bims-ginsta Biomed News
on Genome instability
Issue of 2025–11–30
fifty-six papers selected by
Jinrong Hu, National University of Singapore
  1. Localized Wnt-signaling promotes asymmetric NuMA-dependent oriented divisions and unequal apportioning of mitochondria.
  2. Fate and state transitions during human blood vessel organoid development.
  3. RNA innate immunity constitutes a barrier for interspecies chimerism.
  4. A metabolic atlas of mouse aging.
  5. Stress-induced sympathetic hyperactivation drives hair follicle necrosis to trigger autoimmunity.
  6. A niche-dependent redox rheostat regulates epithelial stem cell fate.
  7. Convergent flow-mediated mesenchymal force drives embryonic foregut constriction and splitting.
  8. Portioning organelles for autophagic clearance.
  9. PCM1 coordinates centrosome asymmetry with polarized endosome dynamics to regulate daughter cell fate.
  10. Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion.
  11. WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response.
  12. Spatially Organized IGF1-mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs.
  13. Vascular organoid model of Hutchinson-Gilford progeria syndrome uncovers repression of the SRF pathway in premature aging.
  14. Phosphatase specificity influences phosphorylation timing of CDK substrates during the cell cycle.
  15. Nuclei sense complex tissue shape and direct intestinal stem cell fate.
  16. Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells.
  17. Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein.
  18. Cortical tension as a mechanical barrier to safeguard against premature differentiation during neurogenesis.
  19. Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury.
  20. BMP4 initiates and patterns ventral-caudal structures in zebrafish and human pluripotent stem cell aggregates.
  21. BAF-1-VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity.
  22. Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress.
  23. Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading.
  24. Heterochromatin boundaries maintain centromere position, size and number.
  25. Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model.
  26. Progressive coevolution of the yeast centromere and kinetochore.
  27. Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis.
  28. Kinetic control of mammalian transcription elongation.
  29. Cadherin Regulation of Endoplasmic Reticulum-Plasma Membrane Contact Sites.
  30. Adherent cells sustain membrane tension gradients independently of migration.
  31. The Somatic Aneuploidy Landscape of Adult Glia Reveals 16p as a Hotspot and Differentiates Mosaicism in Normal Glia from Chromosomal Instability in Glioblastoma.
  32. Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks.
  33. An mTOR-Stat3-Stathmin pathway controls centrosome and microtubule dynamics for oocyte polarization.
  34. Zebrafish otic vesicle and mouse epididymis as model systems for studying columnar epithelial cell division.
  35. Mechanical control of histone serotonylation initiates neural crest migration in vivo.
  36. Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis.
  37. Cell cycle oscillations in a polarity network facilitate state switching by morphogenetic cues.
  38. Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth.
  39. Genetic elements promote retention of extrachromosomal DNA in cancer cells.
  40. Fission yeast cells use distinct cell size control mechanisms for size adaptation to osmotic, oxidative, or low glucose conditions.
  41. Reversing lysosomal dysfunction restores youthful state in aged hematopoietic stem cells.
  42. Iron homeostasis and cell clonality drive cancer-associated intestinal DNA methylation drift in aging.
  43. The CIP2A-TOPBP1 axis facilitates mitotic DNA repair via MiDAS and MMEJ.
  44. Inhibitors supercharge kinase turnover through native proteolytic circuits.
  45. Class-I myosin responds to changes in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells.
  46. Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness.
  47. Integrated single-cell whole genome sequencing and spatial transcriptomics reveal latent intra-tumoral heterogeneity in ovarian cancer.
  48. Intrinsic errors in mitochondrial translation trigger a decline in cell fitness.
  49. Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins.
  50. Mechanisms governing poly(A)-tail-length specificity of the human PAN2-PAN3 deadenylase complex.
  51. Spatiotemporal Crosstalk Between Oocyte and the Microenvironment Governs Preovulatory Follicle Aging.
  52. Polymerase theta repairs persistent G1-induced DNA breaks in S-phase during class switch recombination.
  53. ATR promotes genome instability via CENP-A eviction from centromeres under replication stress.
  54. Xenophagocytosis blockade enhances interspecies chimerism.
  55. MAPK-driven epithelial cell plasticity drives colorectal cancer therapeutic resistance.
  56. Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy.
  1. Nat Commun. 2025 Nov 27. 16(1): 10690
    Localized Wnt-signaling promotes asymmetric NuMA-dependent oriented divisions and unequal apportioning of mitochondria.
    Susanna Eli, Greta Rauso, Paola Ghezzi, James L A Szczerkowski, Michela Bruzzi, Francesca Rizzelli, Fabiola Iommazzo, Alessia Loffreda, Francesco Castagna, Federico Donà, Chiara Gaddoni, Ambra Dondi, Mattia Marenda, Simona Rodighiero, Pierre Tournier, Zeno Lavagnino, Dario Parazzoli, Nils C Gauthier, Simone Tamburri, Diego Pasini, Shukry James Habib, Marina Mapelli.
      In multicellular organisms, the execution of developmental and homeostatic programs often relies on asymmetric cell divisions. These divisions require the alignment of the mitotic spindle axis to cortical polarity cues, and the unequal partitioning of cellular components between progeny cells. Asymmetric divisions are orchestrated by signals from the niche frequently presented in a directional manner, such as Wnt signals. Here we employ bioengineered Wnt-niches to demonstrate that in metaphase NuMA/dynein microtubule motors form a complex with activated LRP6 and β-catenin at the cortical sites of Wnt activation to orient cell division perpendicularly. We show that engagement of LRP6 co-receptors by Wnt ligands locally stabilizes actomyosin contractility through the accumulation of myosin1C. Additionally, we describe a proteomic-based approach to identify mitotic protein complexes enriched at the Wnt-contact site, revealing that mitochondria polarize toward localized Wnt3a sources and are asymmetrically apportioned to the Wnt-proximal daughter cell during Wnt-mediated asymmetric cell division of embryonic stem cells. Mechanistically, we show that CENP-F is required for mitochondria polarization towards localized sites of Wnt3a activation, and that deletion of the Wnt-co-receptor LRP6 impairs the asymmetric apportioning of mitochondria. Our findings enhance the understanding of mitotic Wnt-signaling and elucidate fundamental principles underlying Wnt-dependent mitochondrial polarization.
    DOI:  https://doi.org/10.1038/s41467-025-65775-z
  2. Cell. 2025 Nov 21. pii: S0092-8674(25)01314-5. [Epub ahead of print]
    Fate and state transitions during human blood vessel organoid development.
    Marina T Nikolova, Zhisong He, Makiko Seimiya, Gustav Jonsson, Wuji Cao, Ryo Okuda, Reiner A Wimmer, Ryoko Okamoto, Jonas M Nikoloff, Petra S Dittrich, Josef M Penninger, J Gray Camp, Barbara Treutlein.
      
    DOI:  https://doi.org/10.1016/j.cell.2025.11.018
  3. Cell. 2025 Nov 24. pii: S0092-8674(25)01244-9. [Epub ahead of print]
    RNA innate immunity constitutes a barrier for interspecies chimerism.
    Yingying Hu, Hai-Xi Sun, Masahiro Sakurai, Zhou Luo, Amanda E Jones, Tianlei Cheng, Jia Huang, Lizhong Liu, Canbin Zheng, Jie Li, Yue Lu, Benjamin Ravaux, Bingbing He, Yi Ding, Tianbin Liu, Yan Wu, Zhijian J Chen, John M Abrams, Elizabeth H Chen, Ying Gu, Jun Wu.
      Creating interspecies chimeras with human pluripotent stem cells (hPSCs) offers a promising strategy for modeling human development and generating donor organs; however, poor human cell integration remains a major barrier. Most existing efforts to improve human chimerism focus on genetically modifying donor hPSCs, while altering the host embryo remains largely unexplored. Using an interspecies PSC competition model, we discovered that RNA innate immunity in "winner" mouse cells drives the competitive elimination of hPSCs. Disrupting RNA-sensing pathways reduced the competitiveness and viability of mouse PSCs, and mouse embryos lacking Mavs-a key gene in RNA innate immunity-led to markedly improved human cell survival and chimerism. We also found that contact-dependent horizontal RNA transfer likely underlies this immune activation. Overall, our study uncovers a previously unrecognized role for RNA innate immunity in cell competition and demonstrates that targeting host immune pathways represents a powerful approach to improve human chimerism in animals.
    Keywords:  MAVS; RLR pathway; RNA innate immunity; cell competition; horizontal RNA transfer; human pluripotent stem cells; interspecies PSC co-culture; interspecies chimeras; mouse epiblast stem cells; tunneling nanotube
    DOI:  https://doi.org/10.1016/j.cell.2025.10.039
  4. Cell Metab. 2025 Nov 25. pii: S1550-4131(25)00476-0. [Epub ahead of print]
    A metabolic atlas of mouse aging.
    Steven E Pilley, Dominik Awad, Djakim Latumalea, Connie New, Edgar Esparza, Shuo Wang, Xuanyi Shi, Li Zhang, Maximilian Unfried, Jasinda H Lee, Ernst Schmid, Ipsita Mohanty, Jenna L E Blum, Shivaanishaa Raventhiran, Esther Wong, Preeti R Iyengar, Racheal Mulondo, Sriraksha Bharadwaj Kashyap, Darius Moaddeli, Peter Sajjakulnukit, Damien Sutton, Harrison K A Wong, Yaqi Gao, George Wang, Aeowynn J Coakley, Gilberto Garcia, Ryo Higuchi-Sanabria, Anja Karlstaedt, Timothy L Frankel, Marina Pasca di Magliano, Whitaker Cohn, Sophia Liu, Bingfei Yu, Pieter C Dorrestein, Ernest Fraenkel, Shawn M Davidson, William B Tu, Brian K Kennedy, Costas A Lyssiotis, Peter J Mullen.
      Humans are living longer and experiencing more age-related diseases, many of which involve metabolic dysregulation, but how metabolism changes in multiple organs during aging is not known. Answering this could reveal new mechanisms of aging and therapeutics. Here, we profile metabolic changes in 12 organs in male and female mice at 5 different ages. We also develop organ-specific metabolic aging clocks that identify metabolic drivers of aging, including alpha-ketoglutarate, previously shown to extend lifespan in mice. We also use the clocks to uncover that carglumic acid is a potential driver of aging and show that it is synthesized by human cells. Finally, we validate that hydroxyproline decreases with age in the human pancreas, emphasizing that our approach reveals insights across species. This study reveals fundamental insights into the aging process and identifies new therapeutic targets to maintain organ health.
    Keywords:  LC-MS/MS; MALDI-MSI; aging; aging clocks; healthspan; human tissue; hydroxyproline; metabolism; scRNA-seq; sex
    DOI:  https://doi.org/10.1016/j.cmet.2025.10.016
  5. Cell. 2025 Nov 26. pii: S0092-8674(25)01247-4. [Epub ahead of print]
    Stress-induced sympathetic hyperactivation drives hair follicle necrosis to trigger autoimmunity.
    Emily Scott-Solomon, Shlomi Brielle, Alexander O Mann, Mark J Khoury, Jingyu Peng, Liana Tellez, Mackenzie Harrigan, Myrto Ziogas, H Amalia Pasolli, Monica Cassandras, Adam J Getzler, Rebecca Freeman, Bing Zhang, Yulia Shwartz, Judith Agudo, Ruth A Franklin, Ya-Chieh Hsu.
