bims-ginsta 2025-01-19 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–01–19
28 papers selected by
Jinrong Hu, National University of Singapore

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos.
Mitotic chromatin marking governs the segregation of DNA damage.
Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.
Centromere inactivation during aging can be rescued in human cells.
Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradation.
Vinculin haploinsufficiency impairs integrin-mediated costamere remodeling on stiffer microenvironments.
Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states.
The Balbiani body is formed by microtubule-controlled molecular condensation of Buc in early oogenesis.
Fate mapping in mouse demonstrates early secretory differentiation directly from Lgr5+ intestinal stem cells.
Prolonged persistence of mutagenic DNA lesions in somatic cells.
Spatial transcriptomic characterization of a Carnegie stage 7 human embryo.
A cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program.
Homologous recombination promotes non-immunogenic mitotic cell death upon DNA damage.
Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics.
Sequential recruitment of F-BAR proteins controls cytoskeletal crosstalk at the yeast bud neck.
Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage.
Stored elastic bending tension as a mediator of embryonic body folding.
Exosomal miR-302b rejuvenates aging mice by reversing the proliferative arrest of senescent cells.
LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells.
An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast.
Massively parallel characterization of transcriptional regulatory elements.
Specialized pericyte subtypes in the pulmonary capillaries.
SYS-1/beta-catenin inheritance and regulation by Wnt-signaling during asymmetric cell division.
Somatic mutation as an explanation for epigenetic aging.
BMP and STRA8 act collaboratively to ensure correct mitotic-to-meiotic transition in the fetal mouse ovary.
Brain-wide neuronal circuit connectome of human glioblastoma.
PDGFRα inhibition reduces myofibroblast expansion in the fibrotic rim and enhances recovery after ischemic stroke.
Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability.

Curr Biol. 2025 Jan 04. pii: S0960-9822(24)01587-2. [Epub ahead of print]

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos.

Yitong Xu, Anna Chao, Melissa Rinaldin, Alison Kickuth, Jan Brugués, Stefano Di Talia.

  Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes.1,2,3 The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm.4,5,6,7 Yet, the relationship between spindle size and chromosome movement remains poorly understood. Here, we address this relationship during the cleavage divisions of the Drosophila blastoderm. We show that the speed of chromosome separation gradually decreases during the four nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in spindle length, ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, we find that two processes contribute to controlling the speed at which chromosomes move in anaphase: the activity of molecular motors important for microtubule depolymerization and sliding and the cell cycle oscillator. Specifically, we found that the levels of multiple kinesin-like proteins important for microtubule depolymerization, as well as kinesin-5, contribute to setting the speed of chromosome separation. This observation is further supported by the scaling of poleward flux rate with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, our work suggests a link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, we propose that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase.

Keywords:  Drosophila embryo; anaphase; cell cycle; kinesin; microtubule; mitosis; mitotic kinases; mitotic phosphatases; spindle length

DOI:  https://doi.org/10.1016/j.cub.2024.11.046
Nat Commun. 2025 Jan 16. 16(1): 746

Mitotic chromatin marking governs the segregation of DNA damage.

Juliette Ferrand, Juliette Dabin, Odile Chevallier, Matteo Kane-Charvin, Ariana Kupai, Joel Hrit, Scott B Rothbart, Sophie E Polo.

The faithful segregation of intact genetic material and the perpetuation of chromatin states through mitotic cell divisions are pivotal for maintaining cell function and identity across cell generations. However, most exogenous mutagens generate long-lasting DNA lesions that are segregated during mitosis. How this segregation is controlled is unknown. Here, we uncover a mitotic chromatin-marking pathway that governs the segregation of UV-induced damage in human cells. Our mechanistic analyses reveal two layers of control: histone ADP-ribosylation, and the incorporation of newly synthesized histones at UV damage sites, that both prevent local mitotic phosphorylations on histone H3 serine residues. Functionally, this chromatin-marking pathway controls the segregation of UV damage in the cell progeny with consequences on daughter cell fate. We propose that this mechanism may help preserve the integrity of stem cell compartments during asymmetric cell divisions.

DOI: https://doi.org/10.1038/s41467-025-56090-8
Nat Struct Mol Biol. 2025 Jan 15.

Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.

Michael Uckelmann, Vita Levina, Cyntia Taveneau, Xiao Han Ng, Varun Pandey, Jasmine Martinez, Shweta Mendiratta, Justin Houx, Marion Boudes, Hari Venugopal, Sylvain Trépout, Alex J Fulcher, Qi Zhang, Sarena Flanigan, Minrui Li, Emma Sierecki, Yann Gambin, Partha Pratim Das, Oliver Bell, Alex de Marco, Chen Davidovich.

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organization and dynamics of chromatin compacted by gene-repressing factors are unknown. Here, using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the polycomb repressive complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilized through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provide a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

DOI: https://doi.org/10.1038/s41594-024-01457-6
Mol Cell. 2025 Jan 08. pii: S1097-2765(24)01035-9. [Epub ahead of print]

Centromere inactivation during aging can be rescued in human cells.

Sweta Sikder, Songjoon Baek, Truman McNeil, Yamini Dalal.

  Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres in aged human fibroblasts and tissues and in various cellular senescent models. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to the mitotic rejuvenation of these cells. These results offer insights into a unique mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.

Keywords:  CENP-A; aging; cancer; centromere; chromatin; genome instability; histone demethylase; non-coding transcription; p53; senescence

DOI:  https://doi.org/10.1016/j.molcel.2024.12.018
Cell Rep. 2025 Jan 16. pii: S2211-1247(24)01566-3. [Epub ahead of print]44(1): 115215

Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradation.

