bims-ginsta 2025-11-02 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–11–02
38 papers selected by
Jinrong Hu, National University of Singapore

Maternal factor OTX2 regulates human embryonic genome activation and early development.
Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.
Surface mechanics and compressive stress impact mammalian follicle development.
Dcr1 senses R-loops for RNAPII termination at sites of replication stress and repair pathway choice.
YAP-Induced Glycolysis Drives Fibroinflammation and Disrupts Fibroblast Fidelity.
Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos.
Dissociation of the nuclear basket triggers chromosome loss in aging yeast.
Human heart-macrophage assembloids mimic immune-cardiac interactions and enable arrhythmia disease modeling.
Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration.
Selective RNA sequestration in biomolecular condensates directs cell fate transitions.
Spatiotemporal gene expression and cellular dynamics of the developing human heart.
Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2.
Improved reconstruction of single-cell developmental potential with CytoTRACE 2.
Reevaluation of whether histones are asymmetrically segregated during asymmetric divisions of stem cells in Drosophila.
Ribosome dysregulation and intervention in age-related infertility.
Intestinal fibroblast heterogeneity: unifying RNA-seq studies and introducing consensus-driven nomenclature.
Adrenergic signaling coordinates distant and local responses to amputation in axolotl.
Transcription factor switching drives subtype-specific pancreatic cancer.
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.
Evidence for improved DNA repair in long-lived bowhead whale.
Serum response factor is essential for endometrial function and prevention of inflammatory fibrosis.
KDM4A serves as an α-tubulin demethylase regulating microtubule polymerization and cell mitosis.
Accumulation of succinate suppresses de novo purine synthesis through succinylation-mediated control of the mitochondrial folate cycle.
Structural landscape of activation, desensitization and inhibition in the human TRPM4 channel.
The E3 ligase RNF32 controls the IκB kinase complex and NF-κB signaling in intestinal stem cells.
TDP-43-dependent mis-splicing of KCNQ2 triggers intrinsic neuronal hyperexcitability in ALS/FTD.
H2BK120ub and its reader RNF169 sequentially regulate replication fork remodeling and stability.
Cell autonomous polarization by the planar cell polarity signaling pathway.
Protein restriction reprograms the multi-organ proteomic landscape of mouse aging.
Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.
N6-methyladenosine on L1PA governs the trans-silencing of LTRs and restrains totipotency in naive human embryonic stem cells.
TDP-43 skein-like inclusions are formed by BAG3- and HSP70-guided co-aggregation with actin-binding proteins.
Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response.
Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy.
Close-up of vesicular ER exit sites by volume electron imaging using FIB-SEM.
A single-chain derivative of an integrin-activating antibody potentiates organoid growth in Matrigel and collagen hydrogels.
Mechanisms and regulation of the Hsp70 chaperone network.
PCMD-1 stabilizes the PCM scaffold and facilitates centriole separation.

Nat Genet. 2025 Oct 27.

Maternal factor OTX2 regulates human embryonic genome activation and early development.

Qiuyan Wang, Chuanxin Zhang, Yanna Dang, Jiaqi Sun, Zhuoning Zou, Cheng Li, Shuiying Ma, Zongyu Li, Hui Liu, Xiaonan Ma, Zhen Yang, Lijuan Wang, Keliang Wu, Zi-Jiang Chen, Wei Xie, Han Zhao.

Transcription factors (TFs) are instrumental in kickstarting embryonic genome activation (EGA) in many species, yet their regulatory roles in human embryos remain poorly understood. Here, we show that OTX2, a maternally provided PRD-like homeobox TF, is required for proper human EGA and early development. At the four-cell stage, OTX2 promotes activation of key EGA genes, including TPRX1 and TPRX2, and the EGA-associated repeat HERVL-int and MLT2A1. At EGA targets, OTX2 directly binds promoters and putative enhancers, many of which overlap with Alu and MaLR repetitive elements containing the OTX2 motif, and promotes chromatin accessibility. The transcriptome and developmental defects upon OTX2 knockdown are partially rescued by overexpression of TPRX1 and TPRX2. Finally, joint knockdown of OTX2 and TPRXL, encoding another maternal PRD-like homeobox TF, exacerbates chromatin opening and EGA defects at the 8C stage. These findings establish OTX2 as a crucial maternal TF that awakes the genome at the beginning of human life.

DOI: https://doi.org/10.1038/s41588-025-02350-8
EMBO J. 2025 Oct 29.

Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

Dominik Saul, Diana Jurk, Madison L Doolittle, Robyn Laura Kosinsky, Yeaeun Han, Xu Zhang, Ana Catarina Franco, Sung Y Kim, Saranya P Wyles, Y S Prakash, David G Monroe, Luigi Ferrucci, Nathan K LeBrasseur, Paul D Robbins, Laura J Niedernhofer, Sundeep Khosla, João F Passos.

  Senescent cells drive age-related tissue dysfunction via the induction of a chronic senescence-associated secretory phenotype (SASP). The cyclin-dependent kinase inhibitors p21Cip1 and p16Ink4a have long served as markers of cellular senescence. However, their individual roles remain incompletely elucidated, particularly in vivo. Thus, we conducted a comprehensive examination of multiple single-cell RNA sequencing datasets spanning both murine and human tissues during aging. Our analysis revealed that p21Cip1 and p16Ink4a transcripts demonstrate significant heterogeneity across distinct cell types and tissues, frequently exhibiting a lack of co-expression. Moreover, we identified tissue-specific variations in SASP profiles linked to p21Cip1 or p16Ink4a expression. Using RNA velocity and pseudotime analyses, we discovered that p21+ and p16+ cells follow independent trajectory dynamics, with no evidence of direct transitions between these two states. Despite this heterogeneity, we identified a limited set of shared "core" SASP factors that may drive common senescence-related functions. Our study underscores the substantial diversity of cellular senescence and the SASP, emphasizing that these phenomena are inherently cell- and tissue-dependent.

Keywords:  Aging; Cellular Senescence; Heterogeneity; Senescence-Associated Secretory Phenotype (SASP); Single-Cell Mapping

DOI:  https://doi.org/10.1038/s44318-025-00601-2
Nat Commun. 2025 Oct 31. 16(1): 9578

Surface mechanics and compressive stress impact mammalian follicle development.

Arikta Biswas, Yuting Lou, Boon Heng Ng, Kosei Tomida, Sukhada Darpe, Kim Whye Leong, Zihao Wu, Thong Beng Lu, Xiang Teng, Yusuke Toyama, Isabelle Bonne, Chii Jou Chan.

The maturation of functional eggs in ovaries is essential for successful reproduction in mammals. Despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, using murine ovaries, we report that the theca cells surrounding secondary follicles play a critical role in regulating follicle development through mechanical signalling. Using biophysical approaches, we found that the contractile theca cells exert significant compressive stress to the follicular interior through active assembly of fibronectin. Manipulation of compressive stress by targeting theca cell contractility, basement membrane integrity or intrafollicular pressure leads to changes in follicle size and mechanics, granulosa cell YAP signalling and oocyte-granulosa cell communications. Transcriptomics and quantitative immunofluorescence reveal that compressive stress impacts functional follicle growth through regulating the balance between granulosa cell proliferation and death that drives tissue pressure homeostasis. Altogether, our study uncovers unique mechanical functions of theca cells and provides quantitative evidence of the role of compressive stress in regulating mammalian folliculogenesis.

DOI: https://doi.org/10.1038/s41467-025-65390-y
Mol Cell. 2025 Oct 28. pii: S1097-2765(25)00820-2. [Epub ahead of print]

Dcr1 senses R-loops for RNAPII termination at sites of replication stress and repair pathway choice.

Zihao Wang, Yizheng Zhang, Ting Guo, Ming He, Yingying Xu, Sonali Bhattacharjee, Robert A Martienssen, Jie Ren.

  Stalled RNA polymerase II (RNAPII) threatens genome integrity, yet how cells resolve transcription blocks at difficult-to-terminate sites is unclear. Leveraging the compact genome of fission yeast and termination defects associated with the non-canonical function of Dcr1, we unravel the recognition and release mechanisms of stalled RNAPII. Through dual recognition, Dcr1 senses the difficult-to-terminate context-stalled RNAPII and accumulated R-loops-and recruits the termination factor Dhp1 to ensure efficient RNAPII release. Failure of this mechanism causes termination defects that impede replication forks, necessitating DNA polymerase delta (DNAPδ)-mediated replication fork restart at stalled sites. Moreover, Dcr1 promotes genome stability by repurposing its hybrid-recognition ability to engage Rad51, thereby biasing DNA repair toward high-fidelity homologous recombination. Our work defines a key chromatin context and mechanisms governing RNAPII termination, establishing Dcr1 as a molecular hub that directly couples the fidelity of transcription termination to the stability of the genome during replication and repair.