      Stress has profound effects on health, yet how it damages tissues remains poorly understood. Here, we show that acute stress triggers rapid hair loss and initiates autoimmunity. Under stress, hyperactivated sympathetic nerves release excessive norepinephrine, causing necrosis in rapidly dividing hair follicle transit-amplifying cells (HF-TACs) while sparing most hair follicle stem cells (HFSCs). This differential sensitivity stems from differences in cell death pathways, metabolic strategies, and calcium homeostasis, which render HF-TACs more susceptible to norepinephrine-induced calcium surges. HF-TAC necrosis releases cellular debris that triggers macrophage-mediated clearance and dendritic cell activation, ultimately leading to the activation and amplification of autoreactive T cells that can attack the hair follicle under inflammatory insults. Our findings reveal mechanistically how stress causes immediate tissue damage in highly proliferative HF-TACs via sympathetic nerve-induced necrosis, which in turn fuels the activation of autoreactive T cells capable of mounting future attacks against the same tissue.
    Keywords:  alopecia areata; autoimmune; necrosis; nerve-tissue interaction; neuro-immune interaction; stress; sympathetic neuron
    DOI:  https://doi.org/10.1016/j.cell.2025.10.042
  6. Nat Commun. 2025 Nov 28.
    A niche-dependent redox rheostat regulates epithelial stem cell fate.
    Xi Chen, Krishnan Raghunathan, Bin Bao, Elsy Ngwa, Andrew Kwong, Zhongyang Wu, Stephen Babcock, Clara Baek, George Ye, Anoohya Muppirala, Qianni Peng, Michael Rutlin, Mantu Bhaumik, Daping Yang, Daniel Kotlarz, Unmesh Jadhav, Meenakshi Rao, Eranthie Weerapana, Xu Zhou, Jose Ordovas-Montanes, Scott B Snapper, Jay R Thiagarajah.
      Intestinal stem cells (ISCs) reside in regionally variable niches that provide diverse microenvironmental cues such as tissue oxygen status, and morphogen signaling. Integration of these cues with ISC metabolism and fate remains poorly understood. Here, we show that cellular redox balance orchestrates niche factors with metabolic state to govern cell fate decisions. We demonstrate that hypoxia and Wnt signaling synergistically restrict the reactive oxygen species generating enzyme NADPH oxidase 1 (NOX1) regionally to the crypt base in the distal colon. NOX1 enables maintenance of an oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric ISC self-renewal and lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1α-dependent signaling with post-translational regulation of the metabolic enzyme isocitrate dehydrogenase 1. Our studies show redox balance acts as a cellular rheostat that is central and causative for metabolic control of the ISC cell-cycle.
    DOI:  https://doi.org/10.1038/s41467-025-66636-5
  7. Nat Commun. 2025 Nov 27. 16(1): 10643
    Convergent flow-mediated mesenchymal force drives embryonic foregut constriction and splitting.
    Rui Yan, Ludwig A Hoffmann, Panagiotis Oikonomou, Deng Li, ChangHee Lee, Hasreet K Gill, Alessandro Mongera, Nandan L Nerurkar, L Mahadevan, Clifford J Tabin.
      The transformation of a two-dimensional epithelial sheet into various three-dimensional structures is a critical process in generating the diversity of animal forms. Previous studies of epithelial folding have revealed diverse mechanisms driven by epithelium-intrinsic or -extrinsic forces. Yet little is known about the biomechanical basis of epithelial splitting, which involves extreme folding and eventually a topological transition breaking the epithelial tube. Here, we leverage tracheal-esophageal separation (TES), a critical and highly conserved morphogenetic event during tetrapod embryogenesis, as a model system for interrogating epithelial tube splitting. We identify an evolutionarily conserved, compressive force exerted by the mesenchyme surrounding the epithelium, as being necessary to drive epithelial constriction and splitting. The compressive force is mediated by localized convergent flow of mesenchymal cells towards the epithelium. Sonic hedgehog (SHH) secreted by the epithelium functions as an attractive cue for mesenchymal cells. Removal of the mesenchyme, inhibition of cell migration, or loss of SHH signaling all abrogate TES, which can be rescued by externally applied pressure. These results unveil the biomechanical basis of epithelial splitting and suggest plausible mesenchymal origins of tracheal-esophageal birth defects.
    DOI:  https://doi.org/10.1038/s41467-025-65644-9
  8. Autophagy. 2025 Nov 28.
    Portioning organelles for autophagic clearance.
    Mikhail Rudinskiy, Maurizio Molinari.
      The lysosomal/vacuolar clearance of portions of organelles including the endoplasmic reticulum (ER), mitochondria, the Golgi apparatus and the nucleus, organellophagy, is mediated by autophagy receptors anchored at the surface of their respective organelles. Organellophagy receptors are activated, induced or derepressed in response to stimuli such as nutrient or oxygen deprivation, accumulation of toxic or aged macromolecules, membrane depolarization, pathogen invasion, cell differentiation and many others. Their activation drives the portioning of the homing organelle, and the engagement of Atg8/LC3/GABARAP (LC3) proteins via LC3-interacting regions (LIRs) that results in autophagic clearance. In our latest work, we elaborate on the fact that all known mammalian and yeast organellophagy receptors expose their LIR embedded within intrinsically disordered regions (IDRs), i.e. cytoplasmic stretches of amino acids lacking a fixed three-dimensional structure. Our experiments reveal that the IDR modules of organellophagy receptors are interchangeable, required and sufficient to induce the fragmentation of the organelle that displays them at the limiting membrane, independent of LC3 engagement. LC3 engagement drives lysosomal delivery. Building on these findings, we propose harnessing practical and therapeutic potential of controlled organelle fragmentation and organellophagy through ORGAnelle TArgeting Chimeras (ORGATACs).
    Keywords:  Endoplasmic reticulum (Er)phagy; ORGAnelle TArgeted chimeras (ORGATACs); intrinsically disordered regions (IDRs); mitophagy; organellophagy receptors; targeted organelle degradation
    DOI:  https://doi.org/10.1080/15548627.2025.2597458
  9. Nat Commun. 2025 Nov 28. 16(1): 10728
    PCM1 coordinates centrosome asymmetry with polarized endosome dynamics to regulate daughter cell fate.
    Xiang Zhao, Vincent Mouilleau, Yiqi Wang, Ahmet Can Solak, Jason Q Garcia, Xinye Chen, Xiaoyu Shi, Christopher J Wilkinson, Loïc A Royer, Zhiqiang Dong, Su Guo.
      Vertebrate radial glia progenitors (RGPs) balance self-renewal and differentiation through asymmetric cell division (ACD), which involves unequal centrosome inheritance. How centrosome asymmetry directs cell fate remains poorly understood. Here, we identify Pericentriolar material 1 (Pcm1) as a key player in this process. In zebrafish embryonic RGPs, Pcm1 is asymmetrically associated with Cep83, a mother centrosome marker. Using in vivo time-lapse imaging and nanoscale-resolution expansion microscopy, we detect Pcm1 on Notch ligand-containing endosomes, where it interacts-either directly or indirectly-with Par-3 and dynein. Loss of pcm1 disrupts endosome dynamics, increasing neuronal differentiation at the expense of RGP self-renewal. Mechanistically, Pcm1 facilitates the transition from Rab5b to Rab11a and promotes the assembly of Par-3 and dynein macromolecular complexes on recycling endosomes. Furthermore, we find conserved PARD3-PCM1-CEP83-RAB11 associations in human cortical brain organoids. Our findings uncover that Pcm1 links centrosome asymmetry to polarized endosome trafficking, thereby regulating RGP fate decisions.
    DOI:  https://doi.org/10.1038/s41467-025-65756-2
  10. Nat Commun. 2025 Nov 27.
    Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion.
    Maria T Bejar, Paula Jimenez-Gomez, Ilias Moutsopoulos, Harikrishnan Ajith, Bartomeu Colom, Jamie McGinn, Seungmin Han, Greta Skrupskelyte, Fernando J Calero-Nieto, Berthold Göttgens, Irina I Mohorianu, Benjamin D Simons, Maria P Alcolea.
      The ability of adult epithelial cells to rewire their cell fate programme in response to injury has emerged as a new paradigm in stem cell biology. This plasticity supersedes the concept of strict stem cell hierarchies, granting cells access to a wider repertoire of fate choices. Yet, in order to prevent a disordered cellular response, this process must be finely regulated. Here we investigate the little-known regulatory processes that restrict fate permissibility in adult cells, and keep plasticity in check. Using a 3D regenerative culture system, that enables co-culturing epithelium and stroma of different origins, we demonstrate that oesophageal cells exposed to the ectopic signals of the dermis are capable of switching their identity towards skin. Lineage tracing experiments and histological analysis, however, reveal that the oesophageal-to-skin lineage conversion process is highly inefficient, pointing to the existence of barriers limiting cell fate re-specification. Single-cell RNA sequencing capturing the temporality of this process shows that cells transitioning towards skin identity resist the natural progression towards tissue maturation by remaining in a persistent regenerative state marked by a particularly strong hypoxic signature. Gain and loss of function experiments demonstrate that the HIF1a-SOX9 axis acts as a key modulator of epithelial cell fate plasticity, restricting changes in identity during tissue regeneration. Taken together, our results reveal the existence of lineage conversion barriers that must be resolved for cells to respond to signals instructing alternative fate choices, shedding light on the principles underlying the full regenerative capacity of adult epithelial cells.
    DOI:  https://doi.org/10.1038/s41467-025-66446-9
  11. Nat Commun. 2025 Nov 24.
    WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response.
    Rinskje B Tjeerdsma, Timothy F Ng, Maurits Roorda, Daniëlle Bianchi, Sora Yang, Clara Bonnet, Michael VanInsberghe, Marieke Everts, Femke J Bakker, H Rudolf de Boer, Nathalie Moatti, Nicole Hustedt, Jay Z Yin, Lisa Hoeg, Matthew Leibovitch, Frank Sicheri, Alexander van Oudenaarden, Steven de Jong, Jeroen van den Berg, Marvin E Tanenbaum, Thijn R Brummelkamp, Daniel Durocher, Marcel A T M van Vugt.
      The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibitors (WEE1i) are largely unknown. A genome-wide insertional mutagenesis screen revealed that mutation of EIF2A, a translation regulator, sensitized to WEE1i. Additionally, a genome-wide CRISPR-Cas9 screen revealed that inactivation of integrated stress response (ISR) kinase GCN2 or its co-factor GCN1 rescued WEE1i-mediated cytotoxicity. Conversely, loss of the collided ribosome sensor ZNF598 increased sensitivity to WEE1i. Mechanistically, WEE1i induced paradoxical GCN2 activation, ATF4 upregulation, and altered ribosome dynamics. ISR activation was independent of WEE1 presence, pointing at off-target GCN2 engagement by multiple chemically distinct WEE1i. ISR activation was observed in cancer cells as well as non-transformed cells, and required GCN1 and ongoing translation. Consequently, WEE1i induce multiple independent cellular effects: DNA damage, premature mitotic entry and sensitization to DNA-damaging chemotherapeutics in an ISR-independent fashion, as well as ISR activation independently of CDK1/2 activation. Importantly, low-dose WEE1 inhibition did not induce ISR activation, while it still synergized with PKMYT1 inhibition. Taken together, WEE1i trigger toxic ISR activation and translational shutdown, which can be prevented by low-dose or combination treatments, while retaining the cell cycle checkpoint-perturbing effects.
    DOI:  https://doi.org/10.1038/s41467-025-66514-0
  12. bioRxiv. 2025 Sep 24. pii: 2025.05.08.652851. [Epub ahead of print]
    Spatially Organized IGF1-mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs.
    Kadia Lisst, Da Huo, Stephen M Eacker, Sonya Zhang, Alina Yang, Yuejia Huang, Ted M Dawson, Valina L Dawson, Jin-Chong Xu.
