bims-ginsta Biomed News
on Genome instability
Issue of 2025–10–26
thirty-two papers selected by
Jinrong Hu, National University of Singapore
  1. Live imaging of late-stage preimplantation human embryos reveals de novo mitotic errors.
  2. EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogramming.
  3. Post-replicative initial expression of PAX6 during neuroectoderm differentiation.
  4. Tissue and cellular spatiotemporal dynamics in colon aging.
  5. Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation.
  6. Delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.
  7. Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric oocyte divisions.
  8. Myocardial reprogramming by HMGN1 underlies heart defects in trisomy 21.
  9. Actin cytoskeleton protection by the formin-mediated safety valve.
  10. Sequential verification of transcription by Integrator and Restrictor.
  11. A steady-state pool of calcium-dependent actin is maintained by Homer and controls epithelial mechanosensation.
  12. CENP-E initiates chromosome congression by opposing Aurora kinases to promote end-on attachments.
  13. Kinetochore-centrosome feedback linking CENP-E and Aurora kinases controls chromosome congression.
  14. Enhancer activation from transposable elements in extrachromosomal DNA.
  15. Cluster nanoarchitecture and structural diversity of PIEZO1 at rest and during activation in intact cells.
  16. Mitochondrial and lysosomal signaling orchestrates heterogeneous metabolic states of regulatory T cells.
  17. Hypercontractility and Oxidative Stress Drive Creatine Kinase Dysfunction in Hypertrophic Cardiomyopathy.
  18. Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.
  19. Global analysis of translocon remodeling during protein synthesis at the ER.
  20. A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress.
  21. Cadherin flow translates cortical chirality into left-right asymmetric cell division dynamics in Caenorhabditis elegans embryos.
  22. A multimodal cross-species comparison of pancreas development.
  23. Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function.
  24. Complete genome assemblies of two mouse subspecies reveal structural diversity of telomeres and centromeres.
  25. MED1 IDR deacetylation controls stress responsive genes through RNA Pol II recruitment.
  26. Chromatin activity of IκBα mediates the exit from naïve pluripotency.
  27. Endophilin-Lamellipodin-VASP, key components in fast endophilin-mediated endocytosis, control actin polymerization within liquid-like condensates.
  28. Oligodendrocyte precursor cell-specific blocking of low-glucose-induced activation of AMPK ensures myelination and remyelination.
  29. Ligand and integrin-independent mechano-sensitive EGFR activation in lung cancer cells.
  30. Total cell number influences the timing of Hippo/YAP activation during preimplantation development in mouse tetraploid embryos.
  31. Bottom-up design of Ca2+ channels from defined selectivity filter geometry.
  32. Germ granule localization of nematode Argonaute WAGO-4 ensures fidelity in small RNA loading.
  1. Nat Biotechnol. 2025 Oct 23.
    Live imaging of late-stage preimplantation human embryos reveals de novo mitotic errors.
    Ahmed Abdelbaki, Afshan McCarthy, Anita Karsa, Leila Muresan, Kay Elder, Athanasios Papathanasiou, Phil Snell, Leila Christie, Martin Wilding, Benjamin J Steventon, Kathy K Niakan.
      Existing methods to image chromosome segregation errors are not suitable for studying human embryos at advanced preimplantation stages. As chromosomal errors are a leading cause of miscarriage and infertility, it remains unclear whether missegregation arises postfertilization. Here we optimize nuclear DNA labeling via messenger RNA electroporation and apply light-sheet live imaging to reveal chromosome segregation errors immediately before implantation. We show that embryos at advanced preimplantation stages display missegregation, including multipolar spindle formation, lagging chromosomes, misalignment and mitotic slippage. Most lagging chromosomes are passively inherited rather than reincorporated. To trace individual nuclei, we developed an open-source, semi-automated segmentation method using a customized deep learning model optimized for variability in embryo size, shape and signal. With this approach, we find most labeled cells remain externally positioned, consistent with placental rather than inner cell mass fate. Our findings raise questions about clinical uses of preimplantation genetic testing for aneuploidy, while providing broadly applicable imaging and segmentation methods for studying diverse cellular structures in human embryos.
    DOI:  https://doi.org/10.1038/s41587-025-02851-1
  2. Cell Stem Cell. 2025 Oct 20. pii: S1934-5909(25)00340-6. [Epub ahead of print]
    EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogramming.
    Yitian Zeng, Feng Kong, Zihan Xu, Xukun Lu, Qian Li, Bofeng Liu, Shu Liu, Lijun Dong, Ling Liu, Wenying Wang, Bing Zhu, Wei Xie.
      In mice, the repressive histone mark H3K27me3 undergoes both region-specific inheritance and erasure during the parental-to-embryonic transition, with the underlying mechanisms poorly understood. Here, we show that PRC2, which catalyzes H3K27me3, binds both classic Polycomb targets and noncanonical H3K27me3 domains in growing oocytes but dissociates from chromatin in fully grown oocytes. After fertilization, PRC2 rebinds noncanonical H3K27me3 domains before relocating to Polycomb targets in blastocysts. Interestingly, the binding and activity of PRC2 are restricted by a maternal inhibitory factor, EZH inhibitory protein (EZHIP), which co-binds with PRC2. Upon knockout of Ezhip, hyperactive PRC2 promiscuously deposits H3K27me3 genome-wide. This overwrites H3K27me3 memories at noncanonical imprinted genes and paradoxically causes derepression of H3K27me3 targets, defective X chromosome inactivation, and diluted chromatin PRC2. H3K27me3 restoration at Polycomb targets after implantation is also attenuated, accompanied by sub-lethality. These data unveil principles of epigenetic inheritance that both insufficient and excessive heterochromatic marks cause loss of epigenetic memories and repression.
    Keywords:  EZHIP; H3K27me3; Polycomb regulation; early embryo; epigenetic memory; epigenetic reprogramming; intergenerational inheritance; noncanonical imprinting
    DOI:  https://doi.org/10.1016/j.stem.2025.09.009
  3. EMBO J. 2025 Oct 21.
    Post-replicative initial expression of PAX6 during neuroectoderm differentiation.
    Song Hu, Rongao Kou, Zhuojie Su, Guanchen Li, Shutao Qi, Yanxiao Zhang, Haifeng Wang, Ling-Ling Chen, Hongtao Yu.
