bims-ginsta 2025-03-16 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–03–16
24 papers selected by
Jinrong Hu, National University of Singapore

A tension-induced morphological transition shapes the avian extra-embryonic territory.
Measuring and manipulating mechanical forces during development.
Fetal-like reversion in the regenerating intestine is regulated by mesenchymal asporin.
Engineering mtDNA deletions by reconstituting end joining in human mitochondria.
Tunneling nanotube-like structures regulate distant cellular interactions during heart formation.
Pancreatic alpha and beta cell fate choice is directed by apical-basal polarity dynamics.
A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan.
Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.
Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.
DNA lesions can frequently precede DNA:RNA hybrid accumulation.
Disruption of ER-mitochondria contact sites induces autophagy-dependent loss of P-bodies through the Ca2+-CaMKK2-AMPK pathway.
Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells.
Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM.
c-Kit+ cells that intercalate with crypt Lgr5+ cells are distinctively multipotent in colonic epithelium renewal and repair.
Genetic tracing and topography of spontaneous and stimulated cardiac regeneration in mice.
Hepatic stellate cells control liver zonation, size and functions via R-spondin 3.
GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis.
Cell extrusion drives neural crest cell delamination.
Interleukin-12 signaling drives Alzheimer's disease pathology through disrupting neuronal and oligodendrocyte homeostasis.
Overcoming gene dosage barriers in mammalian development: An imprinting balancing act.
Mucosal macrophages govern intestinal regeneration in response to injury.
Modes of Notch signalling in development and disease.
Myeloid Fatty Acid Metabolism Activates Neighboring Hematopoietic Stem Cells to Promote Heart Failure With Preserved Ejection Fraction.
Aneuploidy as a cancer vulnerability.

Curr Biol. 2025 Mar 07. pii: S0960-9822(25)00191-5. [Epub ahead of print]

A tension-induced morphological transition shapes the avian extra-embryonic territory.

Arthur Michaut, Alexander Chamolly, Aurélien Villedieu, Francis Corson, Jérôme Gros.

  The segregation of the extra-embryonic lineage is one of the earliest events and a key step in amniote development. Whereas the regulation of extra-embryonic cell fate specification has been extensively studied, little is known about the morphogenetic events underlying the formation of this lineage. Here, taking advantage of the amenability of avian embryos to live and quantitative imaging, we investigate the cell- and tissue-scale dynamics of epiboly, the process during which the epiblast expands to engulf the entire yolk. We show that tension arising from the outward migration of the epiblast border on the vitelline membrane stretches extra-embryonic cells, which reversibly transition from a columnar to a squamous morphology. The propagation of this tension is strongly attenuated in the embryonic territory, which concomitantly undergoes fluid-like motion, culminating in the formation of the primitive streak. We formulate a simple viscoelastic model in which the epiblast responds elastically to isotropic stress but, on a similar timescale, flows in response to shear stress, and we show that it recapitulates the flows and deformation of both embryonic and extra-embryonic tissues. Together, our results clarify the mechanical basis of early avian embryogenesis and provide a framework unifying the divergent mechanical behaviors observed in the contiguous embryonic and extra-embryonic territories that make up the epiblast.

Keywords:  epiblast; epiboly; extraembryonic; gastrulation; mechanical forces; morphogenesis; primitive streak; tissue deformation; tissue mechanics; viscoelastic model

DOI:  https://doi.org/10.1016/j.cub.2025.02.028
Nat Cell Biol. 2025 Mar 10.

Measuring and manipulating mechanical forces during development.

Clémentine Villeneuve, Kaitlin P McCreery, Sara A Wickström.

Tissue deformations are a central feature of development, from early embryogenesis, growth and building the body plan to the establishment of functional organs. These deformations often result from active contractile forces generated by cells and cell collectives, and are mediated by changes in their mechanical properties. Mechanical forces drive the formation of functional organ architectures, but they also coordinate cell behaviour and fate transitions, ensuring robustness of development. Advances in microscopy, genetics and chemistry have enabled increasingly powerful tools for measuring, generating and perturbing mechanical forces. Here we discuss approaches to measure and manipulate mechanical forces with a focus on developmental processes, ranging from quantification of molecular interactions to mapping the mechanical properties of tissues. We focus on contemporary methods, and discuss the biological discoveries that these approaches have enabled. We conclude with an outlook to methodologies at the interface of physics, chemistry and biology to build an integrated understanding of tissue morphodynamics.

DOI: https://doi.org/10.1038/s41556-025-01632-x
Cell Stem Cell. 2025 Mar 03. pii: S1934-5909(25)00048-7. [Epub ahead of print]

Fetal-like reversion in the regenerating intestine is regulated by mesenchymal asporin.

