell nuclei, but the mechanism underlying this process remains unclear3,7. Here we identify a family of human genomic elements, termed retention elements, that tether episomes to mitotic chromosomes to increase ecDNA transmission to daughter cells. Using Retain-seq, a genome-scale assay that we developed, we reveal thousands of human retention elements that confer generational persistence to heterologous episomes. Retention elements comprise a select set of CpG-rich gene promoters and act additively. Live-cell imaging and chromosome conformation capture show that retention elements physically interact with mitotic chromosomes at regions that are mitotically bookmarked by transcription factors and chromatin proteins. This activity intermolecularly recapitulates promoter-enhancer interactions. Multiple retention elements are co-amplified with oncogenes on individual ecDNAs in human cancers and shape their sizes and structures. CpG-rich retention elements are focally hypomethylated. Targeted cytosine methylation abrogates retention activity and leads to ecDNA loss, which suggests that methylation-sensitive interactions modulate episomal DNA retention. These results highlight the DNA elements and regulatory logic of mitotic ecDNA retention. Amplifications of retention elements promote the maintenance of oncogenic ecDNA across generations of cancer cells, and reveal the principles of episome immortality intrinsic to the human genome.
    DOI:  https://doi.org/10.1038/s41586-025-09764-8
  5. Cell Rep. 2025 Nov 14. pii: S2211-1247(25)01339-7. [Epub ahead of print]44(11): 116567
    Cadherins modulate the self-organizing potential of pseudo-embryos.
    Alexandre Mayran, Dominique Kolly, Lucille Lopez-Delisle, Yuliia Romaniuk, Maxine Leonardi, Anne-Catherine Cossy, Theo Lacroix, Hocine Rekaik, Ana Rita Amândio, Pierre Osteil, Denis Duboule.
      Embryonic stem cells can be instructed to form gastruloids, an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning, which undergo gastrulation-like processes, illustrating their robust self-organizing capacity to form embryo-like patterns. Here, we study the molecular and cellular mechanisms underlying this remarkable property and report that self-organization competence is associated with a cell-specific coordination of a cadherin switch. E-cadherin repression by Snai1 is indeed critical for this process, with Snai1 triggering the cell-specific pace of pluripotency exit, thus allowing a coordinated transition from E- to N-cadherin to occur. In contrast, we find that N-cadherin inactivation unleashes gastruloids' morphogenetic competence, for it leads to the formation of embryo-like structures with proper rostro-caudal somite patterning without requiring any addition of extracellular matrix. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the self-organizing potential of gastruloids.
    Keywords:  CP: developmental biology; CP: stem cell research; EMT; Snai1; cadherin; chromatin; embryogenesis; gastruloids; pluripotency; self-organization; somitogenesis
    DOI:  https://doi.org/10.1016/j.celrep.2025.116567
  6. Cell Rep. 2025 Nov 13. pii: S2211-1247(25)01229-X. [Epub ahead of print]44(11): 116458
    Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
    Vinayak V Viswanadham, Sonia N Kim, Emre Caglayan, Ryan N Doan, Yanmei Dou, Sara Bizzotto, Sattar Khoshkhoo, August Yue Huang, Rebecca Yeh, Brian H Chhouk, Alex Truong, Kathleen M Chappell, Marc Beaudin, Alison Barton, Shyam K Akula, Yifan Zhao, Lariza Rento, Michael Lodato, Ryan A Szeto, Javier Ganz, Pengpeng Li, Jessica W Tsai, Robert Sean Hill, Peter J Park, Christopher A Walsh.
      The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.
    Keywords:  CP: genomics; CP: neuroscience; cortical development; glutamatergic neurons; interneurons; lineage tracing; single-cell transcriptomics; somatic mutations; spatial genomics; visual cortex
    DOI:  https://doi.org/10.1016/j.celrep.2025.116458
  7. Sci Adv. 2025 Nov 21. 11(47): eady6402
    Capturing aberrant cell behaviors producing defects in human embryos via live imaging.
    Hiroki Akizawa, Ana Domingo-Muelas, Maria Pardo-Figuerez, Blake Hernandez, Goli Ardestani, Robin M Skory, Marta Venturas, Piotr Tetlak, Stephanie Bissiere, Denny Sakkas, Carlos Simon, Nicolas Plachta.
      The generation of human embryos in vitro has revolutionized reproductive medicine, and also made it possible to study fundamental aspects of early human development. However, human preimplantation embryos often display an array of morphological defects associated with poor development and implantation. Here, we used live-embryo imaging and computational analysis to capture how these defects can be produced in real time. We record various forms of mitotic errors including lagging chromosomes producing micronuclei, multipolar spindles causing abnormal chromosome organization recapitulated by daughter cells, and uncontrolled scattering of condensed chromosomes. In addition, we capture abnormal cleavage furrow dynamics during cytokinesis producing binucleated and enucleated cells. Finally, we find cells with disrupted mitotic progression ultimately leading to blebbing and fragmentation. Thus, these results document specific aberrant cell behaviors producing morphological defects in real time, and indicate that errors during mitosis and cytokinesis represent a major cause of developmental failures in human embryos.
    DOI:  https://doi.org/10.1126/sciadv.ady6402
  8. Elife. 2025 Nov 19. pii: RP103074. [Epub ahead of print]14
    Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants.
    Rebecca Garrett Jaszczak, Jay W Zussman, Daniel E Wagner, Diana J Laird.
      Mammalian primordial germ cells (PGCs) migrate asynchronously through the embryonic hindgut and dorsal mesentery to reach the gonads. We previously found that interaction with different somatic niches regulates mouse PGC proliferation along the migration route. To characterize transcriptional heterogeneity of migrating PGCs and their niches, we performed single-cell RNA sequencing of 13,262 mouse PGCs and 7868 surrounding somatic cells during migration (E9.5, E10.5, E11.5) and in anterior vs posterior locations to enrich for leading and lagging migrants. Analysis of PGCs by position revealed dynamic gene expression changes between faster or earlier migrants in the anterior and slower or later migrants in the posterior at E9.5; these differences include migration-associated actin polymerization machinery and epigenetic reprogramming-associated genes. We furthermore identified changes in signaling with various somatic niches, notably strengthened interactions with hindgut epithelium via non-canonical WNT (ncWNT) in posterior PGCs compared to anterior. Reanalysis of a previously published dataset suggests that ncWNT signaling from the hindgut epithelium to early migratory PGCs is conserved in humans. Trajectory inference methods identified putative differentiation trajectories linking cell states across timepoints and from posterior to anterior in our mouse dataset. At E9.5, we mainly observed differences in cell adhesion and actin cytoskeletal dynamics between E9.5 posterior and anterior migrants. At E10.5, we observed divergent gene expression patterns between putative differentiation trajectories from posterior to anterior, including Nodal signaling response genes Lefty1, Lefty2, and Pycr2 and reprogramming factors Dnmt1, Prc1, and Tet1. At E10.5, we experimentally validated anterior migrant-specific Lefty1/2 upregulation via whole-mount immunofluorescence staining for LEFTY1/2 and phosphorylated SMAD2/3, suggesting that elevated autocrine Nodal signaling in migrating PGCs occurs as they near the gonadal ridges. Together, this positional and temporal atlas of mouse PGCs supports the idea that niche interactions along the migratory route elicit changes in proliferation, actin dynamics, pluripotency, and epigenetic reprogramming.
    Keywords:  Nodal; Wnt; cell heterogeneity; cell migration; developmental biology; mouse; primordial germ cell
    DOI:  https://doi.org/10.7554/eLife.103074
  9. Science. 2025 Nov 20. 390(6775): eady5541
    Retinal calcium waves coordinate uniform tissue patterning of the Drosophila eye.