      The development of multicellular organisms requires precise coordination between cell division and differentiation. Cell division generates the necessary number of cells, while differentiation creates distinct cell identities, forming tissues and organs. The transcription factors SOX2 and PAX6 specify neuroepithelial cells, the earliest neural progenitor cells (NPCs) during brain development. How lineage specification is coordinated with the cell cycle is not fully understood. Here, we show that PAX6 expression occurs during a narrow time window after neural induction of human embryonic stem cells (ESCs). Flow cytometry analyses and time-lapse imaging show that PAX6 expression starts during the G2 phase. We identify a novel 500-bp PAX6 promoter that drives its G2-specific expression. PAX6 expression is independent of known regulators of cell cycle-dependent transcription, suggesting the existence of a novel mechanism. S-phase block by hydroxyurea prevents PAX6 expression and differentiation into NPC. Thus, NPC fate specification is coupled to cell cycle progression and occurs after the completion of DNA replication. This post-replicative lineage commitment ensures the creation of two daughter cells of identical cell fate following cell division.
    Keywords:  Cell Cycle; Cell Fate Decision; Neural Progenitor Cells; Neurogenesis; Transcription
    DOI:  https://doi.org/10.1038/s44318-025-00605-y
  4. Nat Biotechnol. 2025 Oct 22.
    Tissue and cellular spatiotemporal dynamics in colon aging.
    Aidan C Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernandez, Olena Kuksenko, Matthew Smith-Erb, Daniel Domovic, Nicholas Van Wittenberghe, Eugene Drokhlyansky, Gabriel K Griffin, Hemali Phatnani, Richard Bonneau, Aviv Regev, Sanja Vickovic.
      Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects but many of the underlying molecular cues remain unclear. Here, we build a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-sequencing profiles. We develop a computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region and sex by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identify cellular and molecular gradients along the adult colonic tract and across the main crypt axis and multicellular programs associated with aging in the large intestine. Our multimodal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
    DOI:  https://doi.org/10.1038/s41587-025-02830-6
  5. J Cell Biol. 2026 Jan 05. pii: e202505038. [Epub ahead of print]225(1):
    Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation.
    Ana M Dias Maia Henriques, Timothy R Davies, Serge Dmitrieff, Nicolas Minc, Julie C Canman, Julien Dumont, Gilliane Maton.
      Chromosome segregation during anaphase occurs through two mechanistically distinct processes: anaphase A, in which chromosomes move toward spindle poles, and anaphase B, in which the anaphase spindle elongates through cortical astral microtubule pulling forces. Caenorhabditis elegans embryos have been thought to rely primarily on anaphase B, with little to no contribution from anaphase A. Here, we uncover a novel anaphase A mechanism in C. elegans embryos, driven by the kinesin-13 KLP-7MCAK and opposed by the kinesin-12 KLP-18. We found that the extent of chromosome segregation during anaphase A is asymmetrically regulated by cell polarity cues and modulated by mechanical tension within the spindle, generated by opposing forces acting on chromosomes and spindle poles. Additionally, we found that the contribution of anaphase A to chromosome segregation increases progressively across early embryonic divisions. These findings uncover an unexpected role for anaphase A in early C. elegans development and reveal a KLP-7MCAK-dependent mechanical coordination between anaphase A- and anaphase B-driven chromosome segregation.
    DOI:  https://doi.org/10.1083/jcb.202505038
  6. Mol Cell. 2025 Oct 20. pii: S1097-2765(25)00815-9. [Epub ahead of print]
    Delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.
    Nils Bertram, Toshiaki Izawa, Felix Thoma, Serena Schwenkert, Stéphane Duvezin-Caubet, Sae-Hun Park, Nikola Wagener, Anne Devin, Christof Osman, Walter Neupert, Dejana Mokranjac.
      Ribosome-associated protein quality control (RQC) protects cells against the toxic effects of faulty polypeptides produced by stalled ribosomes. However, mitochondria are vulnerable to C-terminal alanyl and threonyl (CAT)-tailed proteins that are generated in this process, and faulty nuclear-encoded mitochondrial proteins are handled by the recently discovered mitoRQC. Here, we performed a genome-wide screen in yeast to identify additional proteins involved in mitoRQC. We found that peptidyl-tRNA hydrolase 2 (Pth2), present in the mitochondrial outer membrane, influences aggregation of CAT-tailed proteins without majorly affecting the CAT-tailing process itself. Peptidyl-tRNA hydrolase activity is essential during this process, yet the activity of Pth2 can be substituted by another peptidyl-tRNA hydrolase upon proper localization. Our data suggest that Pth2 acts by modulating protein translocation and that the mitochondrial proteostasis network is relieved through increased access of CAT-tailed proteins to cytosolic chaperones. Other hits obtained in the screen show that, in general, delayed protein translocation protects mitochondria against toxic CAT-tailed proteins.
    Keywords:  RQC; TOM complex; cellular homeostasis; mitoRQC; mitochondria; peptidyl-RNA hydrolase; protein translocation
    DOI:  https://doi.org/10.1016/j.molcel.2025.09.030
  7. J Cell Biol. 2025 Dec 01. pii: e202312140. [Epub ahead of print]224(12):
    Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric oocyte divisions.
    Ivan Avilov, Yehor Horokhovskyi, Pooja Mehta, Luisa Welp, Jasmin Jakobi, Mingfang Cai, Aleksander Orzechowski, Henning Urlaub, Juliane Liepe, Peter Lenart.
      The Mos kinase activates the ERK/MAPK pathway during oocyte meiosis, controlling essential meiotic functions in species across metazoa. However, despite its significance, the molecular targets of Mos-MAPK remain largely unidentified. Here, we addressed this question using starfish oocytes ideally suited to combine cellular assays with phosphoproteomics. This revealed CPE-mediated mRNA polyadenylation as a prominent target of Mos-MAPK, and we show that translation is required to drive the second meiotic division. Secondly, we identify a well-defined subset of cytoskeletal regulators as targets of Mos-MAPK. We show that this regulation is critical to ensure the asymmetry of meiotic divisions, primarily by reducing the growth of astral microtubules. This allows positioning of the spindle directly beneath the cortex and prevents the separation of spindle poles in anaphase, thereby minimizing polar body size. Thus, by phosphoproteomics, we reveal molecular modules controlled by Mos-MAPK, explaining how this single, conserved kinase can act as a switch between the mitotic and meiotic division programs.
    DOI:  https://doi.org/10.1083/jcb.202312140
  8. Nature. 2025 Oct 22.
    Myocardial reprogramming by HMGN1 underlies heart defects in trisomy 21.
    Sanjeev S Ranade, Feiya Li, Sean Whalen, Angelo Pelonero, Lin Ye, Yu Huang, Abigail Brand, Tomohiro Nishino, Rahul Mital, Ryan M Boileau, Frances Koback, Arun Padmanabhan, Victoria Yu, Bastien Cimarosti, Diana Presas-Ramos, Alexander F Merriman, Langley Grace Wallace, Annie Nguyen, Nikolaos Poulis, Mauro W Costa, Casey A Gifford, Katherine S Pollard, Deepak Srivastava.