Yi-Ran Zhang, Shi-Meng Guo, Xiao-Yan Shi, Yi-Wen Ding, Huai-Biao Li, Lei Li, Jia-Wei Xu, Ximiao He, Bing-Xin Ma, Ying Yin, Li-Quan Zhou.

  Quantification of transcription activities in mammalian preimplantation embryos is challenging due to a huge amount of maternally stored transcripts and paucity of research materials. Here, we investigate genome-wide transcription activities of mouse and human preimplantation embryos by quantifying elongating RNA polymerase II. Two transcriptional waves are identified in early mouse embryos, with summits at the 2-cell and 8-cell stages. Gene collections with different expression patterns are obtained, with genes mainly transcribed at the mouse early/late 2-cell stage designated as zygotic genome activation-early/late 2-cell (ZGA-E2C/L2C). ZGA-E2C genes are short and have low promoter CpG density. Protein translation/degradation not only regulates transcription activity through stepwise orchestration of histone modifications, transcriptional initiation, and elongation in early mouse embryos but also controls on/off switching of ZGA-E2C/L2C genes in maternal aged mouse embryos. Genes mainly transcribed at the mouse 2-cell stage can also be transcribed as early as the human 2-cell stage.

Keywords:  CP: Developmental biology; CP: Molecular biology; embryo; maternal aging; preimplantation; transcription activity; zygotic genome activation

DOI:  https://doi.org/10.1016/j.celrep.2024.115215
J Mol Cell Cardiol. 2025 Jan 08. pii: S0022-2828(25)00001-X. [Epub ahead of print]200 1-10

Vinculin haploinsufficiency impairs integrin-mediated costamere remodeling on stiffer microenvironments.

Aileena C Nelson, Thomas G Molley, Gisselle Gonzalez, Natalie J Kirkland, Alyssa R Holman, Evan M Masutani, Neil C Chi, Adam J Engler.

  Vinculin (VCL) is a key adapter protein located in force-bearing costamere complexes, which mechanically couples the sarcomere to the ECM. Heterozygous vinculin frameshift genetic variants can contribute to cardiomyopathy when external stress is applied, but the mechanosensitive pathways underpinning VCL haploinsufficiency remain elusive. Here, we show that in response to extracellular matrix stiffening, heterozygous loss of VCL disrupts force-mediated costamere protein recruitment, thereby impairing cardiomyocyte contractility and sarcomere organization. Analyses of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) harboring either VCL c.659dupA or VCL c.74del7 heterozygous VCL frameshift variants revealed that these VCL mutant hPSC-CMs exhibited heightened contractile strain energy, morphological maladaptation, and sarcomere disarray on stiffened matrix. Mechanosensitive recruitment of costameric talin 2, paxillin, focal adhesion kinase, and α-actinin was significantly reduced in vinculin variant cardiomyocytes. Despite poorly formed costamere complexes and sarcomeres, elevated expression of integrin β1 and cortical actin on stiff substrates may rescue force transmission on stiff substrates, an effect that is recapitulated in WT CMs by ligating integrin receptors and blocking mechanosensation. Together, these data support that heterozygous loss of VCL contributes to adverse cardiomyocyte remodeling by impairing adhesion-mediated force transmission from the costamere to the cytoskeleton. (191 words).

Keywords:  Cardiomyocyte; Contractility; Costamere; Mechanosensation; Sarcomeres

DOI:  https://doi.org/10.1016/j.yjmcc.2025.01.001
Cell Stem Cell. 2025 Jan 13. pii: S1934-5909(24)00441-7. [Epub ahead of print]

Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states.

Terren K Niethamer, Joseph D Planer, Michael P Morley, Apoorva Babu, Gan Zhao, Maria C Basil, Edward Cantu, David B Frank, Joshua M Diamond, Ana N Nottingham, Shanru Li, Arnav Sharma, Hannah Hallquist, Lillian I Levin, Su Zhou, Andrew E Vaughan, Edward E Morrisey.

  Functional regeneration of the lung's gas exchange surface following injury requires the coordination of a complex series of cell behaviors within the alveolar niche. Using single-cell transcriptomics combined with lineage tracing of proliferating progenitors, we examined mouse lung regeneration after influenza injury, demonstrating an asynchronously phased response across different cellular compartments. This longitudinal atlas of injury responses has produced a catalog of transient and persistent transcriptional alterations in cells as they transit across axes of differentiation. These cell states include an injury-induced capillary endothelial cell (iCAP) that arises after injury, persists indefinitely, and shares hallmarks with developing lung endothelium and endothelial aberrations found in degenerative human lung diseases. This dataset provides a foundational resource to understand the complexity of cellular and molecular responses to injury and correlations to responses found in human development and disease.

Keywords:  alveolar; endothelial plasticity; influenza; injury; lineage tracing; lung; pulmonary endothelium; regeneration

DOI:  https://doi.org/10.1016/j.stem.2024.12.002
Curr Biol. 2025 Jan 06. pii: S0960-9822(24)01623-3. [Epub ahead of print]

The Balbiani body is formed by microtubule-controlled molecular condensation of Buc in early oogenesis.

Swastik Kar, Rachael Deis, Adam Ahmad, Yoel Bogoch, Avichai Dominitz, Gal Shvaizer, Esther Sasson, Avishag Mytlis, Ayal Ben-Zvi, Yaniv M Elkouby.