Keywords:  DNA repair pathway choice; DNR:RNA hybrid; Dicer; R-loop; RNA polymerase II; Schizosaccharomyces pombe; chromatin; genome stability; replication stress; transcription termination; transcription-replication conflict

DOI:  https://doi.org/10.1016/j.molcel.2025.10.004
Circ Res. 2025 Oct 30.

YAP-Induced Glycolysis Drives Fibroinflammation and Disrupts Fibroblast Fidelity.

Chang-Ru Tsai, Lin Liu, Yi Zhao, Jong Kim, Paulo Czarnewski, Rich Li, Fansen Meng, Mingjie Zheng, Jeffrey Steimle, Xiaolei Zhao, Francisco Grisanti, Zheng Sun, Jun Wang, Md Abul Hassan Samee, Xiao Li, James F Martin.

   BACKGROUND: Separation of the pulmonic and systemic circulation is essential for terrestrial life, and mammals have evolved distinct cardiac chambers with specialized structures and functions. Transcriptomics profiling revealed cellular heterogeneity between heart chambers. However, the mechanisms underlying chamber-specific transcriptomic and metabolic differences-and their functional significance-remain poorly understood. The Hippo/YAP (yes-associated protein) pathway is a conserved signaling network that regulates diverse cellular processes. The Hippo kinases inhibit YAP in cardiac fibroblasts (CF) to restrict fibrosis and inflammation. Nonetheless, how YAP regulates the metabolic microenvironment during homeostasis and fibroinflammation remains unclear.
METHODS: We investigated YAP and glycolysis activity in the 4 cardiac chambers by scoring the expression of YAP target genes and glycolysis genes in human single-nucleus RNA sequencing data. To compare glucose uptake between the left and right atria, we measured isotope-labeled glucose uptake in isolated mouse atria. To study the role of YAP in CFs, we inactivated the Hippo kinases, Lats1 and Lats2, in mouse CFs and performed metabolic studies, snRNA-seq, single-nucleus assay for transposase-accessible chromatin with sequencing, and spatial transcriptomics.
RESULTS: Metabolic and sequencing approaches revealed that Hippo-deficient CFs activated glycolysis to promote fibroinflammation. Inhibition of glycolysis or lactate production suppressed Hippo-deficient CF-induced fibrosis. Elevated YAP activity disrupted fibroblast lineage fidelity by inducing an osteochondroprogenitor cell state. Blocking macrophage expansion pharmacologically reduced Hippo-deficient CF proliferation and fibrosis. Sequencing and functional studies showed that macrophages secreted IGF1 (insulin-like growth factor 1) to activate IGF1 signaling in Hippo-deficient CFs to increase cell proliferation and fibrosis.
CONCLUSIONS: We discovered that right atrial CFs are more glycolytic and have higher YAP activity than CFs in other heart chambers. YAP activation in CFs induces glycolysis to drive fibrosis. YAP disrupts fibroblast lineage fidelity, driving them to a SOX9 (SRY-box transcription factor 9)-expressing osteochondroprogenitor cell state. Mechanistically, YAP activates the secretion of CSF1 (colony-stimulating factor 1) to promote macrophage expansion. Blocking macrophage expansion reduces Hippo-deficient CF proliferation, osteochondroprogenitor differentiation, and fibrosis, revealing that macrophages signal reciprocally to regulate CF cell states. Genomic and functional studies revealed that the upregulated IGF1 receptor in Hippo-deficient CFs enables them to receive macrophage-secreted IGF1, thereby further enhancing CF proliferation and fibrosis.

Keywords:  fibroblast; fibrosis; glycolysis; inflammation; isotope

DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326480
Development. 2025 Nov 01. pii: dev204638. [Epub ahead of print]152(21):

Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos.

Trine Skuland, Madeleine Fosslie, Sherif Khodeer, Endalkachew Ashenafi Alemu, Jens Vilstrup Johansen, Marie Indahl, Blanca Corral Castroviejo, Yanjiao Li, Mads Lerdrup, John Arne Dahl, Peter Zoltan Fedorcsak, Gareth D Greggains.

  Epigenetic reprogramming and embryonic genome activation (EGA) are crucial events during early development. Establishment of distinctive broad histone H3 lysine 4 trimethylation (H3K4me3) domains in the oocyte is necessary for genome silencing, and their removal in the 2-cell embryo is crucial for EGA and development in mice. However, the stage-specific requirement for broad H3K4me3 domains is unclear. Here, we show that inducing broad H3K4me3 removal in mouse oocytes can relieve genome silencing, impair oocyte maturation timing, and may cause transcriptional reactivation in resulting parthenogenetic 1-cell embryos. We further demonstrate that broad H3K4me3 demethylation precedes EGA but, surprisingly, premature depletion in zygotes or early 2-cell embryos does not alter the transcriptional program. Our findings suggest that broad H3K4me3 domains are required for oocyte genome silencing, timely maturation and post-fertilisation silencing, but onward pre-EGA transcriptional repression is not dependent on the original mark. This work contributes to the understanding of events and mechanisms involved in genome silencing and activation in early development, providing insight into potential modes of failure that may contribute to infertility.

Keywords:  Activation; Embryo; H3K4me3; KDM5B; Oocyte; Silencing

DOI:  https://doi.org/10.1242/dev.204638
Elife. 2025 Oct 30. pii: RP104530. [Epub ahead of print]14

Dissociation of the nuclear basket triggers chromosome loss in aging yeast.

Mihailo Mirkovic, Jordan McCarthy, Anne Cornelis Meinema, Julie Parenteau, Sung Sik Lee, Sherif Abou Elela, Yves Barral.

  In many organisms, aging is a clear risk factor for chromosome missegregation, the main source of aneuploidy. Here, we report that old yeast cells lose chromosomes by partitioning them asymmetrically to their daughter cells together with the pre-existing (old) spindle pole body (SPB, centrosome equivalent in yeast). Strikingly, remodelling of the nuclear pore complex (NPC) and the displacement of its nuclear basket triggered these asymmetric chromosome segregation events. Simultaneously, nuclear basket displacement caused unspliced pre-mRNAs to leak into the cytoplasm. We show that removing the introns of three genes involved in chromosome segregation was sufficient to fully suppress chromosome loss in old cells. Promoting pre-mRNA leakage in young cells also caused asymmetric chromosome partitioning and loss through the same three introns. Therefore, we propose that basket displacement from NPCs and its consequences for pre-mRNA quality control are key triggers of aging phenotypes such as aneuploidy.

Keywords:  NPC; RNA; S. cerevisiae; aging; aneuploidy; cell biology; chromosomes; gene expression; intron; mitosis

DOI:  https://doi.org/10.7554/eLife.104530
Cell Stem Cell. 2025 Oct 27. pii: S1934-5909(25)00367-4. [Epub ahead of print]

Human heart-macrophage assembloids mimic immune-cardiac interactions and enable arrhythmia disease modeling.

Colin O'Hern, Sammantha Caywood, Shakhlo Aminova, Artem Kiselev, Brett Volmert, Weiheng Cao, Fei Wang, Mia Dionise, Merlinda-Loriane Sewavi, Milana Skoric, Hussain Basrai, Freyda Mannering, Priyadharshni Muniyandi, Mirel Popa, George Boulos, Kyle Wolf, Izabelle Brown, Isabel Nuñez-Regueiro, Amanda Huang, Aleksandra Kostina, Lauren Squire, Curtis Wilkerson, Nagib Chalfoun, Sangbum Park, Nureddin Ashammakhi, Chao Zhou, Christopher Contag, Aitor Aguirre.

