bims-ginsta Biomed News
on Genome instability
Issue of 2025–03–02
29 papers selected by
Jinrong Hu, National University of Singapore
  1. ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation during early mouse development.
  2. Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee.
  3. Genome-coverage single-cell histone modifications for embryo lineage tracing.
  4. Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos.
  5. Epigenetic control of cell identities from epiblast to gastrulation.
  6. Spatio-temporal switches in progenitor cell fate govern upper hair follicle growth and maintenance.
  7. A cluster of RNA Polymerase II molecules is stably associated with an active gene.
  8. B cell stimulation changes the structure and higher-order organization of the inactive X chromosome.
  9. Cavity oscillation drives pattern formation in early mammalian embryos.
  10. Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations.
  11. Protein degradation and growth dependent dilution substantially shape mammalian proteomes.
  12. Mammalian oocytes receive maternal-effect RNAs from granulosa cells.
  13. Maternal PRDM10 activates essential genes for oocyte-to-embryo transition.
  14. N-cadherin-triggered myosin II inactivation provides tumor cells with a mechanical cell competition advantage and chemotherapy resistance.
  15. Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis.
  16. MARIGOLD and MitoCIAO, two searchable compendia to visualize and functionalize protein complexes during mitochondrial remodeling.
  17. The functional organisation of the centromere and kinetochore during meiosis.
  18. Multivalent afadin interaction promotes IDR-mediated condensate formation and junctional separation of epithelial cells.
  19. Interferon-responsive intestinal BEST4/CA7+ cells are targets of bacterial diarrheal toxins.
  20. Mitotic transcription ensures ecDNA inheritance through chromosomal tethering.
  21. Cell type-specific 3D-genome organization and transcription regulation in the brain.
  22. Radioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades.
  23. Exploiting the SunTag system to study the developmental regulation of mRNA translation.
  24. Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development.
  25. Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.
  26. ER-mitochondria contact sites: a refuge for mitochondrial mRNAs under ER stress.
  27. ETVs dictate hPSC differentiation by tuning biophysical properties.
  28. Hallmarks of ovarian aging.
  29. Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development.
  1. Development. 2025 Feb 26. pii: dev.204278. [Epub ahead of print]
    ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation during early mouse development.
    Claire S Simon, Woonyung Hur, Vidur Garg, Ying-Yi Kuo, Kathy K Niakan, Anna-Katerina Hadjantonakis.
      Cell fate decisions in early mammalian embryos are tightly regulated processes crucial for proper development. While FGF signaling plays key roles in early embryo patterning, its downstream effectors remain poorly understood. Our study demonstrates that the transcription factors Etv4 and Etv5 are critical mediators of FGF signaling in cell lineage specification and maturation in mouse embryos. We show that loss of Etv5 compromises primitive endoderm formation at pre-implantation stages. Furthermore, Etv4/5 deficiency delays naïve pluripotency exit and epiblast maturation, leading to elevated NANOG and reduced OTX2 expression within the blastocyst epiblast. As a consequence of delayed pluripotency progression, Etv4/5 deficient embryos exhibit anterior visceral endoderm migration defects post-implantation, a process essential for coordinated embryonic patterning and gastrulation initiation. Our results demonstrate the successive roles of these FGF signaling effectors in early lineage specification and embryonic body plan establishment, providing new insights into the molecular control of mammalian development.
    Keywords:  ETV; Epiblast; FGF; Pluripotency; Primitive endoderm
    DOI:  https://doi.org/10.1242/dev.204278
  2. Cell Stem Cell. 2025 Feb 21. pii: S1934-5909(25)00041-4. [Epub ahead of print]
    Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee.
    Tao Huang, Arthur Radley, Ayaka Yanagida, Zhili Ren, Francesca Carlisle, Somayyeh Tahajjodi, Dongwan Kim, Paul O'Neill, James Clarke, Madeline A Lancaster, Zoe Heckhausen, Jingran Zhuo, João Pedro Agostinho de Sousa, Petra Hajkova, Ferdinand von Meyenn, Hiroo Imai, Hiromitsu Nakauchi, Ge Guo, Austin Smith, Hideki Masaki.
      Naive pluripotent stem cells (PSCs) are counterparts of early epiblast in the mammalian embryo. Mouse and human naive PSCs differ in self-renewal requirements and extraembryonic lineage potency. Here, we investigated the generation of chimpanzee naive PSCs. Colonies generated by resetting or reprogramming failed to propagate. We discovered that self-renewal is enabled by inhibition of Polycomb repressive complex 2 (PRC2). Expanded cells show global transcriptome proximity to human naive PSCs and embryo pre-implantation epiblast, with shared expression of a subset of pluripotency transcription factors. Chimpanzee naive PSCs can transition to multilineage competence or can differentiate into trophectoderm and hypoblast, forming tri-lineage blastoids. They thus provide a higher primate comparative model for studying pluripotency and early embryogenesis. Genetic deletions confirm that PRC2 mediates growth arrest. Further, inhibition of PRC2 overcomes a roadblock to feeder-free propagation of human naive PSCs. Therefore, excess deposition of chromatin modification H3K27me3 is an unexpected barrier to naive PSC self-renewal.
    Keywords:  Polycomb; developmental drift; epiblast; higher primate; mammalian early embryo; naive pluripotency; pluripotent stem cells; self-renewal; single-cell transcriptomics; stem cell-based embryo model
    DOI:  https://doi.org/10.1016/j.stem.2025.02.002
  3. Nature. 2025 Feb 26.
    Genome-coverage single-cell histone modifications for embryo lineage tracing.
