bims-ginsta 2025-09-28 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–09–28
34 papers selected by
Jinrong Hu, National University of Singapore

Nuclear rupture in confined cell migration triggers nuclear actin polymerization to limit chromatin leakage.
The kinesin motor Kif9 regulates centriolar satellite positioning during interphase.
Mechanical control of cell fate decisions in the skin epidermis.
Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation.
Principles of protein abundance regulation across single cells in a mammalian tissue.
Nucleosome stability safeguards cell identity, stress resilience and healthy aging.
Collective Cell Migration Strategies: Patterning, Motility, and Directionality of the Posterior Lateral Line Primordium in Zebrafish.
A non-apoptotic caspase-8-meteorin pathway in hepatocytes promotes MASH fibrosis.
Holliday junction-ZMM protein feedback enables meiotic crossover assurance.
Membrane receptors cluster phosphatidylserine to activate LC3-associated phagocytosis.
The nuclear pore complex connects energy sensing to transcriptional plasticity in longevity.
Aging in mice alters regionally enriched striatal astrocytes.
Reprogramming neuroblastoma by diet-enhanced polyamine depletion.
Mitochondria transported by Kinesin-3 prevent localized calcium spiking to inhibit caspase-dependent specialized cell death.
JIP4 and RILPL1 utilize opposing motor force to dynamically regulate lysosomal tubulation.
Quantitative proteomics of formalin-fixed, paraffin-embedded cardiac specimens uncovers protein signatures of specialized regions and patient groups.
Mechanosensitive calcium channels and integrins coordinate the reprogramming of colorectal cancer cells into a fetal-like state.
Patterning in motion: Cell interfaces guide mesenchymal collective migration and morphogenesis.
Ribonucleotide incorporation into mitochondrial DNA drives inflammation.
Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase.
Primitive Means First, Not Worst: Critical Roles for Primitive Endoderm in Embryos and Embryo Models.
Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.
Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression.
A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.
Macrophage/microglia-dependent mechanisms drive retinal pigment epithelium regeneration in zebrafish.
Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging.
Remote control of AMPK via extracellular adenosine controls tissue growth.
Dynamic U2AF cycling defines two phases of cotranscriptional pre-mRNA splicing.
Single-cell-scale spatial transcriptome of the developing and adult mouse ovary.
Engineering synthetic agonists for targeted activation of Notch signaling.
Intrinsic heterogeneity of primary cilia revealed through spatial proteomics.
Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.
Protecting double Holliday junctions ensures crossing over during meiosis.
Cortical tension as a mechanical barrier to safeguard against premature differentiation during neurogenesis.

EMBO J. 2025 Sep 22.

Nuclear rupture in confined cell migration triggers nuclear actin polymerization to limit chromatin leakage.

Christos Kamaras, Dennis Frank, Hong Wang, Friedel Drepper, Pitter F Huesgen, Robert Grosse.

  Upon cell migration in confined space, such as during cancer metastasis, mechanical forces from the extracellular matrix act onto the nucleus leading to nuclear envelope (NE) rupture, chromatin leakage and genomic instability. Here we found that during confined migration, NE rupture triggers dynamic nuclear F-actin formation dependent on the formins DIAPH1 and DIAPH3. We show that DIAPH3 dynamically and transiently relocates to the nucleus upon NE rupture. Interfering with DIAPH1/3 or with nuclear actin polymerization resulted in nuclear instability during confined migration. Notably, nuclear formin activity or actin assembly limit NE rupture-induced chromatin leakage. Similarly, silencing of Ataxia Telangiectasia and Rad3-related protein (ATR) reduced NE rupture-triggered nuclear F-actin assembly and increased chromatin leakage. Consistent with this, ATR promotes the phosphorylation of DIAPH3 at S1072 adjacent to its autoregulatory domain to promote nuclear actin polymerization. Using atomic force microscopy, we found that nuclear actin assembly or nuclear DIAPH3 activity promotes nuclear stiffness in an ATR-dependent manner. Thus, our study identifies an ATR-formin module that regulates nuclear mechanical properties through induction of intranuclear actin scaffolding.

Keywords:  Cancer Cell Invasion; Nuclear Actin; Nuclear Mechanics

DOI:  https://doi.org/10.1038/s44318-025-00566-2
Curr Biol. 2025 Sep 19. pii: S0960-9822(25)01130-3. [Epub ahead of print]

The kinesin motor Kif9 regulates centriolar satellite positioning during interphase.

Juan Jesus Vicente, Michael Wagenbach, Justin Decarreau, Alex Zelter, Michael J MacCoss, Trisha N Davis, Linda Wordeman.

  Centrosomes are the principal microtubule-organizing centers of the cell, are cellular hubs for protein degradation, and play an essential role in mitotic spindle function that ultimately regulates chromosome segregation during mitosis. Centrosome maturation is achieved by strict control of protein acquisition and phosphorylation prior to mitosis. Defects in this process during interphase promote fragmentation of pericentriolar material once cells enter mitosis due to the increased forces exerted over the centrosome by the mitotic spindle, finally culminating in multipolar spindles and chromosome missegregation. Centriolar satellites, membrane-less assemblies of proteins involved in the trafficking of proteins toward and away from the centrosome, are thought to contribute to centrosome biogenesis. Moreover, centriolar satellites also regulate the quantity of proteolytic factors reaching the centrosome. Here, we show that the microtubule plus-end-directed kinesin motor Kif9 localizes to centriolar satellites and regulates their pericentrosomal localization during interphase. Lack of Kif9 leads to aggregation of satellites closer to the centrosome and increased centrosomal protein degradation that disrupts centrosome maturation and results in chromosome congression and segregation defects during mitosis. Our data show that the kinesin Kif9 controls the position of centriolar satellites relative to the centrosome and reveal roles for Kif9 and centriolar satellites in the regulation of cellular proteostasis and mitosis.

Keywords:  Kif9; PCM1; centriolar satellites; centrosome; chromosome congression; chromosome missegregation; kinesin; microtubules; mitosis; pericentriolar material

DOI:  https://doi.org/10.1016/j.cub.2025.08.064
Nat Commun. 2025 Sep 26. 16(1): 8440

Mechanical control of cell fate decisions in the skin epidermis.

Preeti Sahu, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares, Adriana Sánchez-Danés, Edouard Hannezo.

Homeostasis relies on a precise balance of fate choices between renewal and differentiation. Although progress has been done to characterize the dynamics of single-cell fate choices, their underlying mechanistic basis often remains unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation in the basal layer, showing that mechanical competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical heterogeneities between cellular subpopulations. We uncover that relatively small tension heterogeneities, reflected by distinct morphological changes in single-cell shapes, can be sufficient to heavily tilt cellular dynamics towards exponential growth. We thus derive a master relationship between cell shape and long-term clonal dynamics, which we validated during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues.

DOI: https://doi.org/10.1038/s41467-025-62882-9
Dev Cell. 2025 Sep 24. pii: S1534-5807(25)00537-4. [Epub ahead of print]

Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation.