Sharif Iqbal, Simon Andersson, Ernesta Nesta, Nalle Pentinmikko, Ashish Kumar, Sawan Kumar Jha, Daniel Borshagovski, Anna Webb, Nadja Gebert, Emma W Viitala, Alexandra Ritchie, Sandra Scharaw, Emilia Kuuluvainen, Hjalte L Larsen, Tuure Saarinen, Anne Juuti, Ari Ristimäki, Michael Jeltsch, Alessandro Ori, Markku Varjosalo, Kirsi H Pietiläinen, Saara Ollila, Kim B Jensen, Menno J Oudhoff, Pekka Katajisto.

  Mesenchymal cells and the extracellular matrix (ECM) support epithelium during homeostasis and regeneration. However, the role of the mesenchyme in epithelial conversion into a fetal-like regenerative state after damage is not known. We modeled epithelial regeneration by culturing intestinal epithelium on decellularized small intestinal scaffolds (iECM) and identify asporin (Aspn), an ECM-bound proteoglycan, as a critical mediator of epithelial fetal-like reprogramming. After damage, transient increase in Aspn expression by the pericryptal fibroblasts induces epithelial transforming growth factor β (TGF-β)-signaling via CD44 and promotes timely epithelial reprogramming. Temporal control of Aspn is lost in old mice, and after damage, the persistently high level of Aspn stagnates epithelium in the regenerative state. Increase in Wnt signaling can resolve the stagnated regenerative program of the old epithelium, promoting restoration of tissue function. In summary, we establish a platform for modeling epithelial injury responses ex vivo and show that the mesenchymal Aspn-producing niche modulates tissue repair by regulating epithelial fetal-like reprogramming.

Keywords:  CD44; TGF-β signaling; Wnt signaling; aging; asporin; extracellular matrix; fetal-like cellular reprogramming; intestinal stem cells; mesenchyme; regeneration

DOI:  https://doi.org/10.1016/j.stem.2025.02.009
Cell. 2025 Mar 05. pii: S0092-8674(25)00194-1. [Epub ahead of print]

Engineering mtDNA deletions by reconstituting end joining in human mitochondria.

Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B Thompson, Dana Pe'er, Agnel Sfeir.

  Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.

Keywords:  DOGMA-seq; end joining; mitochondrial pathologies; mtDNA; mtDNA deletion

DOI:  https://doi.org/10.1016/j.cell.2025.02.009
Science. 2025 Mar 14. 387(6739): eadd3417

Tunneling nanotube-like structures regulate distant cellular interactions during heart formation.

Lianjie Miao, Yangyang Lu, Anika Nusrat, Guizhen Fan, Shaohua Zhang, Luqi Zhao, Chia-Ling Wu, Hongyan Guo, Trang Le Nu Huyen, Yi Zheng, Zhen-Chuan Fan, Weinian Shou, Robert J Schwartz, Yu Liu, Ashok Kumar, Haixin Sui, Irina I Serysheva, Alan R Burns, Leo Q Wan, Bin Zhou, Sylvia M Evans, Mingfu Wu.

In the developing mammalian heart, the endocardium and the myocardium are separated by so-called cardiac jelly. Communication between the endocardium and the myocardium is essential for cardiac morphogenesis. How membrane-localized receptors and ligands achieve interaction across the cardiac jelly is not understood. Working in developing mouse cardiac morphogenesis models, we used a variety of cellular, imaging, and genetic approaches to elucidate this question. We found that myocardium and endocardium interacted directly through microstructures termed tunneling nanotube-like structures (TNTLs). TNTLs extended from cardiomyocytes (CMs) to contact endocardial cells (ECs) directly. TNTLs transported cytoplasmic proteins, transduced signals between CMs and ECs, and initiated myocardial growth toward the heart lumen to form ventricular trabeculae-like structures. Loss of TNTLs disturbed signaling interactions and, subsequently, ventricular patterning.

DOI: https://doi.org/10.1126/science.add3417
Dev Cell. 2025 Mar 04. pii: S1534-5807(25)00113-3. [Epub ahead of print]

Pancreatic alpha and beta cell fate choice is directed by apical-basal polarity dynamics.

Ulf Tiemann, Chenglei Tian, Florian Hermann, Martin Proks, Emilie Skovgaard, Ivan Kulik, Yilin Di, Jakub Sedzinski, Henrik Semb.

  A central question in cell and developmental biology is how extracellular cues control the differentiation of multipotent progenitors in a dynamically changing niche. Here, we identify apical-basal polarity as the main regulator of the differentiation of multipotent pancreatic Neurogenin3+ endocrine progenitors (EPs) into the beta or alpha cell fates. We show that human EPs dynamically change their apical-basal polarity status. Whereas polarized EPs are predisposed to differentiate into beta cells rather than alpha cells, inhibiting apical-basal polarity selectively suppresses beta cell differentiation. Single-cell RNA sequencing and complementary mechanistic data demonstrate that apical-basal polarity in human EPs promotes beta cell specification via cyclic AMP (cAMP)/PKA-cAMP response element binding protein (CREB)-EGR1-mediated inhibition of ARX expression, while reduced cAMP levels in non-polarized human EPs maintain expression of ARX, leading to alpha cell differentiation. These findings identify the apical-basal polarity status of multipotent EPs as a critical epithelial feature that determines their fate into the alpha or beta cell lineages.