    Min Liu, Yanzhu Yue, Xubin Chen, Kexin Xian, Chao Dong, Ming Shi, Haiqing Xiong, Kang Tian, Yuzhe Li, Qiangfeng Cliff Zhang, Aibin He.
      Substantial epigenetic resetting during early embryo development from fertilization to blastocyst formation ensures zygotic genome activation and leads to progressive cellular heterogeneities1-3. Mapping single-cell epigenomic profiles of core histone modifications that cover each individual cell is a fundamental goal in developmental biology. Here we develop target chromatin indexing and tagmentation (TACIT), a method that enabled genome-coverage single-cell profiling of seven histone modifications across mouse early embryos. We integrated these single-cell histone modifications with single-cell RNA sequencing data to chart a single-cell resolution epigenetic landscape. Multimodal chromatin-state annotations showed that the onset of zygotic genome activation at the early two-cell stage already primes heterogeneities in totipotency. We used machine learning to identify totipotency gene regulatory networks, including stage-specific transposable elements and putative transcription factors. CRISPR activation of a combination of these identified transcription factors induced totipotency activation in mouse embryonic stem cells. Together with single-cell co-profiles of multiple histone modifications, we developed a model that predicts the earliest cell branching towards the inner cell mass and the trophectoderm in latent multimodal space and identifies regulatory elements and previously unknown lineage-specifying transcription factors. Our work provides insights into single-cell epigenetic reprogramming, multimodal regulation of cellular lineages and cell-fate priming during mouse pre-implantation development.
    DOI:  https://doi.org/10.1038/s41586-025-08656-1
  4. Elife. 2025 Feb 27. pii: RP100735. [Epub ahead of print]13
    Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos.
    Yanlin Hou, Zhengwen Nie, Qi Jiang, Sergiy Velychko, Sandra Heising, Ivan Bedzhov, Guangming Wu, Kenjiro Adachi, Hans R Scholer.
      During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression. Oct4 and Sox2 activate the pluripotency-related genes through the putative OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory toward the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.
    Keywords:  Oct4; Sox2; chromatin accessibility; developmental biology; embryonic development; inner cell mass; mouse; transcriptome
    DOI:  https://doi.org/10.7554/eLife.100735
  5. FEBS J. 2025 Feb 22.
    Epigenetic control of cell identities from epiblast to gastrulation.
    Katrin M Schüle, Simone Probst.
      Epigenetic modifications of chromatin are essential for the establishment of cell identities during embryogenesis. Between embryonic days 3.5-7.5 of murine development, major cell lineage decisions are made that discriminate extraembryonic and embryonic tissues, and the embryonic primary germ layers are formed, thereby laying down the basic body plan. In this review, we cover the contribution of dynamic chromatin modifications by DNA methylation, changes of chromatin accessibility, and histone modifications, that in combination with transcription factors control gene expression programs of different cell types. We highlight the differences in regulation of enhancer and promoter marks and discuss their requirement in cell lineage specification. Importantly, in many cases, lineage-specific targeting of epigenetic modifiers is carried out by pioneer or master transcription factors, that in sum mediate the chromatin landscape and thereby control the transcription of cell-type-specific gene programs and thus, cell identities.
    Keywords:  DNA methylation; embryonic stem cells; epigenetics; gastrulation; germ layers; histone modifications; mouse embryo; nucleosome remodeling; transcription factors
    DOI:  https://doi.org/10.1111/febs.70024
  6. J Invest Dermatol. 2025 Feb 24. pii: S0022-202X(25)00287-8. [Epub ahead of print]
    Spatio-temporal switches in progenitor cell fate govern upper hair follicle growth and maintenance.
    Marianne S Andersen, Svetlana Ulyanchenko, Pawel J Schweiger, Edouard Hannezo, Benjamin D Simons, Kim B Jensen.
      The epidermis provides a protective barrier against our hostile environment, yet our knowledge of how this barrier forms during development and is subsequently maintained remains incomplete. The infundibulum (INF) is a cylindrical epidermal tissue compartment that serves as an outlet for the hair-follicle protruding out of the skin and the excretions of the sebaceous glands that are essential for proper skin function. Here, we apply quantitative fate mapping to address how the INF is maintained during adulthood. We show that progenitors build and maintain the tissue through stochastic cell fate choices. Long-term analysis identifies a preferential transient contribution from cells initially located in the bottom of the structure to the maintenance of the tissue with bursts of local progenitor expansion associated to phases of hair growth. Beyond providing compartment-wide insights into progenitor cell dynamics in the INF, these findings demonstrate how spatio-temporal regulation controls transient progenitor dominance.
    Keywords:  Infundibulum; epidermis; quantitative fate mapping; skin; stem cells
    DOI:  https://doi.org/10.1016/j.jid.2025.01.034
  7. bioRxiv. 2025 Feb 11. pii: 2025.02.10.637507. [Epub ahead of print]
    A cluster of RNA Polymerase II molecules is stably associated with an active gene.
    Apratim Mukherjee, Manya Kapoor, Kareena Shankta, Samantha Fallacaro, Raymond D Carter, Puttachai Ratchasanmuang, Yara I Haloush, Mustafa Mir.