Catherine A Tower, Gabriel Manske, Emily L Ferrell, Dilara N Anbarci, Kelsey Jorgensen, Binbin Ma, Mansour Aboelenain, Rajesh Ranjan, Saikat Chakraborty, Lindsay Moritz, Arunika Das, Michele Boiani, Ben E Black, Shawn Chavez, Erica E Marsh, Ariella Shikanov, Karen Schindler, Xin Chen, Saher Sue Hammoud.

  Across metazoan species, the centromere-specific histone variant CENP-A is essential for accurate chromosome segregation, yet its regulation during the mammalian parental-to-zygote transition is poorly understood. To address this, we generated a CENP-A-mScarlet mouse model that revealed sex-specific dynamics: mature sperm retain 10% of the CENP-A levels present in MII oocytes. However, this difference is resolved in zygotes prior to the first mitosis, using maternally inherited cytoplasmic CENP-A. Notably, the increase in CENP-A at paternal centromeres is independent of sensing CENP-A asymmetry or the presence of maternal chromosomes. Instead, CENP-A equalization relies on the asymmetric recruitment of maternal CENP-C to paternal centromeres. Depletion of maternal CENP-A decreases total CENP-A in both pronuclei without disrupting equalization. In contrast, reducing maternal CENP-C or disruption of its dimerization function impairs CENP-A equalization and chromosome segregation. Therefore, maternal CENP-C acts as a key epigenetic regulator that resets centromeric symmetry at fertilization to preserve genome integrity.

Keywords:  CENP-A; CENP-C; MIS18BP1; centromere; epigenetics; intergenerational; mouse; oocyte; sperm; zygote

DOI:  https://doi.org/10.1016/j.devcel.2025.08.017
bioRxiv. 2025 Sep 20. pii: 2025.09.17.676955. [Epub ahead of print]

Principles of protein abundance regulation across single cells in a mammalian tissue.

Andrew Leduc, Gergana Shipkovenska, Yanxin Xu, Alexander Franks, Nikolai Slavov.

Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematically quantify protein synthesis and clearance across over 4,200 cells from a primary tissue. Through integration with single-cell transcriptomics, we report the first quantitative analysis of how individual cell types regulate their proteomes across the continuum of gene expression. Our analysis quantifies the relative contributions of RNA abundance, translation, and protein clearance to the abundance variation of thousands of proteins. These results reveal an putative organizing principle: The contributions of both translation and protein clearance are linearly dependent on the cell growth rate. Further, we find that some proteins are primarily regulated by one mechanism (RNA abundance, translation, or clearance) across all cell types while the abundances of other proteins is dominated by different regulatory mechanisms across cell types. Our reliable multimodal measurements enabled quantifying and functionally interpreting molecular variation across single cells from the same cell type. The protein-protein correlations are substantially stronger than the mRNA-mRNA ones, which is mediated by protein clearance regulation. The protein-protein correlations are stronger not only for directly interacting proteins but also between functional sets of proteins. Further, these protein correlations allow identifying cell-type specific functional clusters. These clusters vary across cell types, revealing differences in metabolic processes coordination, partially mediated by protein clearance regulation. Our approach provides a scalable multiplexed framework for quantifying the regulatory processes shaping mammalian tissues and reveals organizing principles determining the relative contributions of translation and protein clearance to the proteomes of primary mammalian cells.

DOI: https://doi.org/10.1101/2025.09.17.676955
bioRxiv. 2025 Sep 18. pii: 2025.09.17.676776. [Epub ahead of print]

Nucleosome stability safeguards cell identity, stress resilience and healthy aging.

Hiroshi Tanaka, Brenna S McCauley, Clara Guida, Xue Lei, Sha Li, Tatiana M Moreno, K'leigh Guillotte, Zong-Ming Chua, Adrianna Abele, Aashna Lamba, Rouven Arnold, Adarsh Rajesh, Marcos G Teneche, Laurence Haddadin, Anagha Deshpande, Aniruddha J Deshpande, Alexandre Colas, Caroline Kumsta, Michael Petrascheck, Rolf Bodmer, Weiwei Dang, Peter D Adams.

Nucleosomes are the minimal repeating units of chromatin. Their dynamic assembly and disassembly underpins chromatin organization and genome regulation. However, it remains unclear how intrinsic nucleosome stability contributes to higher-level yet fundamental cellular and organismal properties-such as preservation of cell identity, lineage specification, stress resilience and ultimately healthy aging. To address this, we tested the impact of decreased intrinsic nucleosome stability across multiple cell, tissue and organismal models by introducing histone mutants that weaken histone-histone interactions. While nucleosome instability did not broadly alter global chromatin accessibility, DNA damage, cell proliferation or viability, it impaired lineage-specific gene expression programs, altered lineage specification and activated intrinsic inflammatory and stress pathways in a manner reminiscent of aging in mouse tissues and human cells. Consistently, nucleosome instability accelerated the onset of age-associated transcriptional alterations and functional decline in Caenorhabditis elegans and Drosophila melanogaster , and reduced cellular resilience to exogenous perturbations- including environmental, epigenetic and mitotic stress-in human cells and Saccharomyces cerevisiae . These cross-species findings identify nucleosome stability as an evolutionarily conserved epigenetic safeguard that preserves cell identity and stress resilience and supports organismal function and healthy aging.

DOI: https://doi.org/10.1101/2025.09.17.676776
Cold Spring Harb Perspect Biol. 2025 Sep 22. pii: a041751. [Epub ahead of print]

Collective Cell Migration Strategies: Patterning, Motility, and Directionality of the Posterior Lateral Line Primordium in Zebrafish.

Alex V Nechiporuk, Holger Knaut.

During development and homeostasis, tissues move and rearrange to form organs, seal wounds, or-in the case of cancer-spread in the body. To accomplish this, cells in tissues need to communicate with each other, generate force to push themselves forward, and know where to go to-all of this with little to no error. Here, we discuss how a migrating tissue-the zebrafish posterior lateral line primordium-solves these challenges. We focus on the strategies that ensure signaling within the tissue, enable the tissue to generate and transmit force to its substrate for propulsion, and allow robust directional sensing and migration by the tissue. These strategies include facilitated diffusion and ligand trapping for focal signaling, a self-generated attractant gradient for long-distance migration, clamping of the attractant concentration to the attractant receptor's K d for most sensitive signaling, mechanical coupling among cells for averaging directional sensing in a tissue, and large rear traction stresses to propel the tissue forward. Many of these strategies likely apply to collectively migrating cells in other contexts and should thus provide insights with direct relevance to human health.

DOI: https://doi.org/10.1101/cshperspect.a041751
Nat Metab. 2025 Sep 26.

A non-apoptotic caspase-8-meteorin pathway in hepatocytes promotes MASH fibrosis.

Xiaobo Wang, Mary P Moore, Hongxue Shi, Yang Xiao, Jiayu Zhang, Lanuza A P Faccioli, Zhiping Hu, Shareef Khalid, Danish Saleheen, Dwayne G Stupack, Tatiana Kisseleva, Alejandro Soto Gutierrez, Mitchell A Lazar, Ira Tabas.