Keywords:  apical-basal polarity; cAMP; multipotent pancreatic endocrine progenitors; pancreas; pancreatic alpha cells; pancreatic beta cells

DOI:  https://doi.org/10.1016/j.devcel.2025.02.008
Nat Aging. 2025 Mar 07.

A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan.

Lorna Jayne, Aurora Lavin-Peter, Julian Roessler, Alexander Tyshkovskiy, Mateusz Antoszewski, Erika Ren, Aleksandar Markovski, Senmiao Sun, Hanqi Yao, Vijay G Sankaran, Vadim N Gladyshev, Robert T Brooke, Steve Horvath, Eric C Griffith, Sinisa Hrvatin.

Torpor and hibernation are extreme physiological adaptations of homeotherms associated with pro-longevity effects. Yet the underlying mechanisms of how torpor affects aging, and whether hypothermic and hypometabolic states can be induced to slow aging and increase healthspan, remain unknown. Here we demonstrate that the activity of a spatially defined neuronal population in the preoptic area, which has previously been identified as a torpor-regulating brain region, is sufficient to induce a torpor-like state (TLS) in mice. Prolonged induction of TLS slows epigenetic aging across multiple tissues and improves healthspan. We isolate the effects of decreased metabolic rate, long-term caloric restriction, and decreased core body temperature (Tb) on blood epigenetic aging and find that the decelerating effect of TLSs on aging is mediated by decreased Tb. Taken together, our findings provide novel mechanistic insight into the decelerating effects of torpor and hibernation on aging and support the growing body of evidence that Tb is an important mediator of the aging processes.

DOI: https://doi.org/10.1038/s43587-025-00830-4
Mol Cell. 2025 Mar 05. pii: S1097-2765(25)00144-3. [Epub ahead of print]

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.

Tiffany Ge, Donna Garvey Brickner, Kara Zehr, D Jake VanBelzen, Wenzhu Zhang, Christopher Caffalette, Gavin C Moeller, Sara Ungerleider, Nikita Marcou, Alexis Jacob, Vu Q Nguyen, Brian Chait, Michael P Rout, Jason H Brickner.

  Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.

Keywords:  nuclear architecture; nuclear pore complex; transcription; transcription factor

DOI:  https://doi.org/10.1016/j.molcel.2025.02.013
Mol Cell. 2025 Mar 05. pii: S1097-2765(25)00143-1. [Epub ahead of print]

Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.

Nadiya Khyzha, Kami Ahmad, Steven Henikoff.

  Nuclear compartments are membrane-less regions enriched in functionally related molecules. RNA is a major component of many nuclear compartments, but the identity and dynamics of transcripts within nuclear compartments are poorly understood. Here, we applied reverse transcribe and tagment (RT&Tag) to human cell lines to identify the transcript populations of Polycomb domains and nuclear speckles. We also developed SLAM-RT&Tag, which combines RNA metabolic labeling with RT&Tag, to quantify transcript dynamics within nuclear compartments. We observed unique transcript populations with differing structures and dynamics within each compartment. Intriguingly, exceptionally long genes are transcribed adjacent to Polycomb domains and are transiently associated with chromatin. By contrast, nuclear speckles act as quality control checkpoints that transiently confine incompletely spliced polyadenylated transcripts and facilitate their post-transcriptional splicing. In summary, we demonstrate that transcripts at Polycomb domains and nuclear speckles undergo distinct RNA processing mechanisms, highlighting the pivotal role of compartmentalization in RNA maturation.

Keywords:  H3K27me3; Polycomb domains; RNA dynamics; RNA localization; RNA metabolic labeling; RNA sequencing; RT&Tag; compartments; nuclear bodies; nuclear organization; nuclear speckles; post-transcriptional splicing

DOI:  https://doi.org/10.1016/j.molcel.2025.02.012
Nat Commun. 2025 Mar 10. 16(1): 2401

DNA lesions can frequently precede DNA:RNA hybrid accumulation.

Raphaël M Mangione, Steven Pierce, Myriam Zheng, Robert M Martin, Coralie Goncalves, Arun Kumar, Sarah Scaglione, Cristiana de Sousa Morgado, Arianna Penzo, Astrid Lancrey, Robert J D Reid, Ophélie Lautier, Pierre-Henri Gaillard, Peter C Stirling, Sérgio F de Almeida, Rodney Rothstein, Benoit Palancade.