    Ben Jiwon Choi, Yen-Chung Chen, Claude Desplan.
      Optimal neural processing relies on precise tissue patterning across diverse cell types. Here, we show that spontaneous calcium waves arise among non-neuronal support cells in the developing Drosophila eye to drive retinal morphogenesis. These waves are initiated by Cad96Ca receptor tyrosine kinase signaling, triggering phospholipase C-γ-mediated calcium release from the endoplasmic reticulum. A cell type-specific "innexin code" coordinates wave propagation through a defined gap junction network among non-neuronal retinal cells, excluding photoreceptors. Wave intensity scales with ommatidial size, triggering stronger myosin II-driven apical contraction at interommatidial boundaries in larger ommatidia. This size-dependent mechanism compensates for early boundary irregularities, ensuring uniform ommatidial packing that is critical for precise optical architecture. Our findings reveal how synchronized calcium signaling among non-neuronal cells orchestrates tissue patterning in the developing nervous system.
    DOI:  https://doi.org/10.1126/science.ady5541
  10. Nature. 2025 Nov 19.
    Hepatic zonation determines tumorigenic potential of mutant β-catenin.
    Alexander Raven, Kathryn Gilroy, Hu Jin, Joseph A Waldron, Holly Leslie, June Munro, Holly Hall, Rachel A Ridgway, Catriona A Ford, Doga C Gulhan, Nikola Vlahov, Megan L Mills, Andrew Hartley, Eve Anderson, Sheila Bryson, Nathalie Sphyris, Miryam Müller, Stephanie May, Barbara Cadden, Colin Nixon, Scott H Waddell, Rachel Guest, Luke Boulter, Nick Barker, Hans Clevers, Hao Zhu, Johanna Ivaska, Douglas Strathdee, Crispin J Miller, Nigel B Jamieson, Martin Bushell, Peter J Park, Thomas G Bird, Owen J Sansom.
      Oncogenic mutations in phenotypically normal tissue are common across adult organs1,2. This suggests that multiple events need to converge to drive tumorigenesis and that many processes such as tissue differentiation may protect against carcinogenesis. WNT-β-catenin signalling maintains zonal differentiation during liver homeostasis3,4. However, the CTNNB1 oncogene-encoding β-catenin-is also frequently mutated in hepatocellular carcinoma, resulting in aberrant WNT signalling that promotes cell growth5,6. Here we investigated the antagonistic interplay between WNT-driven growth and differentiation in zonal hepatocyte populations during liver tumorigenesis. We found that β-catenin mutations co-operate with exogenous MYC expression to drive a proliferative translatome. Differentiation of hepatocytes to an extreme zone 3 fate suppressed this proliferative translatome. Furthermore, a GLUL and Lgr5-positive perivenous subpopulation of zone 3 hepatocytes were refractory to WNT-induced and MYC-induced tumorigenesis. However, when mutant CTNNB1 and MYC alleles were activated sporadically across the liver lobule, a subset of mutant hepatocytes became proliferative and tumorigenic. These early lesions were characterized by reduced WNT pathway activation and elevated MAPK signalling, which suppresses zone 3 differentiation. The proliferative lesions were also dependent on IGFBP2-mTOR-cyclin D1 pathway signalling, in which inhibition of either IGFBP2 or mTOR suppressed proliferation and tumorigenesis. Therefore, we propose that zonal identity dictates hepatocyte susceptibility to WNT-driven tumorigenesis and that escaping WNT-induced differentiation is essential for liver cancer.
    DOI:  https://doi.org/10.1038/s41586-025-09733-1
  11. bioRxiv. 2025 Sep 30. pii: 2025.09.29.678879. [Epub ahead of print]
    Organ-specific rewiring of mitochondrial integrity through COX7A dictates cellular ploidy control.
    Archan Chakraborty, Sophia DeLuca, Meera Gangasani, Stephen Rogers, Nenad Bursac, Donald T Fox.
      To achieve proper cell and tissue size, cytoplasmic and nuclear growth must be coordinated. Disrupting this coordination causes birth defects and disease. In nature's largest cells, nuclear growth occurs through polyploidization (whole-genome-duplication). How the massive nuclear growth of polyploid cells is coordinated with cytoplasmic growth processes such as mitochondrial biogenesis is relatively unclear. Here, focusing on one of nature's most commonly polyploid organs-the heart-we uncover cross-talk between cytoplasmic mitochondrial biogenesis/integrity and nuclear growth/polyploidy. From a human-to-fly screen, we uncover novel regulators of cardiomyocyte ploidy, including mitochondrial integrity regulators. In comparing these cardiac hits with a parallel screen in another polyploid tissue, the salivary gland, we discovered two opposing roles for Cytochrome-c-oxidase-subunit-7A (COX7A). While salivary gland COX7A preserves mitochondrial integrity to promote polyploidy and optimal organ growth, cardiac COX7A instead suppresses mitochondrial biogenesis to repress polyploidy and prevent hypertrophic organ growth. Among all electron transport chain genes, only COX7A functions as a cardiac growth repressor. Fly hearts with compromised COX7A show abnormally high cardiac output. Human COX7A1, a mitochondrial-localized protein, similarly represses polyploidy of human iPSC-derived cardiomyocytes. In summary, our human-fly-human approach reveals conserved rewiring of mitochondrial integrity in heart tissue that switches COX7A's role from ploidy promotion to repression. Our findings reveal fundamental cross-talk between mitochondrial biogenesis and genome duplication that are critical in growing metazoan tissues.
    DOI:  https://doi.org/10.1101/2025.09.29.678879
  12. bioRxiv. 2025 Oct 01. pii: 2025.09.29.679218. [Epub ahead of print]
    A mechanical origin for implantation defects in embryos from aged females.
    Kate E Cavanaugh, M J Franco-Oñate, Diana J Laird, Patrick W Oakes, Ricard Alert, Orion D Weiner.
      Women over 35 experience a marked reduction in fertility. The origin of these fertility defects appears to reside in the implantation capacity of the embryo itself, but the mechanistic basis of this impairment is not well-understood. Here, we identify a core mechanical defect in embryos from aged mothers that impairs the process of implantation. Using mouse models, we find that reproductive aging yields increased contractility in the extra-embryonic trophectoderm, the outer epithelial tissue responsible for mediating uterine attachment and embryo implantation. This hypercontractile state elevates tissue surface tension and viscosity in the blastocyst, culminating in defective spreading during implantation. Enhanced contractility is necessary and sufficient for this age-related defect in implantation, and early embryo mechanics can be used to predict successful implantation for embryos from both young and aged mothers. Our work represents a potential foundation for improving embryo selection in Assisted Reproductive Technologies to resolve age-related defects in female fertility.
    DOI:  https://doi.org/10.1101/2025.09.29.679218
  13. Nature. 2025 Nov 19.
    ZAK activation at the collided ribosome.
    Vienna L Huso, Shuangshuang Niu, Marco A Catipovic, James A Saba, Timo Denk, Eugene Park, Jingdong Cheng, Otto Berninghausen, Thomas Becker, Rachel Green, Roland Beckmann.
      Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.
    DOI:  https://doi.org/10.1038/s41586-025-09772-8
  14. Sci Signal. 2025 Nov 18. 18(913): eady0398
    IFN-I signaling enhances salivary gland stem and progenitor cell activity after irradiation.
    Davide Cinat, Ryan van der Wal, Mirjam Baanstra, Abel Soto-Gamez, Rufina Maturi, Anne L Jellema-de Bruin, Uilke Brouwer, Marc-Jan van Goethem, Marcel A T M van Vugt, Lara Barazzuol, Rob P Coppes.