Metabolic-dysfunction-associated steatohepatitis (MASH) is the leading cause of chronic liver disease, but an incomplete understanding of MASH-induced liver fibrosis has limited therapeutic options. Here we show that hepatocyte caspase-8 drives MASH fibrosis through an apoptosis-independent mechanism. Hepatic caspase-8 expression correlates with liver fibrosis in both human and experimental MASH, and hepatocyte-specific caspase-8 deletion in male mice with MASH suppressed liver fibrosis and hepatic stellate cell (HSC) activation without affecting hepatocyte apoptosis. Mechanistic studies showed that a caspase-8-YY1 pathway in hepatocytes induces secretory meteorin (Metrn), which activates HSCs via a c-Kit-STAT3 pathway. Meteorin expression was increased in human and male mouse MASH livers and decreased by deletion of hepatocyte caspase-8 in MASH mice and human and mouse primary hepatocytes. Genetic restoration of hepatocyte meteorin in hepatocyte-caspase-8-deleted MASH mice restored HSC activation and liver fibrosis while silencing hepatocyte meteorin lowered liver fibrosis. These findings reveal a therapeutically targetable pathway promoting MASH fibrosis involving a non-apoptotic function of caspase-8 and a newly discovered HSC activator, meteorin.

DOI: https://doi.org/10.1038/s42255-025-01355-1
Nature. 2025 Sep 24.

Holliday junction-ZMM protein feedback enables meiotic crossover assurance.

Adrian Henggeler, Lucija Orlić, Daniel Velikov, Joao Matos.

Holliday junctions (HJs) are branched four-way DNA structures that link recombining chromosomes during double-strand break repair1. Despite posing a risk to chromosome segregation, HJs accumulate during meiotic prophase I as intermediates in the process of crossing-over2,3. Whether HJs have additional regulatory functions remains unclear. Here we establish an experimental system in budding yeast that enables conditional nucleolytic resolution of HJs after the establishment of meiotic chromosome synapsis. We find that HJ resolution triggers complete disassembly of the synaptonemal complex without disrupting the axis-loop organization of chromosomes. Mechanistically, HJs mediate the continued association of ZMM proteins with recombination nodules that form at the axes interface of homologous chromosome pairs. ZMM proteins, in turn, promote polymerization of the synaptonemal complex while simultaneously protecting HJs from processing by non-crossover pathways. Thus, reciprocal feedback between ZMMs, which stabilize HJs, and HJs, which retain ZMM proteins at future crossover sites, maintains chromosome synapsis until HJ-resolving enzymes are activated during exit from prophase I. Notably, by polymerizing and maintaining the synaptonemal complex structure, the HJ-ZMM interplay suppresses de novo double-strand break formation and recombination reinitiation. In doing so, this interplay suppresses the DNA damage response, enabling meiotic progression without unrepaired breaks and supporting crossover assurance.

DOI: https://doi.org/10.1038/s41586-025-09559-x
Nat Cell Biol. 2025 Sep 22.

Membrane receptors cluster phosphatidylserine to activate LC3-associated phagocytosis.

Emilio Boada-Romero, Clifford S Guy, Gustavo Palacios, Luigi Mari, Suresh Poudel, Zhenrui Li, Piyush Sharma, Douglas R Green.

LC3-associated phagocytosis (LAP) represents a non-canonical function of autophagy proteins in which ATG8-family proteins (LC3 and GABARAP proteins) are lipidated onto single-membrane phagosomes as particles are engulfed by phagocytic cells. LAP plays roles in innate immunity, inflammation and anticancer responses, and is initiated following phagocytosis of particles that stimulate Toll-like receptors (TLR) and Fc receptors as well as following engulfment of dying cells. However, how this molecular process is initiated remains elusive. Here we report that receptors that engage LAP enrich phosphatidylserine (PS) in the phagosome membrane via membrane-proximal domains that are necessary and sufficient for LAP to proceed. Subsequently, PS recruits the Rubicon-containing PI3-kinase complex to initiate the enzymatic cascade leading to LAP. Manipulation of plasma membrane PS content, PS binding by Rubicon or the PS-clustering domains of receptors prevents LAP and delays phagosome maturation. Therefore, the initiation of LAP represents a novel mechanism of PS-mediated signal transduction following ligation of surface receptors.

DOI: https://doi.org/10.1038/s41556-025-01749-z
Mol Cell. 2025 Sep 23. pii: S1097-2765(25)00741-5. [Epub ahead of print]

The nuclear pore complex connects energy sensing to transcriptional plasticity in longevity.

Yifei Zhou, Fasih M Ahsan, Sinclair W Emans, Alexander A Soukas.

  As the only gateway governing nucleocytoplasmic transport, the nuclear pore complex (NPC) maintains fundamental cellular processes and deteriorates with age. However, the study of age-related roles of single NPC components remains challenging owing to the complexity of NPC composition. Here, we demonstrate that the central energy sensor, AMP-activated protein kinase (AMPK), post-translationally regulates the abundance of the nucleoporin NPP-16/NUP50 in response to nutrient availability and energetic stress. In turn, NPP-16/NUP50 promotes transcriptional activation of lipid catabolism to extend the lifespan of Caenorhabditis elegans independently of its role in nuclear transport. Rather, the intrinsically disordered region (IDR) of NPP-16/NUP50, through direct interaction with the transcriptional machinery, transactivates the promoters of catabolic genes. Remarkably, elevated NPP-16/NUP50 levels are sufficient to promote longevity and metabolic stress defenses. AMPK-NUP50 signaling is conserved in humans, indicating that bridging energy sensing to metabolic adaptation is an ancient role of this signaling axis.

Keywords:  aging; energy sensing; intrinsically disordered regions; lipid metabolism; longevity; metabolic rewiring; nuclear pore complex; nucleoporins; transcriptional regulation

DOI:  https://doi.org/10.1016/j.molcel.2025.08.035
Nat Commun. 2025 Sep 26. 16(1): 8496

Aging in mice alters regionally enriched striatal astrocytes.

Kay E Linker, Violeta Duran-Laforet, Matthias Ollivier, Xinzhu Yu, Dorothy P Schafer, Baljit S Khakh.

Aging affects multiple organs and within the brain drives distinct molecular changes across different cell types. The striatum encodes motor behaviors that decline with age, but our understanding of how cells within the striatum change remains incomplete. Using single-cell RNA sequencing from young and aged mice we identify molecularly distinct astrocyte subtypes. We show that astrocytes change significantly with age, exhibiting downregulation of genes, reduced diversity, and a shift to more homogenous inflammatory transcriptomic profiles. By exploring where striatal astrocyte subtypes are located with single-cell resolution, we map astrocytes enriched in dorsal, medial, and ventral striatum. Age increases inflammatory marker transcripts in dorsal striatal astrocytes, which display greater age-related changes than ventral striatal astrocytes. We impute molecular interactions between astrocytes and neurons and find that age particularly reduced interactions related to Nrxn2. Our data show that aging alters regionally enriched striatal astrocytes asymmetrically, with dorsal striatal astrocytes exhibiting greater age-related molecular changes.

DOI: https://doi.org/10.1038/s41467-025-63429-8
Nature. 2025 Sep 24.

Reprogramming neuroblastoma by diet-enhanced polyamine depletion.