      Congenital heart defects (CHDs) are the most common developmental abnormalities, affecting around 1% of live births1. Aneuploidy causes around 15% of CHDs, with trisomy 21 (also known as Down syndrome) being the most frequent form2. CHDs occur in around 50% of cases of Down syndrome, with an approximately 1,000-fold enrichment of atrioventricular canal (AVC) defects that disrupt the junction between the atria and ventricles3,4. The AVC contains unique myocardial cells that are essential for valvuloseptal development; however, the specific combination of dosage-sensitive genes on chromosome 21 that are responsible for Down syndrome-associated CHDs have remained unknown. Here, using human pluripotent stem cell and mouse models of Down syndrome, we identify HMGN1, a nucleosome-binding epigenetic regulator encoded on chromosome 21, as a key contributor to these defects. Single-cell transcriptomics showed that trisomy 21 shifts human AVC cardiomyocytes towards a ventricular cardiomyocyte state. A CRISPR-activation single-cell RNA droplet sequencing (CROP-seq) screen of chromosome 21 genes expressed during heart development revealed that HMGN1 upregulation mimics this shift, whereas deletion of one HMGN1 allele in trisomic cells restored normal gene expression. In a mouse model of trisomy 21, a similar transcriptional shift of AVC cardiomyocytes was restored by a reduction in Hmgn1 dosage, leading to rescue of valvuloseptal defects. These findings identify HMGN1 as a dosage-sensitive modulator of AVC development and cardiac septation in Down syndrome. This study offers a paradigm for dissecting aneuploidy-associated pathogenesis using isogenic systems to map causal genes in complex genetic syndromes.
    DOI:  https://doi.org/10.1038/s41586-025-09593-9
  9. Curr Opin Cell Biol. 2025 Oct 16. pii: S0955-0674(25)00131-0. [Epub ahead of print]97 102593
    Actin cytoskeleton protection by the formin-mediated safety valve.
    Fernando R Valencia, Sergey V Plotnikov.
      Mechanical forces shape cellular form and function by regulating key cellular processes; however, when dysregulated, they contribute to disease. Excessive forces can be detrimental to cells, damaging cytoskeleton, deforming nuclei, and even rupturing the cell itself. To counteract these effects, cells deploy protective mechanisms that enhance mechanical resilience. Emerging evidence highlights a novel strategy for rapid tension release via force-dependent actin polymerization mediated by formin-family proteins such as Dia1. Acting as a mechanical "safety valve", Dia1 buffers otherwise damaging stress and promotes zyxin-mediated repair, preserving cytoskeletal architecture, safeguarding the nucleus, and maintaining cellular integrity. Loss of Dia1 disrupts signaling cascades that converge on key mechanotransduction processes governing cell fate and disease progression. In this review, we explore recent advances in force-dependent actin polymerization and its role in cytoskeletal protection, nuclear homeostasis, and cellular adaptation to mechanical forces.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102593
  10. Mol Cell. 2025 Oct 17. pii: S1097-2765(25)00785-3. [Epub ahead of print]
    Sequential verification of transcription by Integrator and Restrictor.
    Chris Estell, Krystian Łazowski, Joshua D Eaton, Steven West.
      The decision between productive elongation and premature termination of promoter-proximal RNA polymerase II (RNAPII) is fundamental to metazoan gene regulation. Integrator and Restrictor complexes are implicated in promoter-proximal termination, but why metazoans utilize two complexes and how they are coordinated remains unknown. Here, we show that Integrator and Restrictor act sequentially to monitor distinct stages of transcription. Integrator predominantly engages with promoter-proximally paused RNAPII to trigger premature termination, which is prevented by cyclin-dependent kinase 7/9 activity. After pause release, RNAPII enters a "restriction zone"-universally imposed by Restrictor. Unproductive RNAPII terminates within this zone, while progression through it is promoted by U1 small nuclear ribonucleoprotein particles (snRNPs), which antagonize Integrator and Restrictor in a U1-70K-dependent manner. These findings reveal the principles of a sequential verification mechanism governing the balance between productive and attenuated transcription, rationalizing the necessity of Integrator and Restrictor complexes in metazoans.
    Keywords:  Integrator; RNA exosome; RNA polymerase II; Restrictor; U1 snRNA; ZC3H4; transcription; transcriptional elongation; transcriptional termination
    DOI:  https://doi.org/10.1016/j.molcel.2025.09.025
  11. Proc Natl Acad Sci U S A. 2025 Oct 28. 122(43): e2509784122
    A steady-state pool of calcium-dependent actin is maintained by Homer and controls epithelial mechanosensation.
    Kenji Matsuzawa, Makoto Suzuki, Yuma Cho, Ryoya Fujinaga, Junichi Ikenouchi.
      Epithelial cells are inherently contractile and in homeostasis, tissue integrity is maintained by balancing the uneven contractile forces in neighboring cells at the cell-cell interface. By contrast, epithelial cells can utilize an imbalance in contractile force to communicate various information to induce tissue-wide response as in wound healing. Contractility is generated and processed at the apical junctional complex (AJC) by the dynamic behavior of the actin cytoskeleton. Calcium signaling can pattern cellular responses based on its reach and amplitude and the actin cytoskeleton is supported by its wide ranging effects on actin regulators. Calcium transients regulate various cell behaviors associated with actin remodeling, such as in damage response and developmental morphogenesis. Here, we report that calcium maintains an adaptive pool of AJC-associated actin that is sensitive to tension and encoded by calcium dynamics. For this, the recently identified epithelial polarity module Homer-MUPP1/PatJ is required. Homer regulates calcium signaling in various tissue contexts through interaction with numerous components of the endoplasmic reticulum (ER) and plasma membrane (PM) calcium signal toolkit. Knockout of either Homer or MUPP1/PatJ attenuated tension-induced calcium response and severely disrupted wound healing migration, which is dependent on guidance input through AJC tension. We also show that Homer is integral to early embryonic neurodevelopment as its suppression causes failure of neural tube closure. Our findings highlight the critical role of localized calcium dynamics on AJC actin remodeling and cellular behavior, elucidating the means of tissue coordination through intercellular tension.
    Keywords:  Homer; MUPP1; PatJ; actin; calcium
    DOI:  https://doi.org/10.1073/pnas.2509784122
  12. Nat Commun. 2025 Oct 21. 16(1): 8537
    CENP-E initiates chromosome congression by opposing Aurora kinases to promote end-on attachments.
    Kruno Vukušić, Iva M Tolić.
      Accurate cell division relies on rapid chromosome congression. The kinetochore motor protein CENP-E/kinesin-7 is uniquely required for congression of polar chromosomes. It is currently assumed that CENP-E drives congression by gliding kinetochores along microtubules independently of their biorientation. Here, by studying chromosome movement under different levels of CENP-E activity, we favor an alternative model in which CENP-E initiates congression by promoting stabilization of end-on attachments. In this way, CENP-E accelerates congression initiation without significantly contributing to subsequent movement. Stabilization of end-on attachments on polar chromosomes without CENP-E is delayed due to Aurora kinase-mediated hyperphosphorylation of microtubule-binding proteins and expansion of the fibrous corona. CENP-E counters this by reducing Aurora B-mediated phosphorylation in a BubR1-dependent manner, thereby stabilizing initial end-on attachments, facilitating removal of the fibrous corona, and triggering biorientation-dependent chromosome movement. These findings support a unified model of chromosome movement in which congression is intrinsically coupled to biorientation.