      The goal of radiotherapy in cancer treatment is to maximize DNA damage in tumors while minimizing harm to surrounding healthy tissues, especially to stem and progenitor cells essential for tissue regeneration and organ function. Here, we investigated the molecular responses to photon and proton irradiation, two key modalities in head and neck cancer treatment. Multiomics and in vitro analyses revealed that both photon and proton irradiation of mouse salivary gland organoids induced similar early responses, including DNA damage, micronuclei formation, increased amounts of the cytosolic DNA sensor cGAS, and type I interferon (IFN-I) signaling. In addition, both types of radiation induced comparable increases in the release of mitochondrial DNA (mtDNA) into the cytoplasm and stimulated the production of ZBP1, a cytosolic nucleic acid sensor involved in mtDNA recognition. However, proton irradiation resulted in a more pronounced loss of heterochromatin regulators and derepression of transposable elements at later times after irradiation, which was accompanied by increased accumulation of intracellular double-stranded RNA (dsRNA) and an enhanced RIG-I-mediated IFN-I response. Genetic and pharmacological modulation demonstrated its critical role for IFN-I signaling in enhancing salivary gland stem and progenitor cell activity after irradiation in vitro and in vivo. Our findings reveal more pronounced molecular changes after proton irradiation as compared with photon irradiation and uncover a proregenerative role of IFN-I signaling in the salivary gland, suggesting this pathway as a promising therapeutic target to mitigate radiation-induced side effects.
    DOI:  https://doi.org/10.1126/scisignal.ady0398
  15. bioRxiv. 2025 Oct 01. pii: 2025.10.01.679696. [Epub ahead of print]
    Novel Tissue Mechanics-Guided Cellular Flows Enable the Evolution of Feather Follicles.
    Hans I-Chen Harn, Ting-Xin Jiang, Chih-Han Huang, Wen-Tau Juan, Tzu-Yu Liu, Tsao-Chi Chuang, Wan-Chi Liao, Yingxiao Wang, Ji Li, Cornelis J Weijer, Ping Wu, Chin-Lin Guo, Cheng-Ming Chuong.
      Complex tissue architecture is achieved through multiple rounds of morphological transitions. Here, we analyzed cellular flows and tissue mechanics during avian skin development. We showed how novel cellular flows initiate chemo-mechanical circuits that guide epithelial protrusion, folding, invagination, and spatial cell fate specification. In the initial feather bud formation, stiff dermal condensates protrude vertically out of the locally softened epithelial sheet. As the bud elongates, it stretches the epithelial cells at the base, which mechanically activates YAP and causes the epithelial sheet to fold downward and form a stiff cylindrical wall that invaginates into the skin. This stiff epithelial tongue is essential to the compaction and formation of the tightly packed dermal papillae. These topological transformational events are mechanically interconnected, and the completion of the previous circuit initializes the next one. On the contrary, during scale development, its rigid epithelial sheet restricts dermal cell flows, preventing other further topological transformation. We generated a topological transformation model to show how the process enables the novel evolution of feather follicles.
    DOI:  https://doi.org/10.1101/2025.10.01.679696
  16. bioRxiv. 2025 Oct 04. pii: 2025.10.02.680008. [Epub ahead of print]
    Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation.
    Ana M Dias Maia Henriques, Tim Davies, Serge Dmitrieff, Nicolas Minc, Julie C Canman, Julien Dumont, Gilliane Maton.
      Chromosome segregation during anaphase occurs through two mechanistically distinct processes: anaphase A, in which chromosomes move toward spindle poles, and anaphase B, in which the anaphase spindle elongates through cortical astral microtubule pulling forces. Caenorhabditis elegans embryos have been thought to rely primarily on anaphase B, with little to no contribution from anaphase A. Here, we uncover a novel anaphase A mechanism in C. elegans embryos, driven by the kinesin-13 KLP-7 MCAK and opposed by the kinesin-12 KLP-18. We found that the extent of chromosome segregation during anaphase A is asymmetrically regulated by cell polarity cues and modulated by mechanical tension within the spindle, generated by opposing forces acting on chromosomes and spindle poles. Additionally, we found that the contribution of anaphase A to chromosome segregation increases progressively across early embryonic divisions. These findings uncover an unexpected role for anaphase A in early C. elegans development and reveal a KLP-7 MCAK -dependent mechanical coordination between anaphase A and anaphase B driven chromosome segregation.
    eTOC summary: Dias Maia Henriques et al. uncover an anaphase A pathway, driven by the kinesin-13 KLP-7 and opposed by the kinesin-12 KLP-18, that contributes to chromosome segregation in early C. elegans embryos. Its activity is regulated by spindle tension, cell polarity cues, and progressively increases during early embryonic divisions.
    DOI:  https://doi.org/10.1101/2025.10.02.680008
  17. Nat Commun. 2025 Nov 18. 16(1): 10107
    Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.
    Xinli Qu, Ehsan Razmara, Ashiq Khader C, Chee Ho H'ng, Kailash K Vinu, Luciano G Martelotto, Maia Zethoven, Fernando J Rossello, Shanika L Amarasinghe, David R Powell, Alberto Rosello-Diez.
      The growth-plate cartilage of the developing long bones is a well-known system of spatially segregated stem/progenitor, transient amplifying and terminally differentiated cells. However, the regulation of the number and activity of long-lived cartilage progenitors (LLCPs) is poorly understood, despite its relevance for understanding human-height variation, the evolution of limb size and proportions and the aetiology of skeletal growth disorders. Moreover, whether their behaviour can adapt to developmental perturbations, generating robustness, has not been explored. Here, we show that Gli1+ cells are the fetal precursors of postnatal LLCPs, and that Gli1+ LLCP precursors remain mostly dormant until postnatal stages. However, in response to genetically-induced cell-cycle arrest targeted to the fetal cartilage, they expand in the cartilage, enabling normal growth. We further show that reparative Gli1+ cells originate from Pdgfra+ cells outside the cartilage, revealing the surrounding tissues as an unexpected CP source. Elucidating how stromal cells become Gli1+ LLCPs could shed light on developmental robustness and lead to growth-boosting therapies.
    DOI:  https://doi.org/10.1038/s41467-025-65029-y
  18. Nat Cell Biol. 2025 Nov 18.
    Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells.
    Lucrezia Della Volpe, Andrew J Lee, Mateusz Antoszewski, Amy A Deik, Ksenia R Safina, Teng Gao, Chun-Jie Guo, Tianyi Ye, Peng Lyu, Jorge D Martin-Rufino, Nicole Castano, Jonathan Good, Yaniris Molina-Aponte, Jiawei Zhao, Clary B Clish, Peter van Galen, Vijay G Sankaran.
      Improved ex vivo expansion of human haematopoietic stem cells (HSCs) would considerably advance transplantation and genome-engineered therapies, yet existing culture methods still allow substantial HSC loss. Here we show that this attrition is driven largely by ferroptosis, a metabolically regulated, iron-dependent cell-death pathway, and that it can be blocked to augment HSC expansion. Inhibiting ferroptosis with liproxstatin-1 or ferrostatin-1 markedly increases the expansion of cord blood and adult HSCs consistently across donors in both widely used serum-free cultures and recently reported chemically defined conditions. The expanded cells retain phenotypic and molecular stem cell identity and mediate improved durable, multilineage engraftment in xenotransplanted mice without genotoxicity or aberrant haematopoiesis. Mechanistically, ferroptosis blockade is accompanied by upregulated ribosome biogenesis and cholesterol synthesis, increasing levels of 7-dehydrocholesterol-a potent endogenous ferroptosis inhibitor that itself promotes HSC expansion. Crucially, this approach enhances yields of therapeutically genome-modified HSCs, paving a path for clinical applications.
