bims-ginsta Biomed News
on Genome instability
Issue of 2025–04–06
25 papers selected by
Jinrong Hu, National University of Singapore
  1. SKAP binding to microtubules reduces friction at the kinetochore-microtubule interface and increases attachment stability under force.
  2. A spatiotemporal cell atlas of cardiopulmonary progenitor cell allocation during development.
  3. Genetically encoded reporters of actin filament organization in living cells and tissues.
  4. Regeneration leads to global tissue rejuvenation in aging sexual planarians.
  5. Pluripotent cell states and fates in human embryo models.
  6. Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.
  7. Meru co-ordinates spindle orientation with cell polarity and cell cycle progression.
  8. Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.
  9. HAND1 level controls the specification of multipotent cardiac and extraembryonic progenitors from human pluripotent stem cells.
  10. Tissue-like multicellular development triggered by mechanical compression in archaea.
  11. Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes.
  12. Somatic NAP1L1 p.D349E promotes cardiac hypertrophy through cGAS-STING-IFN signaling.
  13. Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.
  14. The RAD52 double-ring remodels replication forks restricting fork reversal.
  15. Dual genetic tracing demonstrates the heterogeneous differentiation and function of neuromesodermal progenitors in vivo.
  16. Global analysis of protein turnover dynamics in single cells.
  17. Cellular and molecular regulations of oocyte selection and activation in mammals.
  18. No transcription, no problem: Protein phosphorylation changes and the transition from oocyte to embryo.
  19. Epigenome dynamics in early mammalian embryogenesis.
  20. Ceramide-induced FGF13 impairs systemic metabolic health.
  21. Luteinizing hormone-induced changes in the structure of mammalian preovulatory follicles.
  22. Animal septins contain functional transmembrane domains.
  23. Enteroendocrine Cells Regulate Intestinal Barrier Permeability.
  24. Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.
  25. Engineering sonogenetic EchoBack-CAR T cells.
  1. Curr Biol. 2025 Mar 25. pii: S0960-9822(25)00288-X. [Epub ahead of print]
    SKAP binding to microtubules reduces friction at the kinetochore-microtubule interface and increases attachment stability under force.
    Miquel Rosas-Salvans, Caleb J Rux, Moumita Das, Sophie Dumont.
      The kinetochore links chromosomes to spindle microtubules to drive chromosome segregation at cell division. We recently uncovered that the kinetochore complex Astrin-SKAP, which binds microtubules, reduces rather than increases friction at the mammalian kinetochore-microtubule interface. How it does so is not known. Astrin-SKAP could affect how other kinetochore complexes bind microtubules, reducing their friction along microtubules, or it could itself bind microtubules with similar affinity but lower friction than other attachment factors. Using SKAP mutants unable to bind microtubules, live imaging, and laser ablation, we show that SKAP's microtubule binding is essential for sister kinetochore coordination, force dissipation at the interface, and attachment responsiveness to force changes. Further, we show that SKAP's microtubule binding is essential to prevent chromosome detachment under both spindle forces and microneedle-generated forces. Together, our findings indicate that SKAP's microtubule binding reduces kinetochore friction and increases attachment responsiveness and stability under force. We propose that having complexes with both high and low sliding friction on microtubules, making a mechanically heterogeneous interface, is key to maintaining robust attachments under force and thus accurate segregation.
    Keywords:  Astrin-SKAP; attachment; dynamics; friction; interface; kinetochore; mechanics; microtubule; robustness; spindle
    DOI:  https://doi.org/10.1016/j.cub.2025.03.003
  2. Cell Rep. 2025 Apr 02. pii: S2211-1247(25)00284-0. [Epub ahead of print]44(4): 115513
    A spatiotemporal cell atlas of cardiopulmonary progenitor cell allocation during development.
    Hongbo Wen, Prashant Chandrasekaran, Annabelle Jin, Josh Pankin, MinQi Lu, Derek C Liberti, Jarod A Zepp, Rajan Jain, Edward E Morrisey, Sylvia N Michki, David B Frank.
      The heart and lung co-orchestrate their development during organogenesis. The mesoderm surrounding both the developing heart and anterior foregut endoderm provides instructive cues guiding cardiopulmonary development. Additionally, it serves as a source of cardiopulmonary progenitor cells (CPPs) expressing Wnt2 that give rise to both cardiac and lung mesodermal cell lineages. Despite the mesoderm's critical importance to both heart and lung development, mechanisms guiding CPP specification are unclear. To address this, we lineage traced Wnt2+ CPPs at E8.5 and performed single-cell RNA sequencing on collected progeny across the developmental lifespan. Using computational analyses, we created a CPP-derived cell atlas that revealed a previously underappreciated spectrum of CPP-derived cell lineages, including all lung mesodermal lineages, ventricular cardiomyocytes, and epicardial and pericardial cells. By integrating spatial mapping with computational cell trajectory analysis and transcriptional profiling, we have provided a potential molecular and cellular roadmap for cardiopulmonary development.