  Yolk-sac-derived embryonic cardiac tissue-resident macrophages (TRMPs) colonize the heart early in development and are essential for proper heart development, supporting tissue remodeling, angiogenesis, electrical conduction, efferocytosis, and immune regulation. We present here a human heart-macrophage assembloid (hHMA) model by integrating autologous human pluripotent stem cell (hPSC)-derived embryonic monocytes into heart organoids to generate physiologically relevant TRMPs that persist long-term and contribute to cardiogenesis. Using single-cell transcriptomics, live imaging, and proteomics, we demonstrate that TRMPs modulate cardiac paracrine signaling, perform efferocytosis, and regulate extracellular matrix remodeling and electrical conduction. In a proof-of-concept maturated hHMA model of chronic inflammation, TRMPs adopt pro-inflammatory phenotypes that promote arrhythmogenic activity, consistent with atrial fibrillation through activation of the NOD-like receptor pyrin domain-containing 3 (NLRP3) inflammasome. This system enables detailed mechanistic studies of immune-cardiac interactions and provides a powerful in vitro platform for modeling human heart development and inflammation-driven arrhythmias.

Keywords:  assembloid; atrial fibrillation; cardiac development; disease modeling; embryonic monocyte; human heart organoid; inflammasome; pluripotent stem cell; tissue-resident macrophage

DOI:  https://doi.org/10.1016/j.stem.2025.09.011
Nat Cell Biol. 2025 Oct 31.

Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration.

Qiaochu Li, Konstantin Weiss, Fuateima Niwa, Jan Riemer, Thorsten Hoppe.

The mitochondrial proteome is remodelled to meet metabolic demands, but how metabolic cues regulate mitochondrial protein turnover remains unclear. Here we identify a conserved, nutrient-responsive mechanism in which the amino acid leucine suppresses ubiquitin-dependent degradation of outer mitochondrial membrane (OMM) proteins, stabilizing key components of the protein import machinery and expanding the mitochondrial proteome to enhance metabolic respiration. Leucine inhibits the amino acid sensor GCN2, which selectively reduces the E3 ubiquitin ligase cofactor SEL1L at mitochondria. Depletion of SEL1L phenocopies the effect of leucine, elevating OMM protein abundance and mitochondrial respiration. Disease-associated defects in leucine catabolism and OMM protein turnover impair fertility in Caenorhabditis elegans and render human lung cancer cells resistant to inhibition of mitochondrial protein import. These findings define a leucine-GCN2-SEL1L axis that links nutrient sensing to mitochondrial proteostasis, with implications for metabolic disorders and cancer.

DOI: https://doi.org/10.1038/s41556-025-01799-3
Nat Biotechnol. 2025 Oct 28.

Selective RNA sequestration in biomolecular condensates directs cell fate transitions.

Patrizia Pessina, Mika Nevo, Junchao Shi, Srikanth Kodali, Eduard Casas, Yingzhi Cui, Alicia L Richards, Emily J Park, Xi Chen, Florencia Levin-Ferreyra, Alejandra Rivera Tostado, Erica Stevenson, Nevan J Krogan, Danielle L Swaney, Qilong Ying, Qi Chen, Justin Brumbaugh, Bruno Di Stefano.

Controlling stem cell differentiation is a longstanding goal in biomedical research. Here we explore how cell fate is influenced by RNA condensates, specifically P-bodies, which modulate gene expression posttranscriptionally. We profiled the transcriptomes of biomolecular condensates in diverse developmental contexts spanning multiple vertebrate species. Our analyses revealed conserved, cell type-specific sequestration of untranslated RNAs encoding cell fate regulators. P-body RNA contents do not reflect active gene expression in each cell type but are enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, P-body contents are controlled by microRNAs and can be profoundly reshaped by perturbing AGO2 or polyadenylation site usage. Applying these insights to stem cell differentiation, we show that manipulating P-body assembly or microRNA activity can direct naive mouse and human pluripotent stem cells toward totipotency or primed human embryonic cells toward the germ cell lineage. Our findings link cell fate decisions to RNA condensates across vertebrates and provide a means of controlling cell identity.

DOI: https://doi.org/10.1038/s41587-025-02853-z
Nat Genet. 2025 Oct 29.

Spatiotemporal gene expression and cellular dynamics of the developing human heart.

Enikő Lázár, Raphaël Mauron, Žaneta Andrusivová, Julia Foyer, Mengxiao He, Ludvig Larsson, Nick Shakari, Sergio Marco Salas, Christophe Avenel, Sanem Sariyar, Jan Niklas Hansen, Marco Vicari, Paulo Czarnewski, Emelie Braun, Xiaofei Li, Olaf Bergmann, Christer Sylvén, Emma Lundberg, Sten Linnarsson, Mats Nilsson, Erik Sundström, Igor Adameyko, Joakim Lundeberg.

Heart development relies on topologically orchestrated cellular transitions and interactions, many of which remain poorly characterized in humans. Here, we combined unbiased spatial and single-cell transcriptomics with imaging-based validation across postconceptional weeks 5.5 to 14 to uncover the molecular landscape of human early cardiogenesis. We present a high-resolution transcriptomic map of the developing human heart, revealing the spatial arrangements of 31 coarse-grained and 72 fine-grained cell states organized into distinct functional niches. Our findings illuminate key insights into the formation of the cardiac pacemaker-conduction system, heart valves and atrial septum, and uncover unexpected diversity among cardiac mesenchymal cells. We also trace the emergence of autonomic innervation and provide the first spatial account of chromaffin cells in the fetal heart. Our study, supported by an open-access spatially centric interactive viewer, offers a unique resource to explore the cellular and molecular blueprint of human heart development, offering links to genetic causes of heart disease.

DOI: https://doi.org/10.1038/s41588-025-02352-6
EMBO J. 2025 Oct 30.

Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2.

Marlena Mucha, Zhihao Lai, Nicholas J McKenzie, Francesca Matrà, Marion Boudes, Sarena F Flanigan, Maria Teresa Alejo-Vinogradova, Craig Monger, Qi Zhang, Darragh Nimmo, Evan Healy, Ademar J Silva, Daniel Angelov, David M Reck, Gráinne Holland, Zeynep Eda Atmaca, Helen E King, Maeve Hamilton, Eleanor Glancy, James Nolan, Robert J Weatheritt, Oliver Bell, Michiel Vermeulen, Chen Davidovich, Adrian P Bracken.

  Polycomb Repressive Complex 2 (PRC2) is an essential chromatin regulator responsible for mono-, di- and tri-methylating H3K27. Control of PRC2 activity is a critical process in development and disease, yet no inhibitory cofactor has been identified in somatic cells. Here, we show that the alternative isoforms of its accessory subunit AEBP2, namely AEBP2S (short) and AEBP2L (long), perform opposite functions in modulating PRC2 activity. Contrary to prior assumptions that AEBP2 enhances PRC2 function, we find that the widely expressed AEBP2L isoform inhibits it. AEBP2L is expressed throughout embryogenesis and adulthood and inhibits PRC2 DNA binding, histone methyltransferase activity, and binding to target genes. In contrast, AEBP2S, expressed during early embryogenesis, promotes PRC2 DNA-binding activity and is essential for de novo repression of target genes during the transition from naïve to primed pluripotency. Mechanistically, through high-resolution cryo-EM and mutagenesis, we show that the recently evolved, negatively charged N-terminal region of AEBP2L inhibits PRC2. We propose a scenario in which the N-terminus of AEBP2L arose in vertebrates to restrain PRC2 activity in somatic cells.

Keywords:  AEBP2; Cryo-EM; PRC2; Polycomb; Trithorax

DOI:  https://doi.org/10.1038/s44318-025-00616-9
Nat Methods. 2025 Oct 27.

Improved reconstruction of single-cell developmental potential with CytoTRACE 2.

Minji Kang, Gunsagar S Gulati, Erin L Brown, Zhen Qi, Susanna Avagyan, Jose Juan Almagro Armenteros, Rachel Gleyzer, Wubing Zhang, Chloé B Steen, Jeremy Philip D'Silva, Janella Schwab, Michael F Clarke, Aadel A Chaudhuri, Aaron M Newman.

While single-cell RNA sequencing has advanced our understanding of cell fate, identifying molecular hallmarks of potency-a cell's ability to differentiate into other cell types-remains a challenge. Here we introduce CytoTRACE 2, an interpretable deep learning framework for predicting absolute developmental potential from single-cell RNA sequencing data. Across diverse platforms and tissues, CytoTRACE 2 outperformed previous methods in predicting developmental hierarchies, enabling detailed mapping of single-cell differentiation landscapes and expanding insights into cell potency.

DOI: https://doi.org/10.1038/s41592-025-02857-2
Proc Natl Acad Sci U S A. 2025 Nov 04. 122(44): e2513015122

Reevaluation of whether histones are asymmetrically segregated during asymmetric divisions of stem cells in Drosophila.