      The specification and maintenance of human forebrain neural progenitor cells (NPCs) depend on both intrinsic gene networks and spatially localized niche signals, but the interplay between these cues remains incompletely understood. Here, we identify a spatially organized, paracrine IGF1 signaling architecture that regulates human FOXG1⁺ NPCs through multilayered transcriptional and translational control. Using a pluripotent stem cell-derived forebrain model, we show that FOXG1⁺ NPCs express IGF1 receptors but lack endogenous IGF1, instead depending on neighboring epithelial-like domains that secrete IGF1. IGF1 promotes progenitor proliferation, clonal expansion, and vertical tissue growth by activating PI3K-AKT-mTOR and MEK-ERK pathways. Ribosome profiling and 5'UTR reporter assays reveal that mTOR signaling selectively enhances translation of neurodevelopmental and biosynthetic transcripts- including GSX1 , a ventral fate determinant implicated in interneuron specification and autism. These findings uncover a human-specific regulatory mechanism in which spatially restricted IGF1-mTOR signaling integrates niche signals with translational output to support progenitor identity, biosynthetic capacity, and developmental resilience.
    DOI:  https://doi.org/10.1101/2025.05.08.652851
  13. Dev Cell. 2025 Nov 27. pii: S1534-5807(25)00690-2. [Epub ahead of print]
    Vascular organoid model of Hutchinson-Gilford progeria syndrome uncovers repression of the SRF pathway in premature aging.
    Xiaoyan Sun, Shanshan Che, Hengchao Wang, Yanling Fan, Yingjie Ding, Ansheng Tan, Kuan Yang, Jianli Hu, Yixin Zhang, Miyang Ma, Jinghao Hu, Shuhui Sun, Shuai Ma, Si Wang, Juan Carlos Izpisua Belmonte, Jing Qu, Weiqi Zhang, Guang-Hui Liu.
      Vascular aging is a key driver of cardiovascular disease, yet models capturing its complexity in humans are lacking. Hutchinson-Gilford progeria syndrome (HGPS), a premature aging disorder caused by the LMNA mutation, provides a model to study accelerated vascular decline. Here, we developed a blood vessel organoid (BVO) model from HGPS-mutant human embryonic stem cells (hESCs). These BVOs model HGPS vascular defects and reveal significant downregulation of serum response factor (SRF), a trend also observed in the vasculature of naturally aged primates. We show that SRF regulates angiogenesis-related genes, and that its overexpression rescues endothelial function in HGPS organoids. In summary, we establish a 3D human organoid model of vascular aging, identify SRF as a pivotal regulator and provide a powerful platform for discovering geroprotective therapies.
    Keywords:  Hutchinson-Gilford progeria syndrome; SRF; aging; angiogenesis; blood vessel; endothelial cell; organoid; premature aging; senescence; vascular aging
    DOI:  https://doi.org/10.1016/j.devcel.2025.10.019
  14. Nat Commun. 2025 Nov 24.
    Phosphatase specificity influences phosphorylation timing of CDK substrates during the cell cycle.
    Theresa U Zeisner, Tania Auchynnikava, Emma L Roberts, Paul Nurse.
      Cell cycle events are ordered by cyclin-dependent kinases (CDKs), which phosphorylate hundreds of substrates. Multiple phosphatases oppose these CDK substrates, yet their collective role in regulating phosphorylation timing in vivo remains unclear. Here, we show that four phosphatases (PP2A-B55, PP2A-B56, CDC14, and PP1) each target distinct subsets of CDK substrate sites in vivo in fission yeast, influencing when phosphorylation occurs during G2 and mitosis. On average, sites dephosphorylated by CDC14 and PP2A-B56 are phosphorylated earlier during G2, followed by sites dephosphorylated by PP1 and PP2A-B55. This suggests that these phosphatases set different phosphorylation thresholds at the G2/M transition. Consistent with this, depleting PP2A-B55 or CDC14 accelerates mitotic onset, likely by advancing phosphorylation of their respective CDK substrates, suggesting these phosphorylation thresholds are important for regulating mitotic onset. Our findings establish in vivo phosphatase substrate specificity as a key factor regulating the timing of CDK substrate phosphorylation throughout the cell cycle.
    DOI:  https://doi.org/10.1038/s41467-025-66547-5
  15. bioRxiv. 2025 Oct 24. pii: 2025.10.23.684219. [Epub ahead of print]
    Nuclei sense complex tissue shape and direct intestinal stem cell fate.
    Kaustav Bera, Delaney L McNally, Bruce E Kirkpatrick, Nolan R Petrich, F Max Yavitt, Marilyne Coulombe, Michaela Quintero, Nathaniel P Skillin, Alex Khang, Patrick S McGrath, Linda C Samuelson, Tanmay P Lele, Peter J Dempsey, Kristi S Anseth.
      Tissue architecture and function are influenced by mechanical cues. Yet, how cell nuclei sense forces within 3D tissues and dictate differentiation remains unknown as prior studies focused on isolated mesenchymal cells, which fail to fully predict tissue-level mechanical properties. We fill this knowledge gap utilizing live reporters and material-based organoid models. We posit the nucleus as an active mechanosensor of tissue shape, with levels of the nuclear scaffolding protein lamin-A varying across intestinal stem cell differentiation trajectory. Elevated forces on differentiated Paneth cell nuclei, in both organoids and tissue explants, increase lamin-A and nuclear wrinkling. Enhancing nuclear mechanotransduction primes cell differentiation, in otherwise stem promoting conditions, revealing that nuclear mechanics can direct stem cell fate. By engineering spatiotemporally controlled de novo tissue curvature with photo-degradable hydrogels, we direct spatially patterned lamin-A levels across mouse and human organoids of healthy and diseased origin, uncovering conserved nuclear mechanosensing pathway in epithelial tissues.
    DOI:  https://doi.org/10.1101/2025.10.23.684219
  16. Nat Aging. 2025 Nov 24.
    Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells.
    Eva Mejía-Ramírez, Pablo Iáñez Picazo, Barbara Walter, Sara Montserrat-Vazquez, Francesco Affuso, Stefan Wieser, Fabio Pezzano, Loïc Reymond, Jorge Castillo-Robles, Francesca Matteini, Loris Mularoni, Dídac Maciá, Ángel Raya, Verena Ruprecht, Yi Zheng, Paula Petrone, M Carolina Florian.
      Biomechanical alterations contribute to the decreased regenerative capacity of hematopoietic stem cells (HSCs) upon aging. RhoA is a key regulator of mechanosignaling, but its role in mechanotransduction in stem cell aging remains unclear. Here we show that murine HSCs respond to increased nuclear envelope (NE) tension by inducing NE translocation of P-cPLA2, which cell-intrinsically activates RhoA. Aged HSCs experience physiologically higher intrinsic NE tension, but reducing RhoA activity lowers NE tension in aged HSCs. Feature image analysis of HSC nuclei reveals that chromatin remodeling is associated with RhoA inhibition, including restoration of youthful levels of the heterochromatin marker H3K9me2 and a decrease in chromatin accessibility and transcription at retrotransposons. Finally, we demonstrate that RhoA inhibition upregulates Klf4 expression and transcriptional activity, improving aged HSC regenerative capacity and lympho/myeloid skewing in vivo. Together, our data outline an intrinsic RhoA-dependent mechanosignaling axis, which can be pharmacologically targeted to restore aged stem cell function.
    DOI:  https://doi.org/10.1038/s43587-025-01014-w
  17. Nat Cell Biol. 2025 Nov 24.
    Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein.
    Srivarsha Rajshekar, Omar Adame-Arana, Gaurav Bajpai, Serafin U Colmenares, Hannah Papoi, Lucy D Brennan, Shingo Tsukamoto, Samuel Safran, Gary H Karpen.
      Nucleoli are surrounded by pericentromeric heterochromatin (PCH), reflecting a conserved spatial association between the two largest biomolecular condensates in eukaryotic nuclei. Nucleoli are the sites of ribosome synthesis, whereas the repeat-rich PCH is essential for chromosome segregation, genome stability and transcriptional silencing, yet the mechanisms for their co-assembly are unclear. Here we use high-resolution live imaging during Drosophila embryogenesis and reveal that de novo establishment of PCH-nucleolar associations is highly dynamic, as PCH transitions from extending along the nuclear edge to surrounding the nucleolus. Elimination of the nucleolus by removing the ribosomal RNA genes disrupted this process causing increased PCH compaction, followed by its reorganization into a toroidal structure. Furthermore, in embryos lacking ribosomal RNA genes, nucleolar proteins were redistributed into new bodies or 'neocondensates', including enrichment in the PCH toroidal hole. Combining these in vivo observations with molecular dynamics simulations based on multiphase wetting theory revealed that nucleolar-PCH associations can be mediated by a hierarchy of interaction strengths between PCH, nucleoli and proteins with dual affinities for both compartments. We validate this model by identifying such a protein, a DEAD-box RNA helicase called Pitchoune, and show that modulation of its affinity for either nucleolar or PCH components alters nucleolar-PCH organization. Together, this study unveils a dynamic programme for establishing nucleolar-PCH associations during animal development and demonstrates how interaction hierarchies and dual-affinity molecular linkers co-organize compositionally distinct condensates.
    DOI:  https://doi.org/10.1038/s41556-025-01806-7
  18. Res Sq. 2025 Oct 31. pii: rs.3.rs-7725502. [Epub ahead of print]
    Cortical tension as a mechanical barrier to safeguard against premature differentiation during neurogenesis.
    Hongyan Zou, Daniel Halperin, Chrystian Junqueira Alves, Marcelle Rodrigues Lemos, Swagata Dey, Haochen Tao, Sangjo Kang, Xianting Li, Zhenyu Yue, Jiaxi Li, Rodrigo Alves Dias, Gustavo Rosa, José Rodrigues Furtado de Mendonça, Molly Estill, Yonatan Perez, Susana Ramos, Nadejda Tsankova, Li Shen, Roland Friedel.
      Neuronal differentiation requires coordinated gene reprogramming and morphodynamic remodeling. How mechanical forces integrate with nuclear gene programs during neurogenesis remains unresolved. Here, we identify cortical tension as a mechanical barrier that safeguards against premature neuronal differentiation. Deletion of Plexin-B2, a guidance receptor controlling actomyosin contractility, lowers this barrier, enabling neurite outgrowth and accelerating neuronal lineage commitment. We show that coupling of extrinsic differentiation cues with intrinsic morphodynamics is essential for stabilizing neuronal fate and that cortical barrier and epigenetic barrier act in concert to regulate developmental timing. In cerebral organoids, Plexin-B2 ablation triggered premature cell-cycle exit and differentiation, resulting in progenitor pool depletion and neuroepithelial disorganization, phenotypes echoing intellectual disability in patients with rare pathogenic PLXNB2 variants. Our studies demonstrate that cortical tension functions as mechano-checkpoint that regulates the onset of neurogenesis. Lowering this barrier may provide a strategy to accelerate induced neuron generation and maturation for CNS disease modeling.
    DOI:  https://doi.org/10.21203/rs.3.rs-7725502/v1
  19. bioRxiv. 2025 Nov 11. pii: 2025.11.09.687498. [Epub ahead of print]
    Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury.
    Julian Chua, Lucy Driver, Masahiro Narimatsu, Mardi Fink, Lixia Luo, Jordan Tran, Arshdeep Kaur, Rida Habib, Jatin Roper, David G Kirsch, Jeffrey L Wrana, Chang-Lung Lee, Arshad Ayyaz.