    DOI:  https://doi.org/10.1038/s41556-025-01814-7
  19. Nat Genet. 2025 Nov 18.
    Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulation.
    Takeo Narita, Sinan Kilic, Yoshiki Higashijima, Natalie M Scherer, Georgios Pappas, Elina Maskey, Chunaram Choudhary.
      Cohesin- and CTCF-mediated chromatin loops facilitate enhancer-promoter and promoter-promoter interactions, but their impact on global gene regulation remains debated. Here we show that acute removal of cohesin or CTCF in mouse cells dysregulates hundreds of genes. Cohesin depletion primarily downregulates CBP/p300-dependent putative enhancer targets, whereas CTCF loss both up- and downregulates enhancer targets. Beyond loop anchoring, CTCF directly modulates transcription, acting as an activator or repressor depending on its binding position and orientation at promoters. Mechanistically, when activating, CTCF increases DNA accessibility and promotes RNA polymerase II recruitment; when repressing, it prevents RNA polymerase II binding without altering chromatin accessibility. Promoter-bound CTCF activates housekeeping genes essential for cell proliferation. CTCF's transcriptional activation function-but not its loop anchoring role-is shared with its vertebrate-specific paralog, CTCFL. These findings reconcile architectural and non-architectural roles of cohesin and CTCF, offering a unified model for their functions in enhancer-dependent and enhancer-independent transcription control.
    DOI:  https://doi.org/10.1038/s41588-025-02404-x
  20. bioRxiv. 2025 Sep 30. pii: 2025.09.29.679324. [Epub ahead of print]
    Engineering Inducible Cell Fate Transitions by Harnessing Epigenetic Silencing.
    Oscar A Campos, Alessandro Migliara, Satoshi Toda, Pilar Lopez, Wendell A Lim, Ricardo Almeida.
      During development, cell-cell communication induces a series of cell fate transitions that are maintained by epigenetic gene regulation. Here, we harness endogenous epigenetic silencing machinery to develop synthetic circuits that induce stable gene expression changes. Using synthetic Notch receptors that control the chromatin regulators KRAB and Dnmt3L, we developed input-controlled switches capable of inducing self-sustaining silencing of target loci. We used these modules to construct circuits in which combinatorial inputs specifically direct a choice among multiple alternative cell fates. These epigenetic silencing switches can also be inverted to yield input-induced sustained activation of a target gene. We demonstrate that this epigenetic memory switch can be used to drive morphological fate changes, in response to transient cell signals, that remain stable over many cell divisions, as is observed in development. These synthetic epigenetic circuits represent an important step towards engineering cell populations capable of coordinated multi-cell fate decisions.
    DOI:  https://doi.org/10.1101/2025.09.29.679324
  21. Nat Commun. 2025 Nov 17. 16(1): 9887
    Mechanochemical mechanism underlying intercellular Ca2+ wave propagation and its crucial role in apoptotic cell extrusion.
    Sohei Yamada, Ryohei Yasukuni, Yasumasa Bessho, Yasuyuki Fujita, Yoichiroh Hosokawa, Takaaki Matsui.
      Calcium (Ca2+) wave propagation plays a crucial role in intercellular communication. Elevation of cytosolic Ca2+ (Ca2+ transient) in a single cell is attributed to various Ca2+ channels present in the plasma membrane and endoplasmic reticulum, whereas gap junctions contribute to propagation of Ca2+ waves between cells. However, we found that Ca2+ waves propagate without gap junctions during apoptotic cell extrusion (ACE). Mechanistically, we identified that a chain reaction of mechano-signal transduction from proximal to distal cells through the mechanosensitive Ca2+ channels (MCCs) mediates the Ca2+ wave propagation; an apoptotic cell shrinks accompanied by a Ca2+ transient, followed by pulling the edges of neighboring cells, which opens MCCs in neighboring cells, resulting in Ca2+ transients in these cells. Furthermore, Ca2+ wave propagation promotes Rac-Arp2/3 pathway-mediated polarized collective migration, generating approximately 1 kPa of force toward extruding cells. Our results uncovered a mechanochemical mechanism of Ca2+ wave propagation and its significant role in ACE.
    DOI:  https://doi.org/10.1038/s41467-025-65474-9
  22. Cell Metab. 2025 Nov 20. pii: S1550-4131(25)00443-7. [Epub ahead of print]
    Endothelial senescent-cell-specific clearance alleviates metabolic dysfunction in obese mice.
    Masayoshi Suda, Selim Chaib, Larissa G P Langhi Prata, Yi Zhu, Utkarsh Tripathi, Karl H Paul, Allyson K Palmer, Tamar Pirtskhalava, Vagisha Kulshreshtha, Christina L Inman, Kurt O Johnson, Nino Giorgadze, Runqing Huang, Carolyn M Roos, Luisa F Leon-Sanchez, Jordan D Miller, Thomas White, Linshan Laux, Laura J Niedernhofer, Paul D Robbins, Sara Espinoza, Nicolas Musi, Sundeep Khosla, Stefan G Tullius, Tamar Tchkonia, James L Kirkland.
      Accumulation of senescent cells is a key contributor to multiple diseases across the lifespan, including metabolic dysfunction. We previously demonstrated that elimination of senescent cells using senolytic drugs alleviates obesity-induced metabolic dysfunction. However, the contribution of senescent endothelial cells to metabolic disorders remains elusive. Hence, we crossed mice that allow selective elimination of senescent cells (p16Ink4a-LOX-ATTAC mice) with Tie2-Cre mice (Tie2-Cre;p16Ink4a-LOX-ATTAC) to enable identification and inducible, selective elimination of p16Ink4a+ senescent endothelial cells. Targeted removal of senescent endothelial cells from obese Tie2-Cre;p16Ink4a-LOX-ATTAC mice attenuated the pro-inflammatory senescence-associated secretory phenotype and alleviated metabolic dysfunction. Conversely, transplanting senescent endothelial cells into lean mice caused adipose tissue inflammation and metabolic dysfunction. Consistent with these findings, the senolytic, fisetin, which targets senescent endothelial cells among other senescent cell types, reduced adipose tissue senescent endothelial cell abundance and improved glucose metabolism in obese mice or mice transplanted with senescent mouse endothelial cells. Our results indicate that specifically eliminating p16Ink4a+ senescent endothelial cells is a potential therapeutic strategy for metabolic disease.
    Keywords:  SASP factors; TNFα; cellular senescence; diabetes; endothelial cells; fisetin; glucose intolerance; obesity; p16(Ink4a); senolytics
    DOI:  https://doi.org/10.1016/j.cmet.2025.10.009
  23. PLoS Biol. 2025 Nov;23(11): e3003509
    Chromosome duplication causes premature aging via defects in ribosome quality control.
    Leah E Escalante, James Hose, Jamie M Ahrens, Hollis Howe, Norah Paulsen, Sofia J Liss, Michael Place, Audrey P Gasch.
      Down syndrome, caused by an extra copy of Chromosome 21, causes lifelong problems. One of the most common phenotypes among people with Down syndrome is premature aging, including early tissue decline, neurodegeneration, and shortened life span. Yet the reasons for premature systemic aging are a mystery and difficult to study in humans. Here we show that chromosome amplification in wild yeast also produces premature aging and shortens life span. Chromosome duplication disrupts nutrient-induced cell-cycle arrest, entry into quiescence, and cellular health during chronological aging, across genetic background and independent of which chromosome is amplified. Using a genomic screen, we discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). We show that aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates compared to euploid cells. Although they maintain proteasome activity, aneuploids also show signs of ubiquitin dysregulation and sequestration into foci. Remarkably, inducing ribosome stalling in euploids produces similar aging phenotypes, while up-regulating limiting RQC subunits or poly-ubiquitin alleviates many of the aneuploid defects. We propose that the increased translational load caused by having too many mRNAs accelerates a decline in translational fidelity, contributing to premature aging.
