bims-ginsta 2025-12-21 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–12–21
33 papers selected by
Jinrong Hu, National University of Singapore

The G3BP stress-granule proteins reinforce the integrated stress response translation programme.
Spatial patterning of the epigenome during vertebrate gastrulation.
Mechanical feedback between a transient core cell and a contractile valve ensures robust organ morphogenesis in C. elegans.
Spatiotemporal cellular map of the developing human reproductive tract.
Permeability-driven pressure and cell proliferation control lumen morphogenesis in pancreatic organoids.
Unequal mitochondrial segregation promotes asymmetric fates during neurogenesis.
Escape from X inactivation is directly modulated by Xist noncoding RNA.
5' UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins.
Autophagy-regulated mitochondrial inheritance controls early CD8+ T cell fate commitment.
Modelling co-development between the somites and neural tube in human trunk-like structures.
Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.
Mitochondrial RNA cytosolic leakage drives the SASP.
Nucleophosmin supports WNT-driven hyperproliferation and tumor initiation.
Subcellular In Vivo Cardiac Proteomics Reveals Sarcomere and Ribosome Interactomes and skNAC's Impact on Cardiac Proteostasis.
GDF3 promotes adipose tissue macrophage-mediated inflammation via altered chromatin accessibility during aging.
Multistep genomics on single cells and live cultures in subnanoliter capsules.
Resident phagocytes promote non-cell-autonomous fragmentation of apoptotic cells.
Inhibiting translation elongation by reducing eIF5A activity induces feedback inhibition of initiation, limiting tumour cell proliferation.
Keratin intermediate filaments mechanically position melanin pigments for genome photoprotection.
CRISPRa-mediated disentanglement of the Dux-MERVL axis in the 2C-like state, totipotency, and cell death.
Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment.
Prodrug nanoplatform for triggering ferroptosis to eliminate senescent cells in age-associated pathologies.
Neural stem cell quiescence is actively maintained by the epigenome.
α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis.
HLA export by melanoma cells decoys cytotoxic T cells to promote immune evasion.
TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability.
Abrogation of aberrant glycolytic interactions eliminates senescent cells and alleviates aging-related dysfunctions.
Force Transmission by Minimal Focal Adhesion Complexes Induces Synthetic Cell Deformation.
A Chemically Switchable Synthetic Condensate Platform for Reversible Protein Sequestration and Release.
Human assembloids recapitulate periportal liver tissue in vitro.
Asymmetrical recognition and processing of double-strand breaks formed during DNA replication.
Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell.
TMEM65-dependent Ca2+ extrusion safeguards mitochondrial homeostasis.

Nat Cell Biol. 2025 Dec 19.

The G3BP stress-granule proteins reinforce the integrated stress response translation programme.

Jarrett Smith, David P Bartel.

When mammalian cells are exposed to stress, they co-ordinate the condensation of stress granules (SGs) through the action of proteins G3BP1 and G3BP2 (G3BPs) and, simultaneously, undergo a massive reduction in translation. Although SGs and G3BPs have been linked to this translation response, their overall impact has been unclear. Here we investigate the question of how, and indeed whether, G3BPs and SGs shape the stress translation response. We find that SGs are enriched for mRNAs that are resistant to the stress-induced translation shutdown. Although the accurate recruitment of these stress-resistant mRNAs does require the context of stress, a combination of optogenetic tools and spike-normalized ribosome profiling demonstrates that G3BPs and SGs are necessary and sufficient to both help prioritize the translation of their enriched mRNAs and help suppress cytosolic translation. Together, these results support a model in which G3BPs and SGs reinforce the stress translation programme by prioritizing the translation of their resident mRNAs.

DOI: https://doi.org/10.1038/s41556-025-01834-3
Nat Commun. 2025 Dec 15.

Spatial patterning of the epigenome during vertebrate gastrulation.

Ana Paula Azambuja, Megan Rothstein, Tatiane Y Kanno, Marcos Simoes-Costa.

A central question in developmental biology is how embryonic cells acquire and store positional information during pattern formation. In vertebrates, this process begins with the localized activation of signaling systems that mediate axial specification. How these spatial cues are recorded within the regulatory landscape of cells has remained unclear. Here, we report that the chromatin landscape of embryonic cells is spatially patterned during gastrulation. Using spatially resolved genomic analysis in avian embryos, we observed that the epigenome becomes organized in gradients of accessibility and activity along the embryonic axes. These chromatin gradients are established within the loci of developmental genes at the onset of gastrulation and can be used to infer the position of cells in the embryo. Our results show that axial specification involves the spatial organization of the epigenome, linking patterns of chromatin activity to the emergence of the embryonic body plan.

DOI: https://doi.org/10.1038/s41467-025-67491-0
Curr Biol. 2025 Dec 15. pii: S0960-9822(25)01551-9. [Epub ahead of print]

Mechanical feedback between a transient core cell and a contractile valve ensures robust organ morphogenesis in C. elegans.

Meghna Suhag, Ronen Zaidel-Bar.

  Organ morphogenesis requires tightly coordinated changes in cell shape and position, sometimes aided by transient cellular structures. In the C. elegans reproductive system, formation of the spermatheca-uterine valve involves a transient "core cell," but its function has remained unknown. Using long-term live imaging, cell-specific genetic perturbations, and biophysical assays, we show that the core cell mechanically guides valve morphogenesis through two mechanisms: it directs a sliding cell-cell junction that facilitates expansion of the valve's apical domain, and it promotes assembly of a contractile actomyosin network within the valve cell, essential for valve contraction and animal fertility. Ablation or softening of the transient core cell disrupted valve contractility and revealed a mechanical feedback loop in which resistance from the core cell reinforces actomyosin assembly in the valve. Our findings highlight how transient scaffold cells can coordinate morphogenesis in neighboring cells, ensuring precise and robust organ formation.

Keywords:  C. elegans; actomyosin; cell polarization; cell-cell adhesion; cellular valve; gonad; lumen formation; morphogenesis; reproduction; scaffold

DOI:  https://doi.org/10.1016/j.cub.2025.11.044
Nature. 2025 Dec 17.

Spatiotemporal cellular map of the developing human reproductive tract.

Valentina Lorenzi, Cecilia Icoresi-Mazzeo, Charlotte Cassie, Nadav Yayon, Elias R Ruiz-Morales, Carmen Sancho-Serra, Ryan Colligan, Frederick C K Wong, Magda Marečková, Elizabeth Tuck, Kenny Roberts, Tong Li, Marc-Antoine Jacques, James Ashcroft, Xiaoling He, Berta Crespo, Batuhan Cakir, Simon Murray, Yong Gu, Alexander V Predeus, Martin Prete, Iva Kelava, Roger Barker, Luz Garcia-Alonso, John C Marioni, Roser Vento-Tormo.

