bims-ginsta Biomed News
on Genome instability
Issue of 2025–05–25
thirty-two papers selected by
Jinrong Hu, National University of Singapore



  1. Science. 2025 May 22. 388(6749): eads1234
      Following fertilization, the preimplantation embryo undergoes successive rounds of cell division and must accurately propagate the genetic material to ensure successful development. However, early mammalian embryos lack efficient spindle assembly mechanisms, and it remains unclear how error-free chromosome segregation is achieved. In this work, we imaged early mouse embryos and identified a network of nuclear actin cables that organize prophase chromosomes at the nuclear periphery. Following nuclear envelope breakdown, the network contracts and gathers chromosomes toward the cell center. Network contraction was driven by filament disassembly in a myosin II-independent manner. Additionally, we identified a network of branched actin filaments that attenuates metaphase spindle elongation. We also visualized nuclear actin in human embryos, suggesting a conserved role for actin in ensuring mitotic fidelity during early mammalian development.
    DOI:  https://doi.org/10.1126/science.ads1234
  2. Stem Cell Reports. 2025 May 08. pii: S2213-6711(25)00110-9. [Epub ahead of print] 102506
      Human pluripotent stem cells (hPSCs) maintain diploid populations for generations despite frequent mitotic errors that cause aneuploidy or chromosome imbalances. Consequently, aneuploid hPSC propagation must be prevented to sustain genome stability, but how this is achieved is unknown. Surprisingly, we find that, unlike somatic cells, uniformly aneuploid hPSC populations with heterogeneous abnormal karyotypes proliferate. Instead, in mosaic populations, cell-non-autonomous competition between neighboring diploid and aneuploid hPSCs eliminates less fit aneuploid cells, regardless of specific chromosome imbalances. Aneuploid hPSCs with lower MYC or higher p53 levels relative to diploid neighbors are outcompeted but conversely gain an advantage when MYC and p53 relative abundance switches. Thus, MYC- and p53-driven cell competition preserves hPSC genome integrity despite their low mitotic fidelity and intrinsic capacity to proliferate with an aneuploid genome. These findings have important implications for using hPSCs in regenerative medicine and for how diploid human embryos form during development despite the prevalence of aneuploidy.
    Keywords:  MYC; aneuploidy; cell competition; human pluripotent stem cells; mosaicism; p53; preimplantation embryos
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102506
  3. Cell. 2025 May 15. pii: S0092-8674(25)00458-1. [Epub ahead of print]
      The amnion, an extra-embryonic tissue in mammalian embryos, is thought to provide crucial signaling, structural, and nutritional support during pregnancy. Despite its pivotal importance, studying human amnion formation and function has been hampered by the lack of accurate in vitro models. Here, we present an embryonic stem cell-derived 3D model of the post-gastrulation amnion, post-gastrulation amnioids (PGAs), that faithfully recapitulates extra-embryonic development up to 4 weeks post-fertilization, closely mimicking the functional traits of the human amniotic sac. PGAs self-organize, forming the amnion and the yolk sac, and are surrounded by the extra-embryonic mesoderm. Using PGAs, we show that GATA3 is required and sufficient for amniogenesis and that an autoregulatory feedback loop governs amnion formation, whereby extra-embryonic signals promote amnion specification. The reproducibility and scalability of the PGA system, with its precise cellular, structural, and functional integrity, opens avenues for investigating embryo-amnion interactions beyond gastrulation and offers an ideal platform for large-scale pharmacological and clinical studies.
    Keywords:  BMP4; GATA3; WNT; amnion; extra-embryonic tissues; hESCs; human development; self-organization; stem cell-based models of human development
    DOI:  https://doi.org/10.1016/j.cell.2025.04.025
  4. Cell Stem Cell. 2025 May 19. pii: S1934-5909(25)00177-8. [Epub ahead of print]
      Hepatocytes can reprogram into biliary epithelial cells (BECs) during liver injury, but the underlying epigenetic mechanisms remain poorly understood. Here, we define the chromatin dynamics of this process using single-cell ATAC-seq and identify YAP/TEAD activation as a key driver of chromatin remodeling. An in vivo CRISPR screen highlights the histone acetyltransferase HBO1 as a critical barrier to reprogramming. HBO1 is recruited by YAP to target loci, where it promotes histone H3 lysine 14 acetylation (H3K14ac) and engages the chromatin reader zinc-finger MYND-type containing 8 (ZMYND8) to suppress YAP/TEAD-driven transcription. Loss of HBO1 accelerates chromatin remodeling, enhances YAP binding, and enables a more complete hepatocyte-to-BEC transition. Our findings position HBO1 as an epigenetic brake that restrains YAP-mediated reprogramming, suggesting that targeting HBO1 may enhance hepatocyte plasticity for liver regeneration.