Anqi Li, Dong Tong, Benjamin Ohlstein, Zheng Guo.

  Recent work suggests that asymmetric segregation of preexisting and newly synthesized canonical histone 3.1 (H3.1), but not variant histone 3.3A (H3.3A), plays an important role in the asymmetric outcome of Drosophila germline stem cell (GSC) and intestinal stem cell (ISC) divisions. However, this finding relied on the Gal4/UAS system and Flp-out technology to swap expression of exogenous fluorescent proteins-an approach that decouples H3.1 expression from the cell cycle and may be prone to artifacts. Here, by photoswitching photoconvertible H3-Dendra2 proteins expressed under their native controls in living flies, we find that preexisting and newly synthesized H3.1 and H3.3A are symmetrically segregated in dividing ISCs and somatic cyst stem cells (CySCs) in male testes. While H3.3A was found to be symmetrically segregated during GSC divisions, analysis of the H3.1 segregation in GSCs was complicated by our unexpected finding that H3.1-Dendra2 expressed under its normal control within the context of a histone transgene is not detectable in GSCs, owing to regulatory elements in the 3'UTR that mediate translational repression by the RNA-binding proteins Nanos and Pumilio. Nevertheless, when this repression is obviated by using a 3'UTR devoid of such elements, H3.1-Dendra2 is expressed in GSCs and symmetrically segregated without affecting lineage outcomes. We obtained similar results when the coding sequence of H3.3A was edited to encode H3.1 in the context of an H3.3A-Dendra2 knock-in allele. Our findings thus challenge the prevailing model of asymmetric histone segregation and reveal an unexpected molecular mechanism of posttranscriptional repression of H3.1 in GSCs.

Keywords:  Dendra2; asymmetric division; newly synthesized histones; preexisting histones; symmetric segregation

DOI:  https://doi.org/10.1073/pnas.2513015122
Cell Rep Med. 2025 Oct 27. pii: S2666-3791(25)00497-5. [Epub ahead of print] 102424

Ribosome dysregulation and intervention in age-related infertility.

Jie Li, Honghong Wang, Pengfei Zhu, Haixia Chen, Haiyang Zuo, Chang Liu, Linlin Liu, Xiaoying Ye, Guofeng Feng, Yiwei Wu, Qinli Liu, Tao Yang, David L Keefe, Xiaohong Bai, Wei Shang, Xueqing Wu, Lin Liu.

  Fertility in women decreases with age, but the molecular basis for age-related, unexplained infertility remains elusive. Here, we reveal distinct transcriptome changes in oocytes and surrounding cumulus cells from women in their mid-thirties, as evidenced by notably increased transcription of ribosome genes. Additionally, meiosis genes and actin and cohesin components are downregulated in oocytes with age. Lysosomes and proteostasis are also disrupted in cumulus cells. Moreover, DNA hypomethylation and altered heterochromatin deposition at specific genomic loci are linked to increased transcription of ribosome genes. Rapamycin effectively reduces translation and promotes protein homeostasis in cumulus cells. Remarkably, short-term rapamycin allows patients who fail repeated in vitro fertilization cycles with embryo developmental arrest to achieve high-quality blastocysts that yield successful pregnancy and live birth. These data suggest a causal role for elevated transcription of ribosome genes in aging oocytes and cumulus cells and identify rapamycin as a promising treatment for age-related infertility. This study is registered at Chinese Clinical Trial Registry (ChiCTR2300069828).

Keywords:  aging; cumulus cells; infertility; oocyte; rapamycin; ribosome

DOI:  https://doi.org/10.1016/j.xcrm.2025.102424
J Cell Sci. 2025 Oct 31. pii: jcs.264147. [Epub ahead of print]

Intestinal fibroblast heterogeneity: unifying RNA-seq studies and introducing consensus-driven nomenclature.

Neda Glisovic, Aleksandra Chikina, Noémie Robil, Sonia Lameiras, Reda Bouras, Danijela Matic Vignjevic.

  In the colon, the single-layered epithelium forms crypts that extend into the mucosa and are surrounded by a fibroblast network essential for extracellular matrix (ECM) production, remodeling, and epithelial support. Fibroblasts are heterogeneous, but inconsistent nomenclature and lack of markers have hindered their classification. Using single-cell RNA sequencing (scRNA-seq), we identified six distinct fibroblast subpopulations in mouse colonic mucosa, each with unique molecular profiles and specialized functions. Some fibroblasts focus on ECM production and remodeling, while others show high contractility. Certain subsets secrete cytokines promoting epithelial differentiation or maintaining the stem cell niche. Spatial mapping revealed their organization within the mucosa, and trajectory analysis suggested distinct differentiation pathways. Cell cycle scoring confirmed that fibroblasts remain largely non-proliferative under homeostasis. By integrating our dataset with published ones, we identified conserved fibroblast populations and propose a standardized nomenclature for intestinal fibroblasts. This framework enhances communication and understanding of fibroblast diversity and their roles in gut homeostasis and disease.

Keywords:  Colon; Fibroblasts; Homeostasis

DOI:  https://doi.org/10.1242/jcs.264147
Cell. 2025 Oct 24. pii: S0092-8674(25)01125-0. [Epub ahead of print]

Adrenergic signaling coordinates distant and local responses to amputation in axolotl.

Duygu Payzin-Dogru, Tim Froitzheim, Steven J Blair, Siddhartha G Jena, Hani Singer, Julia C Paoli, Ryan T Kim, Emil Kriukov, Sarah E Wilson, Renzhi Hou, Aaron M Savage, Victor Cat, Louis V Cammarata, S Y Celeste Wu, Vivien Bothe, Burcu Erdogan, Shifa Hossain, Noah Lopez, Julia Losner, Juan Velazquez Matos, Sangwon Min, Sebastian Böhm, Anthony E Striker, Kelly E Dooling, Adam H Freedman, Bobby Groves, Benjamin Tajer, Glory Kalu, Eric Wynn, Alan Y L Wong, Nadia Fröbisch, Petr Baranov, Maksim V Plikus, Jason D Buenrostro, Brian J Haas, Isaac M Chiu, Timothy B Sackton, Jessica L Whited.

  Many species regenerate lost body parts following amputation. Most limb regeneration research has focused on the immediate injury site. Meanwhile, body-wide injury responses remain largely unexplored but may be critical for regeneration. Here, we discovered a role for the sympathetic nervous system in stimulating a body-wide stem cell activation response to amputation that drives enhanced limb regeneration in axolotls. This response is mediated by adrenergic signaling, which coordinates distant cellular activation responses via the α2Α-adrenergic receptor, and local regeneration responses via β-adrenergic receptors. Both α2A- and β-adrenergic signaling act upstream of mTOR signaling. Notably, systemically activated axolotls regenerate limbs faster than naive animals, suggesting a potential selective advantage in environments where injury from cannibalism or predation is common. This work challenges the predominant view that cellular responses underlying regeneration are confined to the injury site and argues instead for body-wide cellular priming as a foundational step that enables localized tissue regrowth.

Keywords:  amputation; limb; mTOR; noradrenaline; norepinephrine; peripheral nervous system; progenitor cells; regeneration; stem cells; systemic responses

DOI:  https://doi.org/10.1016/j.cell.2025.09.025
Nat Genet. 2025 Oct 30.

Transcription factor switching drives subtype-specific pancreatic cancer.

Shalini V Rao, Lisa Young, Danya Cheeseman, Sean Flynn, Niklas Krebs, Dominique-Laurent Couturier, Stephanie Mack, Rebecca Brais, Jill Temple, Amy Smith, Evangelia Papachristou, Catarina Pelicano, Chandra Sekhar Reddy Chilamakuri, Krzysztof Herka, Hideo Baba, Luay Farah, Phyllis F Cheung, Jens Siveke, Stéphane Guerrier, Luca Insolia, Michael Gill, Emily Archer Goode, Steven Kupczak, Yi Cheng, Giacomo Borsari, Duncan Jodrell, Clive D'Santos, Alasdair Russell, Barbara T Grünwald, Eva Serrao, Igor Chernukhin, Jason S Carroll.