      In eukaryotic nuclei, transcription is associated with discrete foci of RNA Polymerase II (RNAPII) molecules. How these clusters interact with genes and their impact on transcriptional activity remain heavily debated. Here we take advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in Drosophila melanogaster embryos to characterize the functional roles of RNAPII clusters in a developmental context. Using single-molecule tracking and lattice light-sheet microscopy, we find that RNAPII cluster formation depends on transcription initiation and that cluster lifetimes are reduced upon transcription elongation. We show that single clusters are stably associated with active gene loci during transcription and that cluster intensities are strongly correlated with transcriptional output. Our data suggest that prior to ZGA, RNAPII clusters prime genes for activation, whereas after ZGA, clusters are composed mostly of elongating molecules at individual genes.
    DOI:  https://doi.org/10.1101/2025.02.10.637507
  8. Cell Rep. 2025 Feb 26. pii: S2211-1247(25)00122-6. [Epub ahead of print]44(3): 115351
    B cell stimulation changes the structure and higher-order organization of the inactive X chromosome.
    Isabel Sierra, Natalie E Toothacre, Robin H van der Weide, Claudia D Lovell, Son C Nguyen, R Jordan Barnett, Ashley L Cook, Han-Seul Ryu, Sarah Pyfrom, Harrison Wang, Daniel Beiting, Jennifer E Philips-Cremins, Eric F Joyce, Montserrat C Anguera.
      X chromosome inactivation (XCI) equalizes X-linked gene expression between sexes. B cells exhibit dynamic XCI, with Xist RNA/heterochromatic marks absent on the inactive X (Xi) in naive B cells but returning following mitogenic stimulation. The impact of dynamic XCI on Xi structure and maintenance was previously unknown. Here, we find dosage compensation of the Xi with state-specific XCI escape genes in naive and in vitro-activated B cells. Allele-specific OligoPaints indicate similar Xi and active X (Xa) territories in B cells that are less compact than in fibroblasts. Allele-specific Hi-C reveals a lack of TAD-like structures on the Xi of naive B cells and stimulation-induced alterations in TAD-like boundary strength independent of gene expression. Notably, Xist deletion in B cells changes TAD boundaries and large-scale Xi compaction. Altogether, our results uncover B cell-specific Xi plasticity, which could underlie sex-biased biological mechanisms.
    Keywords:  B cell stimulation; B cells; CP: Immunology; CP: Molecular biology; TAD remodeling; X chromosome inactivation; XCI escape genes; XCI maintenance; Xist RNA; allele-specific Hi-C; chromosome compartments; chromosome structure; inactive X chromosome; topological associated domains
    DOI:  https://doi.org/10.1016/j.celrep.2025.115351
  9. Cell Rep. 2025 Feb 21. pii: S2211-1247(25)00113-5. [Epub ahead of print]44(3): 115342
    Cavity oscillation drives pattern formation in early mammalian embryos.
    Zheng Guo, Jie Yao, Xu Zheng, Jialing Cao, Xinxin Lv, Zheng Gao, Shuyu Guo, Hangyu Li, Dongshi Guan, Long Li, Dandan Qin, Dong Li, Xiaoxiao Wang, Min Tan, Jing Zhang, Yanli Zhang, Bo Wang, Wanjuan Bu, Jianwen Li, Xinbin Zhao, Fanzhe Meng, Yue Feng, Lei Li, Jing Du, Yubo Fan.
      During the second cell fate in mouse embryos, the inner cell mass (ICM) segregates into the spatially distinct epiblast (EPI) and primitive endoderm (PrE) layers. The mechanism driving this pattern formation, however, remains unresolved. Here, we report that, concomitant with the segregation process of EPI/PrE precursors starting from mid-blastocyst, the blastocyst cavity begins to oscillate cyclically with rapid contraction yet slow expansion, triggering a phase transition in the ICM to a fluid-like state. This asymmetric oscillation of the blastocyst cavity facilitates EPI/PrE segregation by enhancing cell-cell contact fluctuations within the ICM and initiating convergent cell flows, which induce movement of these two cell types in opposite directions, wherein PrE precursors move toward the ICM-lumen interface, whereas EPI precursors move toward the trophectoderm. Last, we found that both PDGFRα expression and YAP nuclear accumulation in PrE precursors increase in response to blastocyst cavity oscillation. This study reveals the foundational role of physical oscillation in driving embryonic pattern formation during early mammalian embryonic development.
    Keywords:  CP: Developmental biology; EPI/PrE segregation; blastocyst; cavity oscillation; early mammalian embryos; pattern formation
    DOI:  https://doi.org/10.1016/j.celrep.2025.115342
  10. Cell Stem Cell. 2025 Feb 19. pii: S1934-5909(25)00012-8. [Epub ahead of print]
    Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations.
    Indranil Singh, Daniel Fernandez-Perez, Pedro Sanchez Sanchez, Alejo E Rodriguez-Fraticelli.
      Cancer cells display wide phenotypic variation even across patients with the same mutations. Differences in the cell of origin provide a potential explanation, but traditional assays lack the resolution to distinguish clonally heterogeneous subsets of stem and progenitor cells. To address this challenge, we developed simultaneous tracking of recombinase activation and clonal kinetics (STRACK), a method to trace clonal dynamics and gene expression before and after the acquisition of cancer mutations. Using mouse models, we studied two leukemic mutations, Dnmt3a-R878H and Npm1c, and found that their effect was highly variable across different stem cell states. Specifically, a subset of differentiation-primed stem cells, which normally becomes outcompeted with time, expands with both mutations. Intriguingly, Npm1c mutations reversed the intrinsic bias of the clone of origin, with differentiation-primed stem cells giving rise to more primitive malignant states. Thus, we highlight the relevance of single-cell lineage tracing to unravel early events in cancer evolution and posit that different cellular histories carry distinct cancer phenotypic potential.