While DNA:RNA hybrids contribute to multiple genomic transactions, their unscheduled formation is a recognized source of DNA lesions. Here, through a suite of systematic screens, we rather observed that a wide range of yeast mutant situations primarily triggering DNA damage actually leads to hybrid accumulation. Focusing on Okazaki fragment processing, we establish that genic hybrids can actually form as a consequence of replication-born discontinuities such as unprocessed flaps or unligated Okazaki fragments. Strikingly, such "post-lesion" DNA:RNA hybrids neither detectably contribute to genetic instability, nor disturb gene expression, as opposed to "pre-lesion" hybrids formed upon defective mRNA biogenesis, e.g., in THO complex mutants. Post-lesion hybrids similarly arise in distinct genomic instability situations, triggered by pharmacological or genetic manipulation of DNA-dependent processes, both in yeast and human cells. Altogether, our data establish that the accumulation of transcription-born DNA:RNA hybrids can occur as a consequence of various types of natural or pathological DNA lesions, yet do not necessarily aggravate their genotoxicity.

DOI: https://doi.org/10.1038/s41467-025-57588-x
J Cell Sci. 2025 Mar 01. pii: JCS263652. [Epub ahead of print]138(5):

Disruption of ER-mitochondria contact sites induces autophagy-dependent loss of P-bodies through the Ca2+-CaMKK2-AMPK pathway.

Nikhil More, Jomon Joseph.

  P-bodies (PBs) and stress granules (SGs) are conserved, non-membranous cytoplasmic condensates of RNA-protein complexes. PBs are implicated in post-transcriptional regulation of gene expression through mRNA decay, translational repression and/or storage. Although much is known about the de novo formation of PBs and SGs involving liquid-liquid phase separation through multiple protein-protein and protein-RNA interactions, their subcellular localization and turnover mechanisms are less understood. Here, we report the presence of a subpopulation of PBs and SGs that are in proximity to ER-mitochondria contact sites (ERMCSs) in mammalian cells. Disruption of ERMCSs, achieved through depletion of ER-mitochondria tethering proteins, leads to the disappearance of PBs but not SGs. This effect can be reversed by inhibiting autophagy through both genetic and pharmacological means. Additionally, we find that the disruption of ERMCSs leads to cytosolic Ca2+-induced activation of CaMKK2 and AMP-activated protein kinase (AMPK), ultimately resulting in an autophagy-dependent decrease in PB abundance. Collectively, our findings unveil a mechanism wherein disturbances in ERMCSs induce autophagy-dependent loss of PBs via activation of the Ca2+-CaMKK2-AMPK pathway, thus potentially linking the dynamics and functions of ERMCS with post-transcriptional gene regulation.

Keywords:  Autophagy; CaMKK2; ER–mitochondria contact sites; P-bodies; Stress granules

DOI:  https://doi.org/10.1242/jcs.263652
Cell. 2025 Mar 06. pii: S0092-8674(25)00196-5. [Epub ahead of print]

Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells.

Nemanja Vukašinović, Che-Wei Hsu, Marco Marconi, Shaopeng Li, Christopher Zachary, Rachel Shahan, Pablo Szekley, Ziv Aardening, Isabelle Vanhoutte, Qian Ma, Lucrezia Pinto, Pavel Krupař, Nathan German, Jingyuan Zhang, Claire Simon-Vezo, Jessica Perez-Sancho, Pepe Cana Quijada, Qianzi Zhou, Laura R Lee, Jianghua Cai, Emmanuelle M Bayer, Matyáš Fendrych, Elisabeth Truernit, Yu Zhou, Sigal Savaldi-Goldstein, Krzysztof Wabnik, Trevor M Nolan, Eugenia Russinova.

  Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging of the Arabidopsis root, we reveal that brassinosteroid activity fluctuates throughout the cell cycle, decreasing during mitotic divisions and increasing during the G1 phase. The post-mitotic recovery of brassinosteroid activity is driven by the intrinsic polarity of the mother cell, resulting in one daughter cell with enhanced brassinosteroid signaling, while the other supports brassinosteroid biosynthesis. The coexistence of these distinct daughter cell states during the G1 phase circumvents a negative feedback loop to facilitate brassinosteroid production while signaling increases. Our findings uncover polarity-guided, uneven mitotic divisions in the meristem, which control brassinosteroid hormone activity to ensure optimal root growth.

Keywords:  brassinosteroids; cell cycle; cell division; cell polarity; live-cell imaging; root meristem; single-cell RNA sequencing

DOI:  https://doi.org/10.1016/j.cell.2025.02.011
J Cell Biol. 2025 Apr 07. pii: e202406054. [Epub ahead of print]224(4):

Vimentin filament transport and organization revealed by single-particle tracking and 3D FIB-SEM.