Sarah Cherkaoui, Christina S Turn, Yuan Yuan, Wenyun Lu, Lifeng Yang, Matthew J McBride, Caroline Eigenmann, George E Allen, Olesya O Panasenko, Lu Zhang, Annette Vu, Kangning Liu, Yimei Li, Om H Gandhi, Lea F Surrey, Sandra D Kienast, Sebastian A Leidel, Michael Wierer, Eileen White, Joshua D Rabinowitz, Michael D Hogarty, Raphael J Morscher.

Neuroblastoma is a highly lethal childhood tumour derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fuelled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, and the inhibitor difluoromethylornithine has shown clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumour differentiation and profound survival gains in the Th-MYCN mouse model. Specifically, an arginine- and proline-free diet decreases the amount of the polyamine precursor ornithine and enhances tumour polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at codons with adenosine in the third position. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by combined dietary and pharmacological intervention, favours a pro-differentiation proteome. These results suggest that the genes of specific cellular programmes have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of paediatric cancers.

DOI: https://doi.org/10.1038/s41586-025-09564-0
Curr Biol. 2025 Sep 19. pii: S0960-9822(25)01165-0. [Epub ahead of print]

Mitochondria transported by Kinesin-3 prevent localized calcium spiking to inhibit caspase-dependent specialized cell death.

Rashna Sharmin, Aladin Elkhalil, Sara Pena, Pranya Gaddipati, Ginger Clark, Pavak K Shah, Mark W Pellegrino, Shai Shaham, Piya Ghose.

Polarized cells (such as neurons) have distinct compartments with differing functions, subcellular architecture, and microenvironments. Like many cell types, they are subject to programmed elimination as a part of normal development and homeostasis. We investigated the mechanism of specialized cell elimination by studying the embryonic cell death program, compartmentalized cell elimination (CCE), in the scaffolding tail-spike epithelial cell (TSC) of C. elegans. CCE, also seen in Cephalic male (CEM) sensory neurons, is stereotyped and ordered, with distinct programs eliminating each cell compartment-the soma and two segments of the single process, the latter resembling neurite pruning. Here, we report the atypical, compartment-specific roles of two kinesins in mitochondrial transport to regulate CCE. We show that UNC-116/Kinesin-1 is required to transport mitochondria out of the TSC process and that its absence results in distal mitochondrial retention and process persistence. We describe UNC-104/Kinesin-3 in the non-canonical role of mitochondrial transport that is negatively regulated by CED-3/caspase. We identify a degenerative hub of the TSC at the junction of the cell soma and process, characterized by local CED-3/caspase activity, Ca2+ increase, and membrane severing. In the absence of CED-3/caspase, early morphological hallmarks of CCE are seen; however, UNC-104/Kinesin-3 is permitted to carry mitochondria that take up local Ca2+, leading to the reversal of CCE and cell recovery. Our study, by highlighting the involvement of region-specific Ca2+ signaling and caspase activity, the different contributions of mitochondria to cytoprotection, and the atypical roles of kinesin motors, sheds light on the molecular machinery of specialized cell elimination, with implications for cellular resilience.

DOI: https://doi.org/10.1016/j.cub.2025.08.065
J Cell Biol. 2025 Nov 03. pii: e202404018. [Epub ahead of print]224(11):

JIP4 and RILPL1 utilize opposing motor force to dynamically regulate lysosomal tubulation.

Luis Bonet-Ponce, Tsion Tegicho, Nuria Fernandez-Martinez, Irene A Rozenberg, Mia Ashriem, Alexandra Beilina, Jillian H Kluss, Yan Li, Mark R Cookson.

Lysosomes are dynamic organelles that remodel their membrane in response to stimuli. We previously uncovered a process we term LYsosomal Tubulation/sorting driven by LRRK2 (LYTL), wherein damaged lysosomes generate tubules sorted into vesicles. LYTL is orchestrated by the Parkinson's disease kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes. JIP4 enhances LYTL tubule extension toward the plus-end of microtubules. To identify new players involved in LYTL, we mapped the lysosomal proteome after LRRK2 kinase inhibition. We found that RILPL1 is recruited to dysfunctional lysosomes in an LRRK2 kinase activity-dependent manner, facilitated by pRAB proteins. Unlike JIP4, RILPL1 induces retraction of LYTL tubules by binding to p150Glued, thereby moving lysosomal tubules toward the minus-end of microtubules. Our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, acting as opposing motor adaptor proteins. These opposing forces create a metastable lysosomal membrane deformation, enabling dynamic tubulation events.

DOI: https://doi.org/10.1083/jcb.202404018
Nat Cardiovasc Res. 2025 Sep 26.

Quantitative proteomics of formalin-fixed, paraffin-embedded cardiac specimens uncovers protein signatures of specialized regions and patient groups.

Jonathan S Achter, Thomas H L Jensen, Paola Pisano, Johan S Bundgaard, Daniel Raaschou-Oddershede, Kasper Rossing, Michael Wierer, Alicia Lundby.

Proteomic technologies have advanced our understanding of disease mechanisms, patient stratification and targeted therapies. However, applying cardiac proteomics in translational research requires overcoming the barrier of tissue accessibility. Formalin-fixed, paraffin-embedded (FFPE) heart tissue, widely preserved in pathology collections, remains a largely untapped resource. Here we demonstrate that proteomic profiles are well preserved in FFPE human heart specimens and compatible with high-resolution, quantitative analysis. Quantifying approximately 4,000 proteins per sample, we show this approach effectively distinguishes disease states and subanatomical regions, revealing distinct underlying protein signatures. Specifically, the human sinoatrial node exhibited enrichment of collagen VI and G protein-coupled receptor signaling. Myocardial biopsies from patients with arrhythmogenic cardiomyopathy were characterized by fibrosis and metabolic/cytoskeletal derangements, clearly separating them from donor heart biopsies. This study establishes FFPE heart tissue as a robust resource for cardiac proteomics, enabling retrospective molecular profiling at scale and unlocking archived specimens for disease discovery and precision cardiology.

DOI: https://doi.org/10.1038/s44161-025-00721-2
Cell Rep. 2025 Sep 22. pii: S2211-1247(25)01079-4. [Epub ahead of print]44(10): 116308

Mechanosensitive calcium channels and integrins coordinate the reprogramming of colorectal cancer cells into a fetal-like state.

Mirjam C van der Net, Marjolein J Vliem, Lars J S Kemp, Carlos Perez-Gonzalez, Tariq S Haddad, Esther A Strating, Ana Krotenberg-Garcia, Ronja M Houtekamer, Willem-Jan Pannekoek, Karen B van den Anker, Susan Zwakenberg, Jooske L Monster, Suzanne E M van der Horst, Hugo J G Snippert, Antoine A Khalil, Jacco van Rheenen, Saskia J E Suijkerbuijk, Onno Kranenburg, Femke Simmer, Iris D Nagtegaal, Danijela Matic Vignjevic, Martijn Gloerich.