The human reproductive tract is essential for species perpetuation and overall health. Its development involves complex processes of sex specification, tissue patterning and morphogenesis, the disruption of which can cause lifelong issues, including infertility1-5. Here we present an extensive single-cell and spatial multi-omic atlas of the human reproductive tract during prenatal development to provide insights beyond those that are possible with smaller-scale, organ-focused studies. We describe potential regulators of sexual dimorphism in reproductive organs and pinpoint previously unknown genes involved in Müllerian duct emergence and regression and urethral canalization of the penis. By combining histological features with gene expression and chromatin accessibility data, we define transcription factors and signalling events potentially involved in the regionalization of the Müllerian and Wolffian ducts. We also refine how the HOX code is established in distinct reproductive organs and reveal that the expression of thoracic HOX genes is increased in the rostral mesenchyme of the fallopian tube and epididymis. Our findings further indicate that epithelial regionalization of the fallopian tube and epididymis, which probably contribute to sperm maturation and capacitation, is established during development. By contrast, later events are necessary for regionalization of the uterocervical canal epithelium. Finally, on the basis of single-cell data and fetal-derived organoids, we show that the fetal uterine epithelium is vulnerable to oestrogen-mimicking endocrine disruptors. By mapping sex-specific reproductive tract regionalization and differentiation at the cellular level, our study provides valuable insights into causes and potential treatments of developmental reproductive disorders.

DOI: https://doi.org/10.1038/s41586-025-09875-2
Nat Cell Biol. 2025 Dec 19.

Permeability-driven pressure and cell proliferation control lumen morphogenesis in pancreatic organoids.

Byung Ho Lee, Kana Fuji, Heike Petzold, Phil Seymour, Siham Yennek, Coline Schewin, Allison Lewis, Daniel Riveline, Tetsuya Hiraiwa, Masaki Sano, Anne Grapin-Botton.

Lumen formation in organ epithelia involves processes such as polarization, secretion, exocytosis and contractility, but what controls lumen shape remains unclear. Here we study how lumina develop spherical or complex structures using pancreatic organoids. Combining computational phase-field modelling and experiments, we found that lumen morphology depends on the balance between cell cycle duration and lumen pressure, low pressure and high proliferation produce complex shapes. Manipulating proliferation and lumen pressure can alter or reverse lumen development both in silico and in vitro. Increasing epithelial permeability reduces lumen pressure, converting from spherical to complex lumina. During pancreas development, the epithelium is initially permeable and becomes sealed, experimentally increasing permeability at late stages impairs ductal morphogenesis. Overall, our work underscores how proliferation, pressure and permeability orchestrate lumen shape, offering insights for tissue engineering and cystic disease treatment.

DOI: https://doi.org/10.1038/s41556-025-01832-5
Nat Commun. 2025 Dec 15. 16(1): 11049

Unequal mitochondrial segregation promotes asymmetric fates during neurogenesis.

Benjamin Bunel, Rémi Leclercq, Rosette Goïame, Arnaud Gautier, Xavier Morin, Evelyne Fischer.

Asymmetric cell division plays a critical role during vertebrate neurogenesis by generating neuronal cells while maintaining a pool of progenitors. It relies on unequal distribution of cell fate determinants during progenitor division. Here, we use live imaging in the chick embryonic neuroepithelium to demonstrate that mitochondria behave as asymmetric fate determinants during mitosis. We show that the frequency of unequal distribution of mitochondria increases in parallel with the rate of asymmetric divisions during development. Furthermore, fate tracking experiments reveals that following progenitor division, a cell inheriting fewer mitochondria than its sister consistently differentiates into a neuron. We set up a chemogenetic approach to experimentally displace mitochondria specifically during mitosis to force their unequal inheritance and find that this drives premature neuronal differentiation. In this work, we establish a direct causal relationship between unequal mitochondrial inheritance and the asymmetric fate of sister cells in vivo, revealing a pivotal mechanism for neurogenesis.

DOI: https://doi.org/10.1038/s41467-025-66932-0
Nat Cell Biol. 2025 Dec 15.

Escape from X inactivation is directly modulated by Xist noncoding RNA.

Antonia Hauth, Jasper Panten, Emma Kneuss, Christel Picard, Nicolas Servant, Isabell Rall, Yuvia A Pérez-Rico, Lena Clerquin, Nila Servaas, Laura Villacorta, Ferris Jung, Christy Luong, Howard Y Chang, Judith B Zaugg, Oliver Stegle, Duncan T Odom, Edith Heard, Agnese Loda.

In placental XX females, one X chromosome is silenced during a narrow developmental time window by X-chromosome inactivation, which is mediated by Xist noncoding RNA. Although most X-linked genes are silenced during X-chromosome inactivation, some genes can escape. Here, by increasing its endogenous level, we show that Xist RNA can silence escapees well beyond early embryogenesis both in vitro, in differentiated cells, as well as in vivo, in mouse pre- and post-implantation embryos. We further demonstrate that Xist RNA plays a role in eliminating topologically associating domain-like structures spanning clusters of escapees, and this is dependent on SPEN. The function of Xist in silencing escapees and eliminating topological domains is initially fully reversible, but sustained Xist upregulation leads to irreversible silencing and CpG island DNA methylation of escapees. Thus, gene activity and three-dimensional topology of the inactive X chromosome are directly controlled by Xist, well beyond an early developmental time window.

DOI: https://doi.org/10.1038/s41556-025-01823-6
Cell Rep. 2025 Dec 12. pii: S2211-1247(25)01434-2. [Epub ahead of print]44(12): 116662

5' UTR-mediated retention of eIF3 on 80S ribosomes promotes co-translational folding of ER membrane proteins.

Baochun Han, Siqiong Zhang, Yurui Zhang, Binbin Yu, Weimin Lin, Yabin Cheng, Haoran Duan, Dieter A Wolf.

  Co-translational folding of nascent polypeptides is essential for protein function and cellular homeostasis. Ribosome-associated chaperones assist in this process, but coordination between their recruitment and translation initiation remains poorly understood. We report here that specific binding sites for eukaryotic translation initiation factor eIF3 within the 5' UTRs of mRNAs promote its retention on 80S ribosomes during the synthesis of select endoplasmic reticulum (ER) membrane proteins. Disruption of these eIF3 binding sites leads to misfolding and sequestration of newly synthesized membrane proteins into ER whorls. Sequestration into ER whorls is exacerbated by HSP70 inhibition but can be rescued by overexpressing HSPA1 and HSPA8. Cross-linking assays reveal that 5' UTR binding sites stabilize eIF3-80S interactions during early elongation, facilitating recruitment of HSPA1 and HSPA8 to ribosomes. These findings indicate that genetic instructions within 5' UTRs direct eIF3-mediated chaperone recruitment, ensuring proper co-translational folding of ER membrane proteins.