    Keywords:  Dnmt3a; Npm1; cancer initiation; cell barcoding; cell of origin; clonal hematopoiesis; lineage tracing; myeloid leukemia; myeloid malignancies; single-cell
    DOI:  https://doi.org/10.1016/j.stem.2025.01.012
  11. bioRxiv. 2025 Feb 12. pii: 2025.02.10.637566. [Epub ahead of print]
    Protein degradation and growth dependent dilution substantially shape mammalian proteomes.
    Andrew Leduc, Nikolai Slavov.
      Cellular protein concentrations are maintained through a balance of synthesis and clearance. Clearance occurs through both protein degradation and growth-dependent dilution. At slow growth, clearance is dominated by degradation, which leads to the accumulation of long lived proteins. At fast growth, however, it is dominated by dilution, preventing this accumulation. Thus, the concentration of long lived proteins will be reduced unless cells compensate by preferentially increasing synthesis rates. To determine the dominant regulatory mechanisms, we quantified the degree of compensation between activated and resting human B cells and across mouse tissues. The results indicate that growth-dependent dilution is insufficiently compensated for by changes in protein synthesis, and it accounts for over a third of the concentration changes between high and low growth conditions. Furthermore, we find that about 25 % of the differences in protein concentration across all tissues are controlled by protein clearance. When comparing only slowly growing tissues such as the brain and pancreas, clearance differences explain as much as 42 %. Within a tissue or cell type, clearance variation is sufficient to account for 50 % of the abundance variation for all measured proteins at slow growth, contrasted with 7 % at fast growth. Thus, our model unifies previous observations with our new results and highlights a context-dependent and larger than previously appreciated contribution of protein degradation in shaping protein variation both across the proteome and across cell states.
    DOI:  https://doi.org/10.1101/2025.02.10.637566
  12. bioRxiv. 2025 Feb 11. pii: 2025.02.10.637575. [Epub ahead of print]
    Mammalian oocytes receive maternal-effect RNAs from granulosa cells.
    Caroline A Doherty, Abdulfatai Tijjani, Steven C Munger, Diana J Laird.
      It is currently thought that growing mammalian oocytes receive only small molecules via gap junctions from surrounding support cells, the granulosa cells. From the study of chimeric preantral oocyte and granulosa cell reaggregations, we provide evidence that growing mouse oocytes receive mRNAs from granulosa cells. Among the >1,000 granulosa-transcribed RNAs we identified in the oocyte, those that contribute to proper oocyte maturation and early embryo development were highly enriched. Predicted motifs for two RNA-binding proteins that function in RNA trafficking, FMRP and TDP43, were abundant in the UTRs of the granulosa-derived transcripts. Immunostaining demonstrated that both FMRP and TDP43 co-localize with the actin-rich granulosa cell protrusions that span the zone pellucida and connect to the oocyte, suggesting their role in importing mRNAs. Our results offer the possibility that oocyte failure may not always reflect an intrinsic oocyte deficiency but could arise from insufficient supply of maternal transcripts by granulosa cells during oocyte growth.
    DOI:  https://doi.org/10.1101/2025.02.10.637575
  13. Nat Commun. 2025 Feb 24. 16(1): 1939
    Maternal PRDM10 activates essential genes for oocyte-to-embryo transition.
    Michelle K Y Seah, Brenda Y Han, Yan Huang, Louise J H Rasmussen, Andrina J Stäubli, Judith Bello-Rodríguez, Andrew Chi-Ho Chan, Maxime Gasnier, Heike Wollmann, Ernesto Guccione, Daniel M Messerschmidt.
      PR/SET domain-containing (PRDM) proteins are metazoan-specific transcriptional regulators that play diverse roles in mammalian development and disease. Several members such as PRDM1, PRDM14 and PRDM9, have been implicated in germ cell specification and homoeostasis and are essential to fertility-related processes. Others, such as PRDM14, PRDM15 and PRDM10 play a role in early embryogenesis and embryonic stem cell maintenance. Here, we describe the first PRDM family member with a maternal effect. Absence of maternal Prdm10 results in catastrophic failure of oocyte-to-embryo transition and complete arrest at the 2-cell stage. We describe multiple defects in oocytes, zygotes and 2-cell stage embryos relating to the failure to accumulate PRDM10 target gene transcripts in the egg. Transcriptomic analysis and integration of genome-wide chromatin-binding data reveals new and essential PRDM10 targets, including the cytoskeletal protein encoding gene Septin11. We demonstrate that the failure to express maternal Septin11, in the absence of maternal PRDM10, disrupts Septin-complex assembly at the polar body extrusion site in MII oocytes. Our study sheds light into the essentiality of maternal PRDM10, the requirement of the maternal Septin-complex and the likely evolutionary conservation of this regulatory axis in human female germ cells.
    DOI:  https://doi.org/10.1038/s41467-025-56991-8
  14. Dev Cell. 2025 Feb 18. pii: S1534-5807(25)00061-9. [Epub ahead of print]
    N-cadherin-triggered myosin II inactivation provides tumor cells with a mechanical cell competition advantage and chemotherapy resistance.
    Zhenlin Dai, Shengkai Chen, Jianbo Shi, Mengyu Rui, Qin Xu.