  Vertebrate oocyte polarity has been observed for two centuries and is essential for embryonic axis formation and germline specification, yet its underlying mechanisms remain unknown. In oocyte polarization, critical RNA-protein (RNP) granules delivered to the oocyte's vegetal pole are stored by the Balbiani body (Bb), a membraneless organelle conserved across species from insects to humans. However, the mechanisms of Bb formation are still unclear. Here, we elucidate mechanisms of Bb formation in zebrafish through developmental biomolecular condensation. Using super-resolution microscopy, live imaging, biochemical, and genetic analyses in vivo, we demonstrate that Bb formation is driven by molecular condensation through phase separation of the essential intrinsically disordered protein Bucky ball (Buc). Live imaging, molecular analyses, and fluorescence recovery after photobleaching (FRAP) experiments in vivo reveal Buc-dependent changes in the Bb condensate's dynamics and apparent material properties, transitioning from liquid-like condensates to a solid-like stable compartment. Furthermore, we identify a multistep regulation by microtubules that controls Bb condensation: first through dynein-mediated trafficking of early condensing Buc granules, then by scaffolding condensed granules, likely through molecular crowding, and finally by caging the mature Bb to prevent overgrowth and maintain shape. These regulatory steps ensure the formation of a single intact Bb, which is considered essential for oocyte polarization and embryonic development. Our work offers insight into the long-standing question of the origins of embryonic polarity in non-mammalian vertebrates, supports a paradigm of cellular control over molecular condensation by microtubules, and highlights biomolecular condensation as a key process in female reproduction.

Keywords:  Oocyte development; RNP granules; Zebrafish oogenesis; balbiani body; cell polarity; mictotubules; molecular condensation; ovary

DOI:  https://doi.org/10.1016/j.cub.2024.11.056
Dev Cell. 2025 Jan 02. pii: S1534-5807(24)00762-7. [Epub ahead of print]

Fate mapping in mouse demonstrates early secretory differentiation directly from Lgr5+ intestinal stem cells.

Isidora Banjac, Martti Maimets, Ingrid H C Tsang, Marius Dioli, Stine Lind Hansen, Kata Krizic, Raul Bardini Bressan, Cecilia Lövkvist, Kim B Jensen.

  The intestinal epithelium has a remarkably high turnover in homeostasis. It remains unresolved how this is orchestrated at the cellular level and how the behavior of stem and progenitor cells ensures tissue maintenance. To address this, we combined quantitative fate mapping in three complementary mouse models with mathematical modeling and single-cell RNA sequencing. Our integrated approach generated a spatially and temporally defined model of crypt maintenance based on two cycling populations: stem cells at the crypt-bottom and transit-amplifying (TA) cells above them. Subsequently, we validated the predictions from the mathematical model, demonstrating that fate decisions between the secretory and absorptive lineages are made within the stem cell compartment, whereas TA cell divisions contribute specifically to the absorptive lineage. These quantitative insights provide further direct evidence for crypt-bottom stem cells as the dominant driver of the intestinal epithelium replenishment.

Keywords:  fate mapping; intestinal stem cells; mathematical modeling

DOI:  https://doi.org/10.1016/j.devcel.2024.12.023
Nature. 2025 Jan 15.

Prolonged persistence of mutagenic DNA lesions in somatic cells.

Michael Spencer Chapman, Emily Mitchell, Kenichi Yoshida, Nicholas Williams, Margarete A Fabre, Anna Maria Ranzoni, Philip S Robinson, Lori D Kregar, Matthias Wilk, Steffen Boettcher, Krishnaa Mahbubani, Kourosh Saeb Parsy, Kate H C Gowers, Sam M Janes, Stanley W K Ng, Matt Hoare, Anthony R Green, George S Vassiliou, Ana Cvejic, Markus G Manz, Elisa Laurenti, Iñigo Martincorena, Michael R Stratton, Jyoti Nangalia, Tim H H Coorens, Peter J Campbell.

DNA is subject to continual damage, leaving each cell with thousands of individual DNA lesions at any given moment1-3. The efficiency of DNA repair means that most known classes of lesion have a half-life of minutes to hours3,4, but the extent to which DNA damage can persist for longer durations remains unknown. Here, using high-resolution phylogenetic trees from 89 donors, we identified mutations arising from 818 DNA lesions that persisted across multiple cell cycles in normal human stem cells from blood, liver and bronchial epithelium5-12. Persistent DNA lesions occurred at increased rates, with distinctive mutational signatures, in donors exposed to tobacco or chemotherapy, suggesting that they can arise from exogenous mutagens. In haematopoietic stem cells, persistent DNA lesions, probably from endogenous sources, generated the characteristic mutational signature SBS1913; occurred steadily throughout life, including in utero; and endured for 2.2 years on average, with 15-25% of lesions lasting at least 3 years. We estimate that on average, a haematopoietic stem cell has approximately eight such lesions at any moment in time, half of which will generate a mutation with each cell cycle. Overall, 16% of mutations in blood cells are attributable to SBS19, and similar proportions of driver mutations in blood cancers exhibit this signature. These data indicate the existence of a family of DNA lesions that arise from endogenous and exogenous mutagens, are present in low numbers per genome, persist for months to years, and can generate a substantial fraction of the mutation burden of somatic cells.

DOI: https://doi.org/10.1038/s41586-024-08423-8
Nat Cell Biol. 2025 Jan 10.

Spatial transcriptomic characterization of a Carnegie stage 7 human embryo.

Lina Cui, Sirui Lin, Xiaolong Yang, Xinwei Xie, Xiaoyan Wang, Nannan He, Jingyu Yang, Xin Zhang, Xiaojian Lu, Xiaodi Yan, Yifei Guo, Bailing Zhang, Ran Li, Hefan Miao, Mei Ji, Runzhao Zhang, Leqian Yu, Zhenyu Xiao, Yulei Wei, Jingtao Guo.