    Keywords:  CP: Developmental biology; WNT; cell fate; development; heart; lung; progenitor cells; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.celrep.2025.115513
  3. Cell. 2025 Apr 01. pii: S0092-8674(25)00276-4. [Epub ahead of print]
    Genetically encoded reporters of actin filament organization in living cells and tissues.
    Carla Silva Martins, François Iv, Shashi Kumar Suman, Thomas C Panagiotou, Clara Sidor, María Ruso-López, Camille N Plancke, Shizue Omi, Rebecca Pagès, Maxime Gomes, Alexander Llewellyn, Sourish Reddy Bandi, Laurie Ramond, Federica Arbizzani, Caio Vaz Rimoli, Frank Schnorrer, François Robin, Andrew Wilde, Loïc LeGoff, Jean-Denis Pedelacq, Antoine Jégou, Stéphanie Cabantous, Sergio A Rincon, Cristel Chandre, Sophie Brasselet, Manos Mavrakis.
      The cytoskeletal protein actin is crucial for cell shape and integrity throughout eukaryotes. Actin filaments perform essential biological functions, including muscle contraction, cell division, and tissue morphogenesis. These diverse activities are achieved through the ability of actin filaments to be arranged into precise architectures. Much progress has been made in defining the proteome of the actin cytoskeleton, but a detailed appreciation of the dynamic organizational state of the actin filaments themselves has been hindered by available tools. Fluorescence polarization microscopy is uniquely placed for measuring actin filament organization by exploiting the sensitivity of polarized light excitation to the orientation of fluorophores attached to actin filaments. By engineering fusions of five widely used actin localization reporters to fluorescent proteins with constrained mobility, we have succeeded in developing genetically encoded, green- and red-fluorescent-protein-based reporters for non-invasive, quantitative measurements of actin filament organization in living cells and tissues by fluorescence polarization microscopy.
    Keywords:  GFP mobility; actin filaments; filament alignment; fluorescence polarization microscopy; molecular order; molecular organization; molecular orientation
    DOI:  https://doi.org/10.1016/j.cell.2025.03.003
  4. Nat Aging. 2025 Apr 03.
    Regeneration leads to global tissue rejuvenation in aging sexual planarians.
    Xiaoting Dai, Xinghua Li, Alexander Tyshkovskiy, Cassandra Zuckerman, Nan Cheng, Peter Lin, David Paris, Saad Qureshi, Leonid Kruglyak, Xiaoming Mao, Jayakrishnan Nandakumar, Vadim N Gladyshev, Scott Pletcher, Jacob Sobota, Longhua Guo.
      The possibility of reversing the adverse impacts of aging could significantly reduce age-related diseases and improve quality of life in older populations. Here we report that the sexual lineage of the planarian Schmidtea mediterranea exhibits physiological decline within 18 months of birth, including altered tissue architecture, impaired fertility and motility, and increased oxidative stress. Single-cell profiling of young and older planarian heads uncovered loss of neurons and muscle, increase of glia, and revealed minimal changes in somatic pluripotent stem cells, along with molecular signatures of aging across tissues. Remarkably, amputation followed by regeneration of lost tissues in older planarians led to reversal of these age-associated changes in tissues both proximal and distal to the injury at physiological, cellular and molecular levels. Our work suggests mechanisms of rejuvenation in both new and old tissues concurring with planarian regeneration, which may provide valuable insights for antiaging interventions.
    DOI:  https://doi.org/10.1038/s43587-025-00847-9
  5. Development. 2025 Apr 01. pii: dev204565. [Epub ahead of print]152(7):
    Pluripotent cell states and fates in human embryo models.
    Berna Sozen, Patrick P L Tam, Martin F Pera.
      Pluripotency, the capacity to generate all cells of the body, is a defining property of a transient population of epiblast cells found in pre-, peri- and post-implantation mammalian embryos. As development progresses, the epiblast cells undergo dynamic transitions in pluripotency states, concurrent with the specification of extra-embryonic and embryonic lineages. Recently, stem cell-based models of pre- and post-implantation human embryonic development have been developed using stem cells that capture key properties of the epiblast at different developmental stages. Here, we review early primate development, comparing pluripotency states of the epiblast in vivo with cultured pluripotent cells representative of these states. We consider how the pluripotency status of the starting cells influences the development of human embryo models and, in turn, what we can learn about the human pluripotent epiblast. Finally, we discuss the limitations of these models and questions arising from the pioneering studies in this emerging field.
    Keywords:  Cell fate; Epiblast; Human embryo model; Peri-implantation development; Pluripotent stem cell
    DOI:  https://doi.org/10.1242/dev.204565
  6. Cell Rep. 2025 Apr 03. pii: S2211-1247(25)00273-6. [Epub ahead of print]44(4): 115502
    Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.