      The concept that mechanical cell competition may contribute to tumor cell expansion has been widely discussed. However, whether this process could occur during natural tumor progression, as well as its underlying mechanisms and clinical implications, remains largely unknown. In this study, we observed that self-seeded tumor cell lines of human oral cancer, SCC9- and SCC25-seeded cells, exhibited a mechanical competitive advantage, outcompeted neighboring cells, and became "winner" cells. Mechanical compression-induced calcium influx activates myosin II in "loser" cells, leading to apoptotic nuclear breakdown and subsequent clearance. N-cadherin/Rac1/PAK1/myosin light-chain kinase (MLCK)-controlled myosin II inactivation endows cells with resistance to mechanical stress and superior cellular flexibility, thus providing a cell competition advantage to self-seeded cells. The activation of the N-cadherin/Rac1/PAK1/MLCK/myosin II signaling axis is associated with drug resistance. Together, these results suggest that N-cadherin/Rac1/PAK1/MLCK signaling-induced myosin II inactivation enables tumor cells to acquire resistance to mechanical stress and a competitive advantage. Our study also provides insights into drug resistance from a stress-sensitivity perspective.
    Keywords:  cellular flexibility; drug resistance; mechanical cell competition; self-seeding
    DOI:  https://doi.org/10.1016/j.devcel.2025.01.020
  15. Nat Biotechnol. 2025 Feb 24.
    Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis.
    Mikael G Pezet, Juan A Torres, Tania A Thimraj, Ivana Matkovic, Nadine Schrode, John W Murray, Anjali Saqi, Kristin G Beaumont, Hans-Willem Snoeck.
      Human lungs contain unique cell populations in distal respiratory airways or terminal and respiratory bronchioles (RA/TRBs) that accumulate in persons with lung injury and idiopathic pulmonary fibrosis (IPF), a lethal lung disease. As these populations are absent in rodents, deeper understanding requires a human in vitro model. Here we convert human pluripotent stem cells (hPS cells) into expandable spheres, called induced respiratory airway progenitors (iRAPs), consisting of ~98% RA/TRB-associated cell types. One hPS cell can give rise to 1010 iRAP cells. We differentiate iRAPs through a stage consistent with transitional type 2 alveolar epithelial (AT2) cells into a population corresponding to mature AT1 cells with 95% purity. iRAPs with deletion of Heřmanský-Pudlák Syndrome 1 (HPS1), which causes pulmonary fibrosis in humans, replicate the aberrant differentiation and recruitment of profibrotic fibroblasts observed in IPF, indicating that intrinsic dysfunction of RA/TRB-associated alveolar progenitors contributes to HPS1-related IPF. iRAPs may provide a system suitable for IPF drug discovery and validation.
    DOI:  https://doi.org/10.1038/s41587-025-02569-0
  16. Cell Metab. 2025 Feb 20. pii: S1550-4131(25)00017-8. [Epub ahead of print]
    MARIGOLD and MitoCIAO, two searchable compendia to visualize and functionalize protein complexes during mitochondrial remodeling.
    Giovanni Rigoni, Enrique Calvo, Christina Glytsou, Marta Carro-Alvarellos, Masafumi Noguchi, Martina Semenzato, Charlotte Quirin, Federico Caicci, Natascia Meneghetti, Mattia Sturlese, Takaya Ishihara, Stefano Moro, Chiara Rampazzo, Naotada Ishihara, Fabrizio Bezzo, Leonardo Salviati, Jesùs Vazquez, Gabriele Sales, Chiara Romualdi, Jose Antonio Enriquez, Luca Scorrano, Maria Eugenia Soriano.
      Mitochondrial proteins assemble dynamically in high molecular weight complexes essential for their functions. We generated and validated two searchable compendia of these mitochondrial complexes. Following identification by mass spectrometry of proteins in complexes separated using blue-native gel electrophoresis from unperturbed, cristae-remodeled, and outer membrane-permeabilized mitochondria, we created MARIGOLD, a mitochondrial apoptotic remodeling complexome database of 627 proteins. MARIGOLD elucidates how dynamically proteins distribute in complexes upon mitochondrial membrane remodeling. From MARIGOLD, we developed MitoCIAO, a mitochondrial complexes interactome tool that, by statistical correlation, calculates the likelihood of protein cooccurrence in complexes. MitoCIAO correctly predicted biologically validated interactions among components of the mitochondrial cristae organization system (MICOS) and optic atrophy 1 (OPA1) complexes. We used MitoCIAO to functionalize two ATPase family AAA domain-containing 3A (ATAD3A) complexes: one with OPA1 that regulates mitochondrial ultrastructure and the second containing ribosomal proteins that is essential for mitoribosome stability. These compendia reveal the dynamic nature of mitochondrial complexes and enable their functionalization.
    Keywords:  ATAD3A; OPA1; cristae remodeling; interactome; mitochondria; mitochondrial complexes; mitoribosome stability
    DOI:  https://doi.org/10.1016/j.cmet.2025.01.017
  17. Curr Opin Cell Biol. 2025 Feb 26. pii: S0955-0674(25)00024-9. [Epub ahead of print]94 102486
    The functional organisation of the centromere and kinetochore during meiosis.
    Lori B Koch, Adele L Marston.
      Meiosis generates gametes through a specialised cell cycle that reduces the genome by half. Homologous chromosomes are segregated in meiosis I and sister chromatids are segregated in meiosis II. Centromeres and kinetochores play central roles in instructing this specialised chromosome segregation pattern. Accordingly, kinetochores acquire meiosis-specific modifications. Here we contextualise recent highlights in our understanding of how centromeres and kinetochores direct the sorting of chromosomes into gametes via meiosis.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102486
  18. Cell Rep. 2025 Feb 21. pii: S2211-1247(25)00106-8. [Epub ahead of print] 115335
    Multivalent afadin interaction promotes IDR-mediated condensate formation and junctional separation of epithelial cells.