Gastrulation marks a pivotal stage in mammalian embryonic development, establishing the three germ layers and body axis through lineage diversification and morphogenetic movements. However, studying human gastrulating embryos is challenging due to limited access to early tissues. Here we show the use of spatial transcriptomics to analyse a fully intact Carnegie stage 7 human embryo at single-cell resolution, along with immunofluorescence validations in a second embryo. Employing 82 serial cryosections and Stereo-seq technology, we reconstructed a three-dimensional model of the embryo. Our findings reveal early specification of distinct mesoderm subtypes and the presence of the anterior visceral endoderm. Notably, primordial germ cells were located in the connecting stalk, and haematopoietic stem cell-independent haematopoiesis was observed in the yolk sac. This study advances our understanding of human gastrulation and provides a valuable dataset for future research in early human development.

DOI: https://doi.org/10.1038/s41556-024-01597-3
Development. 2025 Jan 13. pii: dev.204458. [Epub ahead of print]

A cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program.

Anupama Rao, Andrew Russell, Jose Segura-Bermudez, Charles Franz, Rejenae Dockery, Anton Blatnik, Jacob Panten, Mateo Zevallos, Carson McNulty, Maciej Pietrzak, Joseph Aaron Goldman.

  Zebrafish have a high capacity to regenerate their hearts. Several studies have surveyed transcriptional enhancers to understand how gene expression is controlled during heart regeneration. We have identified REN or the runx1 enhancer that during regeneration regulates the expression of the nearby runx1 gene. We show that runx1 mRNA is reduced with deletion of REN (ΔREN) and cardiomyocyte proliferation is enhanced ΔREN mutants only during regeneration. Interestingly, in uninjured hearts, ΔREN mutants have reduced expression of adamts1, a nearby gene that encodes a Collagen protease. This results in excess Collagen within cardiac valves of uninjured hearts. The ΔREN Collagen phenotype is rescued by an allele with Δrunx1 mutations, suggesting that in uninjured hearts REN regulates adamts1 independently of runx1. Taken together, this suggests that REN is rewired from adamts1 in uninjured hearts to stimulate runx1 transcription during regeneration. Our data point to a previously unappreciated mechanism for gene regulation during zebrafish heart regeneration. We report that an enhancer is rewired from expression in a distal cardiac domain to activate a different gene in regenerating tissue.

Keywords:  Gene regulation; Heart regeneration; Transcription enhancer; Zebrafish

DOI:  https://doi.org/10.1242/dev.204458
Nat Cell Biol. 2025 Jan;27(1): 59-72

Homologous recombination promotes non-immunogenic mitotic cell death upon DNA damage.

Radoslaw Szmyd, Sienna Casolin, Lucy French, Anna G Manjón, Melanie Walter, Léa Cavalli, Christopher B Nelson, Scott G Page, Andrew Dhawan, Eric Hau, Hilda A Pickett, Harriet E Gee, Anthony J Cesare.

Double-strand breaks (DSBs) can initiate mitotic catastrophe, a complex oncosuppressive phenomenon characterized by cell death during or after cell division. Here we unveil how cell cycle-regulated DSB repair guides disparate cell death outcomes through single-cell analysis of extended live imaging. Following DSB induction in S or G2, passage of unresolved homologous recombination intermediates into mitosis promotes non-immunogenic intrinsic apoptosis in the immediate attempt at cell division. Conversely, non-homologous end joining, microhomology-mediated end joining and single-strand annealing cooperate to enable damaged G1 cells to complete the first cell cycle with an aberrant cell division at the cost of delayed extrinsic lethality and interferon production. Targeting non-homologous end joining, microhomology-mediated end joining or single-strand annealing promotes mitotic death, while suppressing mitotic death enhances interferon production. Together the data indicate that a temporal repair hierarchy, coupled with cumulative DSB load, serves as a reliable predictor of mitotic catastrophe outcomes following genome damage. In this pathway, homologous recombination suppresses interferon production by promoting mitotic lethality.

DOI: https://doi.org/10.1038/s41556-024-01557-x
Mol Cell. 2025 Jan 08. pii: S1097-2765(24)01041-4. [Epub ahead of print]

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics.

Xiang Zheng, Andreas Mund, Matthias Mann.

  Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we introduce mipDVP, an advanced approach integrating highly multiplexed imaging, single-cell laser microdissection, and sensitive mass spectrometry to spatially profile the proteomes of distinct cell populations in a human colorectal and tonsil cancer with high sensitivity. In a colorectal tumor-a representative cold tumor-we uncovered spatial compartmentalization of an immunosuppressive macrophage barrier that potentially impedes T cell infiltration. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In a tonsil cancer sample-a hot tumor-we identified significant proteomic heterogeneity among cells influenced by proximity to cytotoxic T cell subtypes. T cells in the tumor parenchyma exhibit metabolic adaptations to hypoxic regions. Our spatially resolved, highly multiplexed strategy deciphers the complex cellular interplay within the tumor microenvironment, offering valuable insights for identifying immunotherapy targets and predictive signatures.

Keywords:  cancer; deep visual proteomics; immunotherapy; mass spectrometry; multiplexed imaging; spatial medicine; spatial proteomics; tumor microenvironment; tumor-infiltrating lymphocytes

DOI:  https://doi.org/10.1016/j.molcel.2024.12.023
Curr Biol. 2025 Jan 03. pii: S0960-9822(24)01651-8. [Epub ahead of print]

Sequential recruitment of F-BAR proteins controls cytoskeletal crosstalk at the yeast bud neck.

Joseph O Magliozzi, Lucas A Runyan, Priyanka Dutta, Gregory J Hoeprich, Bruce L Goode.