Keywords:  5′ UTR; CP: molecular biology; ER membrane proteins; ER whorls; HSP70 chaperones; co-translational folding; eIF3

DOI:  https://doi.org/10.1016/j.celrep.2025.116662
Nat Cell Biol. 2025 Dec 19.

Autophagy-regulated mitochondrial inheritance controls early CD8+ T cell fate commitment.

Mariana Borsa, Ana Victoria Lechuga-Vieco, Amir H Kayvanjoo, Edward Jenkins, Yavuz Yazicioglu, Ewoud B Compeer, Felix C Richter, Simon Rapp, Robert Mitchell, Tom Youdale, Hien Bui, Emilia Kuuluvainen, Michael L Dustin, Linda V Sinclair, Pekka Katajisto, Anna Katharina Simon.

T cell immunity deteriorates with age, accompanied by a decline in autophagy and asymmetric cell division. Here we show that autophagy regulates mitochondrial inheritance in CD8+ T cells. Using a mouse model that enables sequential tagging of mitochondria in mother and daughter cells, we demonstrate that autophagy-deficient T cells fail to clear premitotic old mitochondria and inherit them symmetrically. By contrast, autophagy-competent cells that partition mitochondria asymmetrically produce daughter cells with distinct fates: those retaining old mitochondria exhibit reduced memory potential, whereas those that have not inherited old mitochondria and exhibit higher mitochondrial turnover are long-lived and expand upon cognate-antigen challenge. Multiomics analyses suggest that early fate divergence is driven by distinct metabolic programmes, with one-carbon metabolism activated in cells retaining premitotic mitochondria. These findings advance our understanding of how T cell diversity is imprinted early during division and support the development of strategies to modulate T cell function.

DOI: https://doi.org/10.1038/s41556-025-01835-2
Nat Cell Biol. 2025 Dec;27(12): 2049-2062

Modelling co-development between the somites and neural tube in human trunk-like structures.

Komal Makwana, Louise Tilley, Probir Chakravarty, Jamie Thompson, Peter Baillie-Benson, Ignacio Rodriguez-Polo, Naomi Moris.

Human stem cell-based embryo models provide experimentally amenable in vitro systems for developmental research. A key feature of embryo models is their multi-lineage differentiation, which allows for the study of tissue co-development. Here we develop human trunk-like structures that have morphologically organized somites and a neural tube that form through self-organized, endogenous signalling. Transcriptomic comparison with human embryo datasets suggests that human trunk-like structure cells approximate Carnegie stage 13-14 (28-35 days after fertilization). The absence of a notochord leads to a dorsal identity, but exogenous Sonic Hedgehog signalling activation ventralizes both the somites and the neural tube in a dose-dependent manner. We further identify reciprocal signalling: neural tube-derived cues induce medial ALDH1A2 in somites, which in turn generate retinoic acid signals that drive spontaneous neural-tube patterning. Together, our data highlight the value of modularity in embryo models, which we leverage to explore human trunk co-development.

DOI: https://doi.org/10.1038/s41556-025-01813-8
Nat Commun. 2025 Dec 19.

Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.

Meghana S Oak, Marco Stock, Ana Janeva, Matthias Mezes, Antony M Hynes-Allen, Tobias Straub, Ignasi Forné, Andreas Ettinger, Stephan Hamperl, Axel Imhof, Jelle van den Ameele, Antonio Scialdone, Eva Hörmanseder.

In vertebrate embryos, gene expression is first initiated at zygotic genome activation (ZGA). Maternally expressed transcription factors are essential for this process. However, it is unknown whether active chromatin modifications established in gametes are present in early embryos and contribute to ZGA and embryonic development. Here, we show that in Xenopus laevis, H3K4me3 occurs at common genomic loci in gametes, in transcriptionally quiescent pre-ZGA embryos, and in transcriptionally active ZGA embryos. These loci exhibit high H3K4me3 intensities and breadth, DNA hypomethylation, and elevated CpG content. We show that H3K4 methylation pre-marking is required for successful ZGA and development, including expression of the key ZGA transcription factor Pou5f3.2. We demonstrate that the H3K4 methyltransferase Cxxc1 ensures establishment of H3K4me3 and proper ZGA. These findings reveal a role for H3K4 methylation in defining active chromatin states in Xenopus laevis embryos and highlight its importance for accurate ZGA and embryonic development.

DOI: https://doi.org/10.1038/s41467-025-67692-7
Nat Commun. 2025 Dec 15. 16(1): 10992

Mitochondrial RNA cytosolic leakage drives the SASP.

Stella Victorelli, Madeline Eppard, Hélène Martini, Seung-Hwa Woo, Stacia P A Everts, Gung Lee, Nicholas Pirius, Nuan Han, Eugene Y Liang, Ana Catarina Franco, Yeaeun Han, Dominik Saul, Eva Nóvoa, Rubén Nogueiras, Patrick L Splinter, Steven P O'Hara, Olivia Morgenthaler, Lucía Valenzuela-Pérez, Hyun Se Kim Lee, Diana Jurk, Nicholas F LaRusso, Petra Hirsova, João F Passos.

Senescent cells secrete proinflammatory factors known as the senescence-associated secretory phenotype (SASP), contributing to tissue dysfunction and aging. Mitochondrial dysfunction is a key feature of senescence, influencing SASP via mitochondrial DNA (mtDNA) release and cGAS/STING pathway activation. Here, we demonstrate that mitochondrial RNA (mtRNA) also accumulates in the cytosol of senescent cells, activating RNA sensors RIG-I and MDA5, leading to MAVS aggregation and SASP induction. Inhibition of these RNA sensors significantly reduces SASP factors. Furthermore, BAX and BAK play a key role in mtRNA leakage during senescence, and their deletion diminishes SASP expression in vitro and in a mouse model of Metabolic Dysfunction-Associated Steatohepatitis (MASH). These findings highlight mtRNA's role in SASP regulation and its potential as a therapeutic target for mitigating age-related inflammation.

DOI: https://doi.org/10.1038/s41467-025-66159-z
Nat Genet. 2025 Dec 18.

Nucleophosmin supports WNT-driven hyperproliferation and tumor initiation.