    Shuhei Kuno, Ryu Nakamura, Tetsuhisa Otani, Hideru Togashi.
      In epithelial cells, cell-cell adhesion is mediated by the apical junctional complex (AJC), which consists of tight junctions (TJs) and adherens junctions (AJs) aligned from the apical to the basal axis. However, the mechanism of AJC formation on the apical side and the separation of these junctions within AJCs are poorly understood. We find that multivalent interactions of afadin with adhesion molecules and the cytoskeleton lead to condensate formation in an intrinsically disordered region (IDR)-dependent manner, which promotes efficient accumulation in the linear AJ during initial junction formation. Furthermore, we observe that afadin and ZO-1 induce different condensate formations in the cell and that these molecules are differentially distributed from each other. These properties of afadin explain how it strictly localizes to AJs in epithelial cells and is involved in regulating the segregation of AJs and TJs within the AJC.
    Keywords:  CP: Cell biology; LLPS; afadin; apical junctional complex; cell-cell adhesion; epithelial cells; initial junction formation; liquid-liquid phase separation; zonula adherens
    DOI:  https://doi.org/10.1016/j.celrep.2025.115335
  19. Cell Stem Cell. 2025 Feb 24. pii: S1934-5909(25)00042-6. [Epub ahead of print]
    Interferon-responsive intestinal BEST4/CA7+ cells are targets of bacterial diarrheal toxins.
    Daisong Wang, Willem Kasper Spoelstra, Lin Lin, Ninouk Akkerman, Daniel Krueger, Talya Dayton, Jeroen S van Zon, Sander J Tans, Johan H van Es, Hans Clevers.
      BEST4/CA7+ cells of the human intestine were recently identified by single-cell RNA sequencing. While their gene expression profile predicts a role in electrolyte balance, BEST4/CA7+ cell function has not been explored experimentally owing to the absence of BEST4/CA7+ cells in mice and the paucity of human in vitro models. Here, we establish a protocol that allows the emergence of BEST4/CA7+ cells in human intestinal organoids. Differentiation of BEST4/CA7+ cells requires activation of Notch signaling and the transcription factor SPIB. BEST4/CA7+ cell numbers strongly increase in response to the cytokine interferon-γ, supporting a role in immunity. Indeed, we demonstrate that BEST4/CA7+ cells generate robust CFTR-mediated fluid efflux when stimulated with bacterial diarrhea-causing toxins and find the norepinephrine-ADRA2A axis as a potential mechanism in blocking BEST4/CA7+ cell-mediated fluid secretion. Our observations identify a central role of BEST4/CA7+ cells in fluid homeostasis in response to bacterial infections.
    Keywords:  BEST4/CA7(+) cells; bacterial infection; fluid homeostasis; human intestinal organoids; interferon-γ
    DOI:  https://doi.org/10.1016/j.stem.2025.02.003
  20. bioRxiv. 2025 Feb 16. pii: 2025.02.12.637945. [Epub ahead of print]
    Mitotic transcription ensures ecDNA inheritance through chromosomal tethering.
    Ashley Nichols, Roshan Norman, Yanyang Chen, Yujin Choi, Josefine Striepen, Eralda Salataj, Eleonore Toufektchan, Richard Koche, John Maciejowski.
      Extrachromosomal DNA (ecDNA) are circular DNA bodies that play critical roles in tumor progression and treatment resistance by amplifying oncogenes across a wide range of cancer types. ecDNA lack centromeres and are thus not constrained by typical Mendelian segregation, enabling their unequal accumulation within daughter cells and associated increases in copy number. Despite intrinsic links to their oncogenic potential, the fidelity and mechanisms of ecDNA inheritance are poorly understood. Here, we show that ecDNA are protected against cytosolic mis-segregation through mitotic clustering and by tethering to the telomeric and subtelomeric regions of mitotic chromosomes. ecDNA-chromosome tethering depends on BRD4 transcriptional co-activation and mitotic transcription of the long non-coding RNA PVT1 , which is co-amplified with MYC in colorectal and prostate cancer cell lines. Disruption of ecDNA-chromosome tethering through BRD4 inhibition, PVT1 depletion, or inhibiting mitotic transcription results in cytosolic mis-segregation, ecDNA reintegration, and the formation of homogeneously staining regions (HSRs). We propose that nuclear inheritance of ecDNA is facilitated by an RNA-mediated physical tether that links ecDNA to mitotic chromosomes and thus protects against cytosolic mis-segregation and chromosomal integration.
    DOI:  https://doi.org/10.1101/2025.02.12.637945
  21. Sci Adv. 2025 Feb 28. 11(9): eadv2067
    Cell type-specific 3D-genome organization and transcription regulation in the brain.
    Shiwei Liu, Cosmos Yuqi Wang, Pu Zheng, Bojing Blair Jia, Nathan R Zemke, Peter Ren, Hannah L Park, Bing Ren, Xiaowei Zhuang.
      3D organization of the genome plays a critical role in regulating gene expression. How 3D-genome organization differs among different cell types and relates to cell type-dependent transcriptional regulation remains unclear. Here, we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the size of the cell nucleus to higher-order chromosome structures and radial positioning of chromatin loci within the nucleus. These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. Moreover, we found that the methylated DNA binding protein MeCP2 promotes active-inactive chromatin segregation and regulates transcription in a nuclear radial position-dependent manner that is highly correlated with its function in modulating active-inactive chromatin compartmentalization.