  Colorectal cancer (CRC) cells exhibit high plasticity and transition between different cellular states during the development of metastasis. Lgr5-expressing cancer stem cells fuel the growth of the primary tumor and metastasis, yet disseminated tumor cells arriving at the metastatic site and seeding liver metastases are devoid of Lgr5 expression. Using CRC organoid models, we demonstrate that mechanical interactions with collagen I, a main constituent of the interstitial matrix, instruct the reprogramming of CRC cells. Collagen I-induced pulling forces are sensed by integrins and mechanosensitive calcium channels, which together direct the transition of CRC cells into a cellular state with transcriptional similarities to fetal intestinal cells. CRC cells infiltrating the interstitial stroma show upregulation of this fetal-like transcriptional program, which correlates with the ability of Lgr5-negative cells to initiate metastasis formation. Our findings indicate that mechanical interactions with collagen I regulate cell fate transitions associated with the metastatic cascade of CRC.

Keywords:  CP: Cancer; CP: Cell biology; Lgr5; TRPV4; YAP1; cancer stem cell; colorectal cancer; fetal-like state; integrins; mechanosensitive calcium channels; mechanotransduction

DOI:  https://doi.org/10.1016/j.celrep.2025.116308
J Cell Biol. 2025 Nov 03. pii: e202505198. [Epub ahead of print]224(11):

Patterning in motion: Cell interfaces guide mesenchymal collective migration and morphogenesis.

Maik C Bischoff, Roberto Mayor.

Collective cell migration is a fundamental process in development, wound healing, and cancer. The best-characterized modes of collective migration typically involve cells that retain an epithelial architecture. However, in this review, we explore less well-understood modes of migration driven by cells with a more mesenchymal phenotype. To better understand and compare contact-dependent collective cell behaviors, we propose envisioning each cell as a structure made up of smaller dynamic parts and inferring how these parts behave to understand the overall collective behavior. By examining how local cell shapes influence single-cell behaviors, we can gain insight into how swarm-like behaviors emerge through cell-cell contact. Through this lens, we compare key processes such as contact inhibition of locomotion, mesenchymal cell intercalation, and more complex heterotypic swarm behaviors. Finally, we discuss the emerging concept of contact-mediated rules that regulate motility and have the potential to encode blueprints for complex patterns and even organ shapes.

DOI: https://doi.org/10.1083/jcb.202505198
Nature. 2025 Sep 24.

Ribonucleotide incorporation into mitochondrial DNA drives inflammation.

Amir Bahat, Dusanka Milenkovic, Eileen Cors, Mabel Barnett, Sadig Niftullayev, Athanasios Katsalifis, Marc Schwill, Petra Kirschner, Thomas MacVicar, Patrick Giavalisco, Louise Jenninger, Anders R Clausen, Vincent Paupe, Julien Prudent, Nils-Göran Larsson, Manuel Rogg, Christoph Schell, Isabella Muylaert, Erik Lekholm, Hendrik Nolte, Maria Falkenberg, Thomas Langer.

Metabolic dysregulation can lead to inflammatory responses1,2. Imbalanced nucleotide synthesis triggers the release of mitochondrial DNA (mtDNA) to the cytosol and an innate immune response through cGAS-STING signalling3. However, how nucleotide deficiency drives mtDNA-dependent inflammation has not been elucidated. Here we show that nucleotide imbalance leads to an increased misincorporation of ribonucleotides into mtDNA during age-dependent renal inflammation in a mouse model lacking the mitochondrial exonuclease MGME14, in various tissues of aged mice and in cells lacking the mitochondrial i-AAA protease YME1L. Similarly, reduced deoxyribonucleotide synthesis increases the ribonucleotide content of mtDNA in cell-cycle-arrested senescent cells. This leads to mtDNA release into the cytosol, cGAS-STING activation and the mtDNA-dependent senescence-associated secretory phenotype (SASP), which can be suppressed by exogenously added deoxyribonucleosides. Our results highlight the sensitivity of mtDNA to aberrant ribonucleotide incorporation and show that imbalanced nucleotide metabolism leads to age- and mtDNA-dependent inflammatory responses and SASP in senescence.

DOI: https://doi.org/10.1038/s41586-025-09541-7
Proc Natl Acad Sci U S A. 2025 Sep 30. 122(39): e2506417122

Sperm meet the elevated energy demands to attain fertilization competence by increasing flux through aldolase.

Sara Violante, Aye Kyaw, Lana Kouatli, Kaushik Paladugu, Lauren Apostolakis, Macy Jenks, Amy Johnson, Ryan D Sheldon, Douglas Whitten, Anthony L Schilmiller, Pablo E Visconti, Justin R Cross, Lonny R Levin, Jochen Buck, Melanie Balbach.

  Prior to ejaculation, mammalian sperm are stored in the epididymis in a "resting" metabolic state. Upon ejaculation, sperm must alter their metabolism to generate the energy needed to support the motility and maturation process known as capacitation to reach and fertilize the oocyte. How sperm regulate the capacitation-induced increase in carbon flux is unknown. Here, we use 13C stable isotope labeling in mouse sperm isolated from the cauda epididymis to follow glucose metabolism through central carbon metabolic network before and after sperm activation. As sperm transition from resting to highly activated states, they boost energy yield by increasing flux through glycolysis at the expense of the pentose phosphate pathway. Increased glycolytic activity seems to be achieved via capacitation-induced stimulation of flux through aldolase. In the mitochondria-containing midpiece, glycolytically generated pyruvate feeds the tricarboxylic acid (TCA) cycle to further maximize energy yield via oxidative phosphorylation. In the mitochondria-free principal piece of the flagellum, pyruvate produced from glycolysis is reduced to lactate by lactate dehydrogenase, which also serves to regenerate oxidized nicotinamide adenine dinucleotide (NAD+) ensuring a sufficient supply to support glycolysis. The resultant lactate is at least partially secreted. Finally, we find evidence that there is an as yet unknown endogenous source of energy in sperm, feeding the upregulation of TCA cycle intermediates. These studies provide the most complete picture of the metabolic shift which occurs in capacitating mouse sperm in glucose.

Keywords:  aldolase; glycolysis; metabolic reprogramming; sperm; stable isotope labeling

DOI:  https://doi.org/10.1073/pnas.2506417122
Dev Biol. 2025 Sep 20. pii: S0012-1606(25)00266-0. [Epub ahead of print]

Primitive Means First, Not Worst: Critical Roles for Primitive Endoderm in Embryos and Embryo Models.

Marcelio A Shammami, Alyssa Virola-Iarussi, Ian McCrary, Amy Ralston.

  In mammals, extraembryonic tissues, such as the placenta and yolk sac, are the first cell types to be specified during development because they enable the embryo to take residence and thrive in the uterine environment. Among extraembryonic tissue types, primitive endoderm (PrE), which will eventually contribute to the yolk sac, is especially fascinating. The PrE itself is named for functioning like the embryo's original gut-like tissue. For many years, our understanding of the PrE was limited by the intrinsically challenging nature of accessing and observing this tissue. However, pioneering studies in mouse have gradually revealed that the PrE is more than just nutritive in function. In fact, the PrE lineage gives rise to signaling centers that oversee developmental processes within the fetus - through processes that are very likely conserved between rodents and primates. Thus, understanding the stages between PrE and yolk sac promises clinically relevant models, including stem cell embryo models, which could lead to enhanced success for in vitro fertilization (IVF). Here, we examine the functions of PrE in the context of embryos, stem cells, and embryo models.