    DOI:  https://doi.org/10.1038/s41467-025-64148-w
  13. Nat Commun. 2025 Oct 21. 16(1): 9097
    Kinetochore-centrosome feedback linking CENP-E and Aurora kinases controls chromosome congression.
    Kruno Vukušić, Iva M Tolić.
      Chromosome congression is crucial for accurate cell division, with key roles played by kinetochore components, the molecular motor CENP-E/kinesin-7, and Aurora B kinase. However, Aurora B kinase can both inhibit and promote congression, suggesting the presence of a larger signaling network. Our study demonstrates that centrosomes inhibit congression initiation when CENP-E is inactive by regulating the activity of kinetochore components. Depletion of centrioles via Plk4 kinase inhibition allows chromosomes near acentriolar poles to initiate congression independently of CENP-E. At centriolar poles, high Aurora A kinase enhances Aurora B activity, increasing phosphorylation of microtubule-binding proteins at kinetochores and preventing stable microtubule attachments in the absence of CENP-E. Conversely, inhibition of Aurora A or expression of a dephosphorylatable mutant of the kinetochore microtubule-binding protein Hec1 enables congression initiation without CENP-E. We propose a negative feedback mechanism involving Aurora kinases and CENP-E that regulates the timing of chromosome movement by modulating kinetochore-microtubule attachments and fibrous corona expansion, with the Aurora A activity gradient providing critical spatial cues for the network's function.
    DOI:  https://doi.org/10.1038/s41467-025-64804-1
  14. Nat Cell Biol. 2025 Oct 21.
    Enhancer activation from transposable elements in extrachromosomal DNA.
    Katerina Kraft, Sedona E Murphy, Matthew G Jones, Quanming Shi, Aarohi Bhargava-Shah, Christy Luong, King L Hung, Britney J He, Rui Li, Seung Kuk Park, Michael T Montgomery, Natasha E Weiser, Yanbo Wang, Jens Luebeck, Vineet Bafna, Jef D Boeke, Paul S Mischel, Alistair N Boettiger, Howard Y Chang.
      Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoural heterogeneity in aggressive cancers. While transposable element reactivation is common in cancer, its role on ecDNA remains unexplored. Here we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements-genomic loci enriched for transposable elements that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA-amplified context. Using CRISPR-CATCH, CRISPR interference and reporter assays, we confirm its presence on ecDNA, enhancer activity and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumour evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.
    DOI:  https://doi.org/10.1038/s41556-025-01788-6
  15. Sci Adv. 2025 Oct 24. 11(43): eady8052
    Cluster nanoarchitecture and structural diversity of PIEZO1 at rest and during activation in intact cells.
    Clement Verkest, Lucas Roettger, Nadja Zeitzschel, James Hall, Oscar Sánchez-Carranza, Angela Tzu-Lun Huang, Gary R Lewin, Stefan G Lechner.
      The force-gated ion channel PIEZO1 confers mechanosensitivity to many cell types. While the structure and physiological roles of PIEZO1 are well-described, the subcellular distribution and the impact of the cellular microenvironment on PIEZO1 conformation and function are poorly understood. Here, using MINFLUX nanoscopy, we demonstrate that PIEZO1 channels accumulate in pit-shaped invaginations that are distinct from classical membrane invaginations such as clathrin-coated pits and caveolae, thereby possibly creating hotspots for mechanotransduction. Moreover, by measuring intramolecular distances in individual PIEZO1 channels with nanometer precision, we reveal subcellular compartment-specific differences in PIEZO1 conformation at rest and during activation that correlate with differences in PIEZO1 function and are possibly caused by differences in cytoskeletal architecture. Together, our data provide previously unrecognized insights into the complex interplay of forces that determine how PIEZO1 alters membrane shape and, vice versa, how the membrane together with the cytoskeleton affect the conformation and function of individual PIEZO1 channels.
    DOI:  https://doi.org/10.1126/sciadv.ady8052
  16. Sci Immunol. 2025 Oct 24. 10(112): eads9456
    Mitochondrial and lysosomal signaling orchestrates heterogeneous metabolic states of regulatory T cells.
    Jordy Saravia, Nicole M Chapman, Yu Sun, Xiaoxi Meng, Isabel Risch, Wei Li, Cliff Guy, Hao Shi, Haoran Hu, Yogesh Dhungana, Jia Li, Zhiyuan You, Anil Kc, Seon Ah Lim, Jana L Raynor, Sharad Shrestha, Erienne G Norton, Sarah E La Grange, Camenzind G Robinson, Peter Vogel, Hongbo Chi.
      Immunotherapies targeting regulatory T (Treg) cells often trigger inflammation and autoimmunity. How Treg cells undergo functional reprogramming to reestablish immune homeostasis under these conditions remains unclear. Here, we demonstrate that mitochondrial and lysosomal signaling orchestrates Treg cell metabolic and functional fitness. Treg cell-specific loss of the mitochondrial protein Opa1 led to disrupted immune homeostasis and pronounced inflammation, and reduced the generation of Treg cells with high mitochondrial metabolic and suppressive function. Opa1 deletion triggered mitochondrial bioenergetic stress, associated with increased adenosine monophosphate-activated protein kinase (AMPK) signaling and transcription factor EB (TFEB) activation. Further, Treg cell-specific deletion of the lysosomal signaling protein Flcn partially phenocopied Opa1 deficiency-associated inflammation and aberrant TFEB activation, and these effects were rectified by TFEB codeletion. Flcn-deficient Treg cells were enriched in a terminal "metabolic quiescence reset" state and failed to accumulate in nonlymphoid tissues and suppress antitumor immunity. Our study demonstrates that organelle-directed metabolic and signaling processes and mitochondria-lysosome interplay control Treg cell differentiation and function.
    DOI:  https://doi.org/10.1126/sciimmunol.ads9456
  17. Circulation. 2025 Oct 20.
    Hypercontractility and Oxidative Stress Drive Creatine Kinase Dysfunction in Hypertrophic Cardiomyopathy.