  In vivo functions of the septin and actin cytoskeletons are closely intertwined, yet the mechanisms underlying septin-actin crosstalk have remained poorly understood. Here, we show that the yeast-bud-neck-associated Fes/CIP4 homology Bar-amphiphysin-Rvs (F-BAR) protein suppressor of yeast profilin 1 (Syp1)/FCHo uses its intrinsically disordered region (IDR) to directly bind and bundle filamentous actin (F-actin) and to physically link septins and F-actin. Interestingly, the only other F-BAR protein found at the neck during bud development, Hof1, has related activities and also potently inhibits the bud-neck-associated formin Bnr1. However, we find that Syp1 enhances rather than inhibits Bnr1-mediated actin assembly and fully overcomes Hof1-mediated inhibition of Bnr1. Further, during bud development, Syp1 and Hof1 show reciprocal patterns of arrival and departure from the bud neck, and in vitro Syp1 and Hof1 compete for septin binding. Together, our observations suggest that as the bud grows, the relative levels of these two F-BAR proteins at the bud neck invert, driving changes in septin organization, septin-actin linkage, and formin activity. More broadly, our findings expand the functional roles of Syp1/FCHo family proteins and our understanding of the working relationships among F-BAR proteins in cytoskeletal regulation.

Keywords:  F-BAR protein; actin; cytoskeleton; formin; septin

DOI:  https://doi.org/10.1016/j.cub.2024.12.011
Nat Struct Mol Biol. 2025 Jan 16.

Maternal ELL3 loss-of-function leads to oocyte aneuploidy and early miscarriage.

Shiqi Zhu, Peng Xie, Yi Yang, Yan Wang, Chuanxin Zhang, Yu Zhang, Shuhan Si, Jin Zhang, Jingjing He, Hao Si, Ke Fang, Binbin Ma, Xu Jiang, Lindi Huang, Jiamin Li, Tian Min, Beihong Zheng, Lincui Da, Dianliang Lin, Kun Gao, Yuanyuan Li, Mingtao Huang, Fengchang Qiao, Haiqin Huo, Haoyang Feng, Han Zhao, Zijiang Chen, Zhengfeng Xu, Jing Xie, Hua Cao, Jin Liu, Xuebiao Yao, Wei Xie, Yan Sun, Keliang Wu, Bo Xiong, Ping Hu, Zhuojuan Luo, Chengqi Lin.

Up to an estimated 10% of women experience miscarriage in their lifetimes. Embryonic aneuploidy is a leading cause for miscarriage, infertility and congenital defects. Here we identify variants of ELL3, a gene encoding a transcription elongation factor, in couples who experienced consecutive early miscarriages due to embryonic aneuploidy. Maternal ELL3 knockout leads to mouse oocyte aneuploidy, subfertility and miscellaneous embryonic defects. Mechanistically, we find that ELL3 localizes to the spindle during meiosis, and that ELL3 depletion in both mouse and human oocytes increases the incidence of meiotic spindle abnormality. ELL3 coordinates with TPX2 to ensure the proper function of the microtubule motor KIF11. Live imaging analysis shows that ELL3 is paramount for promoting spindle assembly and driving chromosome movement. Together, our findings implicate maternal ELL3 deficiency in causing oocyte aneuploidy and early miscarriage.

DOI: https://doi.org/10.1038/s41594-024-01471-8
Cell Rep. 2025 Jan 10. pii: S2211-1247(24)01551-1. [Epub ahead of print]44(1): 115200

Stored elastic bending tension as a mediator of embryonic body folding.

Mira Zaher, Ronit Yelin, Alaa A Arraf, Julian Jadon, Manar Abboud Asleh, Sivan Goltzman, Lihi Shaulov, Dieter P Reinhardt, Thomas M Schultheiss.

  During development, amniote vertebrate embryos transform from a flat sheet into a three-dimensional cylindrical form through ventral folding of the lateral sides of the sheet (the lateral plate [LP]) and their fusion in the ventral midline. Using a chick embryo slice system, we find that the flat stage is actually a poised balance of opposing dorsal and ventral elastic bending tensions. An intact extracellular matrix (ECM) is required for generating tension, as localized digestion of ECM dissipates tension, while removal of endoderm or ectoderm layers has no significant effect. As development proceeds, dorsal bending tension dissipates coincident with epithelial-mesenchymal transition in the dorsal LP while ventral tension is maintained, changing the balance of forces to promote ventral folding. Interference with the elastic ECM component fibrillin reduces ventral bending tension and perturbs body folding in vivo. A model is presented for the accumulation and harnessing of LP bending tension to drive body folding.

Keywords:  CP: Developmental biology; biomechanics; chick embryo; epithelial bending; extracellular matrix; lateral mesoderm; morphogenesis

DOI:  https://doi.org/10.1016/j.celrep.2024.115200
Cell Metab. 2025 Jan 13. pii: S1550-4131(24)00481-9. [Epub ahead of print]

Exosomal miR-302b rejuvenates aging mice by reversing the proliferative arrest of senescent cells.

Youkun Bi, Xinlong Qiao, Zhaokui Cai, Hailian Zhao, Rong Ye, Qun Liu, Lin Gao, Yingqi Liu, Bo Liang, Yixuan Liu, Yaning Zhang, Zhiguang Yang, Yanyun Wu, Huiwen Wang, Wei Jia, Changqing Zeng, Ce Jia, Hongjin Wu, Yuanchao Xue, Guangju Ji.

  Cellular senescence, a hallmark of aging, involves a stable exit from the cell cycle. Senescent cells (SnCs) are closely associated with aging and aging-related disorders, making them potential targets for anti-aging interventions. In this study, we demonstrated that human embryonic stem cell-derived exosomes (hESC-Exos) reversed senescence by restoring the proliferative capacity of SnCs in vitro. In aging mice, hESC-Exos treatment remodeled the proliferative landscape of SnCs, leading to rejuvenation, as evidenced by extended lifespan, improved physical performance, and reduced aging markers. Ago2 Clip-seq analysis identified miR-302b enriched in hESC-Exos that specifically targeted the cell cycle inhibitors Cdkn1a and Ccng2. Furthermore, miR-302b treatment reversed the proliferative arrest of SnCs in vivo, resulting in rejuvenation without safety concerns over a 24-month observation period. These findings demonstrate that exosomal miR-302b has the potential to reverse cellular senescence, offering a promising approach to mitigate senescence-related pathologies and aging.