    Holly Merta, Kaitlynn Gov, Tadamoto Isogai, Blessy Paul, Achinta Sannigrahi, Arun Radhakrishnan, Gaudenz Danuser, W Mike Henne.
      The endoplasmic reticulum (ER) is structurally and functionally diverse, yet how its functions are organized within morphological subdomains is incompletely understood. Utilizing TurboID-based proximity labeling and CRISPR knockin technologies, we map the proteomic landscape of the human ER network. Sub-organelle proteomics reveals enrichments of proteins into ER tubules, sheets, and the nuclear envelope. We uncover an ER-enriched actin-binding protein, calmin/CLMN, and define it as an ER-actin tether that localizes to focal adhesions adjacent to ER tubules. Mechanistically, we find that CLMN depletion perturbs adhesion disassembly, actin dynamics, and cell movement. CLMN-depleted cells display decreased polarization of ER-plasma membrane contacts and calcium signaling factor STIM1 and altered calcium signaling near ER-actin interfaces, suggesting that CLMN influences calcium signaling to facilitate F-actin/adhesion dynamics. Collectively, we map the sub-organelle proteome landscape of the ER, identify CLMN as an ER-actin tether, and describe a non-canonical mechanism by which ER tubules engage actin to regulate cell migration.
    Keywords:  CLMN; CP: Cell biology; ER; TurboID; adhesion; calmin; endoplasmic reticulum; migration
    DOI:  https://doi.org/10.1016/j.celrep.2025.115502
  7. EMBO J. 2025 Apr 01.
    Meru co-ordinates spindle orientation with cell polarity and cell cycle progression.
    Melissa M McLellan, Birgit L Aerne, Jennifer J Banerjee Dhoul, Maxine V Holder, Tania Auchynnikava, Nicolas Tapon.
      Correct mitotic spindle alignment is essential for tissue architecture and plays an important role in cell fate specification through asymmetric cell division. Spindle tethering factors such as Drosophila Mud (NuMA in mammals) are recruited to the cell cortex and capture astral microtubules, pulling the spindle in the correct orientation. However, how spindle tethering complexes read the cell polarity axis and how spindle attachment is coupled to mitotic progression remains poorly understood. We explore these questions in Drosophila sensory organ precursors (SOPs), which divide asymmetrically to give rise to epidermal mechanosensory bristles. We show that the scaffold protein Meru, which is enriched at the posterior cortex by the Frizzled/Dishevelled planar cell polarity complex, in turn recruits Mud, linking the spindle tethering and polarity machineries. Furthermore, Cyclin A/Cdk1 associates with Meru at the posterior cortex, promoting the formation of the Mud/Meru/Dsh complex via Meru and Dsh phosphorylation. Thus, Meru couples spindle orientation with cell polarity and provides a cell cycle-dependent cue for spindle tethering.
    Keywords:  Asymmetric Cell Division; Cell Polarity; Development; Drosophila; Spindle Orientation
    DOI:  https://doi.org/10.1038/s44318-025-00420-5
  8. Science. 2025 Apr 04. 388(6742): 52-59
    Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.
    Jorge Diego Martin-Rufino, Alexis Caulier, Seayoung Lee, Nicole Castano, Emily King, Samantha Joubran, Marcus Jones, Seth R Goldman, Uma P Arora, Lara Wahlster, Eric S Lander, Vijay G Sankaran.
      Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb-multiome, to simultaneously profile chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of master transcription factors (TFs). We examined the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within TF-sensitive accessible chromatin regions in erythroid differentiation, although representing <0.3% of the genome, show a ~100-fold enrichment for blood cell phenotype heritability, which is substantially higher than that for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.
    DOI:  https://doi.org/10.1126/science.ads7951
  9. EMBO J. 2025 Mar 31.
    HAND1 level controls the specification of multipotent cardiac and extraembryonic progenitors from human pluripotent stem cells.
    Adam T Lynch, Naomi Phillips, Megan Douglas, Marta Dorgnach, I-Hsuan Lin, Antony D Adamson, Zoulfia Darieva, Jessica Whittle, Neil A Hanley, Nicoletta Bobola, Matthew J Birket.
      Diverse sets of progenitors contribute to the development of the embryonic heart, but the mechanisms of their specification have remained elusive. Here, using a human pluripotent stem cell (hPSC) model, we deciphered cardiac and non-cardiac lineage trajectories in differentiation and identified transcription factors underpinning cell specification, identity and function. We discovered a concentration-dependent, fate determining function for the basic helix-loop-helix transcription factor HAND1 in mesodermal progenitors and uncovered its gene regulatory network. At low expression level, HAND1 directs differentiation towards multipotent juxta-cardiac field progenitors able to make cardiomyocytes and epicardial cells, whereas at high level it promotes the development of extraembryonic mesoderm. Importantly, HAND1-low progenitors can be propagated in their multipotent state. This detailed mechanistic insight into human development has the potential to accelerate the delivery of effective disease modelling, including for congenital heart disease, and cell therapy-based regenerative medicine.