Georgios Kanellos, Chiara Giacomelli, Alexander Raven, Nikola Vlahov, Hu Jin, Pauline Herviou, Sudhir B Malla, Nadia Nasreddin, Patricia P Centeno, Constantinos Alexandrou, Kathryn Gilroy, Rachel L Baird, Kathryn Pennel, June Munro, Joseph A Waldron, Holly Hall, Leah Officer-Jones, Sheila Bryson, Douglas Strathdee, Sergio Lilla, Sara Zanivan, Vivienne Morrison, Colin Nixon, Rachel A Ridgway, Crispin Miller, John R P Knight, Andrew D Campbell, Philip D Dunne, John Le Quesne, Joanne Edwards, Peter J Park, Martin Bushell, Owen J Sansom.

Nucleophosmin (NPM1), a nucleolar protein frequently mutated in hematopoietic malignancies, is overexpressed in several solid tumors with poorly understood functional roles. Here, we demonstrate that Npm1 is upregulated after APC loss in WNT-responsive tissues and supports WNT-driven intestinal and liver tumorigenesis. Mechanistically, NPM1 loss induces ribosome pausing and accumulation at the 5'-end of coding sequences, triggering a protein synthesis stress response and p53 activation, which mediate this antitumorigenic effect. Collectively, our data identify NPM1 as a critical WNT effector that sustains WNT-driven hyperproliferation and tumorigenesis by attenuating the integrated stress response and p53 activation. Notably, NPM1 expression correlates with elevated WNT signaling and proliferation in human colorectal cancer (CRC), while CRCs harboring NPM1 deletions exhibit preferential TP53 inactivation, underscoring the clinical relevance of our findings. Being dispensable for adult epithelial homeostasis, NPM1 represents a promising therapeutic target in p53-proficient WNT-driven tumors, including treatment-refractory KRAS-mutant CRC, and hepatic cancers.

DOI: https://doi.org/10.1038/s41588-025-02408-7
Circ Res. 2025 Dec 15.

Subcellular In Vivo Cardiac Proteomics Reveals Sarcomere and Ribosome Interactomes and skNAC's Impact on Cardiac Proteostasis.

Rami Haddad, Omer Sadeh, Tamar Ziv, Nardeen Shehdeh, Nadav Keren, Izhak Kehat.

   BACKGROUND: Proteostasis and the regulation of protein folding and sorting play a critical role in maintaining cellular homeostasis. The failure of proteostasis contributes to heart failure and aging, but, despite its importance, the mechanisms and factors regulating proteostasis in cardiomyocytes remain poorly characterized.
METHODS: Subcellular proteomes of cardiomyocytes were analyzed in vivo using biotin proximity labeling in mouse hearts. We employed a novel homology-independent targeting integration strategy for genetic tagging and for substitution of the muscle-specific skNAC (skeletal nascent polypeptide-associated complex alpha isoform) isoform with the ubiquitous short isoform in cardiomyocytes.
RESULTS: We identified hundreds of proteins localized to the Z- and M-lines of sarcomeres, the ribosomes, and the desmosomes, including multiple chaperones. A universal homology-independent targeted integration strategy allowed us to genetically tag endogenous genes in the mouse heart and confirm protein localization. We identified the large muscle-specific isoform of the nascent polypeptide-associated complex protein skNAC as a Z-line and ribosome-associated protein. Replacement of skNAC with a ubiquitous isoform induced dilated cardiomyopathy, accompanied by altered ribosome positioning and markedly reduced mitochondrial protein levels.
CONCLUSIONS: We unraveled the cardiomyocyte subcellular proteome and show that skNAC, an isoform downregulated in disease, is a key ribosome and Z-line-associated protein responsible for cardiomyocyte proteostasis.

Keywords:  biotin; desmosomes; heart failure; mitochondria; proteostasis

DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326929
Nat Aging. 2025 Dec 15.

GDF3 promotes adipose tissue macrophage-mediated inflammation via altered chromatin accessibility during aging.

In Hwa Jang, Anna Carey, Victor Kruglov, Katie Nguyen, Jeffrey R Misialek, Stephanie H Cholensky, Declan M Smith, Suxia Bai, Timothy Nottoli, David A Bernlohr, Pamela L Lutsey, Christina D Camell.

Aging is characterized by amplified inflammation, including proinflammatory macrophages and increased susceptibility to endotoxemia. Here we uncover a mechanism by which macrophages maintain their inflammatory phenotype through autocrine GDF3-SMAD2/3 signaling, which ultimately exacerbates endotoxemia. We show that inflammatory adipose tissue macrophages display an age-dependent increase in GDF3, a TGFβ-family cytokine. Lifelong systemic or myeloid-specific Gdf3 deletion leads to reduced endotoxic inflammation. Using pharmacological interventions to modulate the GDF3-SMAD2/3 axis, we demonstrate its role in regulating the inflammatory adipose tissue macrophage phenotype and endotoxemia lethality in old mice. Mechanistically, single-cell RNA sequencing and assay for transposase-accessible chromatin with sequencing analyses suggest that GDF3 induces a shift toward an inflammatory state by limiting methylation-dependent chromatin compaction. Leveraging human adipose tissue samples and 11,084 participants from the atherosclerosis risk in communities study, we validate the relevance of GDF3 to aging in humans. These findings position the GDF3-SMAD2/3 axis as a critical driver of age-associated chromatin remodeling and a promising therapeutic target for mitigating macrophage-related inflammation in aging.

DOI: https://doi.org/10.1038/s43587-025-01034-6
Science. 2025 Dec 18. eady7209

Multistep genomics on single cells and live cultures in subnanoliter capsules.

Ignas Mazelis, Haoxiang Sun, Arpita Kulkarni, Theresa L Torre, Allon M Klein.

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multistep assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and their extension to live-cell assays.

DOI: https://doi.org/10.1126/science.ady7209
Sci Adv. 2025 Dec 19. 11(51): eadz5264

Resident phagocytes promote non-cell-autonomous fragmentation of apoptotic cells.

Jascinta P Santavanond, Georgia K Atkin-Smith, Irene Lozano-González, Joan Roncero-Carol, Lanzhou Jiang, Amy L Hodge, Dilara C Ozkocak, Kelin Zhao, Daniel H D Gray, Marco J Herold, Andrew J Kueh, Gemma F Ryan, Rochelle Tixeira, Michael F Olson, Mark D Hulett, Amy A Baxter, Ivan K H Poon, Esteban Hoijman.