Keywords:  Ccng2; Cdkn1a; aging; cellular senescence; hESC-Exos; miR-302b; proliferative arrest; rejuvenation

DOI:  https://doi.org/10.1016/j.cmet.2024.11.013
Genes Dev. 2024 Dec 20.

LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells.

Lamisa Ataei, Juan Zhang, Simon Monis, Krystyna Giemza, Kirti Mittal, Joshua Yang, Mayu Shimomura, Brian McStay, Michael D Wilson, Miguel Ramalho-Santos.

  The nucleolus is a major subnuclear compartment where ribosomal DNA (rDNA) is transcribed and ribosomes are assembled. In addition, recent studies have shown that the nucleolus is a dynamic organizer of chromatin architecture that modulates developmental gene expression. rDNA gene units are assembled into arrays located in the p-arms of five human acrocentric chromosomes. Distal junctions (DJs) are ∼400 kb sequences adjacent to rDNA arrays that are thought to anchor them at the nucleolus, although the underlying regulatory elements remain unclear. Here we show that DJs display a dynamic chromosome conformation profile in human embryonic stem cells (hESCs). We identified a primate-specific, full-length insertion of the retrotransposon long interspersed nuclear element 1 (LINE1) in a conserved position across all human DJs. This DJ-LINE1 locus interacts with specific regions of the DJ and is upregulated in naïve hESCs. CRISPR-based deletion and interference approaches revealed that DJ-LINE1 contributes to nucleolar positioning of the DJs. Moreover, we found that the expression of DJ-LINE1 is required for maintenance of the structure and transcriptional output of the nucleolus in hESCs. Silencing of DJ-LINE1 leads to loss of self-renewal, disruption of the landscape of chromatin accessibility, and derepression of earlier developmental programs in naïve hESCs. This work uncovers specific LINE1 elements with a fundamental role in nucleolar organization in hESCs and provides new insights into how the nucleolus functions as a key genome-organizing hub.

Keywords:  LINE1; human embryonic stem cells; nucleolus; rDNA arrays

DOI:  https://doi.org/10.1101/gad.351979.124
Development. 2025 Jan 13. pii: dev.204591. [Epub ahead of print]

An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast.

Ashley R G Libby, Tiago Rito, Arthur Radley, James Briscoe.

  Tissue development relies on the coordinated differentiation of stem cells in dynamically changing environments. The formation of the vertebrate neural tube from stem cells in the caudal lateral epiblast (CLE) is a well characterized example. Despite an understanding of the signalling pathways involved, the gene regulatory mechanisms remain poorly defined. To address this, we developed a multiplexed in vivo CRISPR screening approach in chick embryos targeting genes expressed in the caudal epiblast and neural tube. This revealed a role for MLLT3, a component of the super elongation complex, in the specification of neural fate. Perturbation of MLLT3 disrupted neural tube morphology and reduced neural fate acquisition. Mutant forms of Retinoic Acid Receptor A lacking the MLLT3 binding domain similarly reduced neural fate acquisition. Together, these findings validate an in vivo CRISPR screen strategy in chick embryos and identify a previously unreported role for MLLT3 in caudal neural tissue specification.

Keywords:  CRISPR/cas9; Chick; In vivo screen; NMPs; Neural induction; super elongation complex

DOI:  https://doi.org/10.1242/dev.204591
Nature. 2025 Jan 15.

Massively parallel characterization of transcriptional regulatory elements.

Vikram Agarwal, Fumitaka Inoue, Max Schubach, Dmitry Penzar, Beth K Martin, Pyaree Mohan Dash, Pia Keukeleire, Zicong Zhang, Ajuni Sohota, Jingjing Zhao, Ilias Georgakopoulos-Soares, William S Noble, Galip Gürkan Yardımcı, Ivan V Kulakovskiy, Martin Kircher, Jay Shendure, Nadav Ahituv.

The human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific activities that shape both health and many disease states1. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these cCREs. Here we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of more than 680,000 sequences, representing an extensive set of annotated cCREs among three cell types (HepG2, K562 and WTC11), and found that 41.7% of these sequences were active. By testing sequences in both orientations, we find promoters to have strand-orientation biases and their 200-nucleotide cores to function as non-cell-type-specific 'on switches' that provide similar expression levels to their associated gene. By contrast, enhancers have weaker orientation biases, but increased tissue-specific characteristics. Utilizing our lentiMPRA data, we develop sequence-based models to predict cCRE function and variant effects with high accuracy, delineate regulatory motifs and model their combinatorial effects. Testing a lentiMPRA library encompassing 60,000 cCREs in all three cell types further identified factors that determine cell-type specificity. Collectively, our work provides an extensive catalogue of functional CREs in three widely used cell lines and showcases how large-scale functional measurements can be used to dissect regulatory grammar.

DOI: https://doi.org/10.1038/s41586-024-08430-9
EMBO J. 2025 Jan 13.

Specialized pericyte subtypes in the pulmonary capillaries.

Timothy Klouda, Yunhye Kim, Seung-Han Baek, Mantu Bhaumik, Yan Li, Yu Liu, Joseph C Wu, Benjamin A Raby, Vinicio de Jesus Perez, Ke Yuan.

