bims-ginsta Biomed News
on Genome instability
Issue of 2025–03–30
thirty-one papers selected by
Jinrong Hu, National University of Singapore
  1. Single-cell spatial transcriptomic atlas of the whole mouse brain.
  2. Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration.
  3. Lineage contribution of the mesendoderm progenitors in the gastrulating mouse embryo.
  4. Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2.
  5. Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes.
  6. Orchestration of pluripotent stem cell genome reactivation during mitotic exit.
  7. Foxk1 and Foxk2 promote cardiomyocyte proliferation and heart regeneration.
  8. Proteostasis and lysosomal repair deficits in transdifferentiated neurons of Alzheimer's disease.
  9. Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis.
  10. Macrophages harness hepatocyte glutamate to boost liver regeneration.
  11. Noncanonical phagocytosis-like SEAL establishes mammalian fertilization.
  12. The emergence of human primordial germ cell-like cells in stem cell-derived gastruloids.
  13. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq.
  14. Epithelial biology: Holding the corners together.
  15. Vagal pathway activation links chronic stress to decline in intestinal stem cell function.
  16. Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation.
  17. Ceramide mediates cell-to-cell ER stress transmission by modulating membrane fluidity.
  18. Dynamic molecular atlas of cardiac fibrosis at single-cell resolution shows CD248 in cardiac fibroblasts orchestrates interactions with immune cells.
  19. Conservation of dichromatin organization along regional centromeres.
  20. Simultaneous single-cell DNA damage profiling and RNA sequencing by Paired-Damage-seq.
  21. High-dimensional imaging using combinatorial channel multiplexing and deep learning.
  22. Optogenetic control of Nodal signaling patterns.
  23. Enteric neuronal Piezo1 maintains mechanical and immunological homeostasis by sensing force.
  24. Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3.
  25. Single-nucleus multi-omics implicates androgen receptor signaling in cardiomyocytes and NR4A1 regulation in fibroblasts during atrial fibrillation.
  26. Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.
  27. Inward transport of organelles drives outward migration of the spindle during C. elegans meiosis.
  28. Oxidation of retromer complex controls mitochondrial translation.
  29. Plasticity of the mammalian integrated stress response.
  30. The activation of INF2 by Piezo1/Ca2+ is required for mesenchymal-to-amoeboid transition in confined environments.
  31. BRCA2 prevents PARPi-mediated PARP1 retention to protect RAD51 filaments.
  1. Neuron. 2025 Mar 20. pii: S0896-6273(25)00133-3. [Epub ahead of print]
    Single-cell spatial transcriptomic atlas of the whole mouse brain.
    Lei Han, Zhen Liu, Zehua Jing, Yuxuan Liu, Yujie Peng, Huizhong Chang, Junjie Lei, Kexin Wang, Yuanfang Xu, Wei Liu, Zihan Wu, Qian Li, Xiaoxue Shi, Mingyuan Zheng, He Wang, Juan Deng, Yanqing Zhong, Hailin Pan, Junkai Lin, Ruiyi Zhang, Yu Chen, Jinhua Wu, Mingrui Xu, Biyu Ren, Mengnan Cheng, Qian Yu, Xinxiang Song, Yanbing Lu, Yuanchun Tang, Nini Yuan, Suhong Sun, Yingjie An, Wenqun Ding, Xing Sun, Yanrong Wei, Shuzhen Zhang, Yannong Dou, Yun Zhao, Luyao Han, Qianhua Zhu, Junfeng Xu, Shiwen Wang, Dan Wang, Yinqi Bai, Yikai Liang, Yuan Liu, Mengni Chen, Chun Xie, Binshi Bo, Mei Li, Xinyan Zhang, Wang Ting, Zhenhua Chen, Jiao Fang, Shuting Li, Yujia Jiang, Xing Tan, Guolong Zuo, Yue Xie, Huanhuan Li, Quyuan Tao, Yan Li, Jianfeng Liu, Yuyang Liu, Mingkun Hao, Jingjing Wang, Huiying Wen, Jiabing Liu, Yizhen Yan, Hui Zhang, Yifan Sheng, Shui Yu, Xiaoyan Liao, Xuyin Jiang, Guangling Wang, Huanlin Liu, Congcong Wang, Ning Feng, Xin Liu, Kailong Ma, Xiangjie Xu, Tianyue Han, Huateng Cao, Huiwen Zheng, Yadong Chen, Haorong Lu, Zixian Yu, Jinsong Zhang, Bo Wang, Zhifeng Wang, Qing Xie, Shanshan Pan, Chuanyu Liu, Chan Xu, Luman Cui, Yuxiang Li, Shiping Liu, Sha Liao, Ao Chen, Qing-Feng Wu, Jian Wang, Zhiyong Liu, Yidi Sun, Jan Mulder, Huanming Yang, Xiaofei Wang, Chao Li, Jianhua Yao, Xun Xu, Longqi Liu, Zhiming Shen, Wu Wei, Yan-Gang Sun.
      A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.
    Keywords:  Stereo-seq; development; mouse brain; non-coding gene; parcellation; transcriptome
    DOI:  https://doi.org/10.1016/j.neuron.2025.02.015
  2. Nat Commun. 2025 Mar 27. 16(1): 3012
    Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration.
    Yi Xiao, Hao Zhang, Xu Liu, Pengfei Xu, Heng Du, Jiawan Wang, Jianghua Shen, Yujing Li, Yuhan Wang, Chuting He, Haiping Feng, Jingfang Liu, Yanan Zhou, Siqi Liu, Zeyu Gao, Jingyi Zang, Jinmiao Bi, Tie-Shan Tang, Qi Gu, Tuo Wei, Jun Wang, Moshi Song.
      Heart injury has been characterized by the irreversible loss of cardiomyocytes comprising the contractile tissues of the heart and thus strategies enabling adult cardiomyocyte proliferation are highly desired for treating various heart diseases. Here, we test the ability of human induced pluripotent stem cell-derived primitive macrophages (hiPMs) and their conditioned medium (hiPM-cm) to promote human cardiomyocyte proliferation and enhance cardiac regeneration in adult mice. We find that hiPMs promote human cardiomyocyte proliferation, which is recapitulated by hiPM-cm through the activation of multiple pro-proliferative pathways, and a secreted proteome analysis identifies five proteins participating in this activation. Subsequent in vivo experiments show that hiPM-cm promotes adult cardiomyocyte proliferation in mice. Lastly, hiPM-cm enhances cardiac regeneration and improves contractile function in injured adult mouse hearts. Together, our study demonstrates the efficacy of using hiPM-cm in promoting adult cardiomyocyte proliferation and cardiac regeneration to serve as an innovative treatment for heart disease.