      The cellular origin of intestinal epithelial homeostasis and regeneration has been a subject of continued debate, with recent models challenging the primacy of WNT-dependent Lgr5⁺ crypt base columnar (CBC) cells as the central intestinal stem cell population. Here, we revisit this question through quantitative integration of single-cell transcriptomic, chromatin accessibility, spatial, and lineage-tracing analyses across the proximal-to-distal axis of the small intestinal epithelium. Our data show that under homeostatic conditions, Lgr5⁺ cells exclusively sustain epithelial self-renewal in nearly all crypt-villus units along the entire length of the small intestine, a process for which R-spondin is indispensable. Following irradiation or chemotoxic injury, surviving Lgr5⁺ cells and their progeny reprogram into transient fetal-like cell states that initiate epithelial repair. Crucially, successful regeneration depends on the reactivation of canonical WNT/β-catenin signaling, as evidenced by increased TCF motif accessibility and upregulation of WNT target genes in newly forming Lgr5 + stem cells. Accordingly, pharmacological inhibition of WNT signaling blocks the reconstitution of Lgr5⁺ cells and crypt regeneration, leading to epithelial collapse. These findings reconcile prior controversies by demonstrating the central role of Lgr5⁺ CBC cells in epithelial self-renewal and regeneration following injury.
    DOI:  https://doi.org/10.1101/2025.11.09.687498
  20. EMBO J. 2025 Nov 24.
    BMP4 initiates and patterns ventral-caudal structures in zebrafish and human pluripotent stem cell aggregates.
    Yan-Yi Xing, Ying Huang, Tao Cheng, Yi-Meng Tian, Yang Dong, Zi-Xin Jin, Hai-Rong Pu, Tao Luo, Xiang Liu, Hao-Nan Shen, Jing Mo, Jun Ma, Jun-Feng Ji, Peng-Fei Xu.
      The formation of body axes is a key developmental milestone in vertebrate embryos and is guided by specialized groups of cells known as organizers. The molecular nature of organizers has been extensively investigated across the vertebrate kingdom; however, the minimal conditions and factors sufficient to guide embryogenesis and organogenesis-particularly in humans-remain incompletely understood. Here, we show that BMP4 alone, when administered at an appropriate dosage, is sufficient to induce the formation of an organizer for ventral-caudal-like structure (VCLS) formation. This organizer directs endoderm-deficient ventral-caudal cell fate specification and morphogenesis in zebrafish embryos. In 3D human pluripotent stem cell (hPSC) aggregates, BMP4 can induce an elongated embryonic structure that is characterized by ventral-caudal cell fates. Importantly, hPSCs instructed by BMP4 are sufficient to induce a secondary posterior axis when grafted into the animal pole of the zebrafish embryo. Our study thus uncovers BMP4 as the inducer for the formation of a ventral-caudal organizer in the vertebrate embryo.
    Keywords:  BMP4; Human Pluripotent Stem Cells; Morphogenesis; Ventral-caudal Organizer; Zebrafish Explant
    DOI:  https://doi.org/10.1038/s44318-025-00643-6
  21. Nat Commun. 2025 Nov 25. 16(1): 10446
    BAF-1-VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity.
    Dimitra Paouneskou, Antoine Baudrimont, Réka Kelemen, Marwan Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, Verena Jantsch.
      Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)-dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1-VRK-1 module in preserving genome stability in gametes during rapid chromosome movements.
    DOI:  https://doi.org/10.1038/s41467-025-65420-9
  22. Mol Cell. 2025 Nov 24. pii: S1097-2765(25)00900-1. [Epub ahead of print]
    Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress.
    Mostafa Zedan, Alexandra P Schürch, Stephanie Heinrich, Pablo A Gómez-García, Sarah Khawaja, Léona Dörries, Karsten Weis.
      When cells encounter stress, they rapidly mount an adaptive response by switching from pro-growth to stress-responsive gene expression programs. How cells selectively silence pre-existing, pro-growth transcripts yet efficiently translate transcriptionally induced stress mRNA and whether these transcriptional and post-transcriptional responses are coordinated are poorly understood. Here, we show that following acute glucose withdrawal in S. cerevisiae, pre-existing mRNAs are not first degraded to halt protein synthesis, nor are they sequestered away in P-bodies. Rather, their translation is quickly repressed through a sequence-independent mechanism that differentiates between mRNAs produced before and after stress, followed by their decay. Transcriptional induction of endogenous transcripts and reporter mRNAs during stress is sufficient to escape translational repression, while induction prior to stress leads to repression. Our results reveal a timing-controlled coordination of the transcriptional and translational responses in the nucleus and cytoplasm, ensuring a rapid and wide-scale reprogramming of gene expression following environmental stress.
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.004
  23. Nat Commun. 2025 Nov 26.
    Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading.
    Charles Winterhalter, Kathryn J Stratton, Stepan Fenyk, Heath Murray.
      DNA damage occurs in all cells and must be repaired to maintain genome integrity. Many DNA lesions are targeted for removal by repair systems that excise the damage, thereby generating a temporary single-strand discontinuity in the chromosome. If DNA repair has not been completed prior to a round of genome duplication, the single-strand discontinuity (nick or gap) can be converted to a double-strand break (DSB) by an oncoming replication fork. Because the genomic location of nucleobase damage is stochastic, investigating the fate of replication machinery (replisome) at DNA repair sites with single-strand discontinuities has been limited. Here we address this issue by expressing Cas9 nickases in Bacillus subtilis to create site-specific single-strand discontinuities in a bacterial chromosome. We find that a nick in either leading or lagging strand arrests DNA replication, while the fate of the replicative helicase is distinct and depends upon the strand nicked. Genetic, biochemical, and single cell analyses indicate that replisome/nick encounters generate a single-end DSB which requires recombinational repair to enable PriA-dependent replication restart. Together this work defines the physiologically relevant pathway used by B. subtilis to reinitiate DNA synthesis following replication fork inactivation at a single-strand discontinuity.
    DOI:  https://doi.org/10.1038/s41467-025-66550-w
  24. Nat Struct Mol Biol. 2025 Nov 25.
    Heterochromatin boundaries maintain centromere position, size and number.
    Ben L Carty, Danilo Dubocanin, Marina Murillo-Pineda, Marie Dumont, Emilia Volpe, Pawel Mikulski, Julia Humes, Oliver Whittingham, Daniele Fachinetti, Simona Giunta, Nicolas Altemose, Lars E T Jansen.
      Centromeres are defined by a unique single chromatin domain featuring the histone H3 variant, centromere protein A (CENP-A), and ensure proper chromosome segregation. Centromeric chromatin typically occupies a small subregion of low DNA methylation within multimegabase arrays of hypermethylated alpha-satellite repeats and constitutive pericentric heterochromatin. Here, we define the molecular basis of how heterochromatin serves as a primary driver of centromere and neocentromere position, size and number. Using single-molecule epigenomics, we uncover roles for H3K9me3 methyltransferases SUV39H1/H2 and SETDB1, in addition to noncanonical roles for SUZ12, in maintaining H3K9me3 boundaries at centromeres. Loss of these heterochromatin boundaries leads to the progressive expansion and/or repositioning of the primary CENP-A domain, erosion of surrounding DNA methylation and nucleation of additional functional CENP-A domains across the same alpha-satellite sequences. Our study identifies the functional importance and specialization of different H3K9 methyltransferases across centromeric and pericentric domains, crucial for maintaining centromere domain size and suppressing ectopic centromere nucleation events.
    DOI:  https://doi.org/10.1038/s41594-025-01706-2
  25. Sci Adv. 2025 Nov 28. 11(48): eady7682
    Specialized signaling centers direct cell fate and spatial organization in a mesodermal organoid model.
    Evangelia Skoufa, Jixing Zhong, Kelly Hu, Oliver Kahre, Georgios Tsissios, Louise Carrau, Antonio Herrera, Albert Dominguez Mantes, Marion Leleu, Alejandro Castilla-Ibeas, Hwanseok Jang, Martin Weigert, Gioele La Manno, Matthias Lutolf, Marian Ros, Can Aztekin.
      Specialized signaling centers orchestrate robust development and regeneration. Limb morphogenesis, for instance, requires interactions between the mesoderm and the signaling center apical-ectodermal ridge (AER), whose properties and role in cell fate decisions have remained challenging to dissect. To tackle this, we developed mouse embryonic stem cell (mESC)-based heterogeneous cultures and a three-dimensional (3D) organoid model, termed budoids, comprising cells with AER, surface ectoderm, and mesoderm properties. mESCs were first induced into heterogeneous cultures that self-organized into domes in 2D. Aggregating these cultures formed mesodermal organoids with certain limb bud-like features in 3D, exhibiting chondrogenesis-based symmetry breaking and elongation. Using our organoids and quantitative in situ expression profiling, we uncovered that AER-like cells support nearby limb mesoderm and fibroblast identities while enhancing tissue polarization that permits distant cartilage formation. Together, our findings provide a powerful model to study epithelial signaling center-mesoderm interactions during morphogenesis and reveal the ability of signaling center AER cells to concurrently modulate cell fate and spatial organization.
    DOI:  https://doi.org/10.1126/sciadv.ady7682
  26. Nature. 2025 Nov 26.
    Progressive coevolution of the yeast centromere and kinetochore.
    Jana Helsen, Kausthubh Ramachandran, Gavin Sherlock, Gautam Dey.
      During mitosis, stable but dynamic interactions between centromere DNA and the kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore are highly conserved1,2, centromeres are among the fastest evolving regions in a genome3,4, showing extensive variation even on short evolutionary timescales. Here we sought to understand how organisms evolve completely new sets of centromeres that still effectively engage with the kinetochore machinery by identifying and tracking thousands of centromeres across two major fungal clades, including more than 2,500 natural strain isolates and representing over 1,000 million years of evolution. We show that new centromeres spread progressively via drift and subsequent selection and that the kinetochore, which is evolving slowly in relative terms, appears to act as a filter to determine which new centromere variants are tolerated. Together, our findings provide insight into the evolutionary constraints and trajectories shaping centromere evolution.
    DOI:  https://doi.org/10.1038/s41586-025-09779-1
  27. Nat Cell Biol. 2025 Nov 24.
    Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis.
    Alberto Minetti, Omid Omrani, Christiane Brenner, Feyza Cansiz, Shinya Imada, Jonas Rösler, Saleh Khawaled, Gabriele Allies, Sven W Meckelmann, Nadja Gebert, Ivonne Heinze, Norman Rahnis, Jing Lu, Katrin Spengler, Mahdi Rasa, Emilio Cirri, Regine Heller, Ömer Yilmaz, Alpaslan Tasdogan, Francesco Neri, Alessandro Ori.
      Ageing dampens the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent, using proteomic and metabolomic profiling of intestinal tissues together with functional assays. The comparison of regeneration dynamics in mice of different ages revealed the emergence of proteostasis stress and increased levels of polyamines following injury exclusively in old epithelia. We show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and the accumulation of ubiquitylated proteins. The inhibition of the polyamine pathway in vivo further delays regeneration in old mice, whereas its activation by dietary intervention or supplementation of polyamines is sufficient to enhance the regenerative capacity of aged intestines. Our findings highlight the promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with ageing.
    DOI:  https://doi.org/10.1038/s41556-025-01804-9
  28. Nat Struct Mol Biol. 2025 Nov 27.
    Kinetic control of mammalian transcription elongation.
    Yukun Wang, Xizi Chen, Maximilian Kümmecke, John W Watters, Joel E Cohen, Yanhui Xu, Shixin Liu.