Emerging evidence suggests that lineage-specifying transcription factors control the progression of pancreatic ductal adenocarcinoma (PDAC). We have discovered a transcription factor switching mechanism involving the poorly characterized orphan nuclear receptor HNF4G and the putative pioneer factor FOXA1, which drives PDAC progression. Using our unbiased protein interactome discovery approach, we identified HNF4A and HNF4G as reproducible, FOXA1-associated proteins, in both preclinical models and Whipple surgical samples. In the primary tumor context, we consistently find that the dominant transcription factor is HNF4G, where it functions as the driver. A molecular switch occurs in advanced disease, whereby HNF4G expression or activity decreases, unmasking FOXA1's transcriptional potential. Derepressed FOXA1 drives late-stage disease by orchestrating metastasis-specific enhancer-promoter loops to regulate the expression of metastatic genes. Overall survival is influenced by HNF4G and FOXA1 activity in primary tumor growth and in metastasis, respectively. We suggest that the existence of stage-dependent transcription factor activity, triggered by molecular compartmentalization, mediates the progression of PDAC.

DOI: https://doi.org/10.1038/s41588-025-02389-7
Nat Biotechnol. 2025 Oct 30.

High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.

Tianyi Chang, Shihui Zhao, Kunyue Deng, Zhizhao Liao, Mingchuan Tang, Yanxi Zhu, Wuji Han, Chenxi Yu, Wenyi Fan, Mengcheng Jiang, Guanbo Wang, Dongfang Liu, Jirun Peng, Yuhong Pang, Peng Fei, Jianbin Wang, Chunhong Zheng, Yanyi Huang.

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in situ hybridization require sophisticated instrumentation. Here, we introduce 'profiling of RNA in situ through single-round imaging' (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISM's versatility across various tissues by generating a three-dimensional (3D) atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

DOI: https://doi.org/10.1038/s41587-025-02883-7
Nature. 2025 Oct 29.

Evidence for improved DNA repair in long-lived bowhead whale.

Denis Firsanov, Max Zacher, Xiao Tian, Todd L Sformo, Yang Zhao, Gregory Tombline, J Yuyang Lu, Zhizhong Zheng, Luigi Perelli, Enrico Gurreri, Li Zhang, Jing Guo, Anatoly Korotkov, Valentin Volobaev, Seyed Ali Biashad, Zhihui Zhang, Johanna Heid, Alexander Y Maslov, Shixiang Sun, Zhuoer Wu, Jonathan Gigas, Eric C Hillpot, John C Martinez, Minseon Lee, Alyssa Williams, Abbey Gilman, Nicholas Hamilton, Ekaterina Strelkova, Ena Haseljic, Avnee Patel, Maggie E Straight, Nalani Miller, Julia Ablaeva, Lok Ming Tam, Chloé Couderc, Michael R Hoopmann, Robert L Moritz, Shingo Fujii, Amandine Pelletier, Dan J Hayman, Hongrui Liu, Yuxuan Cai, Anthony K L Leung, Zhengdong Zhang, C Bradley Nelson, Lisa M Abegglen, Joshua D Schiffman, Vadim N Gladyshev, Carlo C Maley, Mauro Modesti, Giannicola Genovese, Mirre J P Simons, Jan Vijg, Andrei Seluanov, Vera Gorbunova.

At more than 200 years, the maximum lifespan of the bowhead whale exceeds that of all other mammals. The bowhead is also the second-largest animal on Earth1, reaching over 80,000 kg. Despite its very large number of cells and long lifespan, the bowhead is not highly cancer-prone, an incongruity termed Peto's paradox2. Here, to understand the mechanisms that underlie the cancer resistance of the bowhead whale, we examined the number of oncogenic hits required for malignant transformation of whale primary fibroblasts. Unexpectedly, bowhead whale fibroblasts required fewer oncogenic hits to undergo malignant transformation than human fibroblasts. However, bowhead whale cells exhibited enhanced DNA double-strand break repair capacity and fidelity, and lower mutation rates than cells of other mammals. We found the cold-inducible RNA-binding protein CIRBP to be highly expressed in bowhead fibroblasts and tissues. Bowhead whale CIRBP enhanced both non-homologous end joining and homologous recombination repair in human cells, reduced micronuclei formation, promoted DNA end protection, and stimulated end joining in vitro. CIRBP overexpression in Drosophila extended lifespan and improved resistance to irradiation. These findings provide evidence supporting the hypothesis that, rather than relying on additional tumour suppressor genes to prevent oncogenesis3-5, the bowhead whale maintains genome integrity through enhanced DNA repair. This strategy, which does not eliminate damaged cells but faithfully repairs them, may be contributing to the exceptional longevity and low cancer incidence in the bowhead whale.

DOI: https://doi.org/10.1038/s41586-025-09694-5
Proc Natl Acad Sci U S A. 2025 Nov 04. 122(44): e2510060122

Serum response factor is essential for endometrial function and prevention of inflammatory fibrosis.

Ryan M Marquardt, Sara A Grimm, San-Pin Wu, Peter F Lais, Shu-Yun Li, Xin Xu, Erin Smithberger, David Cunefare, Charan Ganta, David Olson, Eunhee M Jeong, Jae-Wook Jeong, Bruce A Lessey, John P Lydon, Francesco J DeMayo.

  Pregnancy requires a supportive uterine environment facilitated by steroid hormone-regulated differentiation of endometrial stromal fibroblasts into decidual cells and tight control of inflammation. Serum response factor (SRF) is a widely expressed transcription factor essential for mesenchymal cell growth and differentiation with noted roles in hormonal regulation of muscle tissues but little characterization in reproductive organs. Here, we reveal that endometrial SRF is dysregulated in human endometriosis and is critical for female reproductive success in mice through regulation of endometrial stromal and epithelial cells. Immunohistochemical analysis identified decreased endometrial SRF expression in infertile endometriosis patient tissues. RNAi-based SRF knockdown in human endometrial stromal cells resulted in disrupted cytoskeletal structure, viability, and decidual response. Conditional Srf knockout mice (Srfd/d) generated using the PgrCre were infertile with implantation failure, lack of decidual response, and development of severe endometrial fibrosis. Single-cell RNA sequencing identified dramatic changes in Srfd/d endometrial cell populations including large-scale myeloid immune cell infiltration. Srfd/d stromal fibroblasts displayed aberrant cytoskeletal and extracellular matrix gene expression and downregulation of genes important for decidual growth response. Srf-deficient epithelial cells displayed the most prominent dysregulation, strongly overexpressing estrogenic innate inflammatory genes including C3 and Lcn2 and fibrogenic genes Mmp7 and Fbln1, all of which paralleled patterns in human endometriosis patient data that we identified through comparative analysis using a published single-cell atlas. These results demonstrate the profound impact of SRF on endometrial homeostasis with relevance to human endometriosis-related infertility.

Keywords:  decidualization; endometriosis-related infertility; endometrium; inflammatory fibrosis; serum response factor

DOI:  https://doi.org/10.1073/pnas.2510060122
Sci Adv. 2025 Oct 31. 11(44): eadv6637

KDM4A serves as an α-tubulin demethylase regulating microtubule polymerization and cell mitosis.

Suhao Cao, Shaogang Wang, Xuan Xie, Xinyi Tan, Xinyu Hu, Fengxia Shao, Yanling Liu, Xu Zhang, Hong Cheng, Lei Diao, Lan Bao.

Posttranslational modifications of tubulin give microtubule distinct properties to support diverse cellular functions. Trimethylation on lysine-40 of α-tubulin (α-TubK40me3) is involved in cell division and neuronal development. The "writer" (SETD2) and "reader" (PBRM1) of α-TubK40me3 have been identified. However, the "eraser" of α-TubK40me3 and the impact of α-TubK40me3 dynamic balance on cells are still unclear. Here, we report that KDM4A, a member of the histone demethylase family, binds α-tubulin through its catalytic core domain and demethylates α-tubulin. KDM4A knockout significantly enhances α-TubK40me3, inducing microtubule polymerization and mitotic defects. Furthermore, the overpolymerized microtubules and cell mitotic defects caused by KDM4A knockout are rescued by reducing α-TubK40me3 with overexpression of an α-tubulin mutant α-tubulinK40A or depolymerizing microtubules with nocodazole treatment in cells. Together, our study identifies KDM4A as an α-tubulin demethylase, and this demethylation is important for regulating microtubule polymerization and cell mitosis.

DOI: https://doi.org/10.1126/sciadv.adv6637
Mol Cell. 2025 Oct 28. pii: S1097-2765(25)00819-6. [Epub ahead of print]

Accumulation of succinate suppresses de novo purine synthesis through succinylation-mediated control of the mitochondrial folate cycle.