Phagocytosis of apoptotic cells maintains tissue homeostasis and regulates inflammation. A proposed facilitator of apoptotic cell clearance is the fragmentation of these cells into apoptotic bodies (ApoBDs) through cell-autonomous processes involving caspases and cytoskeletal rearrangement. Although this fragmentation process is considered a hallmark of apoptosis, its progression in tissue environments remains underexplored. Here, we examine the in vivo apoptotic dynamics of mouse thymocytes and pluripotent cells from zebrafish embryos. We show that the in vivo biogenesis of ApoBDs is independent of known cell-intrinsic regulators. Instead, fragmentation depends on actin-rich protrusions from neighboring resident phagocytes, which mechanically compress apoptotic cells to break them into smaller particles. Four-dimensional in vivo tracking of apoptotic cells reveals that both phagocyte-mediated fragmentation and phagocytosis are size sensitive, indicating that apoptotic size reduction mediated by phagocytes enhances their own clearance abilities. This non-cell-autonomous fragmentation ensures rapid apoptotic cell clearance, crucial for maintaining tissue homeostasis in physiological settings.

DOI: https://doi.org/10.1126/sciadv.adz5264
Nat Commun. 2025 Dec 13.

Inhibiting translation elongation by reducing eIF5A activity induces feedback inhibition of initiation, limiting tumour cell proliferation.

Aristeidis P Sfakianos, Rebecca M Raven, Tom Smith, Xiao-Ming Sun, Thomas E Mulroney, Mariavittoria Pizzinga, Veronica Dezi, Angela Rubio Tenor, Mark Stoneley, Cameron H Cole, Karam Al-Doori, Hashim Ahmed Nur, Rachel L Pennie, Ian Powley, Leah Officer-Jones, Ritwick Sawarkar, Martin Turner, Marion MacFarlane, Owen J Sansom, Martin Bushell, John Le Quesne, Robert F Harvey, Anne E Willis.

Cancer development is associated with dysregulation of the translatome, and targeting canonical eukaryotic initiation and elongation factors can offer treatment avenues for various neoplasms. Emerging evidence indicates that dysregulated mRNA elongation, involving alterations in eEF2 activity and eIF5A expression, also contributes to tumour cell growth. In this study, we investigate whether targeting eIF5A with the inhibitor GC7 is a viable strategy to curtail aberrant cell growth. Our findings demonstrate that inhibiting elongation by reducing eIF5A activity induces feedback inhibition of initiation through eIF2α phosphorylation, decreasing ternary complex formation and shutting down bulk protein synthesis. Employing dynamic SILAC, we identify proteins impacted by reduced eIF5A activity, and show their decreased translation results from feedback inhibition to initiation or other processes downstream of eIF5A. Decreased eIF5A activity impairs mitochondrial function, which activates signalling through HRI to eIF2α phosphorylation, reducing cancer cell proliferation. These effects are reversed by treatment with the integrated stress response inhibitor, implying that the impact of GC7 on cancer cell proliferation is mediated via translation initiation rather than elongation inhibition. These data suggest that eIF5A inhibition could be used to target cancer cells that depend on mitochondrial function for their proliferation and survival.

DOI: https://doi.org/10.1038/s41467-025-66531-z
Nat Cell Biol. 2025 Dec 15.

Keratin intermediate filaments mechanically position melanin pigments for genome photoprotection.

Silvia Benito-Martínez, Laura Salavessa, Anne-Sophie Macé, Myckaëla Rouabah, Nathan Lardier, Vincent Fraisier, Julia Sirés-Campos, Riddhi Atul Jani, Maryse Romao, Vanessa Roca, Charlène Gayrard, Marion Plessis, Ilse Hurbain, Cécile Nait-Meddour, Sandrine Etienne-Manneville, Etienne Morel, Michele Boniotto, Jean-Baptiste Manneville, Françoise Bernerd, Christine Duval, Graça Raposo, Cédric Delevoye.

Melanin pigments block genotoxic agents by positioning on the sun-exposed side of the nucleus in human skin keratinocytes. How this positioning is regulated and its role in genome photoprotection remain unknown. Here, by developing a model of human keratinocytes internalizing extracellular melanin into pigment organelles, we show that keratin 5 and keratin 14 intermediate filaments and microtubules control the three-dimensional perinuclear position of pigments, shielding DNA from photodamage. Imaging and microrheology in a human-disease-related model identify structural keratin cages surrounding pigment organelles to stiffen their microenvironment and maintain their three-dimensional position. Optimum supranuclear spatialization of pigment organelles is required for DNA photoprotection and relies on intermediate filaments and microtubules bridged by plectin cytolinkers. Thus, the mechanically driven proximity of pigment organelles to the nucleus is a key photoprotective parameter. Uncovering how human skin counteracts solar radiation by positioning the melanin microparasol next to the genome anticipates that dynamic spatialization of organelles is a physiological response to ultraviolet stress.

DOI: https://doi.org/10.1038/s41556-025-01817-4
Sci Adv. 2025 Dec 19. 11(51): eadu9092

CRISPRa-mediated disentanglement of the Dux-MERVL axis in the 2C-like state, totipotency, and cell death.

Paul Chammas, Sheila Q Xie, Lessly P Sepulveda-Rincon, Bryony J Leeke, Marian H Dore, Dirk Dormann, Ryan T Wagner, Ning Chang, Peter L Jones, Michael T McManus, Mohammad M Karimi, George Young, Michelle Percharde.

Transposable elements (TEs) are powerful cis-regulatory drivers of gene expression, particularly during early development when many TEs become de-repressed. MERVL elements are transiently up-regulated in mouse totipotent two-cell (2C) embryos during major zygotic genome activation (ZGA) and 2C-like cells in vitro. One of the most powerful activators of MERVL is the pioneer transcription factor, Dux. However, apparent differences lie in the requirement for Dux versus MERVL activation in embryos. Moreover, sustained Dux activation causes cell toxicity, which may or may not be linked to MERVL. Using a CRISPR activation system, we unpick the relative role of Dux and MERVL in ZGA, totipotent-like characteristics, and cell toxicity. We find that MERVL activation drives a portion of the Dux-dependent transcriptome, sufficient for expanded fate potential, but not other totipotency features. Conversely, Dux-induced pathology is independent of MERVL activation and involves the proapoptotic factor, Noxa. Our study highlights the complexity of the Dux-MERVL transcriptional network and uncovers a previously unknown player in Dux-driven pathology.

DOI: https://doi.org/10.1126/sciadv.adu9092
Nat Commun. 2025 Dec 13.

Targeted CRISPR-Cas9 screening identifies core transcription factors controlling murine haemato-endothelial fate commitment.

Michael Teske, Tobias Wertheimer, Stefan Butz, Pascale Zwicky, Izaskun Mallona, Svenja L Nopper, Christian Münz, Ulrich Elling, Christophe Lancrin, Burkhard Becher, Ana Rita Grosso, Tuncay Baubec, Nina Schmolka.