    Keywords:  HBO1; Hippo-YAP; epigenetic regulation; hepatocyte reprogramming; in vivo CRISPR screen
    DOI:  https://doi.org/10.1016/j.stem.2025.04.010
  5. Nat Aging. 2025 May 19.
      With increased age, the liver becomes more vulnerable to metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis. Deciphering the complex interplay between aging, the emergence of senescent cells in the liver and MASH fibrosis is critical for developing treatments. Here we report an epigenetic mechanism that links liver aging to MASH fibrosis. We find that upregulation of the chromatin remodeler BAZ2B in a subpopulation of hepatocytes (HEPs) is linked to MASH pathology in patients. Genetic ablation or hepatocyte-specific knockdown of Baz2b in mice attenuates HEP senescence and MASH fibrosis by preserving peroxisome proliferator-activated receptor α (PPARα)-mediated lipid metabolism, which was impaired in both naturally aged and MASH mouse livers. Mechanistically, Baz2b downregulates the expression of genes related to the PPARα signaling pathway by directly binding their promoter regions and reducing chromatin accessibility. Thus, our study unravels the BAZ2B-PPARα-lipid metabolism axis as a link from liver aging to MASH fibrosis, suggesting that BAZ2B is a potential therapeutic target for HEP senescence and fibrosis.
    DOI:  https://doi.org/10.1038/s43587-025-00862-w
  6. Sci Adv. 2025 May 23. 11(21): eadt9446
      The adult mammalian heart has limited regenerative capacity due to the low proliferative ability of cardiomyocytes, whereas embryonic cardiomyocytes exhibit robust proliferative potential. Using single-cell RNA sequencing of embryonic hearts, we identified prothymosin α (PTMA) as a key factor driving cardiomyocyte proliferation. Overexpression of PTMA in primary mouse and rat cardiomyocytes significantly promoted cardiomyocyte proliferation and similarly enhanced proliferation in human iPSC-derived cardiomyocytes. Conditional knockout of Ptma in cardiomyocytes impaired neonatal heart regeneration. AAV9-mediated overexpression of Ptma extended the neonatal proliferative window and showed therapeutic promise for enhancing adult heart regeneration. Mechanistically, PTMA interacted with MBD3, inhibiting its deacetylation activity within the MBD3/HDAC1 NuRD complex. This inhibition increased STAT3 acetylation, which positively regulated STAT3 phosphorylation and activation of its target genes. These findings establish PTMA as a critical regulator of heart regeneration and suggest its potential as a therapeutic target for ischemic myocardial injury.
    DOI:  https://doi.org/10.1126/sciadv.adt9446
  7. Curr Opin Genet Dev. 2025 May 20. pii: S0959-437X(25)00049-8. [Epub ahead of print]93 102357
      Stem cell-based embryo models have taken the scientific community by storm as they enable investigation of previously inaccessible stages of human development. Here, we discuss how stem cell-based embryo and placenta models can shine a light on two elusive and intertwined aspects of human development that are critical for successful pregnancy: the implantation of the blastocyst into the endometrium and the subsequent invasion of placental villi deep inside the maternal tissues. Both of these processes are mediated by the trophoblast lineage, which is specified in the preimplantation embryo and can be modeled using naïve pluripotent stem cells. We review how embryo and placenta models built from naïve stem cells can be leveraged to obtain mechanistic insights into human implantation and trophoblast invasion.
    DOI:  https://doi.org/10.1016/j.gde.2025.102357
  8. Nature. 2025 May 21.
      Cell heterogeneity is a universal feature of life. Although biological processes affected by cell-to-cell variation are manifold, from developmental plasticity to tumour heterogeneity and differential drug responses, the sources of cell heterogeneity remain largely unclear1,2. Mutational and epigenetic signatures from cancer (epi)genomics are powerful for deducing processes that shaped cancer genome evolution3-5. However, retrospective analyses face difficulties in resolving how cellular heterogeneity emerges and is propagated to subsequent cell generations. Here, we used multigenerational single-cell tracking based on endogenously labelled proteins and custom-designed computational tools to elucidate how oncogenic perturbations induce sister cell asymmetry and phenotypic heterogeneity. Dual CRISPR-based genome editing enabled simultaneous tracking of DNA replication patterns and heritable endogenous DNA lesions. Cell lineage trees of up to four generations were tracked in asynchronously growing cells, and time-resolved lineage analyses were combined with end-point measurements of cell cycle and DNA damage markers through iterative staining. Besides revealing replication and repair dynamics, damage inheritance and emergence of sister cell heterogeneity across multiple cell generations, through combination with single-cell transcriptomics, we delineate how common oncogenic events trigger multiple routes towards polyploidization with distinct outcomes for genome integrity. Our study provides a framework to dissect phenotypic plasticity at the single-cell level and sheds light onto cellular processes that may resemble early events during cancer development.