Mushtaq A Nengroo, Austin T Klein, Heather S Carr, Olivia Vidal-Cruchez, Umakant Sahu, Daniel J McGrail, Nidhi Sahni, Niklas B Thompson, Peter A Faull, Peng Gao, John M Asara, Hardik Shah, Marc L Mendillo, Issam Ben-Sahra.

  The de novo purine synthesis pathway is fundamental for nucleotide production, yet the role of mitochondrial metabolism in modulating this process remains underexplored. Here, we identify that succinate dehydrogenase (SDH) is essential for maintaining de novo purine synthesis. Genetic or pharmacological inhibition of SDH suppresses purine synthesis, contributing to a decrease in cell proliferation. Mechanistically, SDH inhibition elevates succinate, which in turn promotes the succinylation of serine hydroxymethyltransferase 2 (SHMT2) within the mitochondrial tetrahydrofolate (THF) cycle. This post-translational modification lowers formate output, depriving cells of one-carbon units needed for purine assembly. In turn, cancer cells activate the purine salvage pathway, a metabolic compensatory adaptation that represents a therapeutic vulnerability. Notably, co-inhibition of SDH and purine salvage induces pronounced antiproliferative and antitumoral effects in preclinical models. These findings reveal a signaling role for mitochondrial succinate in tuning nucleotide metabolism and highlight a dual-targeted strategy to exploit metabolic dependencies in cancer.

Keywords:  TCA cycle; cancer; formate; mitochondrial metabolism; nucleotide metabolism; succinate

DOI:  https://doi.org/10.1016/j.molcel.2025.10.002
Nat Struct Mol Biol. 2025 Oct 31.

Structural landscape of activation, desensitization and inhibition in the human TRPM4 channel.

Celso M Teixeira-Duarte, Weizhong Zeng, Youxing Jiang.

TRPM4 is a member of the transient receptor potential melastatin channel subfamily and functions as a Ca2+-activated monovalent-selective cation channel. It is widely expressed in various cells and tissues, where its activation depolarizes the plasma membrane potential and modulates various Ca2+-dependent biological processes. TRPM4 activity is potentiated by membrane phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) and inhibited by cytosolic free adenosine triphosphate (ATP), allowing the channel to transition between different functional states in response to dynamic changes in cellular Ca2+, ATP and PtdIns(4,5)P2 levels during signaling events. Here we present single-particle cryo-electron microscopy structures of human TRPM4 in four distinct states: apo closed, Ca2+-bound putative desensitized, Ca2+-PtdIns(4,5)P2-bound open and ATP-bound inhibited. Combined with mutagenesis and electrophysiological analyses, these structures reveal the molecular mechanisms underlying TRPM4 activation, desensitization and inhibition. Given the central roles of Ca2+, PtdIns(4,5)P2 and ATP in cellular signaling, this work provides a structural foundation to decipher the physiological functions of TRPM4 across diverse biological systems.

DOI: https://doi.org/10.1038/s41594-025-01705-3
Mol Cell. 2025 Oct 29. pii: S1097-2765(25)00822-6. [Epub ahead of print]

The E3 ligase RNF32 controls the IκB kinase complex and NF-κB signaling in intestinal stem cells.

Angela Lauriola, Juliana Haydeé Enriqué Steinberg, Motoharu Sarubo, Elena Maspero, Fabiana Alejandra Rossi, Yasuhiro Mouri, Marco Pedretti, Mohsen Hajisadeghian, Vincenzo Taibi, Andrea Vettori, Nicola Vitulo, Michael Assfalg, Mariapina D'Onofrio, Mario Rossi, Akihiro Yasue, Alessandra Astegno, Simona Polo, Spartaco Santi, Yasusei Kudo, Daniele Guardavaccaro.

Nuclear factor κB (NF-κB) signaling is a central pathway regulating a plethora of cellular functions. Here, we find that RNF32, a RING E3 ubiquitin ligase whose expression is enriched in murine intestinal stem cells, regulates the activity of the IκB kinase (IKK) complex, the signal integration hub for NF-κB activation. The E3 ligase activity of RNF32 depends on calmodulin, the primary calcium sensor in eukaryotic cells. Increased levels of intracellular calcium ion (Ca2+) induce RNF32 binding to calmodulin, RNF32 activation, and autoubiquitylation. In turn, polyubiquitin chains conjugated to RNF32 recruit NEMO, the regulatory subunit of the IKK complex. Moreover, Ca2+ rise triggers RNF32 phase separation, which is required for the formation of NEMO condensates and IKK activation. Finally, we show that RNF32 is required for NF-κB activation triggered by bacterial lipopolysaccharides. Collectively, our findings uncover a mechanism controlling NF-κB signaling in the intestinal epithelium.

DOI: https://doi.org/10.1016/j.molcel.2025.10.005
Nat Neurosci. 2025 Oct 31.

TDP-43-dependent mis-splicing of KCNQ2 triggers intrinsic neuronal hyperexcitability in ALS/FTD.

Brian J Joseph, Kelly A Marshall, Peter Harley, Jacob R Mann, Francesco Alessandrini, Carlos G Vanoye, Wanhao Chi, Mercedes Prudencio, Dina Simkin, Tzu-Ting Kao, Reshma R Desai, Matthew J Keuss, Simone Barattucci, Matteo Zanovello, Puja R Mehta, Jean-Marc DeKeyser, Francesco Limone, Jonathan Lee, Anna-Leigh Brown, Marcel F Leyton-Jaimes, Leslie A Nash, Irune Guerra San Juan, Eleonora Aronica, Brian J Wainger, Mala Shah, Anand Goswami, Neil A Shneider, Dennis W Dickson, Juan Burrone, Chaolin Zhang, Hynek Wichterle, Leonard Petrucelli, Jonathan K Watts, Alfred L George, Pietro Fratta, Kevin Eggan, Evangelos Kiskinis.

Motor neuron hyperexcitability is a broadly observed yet poorly understood feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Nuclear depletion and cytoplasmic aggregation of the RNA splicing protein TAR DNA-binding protein 43 (TDP-43) are observed in most ALS and FTD patients. Here we show that TDP-43 dysfunction causes mis-splicing of KCNQ2, which encodes a voltage-gated potassium channel (Kv7.2) that regulates neuronal excitability. Using iPSC-derived neurons and postmortem ALS/FTD brain and spinal cord tissue we find widespread, disease-specific and TDP-43-specific skipping of an exon encoding the KCNQ2 pore domain. The mis-spliced mRNA escapes degradation and is translated into a nonfunctional protein with severely reduced ion conductance that aggregates in the endoplasmic reticulum and causes intrinsic hyperexcitability in ALS neuronal models. This event, which correlates with higher phosphorylated TDP-43 levels and earlier age of disease onset in patients, can be rescued by splice-modulating antisense oligonucleotides that dampen hyperexcitability in induced pluripotent stem cell cortical neurons and spinal motor neurons with TDP-43 depletion. Our work reveals that nuclear TDP-43 maintains the fidelity of KCNQ2 expression and function and provides a mechanistic link between established excitability disruption in ALS/FTD patients and TDP-43 dysfunction.

DOI: https://doi.org/10.1038/s41593-025-02096-w
EMBO J. 2025 Oct 27.

H2BK120ub and its reader RNF169 sequentially regulate replication fork remodeling and stability.

Filip D Duzanic, Vaishnavi Mohana-Natarajan, Samuele Fisicaro, Collin Bakker, Moses Aouami, Gabriel Amaral, Massimo Lopes, Nitika Taneja, Lorenza Penengo.

  Ubiquitination of the C-terminus of histone H2B (H2BK120ub) is a key histone modification with functions in a wide array of DNA-related processes, best characterized in gene transcription and repair. A role for H2B ubiquitination in DNA replication has been postulated and investigated in yeast but is still elusive in human cells. Here, we uncovered a critical function of H2BK120ub in replication fork dynamics. H2BK120ub is present at replication forks and accumulates upon replication stress in a manner dependent on ATR and RAD51. Loss of RNF20, the main ubiquitin ligase promoting H2BK120ub, leads to RECQ1-mediated unrestrained replication fork progression and defective fork reversal upon mild replication stress, restoring fork stability in BRCA2-deficient cells. Furthermore, we identified RNF169, a factor involved in the DNA damage response and repair, as a reader of the H2BK120ub mark at stalled replication forks, where it is required to protect the nascent DNA from excessive nucleolytic degradation. Hence, RNF20, H2BK120ub and RNF169 are key novel players orchestrating replication stress response and fork plasticity in human cells.