Keywords:  amnion; blastocyst; extraembryonic; naïve; pluripotency; postimplantation; potency; preimplantation; primed; primitive endoderm; stem cells; trophoblast; yolk sac

DOI:  https://doi.org/10.1016/j.ydbio.2025.09.008
Science. 2025 Sep 25. eadl1988

Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.

Brian D Cosgrove, Lexi R Bounds, Carson Key Taylor, Alan L Su, Anthony J Rizzo, Alejandro Barrera, Tongyu Sun, Alexias Safi, Lingyun Song, Thomas Whitlow, Aleksandra Tata, Nahid Iglesias, Yarui Diao, Purushothama Rao Tata, Brenton D Hoffman, Gregory E Crawford, Charles A Gersbach.

Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcription remains largely unmapped. Here, we combine genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq CRISPR screening to identify a class of genomic enhancers that responds to the mechanical microenvironment. These "mechanoenhancers" can be preferentially activated on either soft or stiff extracellular matrix contexts and regulate transcription to influence critical cell functions including apoptosis, adhesion, proliferation, and migration. Epigenetic editing of mechanoenhancers reprograms the cellular response to the mechanical microenvironment and modulates the activation of disease-related genes in lung fibroblasts from healthy and fibrotic donors. Epigenetic editing of mechanoenhancers holds potential for precise targeting of mechanically-driven diseases.

DOI: https://doi.org/10.1126/science.adl1988
Nucleic Acids Res. 2025 Sep 23. pii: gkaf916. [Epub ahead of print]53(18):

Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression.

Marta Milan, Valeria Runfola, Manthan Patel, Lucia Falbo, Roberta Noberini, Chiara Soriani, Simona Rodighiero, Tiziana Bonaldi, Vincenzo Costanzo, Madapura M Pradeepa, Paola Scaffidi.

Histone acetylation is widely assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Despite its established role in X-chromosome hyperactivation in Drosophila, its function in mammalian cells has remained elusive. Here, we show that in human somatic cells, H4K16ac does not substantially affect gene expression, but instead controls the spatiotemporal program of genome replication. By combining a meta-analysis of public datasets and perturbation experiments designed to minimize confounding effects, we found that H4K16ac is neither associated with nor required for transcriptional activity. Rather, H4K16ac depletion resulted in premature replication of heterochromatic regions and widespread alterations in replication timing across the genome. These defects were driven by the aberrant activation of cryptic replication origins at long terminal repeats-repetitive elements typically marked by H4K16ac and whose sequence context resembles that of canonical origins in euchromatic regions. Our findings reveal an unexpected role for one of the most prevalent chromatin modifications and uncover a new regulatory mechanism that safeguards genome replication fidelity.

DOI: https://doi.org/10.1093/nar/gkaf916
Nat Immunol. 2025 Sep 24.

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Lloyd Steele, Bayanne Olabi, Kenny Roberts, Pavel V Mazin, Simon Koplev, Catherine Tudor, Benjamin Rumney, Chloe Admane, Treasa Jiang, Donovan Correa-Gallegos, Keerthi Priya Chakala, Aljes Binkevich, Nusayhah Hudaa Gopee, Alexander Predeus, Martin Prete, Elena Winheim, Karl Annusver, Agnes Forsthuber, Luc Francis, Sophie Frech, Clarisse Ganier, Thomas Layton, Yingzi Liu, Hao Yuan, Johann E Gudjonsson, Beate M Lichtenberger, Satveer Mahil, Jagdeep Nanchahal, Edel A O'Toole, Maksim V Plikus, Yuval Rinkevich, Emanuel Rognoni, Catherine H Smith, Sarah A Teichmann, Maria Kasper, April R Foster, Mohammad Lotfollahi, Muzlifah Haniffa.

Fibroblasts sculpt the architecture and cellular microenvironments of various tissues. Here we constructed a spatially resolved atlas of human skin fibroblasts from healthy skin and 23 skin diseases, with comparison to 14 cross-tissue diseases. We define six major skin fibroblast subtypes in health and three that are disease-specific. We characterize two fibroblast subtypes further as they are conserved across tissues and are immune-related. The first, F3: fibroblastic reticular cell-like fibroblast (CCL19+CD74+HLA-DRA+), is a fibroblastic reticular cell-like subtype that is predicted to maintain the superficial perivascular immune niche. The second, F6: inflammatory myofibroblasts (IL11+MMP1+CXCL8+IL7R+), characterizes early human skin wounds, inflammatory diseases with scarring risk and cancer. F6: inflammatory myofibroblasts were predicted to recruit neutrophils, monocytes and B cells across multiple human tissues. Our study provides a harmonized nomenclature for skin fibroblasts in health and disease, contextualized with cross-tissue findings and clinical skin disease profiles.

DOI: https://doi.org/10.1038/s41590-025-02267-8
Cell Rep. 2025 Sep 19. pii: S2211-1247(25)01096-4. [Epub ahead of print]44(10): 116325

Macrophage/microglia-dependent mechanisms drive retinal pigment epithelium regeneration in zebrafish.

Lyndsay L Leach, Rebecca G Gonzalez, Sayuri U Jayawardena, Jeffrey M Gross.

  The retinal pigment epithelium (RPE) surrounds the posterior eye and maintains the health and function of the photoreceptors. Consequently, RPE dysfunction or damage has a devastating impact on vision. Due to complex etiologies, there are currently no cures for patients with RPE degenerative diseases, which remain some of the most prevalent causes of vision loss worldwide. Further, owing to a limited capacity for mammalian tissue repair, we know little about how the RPE regenerates. Here, we utilize zebrafish to uncover mechanisms driving intrinsic RPE regeneration. We show that microglia are indispensable for repair and present evidence that supports the role of interleukin-34 in recruiting macrophages/microglia to the RPE injury site. Further, we identify aberrant RPE injury site debris accumulation due to decreased macrophage/microglia localization, and we find that phagocytosis is an important mechanism driving debris clearance. Together, our results identify new regenerative functions of macrophages/microglia after RPE damage.

Keywords:  CP: Immunology; CSF1R; interleukin-34; macrophage; microglia; regeneration; retinal pigment epithelium; zebrafish

DOI:  https://doi.org/10.1016/j.celrep.2025.116325
Nat Aging. 2025 Sep 24.

Herbal terpenoids activate autophagy and mitophagy through modulation of bioenergetics and protect from metabolic stress, sarcopenia and epigenetic aging.

Gabriele Civiletto, Dario Brunetti, Giulia Lizzo, Kamila Muller, Guillaume E Jacot, Ioanna Daskalaki, Federico Sizzano, Minji Huh, Ivano Di Meo, Maria Nicol Colombo, José L Sanchez-Garcia, Bertrand J Bétrisey, Alix Zollinger, Patricia Lino, Christopher Neal, Anne-Laure Egesipe, Joy Richard, Myriam Chimen, Aurélie Hermant, Benjamin Brinon, Lorane Texari, Sylviane Metairon, Mohammed Adnan Qureshi, Dhaval S Patel, Siva A Vanapalli, Marco Malavolta, Arwen W Gao, Amelia Lalou, Mauro Provinciali, Fiorenza Orlando, Valeria Tiranti, Robert T Brooke, Steve Horvath, Johan Auwerx, Jerome N Feige, Philipp Gut.