    DOI:  https://doi.org/10.1038/s41467-025-58301-8
  3. Dev Cell. 2025 Mar 18. pii: S1534-5807(25)00120-0. [Epub ahead of print]
    Lineage contribution of the mesendoderm progenitors in the gastrulating mouse embryo.
    V Pragathi Masamsetti, Nazmus Salehin, Hani Jieun Kim, Nicole Santucci, Megan Weatherstone, Riley McMahon, Lee L Marshall, Hilary Knowles, Jane Sun, Josh B Studdert, Nader Aryamanesh, Ran Wang, Naihe Jing, Pengyi Yang, Pierre Osteil, Patrick P L Tam.
      A population of putative mesendoderm progenitors that can contribute cellular descendants to both mesoderm and endoderm lineages is identified in the gastrulating mouse embryo. These progenitor cells are localized to the posterior epiblast, primitive streak, and nascent mesoderm of mid-streak- (E7.0) to late-streak-stage (E7.5) embryos. Lineage tracing in vivo identified that putative mesendoderm progenitors contribute descendants to the definitive endoderm and the axial mesendoderm of E7.75 embryos and to the endoderm of the foregut and hindgut of the E8.5-8.75 embryos. Differentiation of mouse epiblast stem cells identified that the choice between endoderm and mesoderm cell fates depends on the timing of Mixl1 activation upon exit from pluripotency. The knowledge gained on the spatiotemporal distribution of mesendoderm progenitors and the molecular drivers underpinning the divergence of cell lineages in these progenitors enriches our mechanistic understanding of the allocation of the tissue progenitors to germ layer derivatives in early development.
    Keywords:  endoderm; endoderm differentiation; gastrulation; lineage differentiation; mesendoderm; micropattern; mouse embryos; mouse epiblast stem cells; single cell RNA sequencing analyis
    DOI:  https://doi.org/10.1016/j.devcel.2025.02.015
  4. Science. 2025 Mar 28. 387(6741): eadp4319
    Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2.
    Mengyao Li, Zhenhuan Jiang, Xueqiang Xu, Xinglong Wu, Yun Liu, Kexuan Chen, Yuhan Liao, Wen Li, Xiao Wang, Yuqing Guo, Bo Zhang, Lu Wen, Kehkooi Kee, Fuchou Tang.
      In mammals, fertilized eggs undergo genome-wide epigenetic reprogramming to generate the organism. However, our understanding of epigenetic dynamics during preimplantation development at single-cell resolution remains incomplete. Here, we developed scNanoATAC-seq2, a single-cell assay for transposase-accessible chromatin using long-read sequencing for scarce samples. We present a detailed chromatin accessibility landscape of mouse preimplantation development, revealing distinct chromatin signatures in the epiblast, primitive endoderm, and trophectoderm during lineage segregation. Differences between zygotes and two-cell embryos highlight reprogramming in chromatin accessibility during the maternal-to-zygotic transition. Single-cell long-read sequencing enables in-depth analysis of chromatin accessibility in noncanonical imprinting, imprinted X chromosome inactivation, and low-mappability genomic regions, such as repetitive elements and paralogs. Our data provide insights into chromatin dynamics during mammalian preimplantation development and lineage differentiation.
    DOI:  https://doi.org/10.1126/science.adp4319
  5. Cell. 2025 Mar 19. pii: S0092-8674(25)00255-7. [Epub ahead of print]
    Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes.
    Kai Sandvold Beckwith, Andreas Brunner, Natalia Rosalia Morero, Ralf Jungmann, Jan Ellenberg.
      How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is a long-standing open question in biology. Here, we use nanoscale DNA tracing in single dividing cells to directly visualize how the 3D fold of genomic DNA changes during mitosis at scales from single loops to entire chromosomes. Our structural analysis reveals a characteristic genome scaling minimum of 6-8 megabases in mitosis. Combined with data-driven modeling and molecular perturbations, we can show that very large and strongly overlapping loops formed by condensins are the fundamental structuring principle of mitotic chromosomes. These loops compact chromosomes locally and globally to the limit set by chromatin self-repulsion. The characteristic length, density, and increasingly overlapping structure of mitotic loops we observe in 3D fully explain how the rod-shaped mitotic chromosome structure emerges by self-organization during cell division.
    Keywords:  cell division; chromatin tracing; chromosome compaction; condensins; genome organization; loop extrusion; mitosis
    DOI:  https://doi.org/10.1016/j.cell.2025.02.028
  6. Cell Rep. 2025 Mar 27. pii: S2211-1247(25)00257-8. [Epub ahead of print]44(4): 115486
    Orchestration of pluripotent stem cell genome reactivation during mitotic exit.
    Silja Placzek, Ludovica Vanzan, Cédric Deluz, David M Suter.
      Cell identity maintenance faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through division and faithfully re-initiate gene expression during mitotic exit is unclear. Here, we develop a novel reporter system enabling cell cycle synchronization-free separation of pluripotent stem cells in temporal bins of <30 min during mitotic exit. This allows us to quantify genome-wide reactivation of transcription, sequential changes in chromatin accessibility and transcription factor footprints, and re-binding of the pluripotency transcription factors OCT4, SOX2, and NANOG (OSN). We find that transcriptional activity progressively ramps up after mitosis and that OSN rapidly reoccupy the genome during the anaphase-telophase transition. We also demonstrate transcription factor-specific, dynamic relocation patterns and a hierarchical reorganization of the OSN binding landscape governed by OCT4 and SOX2. Our study sheds light on the dynamic orchestration of transcriptional reactivation after mitosis.
    Keywords:  ATAC-seq; CP: Cell biology; CP: Stem cell research; ChIP-seq; NANOG; OCT4; RNA-seq; SOX2; chromatin; mitosis; pluripotent stem cells; transcription factors
    DOI:  https://doi.org/10.1016/j.celrep.2025.115486
  7. Nat Commun. 2025 Mar 24. 16(1): 2877
    Foxk1 and Foxk2 promote cardiomyocyte proliferation and heart regeneration.
    Dongcheng Cai, Chungeng Liu, Haotong Li, Chiyin Wang, Lina Bai, Jie Feng, Miaoqing Hu, Hao Wang, Shen Song, Yifan Xie, Ziwei Chen, Jiajun Zhong, Hong Lian, Zhiwei Yang, Yuhui Zhang, Yu Nie.