Keywords:  DNA Replication Stress Response; Fork Plasticity and Restart; Histone H2B Ubiquitination; RNF169; RNF20/RNF40

DOI:  https://doi.org/10.1038/s44318-025-00602-1
Nat Commun. 2025 Oct 28. 16(1): 9503

Cell autonomous polarization by the planar cell polarity signaling pathway.

Alexis T Weiner, Silas Boye Nissen, Kaye Suyama, Bomsoo Cho, Gandhy Pierre-Louis, Jeffrey D Axelrod.

As epithelial cells polarize in the tissue plane, the Planar Cell Polarity (PCP) signaling module segregates two distinct molecular subcomplexes to opposite sides of cells. Homodimers of the atypical cadherin Flamingo form bridges linking opposite complexes in neighboring cells, coordinating their direction of polarization. Feedback is required for cell polarization, but whether feedback requires intercellular and/or intracellular pathways is unknown. Using novel tools, we show that cells lacking Flamingo, or bearing a homodimerization-deficient Flamingo, polarize autonomously, indicating that functional PCP subcomplexes form and segregate cell-autonomously. Furthermore, we identify feedback pathways and propose an asymmetry amplifying mechanism that operate cell-autonomously. The intrinsic logic of PCP signaling is therefore more similar to that in single cell systems than was previously recognized.

DOI: https://doi.org/10.1038/s41467-025-64563-z
Cell. 2025 Oct 24. pii: S0092-8674(25)01133-X. [Epub ahead of print]

Protein restriction reprograms the multi-organ proteomic landscape of mouse aging.

Tian Lu, Yuting Xie, Yingrui Wang, Xiling Lin, Xue Cai, Yuqi Zhang, Zongxiang Nie, Chang Su, Wanglong Gou, Hong Zhang, Jing Wang, Yan Zhong, Zeyin Lai, Jingjing Xiang, Peng-Fei Shan, Ju-Sheng Zheng, Huijun Wang, Yi Zhu, Tiannan Guo.

  Population aging is accelerating, yet the multi-organ aging process and the geroprotective effects of dietary protein restriction (PR) remain poorly understood. Here, we conducted comprehensive proteomic analyses on 41 mouse tissues during male mouse aging and PR. Our findings identified tissue-specific aging hallmarks, including widespread changes in immunoglobulins and serine protease inhibitors across multiple tissues. PR mitigated age-related tissue-specific protein expression, epigenomic states, and protein phosphorylation patterns, and it significantly improved adipose tissue functions. These findings were supported by independent reduced representation bisulfite sequencing (RRBS), phosphoproteomics, and pathological analyses. Furthermore, analysis of plasma samples from mice and humans confirmed the cardiovascular benefits of PR. We identified sexual and temporal variations in the impact of PR, with middle age being the optimal intervention period. Overall, our study depicts the multi-organ aging process and provides valuable insights into the geroprotective potential of PR.

Keywords:  aging; epigenomics; geroprotective; human; mouse; multi-organ; protein restriction; proteomics; thermogenesis

DOI:  https://doi.org/10.1016/j.cell.2025.10.004
Nat Commun. 2025 Oct 30. 16(1): 9611

Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.

Mohsina Khan, Kyle Bond, Elyse Grilli, Daniel Cameron, Liyang Zhao, Sunder Sims-Lucas, Andrew P McMahon, Thomas J Carroll, Leif Oxburgh.

The proximal tubule of the nephron performs energy-demanding functions such as resorption of water, amino acids and glucose. Formation of the energy-producing machinery is an essential step in proximal tubule epithelial cell differentiation, and this report asks how mitochondria are localized within these cells. We show that mitochondria move from the apical to basolateral side of the proximal tubule cell coincident with the initiation of lumen flow and that proximal tubules deficient in filtration maintain mitochondria in the apical position. Mitochondrial localization depends on the activity of LRRK2 and modeling fluid flow on cultured proximal tubule epithelial cells demonstrates that LRRK2 activity is regulated by fluid shear stress, explaining how onset of flow in the newly differentiated proximal tubule may trigger the apical-to-basolateral dissemination of mitochondria. These findings indicate that mitochondrial redistribution is one component of a cellular program in the nascent proximal tubule that drives function and that this process is triggered by flow.

DOI: https://doi.org/10.1038/s41467-025-64598-2
Cell Stem Cell. 2025 Oct 29. pii: S1934-5909(25)00371-6. [Epub ahead of print]

N6-methyladenosine on L1PA governs the trans-silencing of LTRs and restrains totipotency in naive human embryonic stem cells.

Xuehao Zhu, Zhanhe Chang, Weide Xiao, Xinbao Zhang, Mingli Ma, Jiang Wu, Jindian Hu, Yan Bi, Xiaochen Kou, Yanhong Zhao, Yifan Sheng, Baoxing Dong, Jiaxing Sun, Che Chen, You Wu, Xuelian Liu, Wenqing Ding, Kaiyuan Jia, Yingfan Yao, Lihua Sun, Xianbin Yu, Hong Wang, Jun Liu, Yixuan Wang, Shaorong Gao, Yawei Gao.

  Transposable elements (TEs) occupy nearly half of the genome and drive developmental innovation, yet the mechanisms of silencing long terminal repeats (LTRs) remain incompletely understood. We demonstrate that methyltransferase-like 3 deficiency reverts naive human embryonic stem cells (hESCs) to a totipotent-like state with reactivation and chromatin resetting of 8C-associated genes, eRNAs, and LTRs, particularly ERV1 and ERVL-MaLR. Moreover, m6A on primate-specific L1PA is found to be essential. Mechanistically, L1PA binds 8C-associated LTRs and eRNAs and regulates chromatin through RNA-scaffold complexes with chromatin regulators, where m6A directs protein-binding preference. In naive hESCs, m6A on L1PA suppresses EP300 binding to ERV1 and enhances KAP1 binding to ERVL-MaLR, thereby restricting LTR activity. In parallel, the m6A-L1PA axis or m6A on eRNAs limits EP300/H3K27ac occupancy at 8C enhancers. Our findings reveal a conserved mechanism in which humans and mice employ species-specific long interspersed nuclear element-1 subfamilies with m6A to regulate LTR activity, underscoring the crucial role of transposons in RNA-chromatin crosstalk during cell fate transitions.

Keywords:  RNA m(6)A methylation; human embryonic stem cells; pluripotency; totipotency; transposable elements

DOI:  https://doi.org/10.1016/j.stem.2025.10.003
Nat Cell Biol. 2025 Oct 31.

TDP-43 skein-like inclusions are formed by BAG3- and HSP70-guided co-aggregation with actin-binding proteins.

Shan Lu, Sitao Zhang, Spencer Oung, Jolene K Diedrich, Peng Han, Olatz Arnold-Garcia, Takuya Ohkubo, Olubankole Aladesuyi Arogundade, Sonia Vazquez-Sanchez, Ke Zhang, John Ravits, John R Yates Iii, Don W Cleveland.

In multiple neurodegenerative diseases, the RNA-binding protein TDP-43 forms cytoplasmic aggregates of distinct morphologies, including skein-like, small rounded granular and large spherical inclusions. Here, whereas the N-terminal self-oligomerization domain regulates TDP-43 demixing into cytoplasmic droplets, inhibition of N-terminal self-oligomerization domain-mediated oligomerization is shown to promote the formation of skein-like inclusions. Utilizing proximity labelling-mass spectrometry, cellular stresses are shown to induce TDP-43 association with actin-binding proteins that include filamins and α-actinin. Small interfering RNA-mediated reduction of filamin in Drosophila ameliorates cell loss from cytoplasmic TDP-43, consistent with the filamin-TDP-43 interaction enhancing cytotoxicity. TDP-43's association with actin-binding proteins is mediated by BAG3, a HSP70 family nucleotide exchange factor that regulates the proteostasis of actin-binding proteins. BAG2, another HSP70 nucleotide exchange factor, facilitates the formation of small, rounded TDP-43 inclusions. We demonstrate that both TDP-43 self-oligomerization and its binding partners, including HSP70 and cochaperones BAG2 and BAG3, drive the formation of the different types of TDP-43 inclusion.

DOI: https://doi.org/10.1038/s41556-025-01789-5
Nat Commun. 2025 Oct 28. 16(1): 9502

Pre-established ATF4 occupancy and chromatin organization instruct selective transcription activation during integrated stress response.