    DOI:  https://doi.org/10.1371/journal.pbio.3003509
  24. Circulation. 2025 Nov 18.
    CD4+ Tregs Regulate Heart Growth and Regeneration Through MRG15/TIP60-Mediated Epigenomic Remodeling in Proliferating Cardiomyocytes.
    Yangfeng Hou, Cheng Kiu Ho, Binglin Lai, Jitao Liu, Lilin Li, Jinhai Lin, Hang Qu, Randolph H L Wong, Yu Nie, Qiurong Ding, Bin Zhou, Kathy O Lui.
       BACKGROUND: Cardiovascular disease remains a leading cause of mortality globally, with the adult mammalian heart exhibiting limited regenerative capacity. The chromatin regulatory network plays a crucial role in the dynamic changes in gene expression that orchestrate the regenerative response in the neonatal heart. This study aims to identify key chromatin regulators in neonatal cardiomyocytes and to elucidate their roles in heart regeneration.
    METHODS: We generated genetic knockout mouse models by crossing Mrg15fl/fl and Tip60fl/fl mice with various Cre-driver lines such as Isl1-Cre and Myh6-MerCreMer to evaluate the function of MRG15 (MORF-related gene 15)/TIP60 in cardiac progenitor cells and cardiomyocytes during heart development and regeneration. The epigenetic regulation of cardiomyocyte proliferation by MRG15/TIP60 was investigated through a variety of methods, including histological, cellular, genomic, transcriptomic, computational, and pharmacological approaches. In addition, we assessed the regulation of transient MRG15 induction in the regenerating neonatal heart by CD4+ regulatory T cells through both adoptive transfer and monoclonal antibody-based depletion in mice.
    RESULTS: MRG15, but not its cofactor TIP60, was transiently expressed in neonatal cardiomyocytes, with its expression downregulated as the regenerative potential of the heart declined. We generated knockout mice targeting Mrg15 in cardiac progenitor cells and cardiomyocytes, revealing that MRG15 is critical for neonatal heart regeneration and plays a key role in regulating cardiomyocyte proliferation. Mechanistically, MRG15 forms an activator complex with TIP60, p300, and RNA polymerase II, facilitating histone acetylation at the Ccnd1 enhancer region. Furthermore, regulatory T cells were shown to induce MRG15 expression, promoting cardiomyocyte proliferation through paracrine signaling. Notably, adeno-associated virus 9-mediated overexpression of Mrg15 rescued the impaired heart regeneration after Treg depletion in vivo. Furthermore, recapitulating MRG15 expression into the juvenile heart promoted regeneration by enhancing cardiomyocyte proliferation.
    CONCLUSIONS: This study elucidates the critical role of regulatory T cells in regulating the transient expression of MRG15 in regenerating cardiomyocytes and its subsequent control of cardiomyocyte proliferation and heart regeneration through TIP60-mediated chromatin modification. Our findings highlight the important interplay between the cardiac and the immune system during neonatal development, particularly through the MRG15/TIP60 axis regulated by regulatory T cells. This cross-talk suggests promising therapeutic strategies for enhancing cardiac repair by targeting these pathways.
    Keywords:  T-lymphocytes, regulatory; myocytes, cardiac
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.073890
  25. Nat Commun. 2025 Nov 21. 16(1): 10266
    Tripotent Lgr5 stem cells in the posterior tongue generate lingual, taste, and salivary gland lineages.
    Laurens H G Verweij, Seok-Young Kim, Dimitrios Laskaris, Lin Lin, Gijs J F van Son, Femke C A S Ringnalda, Harry Begthel, Ravian L van Ineveld, Chris Winkel, Jay P Slack, Anne C Rios, Karin Sanders, Jacco van Rheenen, Marc van de Wetering, Hans Clevers.
      The circumvallate papillae and foliate papillae of the posterior tongue contain taste buds in close proximity to specialized salivary glands, known as von Ebner glands. The developmental relationship between taste buds and these salivary glands has been suggested but remains largely unexplored at postnatal and adult stages. Lineage tracing studies in mice have revealed that Lgr5 marks taste bud stem cells. Here, we report single-cell RNA sequencing of the entire circumvallate and foliate papillae of mice, providing a transcriptional atlas of cells from tongue surface epithelium, taste buds, and the associated and non-associated salivary glands. We unveil a developmental trajectory in which taste buds, the associated salivary glands, and the non-taste tongue surface epithelium originate from a common Lgr5 cell. We confirm this tripotency at the clonal level in vitro and with multicolor lineage tracing in vivo. Thus, the circumvallate and foliate papillae harbor chemosensory units composed of taste bud and salivary gland cells derived from the same parental Lgr5-positive stem cell.
    DOI:  https://doi.org/10.1038/s41467-025-65140-0
  26. Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00889-5. [Epub ahead of print]
    Deubiquitinases cleave ubiquitin-fused ribosomal proteins and physically counteract their targeting to the UFD pathway.
    Stephanie Patchett, Seyed Arad Moghadasi, Ankita Shukla, Farid El Oualid, Beatrix M Ueberheide, Shaun K Olsen, Tony T Huang.
      In eukaryotes, each ribosomal subunit includes a ribosomal protein (RP) that is encoded as a fusion protein with ubiquitin (Ub). In yeast, each Ub-RP fusion requires processing by deubiquitylating enzymes (DUBs) to generate ribosome assembly-competent RPs and contribute to the cellular Ub pool. However, how Ub-RP fusions are processed by DUBs in human cells remains unclear. Here, we discovered that Ub-RPs are substrates of the Ub-fusion degradation (UFD) pathway in human cells via lysine 29 and 48 (K29/K48)-specific ubiquitylation and proteasomal degradation. We identified a pool of DUBs that catalytically process Ub-RPs, as well as DUBs that physically occlude Ub-RP interaction with UFD pathway Ub E3 ligases to prevent their degradation in a non-catalytic manner. Our results suggest that DUBs both process and stabilize Ub-RPs, whereas the UFD pathway regulates levels of Ub-RPs that cannot be fully processed by DUBs to fine-tune protein homeostasis.
    Keywords:  Cezanne; DUBs; HUWE1; OTUD7B; RPL40; RPS27a; TRIP12; UBA52; UBA80; UFD; deubiquitinases; deubiquitinating enzymes; ubiquitin fusion degradation pathway
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.028
  27. Curr Biol. 2025 Nov 18. pii: S0960-9822(25)01381-8. [Epub ahead of print]
    TRPM-mediated mechanoreception regulates myosin oscillation during tissue elongation.
    Zhixiang Dong, Heng Wang, Renchang Zhang, Ziqi Guo, Boxin Zhang, Ruoyi Pei, Xuan Guo, Peng Xia, Guangwei Si, Jiong Chen.
      Periodic oscillation of myosin II has been shown to be required for a wide variety of morphogenetic processes, including tissue elongation of Drosophila egg chambers during mid and late oogenesis. But what developmental cues initiate myosin oscillation in the basal region of the somatic follicle cells in stage 9 egg chambers is not clear. Here, we show that increased mechanical pressure caused by the growth of the adjacent germline tissue could serve as a temporal and spatial cue that helps induce basal myosin oscillation in early-mid stage 9 follicle cells through the function of the mechanosensing TRPM (transient receptor potential M) channel. We demonstrate that TRPM is expressed in stage 9 follicle cells and is required for calcium influx, myosin oscillation, and tissue elongation. Furthermore, calcium levels and the propagation of calcium waves across the follicle epithelium-which requires gap junction function-are critical for myosin oscillation, which we show to be regulated by both the CaM-MLCK and Rho1-Rok pathways. Together, our results support a model that, beginning at stage 9 of oogenesis, growth-induced mechanical pressure serves as a developmental cue to initiate periodic basal myosin oscillations through the function of the mechanosensing calcium channel, TRPM, to drive tissue elongation.