Small molecular food components contribute to the health benefits of diets rich in fruits, vegetables, herbs and spices. The cellular mechanisms by which noncaloric bioactives promote healthspan are not well understood, limiting their use in disease prevention. Here, we deploy a whole-organism, high-content screen in zebrafish to profile food-derived compounds for activation of autophagy, a cellular quality control mechanism that promotes healthy aging. We identify thymol and carvacrol as activators of autophagy and mitophagy through a transient dampening of the mitochondrial membrane potential. Chemical stabilization of thymol-induced mitochondrial depolarization blocks mitophagy activation, suggesting a mechanism originating from the mitochondrial membrane. Supplementation with thymol prevents excess liver fat accumulation in a mouse model of diet-induced obesity, improves pink-1-dependent heat stress resilience in Caenorhabditis elegans, and slows the decline of skeletal muscle performance while delaying epigenetic aging in SAMP8 mice. Thus, terpenoids from common herbs promote autophagy during aging and metabolic overload, making them attractive molecules for nutrition-based healthspan promotion.

DOI: https://doi.org/10.1038/s43587-025-00957-4
Nat Cell Biol. 2025 Sep 26.

Remote control of AMPK via extracellular adenosine controls tissue growth.

Yao Zhang, Katrin Strassburger, Aurelio A Teleman.

Adenosine monophosphate (AMP)-activated protein kinase (AMPK) is a regulator of cellular catabolism that is activated by AMP. As AMP accumulates in cells with low ATP, AMPK is considered a stress-activated kinase. While studying organ growth during Drosophila development, we find that AMPK can also be activated by a signalling metabolite not related to stress. Specifically, we find that two physiological inputs known to regulate organ growth rates (ecdysone (a steroid hormone) and dietary protein) modulate expression of adenosine deaminase in the intestine. This, in turn, alters circulating adenosine levels. Circulating adenosine acts as a signalling molecule by entering cells, becoming phosphorylated to AMP and activating AMPK to inhibit organ growth. Thus, AMPK activity is regulated developmentally, and AMPK activity in one tissue can be remote controlled by another tissue via circulating adenosine. Notably, this mechanism accounts for half the effect of dietary protein on tissue growth rates in Drosophila.

DOI: https://doi.org/10.1038/s41556-025-01764-0
Science. 2025 Sep 25. 389(6767): eadj9141

Dynamic U2AF cycling defines two phases of cotranscriptional pre-mRNA splicing.

Changwei Shao, Yajing Hao, Li Jiang, Dong Wang, Rui Wang, Yuanjun Li, Hui Wang, Yaping Ge, Rui Bai, Xiangjuan Du, Xizi Chen, Tan Wu, Lan-Tao Gou, Ruixue Wan, Yanhui Xu, Xiong Ji, Xiang-Dong Fu.

Distinguishing functional splice sites from abundant cryptic sites in precursor messenger RNAs (pre-mRNAs) represents a fundamental challenge in decoding mammalian genomes. We demonstrate that the specific RNA polymerase II (Pol II) subunit RPB9 directly interacts with the 3' AG dinucleotide binding factor U2AF1 to initiate 3' splice site recognition. Combined with recent structural insights into Pol II-mediated 5' splice site selection, these findings support a cotranscriptional mechanism to recognize paired 3' and 5' splice sites across individual exons. These initial exon definition events facilitate the recruitment of U2AF2 to heterodimerize with U2AF1, which also triggers U2AF1 release from elongating Pol II. Collectively, these results reveal dynamic U2AF cycling that partitions Pol II subunit-facilitated splice site recognition and subsequent Pol II-independent spliceosome assembly steps during cotranscriptional splicing.

DOI: https://doi.org/10.1126/science.adj9141
bioRxiv. 2025 Sep 17. pii: 2025.09.16.676655. [Epub ahead of print]

Single-cell-scale spatial transcriptome of the developing and adult mouse ovary.

Anthony S Martinez, Tyler J Gibson, Jennifer McKey.

Mammalian ovary development is essential for female fertility, involving the complex spatial patterning of diverse cell types to establish the finite reserve of ovarian follicles. While single-cell transcriptome analyses have provided important insights into the mechanisms driving specification and developmental trajectories of ovarian cells, they disrupt this crucial spatial context. To overcome this limitation, we used 10X Genomics Visium HD spatial transcriptomics to analyze the developing mouse ovary while maintaining its native cellular architecture. We captured all ovarian cell types at eight key fetal and postnatal timepoints, generating a near single cell resolution library of spatial gene expression across ovarian development. This comprehensive dataset allows analysis of dynamic transcriptional signatures associated with unique spatial patterning throughout development, including the establishment of cortex and medulla and assembly of ovarian follicles in each region. This dataset represents a fundamental resource for the investigation of regulatory mechanisms driving spatial patterning of the ovary and opens new avenues to explore the spatial determinants of female fertility and reproductive longevity.
Short narrative: This report describes a near-single-cell map of spatially resolved gene expression in the developing mouse ovary using 10X Genomics Visium HD, preserving the crucial cellular architecture that is lost in traditional single-cell analyses. This comprehensive dataset, covering eight key developmental timepoints, provides a fundamental resource for investigating how spatial patterning regulates critical ovarian events like follicle assembly.

DOI: https://doi.org/10.1101/2025.09.16.676655
Nat Chem Biol. 2025 Sep 24.

Engineering synthetic agonists for targeted activation of Notch signaling.

David H Perez, Daniel Antfolk, Shiun Chang, Xiomar E Bustos, Elliot Medina, Ahmed A Ramadan, David Gonzalez-Perez, Daniel Abate-Daga, Paulo C Rodriguez, Vincent C Luca.

Notch signaling regulates cell fate decisions and has context-dependent tumorigenic or tumor suppressor functions. Although there are several classes of Notch inhibitors, the mechanical force requirement for Notch activation has hindered attempts to generate soluble agonists. To address this problem, we engineered synthetic Notch agonists (SNAGs) by tethering affinity-matured Notch ligands to proteins that internalize their targets. This bispecific format enables SNAGs to 'pull' on mechanosensitive Notch receptors, triggering their activation in the presence of desired biomarkers. We successfully developed SNAGs targeting six independent surface markers, including the tumor antigens PDL1, CD19 and HER2 and the immunostimulatory receptor CD40. HER2-SNAGs and CD19-SNAGs increased the expression of T cell activation markers and Notch target genes in cocultures with tumor cells, highlighting their potential for immunotherapeutic applications. These insights have broad implications for the pharmacological activation of mechanoreceptors and will expand our ability to modulate Notch signaling in biotechnology.

DOI: https://doi.org/10.1038/s41589-025-02030-y
Cell. 2025 Sep 25. pii: S0092-8674(25)01029-3. [Epub ahead of print]

Intrinsic heterogeneity of primary cilia revealed through spatial proteomics.