Peipei Jiang, Qian Bian.

Cells rapidly and extensively remodel their transcriptome in response to stress to restore homeostasis, but the underlying mechanisms are not fully understood. Here, we characterize the dynamic changes in transcriptome, epigenetics, and 3D genome organization during the integrated stress response (ISR). ISR induction triggers widespread transcriptional changes within 6 h, coinciding with increased binding of ATF4, a key transcriptional effector. Notably, ATF4 binds to hundreds of genes even under non-stress conditions, priming them for stronger activation upon stress. The transcriptional changes at ATF4-bound sites during ISR do not rely on increased H3K27 acetylation, chromatin accessibility, or rewired enhancer-promoter looping. Instead, ATF4-mediated gene activation is linked to the redistribution of CEBPγ from non-ATF4 sites to a subset of ATF4-bound regions, likely by forming an ATF4/CEBPγ heterodimer. CEBPγ preferentially targets the sites pre-occupied by ATF4, as well as genomic regions exhibiting a unique higher-order chromatin structure signature. Thus, the transcriptional responses during ISR are largely pre-wired by intrinsic chromatin properties. These findings provide critical insights into transcriptional remodeling during ISR with broader implications for other stress responses.

DOI: https://doi.org/10.1038/s41467-025-64577-7
Science. 2025 Oct 30. 390(6772): eadu1351

Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy.

Guanlan Dong, Chanthia C Ma, Shulin Mao, Katherine Sun-Mi Brown, Samuel M Naik, Gannon A McDonough, Samadhi P Wijethunga, Junho Kim, Samantha L Kirkham, Diane D Shao, Jonathan D Cherry, Madeline Uretsky, Elizabeth Spurlock, Ann C McKee, August Yue Huang, Michael B Miller, Eunjung Alice Lee, Christopher A Walsh.

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease linked to exposure to repetitive head impacts (RHI), yet little is known about its pathogenesis. Applying two single-cell whole-genome sequencing methods to hundreds of neurons from prefrontal cortex of 15 individuals with CTE and 4 with RHI without CTE, we revealed increased somatic single-nucleotide variants in CTE, exhibiting a pattern previously reported in Alzheimer's disease (AD). Furthermore, we discovered high burdens of somatic small insertions and deletions in a subset of CTE individuals, resembling a known pattern, ID4, also found in AD. Our results suggest that neurons in CTE experience stereotyped mutational processes shared with AD; the absence of similar changes in RHI neurons without CTE suggests that CTE involves mechanisms beyond RHI alone.

DOI: https://doi.org/10.1126/science.adu1351
J Cell Biol. 2026 Jan 05. pii: e202504178. [Epub ahead of print]225(1):

Close-up of vesicular ER exit sites by volume electron imaging using FIB-SEM.

Athul Nair, Akhil Nair, Patrick Stock, Arkash Jain, Elliott Somerville, Anwesha Sanyal, Jose Inacio Costa-Filho, Tom Kirchhausen.

The architecture of ER exit sites (ERES), the first sites of membrane remodeling in protein secretion, remains unclear, with descriptions ranging from vesicular clusters to extended tubular structures. We addressed this divergence by visualizing ERES in cells not overexpressing secretory cargo using large-scale volume-focused ion beam scanning EM (FIB-SEM) after high-pressure freeze substitution. Automated segmentation in EM (ASEM), our 3D U-Net pipeline trained with sparsely labeled 50-70-nm COPI vesicles near the Golgi, accurately detected them in HeLa, SVG-A, and iPSC-derived neurons. Using the same model, we identified abundant clusters of ∼5-40 larger vesicles (∼65-85 nm) confined within ∼250 nm3 regions adjacent to flattened ER domains, consistent with vesicular ERES. Similar assemblies also appeared alongside tubular networks and varicosities extending from enlarged ER domains, previously described as the sole ERES in HeLa cells. These findings reveal that vesicular ERES are widespread and morphologically diverse, resolving longstanding contradictions in early secretory pathway organization.

DOI: https://doi.org/10.1083/jcb.202504178
Nat Biotechnol. 2025 Oct 28.

A single-chain derivative of an integrin-activating antibody potentiates organoid growth in Matrigel and collagen hydrogels.

Wim B M de Lau, Joost J A P M Wijnakker, Gijs J F van Son, Daniel Krueger, Daisong Wang, Matthijs S Abendroth, Robin Schreurs, Claudia Y Janda, Fenna L H van Rijt, Benjamin J P Chalopin, Emma Bokobza, Johan H van Es, Timothy A Springer, Arnoud Sonnenberg, Hans Clevers.

Current methods of culturing human epithelial organoids from adult stem cells may not be compatible with clinical applications as they rely on xenogeneic, chemically undefined or non-standardized components such as the basement membrane extract Matrigel. Matrigel provides a source of extracellular matrix molecules, including laminins and collagen IV, which interact with β1 integrins expressed on organoid cells. Here we describe a single-chain (sc) version of antibody TS2/16 that allosterically activates integrin β1 function in organoids. The addition of monomeric scTS2/16 to organoid medium results in up to a fivefold increase in the yield of all gastrointestinal organoids grown in Matrigel. Moreover, scTS2/16 supports a six- to sevenfold increase in the yield of these organoids when cultured in collagen I hydrogels, both in 3D and 2D. Collagen I is well defined, available in clinical-grade formulations and, when combined with scTS2/16, may support the clinical application of epithelial organoids derived from gastrointestinal tissues and other epithelial sources.

DOI: https://doi.org/10.1038/s41587-025-02874-8
Nat Rev Mol Cell Biol. 2025 Oct 27.

Mechanisms and regulation of the Hsp70 chaperone network.

Anne Wentink, Rina Rosenzweig, Harm Kampinga, Bernd Bukau.

The 70-kDa heat shock protein (Hsp70) chaperone is essential to maintain cellular protein homeostasis, facilitating the folding, assembly, membrane translocation and quality control of proteins. Hsp70s achieve their functions through 'selective promiscuity', interacting with a wide range of substrate proteins while minimizing undesired interactions. J-domain proteins (JDPs) and nucleotide exchange factors (NEFs) are key to substrate recognition, remodelling and release from chaperone complexes. JDPs either target Hsp70s to specific subcellular sites where substrates reside (recruiters) or bind substrates directly by using highly specific (specialists) or multiple, versatile (generalists) binding sites. Through diverse substrate-binding modes and regulatory mechanisms, the 50 human JDPs confer remarkable client specificity to Hsp70s, a function that is comparable to that achieved by close to 600 E3 ubiquitin ligases in targeting proteins for degradation. Moreover, JDPs, together with NEFs, dictate the fate of Hsp70 clients by directing them to distinct protein quality control pathways, resulting in their folding or degradation. These recent mechanistic insights into Hsp70 regulation not only highlight the versatility and complexity of the Hsp70 network but also offer new avenues for more specific interventions in ageing-related and other protein folding diseases.

DOI: https://doi.org/10.1038/s41580-025-00890-9
J Cell Biol. 2025 Dec 01. pii: e202411107. [Epub ahead of print]224(12):

PCMD-1 stabilizes the PCM scaffold and facilitates centriole separation.

Alina Schreiner, Astrid Heim, Luisa Pletschacher, Lisa-Marie Alznauer, Serena Schwenkert, Friederike Wolff, Esther Zanin, Tamara Mikeladze-Dvali.

Centrosomes are highly dynamic organelles, and maintaining their stability is crucial for spindle pole integrity and bipolar spindle formation. Centrosomes consist of a pair of centrioles surrounded by the PCM. In Caenorhabditis elegans, interactions between the scaffold protein SPD-5 and kinase PLK-1 are essential for PCM formation. However, how PCM stability is established and maintained remains unclear. We address this by analyzing the function of PCMD-1, a protein mainly localizing to centrioles. We show that CDK-1 primes PCMD-1 for PLK-1 phosphorylation. Mutations in PLK-1 docking sites abolish PCMD-1 phosphorylation and SPD-5 binding in vitro and destabilize the PCM scaffold in vivo. As a result, microtubule-pulling forces cannot be relayed to centrioles, delaying their separation. Our findings reveal that PCMD-1 is critical for PCM stability and timely centriole separation during PCM disassembly. We propose that PCMD-1 initiates scaffold assembly by biasing the PCM core toward intrinsic order, acting as a seed that propagates throughout the scaffold to ensure structural integrity.

DOI: https://doi.org/10.1083/jcb.202411107