    Anton Xu, David Weissman, Katharina J Ermer, Edoardo Bertero, Jan M Federspiel, Felix Stadler, Elisa Grünler, Melina Tangos, Sevasti Zervou, Mark T Waddingham, James T Pearson, Jan-Christian Reil, Smita Scholtz, Jan Dudek, Michael Kohlhaas, Alexander G Nickel, Lucie Carrier, Thomas Eschenhagen, Michelle Michels, Cris Dos Remedios, Sean Lal, Leticia Prates Roma, Nazha Hamdani, Diederik Kuster, Inês Falcão-Pires, Christopher N Johnson, Craig A Lygate, Jolanda van der Velden, Christoph Maack, Vasco Sequeira.
       BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a prevalent inherited cardiac disorder marked by left ventricular hypertrophy and hypercontractility. This excessive mechanical workload creates an energetic mismatch in which consumption exceeds production, leading to myocardial energy depletion. Although CK (creatine kinase) plays a key role in cardiac energy homeostasis, its involvement in HCM remains unclear. This study investigates how hypercontractility-driven mitochondrial stress and the resulting increase in mitochondrial H2O2 disrupt CK function in HCM.
    METHODS: CK function was analyzed using myocardial left ventricular tissue from 92 patients with HCM (with and without pathogenic sarcomere variants) and 30 non-failing human controls. Myofilament and mitochondrial CK isoforms were measured using mRNA analysis, protein immunoblotting, enzyme activity assays, mass spectrometry, and redox-sensitive proteomics. To explore links between hypercontractility, mitochondrial reactive oxygen species, and CK dysfunction, we used isolated cardiomyocytes from wild-type, mitochondrion-targeted catalase-overexpressing, CK knockout (myofilament and mitochondrial CK deletion), HCM-associated Mybpc3 knockin, and mito-roGFP2-Orp1 mouse models. We also tested the effects of the Ca2+ sensitizer EMD-57033, the CK inhibitor 1-fluoro-2,4-dinitrobenzene, and the myosin inhibitor MYK-581, a mavacamten derivative.
    RESULTS: Our analysis revealed significant reductions in myofilament and mitochondrial CK protein levels, as well as CK activity, in myocardium of patients with HCM, primarily because of oxidative modifications of CK. In isolated mouse cardiomyocytes from wild-type and CK knockouts, hypercontractility induced by EMD-57033 elevated mitochondrial H2O2, causing cellular arrhythmias and CK inactivation. Hypercontractility-induced oxidative stress, arrhythmias, and CK dysfunction were also observed in Mybpc3 knockin cardiomyocytes. Mitochondrion-targeted catalase-overexpressing mice with enhanced H2O2 scavenging were protected against H2O2-induced (EMD-57033-mediated) arrhythmias and CK dysfunction. MYK-581 treatment in Mybpc3 knockin cardiomyocytes reduced hypercontractility, lowered H2O2 production and arrhythmias, and preserved CK function. CK inhibition using 1-fluoro-2,4-dinitrobenzene in wild-type cardiomyocytes elevated mitochondrial H2O2 levels and triggered cellular arrhythmias. This mitochondrial oxidation was independently confirmed in mito-roGFP2-Orp1 cardiomyocytes exposed to 1-fluoro-2,4-dinitrobenzene. Mitochondrion-targeted catalase-overexpressing mice were protected from 1-fluoro-2,4-dinitrobenzene -induced oxidative stress and arrhythmogenic events.
    CONCLUSIONS: This study reveals a mechanistic link between hypercontractility, mitochondrial reactive oxygen species, and CK dysfunction in HCM, perpetuating a cycle of energetic dysfunction. Targeting hypercontractility and oxidative stress through myosin inhibition offers a strategy to restore energy balance and reduce arrhythmic risk in HCM.
    Keywords:  arrhythmias; creatine kinase; hypercontractility; hypertrophic cardiomyopathy; myocardial energetics; oxidative stress
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.074120
  18. Dev Cell. 2025 Oct 20. pii: S1534-5807(25)00602-1. [Epub ahead of print]
    Cell-type-specific RNA polymerase II activity maps in intact tissues provide a gateway to mammalian gene regulatory mechanisms in vivo.
    Gopal Chovatiya, Sean Y Huang, Alex B Wang, Philip Versluis, Chris K Bai, Michael DeBerardine, Yu-Ching Liao, Judhajeet Ray, Abdullah Ozer, John T Lis, Tudorita Tumbar.
      Accessing ongoing RNA polymerase II (RNA Pol II) activity in specific cell types within intact tissue is critical to reveal regulatory mechanisms of development. We developed precision run-on in cell-type-specific in vivo system followed by sequencing (PReCIS-seq), a method combining Cre-inducible GFP tagging of endogenous RNA Pol II with transcriptional run-on and GFP immunoprecipitation, to map transcriptionally engaged RNA Pol II genome-wide in targeted cell types of mouse tissues. Applied to keratinocytes within intact skin, PReCIS-seq demonstrates that transcriptionally activated functions of biological transitions generally employ both RNA Pol II promoter-recruitment and promoter-proximal pause-release mechanisms. A global RNA Pol II regulatory polarization features extreme pausing levels at cellular safeguarding vs. lineage identity genes across development and homeostasis. This polarization is associated with distinct proximal-promoter structures, distinguishing high-paused genes with restricted RNA Pol II pause-release from low-paused genes undergoing rapid RNA Pol II firing into productive elongation. PReCIS-seq also identifies active enhancers based on divergent transcription. This approach enables high-resolution, cell-type-specific analysis of RNA Pol II dynamics in intact tissues across mammalian development, homeostasis, and disease.
    Keywords:  RNA Pol II pausing in vivo; TF motifs and RNA Pol II pausing; active enhancers; cell-type-specific nascent transcriptomics; cellular safeguarding genes; epithelial lineage genes; transcription regulation
    DOI:  https://doi.org/10.1016/j.devcel.2025.09.017
  19. Nat Struct Mol Biol. 2025 Oct 20.
    Global analysis of translocon remodeling during protein synthesis at the ER.
    Arunkumar Sundaram, Qianru Li, Yu Wan, Josephine Tang, Haoxi Wu, Luka Smalinskaitė, Ramanujan S Hegde, Zhe Ji, Robert J Keenan.
      Protein biogenesis at the endoplasmic reticulum requires translocons comprising the Sec61 protein-conducting channel and several dynamically associated accessory factors. Here we used transcriptome-wide selective ribosome profiling in human cells to monitor cotranslational interactions of accessory factors for N-glycosylation (the OST-A complex) and multipass membrane protein synthesis (the GEL, PAT and BOS complexes). OST-A was preferentially recruited to open Sec61 channels engaged in polypeptide translocation; conversely, GEL, PAT and BOS were recruited synchronously to closed Sec61 channels and stabilized by newly inserted transmembrane domains. Translocon composition changed repeatedly and reversibly during the synthesis of topologically complex multipass membrane proteins. These data establish the molecular logic that underlies substrate-driven translocon remodeling, events that are crucial for the efficient biogenesis of secretory and membrane proteins.