Bhuvanasundar Renganathan, Andrew S Moore, Wei-Hong Yeo, Alyson Petruncio, David Ackerman, Aubrey V Weigel, The CellMap Team, H Amalia Pasolli, C Shan Xu, Gleb Shtengel, Harald F Hess, Anna S Serpinskaya, Hao F Zhang, Jennifer Lippincott-Schwartz, Vladimir I Gelfand.

Vimentin intermediate filaments (VIFs) form complex, tightly packed networks; due to this density, traditional imaging approaches cannot discern single-filament behavior. To address this, we developed and validated a sparse vimentin-SunTag labeling strategy, enabling single-particle tracking of individual VIFs and providing a sensitive, unbiased, and quantitative method for measuring global VIF motility. Using this approach, we define the steady-state VIF motility rate, showing a constant ∼8% of VIFs undergo directed microtubule-based motion irrespective of subcellular location or local filament density. Significantly, our single-particle tracking approach revealed uncorrelated motion of individual VIFs within bundles, an observation seemingly at odds with conventional models of tightly cross-linked bundles. To address this, we acquired high-resolution focused ion beam scanning electron microscopy volumes of vitreously frozen cells and reconstructed three-dimensional VIF bundles, finding that they form only loosely organized, semi-coherent structures from which single VIFs frequently emerge to locally engage neighboring microtubules. Overall, this work demonstrates single VIF dynamics and organization in the cellular milieu for the first time.

DOI: https://doi.org/10.1083/jcb.202406054
Cell Death Differ. 2025 Mar 07.

c-Kit+ cells that intercalate with crypt Lgr5+ cells are distinctively multipotent in colonic epithelium renewal and repair.

Qing Xu, Yuting Zeng, Lan Jiang, Yongjie Zhou, Zhenru Wu, Shiyu Liu, Ruoting Men, Shujun Li, Jiayin Yang, Wei Huang, Yujun Shi.

The colonic crypts are principally composed by Lgr5+ stem cells and deep crypt secretory (DCS) cells. c-Kit-expressing cells mark DCS cells and supply Wnt3, EGF, and Notch signals to support their neighboring crypt bottom-intermingled Lgr5+ cells. However, the role of c-Kit+ cells beyond supporting Lgr5+ cells in colonic epithelium remains unexplored. Here, we identify that c-Kit+ cells are a heterogeneous entity and possess stemness potency to differentiate into the entire spectrum of epithelial cells and renew the homeostatic colon. Intriguingly, c-Kit+ cells play a pivotal role in epithelium repair in mouse models of colitis when contemporary Lgr5+ cells are insufficient or absent. Depletion of c-Kit+ cells or inhibition of SCF/c-Kit signaling worsens, while supplementation of SCF alleviates colonic epithelium injury during colitis. Our findings unravel the fate and function of c-Kit+ cells in homeostatic colon and recovery during colonic epithelium injury which has translational implications for human inflammatory bowel diseases.

DOI: https://doi.org/10.1038/s41418-025-01471-1
Nat Cardiovasc Res. 2025 Mar 07.

Genetic tracing and topography of spontaneous and stimulated cardiac regeneration in mice.

Ilaria Secco, Ana Backovic, Mateusz Tomczyk, Antonio Mura, Gang Li, Francesca Bortolotti, Simone Vodret, Matteo Dal Ferro, Elena Chiavacci, Lorena Zentilin, Gianfranco Sinagra, Serena Zacchigna, Miguel Mano, Mauro Giacca.

Despite recent efforts to stimulate endogenous cardiomyocyte proliferation for cardiac regeneration, the lack of reliable in vivo methods for monitoring cardiomyocyte replication has hindered our understanding of its mechanisms. Thymidine analogs, used to label proliferating cells, are unsuitable for long-term cardiac regeneration studies as their DNA incorporation elicits a damage response, leading to their elimination. Here we present CycleTrack, a genetic strategy based on the transcriptional activation of Cre recombinase from a temporally regulated cyclin B2 promoter segment, for permanent labeling of cardiomyocytes passing through the G2/M phase. Using CycleTrack, we visualized cardiomyocyte turnover in neonatal and adult mice under various conditions, including pregnancy, increased ventricular afterload, and myocardial infarction. CycleTrack also provided visual and quantitative evidence of ventricular remuscularization following treatment with pro-regenerative microRNAs. We identify the subendocardium as a key site of mitotic activity and provide a mode of cardiomyocyte division along their short axis. CycleTrack is a powerful tool to monitor cardiomyocyte renewal during regenerative interventions.

DOI: https://doi.org/10.1038/s44161-025-00623-3
Nature. 2025 Mar 12.

Hepatic stellate cells control liver zonation, size and functions via R-spondin 3.