  Pericytes are essential for capillary stability and homeostasis, with impaired pericyte function linked to diseases like pulmonary arterial hypertension. Investigating pericyte biology has been challenging due to the lack of specific markers, making it difficult to distinguish pericytes from other stromal cells. Using bioinformatic analysis and RNAscope, we identified Higd1b as a unique gene marker for pericytes and subsequently generated a knock-in mouse line, Higd1b-CreERT2, that accurately labels pericytes in the lung and heart. Single-cell RNA sequencing revealed two distinct Higd1b+ pericyte subtypes: while Type 1 pericytes support capillary homeostasis, Type 2 pericytes accumulate in arterioles, and co-express smooth muscle markers and higher levels of vimentin under hypoxic conditions. Lastly, healthy human lung pericytes with upregulation of vimentin exhibited increased adhesion, migration, and higher expression levels of the smooth muscle marker SM22 in vitro. These findings highlight the specialization of pulmonary pericytes and their contribution to vascular remodeling during hypoxia-induced pulmonary hypertension.

Keywords:  Capillary; Higd1b; Pericytes; Pulmonary Hypertension; Single-cell RNA Sequence

DOI:  https://doi.org/10.1038/s44318-024-00349-1
Mol Biol Cell. 2025 Jan 15. mbcE24100441

SYS-1/beta-catenin inheritance and regulation by Wnt-signaling during asymmetric cell division.

Maria F Valdes Michel, Bryan T Phillips.

Asymmetric cell division (ACD) allows daughter cells of a polarized mother to acquire different developmental fates. In C. elegans, the Wnt/β-catenin Asymmetry (WβA) pathway regulates many embryonic and larval ACDs; here, a Wnt gradient induces an asymmetric distribution of Wnt signaling components within the dividing mother cell. One terminal nuclear effector of the WβA pathway is the transcriptional activator SYS-1/β-catenin. SYS-1 is sequentially negatively regulated during ACD; first by centrosomal regulation and subsequent proteasomal degradation and second by asymmetric activity of the β-catenin "destruction complex" in one of the two daughter cells, which decreases SYS-1 levels in the absence of WβA signaling. However, the extent to which mother cell SYS-1 influences cell fate decisions of the daughters is unknown. Here, we quantify inherited SYS-1 in the differentiating daughter cells and the role of SYS-1 inheritance in Wnt-directed ACD. Photobleaching experiments demonstrate the GFP::SYS-1 present in daughter cell nuclei is comprised of inherited and de novo translated SYS-1 pools. We used a photoconvertible DENDRA2::SYS-1, to directly observe the dynamics of inherited SYS-1. Photoconversion during mitosis reveals that SYS-1 clearance at the centrosome preferentially degrades older SYS-1 and that newly localized centrosomal SYS-1 depends on dynein trafficking. Photoconversion of DENDRA2::SYS-1 in the EMS cell during Wnt-driven ACD shows daughter cell inheritance of mother cell SYS-1. Additionally, disrupting centrosomal SYS-1 localization in mother cells increased inherited SYS-1 and, surprisingly, loss of centrosomal SYS-1 also resulted in increased levels of de novo SYS-1 in both EMS daughter cells. Lastly, we show that negative regulation of SYS-1 in daughter cells via the destruction complex member APR-1/APC is key to limit both the de novo and the inherited SYS-1 pools in both the E and the MS cells. We conclude that regulation of both inherited and newly translated SYS-1 via centrosomal processing in the mother cell and daughter cell regulation via Wnt signaling are critical to maintain sister SYS-1 asymmetry during ACD.

DOI: https://doi.org/10.1091/mbc.E24-10-0441
Nat Aging. 2025 Jan 13.

Somatic mutation as an explanation for epigenetic aging.

Zane Koch, Adam Li, Daniel S Evans, Steven Cummings, Trey Ideker.

DNA methylation marks have recently been used to build models known as epigenetic clocks, which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In an analysis of multimodal data from 9,331 human individuals, we found that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping allows mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging more rapidly or slowly than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.

DOI: https://doi.org/10.1038/s43587-024-00794-x
Development. 2025 Jan 16. pii: dev.204227. [Epub ahead of print]

BMP and STRA8 act collaboratively to ensure correct mitotic-to-meiotic transition in the fetal mouse ovary.

Fiona K M Cheung, Chun-Wei Allen Feng, Clare Crisp, Yuji Mishina, Cassy M Spiller, Josephine Bowles.

  A successful mitosis-to-meiosis transition in germ cells is essential for fertility in sexually reproducing organisms. In mice and humans, it is established that expression of STRA8 is critical for meiotic onset in both sexes. Here we show that BMP signalling is also essential, not for STRA8 induction but for correct meiotic progression in female mouse fetal germ cells. Largely in agreement with evidence from primordial germ cell-like cells (PGCLCs) in vitro, germ cell-specific deletion of BMP receptor 1A (BMPR1A; ALK3) caused aberrant retention of pluripotency marker OCT4 and meiotic progression was compromised; however, the timely onset of Stra8/STRA8 expression was unaffected. Comparing the transcriptomes of Bmpr1a-cKO and Stra8-null models, we reveal interplay between the effects of BMP signalling and STRA8 function. Our results verify a role for BMP signalling in instructing germ cell meiosis in female mice in vivo, and shed light on the regulatory mechanisms underlying fetal germ cell development.

Keywords:  BMP signalling; Fetal ovarian germ cell; Fetal ovary; Mammalian reproduction; Mitosis-to-meiosis transition; STRA8

DOI:  https://doi.org/10.1242/dev.204227
Nature. 2025 Jan 16.

Brain-wide neuronal circuit connectome of human glioblastoma.