    Keywords:  Epicardial; Gene Regulatory Networks; HAND1; Juxta-cardiac Field; Single Cell
    DOI:  https://doi.org/10.1038/s44318-025-00409-0
  10. Science. 2025 Apr 04. 388(6742): 109-115
    Tissue-like multicellular development triggered by mechanical compression in archaea.
    Theopi Rados, Olivia S Leland, Pedro Escudeiro, John Mallon, Katherine Andre, Ido Caspy, Andriko von Kügelgen, Elad Stolovicki, Sinead Nguyen, Inés Lucía Patop, L Thiberio Rangel, Sebastian Kadener, Lars D Renner, Vera Thiel, Yoav Soen, Tanmay A M Bharat, Vikram Alva, Alex Bisson.
      The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming tissue-like structures. These archaeal tissues are mechanically and molecularly distinct from their unicellular lifestyle, mimicking several eukaryotic features. Archaeal tissues undergo a multinucleate stage followed by tubulin-independent cellularization, orchestrated by active membrane tension at a critical cell size. After cellularization, tissue junction elasticity becomes akin to that of animal tissues, giving rise to two cell types-peripheral (Per) and central scutoid (Scu) cells-with distinct actin and protein glycosylation polarity patterns. Our findings highlight the potential convergent evolution of a biophysical mechanism in the emergence of multicellular systems across domains of life.
    DOI:  https://doi.org/10.1126/science.adu0047
  11. PLoS Genet. 2025 Apr 04. 21(4): e1011645
    Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes.
    Christian R Nelson, Darren R Mallett, Sue Biggins.
      Faithful chromosome segregation depends upon kinetochores, large protein complexes that anchor chromosomes to dynamic microtubules, allowing for their movement at anaphase. Critical microtubule-coupling components of the budding yeast kinetochore, the Dam1 (Dam1c) and Ndc80 (Ndc80c) complexes, work cooperatively to ensure that kinetochores track with the plus-ends of microtubules. Additionally, the Dam1 complex plays a distinct role in ensuring the integrity of the mitotic spindle. However, the events required to orchestrate these diverse functions of Dam1c remain unclear. To identify regulatory events on kinetochores, we performed phosphoproteomics on purified kinetochore proteins and identified many previously unknown phosphorylation events. We demonstrate that Ndc80 is phosphorylated at Thr-248 and Thr-252 to promote the interaction between Ndc80 and the Dam1c. The phosphorylation of T248 is cell cycle regulated and depends on Mps1. Ndc80 phosphorylation at T248 and T252 does not appear to regulate kinetochore function and instead contributes to Dam1c localization to the anaphase spindle. A ndc80 phospho-deficient mutant exhibited a genetic interaction and altered spindle morphology when combined with dam1 mutant alleles. Taken together, we propose that Mps1-dependent phosphorylation of Ndc80 at T248 and T252 is removed at anaphase to allow Dam1c to help organize and stabilize the spindle.
    DOI:  https://doi.org/10.1371/journal.pgen.1011645
  12. Nat Commun. 2025 Apr 01. 16(1): 3140
    Somatic NAP1L1 p.D349E promotes cardiac hypertrophy through cGAS-STING-IFN signaling.
    Cheng Lv, Xiayidan Alimu, Xiao Xiao, Fei Wang, Jizheng Wang, Shuiyun Wang, Guixin Wu, Yu Zhang, Yue Wu, Houzao Chen, Rutai Hui, Lei Song, Yibo Wang.
      Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, often caused by sarcomere gene mutations, though many sporadic cases remain genetically unexplained. Here we show that the somatic variant NAP1L1 p.D349E was involved in cardiac hypertrophy in sporadic HCM patients. Through next generation sequencing, we found that somatic variant NAP1L1 p.D349E was recurrent in the cardiomyocytes of gene-elusive sporadic HCM patients. Subsequent in vivo and in vitro functional analysis confirmed that NAP1L1 p.D349E contributes to HCM by triggering an innate immunity response. This mutation destabilizes nucleosome formation, causing DNA to leak into the cytoplasm. This leakage activates a key immune pathway, cGAS-STING, which leads to the release of inflammatory molecules and promotes heart muscle thickening. Our findings reveal a new mechanism driving HCM and suggest that somatic variants could be important in understanding and management of HCM.
    DOI:  https://doi.org/10.1038/s41467-025-58453-7
  13. Cell. 2025 Mar 26. pii: S0092-8674(25)00270-3. [Epub ahead of print]
    Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.
    Milka Doktorova, Jessica L Symons, Xiaoxuan Zhang, Hong-Yin Wang, Jan Schlegel, Joseph H Lorent, Frederick A Heberle, Erdinc Sezgin, Edward Lyman, Kandice R Levental, Ilya Levental.
      Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.
    Keywords:  cholesterol; lipid asymmetry; lipid diffusion; membrane packing; membrane structure; peripheral protein; permeability; phospholipid; plasma membrane; protein-membrane interactions
    DOI:  https://doi.org/10.1016/j.cell.2025.02.034
  14. Nature. 2025 Apr 02.
    The RAD52 double-ring remodels replication forks restricting fork reversal.
    Masayoshi Honda, Mortezaali Razzaghi, Paras Gaur, Eva Malacaria, Giorgia Marozzi, Ludovica Di Biagi, Francesca Antonella Aiello, Emeleeta A Paintsil, Andrew J Stanfield, Bailey J Deppe, Lokesh Gakhar, Nicholas J Schnicker, M Ashley Spies, Pietro Pichierri, Maria Spies.
      Human RAD52 is a multifunctional DNA repair protein involved in several cellular events that support genome stability, including protection of stalled DNA replication forks from excessive degradation1-4. In its gatekeeper role, RAD52 binds to and stabilizes stalled replication forks during replication stress, protecting them from reversal by SMARCAL1 motor3. The structural and molecular mechanism of the RAD52-mediated fork protection remains elusive. Here, using P1 nuclease sensitivity, biochemical and single-molecule analyses, we show that RAD52 dynamically remodels replication forks through its strand exchange activity. The presence of the single-stranded DNA binding protein RPA at the fork modulates the kinetics of the strand exchange without impeding the reaction outcome. Mass photometry and single-particle cryo-electron microscopy show that the replication fork promotes a unique nucleoprotein structure containing head-to-head arrangement of two undecameric RAD52 rings with an extended positively charged surface that accommodates all three arms of the replication fork. We propose that the formation and continuity of this surface is important for the strand exchange reaction and for competition with SMARCAL1.
    DOI:  https://doi.org/10.1038/s41586-025-08753-1
  15. Proc Natl Acad Sci U S A. 2025 Apr 08. 122(14): e2402305122
    Dual genetic tracing demonstrates the heterogeneous differentiation and function of neuromesodermal progenitors in vivo.
    Hengwei Jin, Zixin Liu, Jialing Mou, Muxue Tang, Xiuzhen Huang, Kuo Liu, Qianyu Zhang, Kathy O Lui, Bin Zhou.
      In recent decades, the traditional paradigm of three distinct germ layers formed during gastrulation has been revised with the identification of neuromesodermal progenitors (NMPs). These progenitors emerge during gastrulation and contribute to both the neural ectoderm, particularly the spinal cord, and the adjacent paraxial mesoderm [D. Henrique et al., Development 142, 2864-2875 (2015); R. J. Garriock et al., Development 142, 1628-1638 (2015); E. Tzouanacou et al., Dev. Cell 17, 365-376 (2009)]. However, effective genetic tools for lineage tracing and functional assessments of NMPs in vivo are currently lacking. Here, we developed a dual recombinase-mediated genetic system to specifically trace and ablate Brachyury+Sox2+ NMPs. Our genetic tracing and single-cell RNA sequencing analyses revealed that NMPs consist of three distinct unipotent and bipotent progenitor populations that progressively differentiate into neural and mesodermal fates. Genetic depletion of NMPs demonstrated their critical role in trunk and tail formation. This study provides in vivo genetic evidence supporting the heterogeneity of NMPs in terms of cell fate determination and their functional roles in the developing embryo.
    Keywords:  Sox2; bi-potent progenitors; brachyury; dual genetic lineage tracing; neuromesodermal progenitors
    DOI:  https://doi.org/10.1073/pnas.2402305122
  16. Cell. 2025 Mar 26. pii: S0092-8674(25)00275-2. [Epub ahead of print]
    Global analysis of protein turnover dynamics in single cells.
    Pierre Sabatier, Maico Lechner, Ulises H Guzmán, Christian M Beusch, Xinlei Zeng, Longteng Wang, Fabiana Izaguirre, Anjali Seth, Olga Gritsenko, Sergey Rodin, Karl-Henrik Grinnemo, Zilu Ye, Jesper V Olsen.
      Single-cell proteomics (SCPs) has advanced significantly, yet it remains largely unidimensional, focusing primarily on protein abundances. In this study, we employed a pulsed stable isotope labeling by amino acids in cell culture (pSILAC) approach to simultaneously analyze protein abundance and turnover in single cells (SC-pSILAC). Using a state-of-the-art SCP workflow, we demonstrated that two SILAC labels are detectable from ∼4,000 proteins in single HeLa cells recapitulating known biology. We performed a large-scale time-series SC-pSILAC analysis of undirected differentiation of human induced pluripotent stem cells (iPSCs) encompassing 6 sampling times over 2 months and analyzed >1,000 cells. Protein turnover dynamics highlighted differentiation-specific co-regulation of protein complexes with core histone turnover, discriminating dividing and non-dividing cells. Lastly, correlating cell diameter with the abundance of individual proteins showed that histones and some cell-cycle proteins do not scale with cell size. The SC-pSILAC method provides a multidimensional view of protein dynamics in single-cell biology.