    Keywords:  Drosophila oogenesis; TRPM; calcium influx; germline tissue; mechanoreception; morphogenesis; myosin II; myosin oscillation; somatic follicle cells; tissue elongation
    DOI:  https://doi.org/10.1016/j.cub.2025.10.038
  28. Nat Protoc. 2025 Nov 19.
    Proteome-wide profiling of S-nitrosylated proteins using the SNOTRAP probe and mass spectrometry-based detection.
    Hongmei Yang, Haitham Amal, Steven R Tannenbaum, Stuart A Lipton.
      Protein S-nitrosylation (SNO) is a ubiquitous post-translational modification, which regulates a broad range of functional parameters, including protein stability; enzymatic, transcriptional and ion channel activity; and cellular signal transduction. Aberrant protein SNO is associated with diverse pathophysiology, from cardiovascular, metabolic and respiratory disorders to neurodegeneration and cancer. Drugs that enhance or inhibit specific SNO reactions are being developed as potential disease-modifying therapeutics. However, owing to a lack of suitable approaches to monitor SNO proteins, which often exist at low abundance with ephemeral expression, a systematic understanding of their roles in disease remains elusive. Here we report a robust and proteome-wide approach for the exploration of the S-nitrosoproteome in human and mouse tissues, using the brain as an example, with a probe named SNOTRAP (a triphenylphosphine thioester linked to a biotin molecule through a polyethylene glycol spacer group) in conjunction with mass spectrometry (MS)-based detection. In this Protocol, we detail tissue sample preparation, synthesis of SNOTRAP under an argon atmosphere and subsequent MS-based identification and analysis of SNO proteins. In situ labeling of SNO proteins is achieved by the SNOTRAP probe, concomitantly yielding a disulfide-iminophosphorane as a labeling tag. The chemically tagged proteins can be digested, followed by streptavidin capture, release by triscarboxyethylphosphine and relabeling of the liberated free Cys with N-ethylmaleimide. This approach selectively enriches SNO-containing peptides at specific sites for label-free quantification by Orbitrap MS. It requires about 5 d for synthesis of the SNOTRAP probe, 2-2.5 d for sample preparation and about 5 d for nano-liquid chromatography-tandem MS measurement and analysis.
    DOI:  https://doi.org/10.1038/s41596-025-01282-1
  29. Nat Biotechnol. 2025 Nov 21.
    Programmable initiation of mRNA translation by trans-RNA.
    Longfei Jia, Tan-Trung Nguyen, Saori Uematsu, Yifei Gu, Shengcho Shi, Yaser Hashem, Shu-Bing Qian.
      Several approaches exist to silence genes, but few tools are available to activate individual mRNAs for translation inside cells. Guiding ribosomes to specific start codons without altering the original sequence remains a formidable task. Here we design capped trans-RNAs capable of directing ribosomes to specific initiation sites on individual mRNAs when the trans-cap is positioned near the target start codon. Structural and biochemical data suggest that the capped trans-RNA facilitates ribosome loading and scanning on the target mRNA through a synergistic mechanism involving alternative cap recognition. The trans-RNA also acts independently of the cap on the target mRNA, enabling translation of circular RNAs lacking internal ribosome entry sites. We apply trans-RNAs in vivo to achieve programmable alternative translation of endogenous genes in mouse liver. Finally, we provide the evidence for the existence of natural transcripts that, similarly to exogenous trans-RNAs, activate translation of endogenous mRNAs.
    DOI:  https://doi.org/10.1038/s41587-025-02897-1
  30. Nat Commun. 2025 Nov 21. 16(1): 10304
    Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase.
    Fritz Nagae, Yutaka Murata, Masataka Yamauchi, Shoji Takada, Tsuyoshi Terakawa.
      Faithful replication of eukaryotic chromatin requires the CMG helicase to translocate directionally along single-stranded DNA (ssDNA) while unwinding double-stranded DNA (dsDNA) and navigating nucleosomes. However, the mechanism by which CMG achieves processive translocation and deals with nucleosomal barriers remains incompletely understood. Here, using coarse-grained molecular dynamics simulations with ATP-driven conformational switching, we show that asymmetric rotational transitions among four distinct ssDNA-binding states enable CMG to achieve directional translocation and DNA unwinding. We further demonstrate that the fork protection complex (Csm3/Tof1) and RPA enhance processivity through distinct mechanisms: Csm3/Tof1 grips the parental duplex to suppress backtracking, while RPA alleviates lagging-strand clogging. Upon nucleosome encounter, Csm3/Tof1 promoted partial unwrapping of the entry DNA, but further progression is energetically restricted near the nucleosomal dyad. The histone chaperone FACT lowers this barrier and simultaneously prevents inappropriate histone transfer to the lagging strand. Our results provide mechanistic insights into how the eukaryotic replisome coordinates helicase activity, nucleosome navigation, histone chaperone function, and histone recycling during eukaryotic DNA replication.
    DOI:  https://doi.org/10.1038/s41467-025-65232-x
  31. Nat Cell Biol. 2025 Nov 17.
    DNA fragmentation factor B suppresses interferon to enable cancer persister cell regrowth.
    August F Williams, David A G Gervasio, Claire E Turkal, Anna E Stuhlfire, Michael X Wang, Brandon E Mauch, Rhea Plawat, Ariel H Nguyen, Michelle H Paw, Mehrshad Hairani, Cooper P Lathrop, Sophie H Harris, Jennifer L Page, Matthew J Hangauer.
      Oncogene-targeted cancer therapies can provide deep responses but frequently suffer from acquired resistance. Therapeutic approaches to treat tumours that have acquired drug resistance are complicated by continual tumour evolution and multiple co-occurring resistance mechanisms. Rather than treating resistance after it emerges, it may be possible to prevent it by inhibiting the adaptive processes that initiate resistance, but these are poorly understood. Here we report that residual cancer persister cells that survive oncogene-targeted therapy are growth arrested by drug stress-induced intrinsic type I interferon signalling. To escape growth arrest, persister cells leverage apoptotic machinery to transcriptionally suppress interferon-stimulated genes (ISGs). Mechanistically, persister cells sublethally engage apoptotic caspases to activate DNA endonuclease DNA fragmentation factor B (also known as caspase-activated DNase), which induces DNA damage, mutagenesis and stress response factor activating transcription factor 3 (ATF3). ATF3 limits activator protein 1-mediated ISG expression sufficiently to allow persister cell regrowth. Persister cells deficient in DNA fragmentation factor B or ATF3 exhibit high ISG expression and are consequently unable to regrow. Therefore, sublethal apoptotic stress paradoxically promotes the regrowth of residual cancer cells that survive drug treatment.
    DOI:  https://doi.org/10.1038/s41556-025-01810-x
  32. Development. 2025 Nov 20. pii: dev.204933. [Epub ahead of print]
    Deletion of an enhancer that controls Wnt gene expression following tissue injury produces increased adipogenesis in regenerated muscle.
    Catriona Y Logan, Xinhong Lim, Matt Fish, Makiko Mizutani, Brooke Swain, Roel Nusse.