Yusha Sun, Xin Wang, Daniel Y Zhang, Zhijian Zhang, Janardhan P Bhattarai, Yingqi Wang, Kristen H Park, Weifan Dong, Yun-Fen Hung, Qian Yang, Feng Zhang, Keerthi Rajamani, Shang Mu, Benjamin C Kennedy, Yan Hong, Jamie Galanaugh, Abhijeet Sambangi, Sang Hoon Kim, Garrett Wheeler, Tiago Gonçalves, Qing Wang, Daniel Geschwind, Riki Kawaguchi, Angela N Viaene, Ingo Helbig, Sudha K Kessler, Ahmet Hoke, Huadong Wang, Fuqiang Xu, Zev A Binder, H Isaac Chen, Emily Ling-Lin Pai, Sara Stone, MacLean P Nasrallah, Kimberly M Christian, Marc Fuccillo, Nicolas Toni, Zhuhao Wu, Hwai-Jong Cheng, Donald M O'Rourke, Minghong Ma, Guo-Li Ming, Hongjun Song.

Glioblastoma (GBM) infiltrates the brain and can be synaptically innervated by neurons, which drives tumor progression1,2. Synaptic inputs onto GBM cells identified so far are largely short-range and glutamatergic3,4. The extent of GBM integration into the brain-wide neuronal circuitry remains unclear. Here we applied rabies virus- and herpes simplex virus-mediated trans-monosynaptic tracing5,6 to systematically investigate circuit integration of human GBM organoids transplanted into adult mice. We found that GBM cells from multiple patients rapidly integrate into diverse local and long-range neural circuits across the brain. Beyond glutamatergic inputs, we identified various neuromodulatory inputs, including synapses between basal forebrain cholinergic neurons and GBM cells. Acute acetylcholine stimulation induces long-lasting elevation of calcium oscillations and transcriptional reprogramming of GBM cells into a more motile state via the metabotropic CHRM3 receptor. CHRM3 activation promotes GBM cell motility, whereas its downregulation suppresses GBM cell motility and prolongs mouse survival. Together, these results reveal the striking capacity for human GBM cells to rapidly and robustly integrate into anatomically diverse neuronal networks of different neurotransmitter systems. Our findings further support a model wherein rapid connectivity and transient activation of upstream neurons may lead to a long-lasting increase in tumor fitness.

DOI: https://doi.org/10.1038/s41586-025-08634-7
J Clin Invest. 2025 Jan 14. pii: e171077. [Epub ahead of print]

PDGFRα inhibition reduces myofibroblast expansion in the fibrotic rim and enhances recovery after ischemic stroke.

Jil Protzmann, Manuel Zeitelhofer, Christina Stefanitsch, Daniel Torrente, Milena Z Adzemovic, Kirils Matjunins, Stella Ji Randel, Sebastian A Lewandowski, Lars Muhl, Ulf Eriksson, Ingrid Nilsson, Enming J Su, Daniel A Lawrence, Linda Fredriksson.

  Ischemic stroke is a major cause of adult disability. Early treatment with thrombolytics and/or thrombectomy can significantly improve outcomes; however, following these acute interventions, treatment is limited to rehabilitation therapies. Thus, the identification of therapeutic strategies that can help restore brain function in the post-acute phase remains a major challenge. Here we report that genetic or pharmacologic inhibition of the PDGF-CC/PDGFRα pathway, which has previously been implicated in stroke pathology, significantly reduced myofibroblast expansion in the border of the fibrotic scar and improved outcome in a sensory-motor integration test after experimental ischemic stroke. This was supported by gene expression analyses of cerebrovascular fragments, showing upregulation of pro-fibrotic/pro-inflammatory genes, including genes of the TGFβ pathway, after ischemic stroke or intracerebroventricular injection of active PDGF-CC. Further, longitudinal intravital two-photon imaging revealed that inhibition of PDGFRα dampened the bi-phasic pattern of stroke-induced vascular leakage and enhanced vascular perfusion in the ischemic lesion. Importantly, we found efficacy of PDGFRα inhibition on functional recovery when initiated 24 hours after ischemic stroke. Our data implicate the PDGF-CC/PDGFRα pathway as a crucial mediator modulating post-stroke pathology and suggest a post-acute treatment opportunity for ischemic stroke patients targeting myofibroblast expansion to foster long-term CNS repair.

Keywords:  Fibrosis; Growth factors; Neuroscience; Stroke; Vascular biology

DOI:  https://doi.org/10.1172/JCI171077
Acta Biomater. 2025 Jan 09. pii: S1742-7061(25)00017-0. [Epub ahead of print]

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability.

Lucia G Brunel, Chris M Long, Fotis Christakopoulos, Betty Cai, Patrik K Johansson, Diya Singhal, Annika Enejder, David Myung, Sarah C Heilshorn.

  Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks. STATEMENT OF SIGNIFICANCE: Collagen hydrogels are widely used as scaffolds for tissue engineering due to their support of cellular activity. However, collagen hydrogels often undergo undesired changes in size and shape due to cell-generated forces, and conventional strategies to mitigate this deformation typically compromise either the fibrillar microstructure or cytocompatibility of the collagen. In this study, we introduce an innovative interpenetrating network (IPN) that combines physically self-assembled, fibrillar collagen-ideal for promoting cell adhesion and spreading-with covalently crosslinked, amorphous collagen-ideal for enhancing bulk hydrogel stability. Our IPN design maintains the native fibrillar structure of collagen while significantly improving resistance against cell-induced contraction, providing a promising solution to enhance the performance and reliability of collagen hydrogels for tissue engineering applications.

Keywords:  Cell morphology; Collagen; Crosslinking; Hydrogel contraction; Interpenetrating network

DOI:  https://doi.org/10.1016/j.actbio.2025.01.009