      Promoting endogenous cardiomyocyte proliferation is a promising strategy for cardiac repair. Identifying key factors that regulate cardiomyocyte proliferation can advance the development of novel therapies for heart regeneration. Here, we identify Foxk1 and Foxk2 as key regulators of cardiomyocyte proliferation, whose expression declines during postnatal heart development. Cardiomyocyte-specific knockout of Foxk1 or Foxk2 impairs neonatal heart regeneration after myocardial infarction (MI) injury. AAV9-mediated Foxk1 or Foxk2 overexpression extends the postnatal cardiomyocyte proliferative window and enhances cardiac repair in adult mice after MI. Mechanistically, Foxk1 and Foxk2 drive cardiomyocyte cell cycle progression by directly activating CCNB1 and CDK1 expression, forming the CCNB1/CDK1 complex that facilitates G2/M transition. Moreover, Foxk1 and Foxk2 promote cardiomyocyte proliferation by upregulating HIF1α expression, which enhances glycolysis and the pentose phosphate pathway (PPP), which further favors cardiomyocyte proliferation. These findings establish Foxk1 and Foxk2 as promising therapeutic targets for cardiac injury.
    DOI:  https://doi.org/10.1038/s41467-025-57996-z
  8. Nat Cell Biol. 2025 Mar 26.
    Proteostasis and lysosomal repair deficits in transdifferentiated neurons of Alzheimer's disease.
    Ching-Chieh Chou, Ryan Vest, Miguel A Prado, Joshua Wilson-Grady, Joao A Paulo, Yohei Shibuya, Patricia Moran-Losada, Ting-Ting Lee, Jian Luo, Steven P Gygi, Jeffery W Kelly, Daniel Finley, Marius Wernig, Tony Wyss-Coray, Judith Frydman.
      Ageing is the most prominent risk factor for Alzheimer's disease (AD). However, the cellular mechanisms linking neuronal proteostasis decline to the characteristic aberrant protein deposits in the brains of patients with AD remain elusive. Here we develop transdifferentiated neurons (tNeurons) from human dermal fibroblasts as a neuronal model that retains ageing hallmarks and exhibits AD-linked vulnerabilities. Remarkably, AD tNeurons accumulate proteotoxic deposits, including phospho-tau and amyloid β, resembling those in APP mouse brains and the brains of patients with AD. Quantitative tNeuron proteomics identify ageing- and AD-linked deficits in proteostasis and organelle homeostasis, most notably in endosome-lysosomal components. Lysosomal deficits in aged tNeurons, including constitutive lysosomal damage and ESCRT-mediated lysosomal repair defects, are exacerbated in AD tNeurons and linked to inflammatory cytokine secretion and cell death. Providing support for the centrality of lysosomal deficits in AD, compounds ameliorating lysosomal function reduce amyloid β deposits and cytokine secretion. Thus, the tNeuron model system reveals impaired lysosomal homeostasis as an early event of ageing and AD.
    DOI:  https://doi.org/10.1038/s41556-025-01623-y
  9. Nat Commun. 2025 Mar 27. 16(1): 3007
    Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis.
    Francesco Cardamone, Annamaria Piva, Eva Löser, Bastian Eichenberger, Mari Carmen Romero-Mulero, Fides Zenk, Emily J Shields, Nina Cabezas-Wallscheid, Roberto Bonasio, Guido Tiana, Yinxiu Zhan, Nicola Iovino.
      The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneity of the blastoderm embryo poses a challenge for gaining mechanistic insights. Using 10× Multiome, we simultaneously analyzed the in vivo epigenomic and transcriptomic states of wild-type, E(z)-, and CBP-depleted embryos during zygotic genome activation at single-cell resolution. We found that pre-zygotic H3K27me3 safeguards tissue-specific gene expression by modulating cis-regulatory elements. Furthermore, we demonstrate that CBP is essential for cell fate specification functioning as a transcriptional activator by stabilizing transcriptional factors binding at key developmental genes. Surprisingly, while CBP depletion leads to transcriptional arrest, chromatin accessibility continues to progress independently through the retention of stalled RNA Polymerase II. Our study reveals fundamental principles of chromatin-mediated gene regulation essential for establishing and maintaining cellular identities during early embryogenesis.
    DOI:  https://doi.org/10.1038/s41467-025-57719-4
  10. Nature. 2025 Mar 26.
    Macrophages harness hepatocyte glutamate to boost liver regeneration.
    María Del Mar Rigual, Mariana Angulo-Aguado, Sladjana Zagorac, Ruth Álvarez-Díaz, Marta Benítez-Mondéjar, Fengming Yi, Carlos Martínez-Garay, Karla Santos-de-Frutos, Eunjeong Kim, Ramón Campos-Olivas, Nabil Djouder.
      Liver regeneration after hepatectomy follows accurate coordination with the body's specific requirements1-3. However, the molecular mechanisms, factors and particular hepatocyte population influencing its efficiency remain unclear. Here we report on a unique regeneration mechanism involving unconventional RPB5 prefoldin interactor 1 (URI1), which exclusively colocalizes with, binds to and activates glutamine synthase (GS) in pericentral hepatocytes. Genetic GS or URI1 depletion in mouse pericentral hepatocytes increases circulating glutamate levels, accelerating liver regeneration after two-third hepatectomy. Conversely, mouse hepatocytic URI1 overexpression hinders liver restoration, which can be reversed by elevating glutamate through supplementation or genetic GS depletion. Glutamate metabolically reprograms bone-marrow-derived macrophages, stabilizing HIF1α, which transcriptionally activates WNT3 to promote YAP1-dependent hepatocyte proliferation, boosting liver regeneration. GS regulation by URI1 is a mechanism that maintains optimal glutamate levels, probably to spatiotemporally fine-tune liver growth in accordance with the body's homeostasis and nutrient supply. Accordingly, in acute and chronic injury models, including in cirrhotic mice with low glutamate levels and in early mortality after liver resection, as well as in mice undergoing 90% hepatectomy, glutamate addition enhances hepatocyte proliferation and survival. Furthermore, URI1 and GS expression co-localize in human hepatocytes and correlate with WNT3 in immune cells across liver disease stages. Glutamate supplementation may therefore support liver regeneration, benefiting patients awaiting transplants or recovering from hepatectomy.
    DOI:  https://doi.org/10.1038/s41586-025-08778-6
  11. Cell Rep. 2025 Mar 25. pii: S2211-1247(25)00234-7. [Epub ahead of print]44(4): 115463
    Noncanonical phagocytosis-like SEAL establishes mammalian fertilization.