    DOI:  https://doi.org/10.1038/s41586-025-08986-0
  9. Methods Mol Biol. 2025 May 22.
      The cellular dynamics during peri-implantation embryogenesis and the concurrent interactions at the embryo-maternal interface are inherently difficult to study due to intrauterine development in mammals. To model certain aspects of these processes in vitro, we have generated a biomimetic environment resembling the mechanical properties of the murine uterine stroma. Here we describe a step-by-step methodology for 3D culture of mouse embryos and ectoplacental cone explants in synthetic hydrogels that allow ex utero trophoblast invasion.
    Keywords:  3D culture; Blastocyst; Ectoplacental cone; Egg cylinder; Hydrogel; Implantation; Invasion; Mouse embryo; Trophoblast; Trophoblast giant cells
    DOI:  https://doi.org/10.1007/7651_2025_646
  10. Nature. 2025 May 21.
      Spatial RNA organization has a pivotal role in diverse cellular processes and diseases1-4. However, functional implications of the spatial transcriptome remain largely unexplored due to limited technologies for perturbing endogenous RNA within specific subcellular regions1,5. Here we present CRISPR-mediated transcriptome organization (CRISPR-TO), a system that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of endogenous RNA localization in live cells. CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments, including the outer mitochondrial membrane, p-bodies, stress granules, telomeres and nuclear stress bodies, across various cell types. It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins, facilitating real-time manipulation and monitoring of RNA localization dynamics in living cells. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips, and co-transport with ribosomes, with β-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.
    DOI:  https://doi.org/10.1038/s41586-025-09020-z
  11. Cell. 2025 May 14. pii: S0092-8674(25)00461-1. [Epub ahead of print]
      Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding for in vivo clonal lineage tracing for bulk tissue and single-cell readout. Embryonic day (E) 5.5 pre-gastrulation embryos were barcoded in utero, and epiblast clones were assessed for their contribution to a wide range of tissues in E12.5 embryos. Some epiblast clones contributed broadly across germ layers, while many were biased toward either blood, ectoderm, mesenchyme, or limbs, across tissue compartments and body axes. Using a stochastic agent-based model of embryogenesis and LoxCode barcoding, we inferred and experimentally validated cell fate biases across tissues in line with shared and segregating differentiation trajectories. Single-cell readout revealed numerous instances of asymmetry in epiblast contribution, including left-versus-right and kidney-versus-gonad fate. LoxCode barcoding enables clonal fate analysis for the study of development and broader questions of clonality in murine biology.
    Keywords:  Cre; barcoding; cell fate; clonal; embryogenesis; epiblast; lineage tracing; mathematical modeling; pedigree; phylogenetics
    DOI:  https://doi.org/10.1016/j.cell.2025.04.026
  12. Methods Mol Biol. 2025 May 22.
      Recent advances in three-dimensional (3D) modeling of post-implantation human embryos using human pluripotent stem cells (hPSCs) have revolutionized our ability to investigate this crucial yet enigmatic stage of development. Here we detail the generation of the human extra-embryoid (hEE), a 3D stem cell-based embryo model that uniquely captures key spatiotemporal events of peri-gastrulation development through the formation and co-development of post-implantation embryonic and extra-embryonic lineages, with high efficiency and robustness across genetic backgrounds. This chapter provides a detailed protocol for generating hEEs in vitro, including guidance on hPSC maintenance, expected cell morphology, troubleshooting strategies, and key culture techniques.
    Keywords:  3D culture; Differentiation; Embryo model; Human embryo; Human embryonic stem cells; Human extra-embryoid; Pluripotency; Post-implantation; Stem cell
    DOI:  https://doi.org/10.1007/7651_2025_647
  13. Nat Commun. 2025 May 24. 16(1): 4823
      The spindle assembly checkpoint (SAC) ensures mitotic exit occurs only after sister chromatid biorientation, but how this coordination is mechanistically achieved remains unclear. Kinetochores, the megadalton complexes linking chromosomes to spindle microtubules, contribute to SAC signaling. However, whether they act solely as docking platforms or actively promote the co-orientation of SAC catalysts such as MAD1:MAD2 and BUB1:BUB3 remains unresolved. Here, we reconstitute kinetochores and SAC signaling in vitro to address this question. We engineer recombinant kinetochore particles that recruit core SAC components and trigger checkpoint signaling upon Rapamycin induction, and test their function using a panel of targeted mutants. At approximately physiological concentrations of SAC proteins, kinetochores are essential for efficient mitotic checkpoint complex (MCC) assembly, the key effector of SAC signaling. Our results suggest that kinetochores serve not only as structural hubs but also as catalytic platforms that concentrate and spatially organize SAC components to accelerate MCC formation and ensure timely checkpoint activation.
