bims-ginsta Biomed News
on Genome instability
Issue of 2025–09–21
thirty-one papers selected by
Jinrong Hu, National University of Singapore
  1. Replisome passage through the cohesin ring.
  2. Signaling reprogramming via Stat3 activation unravels high-fidelity human post-implantation embryo modeling.
  3. Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers.
  4. Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication.
  5. The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking.
  6. Nuclear mechanics as a determinant of nuclear pore complex plasticity.
  7. Cardiac lymphatics retain LYVE-1-dependent macrophages during neonatal mouse heart regeneration.
  8. p53-mediated regulation of epiblast cell numbers predicts reactivation during mouse embryonic diapause.
  9. The dynamics of centromere assembly and disassembly during quiescence.
  10. Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosis.
  11. Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals.
  12. Dynamic recruitment of Munc13 primes docked secretory granules for exocytosis.
  13. Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer.
  14. Advancing biological understanding of cellular senescence with computational multiomics.
  15. Leaflet-specific phospholipid imaging using genetically encoded proximity sensors.
  16. Spindle-localized F-actin regulates polar MTOC organization and the fidelity of meiotic spindle formation.
  17. Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.
  18. Hair Follicle Stem Cell SLC3A2 regulates epithelial regenerative properties.
  19. Proteomics-based multi-omics identifies the roadmap of transcription-translation-protein dynamics in planarian regeneration.
  20. BDH2-driven lysosome-to-mitochondria iron transfer shapes ferroptosis vulnerability of the melanoma cell states.
  21. Targeting Cardiomyocyte PCNA and POLD1 Prevents Pathological Myocardial Hypertrophy.
  22. Tissue geometry and mechanochemical feedback initiate rotational migration in Drosophila.
  23. A model for boundary-driven tissue morphogenesis.
  24. QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sites.
  25. Cellular mechanism linking endoplasmic reticulum inheritance and cell cycle regulation of the nuclear genome.
  26. Single-cell compendium of muscle microenvironment in peripheral artery disease reveals altered endothelial diversity and LYVE1+ macrophage activation.
  27. Systems Age: a single blood methylation test to quantify aging heterogeneity across 11 physiological systems.
  28. ATP-dependent one-dimensional movement maintains immune homeostasis by suppressing spontaneous MDA5 filament assembly.
  29. OGFOD1 enables AML chemo- and nutrient stress resistance by regulating protein synthesis.
  30. An electrostatic repulsion model of centromere organisation.
  31. Spatially patterned kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling.
  1. Cell. 2025 Sep 16. pii: S0092-8674(25)01017-7. [Epub ahead of print]
    Replisome passage through the cohesin ring.
    Samson Glaser, Maxim I Molodtsov, John F X Diffley, Frank Uhlmann.
      Following eukaryotic genome replication, the ring-shaped cohesin complex embraces the two newly synthesized sister chromatids, enabling their faithful segregation during cell divisions. Replisome passage through cohesin rings has been envisioned as a fail-safe mechanism that ensures co-entrapment of replication products-whether replisomes can indeed pass through cohesin rings remains unknown. Here, we use biochemical reconstitution and single-molecule fluorescence microscopy to directly visualize replisome-cohesin encounters. We find that the translocating eukaryotic replicative Cdc45-Mcm2-7-GINS (CMG) helicase, unlike other obstacles of similar size, readily passes through cohesin rings. Fully reconstituted replisomes also pass cohesin rings to leave both replication products trapped inside. Replisome passage is primarily aided by DNA polymerases α and ε, a finding that necessitates re-evaluation of canonical cohesion establishment factor roles. Our findings demonstrate the existence of a simple mechanism that links genome replication with chromosome segregation: replisome passage through cohesin rings.
    Keywords:  DNA replication; chromosome segregation; cohesin; single-molecule fluorescence microscopy; sister chromatid cohesion
    DOI:  https://doi.org/10.1016/j.cell.2025.08.028
  2. Cell Stem Cell. 2025 Sep 16. pii: S1934-5909(25)00303-0. [Epub ahead of print]
    Signaling reprogramming via Stat3 activation unravels high-fidelity human post-implantation embryo modeling.
    Chuanxin Chen, Jinyi Wu, Xinggu Wang, Litao Chang, Kexin Wang, Kaiyi Wu, Mingyue Guo, Huanhuan Li, Fei Sun, Xinxing Jiang, Yanlin Ma, Guangjin Pan, Zhenyu Xiao, José C R Silva.
      Human embryo models hold great promise for advancing medicine, but current systems lack efficiency and fidelity in replicating post-implantation stages. Here, we investigate whether STAT3 activation can reprogram pluripotent stem cells (PSCs) into early fates that self-organize into embryo models. Using a medium enhancing STAT3 activity (SAM), PSCs reprogram within 60 h into hypoblast, trophectoderm, naive epiblast, and extraembryonic mesoderm. Dissociating SAM-treated PSCs at 60-120 h, followed by 3D culture, results in dynamic development of post-implantation embryo-like structures with up to 52.41% ± 8.92% efficiency. Resulting day 6 examples resemble Carnegie stages 5 (CS5) to 7 (CS7) embryos, exhibiting bilaminar disc structure with epiblast and yolk sac, amniotic cavity, mesenchyme, chorionic cavity, and trophoblast. Notably, CS6/7-like examples exhibit gastrulation, including the formation and correct positioning of primitive streak, epithelial-to-mesenchymal transition, mesoderm, and definitive endoderm. The STAT3-mediated embryo model also closely aligns molecularly with CS6/7 embryo references and represents a state-of-the-art platform for advancing human embryogenesis research.
    Keywords:  STAT3 signaling; gastrulation; human post-implantation development; integrated embryo model; pluripotency; reprogramming
    DOI:  https://doi.org/10.1016/j.stem.2025.08.011
  3. Nat Struct Mol Biol. 2025 Sep 15.
    Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers.
    Tianyang Liu, Luyan Cao, Miroslav Mladenov, Guillaume Romet-Lemonne, Michael Way, Carolyn A Moores.
      Branched actin networks nucleated by the Arp2/3 complex have critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated by WISH/DIP/SPIN90-family proteins, Arp2/3 nucleates linear actin filaments. Here we found that human SPIN90 is a dimer that can nucleate bidirectional actin filaments. To understand the basis for this, we determined a 3-Å-resolution structure of human SPIN90-Arp2/3 complex nucleating actin filaments. Our structure shows that SPIN90 dimerizes through a three-helix bundle and interacts with two Arp2/3 complexes. Each SPIN90 molecule binds both Arp2/3 complexes to promote their activation. Our analysis demonstrates that single-filament nucleation by Arp2/3 is mechanistically more like branch formation than previously appreciated. The dimerization domain in SPIN90 orthologs is conserved in metazoans, suggesting that this mode of bidirectional nucleation is a common strategy to generate antiparallel actin filaments.