    Naokazu Inoue, Takako Saito, Ikuo Wada.
      In many forms of sexual reproduction, only the most robust spermatozoa, which overcome multiple physiological challenges, reach the oocyte. However, the exact mechanisms of gamete recognition and fusion are unknown. In the present study, we demonstrated that with the onset of gamete recognition, oocyte microvilli form lamellipodium-like structures, activate actin polymerization, and subsequently engulf spermatozoa to initiate gamete fusion. Gamete fusion occurred via a phagocytosis-like process we termed "sperm engulfment activated by IZUMO1-JUNO linkage and gamete fusion-related factors" (SEAL). Gamete adhesion was strictly regulated by binding of sperm IZUMO1 to oocyte JUNO, while SEAL was primarily mediated by sperm DCST1/2, SPACA6, TMEM95, FIMP, and TMEM81, the essential factors for gamete fusion. Interestingly, JUNO was almost depleted from oocyte surfaces in the region where SEAL enveloped spermatozoa by microvilli without actin polymerization. SEAL formation was recapitulated using JUNO-expressing K562 lymphocytic cells rather than oocytes. Together, these findings suggest that dynamic rearrangement of membrane components facilitates SEAL prior to successful fertilization.
    Keywords:  CP: Cell biology; CP: Developmental biology; IZUMO1; JUNO; SEAL; fertilization; gamete fusion; microvilli; oocyte; oocyte tentacle; phagocytosis; spermatozoon
    DOI:  https://doi.org/10.1016/j.celrep.2025.115463
  12. Sci Adv. 2025 Mar 28. 11(13): eado1350
    The emergence of human primordial germ cell-like cells in stem cell-derived gastruloids.
    Jitesh Neupane, Gabriele Lubatti, Theresa Gross-Thebing, Mayra Luisa Ruiz Tejada Segura, Richard Butler, Sargon Gross-Thebing, Sabine Dietmann, Antonio Scialdone, M Azim Surani.
      Most advances in early human postimplantation development depend on animal studies and stem cell-based embryo models. Here, we present self-organized three-dimensional human gastruloids (hGs) derived from embryonic stem cells. The transcriptome profile of day 3 hGs aligned with Carnegie stage 7 human gastrula, with cell types and differentiation trajectories consistent with human gastrulation. Notably, we observed the emergence of nascent primordial germ cell-like cells (PGCLCs), but without exogenous bone morphogenetic protein (BMP) signaling, which is essential for the PGCLC fate. A mutation in the ISL1 gene affects amnion-like cells and leads to a loss of PGCLCs; the addition of exogenous BMP2 rescues the PGCLC fate, indicating that the amnion may provide endogenous BMP signaling. Our model of early human embryogenesis will enable further exploration of the germ line and other early human lineages.
    DOI:  https://doi.org/10.1126/sciadv.ado1350
  13. Nat Protoc. 2025 Mar 21.
    Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq.
    Haikuo Li, Shuozhen Bao, Negin Farzad, Xiaoyu Qin, Anthony A Fung, Di Zhang, Zhiliang Bai, Bo Tao, Rong Fan.
      The epigenome of a cell is tightly correlated with gene transcription, which controls cell identity and diverse biological activities. Recent advances in spatial technologies have improved our understanding of tissue heterogeneity by analyzing transcriptomics or epigenomics with spatial information preserved, but have been mainly restricted to one molecular layer at a time. Here we present procedures for two spatially resolved sequencing methods, spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq, that co-profile transcriptome and epigenome genome wide. In both methods, transcriptomic readouts are generated through tissue fixation, permeabilization and in situ reverse transcription. In spatial-ATAC-RNA-seq, Tn5 transposase is used to probe accessible chromatin, and in spatial-CUT&Tag-RNA-seq, the tissue is incubated with primary antibodies that target histone modifications, followed by Protein A-fused Tn5-induced tagmentation. Both methods leverage a microfluidic device that delivers two sets of oligonucleotide barcodes to generate a two-dimensional mosaic of tissue pixels at near single-cell resolution. A spatial-ATAC-RNA-seq or spatial-CUT&Tag-RNA-seq library can be generated in 3-5 d, allowing researchers to simultaneously investigate the transcriptomic landscape and epigenomic landscape of an intact tissue section. This protocol is an extension of our previous spatially resolved epigenome sequencing protocol and provides opportunities in multimodal profiling.
    DOI:  https://doi.org/10.1038/s41596-025-01145-9
  14. Curr Biol. 2025 Mar 24. pii: S0960-9822(25)00186-1. [Epub ahead of print]35(6): R232-R235
    Epithelial biology: Holding the corners together.
    Tara M Finegan.
      A new study reveals that the Drosophila follicular epithelium opens its permeability barrier to allow passage of yolk to the oocyte by relaxing, not actively pulling open, cell vertices. This work reshapes our understanding of the mechanical regulation of epithelial permeability.
    DOI:  https://doi.org/10.1016/j.cub.2025.02.023
  15. Cell Stem Cell. 2025 Mar 20. pii: S1934-5909(25)00084-0. [Epub ahead of print]
    Vagal pathway activation links chronic stress to decline in intestinal stem cell function.
    Guoying Zhang, Yannan Lian, Qingguo Li, Shudi Zhou, Lili Zhang, Liting Chen, Junzhe Tang, Hailong Liu, Ni Li, Qiang Pan, Yongqiang Gu, Naiheng Lin, Hanling Wang, Xuege Wang, Jiacheng Guo, Wei Zhang, Zige Jin, Beitao Xu, Xiao Su, Moubin Lin, Qi Han, Jun Qin.
      Chronic stress adversely affects intestinal health, but the specific neural pathways linking the brain to intestinal tissue are not fully understood. Here, we show that chronic stress-induced activation of the central amygdala-dorsal motor nucleus of the vagus (CeA-DMV) pathway accelerates premature aging and impairs the stemness of intestinal stem cells (ISCs). This pathway influences ISC function independently of the microbiota, the hypothalamic-pituitary-adrenal (HPA) axis, the immune response, and the sympathetic nervous system (SNS). Under chronic stress, DMV-mediated vagal activation prompts cholinergic enteric neurons to release acetylcholine (ACh), which engages ISCs via the M3 muscarinic acetylcholine receptor (CHRM3). This interaction activates the p38 mitogen-activated protein kinase (MAPK) pathway, triggering growth arrest and mitochondrial fragmentation, thereby accelerating an aging-like decline in ISCs. Together, our findings provide insights into an alternative neural mechanism that links stress to intestinal dysfunction. Strategies targeting the DMV-associated vagal pathway represent potential therapeutic approaches for stress-induced intestinal diseases.