      Transcription elongation by RNA polymerase II (Pol II) is an integral step in eukaryotic gene expression. The speed of Pol II is controlled by a multitude of elongation factors, but the exact regulatory mechanisms remain incompletely understood, especially for higher eukaryotes. Here we develop a single-molecule platform to visualize the dynamics of individual mammalian transcription elongation complexes (ECs) reconstituted from purified proteins. This platform allows us to follow the elongation and pausing behavior of EC in real time and unambiguously determine the role of each elongation factor in the kinetic control of Pol II. We find that the mammalian EC harbors multiple speed gears dictated by its associated factors and phosphorylation status. Moreover, the elongation factors are not functionally redundant but act hierarchically and synergistically to achieve optimal elongation activity. We propose that such elaborate kinetic regulation underlies the major speed-changing events during the transcription cycle and enables cells to adapt to a changing environment.
    DOI:  https://doi.org/10.1038/s41594-025-01707-1
  29. bioRxiv. 2025 Oct 15. pii: 2025.10.15.682666. [Epub ahead of print]
    Cadherin Regulation of Endoplasmic Reticulum-Plasma Membrane Contact Sites.
    Sonam Lhamo, Navaneetha Krishnan Bharathan, William Giang, Kandice R Levental, Cory L Simpson, Stephanie Zimmer, Andrew P Kowalczyk.
      The spatial organization and dynamics of the endoplasmic reticulum (ER) govern when and where ER tubules engage with other organelles and the plasma membrane. We previously found that ER tubules are closely associated with desmosomes, but the mechanisms of ER recruitment to these adhesive intercellular junctions were unclear. Here, we demonstrate that adherens junctions recruit ER tubules to intercellular junctions in a manner dependent upon E-cadherin association with α-catenin and vinculin. During cell-cell junction assembly, adherens junctions and ER appear nearly simultaneously at nascent cell-cell contacts, followed by desmosome formation. ER recruitment to cell-cell contacts allows the formation of ER-plasma membrane contact sites (ER-PMCS) and the assembly of a complex comprising adherens junctions, ER-PMCS, and desmosomes. Ablating adherens junctions disrupts this tripartite complex and perturbs global cellular lipid levels. Collectively, our findings identify cadherins as key organizers of ER-PMCS positioning and suggest that this complex integrates cellular mechanical elements with plasma membrane homeostasis.
    DOI:  https://doi.org/10.1101/2025.10.15.682666
  30. Nat Commun. 2025 Nov 26. 16(1): 10539
    Adherent cells sustain membrane tension gradients independently of migration.
    Juan Manuel García-Arcos, Amine Mehidi, Julissa Sanchez-Velasquez, Pau Guillamat, Caterina Tomba, Laura Houzet, Laura Capolupo, Javier Espadas, Giovanni D'Angelo, Adai Colom, Elizabeth Hinde, Charlotte Aumeier, Aurélien Roux.
      Tension propagates in lipid bilayers over hundreds of microns within milliseconds, seemingly precluding the formation of tension gradients. Nevertheless, plasma membrane tension gradients have been reported in migrating cells and along growing axons. Here, we show that the mechanosensitive, fluorescent membrane probe Flipper-TR visualizes membrane tension gradients in artificial and cellular membranes. Images of tension gradients allow their quantitative characterization, showing that they are long-ranged and linear in all migratory adherent cells. Using this tool, we unexpectedly reveal that tension gradients also exist in non-migrating adherent cells while they are absent in non-adherent migrating cells. This suggests that actomyosin forces can generate tension gradients even in non-moving cells, but that adhesion to a substrate is needed to sustain these gradients. Treatment of cells with drugs perturbing actomyosin show that branched actin increases tension, creating gradients. Furthermore, specific adhesion mediated by clathrin plaques colocalizes with regions of low tension, and chemical disruption of clathrin plaques strongly affect tension gradients. Altogether, our results show that the combined action of actomyosin and adhesion forces create tension gradients in the plasma membrane of adherent cells, even the ones not migrating.
    DOI:  https://doi.org/10.1038/s41467-025-65571-9
  31. Res Sq. 2025 Nov 04. pii: rs.3.rs-6497851. [Epub ahead of print]
    The Somatic Aneuploidy Landscape of Adult Glia Reveals 16p as a Hotspot and Differentiates Mosaicism in Normal Glia from Chromosomal Instability in Glioblastoma.
    Cristina Montagna, Olivia Albert, Shixiang Sun, Jhih-Rong Lin, Moonsook Lee, Chang Chan, Alexander Maslov, Lisa Ellerby, Anita Huttner, Zhengdong Zhang, Jan Vijg.
      Aneuploidy, an abnormal number of chromosomes, is a hallmark of cancer and has been proposed as an initiating event in tumorigenesis. In glioblastoma (GBM), a highly aggressive brain tumor, cells almost universally display gain of chromosome 7 and loss of chromosome 10. However, it remains unclear whether these alterations arise de novo during malignant transformation or reflect pre-existing chromosomal instability in normal brain tissue. Here, we used single-nucleus whole-genome sequencing (snWGS) on 225 NeuN-negative (non-neuronal) cortical nuclei from 12 healthy individuals and 6 GBM patients, including matched tumor cores and non-tumor brain regions. In healthy brains, approximately 15% of glial nuclei harbored somatic aneuploidies, most often involving chromosome arms, with recurrent 16p alterations detected in up to 3% of nuclei from both healthy controls and GBM non-tumor tissue. These findings establish 16p is a hotspot of structural variation in adult glia. Non-tumor regions in GBM patients closely resembled healthy controls in aneuploidy burden and chromosomal instability metrics and lacked hallmark tumor alterations. In contrast, GBM tumors exhibited significantly elevated aneuploidy (~50%), enrichment for canonical chromosomal instability-driven events, and sex-specific karyotype patterns, consistent with transformation-associated chromosomal instability. Thus, aneuploidy is a recurrent but constrained feature of normal adult glia, whereas chromosome instability and GBM-defining aneuploidies emerge only during malignant transformation.
    DOI:  https://doi.org/10.21203/rs.3.rs-6497851/v1
  32. Nat Methods. 2025 Nov 24.
    Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks.
    Xin Sui, Jennifer A Lo, Shuchen Luo, Yichun He, Zefang Tang, Zuwan Lin, Dániel L Barabási, Yiming Zhou, Wendy Xueyi Wang, Jia Liu, Xiao Wang.
      Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 µm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D in situ quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 60-200-µm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.
    DOI:  https://doi.org/10.1038/s41592-025-02867-0
  33. Curr Biol. 2025 Nov 26. pii: S0960-9822(25)01466-6. [Epub ahead of print]
    An mTOR-Stat3-Stathmin pathway controls centrosome and microtubule dynamics for oocyte polarization.
    Amal Shawahny, Yoel Bogoch, Neta Hart, Yaniv M Elkouby.
      In animals and plants, egg production is essential for fertility, reproduction, and embryonic development. However, our understanding of the regulatory mechanisms underlying the cellular and developmental programs of oogenesis is lacking. Here, we aimed to identify overlooked regulators of early oogenesis in zebrafish. First, we established a long-term ovary culture system that enables physiological oocyte development from oogonia to primordial follicles, providing an effective ex vivo platform for rapid investigation. Next, we utilized this system for functional screening of candidates from stage-specific oocyte transcriptomic data. We identified mammalian target of rapamycin (mTOR), signal transducer and activator of transcription 3 (Stat3), and the microtubule-destabilizing protein Stathmin as novel regulators of oocyte polarity. In zebrafish and most species, oocyte polarity is essential for oogenesis and embryonic development. In polarization, microtubules control the localization of the polarity regulator Buc to the centrosome, as well as its condensation into the Balbiani body, an oocyte membraneless compartment. Through a combination of genetics and pharmacological manipulations in vivo and ex vivo, we show that loss of mTOR or Stat3 functions, as well as overactivation of Stathmin, disrupted centrosome regulation and destabilized microtubules, leading to dispersed Buc condensates and loss of polarity. We demonstrate that mTOR acts upstream of Stat3 in oocytes, and inhibition of Stathmin in either stat3-/- or mTOR-deficient ovaries rescued both cytoskeletal and polarity defects. Thus, we established an unpredicted but essential mTOR-Stat3-Stathmin pathway that controls centrosome and microtubule dynamics to drive oocyte polarity. We propose that through cytoskeletal regulation, this pathway provides oocytes with polarization competence, a likely common step in cell polarity.
    Keywords:  Balbiani body; Buc molecular condensation; Bucky ball molecular condensation; Stat3; Stathmin; aebrafish oogenesis and ovary development; cell polarity; centrosome MTOC; mTOR; microtubules
    DOI:  https://doi.org/10.1016/j.cub.2025.10.085
  34. bioRxiv. 2025 Oct 29. pii: 2025.10.28.683518. [Epub ahead of print]
    Zebrafish otic vesicle and mouse epididymis as model systems for studying columnar epithelial cell division.
    Yu Xia, Björn Perder, Alvin Gea Chen Yao, Miaoyan Qiu, Jingli Cao.
      Epithelial cell division maintains tissue architecture through coordinated nuclear migration, cell shape changes, and spindle orientation. In columnar epithelia, interkinetic nuclear migration (INM) involves apical nuclear translocation in G2 and basal return post-mitosis, yet its regulation and physiological significance remain understudied due to limited live imaging in vivo models. We adapted the zebrafish embryonic otic vesicle as an in vivo model to study epithelial division dynamics using high-resolution live imaging and genetic tools. We find that apical INM initiates in mid-to-late G2 and is driven by dynein, not myosin II. Mitotic rounding is achieved via actomyosin-mediated basolateral constriction while maintaining basal attachment. Inhibiting myosin II impairs rounding and planar division, causing apical retention of daughter cells, suggesting planar division ensures proper integration. We extend our analysis to the mouse epididymis epithelium, comparing nuclear migration, cell shape, and spindle orientation across species. Our work introduces optimized in vivo models and reveals conserved and tissue-specific mechanisms maintaining structure and function of columnar epithelia.
    DOI:  https://doi.org/10.1101/2025.10.28.683518
  35. bioRxiv. 2025 Oct 21. pii: 2025.10.21.683626. [Epub ahead of print]
    Mechanical control of histone serotonylation initiates neural crest migration in vivo.
    Joana E Saraiva, Artemis G Korovesi, Xiaoran Wei, Jaime A Espina, Miguel Ribeiro, Ian Maze, Elias H Barriga.
      Collective cell migration (CCM) is pivotal in several biological contexts, and posttranslational modifications of histones are essential to initiate this process1-3. Here, we show that a recently discovered chromatin mark, termed histone serotonylation4, is involved in the collective migration of cranial neural crest cells - an embryonic multipotent stem cell population5. Our in vivo data reveal that histone serotonylation appears in neural crest cells just before they start migrating and that its occurrence is essential to initiate their CCM. Surprisingly, we found that stiffening of the neural crest migratory substrate, the mesoderm, induces histone serotonylation by promoting nuclear translocation of transglutaminase 2 (Tgm2), the enzyme responsible for adding serotonin to histones4. Moreover, mechanical and molecular perturbations demonstrate that mechanical shuttling of Tgm2 into the nucleus, with concomitant increases in histone serotonylation, are both required and sufficient to allow CCM in vivo. Furthermore, integrated chromatin immunoprecipitation and RNA sequencing analyses uncover a transcriptional module, which is enabled by histone serotonylation in response to mesoderm stiffening. Altogether, our results provide in vivo evidence showing that tissue stiffening leads to increased levels of histone serotonylation to reinforce permissive patterns of gene expression, supporting the switch from non-migratory to migratory cell states.