During development, blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm forming haematopoietic progenitors. This study aims to identify the crucial molecular regulators of haemato-endothelial mesoderm formation and to extend our knowledge of the process in an unbiased way. We employ a murine embryonic stem cell model that recapitulates embryonic blood development, and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. We identify the transcription factors ETV2, LDB1, SMAD1, SIX4 and ZBTB7b as regulators of haemato-endothelial mesoderm commitment. Embryonic stem cells lacking these regulators give rise to mesodermal subsets with a defined lineage differentiation bias, while transcriptome analysis of these cells uncovers the precise impact of each factor on gene expression in the developing mesoderm. Our study reveals molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification and paves the way for future advances in haematopoietic stem cell applications.

DOI: https://doi.org/10.1038/s41467-025-66230-9
Nat Commun. 2025 Dec 13.

Prodrug nanoplatform for triggering ferroptosis to eliminate senescent cells in age-associated pathologies.

Chengkang Jin, Xiaoling Xu, Ning Yao, Hairui Zhang, Changjiang Chen, Lingyao Zeng, Zhiyun Liu, Lanjie Lei, Shumao Cui, Chengping Wen, Liyun Shi.

Accumulation of senescent cells is associated with aging and age-related diseases. However, current clearance therapies targeting senescent cells are often limited by low efficiency, poor specificity, and insufficient penetration. Here we develop a nano-platform composed of a probe (GD) that can be specifically activated by senescent cells, a photosensitizer (Ce6), and a peptide (HK) for targeting ferritin, named HK-PCGC. We show that upon entering senescent cells, GD is activated by high levels of β-galactosidase, releasing fluorescence to excite Ce6. Ce6 then generates reactive oxygen species to eliminate these cells. Additionally, we find that under the guidance of the peptide HK, our system degrades ferritin to trigger ferroptosis, further eliminating senescent cells. Collectively, we demonstrate that HK-PCGC can effectively eliminate senescent cells, reduce the senescence-associated secretory phenotype, and safely improve the physical fitness of aged mice. This study integrates senescent cell responsiveness, laser-free photodynamic therapy, and induction of ferroptosis, offering a potential approach for delaying aging.

DOI: https://doi.org/10.1038/s41467-025-67364-6
Cell Rep. 2025 Dec 18. pii: S2211-1247(25)01504-9. [Epub ahead of print]45(1): 116732

Neural stem cell quiescence is actively maintained by the epigenome.

Anna Malkowska, Jan Ander, Andrea H Brand.

  Homeostasis of the nervous system is maintained by a population of resident neural stem cells (NSCs) retained in a state of reversible cell-cycle arrest called quiescence. Quiescent NSCs can resume proliferation in response to different physiological stimuli. Reactivation requires changes in gene expression, much of which is regulated at the epigenomic level. We mapped epigenomic changes in NSC chromatin during stem cell quiescence and reactivation in Drosophila in vivo. Contrary to expectations, chromatin accessibility is increased in quiescent NSCs. Surprisingly, genes crucial for cell-cycle progression are repressed while remaining within permissive H3K36me3-bound euchromatin. At the same time, genes necessary for cell-cell communication are derepressed by eviction of histone H1 and transition to an SWI/SNF-enriched active state. Our results reveal global expansion of accessible chromatin in quiescent NSCs without concomitant transcriptional activation. Strikingly, this process reverses upon reactivation, indicating that opening of chromatin is a quiescence-specific event.

Keywords:  CP: molecular biology; CP: stem cell research; Targeted DamID; chromatin; histone modification; quiescence; stem cell

DOI:  https://doi.org/10.1016/j.celrep.2025.116732
bioRxiv. 2025 Dec 08. pii: 2025.12.04.692378. [Epub ahead of print]

α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis.

Xinyu Dong, Fabian Bock, Ali Hashmi, Nada Bulus, Glenda Mernaugh, Gema Bolas, Shensen Li, Wanying Zhu, Meiling Melzer, Kyle Brown, Colton Miller, Olga Viquéz, Eloi Montañez, Ambra Pozzi, Sara A Wickström, Roy Zent.

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangements is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangements during branching morphogenesis is poorly understood. Here we used 3D live imaging of mouse ureteric bud branching to show that α-parvin, a component of the integrin binding ILK-PINCH-Parvin (IPP) complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, α-parvin promotes actin turnover by inhibiting activation of the small GTPases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis.
Teaser: Scaffold protein α-parvin limits cell adhesion and actin polymerization, enabling cell rearrangements that drive kidney branching.

DOI: https://doi.org/10.64898/2025.12.04.692378
Cell. 2025 Dec 15. pii: S0092-8674(25)01316-9. [Epub ahead of print]

HLA export by melanoma cells decoys cytotoxic T cells to promote immune evasion.

Yoav Chemla, Orit Itzhaki, Stav Melamed, Chen Weller, Yuval Sade, Paulee Manich, Keren Reshef, Nicolas Xenidis, Avishai Maliah, Gilad Levy, Roma Parikh, Osnat Bartok, Opal Levy, Itay Tal, Gal Aziel, Abraham Nissani, Sharon Yunger, Daniela Likonen, Vitaly Kliminsky, Tamar Golan, Coralie Capron, Valentina Ace, Ronen Levy, Diana Rasoulouniriana, Zohar Eyal, Yuval Barzilay, Roi Balaban, Aseel Khateeb, Rami Khosravi, Amir Grau, Tamar Ziv, Polina Greenberg, Dvir Netanely, Hananya Vaknin, Xunwei Wu, Yael Amitay, Ronen Brenner, Julia María Martínez Gómez, Dov Hershkovitz, Tal Yardeni, Valentina Zemser-Werner, Oren Kobiler, Yael Friedmann, David Bassan, Ron Shamir, Lea Eisenbach, Nadine Santana-Magal, Michael Milyavsky, Galit Eisenberg, Leeat Keren, Merav Cohen, Dvir Gur, Boaz Barak, Michal Lotem, David Sprinzak, Shoshana Greenberger, David Fisher, Michal J Besser, Mehdi Khaled, Pierre Close, Ronnie Shapira, Sebastien Apcher, Asaf Madi, Mitchell P Levesque, Francessca Rapino, Yaron Carmi, Shivang Parikh, Yardena Samuels, Carmit Levy.

  While melanoma cells often express a high burden of mutated proteins, the infiltration of reactive T cells rarely results in tumor-eradicating immunity. We discovered that large extracellular vesicles, known as melanosomes, secreted by melanoma cells are decorated with major histocompatibility complex (MHC) molecules that stimulate CD8+ T cells through their T cell receptor (TCR), causing T cell dysfunction and apoptosis. Immunopeptidomic and T cell receptor sequencing (TCR-seq) analyses revealed that these melanosomes carry MHC-bound tumor-associated antigens with higher affinity and immunogenicity, which compete with their tumor cell of origin for direct TCR-MHC interactions. Analysis of biopsies from melanoma patients confirmed that melanosomes trap infiltrating lymphocytes, induce partial activation, and decrease CD8+ T cell cytotoxicity. Inhibition of melanosome secretion in vivo significantly reduced tumor immune evasion. These findings suggest that MHC export protects melanoma from the cytotoxic effects of T cells. Our study highlights a novel immune evasion mechanism and proposes a therapeutic avenue to enhance tumor immunity.