    Keywords:  aging; chronic stress; intestinal stem cells; p38; the brain-gut axis; vagus
    DOI:  https://doi.org/10.1016/j.stem.2025.02.016
  16. Cell Stem Cell. 2025 Mar 20. pii: S1934-5909(25)00088-8. [Epub ahead of print]
    Glucose modulates IRF6 transcription factor dimerization to enable epidermal differentiation.
    Vanessa Lopez-Pajares, Aparna Bhaduri, Yang Zhao, Gayatri Gowrishankar, Laura K H Donohue, Margaret G Guo, Zurab Siprashvili, Weili Miao, Duy T Nguyen, Xue Yang, Albert M Li, Alan Sheng-Hwa Tung, Ronald L Shanderson, Marten C G Winge, Lindsey M Meservey, Suhas Srinivasan, Robin M Meyers, Angela Guerrero, Andrew L Ji, Omar S Garcia, Shiying Tao, Sanjiv S Gambhir, Jonathan Z Long, Jiangbin Ye, Paul A Khavari.
      Non-energetic roles for glucose are largely unclear, as is the interplay between transcription factors (TFs) and ubiquitous biomolecules. Metabolomic analyses uncovered elevation of intracellular glucose during differentiation of diverse cell types. Human and mouse tissue engineered with glucose sensors detected a glucose gradient that peaked in the outermost differentiated layers of the epidermis. Free glucose accumulation was essential for epidermal differentiation and required the SGLT1 glucose transporter. Glucose affinity chromatography uncovered glucose binding to diverse regulatory proteins, including the IRF6 TF. Direct glucose binding enabled IRF6 dimerization, DNA binding, genomic localization, and induction of IRF6 target genes, including essential pro-differentiation TFs GRHL1, GRHL3, HOPX, and PRDM1. These data identify a role for glucose as a gradient morphogen that modulates protein multimerization in cellular differentiation.
    Keywords:  IRF6; differentiation; glucose
    DOI:  https://doi.org/10.1016/j.stem.2025.02.017
  17. J Cell Biol. 2025 May 05. pii: e202405060. [Epub ahead of print]224(5):
    Ceramide mediates cell-to-cell ER stress transmission by modulating membrane fluidity.
    Yazhen Huo, Xinlu Liu, Chen Lu, Tao Li, Zaili Yang, Fenfen Xu, Si Chen, Kailin Yin, Likun Wang.
      Under endoplasmic reticulum (ER) stress (ERS), cells initiate the unfolded protein response (UPR) to maintain ER homeostasis. Recent studies revealed ERS transmission between cells and tissues, by activating the cell-nonautonomous UPR in cells that do not experience ERS directly. Here, we report that ERS triggers a rapid release of ceramide independent of the UPR, but requiring the acid sphingomyelinase activity. Carried by lipoproteins, ceramide is delivered to receiving cells to induce the UPR and regulate cell functions at multiple aspects, including lipid accumulation, cell death, and cytokine production. Mechanistically, extracellular ceramide stimulates ceramide synthesis at the transcription level in receiving cells, leading to ceramide accumulation in the ER so as to reduce membrane fluidity to disrupt ER calcium homeostasis, thus activating the UPR. Sphingomyelin counterbalanced the effect of ceramide. UPR induction is the frontline response to protect cells from ceramide insult. Our study suggests ceramide-mediated ERS transmission as a universal cell-cell communication model regulating a wide range of physiological events.
    DOI:  https://doi.org/10.1083/jcb.202405060
  18. Nat Cardiovasc Res. 2025 Mar 27.
    Dynamic molecular atlas of cardiac fibrosis at single-cell resolution shows CD248 in cardiac fibroblasts orchestrates interactions with immune cells.
    Guohua Li, Cheng Ni, Jiacheng Wang, Feimu Zhang, Zaiyang Fu, Lingjun Wang, Biqing Wang, Ye Liu, Jing Zhao, Mo Li, Hao Lin, Fei Liao, Shuchang Ye, Yu Zhang, Jiayue Cai, Shaohui Shi, Zhiwei Zhong, Yanna Shi, Junhua He, Xushen Xiong, Yang Xu, Jinghai Chen, Wei Zhu, Yibin Wang, Jian'an Wang, Xinyang Hu.
      Post-injury remodeling is a complex process involving temporal specific cellular interactions in the injured tissue where the resident fibroblasts play multiple roles. Here, we performed single-cell and spatial transcriptome analysis in human and mouse infarcted hearts to dissect the molecular basis of these interactions. We identified a unique fibroblast subset with high CD248 expression, strongly associated with extracellular matrix remodeling. Genetic Cd248 deletion in fibroblasts mitigated cardiac fibrosis and dysfunction following ischemia/reperfusion. Mechanistically, CD248 stabilizes type I transforming growth factor beta receptor and thus upregulates fibroblast ACKR3 expression, leading to enhanced T cell retention. This CD248-mediated fibroblast-T cell interaction is required to sustain fibroblast activation and scar expansion. Disrupting this interaction using monoclonal antibody or chimeric antigen receptor T cell reduces T cell infiltration and consequently ameliorates cardiac fibrosis and dysfunction. Our findings reveal a CD248+ fibroblast subpopulation as a key regulator of immune-fibroblast cross-talk and a potential therapy to treat tissue fibrosis.
    DOI:  https://doi.org/10.1038/s44161-025-00617-1
  19. Cell Genom. 2025 Mar 21. pii: S2666-979X(25)00075-8. [Epub ahead of print] 100819
    Conservation of dichromatin organization along regional centromeres.
    Danilo Dubocanin, Gabrielle A Hartley, Adriana E Sedeño Cortés, Yizi Mao, Sabrine Hedouin, Jane Ranchalis, Aman Agarwal, Glennis A Logsdon, Katherine M Munson, Taylor Real, Benjamin J Mallory, Evan E Eichler, Sue Biggins, Rachel J O'Neill, Andrew B Stergachis.