      The capacity to detect and respond to injury is critical for the recovery and long-term survival of many organisms. Wnts are commonly induced by tissue damage but how they become activated transcriptionally is not well understood. Here, we report that mouse Wnt1 and Wnt10b are induced following injury in both lung and muscle. These Wnts occupy the same chromosome and are transcribed in opposite directions with 12kb between them. We identified a highly conserved cis-acting regulatory region (enhancer) residing between Wnt1 and Wnt10b that, when fused to a LacZ reporter, is activated post-injury. This enhancer harbors putative AP-1 binding sites that are required for reporter activity, a feature observed in other injury-responsive enhancers. Injured muscles in mice carrying a germ-line deletion of the enhancer region display reduced Wnt1 and Wnt10b expression and show elevated intramuscular adipogenesis which can be a hallmark of impaired muscle regeneration or tissue maintenance. Enhancer redundancy is common in development, but our in vivo analysis shows that loss of a single injury-responsive regulatory region in adult tissues can produce a detectable phenotype.
    Keywords:  Enhancer; Injury; Muscle; Regeneration; Wnt
    DOI:  https://doi.org/10.1242/dev.204933
  33. EMBO J. 2025 Nov 17.
    Homeostatic control of energy metabolism by monocyte-derived macrophages.
    Rui Martins, Birte Blankehaus, Faouzi Braza, Miguel Mesquita, Pedro Ventura, Sumnima Singh, Sebastian Weis, Maria Pires, Sara Pagnotta, Qian Wu, Sílvia Cardoso, Elisa Jentho, Ana Figueiredo, Pedro Faísca, Ana Nóvoa, Vanessa Alexandra Morais, Stefanie K Wculek, David Sancho, Moises Mallo, Miguel P Soares.
      Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing and responding to deviations of those parameters to sustain organismal homeostasis. Here, we demonstrate that dysregulation of iron (Fe) metabolism, imposed by the deletion of ferritin H chain (FTH) in mouse parenchymal cells, is sensed by monocyte-derived macrophages. In response, monocyte-derived macrophages support tissue function, energy metabolism, and thermoregulation via a mechanism that sustains the mitochondria of parenchymal cells. Mechanistically, FTH supports a transcriptional program promoting mitochondrial biogenesis in macrophages, involving mitochondrial transcription factor A (TFAM). Moreover, FTH sustains macrophage viability and supports intercellular mitochondrial transfer from donor parenchymal cells. In conclusion, monocyte-derived macrophages cross-regulate iron and energy metabolism to support tissue function and organismal homeostasis.
    Keywords:  Ferritin; Homeostasis; Macrophages; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1038/s44318-025-00622-x
  34. Aging Cell. 2025 Nov 17. e70288
    Spatial Transcriptomic Characteristics of the Aging Human Ovary.
    Meiling Zhang, Fanghao Guo, Qing Zhang, Qianhui Hu, Di Sun, Yongjian Ma, Yanquan Li, Mengxi Guo, Haixia Ding, Ying Guo, Baicai Yang, Songmao Li, Ningxia Sun, Yuxuan Zheng, Wen Li.
      Ovarian aging is a complex process that compromises fertility and elevates the risk of reproductive disorders. To elucidate its spatiotemporal dynamics, we integrated single-nucleus RNA sequencing and spatial transcriptomics to construct a comprehensive aging atlas of 12 human ovarian tissues spanning ages 12-54 (prepubertal, age 12, n = 1; young, ages 23-29, n = 4; middle-aged, ages 32-34, n = 2; and older-aged, ages 42-54, n = 5). Our analysis revealed aging-related transcriptomic shifts, including impaired mitochondrial oxidative phosphorylation and reproductive structure development in aged human ovaries. We identified a novel endothelial cell (EDC) subtype, CLDN5+ blood EDCs, which exhibited unique functional specialization as semiprofessional antigen-presenting cells. In contrast to other cell types that lost cell identity during aging, CLDN5+ blood EDCs displayed transcriptomic sensitivity to aging, characterized by enhanced antigen-presenting capabilities, and heightened inflammatory activity. Spatial mapping further uncovered immunoglobulin-expressing (IGHG1+/IGKC+) cell accumulation in the ovarian periphery, correlating with advancing age. Critically, aging disrupted global cellular connectivity while amplifying the DLK1:NOTCH3 axis between theca cells and CLDN5+ blood EDCs, which may contribute to the dysregulation of ovarian functions. We also detected the upregulation of DLK1 in granulosa cells from patients with primary ovarian insufficiency. This study significantly enhances our comprehension of the underlying mechanisms of human ovarian aging and concurrently pinpoints potential therapeutic avenues for addressing related disorders.
    DOI:  https://doi.org/10.1111/acel.70288
  35. Cell. 2025 Nov 19. pii: S0092-8674(25)01235-8. [Epub ahead of print]
    Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy.
    Michelle von Locquenghien, Pascale Zwicky, Ken Xie, Diego Adhemar Jaitin, Fadi Sheban, Adam Yalin, Florian Uhlitz, Chamutal Gur, Reut Sharet Eshed, Eyal David, Kfir Mazuz, Caroline Jennings Marin, Ankita Sankar, Devin Mediratta, Roberto Avellino, Assaf Weiner, Ido Amit.
      Tumor-associated macrophages (TAMs) expressing the myeloid checkpoint TREM2 are key immunosuppressive cells in the tumor microenvironment (TME), driving tumor progression and contributing to poor prognosis in cancer patients. Due to their pivotal role, TAMs have emerged as a promising target for immunotherapies. However, current TAM-targeting monotherapies show limited efficacy, highlighting the need for strategies engaging multiple immune modalities. Here, we developed myeloid-targeted immunocytokines and natural killer (NK)/T cell enhancers (MiTEs) harnessing myeloid and lymphoid synergy for immunotherapy. MiTEs are trans-acting immunocytokines with tumor-specific activation, allowing dual targeting of TAMs and lymphocytes by TREM2 antagonism and cytotoxic effector cell activation through interleukin (IL)-2. To avoid off-target toxicities, MiTEs contain an IL-2 masking moiety, which is cleaved by a TAM-specific protease. MiTEs demonstrate high efficacy in preclinical tumor models through extensive immune reprogramming spanning TAM, T, and NK cell compartments. MiTEs show transformative potential for treating solid cancers by inducing potent multi-axis anti-tumor immunity while minimizing toxicities.
    Keywords:  T and NK cell synergy; TME-conditional IL-2; TREM2; cancer immunotherapy; cytokines; myeloid checkpoints; myeloid-targeted immunocytokine; single-cell genomics; synthetic immunology; tumor-associated macrophages; tumor-microenvironment modulation
    DOI:  https://doi.org/10.1016/j.cell.2025.10.030
  36. Nature. 2025 Nov 19.
    Structural basis of regulated N-glycosylation at the secretory translocon.
    Melvin Yamsek, Mengxiao Ma, Roshan Jha, Yu Wan, Qianru Li, Frank Zhong, Katherine DeLong, Zhe Ji, Rajat Rohatgi, Robert J Keenan.
      Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase (OST) complexes as they enter the endoplasmic reticulum (ER)1-3. Recent work revealed a substrate-assisted mechanism by which N-glycosylation of the chaperone glucose-regulated protein 94 (GRP94) is regulated to control cell surface receptor signalling4. Here we report the structure of a natively isolated GRP94 folding intermediate tethered to a specialized CCDC134-bound translocon. Together with functional analysis, the data reveal how a conserved N-terminal extension in GRP94 inhibits OST-A and how structural rearrangements within the translocon shield the tethered nascent chain from inappropriate OST-B glycosylation. These interactions depend on a hydrophobic CCDC134 groove, which recognizes a non-native conformation of nascent GRP94. Our results define a mechanism of regulated N-glycosylation and illustrate how the nascent chain remodels the translocon to facilitate its own biogenesis.