Jan N Hansen, Huangqingbo Sun, Konstantin Kahnert, Eini Westenius, Alexandra Johannesson, Carmela Villegas, Trang Le, Kalliopi Tzavlaki, Casper Winsnes, Emmie Pohjanen, Anna Mäkiniemi, Jenny Fall, Frederic Ballllosera Navarro, Anna Bäckström, Cecilia Lindskog, Fredric Johansson, Kalle von Feilitzen, Angelica M Delgado-Vega, Anna Martinez Casals, Diana Mahdessian, Mathias Uhlén, Shu-Hsien Sheu, Anna Lindstrand, Ulrika Axelsson, Emma Lundberg.

  Primary cilia are critical organelles found on most human cells. Their dysfunction is linked to hereditary ciliopathies with a wide phenotypic spectrum. Despite their significance, the specific roles of cilia in different cell types remain poorly understood due to limitations in analyzing ciliary protein composition. We employed antibody-based spatial proteomics to expand the Human Protein Atlas to primary cilia. Our analysis identified the subciliary locations of 715 proteins across three cell lines, examining 128,156 individual cilia. We found that 69% of the ciliary proteome is cell-type specific, and 78% exhibited single-cilia heterogeneity. Our findings portray cilia as sensors tuning their proteome to effectively sense the environment and compute cellular responses. We reveal 91 cilia proteins and found a genetic candidate variant in CREB3 in one clinical case with features overlapping ciliopathy phenotypes. This open, spatial cilia atlas advances research on cilia and ciliopathies.

Keywords:  3D images; cell-type specificity; cellular heterogeneity; cilia; ciliopathies; immunofluorescence microscopy; primary cilia; signaling; signaling microdomains; spatial proteomics

DOI:  https://doi.org/10.1016/j.cell.2025.08.039
Cell. 2025 Sep 22. pii: S0092-8674(25)01027-X. [Epub ahead of print]

Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.

Zizhu Tan, Chia-Heng Hsiung, Jiahui Feng, Yangye Zhang, Yihan Wan, Junlin Chen, Ke Sun, Peilong Lu, Jianyang Zang, Wenxing Yang, Ya Gao, Jiabin Yin, Tong Zhu, Yang Lu, Zijian Pan, Yilong Zou, Can Liao, Xiaosong Li, Yuxuan Ye, Yu Liu, Xin Zhang.

  Fluorescence microscopy has been widely applied in the life sciences. While intensity as a steady-state signal is widely used, the time-resolved (tr) signal using fluorescence lifetime remains underexplored. Herein, we present a family of time-resolved fluorescent proteins (tr-FPs) with rationally controlled lifetimes. Using a strategy that regulates lifetime without affecting the spectra of FPs, we have developed a series of tr-FPs that cover the visible spectrum and a wide range of lifetimes. The tr-FPs are employed in temporal-spectral resolved microscopy, allowing for the simultaneous imaging of 9 different proteins in live cells and the correlation of multiple activities to cell cycles. Furthermore, tr-FPs enable multiplexing super-resolution microscopy that concurrently visualizes 4 proteins using the lifetime signal and are demonstrated to quantify the stoichiometry of cellular proteins. Our work introduces the concept and development of tr-FPs as a transformative toolset, presenting opportunities to integrate system complexity and quantitative accuracy into biological research.

Keywords:  cell cycle; ferroptosis; fluorescence lifetime; fluorescence lifetime microscopy; multiplexed imaging; oxidative stress; protein stoichiometry quantification; quantitative imaging; super-resolution microscopy; time-resolved fluorescent protein

DOI:  https://doi.org/10.1016/j.cell.2025.08.035
Nature. 2025 Sep 24.

Protecting double Holliday junctions ensures crossing over during meiosis.

Shangming Tang, Sara Hariri, Regina Bohn, John E McCarthy, Jennifer Koo, Mohammad Pourhosseinzadeh, Emerald Nguyen, Natalie Liu, Christopher Ma, Hanyu Lu, Monica Lee, Neil Hunter.

Chromosomal linkages formed through crossover recombination are essential for the accurate segregation of homologous chromosomes during meiosis1. The DNA events of recombination are linked to structural components of meiotic chromosomes2. Imperatively, the biased resolution of double Holliday junction (dHJ) intermediates into crossovers3,4 occurs within the synaptonemal complex (SC), the meiosis-specific structure that mediates end-to-end synapsis of homologues during the pachytene stage5,6. However, the role of the SC in crossover-specific dHJ resolution remains unclear. Here we show that key SC components function through dependent and interdependent relationships to protect dHJs from aberrant dissolution into non-crossover products. Conditional ablation experiments reveal that cohesin, the core of SC lateral elements, is required to maintain both synapsis and dHJ-associated crossover recombination complexes (CRCs) during pachytene. The SC central region transverse-filament protein is also required to maintain CRCs. Reciprocally, the stability of the SC central region requires the continuous presence of CRCs effectively coupling synapsis to dHJ formation and desynapsis to resolution. However, dHJ protection and CRC maintenance can occur without end-to-end homologue synapsis mediated by the central element of the SC central region. We conclude that local ensembles of SC components are sufficient to enable crossover-specific dHJ resolution to ensure the linkage and segregation of homologous chromosomes.

DOI: https://doi.org/10.1038/s41586-025-09555-1
bioRxiv. 2025 Sep 20. pii: 2025.09.19.677444. [Epub ahead of print]

Cortical tension as a mechanical barrier to safeguard against premature differentiation during neurogenesis.

Daniel Halperin, Chrystian Junqueira Alves, Marcelle Rodrigues Lemos, Swagata Dey, Haochen Tao, Sangjo Kang, Xianting Li, Zhenyu Yue, Jiaxi Li, Rodrigo Alves Dias, Gustavo de Oliveira Rosa, José P Rodrigues Furtado de Mendonça, Molly Estill, Yonatan Perez, Susana I Ramos, Nadejda M Tsankova, Li Shen, Roland H Friedel, Hongyan Zou.

Neuronal differentiation requires coordinated gene reprogramming and morphodynamic remodeling. How mechanical forces integrate with nuclear gene programs during neurogenesis remains unresolved. Here, we identify cortical tension as a mechanical barrier that safeguards against premature neuronal differentiation. Deletion of Plexin-B2, a guidance receptor controlling actomyosin contractility, lowers this barrier, enabling neurite outgrowth and accelerating neuronal lineage commitment. We show that coupling of extrinsic differentiation cues with intrinsic morphodynamics is essential for stabilizing neuronal fate and that cortical barrier and epigenetic barrier act in concert to regulate developmental timing. In cerebral organoids, Plexin-B2 ablation triggered premature cell-cycle exit and differentiation, resulting in progenitor pool depletion and neuroepithelial disorganization, phenotypes echoing intellectual disability in patients with rare pathogenic PLXNB2 variants. Our studies demonstrate that cortical tension functions as mechano-checkpoint that regulates the onset of neurogenesis. Lowering this barrier may provide a strategy to accelerate induced neuron generation and maturation for CNS disease modeling.

DOI: https://doi.org/10.1101/2025.09.19.677444