    Keywords:  Chromatin; Histone serotonylation; Tgm2; Xenopus; cell states transitions; collective cell migration; neural crest; tissue mechanics
    DOI:  https://doi.org/10.1101/2025.10.21.683626
  36. bioRxiv. 2025 Nov 14. pii: 2025.11.13.688366. [Epub ahead of print]
    Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis.
    Rishabh Sharan, XinXin Du, Liliya Leybova, Anyoko Sewavi, Abhishek Biswas, Danelle Devenport.
      During epithelial morphogenesis, cell polarity aligns individual cell behaviors into collective motions that shape developing tissues. Here, we combine experiments with computational modeling to investigate how cell-scale forces oriented by Planar Cell Polarity (PCP) direct the collective, counter-rotational cell flows that occur during hair placode morphogenesis. We rule out that PCP directs apical neighbor exchanges, as junctional myosin and PCP protein localization are not co-correlated with junction shrinkage. Instead, we find that PCP directs anterior-directed crawling of placode cells along the basal surface of the tissue through a mechanism that requires cell crawling regulator Rac1. Modeling the placode as a continuum viscoelastic fluid, we find that active forces from cell crawling at the basal surface is sufficient to generate the experimentally observed counter-rotational cell motion at the apical surface. Our results show an unexpected role for PCP in epithelial morphogenesis, centering the basal surface as the site of force generation.
    DOI:  https://doi.org/10.1101/2025.11.13.688366
  37. bioRxiv. 2025 Oct 13. pii: 2025.10.12.681824. [Epub ahead of print]
    Cell cycle oscillations in a polarity network facilitate state switching by morphogenetic cues.
    KangBo Ng, Hadjar Sebaa, Nisha Hirani, Alex Chizh, Zeno Messi, Tom Bland, Kenji Sugioka, Nathan W Goehring.
      The proper establishment of cell form, fate, and function during morphogenesis requires precise coordination between cell polarity and developmental cues. To achieve this, cells must establish polarity domains that are stable yet sensitive to guiding cues. Here we show that C. elegans germline blastomeres resolve this trade-off by creating a time-varying polarization landscape. Specifically, coupling the PAR polarity network to the cell-cycle kinase CDK-1 ensures that newborn cells operate in a low-feedback regime that lowers barriers to polarity state switching, allowing spatial cues to induce and orient PAR protein asymmetries. As CDK-1 activity rises at mitotic entry, increasing molecular feedback reinforces cue-induced asymmetries to yield robust and stable patterning of PAR domains. Consistent with this model, optogenetic and chemical perturbations show that low-CDK/low-feedback regimes destabilize PAR domains but are required for both de novo polarization and the reorientation of polarity in response to inductive cues. We propose that mitotic oscillations in cell polarity circuits dynamically optimize the polarization landscape to enable coordination of polarity with morphogenesis. Such temporal control of developmental networks is likely a general mechanism to balance robustness of cellular states with sensitivity to signal-induced state switching.
    Keywords:  C. elegans; Cell cycle; cell fate; cell polarity; dynamic systems; oscillations; robustness
    DOI:  https://doi.org/10.1101/2025.10.12.681824
  38. Nat Commun. 2025 Nov 26.
    Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth.
    Anna Maekiniemi, Philipp Savakis, Kelly van Rossum, Jacky L Snoep, Markus Seiler, David D van Niekerk, Kathi Zarnack, Robert H Singer, Evelina Tutucci.
      Clb2 is a conserved B-type cyclin essential for mitotic progression in Saccharomyces cerevisiae, with expression tightly regulated at transcriptional and proteolytic levels. However, it remains unclear whether Clb2 protein synthesis is regulated and responsive to cell growth. Here, we show that CLB2 mRNA localizes to the bud via the She2/She3 complex, while Clb2 protein accumulates in the mother nucleus. This mRNA localization enhances translation without affecting protein localization. A structured RNA element, a ZIP-code, is located within the coding sequence and is required, but not sufficient, for both mRNA transport and protein expression. Mutation of this ZIP code disrupts mRNA localization, reduces Clb2 synthesis, increases budded phase duration and daughter cell size. In wild-type cells, Clb2 protein levels scale with bud growth, a coupling lost in ZIP code mutants. These findings reveal a mechanism by which mRNA localization and translation are coordinated to link cell growth with cell cycle progression.
    DOI:  https://doi.org/10.1038/s41467-025-66623-w
  39. bioRxiv. 2025 Oct 12. pii: 2025.10.10.681495. [Epub ahead of print]
    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 cancer 1,2 . Circular megabase-sized ecDNAs lack centromeres and segregate stochastically during cell division 3-6 yet persist over many generations. EcDNAs were first observed to hitchhike on mitotic chromosomes into daughter cell nuclei over 40 years ago with unknown mechanism 3,7 . 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. We develop Retain-seq, a genome-scale assay that reveals thousands of human retention elements conferring generational persistence to heterologous episomes. Retention elements comprise a select set of CpG-rich gene promoters and act additively. Live-cell imaging and chromatin conformation capture show that retention elements physically interact with mitotic chromosomes at regions which are mitotically bookmarked by transcription factors and chromatin proteins, intermolecularly recapitulating 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, suggesting 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, revealing the principles of episome immortality intrinsic to the human genome.
    DOI:  https://doi.org/10.1101/2025.10.10.681495
  40. bioRxiv. 2025 Nov 05. pii: 2025.11.04.686600. [Epub ahead of print]
    Fission yeast cells use distinct cell size control mechanisms for size adaptation to osmotic, oxidative, or low glucose conditions.
    Elena J Cabral, Pablo Andres, Geraldin Argandona, Paige Duggan, Benjamin M Kuran, Kristi E Miller.
      Cells maintain an appropriate size to function, yet the mechanisms that enable size adaptation to environmental stress remain poorly understood. Fission yeast cells enter mitosis and divide at a threshold size when cyclin-dependent kinase (Cdk1) is activated through size- and time-dependent scaling of its regulators: Cdr2 kinase with cell surface area, Cdc25 phosphatase with cell volume, and mitotic cyclin Cdc13 with cell cycle time. This integrated size control network is characterized in nutrient-rich conditions, but under stress it remains unclear which size parameters cells monitor, and which size- or time-sensing pathways mediate adaptation. Using high-throughput image analysis, we quantified the geometry of dividing cells under osmotic, oxidative, and low glucose conditions. Wild-type cells increased their surface area-to-volume (SA:Vol) ratio in low glucose but decreased it under osmotic or oxidative stress, revealing distinct geometric strategies for environmental size adaptation. Genetic perturbations of size- and time-sensing pathways revealed that Cdc25 is required for volume-based adaptation to oxidative and osmotic stress, Cdc13 contributes to osmotic stress response, and Cdr2 promotes surface area-based expansion in low glucose. Although disrupting individual pathways altered normal geometric responses, cells remained viable, suggesting that a modular size control system enables flexible geometric adaptation to changing environments.
    DOI:  https://doi.org/10.1101/2025.11.04.686600
  41. Cell Stem Cell. 2025 Nov 24. pii: S1934-5909(25)00405-9. [Epub ahead of print]
    Reversing lysosomal dysfunction restores youthful state in aged hematopoietic stem cells.
    Tasleem Arif, Jiajing Qiu, Hossein Khademian, Anusree Lohithakshan, Anagha Menon, Vijay Menon, Mary Slavinsky, Maxime Batignes, Miao Lin, Robert Sebra, Kristin G Beaumont, Deanna L Benson, Nikolaos Tzavaras, Mickaël M Ménager, Saghi Ghaffari.
      Aging impairs hematopoietic stem cells (HSCs), driving clonal hematopoiesis, myeloid malignancies, and immune decline. The role of lysosomes in HSC aging-beyond their passive mediation of autophagy-is unclear. We show that lysosomes in aged HSCs are hyperacidic, depleted, damaged, and aberrantly activated. Single-cell transcriptomics and functional analyses reveal that suppression of hyperactivated lysosomes using a vacuolar ATPase (v-ATPase) inhibitor restores lysosomal integrity and metabolic and epigenetic homeostasis in old HSCs. This intervention reduces inflammatory and interferon-driven programs by improving lysosomal processing of mitochondrial DNA and attenuating cyclic GMP-AMP synthase-stimulator of interferon gene (cGAS-STING) signaling. Strikingly, ex vivo lysosomal inhibition boosts old HSCs' in vivo repopulation capacity by over eightfold and improves their self-renewal. Thus, lysosomal dysfunction emerges as a key driver of HSC aging. Targeting hyperactivated lysosomes reinstates a youthful state in old HSCs, offering a promising strategy to restore hematopoietic function in the elderly.
    Keywords:  MMP; aging; cGas-STING; hematopoietic stem cell; inflammation; interferon; lysosomes; mitochondria; mtDNA; quiescence
    DOI:  https://doi.org/10.1016/j.stem.2025.10.012
  42. Nat Aging. 2025 Nov 26.
    Iron homeostasis and cell clonality drive cancer-associated intestinal DNA methylation drift in aging.
    Anna Krepelova, Mahdi Rasa, Francesco Annunziata, Jing Lu, Chiara Giannuzzi, Omid Omrani, Elisabeth Wyart, Paolo Ettore Porporato, Ihab Ansari, Dor Bilenko, Yehudit Bergman, Francesco Neri.
      Epigenetic drift is a key feature of aging and is associated with age-related diseases including cancer, yet the underlying molecular mechanisms remain unclear. Here, by analyzing DNA methylation and gene expression data from healthy and cancerous human colon samples, we identify an aging and colon cancer-associated DNA methylation (DNAm) drift. We find evidence that this drift is conserved in the mouse intestinal epithelium, where we demonstrate its origin within intestinal stem cells and identify its cell-intrinsic and non-mitotic characteristics, finding that its expansion is regulated via crypt clonality and fission. Mechanistically, we find that this drift is driven by age-related inflammation and reduced Wnt signaling, which dysregulate iron metabolism and impair TET activity. Despite CpG-level heterogeneity, we find that DNAm changes are consistent at the gene level, suggesting potential functionality. Our findings shed light on the epigenetic mechanisms of aging and provide a mechanistic basis for the hypermethylation observed in cancer.
    DOI:  https://doi.org/10.1038/s43587-025-01021-x
  43. Nat Commun. 2025 Nov 27. 16(1): 10623
    The CIP2A-TOPBP1 axis facilitates mitotic DNA repair via MiDAS and MMEJ.
    Peter R Martin, Jadwiga Nieminuszczy, Zuza Kozik, Nihal Jakub, Szymon Kowalski, Maxime Lecot, Julia Vorhauser, Karen A Lane, Alexandra Kanellou, Jörg Mansfeld, Laurence H Pearl, Antony W Oliver, Jessica A Downs, Jyoti S Choudhary, Matthew Day, Wojciech Niedzwiedz.
      Mitotic DNA double-strand breaks (DSBs) accumulate in response to replication stress or BRCA1/2 deficiency posing a significant threat to genome stability as repair by non-homologous end-joining (NHEJ) and homologous recombination (HR) is largely inactivated in mitosis. Instead, mitotic cells rely on alternative repair processes such as microhomology-mediated end-joining (MMEJ) and mitotic DNA synthesis (MiDAS). How these mitotic DNA repair pathways are functionally regulated remains unclear. Here we reveal that the CIP2A-TOPBP1 complex plays an essential regulatory role by facilitating the mitotic recruitment of both SMX complex components and Polθ to mitotic chromatin. Recruitment of the SMX complex components is driven by CDK1-dependent phosphorylation of SLX4 at Thr1260, enabling its interaction with TOPBP1 BRCT domains 1/2, thereby promoting MiDAS. Concurrently, CIP2A promotes efficient mitotic localisation of Polθ to facilitate MMEJ. The simultaneous functional disruption of both MiDAS and MMEJ pathways upon CIP2A loss provides rationale for the synthetic lethality observed in BRCA1 or 2-deficient cells. These findings position the CIP2A-TOPBP1 axis as a central regulatory hub for mitotic DNA repair, highlighting therapeutic opportunities in tumours characterised by HR deficiency or elevated replication stress.