      The attachment of the kinetochore to the centromere is essential for genome maintenance, yet the highly repetitive nature of satellite regional centromeres limits our understanding of their chromatin organization. We demonstrate that single-molecule chromatin fiber sequencing (Fiber-seq) can uniquely co-resolve kinetochore and surrounding chromatin architectures along point centromeres, revealing largely homogeneous single-molecule kinetochore occupancy. In contrast, the application of Fiber-seq to regional centromeres exposed marked per-molecule heterogeneity in their chromatin organization. Regional centromere cores uniquely contain a dichotomous chromatin organization (dichromatin) composed of compacted nucleosome arrays punctuated with highly accessible chromatin patches. CENP-B occupancy phases dichromatin to the underlying alpha-satellite repeat within centromere cores but is not necessary for dichromatin formation. Centromere core dichromatin is conserved between humans and primates, including along regional centromeres lacking satellite repeats. Overall, the chromatin organization of regional centromeres is defined by marked per-molecule heterogeneity, buffering kinetochore attachment against sequence and structural variability within regional centromeres.
    Keywords:  Alpha-satellite; CENP-B; Fiber-seq; centromere; chromatin; kinetochore; single molecule
    DOI:  https://doi.org/10.1016/j.xgen.2025.100819
  20. Nat Methods. 2025 Mar 24.
    Simultaneous single-cell DNA damage profiling and RNA sequencing by Paired-Damage-seq.
      
    DOI:  https://doi.org/10.1038/s41592-025-02634-1
  21. Nat Biotechnol. 2025 Mar 25.
    High-dimensional imaging using combinatorial channel multiplexing and deep learning.
    Raz Ben-Uri, Lior Ben Shabat, Dana Shainshein, Omer Bar-Tal, Yuval Bussi, Noa Maimon, Tal Keidar Haran, Idan Milo, Inna Goliand, Yoseph Addadi, Tomer Meir Salame, Alexander Rochwarger, Christian M Schürch, Shai Bagon, Ofer Elhanani, Leeat Keren.
      Understanding tissue structure and function requires tools that quantify the expression of multiple proteins at single-cell resolution while preserving spatial information. Current imaging technologies use a separate channel for each protein, limiting throughput and scalability. Here, we present combinatorial multiplexing (CombPlex), a combinatorial staining platform coupled with an algorithmic framework to exponentially increase the number of measured proteins. Every protein can be imaged in several channels and every channel contains agglomerated images of several proteins. These combinatorically compressed images are then decompressed to individual protein images using deep learning. We achieve accurate reconstruction when compressing the stains of 22 proteins to five imaging channels. We demonstrate the approach both in fluorescence microscopy and in mass-based imaging and show successful application across multiple tissues and cancer types. CombPlex can escalate the number of proteins measured by any imaging modality, without the need for specialized instrumentation.
    DOI:  https://doi.org/10.1038/s41587-025-02585-0
  22. Development. 2025 Mar 27. pii: dev.204506. [Epub ahead of print]
    Optogenetic control of Nodal signaling patterns.
    Harold M McNamara, Alison M Guyer, Bill Z Jia, Vicente J Parot, Caleb D Dobbs, Alexander F Schier, Adam E Cohen, Nathan D Lord.
      A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creating designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
    Keywords:  Gastrulation; Mesendodermal patterning; Morphogen; Nodal signaling; Optogenetics; Zebrafish
    DOI:  https://doi.org/10.1242/dev.204506
  23. Cell. 2025 Mar 20. pii: S0092-8674(25)00258-2. [Epub ahead of print]
    Enteric neuronal Piezo1 maintains mechanical and immunological homeostasis by sensing force.
    Zili Xie, Lillian Rose, Jing Feng, Yonghui Zhao, Yisi Lu, Harry Kane, Timothy J Hibberd, Xueming Hu, Zhen Wang, Kaikai Zang, Xingliang Yang, Quentin Richardson, Rahmeh Othman, Olivia Venezia, Ademi Zhakyp, Fang Gao, Nobuya Abe, Keren Vigeland, Hongshen Wang, Camren Branch, Coco Duizer, Liwen Deng, Xia Meng, Lydia Zamidar, Max Hauptschein, Ronan Bergin, Xinzhong Dong, Issac M Chiu, Brian S Kim, Nick J Spencer, Hongzhen Hu, Ruaidhrí Jackson.
      The gastrointestinal (GI) tract experiences a myriad of mechanical forces while orchestrating digestion and barrier immunity. A central conductor of these processes, the enteric nervous system (ENS), detects luminal pressure to regulate peristalsis independently of extrinsic input from the central and peripheral nervous systems. However, how the ∼500 million enteric neurons that reside in the GI tract sense and respond to force remains unknown. Herein, we establish that the mechanosensor Piezo1 is functionally expressed in cholinergic enteric neurons. Optogenetic stimulation of Piezo1+ cholinergic enteric neurons drives colonic motility, while Piezo1 deficiency reduces cholinergic neuronal activity and slows peristalsis. Additionally, Piezo1 deficiency in cholinergic enteric neurons abolishes exercise-induced acceleration of GI motility. Finally, we uncover that enteric neuronal Piezo1 function is required for motility alterations in colitis and acts to prevent aberrant inflammation and tissue damage. This work uncovers how the ENS senses and responds to mechanical force.
    Keywords:  Piezo1; cholinergic neurons; enteric nervous system; inflammation; inflammatory bowel disease; mechanosensation; motility; neuro-immune; peristalsis
    DOI:  https://doi.org/10.1016/j.cell.2025.02.031
  24. Nature. 2025 Mar 26.
    Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3.
    Kelvin Y Chen, Tatsuya Kibayashi, Ambre Giguelay, Mayu Hata, Shunsuke Nakajima, Norihisa Mikami, Yusuke Takeshima, Kenji Ichiyama, Ryusuke Omiya, Leif S Ludwig, Kunihiro Hattori, Shimon Sakaguchi.
      Regulatory T (Treg) cells, which specifically express the master transcription factor FOXP3, have a pivotal role in maintaining immunological tolerance and homeostasis and have the potential to revolutionize cell therapies for autoimmune diseases1-3. Although stimulation of naive CD4+ T cells in the presence of TGFβ and IL-2 can induce FOXP3+ Treg cells in vitro (iTreg cells), the resulting cells are often unstable and have thus far hampered translational efforts4-6. A systematic approach towards understanding the regulatory networks that dictate Treg differentiation could lead to more effective iTreg cell-based therapies. Here we performed a genome-wide CRISPR loss-of-function screen to catalogue gene regulatory determinants of FOXP3 induction in primary human T cells and characterized their effects at single-cell resolution using Perturb-icCITE-seq. We identify the RBPJ-NCOR repressor complex as a novel, context-specific negative regulator of FOXP3 expression. RBPJ-targeted knockout enhanced iTreg differentiation and function, independent of canonical Notch signalling. Repeated cytokine and T cell receptor signalling stimulation in vitro revealed that RBPJ-deficient iTreg cells exhibit increased phenotypic stability compared with control cells through DNA demethylation of the FOXP3 enhancer CNS2, reinforcing FOXP3 expression. Conversely, overexpression of RBPJ potently suppressed FOXP3 induction through direct modulation of FOXP3 histone acetylation by HDAC3. Finally, RBPJ-ablated human iTreg cells more effectively suppressed xenogeneic graft-versus-host disease than control iTreg cells in a humanized mouse model. Together, our findings reveal novel regulators of FOXP3 and point towards new avenues to improve the efficacy of adoptive cell therapy for autoimmune disease.