    DOI:  https://doi.org/10.1038/s41594-025-01691-6
  20. Genome Res. 2025 Oct 22.
    A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress.
    Taylor Anglen, Irene M Kaplow, Baekgyu Choi, Enya Dewars, Robin M Perelli, Kevin T Hagy, Duc Tran, Megan E Ramaker, Svati H Shah, Inkyung Jung, Andrew P Landstrom, Ravi Karra, Yarui Diao, Charles A Gersbach.
      A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs has compensatory effects during heart failure, depending on the type and stage of the underlying cardiomyopathy. Thousands of putative cardiac gene regulatory elements have been identified that may control these programs, but their functions are largely unknown. Here, we profile genome-wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for regulating MYH6 expression, which encodes human fetal myosin. Using chromatin conformation assays in combination with epigenome editing, we find that gene regulation is mediated by a direct interaction between MYH6 and the enhancer. We also find that enhancer activation alters cardiomyocyte response to the hypertrophy-inducing peptide endothelin-1. Enhancer activation prevents polyploidization as well as changes in calcium dynamics and metabolism following stress with endothelin-1. Collectively, these results identify regulatory mechanisms of cardiac gene programs that modulate cardiomyocyte maturation, affect cellular stress response, and could serve as potential therapeutic targets.
    DOI:  https://doi.org/10.1101/gr.280825.125
  21. Curr Biol. 2025 Oct 22. pii: S0960-9822(25)01252-7. [Epub ahead of print]
    Cadherin flow translates cortical chirality into left-right asymmetric cell division dynamics in Caenorhabditis elegans embryos.
    Mi Jing Khor, Yuxuan Rain Xiong, Gaganpreet Sangha, Kenji Sugioka.
      Diverse strategies have evolved in bilaterians to establish left-right (L-R) asymmetry. One driver of L-R asymmetry conserved across phyla is the chiral mechanics of the actomyosin-rich cell cortex, a surface layer that governs cell shape and dynamics. However, how cortical chirality is converted into cellular L-R asymmetry remains obscure. Here, we identify cortical-flow-dependent chiral adhesion pattern formation as a key mechanism driving L-R symmetry breaking of cell division in the two-cell-stage Caenorhabditis elegans embryo. Using high-resolution 4D imaging, we show that the classical cadherin HMR-1 exhibits an early ventral flow followed by a later L-R asymmetric flow during cytokinesis. These ventral and chiral cadherin flows, driven by the extracellular matrix coat surrounding the embryos and by RhoA signaling, respectively, together generate a chiral cadherin pattern at the cell-cell contact. The chiral cadherin patch interacts asymmetrically with the cytokinetic contractile ring, selectively slowing its closure on the embryo's right side via inhibition of ring-directed cortical flow. Disrupting cadherin flow or its interaction with the ring abolishes the rightward displacement of the contractile ring-the earliest detectable L-R asymmetry in C. elegans development. Although cadherin flow is known to facilitate junctional remodeling across organisms, our findings reveal its unexpected role in translating cortical chirality into asymmetric cell division dynamics.
    Keywords:  C. elegans; cadherin; cell division; cell-cell adhesion; chirality; cortical flow; cytokinesis; cytoskeleton; left-right asymmetry
    DOI:  https://doi.org/10.1016/j.cub.2025.09.052
  22. Nat Commun. 2025 Oct 22. 16(1): 9355
    A multimodal cross-species comparison of pancreas development.
    Kaiyuan Yang, Hannah Spitzer, Michael Sterr, Karin Hrovatin, Sean de la O, Xinghao Zhang, Eunike Sawitning Ayu Setyono, Minhaz Ud-Dean, Thomas Walzthoeni, Krzysztof Flisikowski, Tatiana Flisikowska, Angelika Schnieke, Katharina Scheibner, James M Wells, Julie B Sneddon, Barbara Kessler, Eckhard Wolf, Elisabeth Kemter, Fabian J Theis, Heiko Lickert.
      Human pancreas development remains incompletely characterized due to restricted sample access. We investigate whether pigs resemble humans in pancreas development, offering a complementary large-animal model. As pig pancreas organogenesis is unexplored, we first annotate developmental hallmarks throughout its 114-day gestation. Building on this, we construct a pig single-cell multiome pancreas atlas across all trimesters. Cross-species comparisons reveal pigs resemble humans more closely than mice in developmental tempo, epigenetic and transcriptional regulation, and gene regulatory networks. This further extends to progenitor dynamics and endocrine fate acquisition. Transcription factors regulated by NEUROG3, the endocrine master regulator, are over 50% conserved between pig and human, many being validated in human stem cell models. Notably, we uncover that during embryonic development, emerging beta-cell heterogeneity coincides with a species-conserved primed endocrine cell (PEC) population alongside NEUROG3-expressing cells. Overall, our work lays the foundation for comparative investigations and offers unprecedented insights into evolutionarily conserved pancreas organogenesis mechanisms across animal models.
    DOI:  https://doi.org/10.1038/s41467-025-64774-4
  23. Sci Adv. 2025 Oct 24. 11(43): eady1742
    Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function.
    Gary Loughran, Raffaella De Pace, Ningyu Ding, Jianchao Zhang, Irwin Jungreis, Gionmattia Carancini, Jonathan M Mudge, Ji Wang, Manolis Kellis, John F Atkins, Pavel V Baranov, Andrew E Firth, Xiaowei Li, Juan S Bonifacino, Yousuf A Khan.
      Programmed ribosomal frameshifting is a process where a proportion of ribosomes change their reading frame on an mRNA. While frameshifting is commonly used by viruses, very few phylogenetically conserved examples are known in nuclear encoded genes. Here, we report a +1 frameshifting event during decoding of the human gene PLEKHM2 that provides access to a second internally overlapping ORF. The new carboxyl-terminal domain of this frameshift protein forms an α helix, which relieves PLEKHM2 from autoinhibition and allows it to move to the tips of cells without activation by ARL8. Reintroducing both the canonically translated and frameshifted protein are necessary to restore normal contractile function of PLEKHM2 knockout cardiomyocytes, demonstrating the necessity of frameshifting for normal cardiac activity.
    DOI:  https://doi.org/10.1126/sciadv.ady1742
  24. Nat Genet. 2025 Oct 21.
    Complete genome assemblies of two mouse subspecies reveal structural diversity of telomeres and centromeres.
    Bailey A Francis, Landen Gozashti, Kevin Costello, Takaoki Kasahara, Olivia S Harringmeyer, Jingtao Lilue, Tianzhen Wu, Katarzyna Zoltowska, Mohab Helmy, Tadafumi Kato, Anne Czechanski, Iraad F Bronner, Emma Dawson, Michael A Quail, Anne Ferguson-Smith, Laura Reinholdt, David J Adams, Thomas M Keane.