    DOI:  https://doi.org/10.1038/s41467-025-65594-2
  44. Nature. 2025 Nov 26.
    Inhibitors supercharge kinase turnover through native proteolytic circuits.
    Natalie S Scholes, Martino Bertoni, Arnau Comajuncosa-Creus, Katharina Kladnik, Xuefei Guo, Fabian Frommelt, Matthias Hinterndorfer, Hlib Razumkov, Polina Prokofeva, Martin P Schwalm, Florian Born, Sandra Roehm, Hana Imrichova, Brianda L Santini, Eleonora Barone, Caroline Schätz, Miquel Muñoz I Ordoño, Severin Lechner, Andrea Rukavina, Iciar Serrano, Miriam Abele, Anna Koren, Stefan Kubicek, Stefan Knapp, Nathanael S Gray, Giulio Superti-Furga, Bernhard Kuster, Yigong Shi, Patrick Aloy, Georg E Winter.
      Targeted protein degradation is a pharmacological strategy that relies on small molecules such as proteolysis-targeting chimeras (PROTACs) or molecular glues, which induce proximity between a target protein and an E3 ubiquitin ligase to prompt target ubiquitination and proteasomal degradation1. Sporadic reports indicated that ligands designed to inhibit a target can also induce its destabilization2-4. Among others, this has repeatedly been observed for kinase inhibitors5-7. However, we lack an understanding of the frequency, generalizability and mechanistic underpinnings of these phenomena. Here, to address this knowledge gap, we generated dynamic abundance profiles of 98 kinases after cellular perturbations with 1,570 kinase inhibitors, revealing 160 selective instances of inhibitor-induced kinase destabilization. Kinases prone to degradation are frequently annotated as HSP90 clients, therefore affirming chaperone deprivation as an important route of destabilization. However, detailed investigation of inhibitor-induced degradation of LYN, BLK and RIPK2 revealed a differentiated, common mechanistic logic whereby inhibitors function by inducing a kinase state that is more efficiently cleared by endogenous degradation mechanisms. Mechanistically, effects can manifest by ligand-induced changes in cellular activity, localization or higher-order assemblies, which may be triggered by direct target engagement or network effects. Collectively, our data suggest that inhibitor-induced kinase degradation is a common event and positions supercharging of endogenous degradation circuits as an alternative to classical proximity-inducing degraders.
    DOI:  https://doi.org/10.1038/s41586-025-09763-9
  45. bioRxiv. 2025 Nov 13. pii: 2025.11.12.688091. [Epub ahead of print]
    Class-I myosin responds to changes in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells.
    Samantha L Smith, Tong Zhan, Wan Li, Henry De Belly, Qing Zhang, Ke Xu, Orion D Weiner, David G Drubin.
      Clathrin-mediated endocytosis (CME) is an essential cellular process that needs to operate efficiently across a wide range of conditions. Internalization of the endocytic site involves forces generated by membrane-bound proteins and Arp2/3-mediated branched actin filament assembly to bend the plasma membrane (PM) from flat to omega-shaped. In mammalian CME, the requirement for a branched actin filament network varies depending on cell type and differences in membrane tension. However, how the actin network adapts to changes in load in order to ensure robustness of this process over a range of membrane tensions is not understood. Here, we combine live-cell imaging and super-resolution microscopy of genome-edited human induced pluripotent stem cells (hiPSCs) to investigate the role of the mammalian class-I myosin, Myosin1E (Myo1E), in load adaptation. Under normal conditions, sites that recruit Myo1E are rare and exhibit slow CME dynamics. However, as membrane tension increases and CME dynamics are slowed globally, Myo1E is recruited to more sites, likely to assemble more branched actin, resulting in increased force generation to rescue stalled sites and promote internalization. Loss of Myo1E results in increased Arp2/3 complex lifetime at CME sites under normal conditions, and at high membrane tension, these sites fail to recruit as many Arp2/3 molecules. We propose that Myo1E is recruited to CME sites that have stalled due to increased membrane tension, where it helps build a more effective branched actin network by generating force through motor activity and recruiting additional Arp2/3 complexes to rescue stalled sites.
    Significance: For mammalian cells to internalize extracellular cargo via clathrin-mediated endocytosis (CME), specific regions of the plasma membrane (PM) must bend from flat to inwardly curved, a process that requires force-generating proteins. One key component in generating this force during CME is the branched actin network, in which actin filaments polymerize against the plasma membrane. When PM tension increases, more force is required to generate curvature, prompting the assembly of actin and actin associated proteins to aid the process. We demonstrate that the class-I myosin motor, Myosin1E (Myo1E), becomes increasingly crucial as membrane tension rises, presumably to build a more effective branched actin network to facilitate internalization of slowed sites.
    DOI:  https://doi.org/10.1101/2025.11.12.688091
  46. Nat Aging. 2025 Nov 25.
    Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness.
    Onur Eskiocak, Joseph Gewolb, Vyom Shah, James A Rouse, Saria Chowdhury, Erdogan O Akyildiz, Inés Fernández-Maestre, Jacob A Boyer, Aveline Filliol, Alexander S Harris, Raditya Utama, Guangran Guo, Carolina Castro-Hernández, Emmanuella Nnuji-John, Charlie Chung, Arianna Anderson, Sara Flowers, Jill Habel, Paul B Romesser, Ross L Levine, Scott W Lowe, Michel Sadelain, Semir Beyaz, Corina Amor.
      Intestinal stem cells (ISCs) drive the rapid regeneration of the gut epithelium. However, during aging, their regenerative capacity wanes, possibly through senescence and chronic inflammation, albeit little is known about how aging-associated dysfunction arises in the intestine. We previously identified the urokinase plasminogen activator receptor (uPAR) as a senescence-associated protein and developed CAR T cells able to efficiently target it. Harnessing them, here, we identify the accumulation of mostly epithelial uPAR-positive cells in the aging gut and uncover their detrimental impact on ISC function in aging. Thus, both therapeutic and prophylactic treatment with anti-uPAR CAR T cells improved barrier function, regenerative capacity, inflammation, mucosal immune function and microbiome composition in aged mice. Overall, these findings reveal the deleterious role of uPAR-positive cells on intestinal aging in vivo and provide proof of concept for the potential of targeted immune-based cell therapies to enhance tissue regeneration in aging organisms.
    DOI:  https://doi.org/10.1038/s43587-025-01022-w
  47. bioRxiv. 2025 Oct 09. pii: 2025.10.08.676897. [Epub ahead of print]
    Integrated single-cell whole genome sequencing and spatial transcriptomics reveal latent intra-tumoral heterogeneity in ovarian cancer.
    Rania Bassiouni, Yuxin Jin, Lee D Gibbs, Jing Qian, Solomon O Rotimi, Heather Miller, Michelle G Webb, Seeta Rajpara, Javier Arias-Stella, David W Craig, Lynda Roman, John D Carpten.
      The mortality rate of ovarian cancer remains disproportionately high compared to its incidence. This is partly due to a high level of intra-tumoral heterogeneity that promotes disease recurrence and treatment failure. In this study, we describe degrees of heterogeneity revealed by single-cell whole genome sequencing and spatial transcriptomics of five epithelial ovarian carcinomas. At the cellular level, we describe pseudo-diploid cells that match the malignant cell population in both somatic variant and copy number patterns. At the clonal and subclonal levels, we describe diversification associated with copy number gains and whole genome doubling. In multi-clonal samples, we infer evolutionary relationships from single cell copy number, loss of heterozygosity analysis, and somatic variant detection, and correlate these with tissue histology and gene expression programs. In one sample, we identify functionally consequential copy number alterations that contribute to molecular diversity, cell proliferation, and inflammation in a minor clone that persisted without major expansion alongside a more complex major clone. In another, we describe a complex evolutionary history including a spontaneous reversion of a driver mutation in a secondary clone, which correlated with a switch in oncogenic expression programs.
    DOI:  https://doi.org/10.1101/2025.10.08.676897
  48. bioRxiv. 2025 Oct 15. pii: 2025.10.13.682189. [Epub ahead of print]
    Intrinsic errors in mitochondrial translation trigger a decline in cell fitness.
    Güleycan Lutfullahoglu Bal, Kah Ying Ng, Eli Berzell, Ani Akpinar, Alex E Ekvik, Lidiia Koludarova, Seyedehshima Naddafi, Clemens Raths, Tania Vane-Tempest, Jordyn J VanPortfliet, Sarah O'Keefe, Arafath K Najumudeen, Tuula A Nyman, James B Stewart, A Phillip West, Brendan J Battersby.
      Defects in the faithful expression of the human mitochondrial genome underlies disease states, from rare inherited disorders to common pathologies and the aging process itself. The ensuing decrease in the capacity for oxidative phosphorylation alone cannot account for the phenotype complexity associated with disease. Here, we address how aberrations in mitochondrial nascent chain synthesis per se exert a decline in cell fitness using a classic model of mitochondrial induced premature aging. We identify how intrinsic errors during mitochondrial nascent chain synthesis destabilize organelle gene expression, triggering intracellular stress responses that rewire cellular metabolism and cytokine secretion. Further, we show how these mechanisms extend to pathogenic variants associated with inherited human disorders. Together, our findings reveal how aberrations in mitochondrial protein synthesis can sensitize a cell to metabolic challenges associated with disease and pathogen infection independent of oxidative phosphorylation.
    Teaser/One-Sentence Summary: Aberrations in mitochondrial translation elongation trigger activation of intracellular stress responses associated with disease and aging.
    DOI:  https://doi.org/10.1101/2025.10.13.682189
  49. bioRxiv. 2025 Oct 13. pii: 2025.10.13.682107. [Epub ahead of print]
    Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins.
    Frederick Rehfeld, Claire Lundstrom, He Zhang, Joshua T Mendell.
      Selenocysteine, incorporated into polypeptides at recoded termination codons, plays an essential role in redox biology. Using GPX1 and GPX4, selenoenzymes that mitigate oxidative stress, as reporters, we performed genome-wide knockout screens to identify regulators of selenocysteine incorporation. This revealed that selenoprotein production is limited by ribosome collisions that occur at inefficiently decoded selenocysteine codons. Accordingly, slowed translation elongation reduced collisions and enhanced selenocysteine decoding. Oxidative stress also slowed translation elongation and augmented selenoprotein production. We identified translation elongation factor EEF1G as a sensor of oxidized glutathione that couples the cellular redox state to translation elongation rate. Oxidative stress sensing by EEF1G slows translation, enhancing production of detoxifying selenoproteins to restore homeostasis. These findings reveal how programmed ribosome collisions enable gene regulation in response to stress.
    DOI:  https://doi.org/10.1101/2025.10.13.682107
  50. Cell Rep. 2025 Nov 22. pii: S2211-1247(25)01381-6. [Epub ahead of print]44(12): 116609
    Mechanisms governing poly(A)-tail-length specificity of the human PAN2-PAN3 deadenylase complex.
    Jana C Albrecht, Timo Reitinger, Jérôme Basquin, Steffen Schüssler, Margot Riggi, Ingmar B Schäfer, Elena Conti.