    DOI:  https://doi.org/10.1038/s41594-025-01665-8
  4. Mol Cell. 2025 Sep 16. pii: S1097-2765(25)00711-7. [Epub ahead of print]
    Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication.
    Masashi Minamino, John F X Diffley, Frank Uhlmann.
      Concomitant with DNA replication, the ring-shaped cohesin complex encircles both newly synthesized sister chromatids, enabling their faithful segregation during cell divisions. Our molecular understanding of how cohesin co-entraps both replication products remains incomplete. Here, we reconstitute sister chromatid cohesion establishment using purified budding yeast proteins. Cohesin rings, initially loaded onto template DNA, remain DNA bound during complete DNA synthesis. Some of these cohesin rings encircle both sister chromatids, consistent with the idea that replisomes traverse through cohesin rings. Often, however, cohesin ends up embracing only one of the two replication products, suggesting that a two-step capture mechanism operates during cohesion establishment. Additionally, DNA replication initiates new cohesin recruitment as a further means to generate sister chromatid cohesion. Our results illustrate that more than one pathway leads to sister chromatid cohesion, and they make cohesion establishment amenable to direct biochemical exploration.
    Keywords:  S. cerevisiae; biochemical reconstitution; chromosome replication; chromosome segregation; cohesin; sister chromatid cohesion
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.026
  5. Nat Struct Mol Biol. 2025 Sep 19.
    The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking.
    Grant A Pellowe, Tomas B Voisin, Laura Karpauskaite, Sarah L Maslen, Alžběta Roeselová, J Mark Skehel, Chloe Roustan, Roger George, Andrea Nans, Svend Kjær, Ian A Taylor, David Balchin.
      Proteins with multiple domains are intrinsically prone to misfold, yet fold efficiently during their synthesis on the ribosome. This is especially important in eukaryotes, where multidomain proteins predominate. Here we sought to understand how multidomain protein folding is modulated by the eukaryotic ribosome. We used hydrogen-deuterium exchange mass spectrometry and cryo-electron microscopy to characterize the structure and dynamics of partially synthesized intermediates of a model multidomain protein. We find that nascent subdomains fold progressively during synthesis on the human ribosome, templated by interactions across domain interfaces. The conformational ensemble of the nascent chain is tuned by its unstructured C-terminal segments, which keep interfaces between folded domains in dynamic equilibrium until translation termination. This contrasts with the bacterial ribosome, on which domain interfaces form early and remain stable during synthesis. Delayed domain docking may avoid interdomain misfolding to promote the maturation of multidomain proteins in eukaryotes.
    DOI:  https://doi.org/10.1038/s41594-025-01676-5
  6. Nat Cell Biol. 2025 Sep 19.
    Nuclear mechanics as a determinant of nuclear pore complex plasticity.
    C Patrick Lusk, Kimberly J Morgan, Megan C King.
      Thousands of nuclear pore complexes (NPCs) cover the nuclear surface of mammalian cells and establish selective transport conduits that biochemically segregate the nucleoplasm and cytoplasm. Although the molecular composition and structure of archetypical NPCs are well understood, distinct NPCs composed of varying nucleoporins exist in different cell types and even within individual cells. Furthermore, the integration of NPCs within mechanosensitive networks impacts their dilation state. However, whether (and how) the dilation or compositional plasticity of NPCs impacts their primary role as selective transport channels remains unclear. Based on our current understanding of NPC plasticity, we propose here that nuclear membrane tension and the resulting dilation of nuclear pores is a determinant of the compositional plasticity of NPCs, thus providing a framework to interpret how nucleoporins may influence cell fate decisions and explain the tissue-specificity of some NPC-related diseases.
    DOI:  https://doi.org/10.1038/s41556-025-01768-w
  7. Nat Cardiovasc Res. 2025 Sep 17.
    Cardiac lymphatics retain LYVE-1-dependent macrophages during neonatal mouse heart regeneration.
    Benjamin G Chapman, Konstantinos Klaourakis, Carla de Villiers, Mala Gunadasa-Rohling, Maria-Alexa Cosma, Susanna T E Cooper, Kshitij Mohan, Michael Weinberger, Carolyn A Carr, David R Greaves, David G Jackson, Daniela Pezzolla, Robin P Choudhury, Joaquim M Vieira, Paul R Riley.
      In adult mice, myocardial infarction (MI) activates the cardiac lymphatics, which undergo sprouting angiogenesis (lymphangiogenesis), drain interstitial fluid and traffic macrophages to mediastinal lymph nodes (MLNs). This prevents edema and reduces inflammatory/fibrotic immune cell content to improve cardiac function. Here we investigated the role of cardiac lymphatics and macrophage clearance across the neonatal mouse regenerative window. The response to injury revealed limited lymphangiogenesis and clearance of macrophages from postnatal day 1 compared to postnatal day 7 infarcted hearts. This coincides with the maturation of lymphatic endothelial cell junctions from impermeable to permeable and with altered signaling between lymphatic endothelial cells and macrophages. Mice lacking the lymphatic endothelial receptor-1 (LYVE-1), where macrophage lymphatic trafficking is impaired in adults, experienced worse long-term outcomes after MI induced at postnatal day 1, suggesting an alternative role for LYVE-1 in macrophages. Macrophage-specific deletion of Lyve1 during neonatal heart injury impaired heart regeneration. This study demonstrates that immature cardiac lymphatics are impermeable to clearance in early neonates, ensuring retention of pro-regenerative LYVE-1-dependent macrophages.
    DOI:  https://doi.org/10.1038/s44161-025-00711-4
  8. Cell Rep. 2025 Sep 17. pii: S2211-1247(25)01069-1. [Epub ahead of print]44(10): 116298
    p53-mediated regulation of epiblast cell numbers predicts reactivation during mouse embryonic diapause.
    Megumi Murata, Akihito Harada, Haruka Hirose, Hinako Maeda, Teppei Shimamura, Yasuyuki Ohkawa, Tatsuya Takemoto, Katsuyoshi Takaoka.
      Embryonic diapause is a temporary suspension of proliferation in mammalian pre-implantation embryos, allowing for reactivation later. Cells in mouse diapause embryos enter the G0 phase within 7 days of diapause initiation. Here, we show that approximately 5% of cells in embryonic tissues continue to proliferate even after 7 days of diapause. Transcriptome and phenotypic analyses reveal that p53 facilitated DNA damage repair via p21-mediated cell cycle arrest and regulated epiblast cell numbers via Bax-mediated apoptosis. Moreover, epiblast cell numbers strongly correlated with reactivation rates, with deviations from optimal levels impairing successful reactivation. Our findings call into question the conventional view that all cells in diapause embryos uniformly enter G0. We established epiblast characteristics as predictive factors for determining reactivation success, the defining event of diapause.