    Keywords:  Chip-Tip; Evosep; Orbitrap Astral; cellenONE; histone; iPSC differentiation; mass spectrometry; protein turnover; pulsed SILAC; single-cell proteomics
    DOI:  https://doi.org/10.1016/j.cell.2025.03.002
  17. Curr Top Dev Biol. 2025 ;pii: S0070-2153(24)00114-5. [Epub ahead of print]162 283-315
    Cellular and molecular regulations of oocyte selection and activation in mammals.
    Xuebing Yang, Yan Zhang, Hua Zhang.
      Oocytes, a uniquely pivotal cell population, play a central role in species continuity. In mammals, oogenesis involves distinct processes characterized by sequential rounds of selection, arrest, and activation to produce a limited number of mature eggs, fitting their high-survival yet high-cost fertility. During the embryonic phase, oocytes undergo intensive selection via cytoplasmic and organelle enrichment, accompanied by the onset and arrest of meiosis, thereby establishing primordial follicles (PFs) as a finite reproductive reserve. Subsequently, the majority of primary oocytes enter a dormant state and are gradually recruited through a process termed follicle activation, essential for maintaining orderly fertility. Following activation, oocytes undergo rapid growth, experiencing cycles of arrest and activation regulated by endocrine and paracrine signals, ultimately forming fertilizable eggs. Over the past two decades, advancements in genetically modified animal models, high-resolution imaging, and omics technologies have significantly enhanced our understanding of the cellular and molecular mechanisms that govern mammalian oogenesis. These advances offer profound insights into the regulatory mechanisms of mammalian reproduction and associated female infertility disorders. In this chapter, we provide an overview of current knowledge in mammalian oogenesis, with a particular emphasis on oocyte selection and activation in vivo.
    Keywords:  Oocyte activation; Oocyte dormancy; Oogenesis; Ovarian reserve; Primordial follicle
    DOI:  https://doi.org/10.1016/bs.ctdb.2024.11.003
  18. Curr Top Dev Biol. 2025 ;pii: S0070-2153(25)00010-9. [Epub ahead of print]162 165-205
    No transcription, no problem: Protein phosphorylation changes and the transition from oocyte to embryo.
    Jonathon M Thomalla, Mariana F Wolfner.
      Although mature oocytes are arrested in a differentiated state, they are provisioned with maternally-derived macromolecules that will start embryogenesis. The transition to embryogenesis, called 'egg activation', occurs without new transcription, even though it includes major cell changes like completing stalled meiosis, translating stored mRNAs, cytoskeletal remodeling, and changes to nuclear architecture. In most animals, egg activation is triggered by a rise in free calcium in the egg's cytoplasm, but we are only now beginning to understand how this induces the egg to transition to totipotency and proliferation. Here, we discuss the model that calcium-dependent protein kinases and phosphatases modify the phosphorylation landscape of the maternal proteome to activate the egg. We review recent phosphoproteomic mass spectrometry analyses that revealed broad phospho-regulation during egg activation, both in number of phospho-events and classes of regulated proteins. Our interspecies comparisons of these proteins pinpoints orthologs and protein families that are phospho-regulated in activating eggs, many of which function in hallmark events of egg activation, and others whose regulation and activity warrant further study. Finally, we discuss key phospho-regulating enzymes that may act apically or as intermediates in the phosphorylation cascades during egg activation. Knowing the regulators, targets, and effects of phospho-regulation that cause an egg to initiate embryogenesis is crucial at both fundamental and applied levels for understanding female fertility, embryo development, and cell-state transitions.
    Keywords:  Calcineurin; Calcium; CamKII; Egg activation; Embryogenesis; Fertilization; Meiotic arrest; Oocyte; Post-translational control; Protein phosphorylation; Translation; Zygote
    DOI:  https://doi.org/10.1016/bs.ctdb.2025.01.001
  19. Nat Rev Genet. 2025 Apr 03.
    Epigenome dynamics in early mammalian embryogenesis.
    Adam Burton, Maria-Elena Torres-Padilla.
      During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.
    DOI:  https://doi.org/10.1038/s41576-025-00831-4
  20. Cell Metab. 2025 Mar 26. pii: S1550-4131(25)00105-6. [Epub ahead of print]
    Ceramide-induced FGF13 impairs systemic metabolic health.