    DOI:  https://doi.org/10.1038/s41467-025-59970-1
  14. Nat Commun. 2025 May 21. 16(1): 4688
      Extraembryonic mesoderm (ExM) is crucial for human development, yet its specification is poorly understood. Human embryonic stem cell (hESC)-based models, including embryoids and differentiated derivatives, are emerging as promising tools for studying ExM development. Despite this, the signaling mechanisms and developmental dynamics that underlie ExM specification from hESCs remain challenging to study. Here, we report that the modulation of BMP, WNT, and Nodal signaling pathways can rapidly (4-5 days) and efficiently ( ~90%) induce the differentiation of both naive and primed hESCs into ExM-like cells (ExMs). We reveal that ExM specification from hESCs predominantly proceeds through intermediates exhibiting a primitive streak (PS)-like gene expression pattern and delineate the regulatory roles of WNT and Nodal signaling in this process. Furthermore, we find that the initial pluripotent state governs hESC-based ExM specification by influencing signal response, cellular composition, developmental progression, and transcriptional characteristics of the resulting ExMs. Our study provides promising models for dissecting human ExM development and sheds light on the signaling principles, developmental dynamics, and influences of pluripotency states underlying ExM specification from hESCs.
    DOI:  https://doi.org/10.1038/s41467-025-59491-x
  15. Cell. 2025 May 14. pii: S0092-8674(25)00507-0. [Epub ahead of print]
      In a human cell, DNA is packed with histones, RNA, and chromatin-associated proteins, forming a cohesive gel. At any given moment, only a subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair, and other essential molecular functions. We have developed a "zero-distance" photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells. Collecting DNA interactomes from human breast cancer cells, we present an atlas of over one thousand proteins with physical access to DNA and hundreds of peptide-nucleotide crosslinks pinpointing protein-DNA interfaces with single-amino-acid resolution. Quantitative comparisons of DNA interactomes from differentially treated cells recapitulate the recruitment of key transcription factors as well as DNA repair proteins and uncover fast-acting restrictors of chromatin accessibility on a timescale of minutes. This opens a direct way to explore genomic regulation in a hypothesis-free manner, applicable to many organisms and systems.
    Keywords:  DNA-binding domains; DNA-binding proteins; DNA-interacting proteome; IDRs; chromatin proteomics; intrinsically disordered regions; mass spectrometry; nucleotide-peptide hybrids; photo-crosslinking; physical protein-DNA interactions; transcription factors
    DOI:  https://doi.org/10.1016/j.cell.2025.04.037
  16. JCI Insight. 2025 May 20. pii: e172370. [Epub ahead of print]
      DNA repair is essential for preserving genome integrity. Podocytes, post-mitotic epithelial cells of the kidney filtration unit, bear limited regenerative capacity, yet their survival is indispensable for kidney health. Podocyte loss is a hallmark of the aging process and of many diseases, but the underlying factors remain unclear. We investigated the consequences of DNA damage in a podocyte-specific knockout mouse model for Ercc1 and in cultured podocytes under genomic stress. Furthermore, we characterized DNA damage-related alterations in mouse and human renal tissue of different ages and patients suffering from minimal change disease and focal segmental glomerulosclerosis. Ercc1 knockout resulted in accumulation of DNA damage, ensuing albuminuria and kidney disease. Podocytes reacted to genomic stress by activating mTORC1 signaling in vitro and in vivo. This was abrogated by inhibiting DNA damage signaling through DNA-PK and ATM kinases and inhibition of mTORC1 modulated the development of glomerulosclerosis. Perturbed DNA repair gene expression and genomic stress in podocytes was also detected in focal segmental glomerulosclerosis. Beyond that, DNA damage signaling occurred in podocytes of healthy aging mice and humans. We provide evidence that genome maintenance in podocytes is linked to the mTORC1 pathway, involved in the aging process and the development of glomerulosclerosis.