    Keywords:  CP: Developmental biology; G0 stage; apoptosis; blastocyst; cell differentiation; cell proliferation; embryonic diapause; implantation
    DOI:  https://doi.org/10.1016/j.celrep.2025.116298
  9. bioRxiv. 2025 Sep 08. pii: 2025.09.08.674938. [Epub ahead of print]
    The dynamics of centromere assembly and disassembly during quiescence.
    Océane Marescal, Kuan-Chung Su, Brittania Moodie, Noah J L Taylor, Iain M Cheeseman.
      Quiescence is a state in which cells undergo a prolonged proliferative arrest while maintaining their capacity to reenter the cell cycle. Here, we analyze entry and exit from quiescence, focusing on how cells regulate the centromere, a structure involved in chromosome segregation. Despite the constitutive localization of centromere proteins throughout the cell cycle, we find that cells rapidly disassemble most centromere proteins during quiescence entry, while preserving those required to maintain centromere identity. During quiescence exit, the centromere is reassembled and rapidly regains normal homeostatic levels of centromere proteins. Although the histone variant CENP-A is typically deposited during G1, we find that CENP-A deposition does not occur during the G1 immediately following quiescence exit, and instead occurs after cells complete their first mitosis. In contrast, other centromere proteins relocalize during the first S phase independent of DNA replication. These findings reveal centromere dynamics during quiescence entry and exit and highlight paradigms for the timing and control of centromere protein deposition.
    DOI:  https://doi.org/10.1101/2025.09.08.674938
  10. Nat Cardiovasc Res. 2025 Sep 16.
    Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of the RNA sensor MDA5 in atherosclerosis.
    Chad S Weldy, Qin Li, João P Monteiro, Tim S Peters, Hongchao Guo, Drew Galls, Wenduo Gu, Paul P Cheng, Markus Ramste, Daniel Li, Brian T Palmisano, Disha Sharma, Matthew D Worssam, Quanyi Zhao, Amruta Bhate, Ramendra K Kundu, Trieu Nguyen, Michal Mokry, Clint L Miller, Sander W van der Laan, Jin Billy Li, Thomas Quertermous.
      Although genetic risk in coronary artery disease (CAD) is linked to changes in gene expression, recent discoveries have revealed a major role for A-to-I RNA editing in CAD. ADAR1 edits immunogenic double-stranded RNA (dsRNA), preventing activation of the dsRNA sensor MDA5 (IFIH1) and downstream interferon-stimulated gene signaling. Using human plaque analysis and human coronary artery smooth muscle cells (SMCs), here, we show that SMCs uniquely require RNA editing and that MDA5 activation regulates SMC phenotype. In a conditional SMC-specific Adar deletion mouse model on an atherosclerosis-prone background, combined with Ifih1 deletion and single-cell RNA sequencing, we demonstrate that ADAR1 preserves vascular integrity and limits atherosclerosis and calcification by suppressing MDA5 activation. Analysis of the Athero-Express carotid endarterectomy cohort further shows that interferon-stimulated gene expression correlates with SMC modulation, plaque instability and calcification. These findings reveal a fundamental mechanism of CAD, where cell type and context-specific RNA editing modulates genetic risk and vascular disease progression.
    DOI:  https://doi.org/10.1038/s44161-025-00710-5
  11. Cell Stem Cell. 2025 Sep 17. pii: S1934-5909(25)00330-3. [Epub ahead of print]
    Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals.
    Chenghao Fan, Shen Song, Yu Han, Dongcheng Cai, Anteng Shi, Fangfang Wan, Jie Feng, Jiajun Zhong, Yifan Xie, Fei Xu, Jiangping Song, Shengshou Hu, Yu Nie, Hui Zhang.
      Adult mammalian hearts are non-regenerative, and a majority of studies examining repair and potential regeneration post-myocardial infarction (MI) have focused on cardiomyocyte (CM) proliferation and infarcted zones. Here, we observed aberrantly high expression of lysozyme 2 (Lyz2) in injured mouse hearts at both local injury sites and at remote zones, with sustained Lyz2 expression conspicuous in endocardial cells of non-regenerative hearts. Although traditionally conceptualized as a myeloid marker, we demonstrate that LYZ2 functions as an injury-specific, positive regulator of lysosomal degradation capacity that mediates pathogenic degradation of the extracellular matrix. We observed an anti-apoptotic benefit to CMs upon disrupting LYZ2/LYZ function in mice and in a human endomyocardium experimental model. Harnessing these insights, we show that both Lyz2 knockout (KO) and pharmacological inhibition of lysosomal degradation confer rapid functional recovery in injured non-regenerative hearts. Thus, targeting a remote injury response in a non-CM cell type rapidly promotes post-MI recovery of non-regenerative hearts.
    Keywords:  HSPG; Lyz2; apilimod; cardiac repair; endocardial cells; injury responses; lysosomal degradability; lysosome; regeneration
    DOI:  https://doi.org/10.1016/j.stem.2025.08.015
  12. Cell Rep. 2025 Sep 17. pii: S2211-1247(25)01072-1. [Epub ahead of print]44(10): 116301
    Dynamic recruitment of Munc13 primes docked secretory granules for exocytosis.
    Santiago Echeverry, Jan Saras, Per-Eric Lund, Johan Dunevall, Nikhil R Gandasi, Sebastian Barg.
      Munc13 proteins are essential for regulated exocytosis in neurons and endocrine cells. They consist of an elongated MUN domain that templates SNARE complex formation during priming, flanked by regulatory membrane-associated C1 and C2 domains. Here, we show, using quantitative high-resolution imaging, that priming of insulin granules coincides with recruitment of on average six copies of Munc13 to individual docked granules, similar to estimates of SNARE complexes formed during exocytosis. Intracellular Ca2+- or lipid-signaling accelerates granule priming by promoting C2B-dependent translocation of Munc13 to the plasma membrane, followed by slower (tens of seconds) C2A-domain dependent accumulation at docked granules. Exocytosis in human β-cells also exhibits rapid Ca2+-dependent short-term facilitation that involves Ca2+/C2B-dependent activation of Munc13 but not further accumulation at the release site. Thus, Munc13 controls secretory granule release probability by two separate C2B-dependent mechanisms that affect its recruitment to the release site and its subsequent activation by Ca2+.
    Keywords:  CP: Cell biology; Ca2+-dependent facilitation; Munc13; SNARE; exocytosis; insulin release; β cells
    DOI:  https://doi.org/10.1016/j.celrep.2025.116301
  13. Nature. 2025 Sep 17.
    Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer.