    DOI:  https://doi.org/10.1126/sciadv.adv2067
  22. Nat Biomed Eng. 2025 Feb 26.
    Radioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades.
    Ameya R Kirtane, Jianling Bi, Netra U Rajesh, Chaoyang Tang, Miguel Jimenez, Emily Witt, Megan K McGovern, Arielle B Cafi, Samual J Hatfield, Lauren Rosenstock, Sarah L Becker, Nicole Machado, Veena Venkatachalam, Dylan Freitas, Xisha Huang, Alvin Chan, Aaron Lopes, Hyunjoon Kim, Nayoon Kim, Joy E Collins, Michelle E Howard, Srija Manchkanti, Theodore S Hong, James D Byrne, Giovanni Traverso.
      Patients undergoing radiation therapy experience debilitating side effects because of toxicity arising from radiation-induced DNA strand breaks in normal peritumoural cells. Here, inspired by the ability of tardigrades to resist extreme radiation through the expression of a damage-suppressor protein that binds to DNA and reduces strand breaks, we show that the local and transient expression of the protein can reduce radiation-induced DNA damage in oral and rectal epithelial tissues (which are commonly affected during radiotherapy for head-and-neck and prostate cancers, respectively). We used ionizable lipid nanoparticles supplemented with biodegradable cationic polymers to enhance the transfection efficiency and delivery of messenger RNA encoding the damage-suppressor protein into buccal and rectal tissues. In mice with orthotopic oral cancer, messenger RNA-based radioprotection of normal tissue preserved the efficacy of radiation therapy. The strategy may be broadly applicable to the protection of healthy tissue from DNA-damaging agents.
    DOI:  https://doi.org/10.1038/s41551-025-01360-5
  23. J Cell Sci. 2025 Feb 24. pii: jcs.263457. [Epub ahead of print]
    Exploiting the SunTag system to study the developmental regulation of mRNA translation.
    Alastair Pizzey, Catherine Sutcliffe, Jennifer C Love, Emmanuel Akabuogu, Magnus Rattray, Mark P Ashe, Hilary L Ashe.
      The ability to quantitatively study mRNA translation using SunTag imaging is transforming our understanding of the translation process. Here, we expand the SunTag method to study new aspects of translation regulation in Drosophila. Repression of the maternal hunchback (hb) mRNA in the posterior of the Drosophila embryo is a textbook example of translational control. Using SunTag imaging to quantitate translation of maternal SunTag-hb mRNAs, we show that repression in the posterior is leaky as ∼5% of SunTag-hb mRNAs are translated. In the anterior of the embryo, the maternal and zygotic SunTag-hb mRNAs show similar translation efficiency despite having different UTRs. We demonstrate that the SunTag-hb mRNA can be used as a reporter to study ribosome pausing at single-mRNA resolution, by exploiting the conserved xbp1 mRNA and A60 pausing sequences. Finally, we adapt the detector component of the SunTag system to visualise and quantitate translation of the short gastrulation (sog) mRNA, encoding an essential secreted extracellular BMP regulator, at the endoplasmic reticulum in fixed and live embryos. Together, these tools will facilitate the future dissection of translation regulatory mechanisms during development.
    Keywords:   Drosophila embryo; Hunchback; Ribosome pausing; Sog; SunTag; Translation
    DOI:  https://doi.org/10.1242/jcs.263457
  24. Nat Commun. 2025 Feb 23. 16(1): 1900
    Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development.
    Feifei Yuan, Jihong Yang, Fanglin Ma, Zhe Hu, Vikas Malik, Ruge Zang, Dan Li, Xianle Shi, Xin Huang, Hongwei Zhou, Jianlong Wang.
      Testis-specific transcript 10 (Tex10) is highly expressed in the testis, embryonic stem cells (ESCs), and primordial germ cells (PGCs). We previously generated a Tex10 knockout mouse model demonstrating its critical roles in ESC pluripotency and preimplantation development. Here, using conditional knockout mice and dTAG-degron ESCs, we show Tex10 is required for spermatogenesis and ESC-to-PGCLC differentiation. Specifically, Tex10-null spermatocytes arrest at metaphase I, compromising round spermatid formation. Tex10 depletion and overexpression compromise and enhance ESC-to-PGCLC differentiation, respectively. Mechanistically, bulk and single-cell RNA sequencing reveals that Tex10 depletion downregulates genes involved in pluripotency, PGC development, and spermatogenesis while upregulating genes promoting somatic programs. Chromatin occupancy study reveals that Tex10 binds to H3K4me3-marked promoters of Psmd3 and Psmd7, negative regulators of Wnt signaling, and activates their expression, thereby restraining Wnt signaling. Our study identifies Tex10 as a previously unappreciated factor in spermatogenesis and PGC development, offering potential therapeutic insights for treating male infertility.
    DOI:  https://doi.org/10.1038/s41467-025-57165-2
  25. Nat Cell Biol. 2025 Feb 26.
    Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.
    Longda Jiang, Carol Dalgarno, Efthymia Papalexi, Isabella Mascio, Hans-Hermann Wessels, Huiyoung Yun, Nika Iremadze, Gila Lithwick-Yanai, Doron Lipson, Rahul Satija.
      Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but predicting causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single-cell sequencing (Perturb-seq) to systematically identify the targets of signalling regulators in diverse biological contexts. We demonstrate how Perturb-seq is compatible with recent and commercially available advances in combinatorial indexing and next-generation sequencing, and perform more than 1,500 perturbations split across six cell lines and five biological signalling contexts. We introduce an improved computational framework (Mixscale) to address cellular variation in perturbation efficiency, alongside optimized statistical methods to learn differentially expressed gene lists and conserved molecular signatures. Finally, we demonstrate how our Perturb-seq derived gene lists can be used to precisely infer changes in signalling pathway activation for in vivo and in situ samples. Our work enhances our understanding of signalling regulators and their targets, and lays a computational framework towards the data-driven inference of an 'atlas' of perturbation signatures.
    DOI:  https://doi.org/10.1038/s41556-025-01622-z
  26. Trends Cell Biol. 2025 Feb 25. pii: S0962-8924(25)00036-4. [Epub ahead of print]
    ER-mitochondria contact sites: a refuge for mitochondrial mRNAs under ER stress.
    Philippe Pihán, Lisa M Ellerby, Claudio Hetz.
      Tight mitochondria-endoplasmic reticulum (ER) contacts (MERCS) play essential roles in cellular homeostasis. Brar et al. reveal a novel mechanism where mitochondrial mRNAs escape global translational repression at novel context-specific MERCS during ER stress, uncovering spatially regulated translation as a critical adaptive strategy to cope with cellular stress.
    Keywords:  ATAD3A; PERK; endoplasmic reticulum stress; mitochondria–ER contact sites (MERCS); spatial translation regulation
    DOI:  https://doi.org/10.1016/j.tcb.2025.02.002
  27. Nat Commun. 2025 Feb 26. 16(1): 1999
    ETVs dictate hPSC differentiation by tuning biophysical properties.
    Natalia M Ziojła, Magdalena Socha, M Cecilia Guerra, Dorota Kizewska, Katarzyna Blaszczyk, Edyta Urbaniak, Sara Henry, Malgorzata Grabowska, Kathy K Niakan, Aryeh Warmflash, Malgorzata Borowiak.
      Stem cells maintain a dynamic dialog with their niche, integrating biochemical and biophysical cues to modulate cellular behavior. Yet, the transcriptional networks that regulate cellular biophysical properties remain poorly defined. Here, we leverage human pluripotent stem cells (hPSCs) and two morphogenesis models - gastruloids and pancreatic differentiation - to establish ETV transcription factors as critical regulators of biophysical parameters and lineage commitment. Genetic ablation of ETV1 or ETV1/ETV4/ETV5 in hPSCs enhances cell-cell and cell-ECM adhesion, leading to aberrant multilineage differentiation including disrupted germ-layer organization, ectoderm loss, and extraembryonic cell overgrowth in gastruloids. Furthermore, ETV1 loss abolishes pancreatic progenitor formation. Single-cell RNA sequencing and follow-up assays reveal dysregulated mechanotransduction via the PI3K/AKT signaling. Our findings highlight the importance of transcriptional control over cell biophysical properties and suggest that manipulating these properties may improve in vitro cell and tissue engineering strategies.
    DOI:  https://doi.org/10.1038/s41467-025-56591-6
  28. Trends Endocrinol Metab. 2025 Feb 24. pii: S1043-2760(25)00018-9. [Epub ahead of print]
    Hallmarks of ovarian aging.
    Chuqing Wu, Dan Chen, Michael B Stout, Meng Wu, Shixuan Wang.
      Ovarian aging is considered to be the pacemaker of female aging, and is linked to various comorbidities such as osteoporosis, cardiovascular diseases, and cognitive decline. Many efforts have been made to determine the mechanisms underlying ovarian aging, but their potential to act as hallmarks to predict and intervene in this process currently remains unclear. In this review we propose nine hallmarks as common features of ovarian aging: genomic instability, telomere attrition, epigenetic alterations, impaired autophagy, cellular senescence, deregulated nutrient-sensing, mitochondrial dysfunction, oxidative stress, and chronic inflammation. Understanding the interaction between these hallmarks poses a significant challenge but may also pave the way to the identification of pharmaceutical targets that can attenuate ovarian aging.
    Keywords:  endocrine; fertility; hallmarks; oocyte; ovarian aging
    DOI:  https://doi.org/10.1016/j.tem.2025.01.005
  29. Dev Cell. 2025 Feb 24. pii: S1534-5807(25)00064-4. [Epub ahead of print]
    Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development.
    Shreeta Chakraborty, Nina Wenzlitschke, Matthew J Anderson, Ariel Eraso, Manon Baudic, Joyce J Thompson, Alicia A Evans, Lilly M Shatford-Adams, Raj Chari, Parirokh Awasthi, Ryan K Dale, Mark Lewandoski, Timothy J Petros, Pedro P Rocha.
      Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysregulation and phenotypes. We tested whether perturbing a domain with multiple developmental regulators would lead to more severe outcomes. We chose a domain with three FGF ligand genes-Fgf3, Fgf4, and Fgf15-that control different murine developmental processes. Heterozygous deletion of a 23.9-kb boundary defined by four CTCF sites led to ectopic interactions of the FGF genes with enhancers active in the brain and induced FGF expression. This caused orofacial clefts, encephalocele, and fully penetrant perinatal lethality. Loss of the single CTCF motif oriented toward the enhancers-but not the three toward the FGF genes-recapitulated these phenotypes. Our works shows that small sequence variants at particular domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation in development and disease.
    Keywords:  CTCF; FGF; epigenetics; gene regulation; nuclear organization
    DOI:  https://doi.org/10.1016/j.devcel.2025.02.002
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