      The lifespan of most eukaryotic mRNAs is modulated by the gradual shortening of the poly(A) tail and removal of the associated poly(A)-binding protein. The human PAN2-PAN3 complex catalyzes initial deadenylation by shortening long poly(A) tails associated with PABPC1. Both PAN2-PAN3 and PABPC1 are evolutionarily conserved from fungi to humans. How the human complex has adapted to recognize and act on longer poly(A) tails characteristic of mammalian mRNAs remains unclear. Here, we report a method to obtain homo-polymeric poly(A) RNAs up to 240 nt, mimicking the synthesis length of poly(A) tails in mammals. We recapitulate human deadenylation properties in vitro, with PAN2-PAN3 showing greater activity on long poly(A)-PABPC1 ribonucleoprotein substrates. Single-particle cryo-electron microscopy (cryo-EM) analyses of PAN2-PAN3 bound to poly(A)-PABPC1 ribonucleoproteins uncover a longer substrate-binding path in the case of the human deadenylase compared to fungi. Altogether, these data provide a rationale for the co-evolution of deadenylase properties and poly(A) tail lengths.
    Keywords:  CCR4-NOT; CP: molecular biology; PABPC1; PAN2-PAN3; cryo-EM; deadenylation; mRNA degradation; poly(A) tail; ribonucleoproteins
    DOI:  https://doi.org/10.1016/j.celrep.2025.116609
  51. Aging Cell. 2025 Nov 23. e70302
    Spatiotemporal Crosstalk Between Oocyte and the Microenvironment Governs Preovulatory Follicle Aging.
    Xin Yi Koh, Kah Junn Tan, Zeng Hao Lim, Shi Chee Ong, Sophie Emma Tan, Jing Xuan Lu, Zhongwei Huang, Jun Wei Pek.
      Preovulatory follicle aging is the period between formation and ovulation of a mature follicle. Previous studies had shown that mammalian preovulatory follicle aging is associated with chromosomal abnormalities and developmental defects such as decreased implantation, increased malformation and mortality and lower embryonic weight. Our understanding of the molecular events governing this process has been hampered by the difficulty in accessing them in vivo under natural conditions. We hypothesize that the quality of the mature oocyte is regulated by crosstalk between the oocyte and the somatic microenvironment during extended storage prior to ovulation. By combining temporal profiling and tissue-specific functional analyzes in Drosophila, we characterize a spatiotemporal crosstalk between the oocyte and the granulosa cells that governs preovulatory follicle aging in vivo. Preovulatory follicle aging is characterized by two distinct phases-early oocyte protective and late degenerative phases. The degenerative phase involves a positive feedback loop between oocyte mitochondrial dysfunction mediated by a mitochondrial-localized microprotein PIGBOS, and granulosa cell functional decline through a circular RNA circdlg1. Activation of the feedback loop is suppressed by germline Sestrin during the early phase. Our findings highlight that natural preovulatory follicle aging in vivo is governed by a mechanism that represses an oocyte-degenerative positive feedback loop between oocyte and granulosa cells.
    Keywords:   drosophila ; sestrin ; PIGBOS; Preovulatory oocyte; aging; circRNA; granulosa cell; mitochondria
    DOI:  https://doi.org/10.1111/acel.70302
  52. Nat Commun. 2025 Nov 26. 16(1): 10536
    Polymerase theta repairs persistent G1-induced DNA breaks in S-phase during class switch recombination.
    Timea Marton, Jinglong Wang, Amaury Vaysse, Wei Yu, Pierre-Henri Commere, Quentin Holleville, Tristan Espie-Caullet, Richard Frock, Ludovic Deriano.
      Non-homologous end joining (NHEJ) is the primary pathway for repairing G1 phase-induced DNA double-strand breaks (DSBs) during immunoglobulin heavy chain (Igh) class switch recombination (CSR) in B lymphocytes. In B cells lacking NHEJ (XRCC4) or DSB end protection (SHLD1), end joining during CSR proceeds through an alternative end-joining pathway. Polymerase theta (Pol θ) is widely regarded as a mediator of this pathway, essential for repairing replication-associated DSBs during mitosis when homologous recombination is unavailable. In this study, we examined CSR in primary B cells lacking XRCC4, SHLD1, and/or Pol θ, revealing two repair pathways: Pol θ-independent productive switching and Pol θ-dependent unproductive switching characterized by end resection, inversion and microhomology. Furthermore, we show that Pol θ-mediated repair under NHEJ-deficiency coincides with G1-to-S phase transition and occurs independently of RHINO and PLK1. Thus, in the absence of NHEJ, Pol θ repairs persistent G1-phase DSBs during S-phase rather than mitosis.
    DOI:  https://doi.org/10.1038/s41467-025-65555-9
  53. bioRxiv. 2025 Oct 20. pii: 2025.10.20.683416. [Epub ahead of print]
    ATR promotes genome instability via CENP-A eviction from centromeres under replication stress.
    Denis Ostapenko, Hang Li, Isabelle Trier, Ross Shamby, Eleanor Zagoren, Carla Becerra Sabrera, Kaelyn Sumigray, Lilian Kabeche.
      Replication stress leads to genome instability in part by promoting missegregation of chromosomes lacking centromeres. Yet the molecular mechanism linking replication stress to centromere dysfunction has remained elusive. Here, we show that sustained replication stress induces eviction of the histone H3 variant CENP-A. Displaced CENP-A relocalizes to nucleoli. This process is dependent on the DNA damage response kinase, ATR, and occurs in both human and mouse cells. We show that ATR promotes CENP-A eviction by recruiting the AAA+ ATPase VCP to centromeres, destabilizing CENP-A-containing nucleosomes. The canonical CENP-A chaperone, HJURP, but not H3 histone chaperones DAXX or ATRX, is necessary for nucleolar CENP-A localization. Importantly, ATR-dependent CENP-A eviction endures after cell-cycle re-entry and correlates with the emergence of acentric chromosomes, linking replication stress directly to segregation defects. Our findings reveal an undiscovered role for ATR in regulating centromere identity under stress and uncover a mechanistic pathway that drives genome instability.
    DOI:  https://doi.org/10.1101/2025.10.20.683416
  54. bioRxiv. 2025 Oct 15. pii: 2025.10.14.682291. [Epub ahead of print]
    Xenophagocytosis blockade enhances interspecies chimerism.
    Sicong Wang, Kouta Niizuma, Daniel Dan Liu, Fabian P Suchy, Hideyuki Sato, Ayaka Yanagida, Hideki Masaki, Masashi Miyauchi, Saman Tabatabaee, Nathan Hidajat, Joydeep Bhadury, Carsten T Charlesworth, Jinyu Zhang, Irving L Weissman, Hiromitsu Nakauchi.
      Organ shortage remains a major challenge in transplantation medicine. Interspecies blastocyst complementation is a promising approach to generate human organs in livestock hosts. However, getting xenogeneic donor cells to engraft and expand at early stages remains challenging. Here we identify an innate immune barrier, wherein host macrophages selectively recognize and eliminate viable xenogeneic donor cells. These events represent a form of phagoptosis and highlight a xenogeneic clearance process that we term xenophagocytosis. We identify the mechanism by which host macrophages selectively phagocytize xenogeneic donor cells: xenogeneic cells display elevated phosphatidylserine, an "eat-me" signal recognized by host macrophages through phagocytic receptor Axl. Xenophagocytosis blockade improves both rat and human donor chimerism in mouse embryos, indicating a conserved mechanism. These findings reveal potential mechanisms by which innate immune cells eliminate xenogeneic cells in early embryogenesis to preserve species integrity and offer improved strategies for generating human organs in livestock.
    DOI:  https://doi.org/10.1101/2025.10.14.682291
  55. Nature. 2025 Nov 24.
    MAPK-driven epithelial cell plasticity drives colorectal cancer therapeutic resistance.
    Mark White, Megan L Mills, Laura M Millett, Kathryn Gilroy, Yourae Hong, Lucas B Zeiger, Rosalin J Simpson, Shania M Corry, Amelia Ligeza, Tamsin R M Lannagan, Susanti Susanti, Rachel A Ridgway, Ayse S Yazgili, Lucile Grzesiak, Raheleh Amirkhah, Catriona A Ford, Nikola Vlahov, Hannah Tovell, Leah Officer-Jones, Catherine Ficken, Rachel Pennie, Arafath K Najumudeen, Alexander Raven, Nadia Nasreddin, Ekansh Chauhan, Andrew S Papanastasiou, Colin Nixon, Vivienne Morrison, Rene Jackstadt, Janet S Graham, Crispin J Miller, Sarah J Ross, Simon T Barry, Valeria Pavet, Richard H Wilson, John Le Quesne, Philip D Dunne, Sabine Tejpar, Simon Leedham, Andrew D Campbell, Owen J Sansom.
      The colorectal epithelium is rapidly renewing, with remarkable capacity to regenerate following injury. In colorectal cancer (CRC), this regenerative capacity can be co-opted to drive epithelial plasticity. While oncogenic MAPK signalling in CRC is common, with frequent mutations of both KRAS (40-50%) and BRAF (10%)1, inhibition of this pathway typically drives resistance clinically. Given the development of KRAS inhibitors, and licensing of BRAF inhibitor combinations2-4, we have interrogated key mechanisms of resistance to these agents in advanced preclinical CRC models. We show that oncogenic MAPK signalling induces epithelial state changes in vivo, driving adoption of a regenerative/revival stem like population, while inhibition leads to rapid transcriptional remodeling of both Kras- and Braf-mutant tumours, favoring a Wnt-associated, canonical stem phenotype. This drives acute therapeutic resistance in Kras- and delayed resistance in Braf-driven models. Importantly, where plasticity is restrained, such as in early metastatic disease, or through targeting ligand-dependent Wnt-pathway Rnf43 mutations, marked therapeutic responses are observed. This explains the super response to BRAF+EGFR targeted therapies previously observed in a BRAF/RNF43 co-mutant patient population, highlighting the criticality of cellular plasticity in therapeutic response. Together, our data provides clear insight into the mechanisms underpinning resistance to MAPK targeted therapies in CRC. Moreover, strategies that aim to corral stem cell fate, restrict epithelial plasticity or intervene when tumours lack heterogeneity may improve therapeutic efficacy of these agents.
    DOI:  https://doi.org/10.1038/s41586-025-09916-w
  56. Nat Commun. 2025 Nov 27. 16(1): 10674
    Loss of cell-autonomously secreted laminin-α2 drives muscle stem cell dysfunction in LAMA2-related muscular dystrophy.
    Timothy J McGowan, Judith R Reinhard, Nicolas Lewerenz, Marta Białobrzeska, Shuo Lin, Jacek Stępniewski, Krzysztof Szade, Józef Dulak, Markus A Rüegg.
      The extracellular matrix protein laminin-α2 is essential for preserving the integrity of skeletal muscle fibers during contraction. Its importance is reflected by the severe, congenital LAMA2-related muscular dystrophy (LAMA2 MD) caused by loss-of-function mutations in the LAMA2 gene. While laminin-α2 has an established role in structurally supporting muscle fibers, it remains unclear whether it exerts additional functions that contribute to the maintenance of skeletal muscle integrity. Here, we report that in healthy muscle, activated muscle stem cells (MuSCs) express Lama2 and remodel their microenvironment with laminin-α2. By characterizing LAMA2 MD-afflicted MuSCs and generating MuSC-specific Lama2 knockouts, we show that MuSC-derived laminin-α2 is essential for rapid MuSC expansion and regeneration. In humans, we identify LAMA2 expression in MuSCs and demonstrate that loss-of-function mutations impair cell-cycle progression of myogenic precursors. In summary, we show that self-secreted laminin-α2 supports MuSC proliferation post-injury, thus implicating MuSC dysfunction in LAMA2 MD pathology.
    DOI:  https://doi.org/10.1038/s41467-025-65703-1
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