    Abbie S Ireland, Daniel A Xie, Sarah B Hawgood, Margaret W Barbier, Lisa Y Zuo, Benjamin E Hanna, Scarlett Lucas-Randolph, Darren R Tyson, Benjamin L Witt, Ramaswamy Govindan, Afshin Dowlati, Justin C Moser, Anish Thomas, Sonam Puri, Charles M Rudin, Joseph M Chan, Andrew Elliott, Trudy G Oliver.
      Neuroendocrine and tuft cells are rare chemosensory epithelial lineages defined by the expression of ASCL1 and POU2F3 transcription factors, respectively. Neuroendocrine cancers, including small cell lung cancer (SCLC), frequently display tuft-like subsets, a feature linked to poor patient outcomes1-9. The mechanisms driving neuroendocrine-tuft tumour heterogeneity and the origins of tuft-like cancers are unknown. Using multiple genetically engineered animal models of SCLC, we demonstrate that a basal cell of origin (but not the accepted neuroendocrine origin) generates neuroendocrine-tuft-like tumours that highly recapitulate human SCLC. Single-cell clonal analyses of basal-derived SCLC further uncovered unexpected transcriptional states, including an Atoh1+ state, and lineage trajectories underlying neuroendocrine-tuft plasticity. Uniquely in basal cells, the introduction of genetic alterations enriched in human tuft-like SCLC, including high MYC, PTEN loss and ASCL1 suppression, cooperates to promote tuft-like tumours. Transcriptomics of 944 human SCLCs revealed a basal-like subset and a tuft-ionocyte-like state that altogether demonstrate notable conservation between cancer states and normal basal cell injury response mechanisms10-13. Together, these data indicate that the basal cell is a probable origin for SCLC and other neuroendocrine-tuft cancers that can explain neuroendocrine-tuft heterogeneity, offering new insights for targeting lineage plasticity.
    DOI:  https://doi.org/10.1038/s41586-025-09503-z
  14. Nat Genet. 2025 Sep 15.
    Advancing biological understanding of cellular senescence with computational multiomics.
    SenNet Consortium
      Cellular senescence is a complex biological process that plays a pathophysiological role in aging and age-related diseases. The biological understanding of senescence at the cellular and tissue levels remains incomplete due to the lack of specific biomarkers as well as the relative rarity of senescent cells, their phenotypic heterogeneity and dynamic features. This Review provides a comprehensive overview of multiomic approaches for the characterization and biological understanding of cellular senescence. The technical capability and challenges of each approach are discussed, and practical guidelines are provided for selecting tools for identifying, characterizing and spatially mapping senescent cells. The importance of computational analyses in multiomics research, including senescent cell identification, signature detection and interactions of senescent cells with microenvironments, is highlighted. Moreover, tissue-specific case studies and experimental design considerations for individual organs are presented. Finally, future directions and the potential impact of multiomic approaches on the biological understanding of cellular senescence are discussed.
    DOI:  https://doi.org/10.1038/s41588-025-02314-y
  15. Nat Chem Biol. 2025 Sep 15.
    Leaflet-specific phospholipid imaging using genetically encoded proximity sensors.
    William M Moore, Roberto J Brea, Caroline H Knittel, Ellen Wrightsman, Brandon Hui, Jinchao Lou, Christelle F Ancajas, Michael D Best, Christopher J Obara, Neal K Devaraj, Itay Budin.
      The lipid composition of cells varies widely across organelles and between individual membrane leaflets. Transport proteins are thought to generate this heterogeneity, but measuring their functions in vivo has been hampered by limited tools for imaging lipids at relevant spatial resolutions. Here we present fluorogen-activating coincidence encounter sensing (FACES), a chemogenetic tool capable of quantitatively imaging subcellular lipid pools and reporting their transbilayer orientation in living cells. FACES combines bioorthogonal chemistry with genetically encoded fluorogen-activating proteins (FAPs) for reversible proximity sensing of conjugated molecules. We first apply this approach to identify roles for lipid transfer proteins that traffic phosphatidylcholine pools between the ER and mitochondria. We then show that transmembrane domain-containing FAPs can reveal the membrane asymmetry of multiple lipid classes in the trans-Golgi network and be used to investigate the mechanisms that generate it. Finally, we present that FACES can be applied to measure glycans and other molecule classes.
    DOI:  https://doi.org/10.1038/s41589-025-02021-z
  16. Nat Commun. 2025 Sep 19. 16(1): 8323
    Spindle-localized F-actin regulates polar MTOC organization and the fidelity of meiotic spindle formation.
    Edgar J Soto-Moreno, Nourhan N Ali, Florian Küllmer, Veselin Nasufovic, Michaela Frolikova, Olga Tepla, Jaromir Masata, Dirk Trauner, Amanda A Patterson, Hans-Dieter Arndt, Katerina Komrskova, Magdalena Zernicka-Goetz, David M Glover, Ahmed Z Balboula.
      Mammalian oocytes are notoriously prone to chromosome segregation errors leading to aneuploidy. The spindle provides the machinery for accurate chromosome segregation during cell division. Mammalian oocytes lack centrioles and, therefore, mouse meiotic spindle relies on the organization of numerous acentriolar microtubule organizing centers into two poles (polar microtubule organizing centers, pMTOCs). The traditional view is that, in mammalian oocytes, microtubules are the sole cytoskeletal component responsible for regulating pMTOC organization and spindle assembly. We identify a previously unrecognized F-actin pool that surrounds pMTOCs, forming F-actin cage-like structure. We demonstrate that F-actin localization on the spindle depends on unconventional myosins X and VIIb. Selective disruption of spindle-localized F-actin, using myosin X/VIIb knockdown oocytes or photoswitchable Optojasp-1, perturbs pMTOC organization, leading to unfocused spindle poles and chromosome missegregation. Here, we unveil an important function of spindle-localized F-actin in regulating pMTOC organization, a critical process for ensuring the fidelity of meiotic spindle formation and proper chromosome segregation.
    DOI:  https://doi.org/10.1038/s41467-025-63586-w
  17. Nat Struct Mol Biol. 2025 Sep 15.
    Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.
    Justus Francis, Achyutha Krishna Pathri, Kankipati Teja Shyam, Sridhar Sripada, Rishav Mitra, Heidy Y Narvaez-Ortiz, Kiran Vyshnav Eliyan, Brad J Nolen, Saikat Chowdhury.