    DOI:  https://doi.org/10.1038/s41586-025-09756-8
  37. Dev Cell. 2025 Nov 17. pii: S1534-5807(25)00638-0. [Epub ahead of print]60(22): 2997-2999
    Epithelial-derived basement membranes help orchestrate crypt-villus patterning in vitro.
    Janny Pineiro-Llanes, Mashael F Aldossari, Rodrigo Cristofoletti.
      Intestinal organoid culture has widely depended on exogenous laminin-rich matrices to provide a supportive environment for organoid development. In this issue of Developmental Cell, Chrisnandy and Lütolf now report that human and mouse intestinal epithelial cells can secrete their own basement membrane, enabling organoid formation even without exogenous laminin.
    DOI:  https://doi.org/10.1016/j.devcel.2025.10.008
  38. bioRxiv. 2025 Sep 29. pii: 2025.09.29.678932. [Epub ahead of print]
    Computational design of pH-sensitive binders.
    Green Ahn, Brian Coventry, Ella Haefner, Shayan Sadre, Jenny Hu, Mimosa Van, Buwei Huang, Isaac Sappington, Adam J Broerman, Mauriz A Lichtenstein, Matthias Glögl, Inna Goreshnik, Dionne Vafeados, David Baker.
      pH gradients are central to physiology, from vesicle acidification to the acidic tumor microenvironment. While therapeutics have been developed to exploit these pH changes to modulate activity across different physiological environments, current approaches for generating pH-dependent binders, such as combinatorial histidine scanning and display-based selections, are largely empirical and often labor-intensive. Here we describe two complementary principles and associated computational methods for designing pH-dependent binders: (i) introducing histidine residues adjacent to positively charged residues at binder-target interfaces to induce electrostatic repulsion and weaken binding at low pH, and (ii) introducing buried histidine-containing charged hydrogen-bonding networks in the binder core such that the protein is destabilized under acidic conditions. Using these methods, we designed binders that dissociate at acidic pH against ephrin type-A receptor 2, tumor necrosis factor receptor 2, interleukin-6, proprotein convertase subtilisin/kexin type 9, and the interleukin-2 mimic Neo2. Fusions of the designs to pH-independent binders of lysosomal trafficking receptors function as catalytic degraders, inducing target degradation at substoichiometric levels. Our methods should be broadly useful for designing pH-sensitive protein therapeutics.
    DOI:  https://doi.org/10.1101/2025.09.29.678932
  39. bioRxiv. 2025 Oct 01. pii: 2025.09.30.679609. [Epub ahead of print]
    Improved T cell surfaceomics by depleting intracellularly labelled dead cells.
    Christofer Daniel Sánchez, Aswath Balakrishnan, Blake Krisko, Bulbul Ahmmed, Luna Witchey, Oceani Valenzuela, Minas Minasyan, Anthony Pak, Haik Mkhikian.
      Although the plasma membrane (PM) is among the most biologically important and therapeutically targeted cellular compartments, it is among the most challenging to faithfully capture using proteomic approaches. The quality of quantitative surfaceomics data depends heavily on the effectiveness of the cell surface enrichment used during sample preparation. Enrichment improves sensitivity for low abundance PM proteins and ensures that the changes detected reflect PM expression changes rather than whole cell changes. Cell surface biotinylation with PM-impermeable, amine-reactive reagents is a facile, accessible, and unbiased approach to enrich PM proteins. For unclear reasons however, it results in unexpectedly high contamination with intracellular proteins, reducing its utility. We report that biotinylating human cells with amine-reactive reagents intracellularly labels a small but reproducible population of non-viable cells. Although these dead cells represent only 5±2% of the total, we find that in T cell preparations the dead cells account for 90% of labelled proteins. Depleting Annexin V positive dead T cells post-labelling removes ∼99% of the intracellularly labelled cells, resulting in markedly improved PM identifications, peptide counts, and iBAQ intensities. Correspondingly, we found substantial depletion of intracellular proteins, particular of nuclear origin. Overall, the cumulative intensity of PM proteins increased from 4% to 55.8% with dead cell depletion. Finally, we demonstrate that immature ER/Golgi glycoforms of CD11a and CD18 are selectively removed by dead-cell depletion. We conclude that high intracellular labelling of non-viable cells is the major source of intracellular protein contaminants in amine-reactive surface enrichment methods and can be reduced by dead-cell depletion post-labelling, improving both sensitivity and accuracy of plasma membrane proteomics.
    DOI:  https://doi.org/10.1101/2025.09.30.679609
  40. Circ Res. 2025 Nov 19.
    Non-Muscle α-Actinin-4 Couples Sarcomere Function to Cardiac Remodeling.
    James B Hayes, Dharmendra Choudhary, Dylan Ritter, Abigail C Neininger-Castro, Alaina H Willet, Leah R Caplan, Yu Wang, Xiao Liu, Nilay Taneja, Zachary C Sanchez, Kyra Smart, David W J Armstrong, Cynthia A Reinhart-King, Qi Liu, Matthew J Tyska, Erdem D Tabdanov, W David Merryman, Quinn S Wells, Ela W Knapik, Dylan T Burnette.
       BACKGROUND: Cardiac sarcomeres generate the fundamental forces of each heartbeat. Cardiac myocytes (CMs) express nonmuscle versions of muscle-specific sarcomere proteins, which have unknown relevance to sarcomere function or heart physiology.
    METHODS: Expression levels of nonmuscle cytoskeletal proteins versus muscle-specific counterparts in CMs were directly compared. Function and subcellular localization of the nonmuscle protein ACTN4 (alpha-actinin 4) in induced pluripotent stem cell-derived CMs were determined using small interfering RNA-mediated knockdown, overexpression, and pharmacological perturbation. Impacts of ACTN4 depletion or knockout on cardiac structure function were evaluated in zebrafish embryos. Left ventricular actn4 levels were evaluated in a mouse model of chronic pressure overload. Human ACTN4 gene variants were tested for association with heart failure with preserved ejection fraction using the BioVU biobank. A meta-analysis was conducted on ventricular data sets of human cardiomyopathies.
    RESULTS: ACTN4 expression in human CMs met or exceeded some muscle-specific genes (eg, MYH6). Anti-ACTN4 antibodies colocalized with anti-ACTN2 (alpha-actinin 2) at the sarcomere Z-disc in human, mouse, and zebrafish ventricular tissue. Coimmunoprecipitation and structural modeling suggest a Z-disc ACTN4:ACTN2 complex. ACTN4 depletion from induced pluripotent stem cell-derived CMs resulted in increased sarcomere assembly, decreased sarcomere component turnover, elevated contractile force, and contractility-dependent cellular hypertrophy. Overexpression of an ACTN4 actin-binding chimera suppressed sarcomere assembly. In zebrafish embryos, ACTN4 depletion/knockout induced ventricular hypercontractility and atrial enlargement. Selective modulation of ventricular contractility was sufficient to prevent or phenocopy atrial remodeling. In mice, actn4, but not actn2, was upregulated in the left ventricular following pressure overload. One of 14 ACTN4 single-nucleotide polymorphisms was associated with reduced heart failure with preserved ejection fraction risk in humans, and prepublished studies suggest a pattern of ventricular ACTN4 upregulation in certain human cardiomyopathies.
    CONCLUSIONS: A nonmuscle actinin (ACTN4) populates the cardiac Z-disc. ACTN4 regulates sarcomeric architecture in CMs. ACTN4 influences fractional shortening at the cell level and contractility at the tissue level. Changes in ventricular ACTN4 levels are associated with remodeling and may influence clinical outcomes related to heart failure.
    Keywords:  heart failure; microscopy, atomic force; myocytes, cardiac; sarcomeres; stroke volume
    DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326412
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