bims-ginsta Biomed News
on Genome instability
Issue of 2026–09–13
forty papers selected by
Jinrong Hu, National University of Singapore



  1. J Cell Biol. 2026 Oct 05. pii: e202412222. [Epub ahead of print]225(10):
      Early embryo development features autonomous, maternally driven cell divisions that self-organize the multicellular blastula or blastocyst tissue. Maternal control cedes to the zygote starting with the onset of widespread zygotic genome activation (ZGA), which is essential for subsequent cell fate determination and morphogenesis. Intriguingly, although ZGA onset is highly regulated at the level of the whole embryo, it can be non-homogenous and precisely patterned at the single-cell level. We previously demonstrated a stereotyped spatial and temporal ordering of ZGA in a model vertebrate embryo. Unknown, however, was whether this precise ZGA patterning was required for development. To address this fundamental question, we devised a strategy to spatially control cell divisions that perturb blastula embryo organization. We demonstrate the feasibility of spatially inverting the cell size pattern of embryos and find that these inverted embryos exhibit a flipped pattern of ZGA. Mispatterned ZGA along the animal-vegetal axis triggers embryo apoptosis, revealing that gastrula embryos have a built-in quality control system to sense inappropriate ZGA patterning, including regionalized defects in transcriptional onset. The quality control response is nonautonomous, dependent on an anti-apoptotic signal that suppresses cell death outside the animal hemisphere. These results reveal the requirement of properly patterned ZGA for normal development and the existence of a surveillance system of embryo quality control exquisitely tuned to the spatial and temporal ordering of genome activation and zygotic gene expression.
    DOI:  https://doi.org/10.1083/jcb.202412222
  2. J Cell Sci. 2026 Sep 10. pii: jcs.264827. [Epub ahead of print]
      The cell cycle is tightly regulated by checkpoint mechanisms that ensure faithful duplication and segregation of the genome. Here, we induced cell-cell fusion between mitotic and interphase cells to study how nuclei from different cell cycle stages behave in a shared cytoplasm. We found that mitosis is a dominant cell cycle state: the mitotic cytoplasm can drive interphase nuclei into mitosis, whereas, in high ratios of interphase versus mitotic nuclei, fusion forced mitotic nuclei to exit mitosis. Both outcomes represent checkpoint override events with impactful consequences. Interphase nuclei forced into mitosis form aberrant mitotic spindles, show partially condensed DNA and ultimately undergo mitotic catastrophe. Conversely, forced mitotic exit resulted in reformation of nuclear envelope membranes around condensed chromosomes, forming nuclei with a defective nuclear import machinery. Altogether, cell-cell fusion revealed the consequences of checkpoint override, forcing nuclei through untimely cell cycle transitions, and highlight how cell-cell fusion experiments can be a powerful system to study how competing cytoplasmic states are integrated in a shared cytoplasm, such as in muscle, placenta formation and in cancer.
    Keywords:  Cell cycle; Cell-cell fusion; Mitosis
    DOI:  https://doi.org/10.1242/jcs.264827
  3. Nat Cell Biol. 2026 Sep 07.
      Embryonic myeloid (EM) cells are the first immune-cell population to emerge during development and must disperse throughout the embryo to act as the first line of defence against infection. Although EM cells migrate directionally toward wounds, how they navigate through unwounded tissues during early colonization remains unclear. Here we show that EM cell dispersion in Xenopus embryos is driven, at least in part, by cell-on-cell migration, an important yet underappreciated phenomenon, guided by dynamic tissue flows. We have established a new ex vivo EM cell migration system that allows for live imaging, computational analyses and optogenetic manipulation. We find that local ectodermal tissue flows repolarize EM cell protrusions and bias their directional migration. Disrupting these flows, both ex vivo and in vivo, either genetically or mechanically, impairs EM cell dispersion. Our findings reveal that mechanical cues generated by surrounding tissue flows coordinate immune-cell migration during development, highlighting an overlooked mechanism by which collective tissue dynamics guide individual cell behaviour.
    DOI:  https://doi.org/10.1038/s41556-026-02058-9
  4. Nat Cell Biol. 2026 Sep;28(9): 1857-1874
      RNA localization adds a fundamental layer to gene expression by determining when and where translation-ready mRNAs become available, yet how this timing is coordinated with nuclear architecture and cell-cycle progression remains unclear. Here we identify a subnuclear RNA niche at the nuclear speckle periphery that couples intron retention to cell-cycle-timed RNA release. Using compartment-resolved transcriptional inhibition, sequence-based deep learning and single-molecule and super-resolution RNA imaging in human pluripotent stem cells, we define a class of nuclear RNAs with long-lived retained introns that persist for hours and are enriched in transcripts encoding regulators of genome maintenance and mitosis, including centromere and kinetochore assembly, DNA repair and telomere maintenance. Long-lived retained introns exhibit elevated GC content, predicted structural stability and enrichment for nuclear speckle-associated RNA-binding proteins. In interphase, these RNAs localize to a distinct nuclear speckle-peripheral RNA niche in a spatial arrangement conserved across cell types. During mitotic remodelling, they undergo coordinated, kinase-dependent splicing and are released into the cytoplasm of early G1 daughter cells. Together, these findings link cis-encoded intronic features, subnuclear organization and mitotic remodelling to temporal control of RNA fate.