      Arp2/3 complex is a key nucleator of actin filaments. It requires activation by nucleation-promoting factors (NPFs). WISH/DIP1/SPIN90 (WDS) proteins represent a unique class of NPFs that activate the Arp2/3 complex independently of preexisting filaments, promoting linear actin-filament nucleation. In fission yeast, Dip1 binds to the clamp subunits in Arp2/3 complex to induce the short-pitch conformation, where Arp2 moves closer to Arp3 to mimic a filamentous actin dimer. However, how WDS proteins stimulate subunit flattening in Arp subunits, a 'scissor-like' conformational change akin to what is observed in an actin monomer during filament formation, remained unclear. Here we present cryo-electron microscopy structures of human SPIN90 bound to activated bovine Arp2/3 complex on an actin filament pointed end. The structures show that SPIN90 dimerizes through a metazoan-specific domain in the middle segment, engaging both the clamp and the Arp3/ARPC3 interface, to drive the activating conformational changes in Arp2/3 complex. Remarkably, a single SPIN90 dimer can also bridge two Arp2/3 complexes, enabling bidirectional actin nucleation and suggesting a mechanism for rapidly assembling complex actin network architectures.
    DOI:  https://doi.org/10.1038/s41594-025-01673-8
  18. J Invest Dermatol. 2025 Sep 12. pii: S0022-202X(25)02426-1. [Epub ahead of print]
    Hair Follicle Stem Cell SLC3A2 regulates epithelial regenerative properties.
    Soline Estrach, Etienne Boulter, Laurence Cailleteau, Charles-Maxime Vivier, Lionel Tosello, Ludovic Cervera, Floriane Tissot, Chloé C Féral.
      SLC3A2, an essential enhancer of integrin signaling, regulates skin homeostasis. We deleted SLC3A2 in hair follicle stem cells (HFSC) to get insights into its role in cell fate decision. Epidermal SLC3A2 is required for SC population maintenance. We show that SLC3A2 itself is expressed in HFSCs. Deleting this gene in multiple HF stem population (K19, Lrig1) resulted in a drastic loss of HF stem cells leading to HF growth defect. SLC3A2 is required for HFSC proper location. In the absence of SLC3A2, stem cells failed to differentiate into follicular keratinocytes, instead they adopted an interfollicular epidermis destiny, making SLC3A2 essential for stem cell fate decisions. HF growth blockade was also associated with decreased fibronectin matrix expression. Using an in vivo skin reconstitution assay, we demonstrate that SLC3A2 preserves HFSC autonomous functions. We found that HFSC SLC3A2-integrin controls stem cell fate and skin regenerative properties, through a YAP/Taz dependent pathway. Finally, SLC3A2 depletion in primary keratinocytes led to defective sphingomyelin synthesis and reduced CerS4 expression, showing that sphingolipid metabolism, downstream of SLC3A2, is crucial for HFSC compartment establishment.
    DOI:  https://doi.org/10.1016/j.jid.2025.09.003
  19. Dev Cell. 2025 Sep 16. pii: S1534-5807(25)00536-2. [Epub ahead of print]
    Proteomics-based multi-omics identifies the roadmap of transcription-translation-protein dynamics in planarian regeneration.
    Yuqing Ying, Yuanyi Zhou Xiong, Xue Pan, Qiushi Zhang, Jiajia Chen, Yun Zhao, Xue Cai, Xiao Yi, Yi Zhu, Tiannan Guo, Kai Lei.
      Identifying regulators for tissue regeneration is fundamental for regenerative biology. While transcription dynamics control planarian regeneration initiation, how protein machinery controls regeneration remains unclear, as transcript levels often fail to predict protein abundance. To address this gap, we performed mass-spectrometry-based proteomic analyses of the planarian Schmidtea mediterranea, establishing a spectral library covering ∼10,000 proteins, and employed quantitative approaches to measure proteome dynamics during regeneration. Our study identified upregulated ribosomal proteins, which were supported by ribosome profiling sequencing (Ribo-seq). Combining RNA sequencing (RNA-seq) and Ribo-seq analyses categorized the increased protein abundance into regulatory modes at transcriptional, translational, and protein stability levels. Functional examination identified 25 proteins essential for planarian regeneration. Troponin T was identified as a regulator of regeneration initiation, showing increased protein abundance before upregulation at transcriptional and translational levels, suggesting a regulation of protein stability. In summary, our study demonstrates previously unexplored ribosome-mediated and transcription-independent protein machinery essential for planarian regeneration initiation.
    Keywords:  DIA; Ribo-seq; TMT; blastema; post-transcriptional regulation; proteomics; regeneration; ribosome; troponin complex; wound response
    DOI:  https://doi.org/10.1016/j.devcel.2025.08.015
  20. Nat Metab. 2025 Sep 16.
    BDH2-driven lysosome-to-mitochondria iron transfer shapes ferroptosis vulnerability of the melanoma cell states.
    Francesca Rizzollo, Abril Escamilla-Ayala, Nicola Fattorelli, Natalia Barbara Lysiak, Sanket More, Pablo Hernández Varas, Lucia Barazzuol, Chris Van den Haute, Joris Van Asselberghs, David Nittner, Jonathan Coene, Vivek Venkataramani, Bernhard Michalke, Christine Gaillet, Tatiana Cañeque, Irwin Davidson, Steven H L Verhelst, Peter Vangheluwe, Tito Calì, Jean-Christophe Marine, Raphaël Rodriguez, Julie Bonnereau, Patrizia Agostinis.
      Iron sustains cancer cell plasticity, yet it also sensitizes the mesenchymal, drug-tolerant phenotype to ferroptosis. This posits that iron compartmentalization must be tightly regulated. However, the molecular machinery governing organelle Fe(II) compartmentalization remains elusive. Here, we show that BDH2 is a key effector of inter-organelle Fe(II) redistribution and ferroptosis vulnerability during melanoma transition from a melanocytic (MEL) to a mesenchymal-like (MES) phenotype. In MEL cells, BDH2 localizes at the mitochondria-lysosome contacts (MLCs) to generate the siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA), which ferries iron into the mitochondria. Fe(II) transfer by BDH2 supports mitochondrial bioenergetics, which is required to maintain lysosomal acidification and MLC formation. Loss of BDH2 alters lysosomal pH and MLC tethering dynamics, causing lysosomal iron sequestration, which primes MES cells for ferroptosis. Rescuing BDH2 expression, or supplementing 2,5-DHBA, rectifies lysosomal pH and MLCs, protecting MES cells from ferroptosis and enhancing their ability to metastasize. Thus, we unveil a BDH2-dependent mechanism that orchestrates inter-organelle Fe(II) transfer, linking metabolic regulation of lysosomal pH to the ferroptosis vulnerability of the mesenchymal, drug-tolerant cancer cells.
    DOI:  https://doi.org/10.1038/s42255-025-01352-4
  21. Circ Res. 2025 Sep 15.
    Targeting Cardiomyocyte PCNA and POLD1 Prevents Pathological Myocardial Hypertrophy.
    Soumojit Pal, Michael S Glennon, Benjamin R Nixon, Ethan J Chetkof, Puneeth Shridhar, Chintha M Kathiresan, Morgan B Glasser, Christina J Waldron, Lanping Guo, Nicolas G Clavere, Dipanjan Banerjee, Jenny H Kim, Jason R Becker.