    Keywords:  Aging; Cell biology; Chronic kidney disease; DNA repair; Nephrology
    DOI:  https://doi.org/10.1172/jci.insight.172370
  17. Nat Metab. 2025 May 19.
    CRUK Rosetta Grand Challenge Consortium
      Transcriptomic studies have attempted to classify glioblastoma (GB) into subtypes that predict survival and have different therapeutic vulnerabilities1-3. Here we identified three metabolic subtypes: glycolytic, oxidative and a mix of glycolytic and oxidative, using mass spectrometry imaging of rapidly excised tumour sections from two patients with GB who were infused with [U-13C]glucose and from spatial transcriptomic analysis of contiguous sections. The phenotypes are not correlated with microenvironmental features, including proliferation rate, immune cell infiltration and vascularization, are retained when patient-derived cells are grown in vitro or as orthotopically implanted xenografts and are robust to changes in oxygen concentration, demonstrating their cell-intrinsic nature. The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes is large enough to be detected using clinically applicable metabolic imaging techniques. A limitation of the study is that it is based on only two patient tumours, albeit on multiple sections, and therefore represents a proof-of-concept study.
    DOI:  https://doi.org/10.1038/s42255-025-01293-y
  18. Science. 2025 May 22. eadr3498
      Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, central mechanisms underlying mitochondrial gene expression remain enigmatic. A lack of suitable technologies to target mitochondrial protein synthesis in cells has limited experimental access. Here, we silenced the translation of specific mitochondrial mRNAs in living human cells by delivering synthetic peptide-morpholino chimeras. This approach allowed us to perform a comprehensive temporal monitoring of cellular responses. Our study provides insights into mitochondrial translation, its integration into cellular physiology, and provides a strategy to address mitochondrial gene expression in living cells. The approach can potentially be used to analyze mechanisms and pathophysiology of mitochondrial gene expression in a range of cellular model systems.
    DOI:  https://doi.org/10.1126/science.adr3498
  19. Nat Struct Mol Biol. 2025 May 23.
      Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role in dynein activation. We recently identified a structure of partially autoinhibited dynein bound to Lis1, which suggests an intermediate state in dynein's activation pathway. However, other structural information is needed to fully understand how Lis1 activates dynein. Here, we used cryo-EM and yeast dynein and Lis1 incubated with ATP at different time points to reveal conformations that we propose represent additional intermediate states in dynein's activation pathway. We solved 16 high-resolution structures, including 7 distinct dynein and dynein-Lis1 structures from the same sample. Our data support a model in which Lis1 relieves dynein autoinhibition by increasing its basal ATP hydrolysis rate and promoting conformations compatible with complex assembly and motility. Together, this analysis advances our understanding of dynein activation and the contribution of Lis1 to this process.
    DOI:  https://doi.org/10.1038/s41594-025-01558-w
  20. Methods Mol Biol. 2025 May 20.
      Trophoblast stem cells (TSCs), equivalent to first-trimester cytotrophoblasts, serve as valuable models for studying placental diseases and understanding early embryogenesis. Recent studies have demonstrated that human-induced trophoblast stem cells (hiTSCs) can be generated either by overexpressing the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) in fibroblasts or through the transdifferentiation of pluripotent stem cells. In this chapter, we describe a methodology for directly converting fibroblasts into fully functional hiTSCs using the transcription factors GATA3, OCT4, KLF4, and MYC (GOKM). This approach circumvents the need for inducing full pluripotency and avoids the expression of pluripotency factors per se. Moreover, the GOKM method seems to be superior technique, as it yields high number of colonies and a transcriptomic profile closely resembling blastocyst/first trimester-derived TSCs.
    Keywords:  Direct conversion; Human trophoblast stem cells; Placenta; Reprogramming; Transcription factors
    DOI:  https://doi.org/10.1007/7651_2025_648
  21. FEBS J. 2025 May 19.
      Senescence is a cellular state induced by various stressors or extracellular signals, but a universal pathway that triggers this process irrespective of the initial stressor has yet to be identified. Recent data indicate that chromatin opening, particularly in the noncoding genome, is a hallmark of cellular senescence. We propose a model in which this increased chromatin accessibility mediated by transcription factors downstream of the senescence-inducing stressors acts as a decisive factor to commit cells toward the senescence fate. Engagement toward senescence is then determined by the balance between mechanisms that increase or decrease chromatin accessibility and can be influenced by modulating the activity of specific histone-modifying complexes. Traits of senescent cells, such as increased nuclear and nucleolar size, the secretion of pro-inflammatory cytokines, reduced rRNA biogenesis, telomere dysfunction, expression of retrotransposons and endogenous retroviruses, as well as DNA damage, can all be attributed to increased chromatin accessibility. This concept suggests potential targets to tilt the balance toward the senescence response in the context of future therapies against cancer and age-related diseases.