Atsushi Sugimoto, Yoshinobu Saito, Guanxiong Wang, Qiuyan Sun, Chuan Yin, Ki Hong Lee, Yana Geng, Presha Rajbhandari, Celine Hernandez, Marcella Steffani, Jingran Qie, Thomas Savage, Dhruv M Goyal, Kevin C Ray, Taruna V Neelakantan, Deqi Yin, Johannes Melms, Brandon M Lehrich, Tyler M Yasaka, Silvia Liu, Michael Oertel, Tian Lan, Adrien Guillot, Moritz Peiseler, Aveline Filliol, Hiroaki Kanzaki, Naoto Fujiwara, Samhita Ravi, Benjamin Izar, Mario Brosch, Jochen Hampe, Helen Remotti, Josepmaria Argemi, Zhaoli Sun, Timothy J Kendall, Yujin Hoshida, Frank Tacke, Jonathan A Fallowfield, Storm K Blockley-Powell, Rebecca A Haeusler, Jonathan B Steinman, Utpal B Pajvani, Satdarshan P Monga, Ramon Bataller, Mojgan Masoodi, Nicholas Arpaia, Youngmin A Lee, Brent R Stockwell, Hellmut G Augustin, Robert F Schwabe.

Hepatic stellate cells (HSCs) have a central pathogenetic role in the development of liver fibrosis. However, their fibrosis-independent and homeostatic functions remain poorly understood1-5. Here we demonstrate that genetic depletion of HSCs changes WNT activity and zonation of hepatocytes, leading to marked alterations in liver regeneration, cytochrome P450 metabolism and injury. We identify R-spondin 3 (RSPO3), an HSC-enriched modulator of WNT signalling, as responsible for these hepatocyte-regulatory effects of HSCs. HSC-selective deletion of Rspo3 phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, liver size, regeneration and cytochrome P450-mediated detoxification, and exacerbates alcohol-associated and metabolic dysfunction-associated steatotic liver disease. RSPO3 expression decreases with HSC activation and is inversely associated with outcomes in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These protective and hepatocyte-regulating functions of HSCs via RSPO3 resemble the R-spondin-expressing stromal niche in other organs and should be integrated into current therapeutic concepts.

DOI: https://doi.org/10.1038/s41586-025-08677-w
Elife. 2025 Mar 13. pii: RP100797. [Epub ahead of print]13

GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis.

Joseph A Bisson, Miriam Gordillo, Ritu Kumar, Neranjan de Silva, Ellen Yang, Kelly M Banks, Zhong-Dong Shi, Kihyun Lee, Dapeng Yang, Wendy K Chung, Danwei Huangfu, Todd Evans.

  Haploinsufficiency for GATA6 is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers, suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hr of cardiac differentiation is sufficient to partially rescue CPC and CM defects in GATA6 heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by human GATA6 mutations.

Keywords:  cardiac progenitors; congenital heart disease; developmental biology; eomesodermin; heart development; human; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.100797
Proc Natl Acad Sci U S A. 2025 Mar 18. 122(11): e2416566122

Cell extrusion drives neural crest cell delamination.

Emma L Moore Zajic, Ruonan Zhao, Mary C McKinney, Kexi Yi, Christopher Wood, Paul A Trainor.

  Neural crest cells (NCC) comprise a heterogeneous population of cells with variable potency that contribute to nearly every tissue and organ throughout the body. Considered unique to vertebrates, NCC are transiently generated within the dorsolateral region of the neural plate or neural tube during neurulation. Their delamination and migration are crucial for embryo development as NCC differentiation is influenced by their final resting locations. Previous work in avian and aquatic species revealed that NCC delaminate via an epithelial-mesenchymal transition (EMT), which transforms these progenitor cells from static polarized epithelial cells into migratory mesenchymal cells with fluid front and back polarity. However, the cellular and molecular mechanisms facilitating NCC delamination in mammals are poorly understood. Through time-lapse imaging of NCC delamination in mouse embryos, we identified a subset of cells that exit the neuroepithelium as isolated round cells, which then halt for a short period prior to acquiring the mesenchymal migratory morphology classically associated with delaminating NCC. High-magnification imaging and protein localization analyses of the cytoskeleton, together with measurements of pressure and tension of delaminating NCC and neighboring neuroepithelial cells, revealed that round NCC are extruded from the neuroepithelium prior to completion of EMT. Furthermore, cranial NCC are extruded through activation of the mechanosensitive ion channel, PIEZO1. Our results support a model in which cell density, pressure, and tension in the neuroepithelium result in activation of the live cell extrusion pathway and delamination of a subpopulation of NCC in parallel with EMT, which has implications for cell delamination in development and disease.

Keywords:  cell extrusion; delamination; epithelial to mesenchymal transition; mouse embryo; neural crest cells

DOI:  https://doi.org/10.1073/pnas.2416566122
Nat Aging. 2025 Mar 13.

Interleukin-12 signaling drives Alzheimer's disease pathology through disrupting neuronal and oligodendrocyte homeostasis.