Keywords:  CD8 T cells; HLA-peptidomics; MHC; TCR-seq; extracellular vesicles; immunotherapy; melanoma; melanosomes; tumor microenvironment; tumor-infiltrating lymphocytes

DOI:  https://doi.org/10.1016/j.cell.2025.11.020
EMBO J. 2025 Dec 15.

TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability.

Charlie Moffatt, Ankita Arora, Katherine F Vaeth, Bryan B Guzman, Gurprit Bhardwaj, Audrey Hoelscher, Levi B Gifford, Holger A Russ, Daniel Dominguez, J Matthew Taliaferro.

  The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanisms that govern their localization are unknown. Here, using subcellular fractionation and single-molecule RNA FISH, we found that loss of TDP-43 results in increased accumulation of hundreds of mRNAs in neurites. Using high-throughput functional assays in cells and high-throughput binding assays in vitro, we subsequently identified specific regions within these mRNAs that mediate their TDP-43-dependent localization and interaction with TDP-43. We found that the same regions also mediated TDP-43-dependent mRNA instability, suggesting a mechanism by which TDP-43 regulates mRNA localization. ALS-associated mutations in TDP-43 resulted in similar mRNA mislocalization phenotypes as did TDP-43 loss in mouse dorsal root ganglia and human iPS-derived motor neurons. These findings establish TDP-43 as a direct negative regulator of mRNA abundance in neurites and suggest that mislocalization of specific transcripts may occur in ALS patients.

Keywords:  ALS; RNA Localization; RNA Stability; RNA Trafficking; TDP-43

DOI:  https://doi.org/10.1038/s44318-025-00653-4
Signal Transduct Target Ther. 2025 Dec 15. 10(1): 402

Abrogation of aberrant glycolytic interactions eliminates senescent cells and alleviates aging-related dysfunctions.

Takumi Mikawa, Masahiro Kameda, Sumiko Ikari, Eri Shibata, Shuyu Liu, Sawa Miyagawa, Koh Ono, Tomiko Ito, Akihiko Yoshizawa, Masataka Sugimoto, Shuichi Shibuya, Takahiko Shimizu, Julio Almunia, Noboru Ogiso, Gwladys Revêchon, Alberta Palazzo, David Bernard, Hiroaki Kanda, Tomoyoshi Soga, Keiyo Takubo, Shin Morioka, Junko Sasaki, Takehiko Sasaki, Akihiro Itamoto, Takayuki Fujii, Hiroshi Seno, Nobuya Inagaki, Hiroshi Kondoh.

Cellular senescence is deeply involved in physiological homeostasis, development, tissue repair, aging, and diseases. Senescent cells (SnCs) accumulate in aged tissues and exert deleterious effects by secreting proinflammatory molecules that contribute to chronic inflammation and aging-related diseases. We revealed that an aberrant interaction between glycolytic PGAM1 and Chk1 kinase is augmented in SnCs associated with increased glycolysis, whose byproduct, lactate, promotes this binding in a noncell autonomous manner. The pseudo-Warburg effect of SnCs with enhanced PPP (pentose phosphate pathway) activity is maintained by HIF-2α phosphorylation by Chk1 and subsequent upregulation of glycolytic enzymes, creating a vicious cycle reprogramming the glycolytic pathway in SnCs. HIF-2α also activates FoxM1 expression, which transcriptionally suppresses proapoptotic profiles, including BIM, and upregulates DNA repair machineries in SnCs. FoxM1 thus supports the genomic integrity and survival capacity of SnCs during their glycolytic changes. Chemical abrogation of PGAM1-Chk1 binding reverts these phenotypes and eliminates SnCs through senolysis. Inhibition of the PGAM1-Chk1 interaction improves physiological parameters during aging and inhibits lung fibrosis in mouse models. Our study highlights a novel pathway contributing to the metabolic reprogramming of SnCs and how the use of a new senolytic molecule that targets the PGAM-Chk1 interaction creates a specific vulnerability of those cells to potentially fight age-related diseases.

DOI: https://doi.org/10.1038/s41392-025-02502-6
ACS Synth Biol. 2025 Dec 17.

Force Transmission by Minimal Focal Adhesion Complexes Induces Synthetic Cell Deformation.

Natalie Huhn, Chiao-Peng Hsu, Timon Nast-Kolb, Arsenii Hordeichyk, Andreas R Bausch.

  Cells sense and respond to mechanical cues through focal adhesions-dynamic, multiprotein assemblies linking the actin cytoskeleton to the extracellular matrix. These complexes are essential to processes from cell migration to tissue morphogenesis, yet the minimal physical requirements for their force-transmitting and mechanosensing functions remain unclear. Here, we reconstitute minimal focal adhesion-like complexes in giant unilamellar vesicles (GUVs) using kindlin-2, talin-1, FAK, paxillin, zyxin, and VASP anchored to membranes containing PIP2 and integrin β1 tails. These assemblies nucleate and anchor actin filaments into networks spanning the vesicle surface. Upon addition of nonmuscle myosin IIa, actomyosin contraction thickens filament bundles, aligns the complexes, and deforms the GUVs, while the assemblies remain stably membrane-bound. Our findings show that actin recruitment, force transmission, and structural stability under load can emerge from defined protein-membrane interactions alone. This minimal, three-dimensional platform offers a controllable synthetic biology system for probing mechanosensing and engineering force-responsive biomimetic systems.

Keywords:  actin; actomyosin; contractile force transmission; focal adhesion; protein complex; reconstitution

DOI:  https://doi.org/10.1021/acssynbio.5c00645
ACS Chem Biol. 2025 Dec 14.

A Chemically Switchable Synthetic Condensate Platform for Reversible Protein Sequestration and Release.

Yoko Fukaya, Masaru Yoshikawa, Kazuhiro Aoki, Helen Farrants, Kai Johnsson, Shinya Tsukiji.