      It has been more than 20 years since the publication of the C57BL/6J mouse reference genome, which has been a key catalyst for understanding the biology of mammalian diseases. However, the mouse reference genome still lacks telomeres and centromeres, contains 281 chromosomal sequence gaps and only partially represents many biomedically relevant loci. Here we present the first telomere-to-telomere (T2T) mouse genomes for two key inbred strains, C57BL/6J and CAST/EiJ. These T2T genomes reveal substantial variability in telomere and centromere sizes and structural organization. We thus add an additional 213 Mb of new sequence to the reference genome, which contains 517 protein-coding genes. We also examined two important but incomplete loci in the mouse genome-the pseudoautosomal region (PAR) on the sex chromosomes and KRAB zinc-finger protein loci. We identified distant locations of the PAR boundary, different copy numbers and sizes of segmental duplications and a multitude of amino acid substitution mutations in PAR genes.
    DOI:  https://doi.org/10.1038/s41588-025-02367-z
  25. Nat Chem Biol. 2025 Oct 23.
    MED1 IDR deacetylation controls stress responsive genes through RNA Pol II recruitment.
    Ran Lin, Yan Mo, Douglas Barrows, Wenbin Mei, Takashi Onikubo, Jianfeng Sun, Zhiguo Zhang, Effie Apostolou, Sohail F Tavazoie, Robert G Roeder.
      Cells fine-tune gene expression in response to cellular stress, a process critical for tumorigenesis. However, mechanisms governing stress-responsive transcription remain incompletely understood. This study shows that the MED1 subunit of the Mediator coactivator complex is acetylated in its intrinsically disordered region (IDR). Under stress, SIRT1 associates with the super elongation complex to deacetylate MED1 in promoter-proximal regions. The deacetylated (or acetylation-defective mutant) MED1 amplified stress-activated cytoprotective genes and rescued stress-suppressed growth-supportive genes in estrogen-receptor-positive breast cancer (ER+ BC) cells. Mechanistically, deacetylated MED1 promotes chromatin incorporation of RNA polymerase II (Pol II) through IDR-mediated interactions. Functionally, ER+ BC cells with deacetylated MED1 exhibit faster growth and enhanced stress resistance in culture and in an orthotopic mouse model. These findings advance our understanding of Pol II regulation under cellular stress and potentially suggest therapeutic strategies targeting oncogenic transcription driven by MED1 and Mediator.
    DOI:  https://doi.org/10.1038/s41589-025-02035-7
  26. Elife. 2025 Oct 22. pii: RP102784. [Epub ahead of print]14
    Chromatin activity of IκBα mediates the exit from naïve pluripotency.
    Luis G Palma, Daniel Alvarez-Villanueva, Maria Maqueda, Mercedes Barrero, Arnau Iglesias, Joan Bertran, Damiana Alvarez, Carlos A Garcia-Prieto, Cecilia Ballare, Virginia Rodriguez-Cortez, Clara Bueno, August Vidal, Alberto Villanueva, Pablo Menendez, Gregoire Stik, Luciano Di Croce, Bernhard Payer, Manel Esteller, Lluis Espinosa, Anna Bigas.
      Maintenance of pluripotency is a multifactorial process in which NF-κB is a negative regulator. Our previous work identified a chromatin role for IκBα, the master regulator of NF-κB signaling, that is critical for the proper regulation of various tissue stem cells. Here, we found that IκBα accumulates specifically in the chromatin fraction of mouse pluripotent stem cells. IκBα depletion does not affect NF-kB-dependent transcription, but causes a profound epigenetic rewiring in pluripotent stem cells, including alterations in H3K27me3, a histone mark catalyzed by Polycomb repression complex 2. Chromatin changes induced by IκBα depletion affect a subset of pluripotency genes and are associated with altered gene transcription. At the cellular level, IκBα-deficient embryonic stem cells are arrested in a naive pluripotency state when cultured in serum/LIF conditions and fail to exit pluripotency under differentiation conditions. By constructing separation-of-function mutants, we show that the effects of IκBα in regulating stem cell pluripotency are NF-κB-independent, but mainly rely on its chromatin-related function. Taken together, our results reveal a novel mechanism by which IκBα participates in the regulation of the pluripotent state of mouse embryonic stem cells and shed light on the interplay between inflammatory signals and the regulation of pluripotency.
    Keywords:  NFKB; NFKBIA; PRC2; embryonic stem cells; ikappabalpha; mouse; pluripotency exit; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.102784
  27. J Biol Chem. 2025 Oct 16. pii: S0021-9258(25)02686-9. [Epub ahead of print] 110834
    Endophilin-Lamellipodin-VASP, key components in fast endophilin-mediated endocytosis, control actin polymerization within liquid-like condensates.
    Karthik B Narayan, Honey Priya James, Jonathan Cope, Samsuzzoha Mondal, Laura Baeyens, Francesco Milano, Jason Zheng, Matthias Krause, Tobias Baumgart.
      Actin polymerization is essential in several clathrin-independent endocytic pathways including fast endophilin mediated endocytosis (FEME), however the actin machinery involved in FEME has been elusive. Here, we show that the actin polymerase VASP colocalizes and interacts directly with the FEME priming complex. We identify Endophilin as a VASP binding partner and establish novel non-canonical interactions between the SH3 domain of Endophilin and the EVH1 and EVH2 domains of VASP. We show that liquid-like condensates formed by Endophilin, Lamellipodin and VASP localize actin polymerization both in solution and on lipid membranes, and result in the formation of torus-shaped condensates in the bulk. We establish a new role for multivalent Endophilin-Lamellipodin interactions in the regulation of actin polymerization, and we identify a novel function for Endophilin as a promoter of actin bundling. Our findings support a model that explains the connection between local actin polymerization and dynamic formation and dissolution of endocytic priming patches in FEME.
    DOI:  https://doi.org/10.1016/j.jbc.2025.110834
  28. Nat Metab. 2025 Oct 22.
    Oligodendrocyte precursor cell-specific blocking of low-glucose-induced activation of AMPK ensures myelination and remyelination.
    Yuxia Sun, Wei-Wei Zhang, Lu Men, Jianfeng Wu, Luming Yao, Xi Huang, Yaying Wu, Cixiong Zhang, Ying Chen, David Carling, Chen-Song Zhang, Sheng-Cai Lin.
      It has been shown that in most cells, low glucose leads to activation of AMP-activated protein kinase (AMPK) via the lysosomal glucose-sensing pathway, where glycolytic aldolase acts as the glucose sensor. Here, we show that ALDOC (aldolase C), the predominant isozyme of aldolase in mouse and rat oligodendrocyte precursor cells (OPCs), is acetylated at lysine 14, making the lysosomal glucose-sensing AMPK pathway unable to operate. We find that the blockage of AMPK activation is required for the proper proliferation and differentiation of OPCs into mature oligodendrocytes for myelination during development and for remyelination in areas of demyelination where the local glucose levels are low. Therefore, the acetylation of aldolase acts as a checkpoint for AMPK activation in response to low glucose to ensure the proliferation and differentiation of OPCs for myelination, and remyelination of demyelinated neurons.