       BACKGROUND: Activation of cell cycle regulatory pathways has been detected during pathological cardiomyocyte growth. However, it has remained unclear whether DNA synthesis pathways play a direct role in cardiomyocyte hypertrophy. We previously discovered in a mouse model of hypertrophic cardiomyopathy that there was increased DNA synthesis, which led to cardiomyocyte endoreplication and replication stress-induced DNA damage. We hypothesized that targeting cardiomyocyte endoreplication pathways could reduce pathological myocardial hypertrophy.
    METHODS: We utilized murine models of hypertrophic cardiomyopathy secondary to mutations in cardiac Mybpc3 (myosin-binding protein C3)-/- or Myh6 (myosin heavy chain 6)R404Q and transverse aortic constriction as a model of pressure overload cardiomyocyte hypertrophy. We manipulated in vivo p21 protein levels using transgenic mouse models or viral transduction. Cardiomyocyte endoreplication was assessed using flow cytometry and immunohistochemistry of cardiomyocyte nuclei. We also utilized proteomics, proximity ligation assays, and human-induced pluripotent stem cell-derived cardiomyocytes.
    RESULTS: We discovered that p21 protein peaked during the early stages of hypertrophic growth in both murine hypertrophic cardiomyopathy models and a pressure overload hypertrophy model. Using genetic manipulation of p21 expression, we discovered that cardiomyocyte endoreplication and hypertrophic growth were negatively correlated with p21 expression. Mechanistically, we discovered that p21 bound to PCNA (proliferating cell nuclear antigen), which led to a reduction of PCNA binding to POLD1 (DNA polymerase delta 1). Directly targeting PCNA or POLD1 prevented cardiomyocyte DNA synthesis and hypertrophic cardiomyocyte growth. Cardiomyocyte-selective overexpression of p21 using an adeno-associated virus vector reduced long-term pathological left ventricular hypertrophy and improved diastolic function in a preclinical murine model of hypertrophic cardiomyopathy (Myh6R404Q).
    CONCLUSIONS: Our results demonstrate that PCNA-POLD1-mediated cardiomyocyte endoreplication drives hypertrophic cardiomyocyte growth, and p21 serves as a negative regulator of this process. Targeting these pathways demonstrates therapeutic potential in preventing pathological myocardial hypertrophy.
    Keywords:  cardiomyopathy, hypertrophic; cytokinesis; disease models, animal; heart failure; myocytes, cardiac
    DOI:  https://doi.org/10.1161/CIRCRESAHA.124.325647
  22. bioRxiv. 2025 Sep 04. pii: 2025.09.03.674060. [Epub ahead of print]
    Tissue geometry and mechanochemical feedback initiate rotational migration in Drosophila.
    Sierra Schwabach, Sreejith Santhosh, Audrey Miller Williams, Maureen Cetera, Mattia Serra, Sally Horne-Badovinac.
      Collective migration of epithelial cells drives diverse tissue remodeling processes. In many cases, a free tissue edge polarizes the cells to promote directed motion, but how edge-free or closed epithelia initiate migration remains unclear. Here, we show that the rotational migration of follicular epithelial cells in the Drosophila egg chamber is a self-organizing process. Combining experiments and theoretical modeling, we identify a positive feedback loop in which the mechanosensitive behavior of the atypical cadherin Fat2 synergizes with the rigid-body dynamics of the egg chamber to both initiate and sustain rotation. Mechanical constraints arising from cell-cell interactions and tissue geometry further align this motion around the egg chamber's anterior-posterior axis. Our findings reveal a biophysical mechanism - combining Fat2-mediated velocity-polarity alignment, rigid-body dynamics, and tissue geometry - by which a closed epithelial tissue self-organizes into persistent, large-scale rotational migration in vivo, expanding current flocking theories.
    DOI:  https://doi.org/10.1101/2025.09.03.674060
  23. Proc Natl Acad Sci U S A. 2025 Sep 23. 122(38): e2505160122
    A model for boundary-driven tissue morphogenesis.
    Daniel S Alber, Shiheng Zhao, Alexandre O Jacinto, Eric F Wieschaus, Stanislav Y Shvartsman, Pierre A Haas.
      Tissue deformations during morphogenesis can be active, driven by internal processes, or passive, resulting from stresses applied at their boundaries. Here, we introduce the Drosophila hindgut primordium as a model for studying boundary-driven tissue morphogenesis. We characterize its deformations and show that its complex shape changes can be a passive consequence of the deformations of the active regions of the embryo that surround it. First, we find an intermediate characteristic "triangular keyhole" shape in the 3D deformations of the hindgut. We construct a minimal model of the hindgut primordium as an elastic ring deformed by active midgut invagination and germ band extension on an ellipsoidal surface, which robustly captures the symmetry-breaking into this triangular keyhole shape. We then quantify the 3D kinematics of the tissue by a set of contours and find that the hindgut deforms in two stages: An initial translation on the curved embryo surface followed by a rapid breaking of shape symmetry. We extend our model to show that the contour kinematics in both stages are consistent with our passive picture. Our results suggest that the role of in-plane deformations during hindgut morphogenesis is to translate the tissue to a region with anisotropic embryonic curvature and show that uniform boundary conditions are sufficient to generate the observed nonuniform shape change. Our work thus provides a possible explanation for the various characteristic shapes of blastopore-equivalents in different organisms and a framework for the mechanical emergence of global morphologies in complex developmental systems.
    Keywords:  Drosophila development; mechanical bifurcation; morphogenesis; tissue mechanics
    DOI:  https://doi.org/10.1073/pnas.2505160122
  24. bioRxiv. 2025 Sep 07. pii: 2025.09.04.674271. [Epub ahead of print]
    QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sites.
    Maureen V Akinyi, Wenjie Yao, Jakub Zeman, Clara Hipp, Deniz Bartsch, Laurence Heaven, Charlotte A Le Roux, Anne C Starner, Fei Yuan, Mason D Bartels, Fangyu Zhao, Hang Le Ha, Riddhi Sharma, Bhumika Choudhary, Josep Biayna, Ralf P Brandes, Gabrijela Dumbović, Arjun Ray, Ilka Wittig, Christian Muench, Michael Sattler, Eric L Van Nostrand, Leo Kurian.