Creating artificial organelles that sequester and release specific proteins in response to a small molecule in mammalian cells is an attractive approach for regulating protein function. In this work, by combining phase-separated condensates formed by the tandem fusion of two oligomeric proteins with a trimethoprim (TMP)-responsive nanobody switch for GFP (GFPLAMA; ligand-modulated antibody fragment), we developed a synthetic condensate system that initially sequesters GFP-tagged proteins within condensates and rapidly releases them into the cytoplasm upon TMP treatment. The released proteins can then be resequestered by washing out the TMP. This system enabled user-defined, temporal, rapid, and reversible control of cellular processes, including membrane ruffling mediated by exogenously expressed GFP-Vav2 and modulation of the cellular localization of endogenous ERK2-GFP generated by genome knock-in. Our results highlight the utility of the GFPLAMA-based synthetic condensate platform as a novel, chemically switchable tool for regulating protein function through controlled protein sequestration and release in mammalian cells.

DOI: https://doi.org/10.1021/acschembio.5c00719
Nature. 2025 Dec 17.

Human assembloids recapitulate periportal liver tissue in vitro.

Lei Yuan, Sagarika Dawka, Yohan Kim, Anke Liebert, Fabian Rost, Robert Arnes-Benito, Franziska Baenke, Christina Götz, David Long Hin Tsang, Andrea Schuhmann, Anna Shevchenko, Roberta Rezende de Castro, Seunghee Kim, Aleksandra Sljukic, Anna M Dowbaj, Andrej Shevchenko, Daniel Seehofer, Dongho Choi, Georg Damm, Daniel E Stange, Meritxell Huch.

The development of complex multicellular human in vitro systems holds great promise for modelling disease and advancing drug discovery and tissue engineering1. In the liver, despite the identification of key signalling pathways involved in hepatic regeneration2,3, in vitro expansion of human hepatocytes directly from fresh patient tissue has not yet been achieved, limiting the possibility of modelling liver composite structures in vitro. Here we first developed human hepatocyte organoids (h-HepOrgs) from 28 different patients. Patient-derived hepatocyte organoids sustained long-term expansion of hepatocytes in vitro and maintained patient-specific gene expression and bile canaliculus features and function of the in vivo tissue. After transplantation, expanded h-HepOrgs rescued the phenotype of a mouse model of liver disease. By combining h-HepOrgs with portal mesenchyme and our previously published cholangiocyte organoids4-6, we generated patient-specific periportal liver assembloids that retain the histological arrangement, gene expression and cell interactions of periportal liver tissue, with cholangiocytes and mesenchyme embedded in the hepatocyte parenchyma. We leveraged this platform to model aspects of biliary fibrosis. Our human periportal liver assembloid system represents a novel in vitro platform to investigate human liver pathophysiology, accelerate drug development, enable early diagnosis and advance personalized medicine.

DOI: https://doi.org/10.1038/s41586-025-09884-1
Proc Natl Acad Sci U S A. 2025 Dec 23. 122(51): e2517830122

Asymmetrical recognition and processing of double-strand breaks formed during DNA replication.

Matthew J Johnson, Michael T Kimble, Seoyeon Jeong, Aakanksha Sane, Lorraine S Symington.

  DNA end resection to generate 3' single-stranded DNA (ssDNA) overhangs is the first step in homology-directed mechanisms of double-strand break (DSB) repair. While end resection has been extensively studied in the repair of endonuclease-induced DSBs, little is known about how resection proceeds at DSBs generated during DNA replication. We previously established a system to generate replication-dependent double-ended DSBs at the sites of nicks induced by the Cas9D10A nickase in the budding yeast genome. Here, we suggest that these DSB ends form in an asymmetric manner, with one being blunt or near blunt and the other bearing a 3' ssDNA overhang of up to the size of an Okazaki fragment. We find that Mre11 preferentially binds blunt ends and is required to evict Ku from these DSB ends and to promote end resection. In contrast, the ends predicted to have 3' overhangs have minimal Ku binding, and resection at these break ends can proceed in a mostly Mre11-independent manner through either the Exo1 or Dna2-Sgs1 long-range resection mechanisms. These findings indicate that resection proceeds differently at replication-dependent DSBs than at canonical DSBs and reveal that Ku selectively binds blunt ends, potentially explaining why replication-dependent DSBs are poorly repaired by nonhomologous end joining.

Keywords:  DNA double-strand break; DNA replication; Ku; Mre11; end resection

DOI:  https://doi.org/10.1073/pnas.2517830122
Biophys J. 2025 Dec 18. pii: S0006-3495(25)00767-2. [Epub ahead of print]

Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell.

Luis Perez, Xue Wen Ng, Michael Mohs, David W Piston, Shankar Mukherji.

The compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. Although functionally significant mitochondrial localization has been demonstrated in cells such as neurons, it remains unclear how general these cell principles are. Here, we examine the spatial organization of mitochondria within MIN6 pancreatic beta cells under variable glucose conditions. We observe glucose-dependent redistributions of mitochondria, favoring peripheral localization at elevated glucose levels. Our results, formalized into a stochastic model of mitochondrial trafficking, suggest that active mitochondrial transport along microtubules and PKA signaling activity, but not ATP synthesis, are critical regulators of this redistribution. These results suggest that environmentally responsive mitochondrial subcellular positioning may represent a general regulatory mechanism in even nonpolarized cell types.

DOI: https://doi.org/10.1016/j.bpj.2025.11.018
Nat Commun. 2025 Dec 17.

TMEM65-dependent Ca2+ extrusion safeguards mitochondrial homeostasis.

Massimo Vetralla, Lena Wischhof, Asrat Kahsay, Vanessa Cadenelli, Enzo Scifo, Beijia Xie, Miriana Sbrissa, Maëlle Sandhira Habert, Dan Ehninger, Rosario Rizzuto, Daniele Bano, Diego De Stefani.

The bidirectional transport of Ca2+ into and out of mitochondria regulates metabolism, signaling, and cell fate. While influx is mediated by the Mitochondrial Calcium Uniporter (MCU) complex, efflux mechanisms are more diversified, involving Na⁺ or H⁺ exchange pathways. We here demonstrate that TMEM65 is a fundamental component of the Ca2+ efflux machinery of mitochondria. Its overexpression specifically enhances Na⁺- and Li⁺-dependent mitochondrial Ca²⁺ extrusion. This effect is inhibited by CGP-37157 and does not depends on NCLX, currently considered the bona fide mitochondrial Na+/Ca2+ exchanger. Its downregulation chronically elevates basal [Ca²⁺]mt and impairs efflux upon stimulation. In Caenorhabditis elegans, deletion of TMEM65 homologs compromises embryonic development under mild thermal stress, causing necrotic lesions that are suppressed by genetic inhibition of MCU-1. These findings highlight a molecular component that may be relevant in pathological settings in which excessive mitochondrial Ca2+ accumulation critically contribute to degenerative pathways.

DOI: https://doi.org/10.1038/s41467-025-67647-y