    Keywords:  ERK signaling; cancer; chromatin; epigenetics; heterochromatin; nucleolus; senescence; transposons
    DOI:  https://doi.org/10.1111/febs.70136
  22. Nature. 2025 May 21.
      To grow at distant sites, metastatic cells must overcome major challenges posed by the unique cellular and metabolic composition of secondary organs1. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that metastasizes to the liver and lungs. Despite evidence of metabolic reprogramming away from the primary site, the key drivers that dictate the ability of PDAC cells to colonize the liver or lungs and survive there remain undefined. Here we identified PCSK9 as predictive of liver versus lung colonization by integrating metastatic tropism data of human PDAC cell lines2, in vivo metastasis modelling in mice and gene expression correlation analysis. PCSK9 negatively regulates low density lipoprotein (LDL)-cholesterol import and, accordingly, PCSK9-low PDAC cells preferentially colonize LDL-rich liver tissue. LDL-cholesterol taken up by liver-avid PCSK9-low cells supports activation of pro-growth mTORC1 activation at the lysosome, and through conversion into the signalling oxysterol, 24(S)-hydroxycholesterol, reprogrammes the microenvironment to release nutrients from neighbouring hepatocytes. Conversely, PCSK9-high, lung-avid PDAC cells rely on transcriptional upregulation of the distal cholesterol synthesis pathway to generate intermediates-7-dehydrocholesterol and 7-dehydrodesmosterol-with protective action against ferroptosis, a vulnerability in the oxygen-rich microenvironment of the lung. Increasing the amount of PCSK9 redirected liver-avid cells to the lung whereas ablating PCSK9 drove lung-avid cells to the liver, thereby establishing PCSK9 as necessary and sufficient for secondary organ site preference. Our studies reveal PCSK9-driven differential utilization of the distal cholesterol synthesis pathway as a key and potentially actionable driver of metastatic growth in PDAC.
    DOI:  https://doi.org/10.1038/s41586-025-09017-8
  23. Semin Cell Dev Biol. 2025 May 20. pii: S1084-9521(25)00028-X. [Epub ahead of print]172 103618
      Somatic polyploidy, a non-inheritable form of genome multiplication, plays cell-type specific and context-dependent roles in organ development and regeneration. In the mammalian heart, embryonic cardiomyocytes are primarily diploid, which lose their ability to complete cell division and become polyploid as they mature. Unlike lower vertebrates like zebrafish, polyploid cardiomyocytes are commonly found across mammals, including humans. Intriguingly, the degree, timing, and modes of cardiomyocyte polyploidization vary greatly between species. In addition to the association with cardiomyocyte development and maturation, recent studies have established polyploidy as a barrier against cardiomyocyte proliferation and heart regeneration following cardiac injury. Hence, a thorough understanding of how and why cardiomyocyte become polyploid will provide insights into heart development and may help develop therapeutic strategies for heart regeneration. Here, we review the dynamics of cardiomyocyte polyploidization across species and how cardiomyocyte-intrinsic, -extrinsic, and environmental factors regulate this process as well as the impact of cardiomyocyte polyploidization on heart development and regeneration.
    Keywords:  Cardiac development; Cardiac regeneration; Cardiomyocytes; Heart; Polyploidy
    DOI:  https://doi.org/10.1016/j.semcdb.2025.103618
  24. Nature. 2025 May 21.
    COPL Consortium
      Every generation, the human genome is shuffled during meiosis and a single fertilized egg gives rise to all of the cells of the body1. Meiotic errors leading to chromosomal abnormalities are known causes of pregnancy loss2,3, but genetic aetiologies of euploid pregnancy loss remain largely unexplained4. Here we characterize sequence diversity in early pregnancy loss through whole-genome sequencing of 1,007 fetal samples and 934 parental samples from 467 trios affected by pregnancy loss (fetus, mother and father). Sequenced parental genomes enabled us to determine both the parental and meiotic origins of chromosomal abnormalities, detected in half of our set. It further enabled us to assess de novo mutations on both homologous chromosomes from parents transmitting extra chromosomes, and date them, revealing that 6.6% of maternal mutations occurred before sister chromatid formation in fetal oocytes. We find a similar number of de novo mutations in the trios affected by pregnancy loss as in 9,651 adult trios, but three times the number of pathogenic small (<50 bp) sequence variant genotypes in the loss cases compared with adults. Overall, our findings indicate that around 1 in 136 pregnancies is lost due to a pathogenic small sequence variant genotype in the fetus. Our results highlight the vast sequence diversity that is lost in early pregnancy.