Shirin Schneeberger, Seung Joon Kim, Maria N Geesdorf, Ekaterina Friebel, Pascale Eede, Marina Jendrach, Anastasiya Boltengagen, Caroline Braeuning, Torben Ruhwedel, Andreas J Hülsmeier, Niclas Gimber, Marlene Foerster, Juliane Obst, Myrto Andreadou, Sarah Mundt, Jan Schmoranzer, Stefan Prokop, Wiebke Kessler, Tanja Kuhlmann, Wiebke Möbius, Klaus-Armin Nave, Thorsten Hornemann, Burkhard Becher, Julia M Edgar, Nikos Karaiskos, Christine Kocks, Nikolaus Rajewsky, Frank L Heppner.

Neuroinflammation including interleukin (IL)-12/IL-23-signaling is central to Alzheimer's disease (AD) pathology. Inhibition of p40, a subunit of IL-12/IL-23, attenuates pathology in AD-like mice; however, its signaling mechanism and expression pattern remained elusive. Here we show that IL-12 receptors are predominantly expressed in neurons and oligodendrocytes in AD-like APPPS1 mice and in patients with AD, whereas IL-23 receptor transcripts are barely detectable. Consistently, deletion of the IL-12 receptor in neuroectodermal cells ameliorated AD pathology in APPPS1 mice, whereas removal of IL-23 receptors had no effect. Genetic ablation of IL-12 signaling alone reverted the loss of mature oligodendrocytes, restored myelin homeostasis, rescued the amyloid-β-dependent reduction of parvalbumin-positive interneurons and restored phagocytosis-related changes in microglia of APPPS1 mice. Furthermore, IL-12 protein expression was increased in human AD brains compared to healthy age-matched controls, and human oligodendrocyte-like cells responded profoundly to IL-12 stimulation. We conclude that oligodendroglial and neuronal IL-12 signaling, but not IL-23 signaling, are key in orchestrating AD-related neuroimmune crosstalk and that IL-12 represents an attractive therapeutic target in AD.

DOI: https://doi.org/10.1038/s43587-025-00816-2
Cell Stem Cell. 2025 Mar 06. pii: S1934-5909(25)00044-X. [Epub ahead of print]32(3): 333-335

Overcoming gene dosage barriers in mammalian development: An imprinting balancing act.

Zhengfeng Liu, Marisa S Bartolomei.

Genomic imprinting ensures parent-of-origin gene expression and prevents uniparental development. In this issue of Cell Stem Cell, Li et al.1 extensively engineered androgenic haploid embryonic stem cells to overcome imprinting barriers, producing adult bi-paternal mice, albeit with low efficiency, and providing insights into roles of imprinted genes in development.

DOI: https://doi.org/10.1016/j.stem.2025.02.005
Gastroenterology. 2025 Mar 03. pii: S0016-5085(25)00465-2. [Epub ahead of print]

Mucosal macrophages govern intestinal regeneration in response to injury.

Ilias Moraitis, Jasin Taelman, Borja Arozamena, Loris Mularoni, Olga Wienskowska, Xavier Sanjuan Garriga, Laura Arregui, Milica Stefanovic, Ignasi Modolell Farré, Ferran Guedea, Mònica Diaz, Jordi Guiu.

   BACKGROUND & AIMS: Cancer patients treated with radiotherapy in the abdominal and pelvic cavity develop radiation-induced enteritis, a condition that impairs their quality of life. Radiation injury depletes proliferative intestinal stem cells (ISCs); in response to this, the epithelium activates a regenerative program that facilitates the healing of the intestine. However, the mechanisms that induce the activation of the intestinal regenerative program are poorly characterized.
METHODS: In this study, we induced radiation-induced enteritis in mice through abdominal irradiation, mimicking clinical scenarios. Through imaging and flow cytometric analysis, we investigated the recruitment of macrophages to the small intestine during injury and healing. Additionally, we developed a co-culture system for mouse and human intestinal organoids and macrophages to explore the crosstalk between these cells. Then combining in vivo ablation of macrophages, fluorescent lineage tracing, imaging, bulk RNA-sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), human intestinal organoids and cell trajectory analysis, we study at cellular and molecular level the macrophage induction of intestinal regeneration.
RESULTS: Our findings revealed that macrophages are recruited around the intestinal stem cell compartment upon radiation injury, promoting a fetal-like reprogramming and proliferation of epithelial cells that drives the regeneration process. In contrast macrophage ablation led to compromised regeneration. Moreover, our scRNA-seq analysis identified key secreted molecules, nrg1 and spp1, as pivotal players in regulating this process. Additionally, characterization of human macrophage/organoid co-cultures and cell trajectory inference confirmed the conservation of macrophages' role in triggering the regenerative program in primary human cells.
CONCLUSIONS: This study identifies macrophages as essential contributors to intestinal regeneration beyond their innate immune response. Targeting macrophages therapeutically may hold promise in enhancing regeneration and improving the quality of life for cancer survivors.