    Jamal Naderi, Amanda Kelsey Johnson, Himani Thakkar, Bhawna Chandravanshi, Alec Ksiazek, Ajay Anand, Vinnyfred Vincent, Aaron Tran, Anish Kalimireddy, Pratibha Singh, Ayushi Sood, Aasthika Das, Chad Lamar Talbot, Isabella A Distefano, J Alan Maschek, James Cox, Ying Li, Scott A Summers, Donald J Atkinson, Tursun Turapov, Jason A Ratcliff, Javis Fung, Asim Shabbir, M Shabeer Yassin, Sue-Anne Toh Ee Shiow, William L Holland, Geoffrey S Pitt, Bhagirath Chaurasia.
      Ceramide accumulation impairs adipocytes' ability to efficiently store and utilize nutrients, leading to energy and glucose homeostasis deterioration. Using a comparative transcriptomic screen, we identified the non-canonical, non-secreted fibroblast growth factor FGF13 as a ceramide-regulated factor that impairs adipocyte function. Obesity robustly induces FGF13 expression in adipose tissue in mice and humans and is positively associated with glycemic indices of type 2 diabetes. Pharmacological or genetic inhibition of ceramide biosynthesis reduces FGF13 expression. Using mice with loss and gain of function of FGF13, we demonstrate that FGF13 is both necessary and sufficient to impair energy and glucose homeostasis independent of ceramides. Mechanistically, FGF13 exerts these effects by inhibiting mitochondrial content and function, metabolic elasticity, and caveolae formation, which cumulatively impairs glucose utilization and thermogenesis. These studies suggest the therapeutic potential of targeting FGF13 to prevent and treat metabolic diseases.
    Keywords:  FGF13; adipocytes; ceramides; diabetes; insulin resistance; lipotoxicity; obesity; sphingolipids
    DOI:  https://doi.org/10.1016/j.cmet.2025.03.002
  21. Curr Top Dev Biol. 2025 ;pii: S0070-2153(24)00111-X. [Epub ahead of print]162 259-282
    Luteinizing hormone-induced changes in the structure of mammalian preovulatory follicles.
    Corie M Owen, Laurinda A Jaffe.
      Ovulation of a mammalian oocyte from its follicle, which occurs in response to luteinizing hormone (LH), requires complex restructuring of the ∼20 layers of surrounding somatic cells. This chapter describes the cellular architecture of preovulatory follicles, the localization of the receptors for LH, and the LH-induced changes in follicular structure, focusing on mice and other small mammals. The multiple interrelated processes that result in ovulation include breakdown of existing extracellular matrix, generation of new extracellular matrix, thinning of the follicular apex where the oocyte will be released, invagination of the follicular surface, and responses of the vascular system to support these dynamic changes. However, much remains unknown about how these events function together to release a fertilizable egg.
    Keywords:  Luteinizing hormone; Mammal; Ovary; Ovulation; Preovulatory follicle
    DOI:  https://doi.org/10.1016/bs.ctdb.2024.10.011
  22. Curr Biol. 2025 Mar 25. pii: S0960-9822(25)00289-1. [Epub ahead of print]
    Animal septins contain functional transmembrane domains.
    Jenna A Perry, Michael E Werner, Shizue Omi, Bryan W Heck, Paul S Maddox, Manos Mavrakis, Amy S Maddox.
      Septins are a highly conserved family of proteins that form palindromic hetero-oligomeric rods, which anneal into non-polar filaments. Via association with the plasma membrane, septin filaments recognize micron-scale membrane curvature, create diffusion barriers, and regulate cell morphogenic events via scaffolding other cytoskeletal polymers (i.e., filamentous actin [F-actin] and microtubules) and biochemical regulators of cell division, cell migration, and polarity establishment.1,2 Although interaction with cellular membranes is thought to be crucial for septin polymer dynamics and function, how septins associate with membranes is not understood. Three polybasic regions (PB1, PB2, and PB3) and an amphipathic helix (AH) are each sufficient for membrane interaction in vitro, and while the AH domain has been implicated in conferring membrane curvature sensing in vivo in the filamentous fungus Ashbya, the functionality of these domains in the context of intact septin complexes in vivo is still incompletely defined.3,4,5,6,7,8,9 We identified and characterized an isoform of Caenorhabditis elegans septin UNC-61 that was predicted to contain a transmembrane domain (TMD; UNC-61a). UNC-61a was expressed in a subset of tissues where the known septins act, and the TMD was required for tissue integrity of the egg-laying apparatus. We found predicted TMD-containing septins across much of opisthokont phylogeny and demonstrated that the TMD-containing sequence of a primate TMD-septin is sufficient for localization to cellular membranes. Together, our findings reveal a novel mechanism of septin-membrane association with profound implications for septin dynamics and regulation.
    Keywords:  C. elegans; cytoskeleton; phylogeny; primate; subcellular localization; tissue morphogenesis
    DOI:  https://doi.org/10.1016/j.cub.2025.03.004
  23. bioRxiv. 2025 Mar 12. pii: 2025.03.07.642036. [Epub ahead of print]
    Enteroendocrine Cells Regulate Intestinal Barrier Permeability.