    DOI:  https://doi.org/10.1038/s41586-025-09031-w
  25. Genes Dev. 2025 May 19.
      The TEAD family of transcription factors is best known as the DNA-binding factor in the Hippo pathway, where these factors act by interacting with transcriptional coactivators YAP and TAZ (YAP/TAZ). Despite the importance of the Hippo pathway, the in vivo functions of TEAD in mammals have not been well established. By comparing mouse mutants lacking TEAD1 and TEAD2 (TEAD1/2) with those lacking YAP/TAZ, we found that TEAD1/2 have both YAP/TAZ-dependent and YAP/TAZ-independent functions during ventral telencephalon development. TEAD1/2 loss and YAP/TAZ loss similarly disrupt neuroepithelial apical junctions. However, the impacts of their losses on progenitor lineage progression are essentially opposite: YAP/TAZ loss depletes early progenitors and increases later progenitors, consistent with their established function in promoting progenitor self-renewal and proliferation, whereas TEAD1/2 loss expands early progenitors and reduces late progenitors, indicating that TEAD1/2 promote lineage progression. We further show that TEAD1/2 promote neural progenitor lineage progression by at least in part inhibiting Notch signaling and by cooperating with insulinoma-associated 1 (INSM1). Orthologs of TEAD and INSM1 have been shown to cooperatively regulate neuronal cell fate decisions in worms and flies. Our study reveals a remarkable evolutionary conservation of the function of this transcription factor complex during metazoan neural development.
    Keywords:  apical progenitor; basal ganglia; basal progenitor; intermediate progenitor; interneuron; medial ganglionic eminence (MGE); neurogenesis; radial glia; subapical progenitor; subpallium
    DOI:  https://doi.org/10.1101/gad.352632.125
  26. Curr Opin Cell Biol. 2025 May 16. pii: S0955-0674(25)00068-7. [Epub ahead of print]95 102530
      The cell nucleus is a fascinating organelle. The myriad of fundamental processes that ensure that the genetic information is read correctly and faithfully transmitted provides a rich subject of research across time scales and model systems. Topics ranging from chromosome 'metascale' organization and division, enabled by molecular machineries like the kinetochore, to the organization of the genome that ensues cell division during interphase, which enables fine tuning of gene regulation, are subjects that we cover in the 'Cell Nucleus' issue of Current Opinion in Cell Biology.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102530
  27. Curr Opin Cell Biol. 2025 May 21. pii: S0955-0674(25)00071-7. [Epub ahead of print]95 102533
      Intracellular organelles are essential for cellular architecture and function, and their size regulation is critical for maintaining cellular homeostasis. Organelle size often scales with cell size, governed by mechanisms that integrate resource allocation, stochastic dynamics, and feedback controls. Here we review these underlying biophysical principles of organelle size control, including the limiting pool hypothesis, stochastic assembly processes, and feedback-driven growth dynamics. We discuss how negative feedback motifs stabilize size, while positive feedback can amplify growth and maintain size under specific conditions. Additionally, we discuss recent advances in modeling size control for organelles with nucleation and fission-fusion dynamics. By integrating experimental observations with theoretical insights, this review provides a conceptual understanding of the design principles governing organelle size regulation in dynamic cellular environments.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102533
  28. Dev Cell. 2025 May 15. pii: S1534-5807(25)00287-4. [Epub ahead of print]
      Glioblastoma (GBM) is the most aggressive primary intracranial tumor, with glioblastoma stem cells (GSCs) enforcing the intratumoral hierarchy. The inflammatory microenvironment influences tumor development at varying stages, while the underlying mechanism of GSCs facing pro-inflammatory stress remains unclear. Here, we show that, in human GBM, pro-inflammatory stress from pro-inflammatory macrophages (pTAMs) maintains GSC proliferation and self-renewal. Tumor necrosis factor alpha-induced protein 6 (TNFAIP6), as a responder in patient-derived GSCs to pro-inflammatory stress tumor necrosis factor alpha (TNF-α) from human pTAMs, promotes tumor growth through binding epidermal growth factor (EGF) and prolonging EGF receptor (EGFR)-phosphatidylinositol 3-kinase (PI3K)-protein kinase B (AKT) signaling activation. Meanwhile, pro-inflammatory stress-induced patient-derived GSCs secrete TNFAIP6 to transform macrophage phenotype from pTAMs to inflammatory-suppressive macrophages (sTAMs). Collectively, pharmacological or genetic disruption of TNFAIP6 autocrine and paracrine communication between patient-derived GSCs and TAMs inhibited GSC proliferation and self-renewal in vitro and in patient-derived xenograft tumor-bearing mice, suggesting that TNFAIP6 is an effective target for GBM therapy.