    DOI:  https://doi.org/10.1038/s41586-025-08795-5
  25. Nat Cardiovasc Res. 2025 Mar 25.
    Single-nucleus multi-omics implicates androgen receptor signaling in cardiomyocytes and NR4A1 regulation in fibroblasts during atrial fibrillation.
    Francis J A Leblanc, Chi Him Kendrick Yiu, Lucia M Moreira, Aaron M Johnston, Neelam Mehta, Antonios Kourliouros, Rana Sayeed, Stanley Nattel, Svetlana Reilly, Guillaume Lettre.
      The dysregulation of gene expression programs in the human atria during persistent atrial fibrillation (AF) is not completely understood. Here, we reanalyze bulk RNA-sequencing datasets from two studies (N = 242) and identified 755 differentially expressed genes in left atrial appendages of individuals with persistent AF and non-AF controls. We combined the bulk RNA-sequencing differentially expressed genes with a left atrial appendage single-nucleus multi-omics dataset to assign genes to specific atrial cell types. We found noncoding genes at the IFNG locus (LINC01479, IFNG-AS1) strongly dysregulated in cardiomyocytes. We defined a gene expression signature potentially driven by androgen receptor signaling in cardiomyocytes from individuals with AF. Cell-type-specific gene expression modules suggested an increase in T cell and a decrease in adipocyte and neuronal cell gene expression in AF. Lastly, we showed that reducing NR4A1 expression, a marker of a poorly characterized human atrial fibroblast subtype, fibroblast activation markers, extracellular matrix remodeling and cell proliferation decreased.
    DOI:  https://doi.org/10.1038/s44161-025-00626-0
  26. Mol Cell. 2025 Mar 21. pii: S1097-2765(25)00187-X. [Epub ahead of print]
    Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.
    Leonard Schärfen, Isaac W Vock, Matthew D Simon, Karla M Neugebauer.
      RNA's catalytic, regulatory, or coding potential depends on structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and dictate the formation of functional conformations. These co-transcriptional states remain mostly unknown. Here, we develop co-transcriptional structure tracking (CoSTseq), which detects nascent RNA base pairing within and upon exit from RNA polymerases (Pols) transcriptome wide in living yeast cells. Monitoring each nucleotide's base pairing activity during transcription, CoSTseq reveals predominantly rapid pairing-within 25 bp of transcription after addition to the nascent chain. Moreover, ∼23% of rRNA nucleotides attain their final base pairing state near Pol I, while most other nucleotides must undergo changes in pairing status during later steps of ribosome biogenesis. We show that helicases act immediately to remodel structures across the rDNA locus to facilitate ribosome biogenesis. By contrast, nascent pre-mRNAs attain local structures indistinguishable from mature mRNAs, suggesting that refolding behind elongating ribosomes resembles co-transcriptional folding behind Pol II.
    Keywords:  RNA base pairing; RNA chemical probing; RNA helicase; RNA structure; U2 snRNA; co-transcriptional RNA processing; eukaryotic RNA polymerases; nascent RNA; polymerase exit channel; pre-rRNA processing; transcription elongation; transcriptome-wide structure probing
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.025
  27. Cell Rep. 2025 Mar 22. pii: S2211-1247(25)00229-3. [Epub ahead of print]44(4): 115458
    Inward transport of organelles drives outward migration of the spindle during C. elegans meiosis.
    Alma P Aquino, Wenzhe Li, Aastha Lele, Denisa Lazureanu, Megan F Hampton, Rebecca M Do, Melissa C Lafrades, Maria G Barajas, Antonio A Batres, Francis J McNally.
      Cortical positioning of the meiotic spindle within an oocyte is required to expel chromosomes into polar bodies to generate a zygote with the correct number of chromosomes. In C. elegans, yolk granules and mitochondria are packed inward, away from the cortex, while the spindle moves outward, both in a kinesin-dependent manner. The kinesin-dependent inward packing of yolk granules suggests the existence of microtubules with minus ends at the cortex and plus ends extending inward, making it unclear how kinesin moves the spindle outward. We hypothesize that the inward packing of organelles might indirectly force the spindle outward by volume exclusion. To test this hypothesis, we generate a strain in which the only kinesin consists of motor domains with no cargo-binding tail optogenetically attached to mitochondria. This mitochondria-only kinesin packs mitochondria into a tight ball and efficiently moves the meiotic spindle to the cortex, supporting the volume exclusion hypothesis.
    Keywords:  CP: Cell biology; kinesin; meiosis; meiotic spindle; oocyte
    DOI:  https://doi.org/10.1016/j.celrep.2025.115458
  28. Nature. 2025 Mar 26.
    Oxidation of retromer complex controls mitochondrial translation.
    Junbing Zhang, Md Yousuf Ali, Harrison Byron Chong, Pei-Chieh Tien, James Woods, Carolina Noble, Tristan Vornbäumen, Zehra Ordulu, Anthony P Possemato, Stefan Harry, Jay Miguel Fonticella, Lina Fellah, Drew Harrison, Maolin Ge, Neha Khandelwal, Yingfei Huang, Maëva Chauvin, Anica Tamara Bischof, Grace Marie Hambelton, Magdy Farag Gohar, Siwen Zhang, MinGyu Choi, Sara Bouberhan, Esther Oliva, Mari Mino-Kenudson, Natalya N Pavlova, Michael Lawrence, Justin F Gainor, Sean A Beausoleil, Nabeel Bardeesy, Raul Mostoslavsky, David Pépin, Christopher J Ott, Brian Liau, Liron Bar-Peled.