    Jennifer G Nwako, Sparsh D Patel, Taevon J Roach, Saanvi R Gupte, Samara G Williams, Anne Marie Riedman, Heather A McCauley.
      The intestinal epithelial barrier is essential for nutrient absorption and protection against ingested pathogens and foreign substances. Barrier integrity is maintained by tight junctions which are sensitive to inflammatory signals, thus creating a feed-forward loop with an increasingly permeable barrier that further drives inflammation and is the hallmark of inflammatory bowel disease. There are currently no therapeutic strategies to improve the intestinal epithelial barrier. We hypothesized that enteroendocrine cells may play an unappreciated role in maintaining barrier integrity. To test this hypothesis, we seeded human intestinal enteroids with genetic loss of enteroendocrine cells on Transwell filters and evaluated transepithelial electrical resistance, paracellular permeability, and the localization and abundance of junctional proteins. We found that enteroendocrine cells were required to maintain a healthy barrier in crypt-like "stem" and villus-like differentiated cultures. Additionally, exogenous supplementation of enteroendocrine-deficient cultures with the hormones peptide tyrosine tyrosine (PYY) and the somatostatin analog octreotide was sufficient to rescue many aspects of this barrier defect both at baseline and in the presence of the inflammatory cytokine tumor necrosis factor (TNF). Surprisingly, these improvements in barrier function occurred largely independently of changes in protein abundance of junctional proteins zona-occludens 1, occludin, and claudin-2. These findings support a novel role for enteroendocrine cells in augmenting epithelial barrier function in the presence of inflammatory stimuli and present an opportunity for developing therapies to improve the intestinal barrier.
    Keywords:  Enteroendocrine cells; barrier function; intestinal organoids; peptide YY; tight junctions
    DOI:  https://doi.org/10.1101/2025.03.07.642036
  24. Nat Commun. 2025 Mar 28. 16(1): 3033
    Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.
    Bingxin Lu, Samuel Winnall, William Cross, Chris P Barnes.
      Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic structural variants (SVs) are intimately related to copy number alterations but the two types of variant are often studied independently. Additionally, despite numerous studies on detecting various SV patterns, there are still no general quantitative models of SV generation. To address this issue, we develop a computational cell-cycle model for the generation of SVs from end-joining repair and replication after double-strand break formation. Our model provides quantitative information on the relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, and extra-chromosomal circular DNA. Given whole-genome sequencing data, the model also allows us to infer important parameters in SV generation with Bayesian inference. Our quantitative framework unifies disparate genomic patterns resulted from CIN, provides a null mutational model for SV, and reveals deeper insights into the impact of genome rearrangement on tumour evolution.
    DOI:  https://doi.org/10.1038/s41467-025-58245-z
  25. Cell. 2025 Mar 23. pii: S0092-8674(25)00271-5. [Epub ahead of print]
    Engineering sonogenetic EchoBack-CAR T cells.
    Longwei Liu, Peixiang He, Yuxuan Wang, Fengyi Ma, Dulei Li, Zhiliang Bai, Yunjia Qu, Linshan Zhu, Chi Woo Yoon, Xi Yu, Yixuan Huang, Zhengyu Liang, Yiming Zhang, Kunshu Liu, Tianze Guo, Yushun Zeng, Qifa Zhou, H Kay Chung, Rong Fan, Yingxiao Wang.
      Chimeric antigen receptor (CAR) T cell therapy for solid tumors encounters challenges such as on-target off-tumor toxicity, exhaustion, and limited T cell persistence. Here, we engineer sonogenetic EchoBack-CAR T cells using an ultrasensitive heat-shock promoter screened from a library and integrated with a positive feedback loop from CAR signaling, enabling long-lasting CAR expression upon focused-ultrasound (FUS) stimulation. EchoBack-hGD2CAR T cells, targeting disialoganglioside GD2, exhibited potent cytotoxicity and persistence in 3D glioblastoma (GBM) models. In mice, EchoBack-hGD2CAR T cells suppressed GBM without off-tumor toxicity and outperformed their constitutive counterparts. Single-cell RNA sequencing revealed enhanced cytotoxicity and reduced exhaustion in EchoBack-CAR T cells compared with the standard CAR T cells. This EchoBack design was further adapted to target prostate-specific membrane antigen (EchoBack-PSMACAR) for prostate cancer treatment, demonstrating long-lasting tumor suppression with minimal off-tumor toxicity. Thus, the sonogenetic EchoBack-CAR T cells can serve as a versatile, efficient, and safe strategy for solid tumor treatment.
    Keywords:  CAR T; feedback engineering; immunotherapy; inducible gene expression; promoter library screening; solid tumor; sonogenetics; spatiotemporal CAR regulation; ultrasound controled CAR-T
    DOI:  https://doi.org/10.1016/j.cell.2025.02.035
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