      During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5' splice sites (5'SS) yet are spliced with high precision, implying unknown yet active splicing fidelity mechanisms. By combining transcriptome and alternative splicing profiling with temporal eCLIP mapping of RNA interactions across development, we identify the RNA-binding protein QKI as an essential direct regulator of splicing fidelity in key cardiac transcripts. Although QKI is dispensable for cardiac specification, its loss disrupts sarcomere assembly despite intact expression of sarcomere mRNAs through exon skipping and nuclear retention of mis-spliced RNAs. QKI-dependent exons in essential cardiac genes have weak 5'SS and frequently show poor complementarity with U6 snRNA. We show that QKI directly interacts with U6 snRNA using an overlapping interface to its traditional intronic binding activity, securing U4/U6·U5 tri-snRNP to ensure splicing fidelity. Thus, QKI exemplifies how context-aware RBPs enforce splicing fidelity at structurally vulnerable splice sites during organogenesis.
    DOI:  https://doi.org/10.1101/2025.09.04.674271
  25. bioRxiv. 2025 Sep 04. pii: 2025.09.04.674221. [Epub ahead of print]
    Cellular mechanism linking endoplasmic reticulum inheritance and cell cycle regulation of the nuclear genome.
    Ya-Shiuan Lai, Jesse Chao, Maho Niwa.
      Endoplasmic reticulum (ER) stress triggers activation of the ER surveillance (ERSU) pathway- a critical protective mechanism that transiently halts cortical ER inheritance to daughter cells and arrests cytokinesis by septin ring subunit Shs1 re-localization to the bud scar in response to ER stress. Once ER functional homeostasis is re-established, cells resume normal cell cycle progression; however, the molecular circuitry linking ER integrity to cell cycle regulation has remained largely unresolved. Here, we show that ER stress selectively disperse Bud2, a GAP for Bud1/Rsr1, severing its canonical role in cell polarity while integrating it into ER homeostasis signaling. Bud2 dispersion results in accelerated spindle pole body (SPB) duplication, spindle misorientation, defects in nuclear migration, and genome segregation errors under ER stress. Strikingly, a C-terminal truncation of Shs1 ( shs1-ΔCTD ) recapitulated the ER stress-induced dispersion of Bud2 phenotype even in the absence of ER stress, and delayed cell-cycle re-entry after ER homeostasis was regained-despite normal occurrence of typical ERSU hallmark events. Notably, Bud2 overexpression rescued the growth defects of shs1-ΔCTD mutants after ER homeostasis was re-established. Collectively, our findings reveal a new mechanistic axis whereby ER integrity coordinates organelle inheritance, cytoskeletal organization, and nuclear division via selective control of Bud2 and Shs1, establishing a direct regulatory bridge between ER status and mitotic fidelity.
    DOI:  https://doi.org/10.1101/2025.09.04.674221
  26. Nat Cardiovasc Res. 2025 Sep 15.
    Single-cell compendium of muscle microenvironment in peripheral artery disease reveals altered endothelial diversity and LYVE1+ macrophage activation.
    Guillermo Turiel, Thibaut Desgeorges, Evi Masschelein, Zheng Fan, David Lussi, Christophe M Capelle, Giulia Bernardini, Raphaela Ardicoglu, Katharina Schönberger, Manuela Birrer, Sandro F Fucentese, Jing Zhang, Daniela Latorre, Stephan Engelberger, Katrien De Bock.
      Peripheral artery disease (PAD) results from atherosclerosis and chronic narrowing of lower limb arteries, leading to decreased muscle perfusion. Current treatments are suboptimal, partly due to limited understanding of PAD muscle pathology. Here we used single-cell RNA sequencing and spatial transcriptomics to analyze the composition of the muscle microenvironment in non-ischemic patients and patients with PAD. We identified ATF3/ATF4+ endothelial cells (ECs) that exhibit altered angiogenic and immune regulatory profiles during PAD and confirmed that ATF4 signaling in ECs is required for effective ischemia recovery. In addition, capillary ECs display features of endothelial-to-mesenchymal transition. Furthermore, LYVE1hiMHCIIlow macrophages are the dominant macrophage population in human muscle, adopting a more pro-inflammatory profile during PAD. Finally, we analyzed alterations in intercellular communication within the muscle microenvironment during PAD and confirmed that EC-derived factors can influence macrophage polarization. This dataset deeply characterizes the PAD muscle microenvironment and provides a resource for exploration of targeted therapies.
    DOI:  https://doi.org/10.1038/s44161-025-00709-y
  27. Nat Aging. 2025 Sep;5(9): 1880-1896
    Systems Age: a single blood methylation test to quantify aging heterogeneity across 11 physiological systems.
    Raghav Sehgal, Yaroslav Markov, Chenxi Qin, Margarita Meer, Courtney Hadley, Aladdin H Shadyab, Ramon Casanova, JoAnn E Manson, Parveen Bhatti, Ann Z Moore, Eileen M Crimmins, Sara Hagg, Themistocles L Assimes, Eric A Whitsel, Albert T Higgins-Chen, Morgan Levine.
      Aging occurs at different rates across individuals and physiological systems, but most epigenetic clocks provide a single age estimate, overlooking within-person variation. Here we developed systems-based DNA methylation clocks that measure aging in 11 distinct physiological systems-Heart, Lung, Kidney, Liver, Brain, Immune, Inflammatory, Blood, Musculoskeletal, Hormone and Metabolic-using data from a single blood draw. By integrating supervised and unsupervised machine learning with clinical biomarkers, functional assessments and mortality risk, we derived system-specific scores that outperformed existing global clocks in predicting relevant diseases and aging phenotypes. We also created a composite Systems Age score to capture overall multisystem aging. Clustering individuals based on these scores revealed distinct biological aging subtypes, each associated with unique patterns of health decline and disease risk. This framework enables a more granular and clinically relevant assessment of biological aging and may support personalized approaches to monitor and target system-specific aging processes.
    DOI:  https://doi.org/10.1038/s43587-025-00958-3
  28. Cell Res. 2025 Sep 19.
    ATP-dependent one-dimensional movement maintains immune homeostasis by suppressing spontaneous MDA5 filament assembly.
    Xiao-Peng Han, Ming Rao, Yu Chang, Jun-Yan Zhu, Jun Cheng, Yu-Ting Li, Wu Qiong, Si-Chao Ye, Qiurong Zhang, Shao-Qing Zhang, Ling-Ling Chen, Fajian Hou, Jin Zhong, Jiaquan Liu.
      MDA5 is a RIG-I-like receptor (RLR) that recognizes viral double-stranded RNA (dsRNA) to initiate the innate immune response. Its activation requires filament formation along the dsRNA, which triggers the oligomerization of N-terminal caspase activation and recruitment domains. The ATPase activity of MDA5 is critical for immune homeostasis, likely by regulating filament assembly. However, the molecular basis underlying this process remains poorly understood. Here, we show that MDA5 operates as an ATP-hydrolysis-driven motor that translocates along dsRNA in a one-dimensional (1D) manner. Multiple MDA5 motors can cooperatively load onto a single dsRNA, but their movements rarely synchronize, inhibiting spontaneous filament formation and activation. LGP2, a key regulator of MDA5 signaling, recognizes MDA5 motors and blocks their movement, thereby promoting filament assembly through a translocation-directed mechanism. This unique assembly strategy underscores the role of 1D motion in higher-order protein oligomerization and reveals a novel mechanism for maintaining immune homeostasis.