      Reactive oxygen species (ROS) underlie human pathologies including cancer and neurodegeneration1,2. However, the proteins that sense ROS levels and regulate their production through their cysteine residues remain ill defined. Here, using systematic base-editing and computational screens, we identify cysteines in VPS35, a member of the retromer trafficking complex3, that phenocopy inhibition of mitochondrial translation when mutated. We find that VPS35 underlies a reactive metabolite-sensing pathway that lowers mitochondrial translation to decrease ROS levels. Intracellular hydrogen peroxide oxidizes cysteine residues in VPS35, resulting in retromer dissociation from endosomal membranes and subsequent plasma membrane remodelling. We demonstrate that plasma membrane localization of the retromer substrate SLC7A1 is required to sustain mitochondrial translation. Furthermore, decreasing VPS35 levels or oxidation of its ROS-sensing cysteines confers resistance to ROS-generating chemotherapies, including cisplatin, in ovarian cancer models. Thus, we identify that intracellular ROS levels are communicated to the plasma membrane through VPS35 to regulate mitochondrial translation, connecting cytosolic ROS sensing to mitochondrial ROS production.
    DOI:  https://doi.org/10.1038/s41586-025-08756-y
  29. Nature. 2025 Mar 26.
    Plasticity of the mammalian integrated stress response.
    Chien-Wen Chen, David Papadopoli, Krzysztof J Szkop, Bo-Jhih Guan, Mohammed Alzahrani, Jing Wu, Raul Jobava, Mais M Asraf, Dawid Krokowski, Anastasios Vourekas, William C Merrick, Anton A Komar, Antonis E Koromilas, Myriam Gorospe, Matthew J Payea, Fangfang Wang, Benjamin L L Clayton, Paul J Tesar, Ashleigh Schaffer, Alexander Miron, Ilya Bederman, Eckhard Jankowsky, Christine Vogel, Leoš Shivaya Valášek, Jonathan D Dinman, Youwei Zhang, Boaz Tirosh, Ola Larsson, Ivan Topisirovic, Maria Hatzoglou.
      An increased level of phosphorylation of eukaryotic translation initiation factor 2 subunit-α (eIF2α, encoded by EIF2S1; eIF2α-p) coupled with decreased guanine nucleotide exchange activity of eIF2B is a hallmark of the 'canonical' integrated stress response (c-ISR)1. It is unclear whether impaired eIF2B activity in human diseases including leukodystrophies2, which occurs in the absence of eIF2α-p induction, is synonymous with the c-ISR. Here we describe a mechanism triggered by decreased eIF2B activity, distinct from the c-ISR, which we term the split ISR (s-ISR). The s-ISR is characterized by translational and transcriptional programs that are different from those observed in the c-ISR. Opposite to the c-ISR, the s-ISR requires eIF4E-dependent translation of the upstream open reading frame 1 and subsequent stabilization of ATF4 mRNA. This is followed by altered expression of a subset of metabolic genes (for example, PCK2), resulting in metabolic rewiring required to maintain cellular bioenergetics when eIF2B activity is attenuated. Overall, these data demonstrate a plasticity of the mammalian ISR, whereby the loss of eIF2B activity in the absence of eIF2α-p induction activates the eIF4E-ATF4-PCK2 axis to maintain energy homeostasis.
    DOI:  https://doi.org/10.1038/s41586-025-08794-6
  30. Curr Biol. 2025 Mar 16. pii: S0960-9822(25)00280-5. [Epub ahead of print]
    The activation of INF2 by Piezo1/Ca2+ is required for mesenchymal-to-amoeboid transition in confined environments.
    Neelakshi Kar, Alexa P Caruso, Nicos Prokopiou, Alleah Abrenica, Jeremy S Logue.
      To invade tissues, cells may undergo a mesenchymal-to-amoeboid transition (MAT). However, the mechanisms regulating this transition are poorly defined. In melanoma cells, we demonstrate that intracellular [Ca2+] increases with the degree of confinement in a Piezo1-dependent fashion. Moreover, Piezo1/Ca2+ is found to drive amoeboid and not mesenchymal migration in confined environments. Consistent with a model in which Piezo1 senses tension at the plasma membrane, the percentage of cells using amoeboid migration is further increased in undulating microchannels. Surprisingly, amoeboid migration was not promoted by myosin light-chain kinase (MLCK), which is sensitive to intracellular [Ca2+]. Instead, we report that Piezo1/Ca2+ activates inverted formin-2 (INF2) to induce widespread actin cytoskeletal remodeling. Strikingly, the activation of INF2 promotes de-adhesion, which in turn facilitates migration across micropatterned surfaces. Thus, we reveal a novel Piezo1/Ca2+/INF2 signaling cascade that regulates MAT, enabling cancer cells to adapt their migration mode in response to varying mechanochemical environments.
    Keywords:  INF2; Piezo1; ROCK2; amoeboid; bleb; cancer; cell migration; mechanotransduction; metastasis; microenvironment
    DOI:  https://doi.org/10.1016/j.cub.2025.02.066
  31. Nature. 2025 Mar 26.
    BRCA2 prevents PARPi-mediated PARP1 retention to protect RAD51 filaments.
    Sudipta Lahiri, George Hamilton, Gemma Moore, Liana Goehring, Tony T Huang, Ryan B Jensen, Eli Rothenberg.
      The tumour-suppressor protein BRCA2 has a central role in homology-directed DNA repair by enhancing the formation of RAD51 filaments on resected single-stranded DNA generated at double-stranded DNA breaks and stimulating RAD51 activity1,2. Individuals with BRCA2 mutations are predisposed to cancer; however, BRCA2-deficient tumours are often responsive to targeted therapy with PARP inhibitors (PARPi)3-6. The mechanism by which BRCA2 deficiency renders cells sensitive to PARPi but with minimal toxicity in cells heterozygous for BRCA2 mutations remains unclear. Here we identify a previously unknown role of BRCA2 that is directly linked to the effect of PARP1 inhibition. Using biochemical and single-molecule approaches, we demonstrate that PARPi-mediated PARP1 retention on a resected DNA substrate interferes with RAD51 filament stability and impairs RAD51-mediated DNA strand exchange. Full-length BRCA2 protects RAD51 filaments and counteracts the instability conferred by PARPi-mediated retention by preventing the binding of PARP1 to DNA. Extending these findings to a cellular context, we use quantitative single-molecule localization microscopy to show that BRCA2 prevents PARPi-induced PARP1 retention at homologous-recombination repair sites. By contrast, BRCA2-deficient cells exhibit increased PARP1 retention at these lesions in response to PARPi. These results provide mechanistic insights into the role of BRCA2 in maintaining RAD51 stability and protecting homologous-recombination repair sites by mitigating PARPi-mediated PARP1 retention.
    DOI:  https://doi.org/10.1038/s41586-025-08749-x
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