    DOI:  https://doi.org/10.1038/s42255-025-01386-8
  29. J Cell Sci. 2025 Oct 23. pii: jcs.264107. [Epub ahead of print]
    Ligand and integrin-independent mechano-sensitive EGFR activation in lung cancer cells.
    Aneesa Shaikh, Aarmann Mohan, Milan Collins, George Santis, Maddy Parsons.
      Epidermal Growth Factor Receptor (EGFR) is a transmembrane receptor tyrosine kinase that plays important roles in cell proliferation, differentiation, and migration. EGFR overexpression or mutation is a hallmark of some cancers, leading to hyperactivation of downstream signalling. Co-regulation between EGF-dependent EGFR signalling and extracellular matrix (ECM) adhesion occurs in both healthy and malignant cells. Increasing ECM stiffness can contribute to lung cancer progression and is sensed by integrins to promote proliferation and invasion. Emerging evidence suggests non-canonical roles for EGFR in mechano-sensing, but the molecular mechanisms and functional consequences remain unclear. Here we demonstrate that EGFR is activated in human lung cancer cells upon early adhesion to ECM substrates with physiologically relevant stiffness (28 kPa vs. 1.5 kPa), independently of canonical ligands and integrins. Mechano-induced EGFR activation correlates with and requires active Src, F-actin and is coupled to stiffness-dependent plasma membrane retention of EGFR within disordered lipid microdomains. Early stiffness-dependent EGFR activation is required for enhanced migration. These findings uncover a non-canonical role for EGFR in early adhesion related mechano-sensing with potential implications for treatment of lung cancer.
    Keywords:  Cytoskeleton; EGFR; Membrane domains; Migration; Src; Substrate stiffness
    DOI:  https://doi.org/10.1242/jcs.264107
  30. Biochem Biophys Res Commun. 2025 Oct 17. pii: S0006-291X(25)01527-X. [Epub ahead of print]788 152811
    Total cell number influences the timing of Hippo/YAP activation during preimplantation development in mouse tetraploid embryos.
    Kaoru Fujino, Hiroyuki Imai, Sumito Matsuya, Ken Takeshi Kusakabe, Kiyoshi Kano.
      Total cell number may determine the timing of Hippo/YAP activity during first lineage specification. We combined mouse tetraploid embryos (reduced cell numbers) with a 2 × 4n aggregation approach (increasing cell numbers) to test whether YAP nuclear entry in inner cell mass (ICM) cells is temporally shifted. Tetraploids reached the blastocyst stage with approximately half the cells of diploids and exhibited delayed nuclear YAP in ICM at mid-blastocyst, despite overall ICM/trophectoderm patterning and pluripotency markers (Oct4, Nanog, Sox2) being comparable. Increasing total cell number by aggregating two tetraploids restored YAP timing to that of diploids. By the late-blastocyst stage, most tetraploid ICM cells displayed nuclear YAP, indicating that this delay is transient. These findings support a model in which total cell number -not ploidy per se-is associated with the timing of Hippo/YAP activation in the preimplantation embryo.
    Keywords:  Blastocyst; Cell number; Hippo signaling; Preimplantation development; Tetraploid embryo; YAP
    DOI:  https://doi.org/10.1016/j.bbrc.2025.152811
  31. Nature. 2025 Oct 22.
    Bottom-up design of Ca2+ channels from defined selectivity filter geometry.
    Yulai Liu, Connor Weidle, Ljubica Mihaljević, Joseph L Watson, Zhe Li, Le Tracy Yu, Sagardip Majumder, Andrew J Borst, Kenneth D Carr, Ryan D Kibler, Tamer M Gamal El-Din, William A Catterall, David Baker.
      Native ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices1,2. Protein design has been harnessed to generate pore-containing transmembrane proteins, but the design of selectivity filters with precise arrangements of amino acid side chains specific for a target ion, a crucial feature of native ion channels3, has been constrained by the lack of methods for placing the metal-coordinating residues with atomic-level precision. Here we describe a bottom-up RFdiffusion-based approach to construct Ca2+ channels from defined selectivity filter residue geometries, and use this approach to design symmetric oligomeric channels with Ca2+ selectivity filters having different coordination numbers and different geometries at the entrance of a wider pore buttressed by multiple transmembrane helices. The designed channel proteins assemble into homogeneous pore-containing particles and, for both tetrameric and hexameric ion-coordinating configurations, patch-clamp experiments show that the designed channels have higher conductances for Ca2+ than for Na+ and other divalent ions (Sr2+ and Mg2+) that are eliminated after mutation of selectivity filter residues. Cryogenic electron microscopy indicates that the design method has high accuracy: the structure of the hexameric Ca2+ channel is nearly identical to that of the design model. Our bottom-up design approach now enables the testing of hypotheses relating filter geometry to ion selectivity by direct construction, and provides a roadmap for creating selective ion channels for a wide range of applications.
    DOI:  https://doi.org/10.1038/s41586-025-09646-z
  32. EMBO J. 2025 Oct 22.
    Germ granule localization of nematode Argonaute WAGO-4 ensures fidelity in small RNA loading.
    Stela Jelenic, Mathias S Renaud, Samantha Del Borrello, Joseph Gokcezade, Janos Bindics, Lisa Frasz, Philipp Czermak, Peter Duchek, Julie M Claycomb.
      Germ granules are liquid-like condensates that regulate small RNA pathways and gene expression, ensuring genome stability and fertility in animals. In C. elegans, several Argonaute proteins, central players of small RNA pathways, localize to germ granules, yet the functional significance of this spatial enrichment remains unclear. Here, we disrupted the localization of the Argonaute WAGO-4 to germ granules by introducing targeted mutations in the FG repeats of Vasa-like GLH proteins. These mutations did not disrupt overall germ granule architecture but significantly reduced WAGO-4 partitioning, leading to its predominant localization in the cytoplasm. Functional analyses revealed that this mislocalization partially compromised WAGO-4 activity, resulting in reduced WAGO-4 binding of small RNAs targeting specific genes, particularly those not co-regulated by the Argonaute CSR-1. This selective effect highlights the importance of WAGO-4's spatial localization for efficient small RNA loading and gene regulation. Our findings demonstrate that germ granules serve as specialized compartments that fine-tune Argonaute function, emphasizing the role of phase-separated condensates in modulating RNA pathways and gene regulatory networks.
    Keywords:   C. elegans Germline; Argonautes; Biomolecular Condensates; Germ Granules; Small RNA Pathways
    DOI:  https://doi.org/10.1038/s44318-025-00606-x
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