    Keywords:  glioblastoma; glioblastoma stem cells; pro-inflammatory stress; tumor necrosis factor alpha-induced protein 6; tumor-associated macrophage
    DOI:  https://doi.org/10.1016/j.devcel.2025.04.027
  29. Nat Cell Biol. 2025 May 22.
      Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved. We previously showed that secretion of LTB4-containing exosomes via nuclear envelope-derived multivesicular bodies is required for effective neutrophil infiltration during inflammation. Here we report that the co-secretion of these exosomes with nuclear DNA facilitates the resolution of the neutrophil infiltrate in a mouse skin model of sterile inflammation. Activated neutrophils exhibit rapid and repetitive DNA secretion as they migrate directionally using a mechanism distinct from suicidal neutrophil extracellular trap release and cell death. Packaging of DNA in the lumen of nuclear envelope-multivesicular bodies is mediated by lamin B receptor and chromatin decondensation. These findings advance our understanding of neutrophil functions during inflammation and the physiological relevance of DNA secretion.
    DOI:  https://doi.org/10.1038/s41556-025-01671-4
  30. Nat Commun. 2025 May 22. 16(1): 4754
      The platelet-derived growth factor receptor (PDGFR) family of receptor tyrosine kinases consists of two receptors, PDGFRα and PDGFRβ, that homodimerize and heterodimerize upon ligand binding. Here, we tested the hypothesis that differential internalization and trafficking dynamics of the various PDGFR dimers underlie differences in downstream intracellular signaling and cellular behavior. Using a bimolecular fluorescence complementation approach, we demonstrated that PDGFRα/β heterodimers are rapidly internalized into early endosomes. We showed that PDGFRα/β heterodimer activation does not induce downstream phosphorylation of ERK1/2 and significantly inhibits cell proliferation. Further, we identified MYO1D as a protein that preferentially binds PDGFRα/β heterodimers and demonstrated that knockdown of MYO1D leads to retention of PDGFRα/β heterodimers at the plasma membrane, increased phosphorylation of ERK1/2 and increased cell proliferation. Collectively, our findings impart valuable insight into the molecular mechanisms by which specificity is introduced downstream of PDGFR activation to differentially propagate signaling and generate distinct cellular responses.
    DOI:  https://doi.org/10.1038/s41467-025-59938-1
  31. Nature. 2025 May 21.
      Around 40% of the US population and 1 in 6 individuals worldwide have obesity, with the incidence surging globally1,2. Various dietary interventions, including carbohydrate, fat and, more recently, amino acid restriction, have been explored to combat this epidemic3-6. Here we investigated the impact of removing individual amino acids on the weight profiles of mice. We show that conditional cysteine restriction resulted in the most substantial weight loss when compared to essential amino acid restriction, amounting to 30% within 1 week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, partly explaining the phenotype7-9. Notably, we observed lower levels of tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective tricarboxylic acid cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen-rich compounds and amino acids. In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism and stress signalling compared with other amino acid restrictions. These findings suggest strategies for addressing a range of metabolic diseases and the growing obesity crisis.
    DOI:  https://doi.org/10.1038/s41586-025-08996-y
  32. EMBO Rep. 2025 May 19.
      Epithelial cells exhibit strong interconnections that are crucial for tissue mechanical properties. In homeostasis, these properties, termed mechanical homeostasis, depend on the balance between intercellular tension and extracellular matrix (ECM) adhesion forces. While age-related ECM remodeling is linked to outer retinal disease, its fundamental role in mechanical homeostasis remains unclear. In our study, we quantified changes in the mechanical state of retinal pigment epithelium (RPE), revealing a correlation with gradients of basement membrane laminins and their integrin receptors, β1 and β4. This relationship is related to regional phagocytic demand for recycling photoreceptor outer segments. Using a reductionist approach, we found that laminin 332 and laminin 511 isoforms differentially influence engagement with β1 and β4 integrins at low densities. Notably, laminin 511 enhances RPE contractility by reducing the β4 to β1 integrin engagement ratio, which subsequently diminishes phagocytic efficiency. Our findings suggest that the ECM-defined mechanical status of RPE serves as a novel parameter for visual function.
    Keywords:  ECM; Laminin; Mechanical Homeostasis; RPE
    DOI:  https://doi.org/10.1038/s44319-025-00475-9