Keywords:  Inflammation; Macrophages; Nrg1; Radiation-induced enteritis; Spp1; intestinal organoids; intestinal regeneration

DOI:  https://doi.org/10.1053/j.gastro.2025.01.252
Nat Rev Mol Cell Biol. 2025 Mar 10.

Modes of Notch signalling in development and disease.

Sarah J Bray, Anna Bigas.

Many different animal developmental and homeostatic processes rely on signalling via the highly conserved Notch pathway. Often Notch signalling has iterative roles during cell specification and differentiation, controlling not only the state of progenitor cells but also the fate and function of their progeny. Its roles continue throughout the lifespan of the organism, regulating normal tissue maintenance, as well as operating in response to damage. Consistent with such fundamental roles, the pathway has been associated with numerous diseases, including cancers. Understanding how Notch signalling is orchestrated to bring about different outcomes is challenging, given that it has many diverse functions. Classic models proposed that stochastic differences in cell states were important to polarise signalling during cell fate decisions. Subsequently, the importance of oscillatory Notch signalling was uncovered, and it became clear that it operates in different modalities depending on the regulatory inputs. With the advent of ever-more-sensitive live-imaging and quantitative approaches, it is becoming evident that differences in the dynamics, levels and architectures of Notch signalling are critical in shaping and maintaining tissues. This Review focuses on the cellular and molecular mechanisms involved in conferring different modalities on Notch pathway operations and how these enable different types of functional outcomes from pathway activation. We also discuss their dysregulation in cancer.

DOI: https://doi.org/10.1038/s41580-025-00835-2
Circulation. 2025 Mar 12.

Myeloid Fatty Acid Metabolism Activates Neighboring Hematopoietic Stem Cells to Promote Heart Failure With Preserved Ejection Fraction.

Mallory Filipp, Zhi-Dong Ge, Matthew DeBerge, Connor Lantz, Kristofor Glinton, Peng Gao, Sasha Smolgovsky, Jingbo Dai, You-Yang Zhao, Laurent Yvan-Charvet, Pilar Alcaide, Samuel E Weinberg, Gabriele G Schiattarella, Joseph A Hill, Matthew J Feinstein, Sanjiv J Shah, Edward B Thorp.

   BACKGROUND: Despite the high morbidity and mortality of heart failure with preserved ejection fraction (HFpEF), treatment options remain limited. The HFpEF syndrome is associated with a high comorbidity burden, including high prevalence of obesity and hypertension. Although inflammation is implicated to play a key role in HFpEF pathophysiology, underlying causal mechanisms remain unclear.
METHODS: Comparing patient samples and animal models, we defined the innate immune response during HFpEF in situ and through flow cytometry and single-cell RNA sequencing. After identifying transcriptional and cell signatures, we implemented a high-fat diet and hypertensive model of HFpEF and tested roles for myeloid and hematopoietic stem cells during HFpEF. Contributions of macrophage metabolism were also evaluated, including through mass spectrometry and carbon labeling. Primary macrophages were studied ex vivo to gain insight into complementary cell-intrinsic mechanisms.
RESULTS: Here we report evidence that patients with cardiometabolic HFpEF exhibit elevated peripheral blood hematopoietic stem cells. This phenotype was conserved across species in a murine mode of high-fat diet and hypertension. Hematopoietic stem cell proliferation was coupled to striking remodeling of the peripheral hematopoietic stem cell niche and expression of the macrophage adhesion molecule Vcam1. This could be partially inhibited by sodium-glucose cotransporter-2 inhibitors and explained by elevated fatty acid metabolism in macrophage mitochondria, which in turn remodeled the Vcam1 promoter to enhance its expression.
CONCLUSIONS: These findings identify a significant new stem cell signature of cardiometabolic HFpEF and support a role for myeloid maladaptive fatty acid metabolism in the promotion of systemic inflammation and cardiac diastolic dysfunction.

Keywords:  heart failure; hematopoiesis; inflammation; macrophages; metabolism; stem cells

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.124.070248
Curr Opin Cell Biol. 2025 Mar 06. pii: S0955-0674(25)00028-6. [Epub ahead of print]94 102490

Aneuploidy as a cancer vulnerability.

Jinghui Cao, Cai Liang, Hongtao Yu.

Aneuploidy is prevalent in cancer and has complicated roles in tumorigenesis. Paradoxically, artificially engineered aneuploidy in normal cells reduces cellular fitness by inducing proteotoxic and genotoxic stresses. A better molecular understanding of the multifaceted roles of aneuploidy in cancer evolution offers promising avenues for future cancer therapies. Here, we discuss the patterns and consequences of aneuploidy in human cancer. We highlight recent efforts to explore aneuploidy as a cancer vulnerability and new interventions that exploit this vulnerability for cancer treatment.

DOI: https://doi.org/10.1016/j.ceb.2025.102490