    DOI:  https://doi.org/10.1038/s41422-025-01183-8
  29. Cell Metab. 2025 Sep 16. pii: S1550-4131(25)00381-X. [Epub ahead of print]
    OGFOD1 enables AML chemo- and nutrient stress resistance by regulating protein synthesis.
    Christina Mayerhofer, Dan Li, Trine Kristiansen, Ernst Mayerhofer, Azeem Sharda, Giulia Schiroli, Karin Gustafsson, Lingli He, Michael Mazzola, Sam Keyes, Anna Kiem, Eve Crompton, Yanxin Xu, Sovannarith Korm, Zhixun Dou, Charles Vidoudez, Peter G Miller, Nick van Gastel, Timothy A Graubert, David T Scadden.
      Acute myeloid leukemia (AML) commonly relapses after initial chemotherapy response. We assessed metabolic adaptations in chemoresistant cells in vivo before overt relapse, identifying altered branched-chain amino acid (BCAA) levels in patient-derived xenografts (PDXs) and immunophenotypically identified leukemia stem cells from AML patients. Notably, this was associated with increased BCAA transporter expression with low BCAA catabolism. Restricting BCAAs further reduced chemoresistant AML cells, but relapse still occurred. Among the persisting cells, we found an unexpected increase in protein production. This was accompanied by elevated translation of 2-oxoglutarate- and iron-dependent oxygenase 1 (OGFOD1), a known ribosomal dioxygenase that adjusts the fidelity of tRNA anticodon pairing with coding mRNA. We found that OGFOD1 upregulates protein synthesis in AML, driving disease aggressiveness. Inhibiting OGFOD1 impaired translation processing, decreased protein synthesis and improved animal survival even with chemoresistant AML while sparing normal hematopoiesis. Leukemic cells can therefore persist despite the stress of chemotherapy and nutrient deprivation through adaptive control of translation. Targeting OGFOD1 may offer a distinctive, translation-modifying means of reducing the chemopersisting cells that drive relapse.
    Keywords:  BCAA; OGFOD1; Ribo-seq; acute myeloid leukemia; chemoresistance; metabolism; protein biosynthesis; ribosome pausing; translation accuracy
    DOI:  https://doi.org/10.1016/j.cmet.2025.08.008
  30. bioRxiv. 2025 Sep 02. pii: 2025.09.01.673455. [Epub ahead of print]
    An electrostatic repulsion model of centromere organisation.
    Caelan Bell, Lifeng Chen, M Julia Maristany, Claudia Blaukopf, Huabin Zhou, Jan Huertas, Jose I Perez Lopez, Christoph C H Langer, Thomas L Steinacker, Nikki Schuette, Lynda Doolittle, Jorge R Espinosa, Sy Redding, Rosana Collepardo-Guevara, Michael K Rosen, Daniel W Gerlich.
      During cell division, chromosomes reorganise into compact bodies in which centromeres localise precisely at the chromatin surface to enable kinetochore-microtubule interactions essential for genome segregation. The physical principles guiding this centromere positioning remain unknown. Here, we reveal that human core centromeres are directed to the chromatin surface by repulsion of centromere-associated proteins - independent of condensin-mediated loop extrusion and microtubule engagement. Using cellular perturbations, biochemical reconstitution, and multiscale molecular dynamics simulations, we show that chromatin surface localisation emerges from repulsion between condensed chromatin and both the kinetochore and the highly negatively charged centromere protein, CENP-B. Together, these elements form a centromeric region composed of two domains with opposing affinities, one favouring integration within the mitotic chromosome and the other favouring exposure to the surrounding cytoplasm, thereby driving surface positioning. Tethering synthetic negatively charged proteins to chromatin was sufficient to recapitulate this surface localisation in cells and in vitro, indicating that electrostatic repulsion is a key determinant of surface localisation. These findings demonstrate that centromere layering is not hardwired by chromatin folding patterns but instead emerges from phase separation in chromatin. Our work uncovers electrostatic polarity as a general and programmable mechanism to spatially organise chromatin.
    DOI:  https://doi.org/10.1101/2025.09.01.673455
  31. Cell Stem Cell. 2025 Sep 17. pii: S1934-5909(25)00328-5. [Epub ahead of print]
    Spatially patterned kidney assembloids recapitulate progenitor self-assembly and enable high-fidelity in vivo disease modeling.
    Biao Huang, Pedro Medina, Jincan He, Zipeng Zeng, Sunghyun Kim, Janet Romo, Kari Koppitch, Chennan C Zhang, Georgina Gyarmati, Yohan Park, Ruslan Bohovyk, Pierre-Emmanuel Yoann N'Guetta, Jinjin Guo, Tianyi Ma, Megan E Schreiber, Cong Xu, Jessica Pham, Riana K Parvez, Jackson Su, Mateo W Xia, Zhenqing Liu, Laura Perin, Danny El-Nachef, Charles E Murry, Sanjeev Kumar, Lori O'Brien, Kurt A Zimmerman, Justin Ichida, Nils O Lindström, Nuria M Pastor-Soler, Kenneth R Hallows, Alexander Staruschenko, Janos Peti-Peterdi, Cizhong Jiang, Andrew P McMahon, Zhongwei Li.
      Current kidney organoids do not recapitulate the kidney's complex spatial patterning and function, limiting their applications. The human kidney comprises one million nephrons, derived from nephron progenitor cells, that connect to an arborized ureteric progenitor cell-derived collecting system. Here, we develop spatially organized mouse and human kidney progenitor assembloid (KPA) models in which the nephrons undergo extensive development and fuse to a centrally located collecting system, recapitulating kidney progenitor self-assembly processes observed in vivo. KPAs show dramatically improved cellular complexity and maturity and exhibit several aspects of major kidney functions in vitro and in vivo. Modeling human autosomal dominant polycystic kidney disease (ADPKD) with genome-edited, in vivo-grown human KPAs recapitulated the cystic phenotype and the molecular and cellular hallmarks of the disease and highlighted the crosstalk among cyst epithelium, stroma, and macrophages. The KPA platform opens new avenues for high-fidelity disease modeling and lays a strong foundation for kidney regenerative medicine.
    Keywords:  collecting duct; functional maturation; kidney organoid; nephron; nephron patterning; nephron progenitor cell; pluripotent stem cell; polycystic kidney disease; progenitor plasticity; ureteric progenitor cell
    DOI:  https://doi.org/10.1016/j.stem.2025.08.013
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