    DOI:  https://doi.org/10.1038/s41556-026-02040-5
  5. Mol Cell. 2026 Sep 08. pii: S1097-2765(26)00562-9. [Epub ahead of print]
      Eukaryotic tailless complex polypeptide 1 ring complex/Chaperonin containing tailless complex polypeptide 1 (TRiC/CCT) chaperonin is typically considered a cytosolic machine mediating polypeptide folding and assembly of protein complexes. Here, we investigated the nuclear role of TRiC/CCT. Use of a TRiC/CCT temperature-sensitive allele revealed increased production of nascent RNA leading to the accumulation of noncoding transcripts. TRiC/CCT was associated with RNA polymerase II (RNAPII) in vitro and in vivo, including when bound to DNA. Heat treatment of the TRiC/CCT ts chaperonin stabilized the RNAPII complex association and binding to the actin and tubulin substrates. Expression of the Huntingtin protein Htt correlated with lowered RNA production and a decreased association between the RNAPII and TRiC/CCT complexes. Together, our presented data support a model where TRiC/CCT regulates the global activity of RNAPII in reaction to the status of proteostasis. Overall, our work reveals an avenue by which TRiC/CCT contributes to homeostasis by regulating the activity of nuclear RNAPII.
    Keywords:  CCT; Chaperonin; RNA polymerase II; TRiC; cryptic RNA; molecular chaperone; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2026.08.015
  6. Curr Opin Cell Biol. 2026 Sep 08. pii: S0955-0674(26)00074-8. [Epub ahead of print]103 102686
      Recent studies have revealed that cytokinetic abscission is developmentally regulated in a wide range of stem cell systems. Rather than a constitutive endpoint of cell division, abscission can be delayed, accelerated, or arrested altogether depending on developmental context. In this review, we highlight recent advances from Drosophila and mammalian models showing how stem cells modulate their link with daughter cells to regulate cell fate decisions and tissue development. Work in Drosophila germline and neural stem cells has uncovered how conserved regulators of cytokinesis, including endosomal sorting complex required for transport (ESCRT) proteins, mitotic kinases, and ubiquitin-dependent pathways, control intercellular bridge stability, midbody dynamics, and cell fate specification. In parallel, studies in mammalian embryonic and neural stem cells have linked delayed abscission to the maintenance of pluripotency, symmetric fate outcomes, and the regulation of differentiation. Emerging evidence also suggests that persistent intercellular bridges and postabscission midbody remnants can contribute to developmental signalling and stem cell behaviour. Together, these findings support a model in which stem cells actively regulate abscission to coordinate cell-cycle progression, fate transitions, and tissue organization.
    DOI:  https://doi.org/10.1016/j.ceb.2026.102686
  7. Cell Rep. 2026 Sep 07. pii: S2211-1247(26)00969-1. [Epub ahead of print]45(9): 117891
      The epithelial tree of the lung is shaped proximo-distally by airway smooth muscle cells (ASMCs), ductal myofibroblasts (DMFs), and, transiently, alveolar myofibroblasts (AMFs). Lineage tracing and snapshot imaging suggest the clearance of AMFs via apoptosis post-alveologenesis, although definitive evidence is lacking. Here, we generate an inducible BCL2 overexpression mouse allele to inhibit AMF apoptosis. Using three independent Cre drivers and single-cell RNA sequencing, we show that BCL2-rescued AMFs persist around distal alveolar ducts and alveoli and, unexpectedly, mature toward DMFs. Both normal DMFs and rescued DMF-like cells upregulate contractile proteins in a house dust mite-induced asthma model. Our findings demonstrate apoptosis as the chief mechanism of AMF clearance, as well as fate plasticity and pathophysiological convergence of lung mesenchymal cells of the epithelial axis.
    Keywords:  CP: developmental biology; alveolar myofibroblast; alveologenesis; apoptosis; cell fate plasticity and reprogramming; lung development
    DOI:  https://doi.org/10.1016/j.celrep.2026.117891
  8. Development. 2026 Sep 07. pii: dev.205461. [Epub ahead of print]
      Epithelial remodeling is powered by contractile forces exerted by the actomyosin cytoskeleton. In invertebrates, pulsatile contractile flows of the medio-apical actomyosin cortex have been shown to be critical in promoting junction contraction, ultimately driving cell rearrangements, apical constriction, and cell extrusion. However, how actomyosin dynamics drive epithelial remodeling in vertebrates, especially amniotes, remains poorly understood. In this study, we generated transgenic quail lines reporting actin and myosin and investigated their dynamics in gastrulating embryos. We show that during this process, epithelial remodeling events are closely associated with the contraction of junctional myosin. Although we observe medio-apical contractile flows, these are irregular, produce only transient or subtle cell and junctional deformations, and are not consistently associated with junctional or cellular contraction during convergent extension of the primitive streak or during mesendodermal cell ingression. Notably, by characterizing live and apoptotic cell extrusions and their associated actomyosin dynamics, we provide new insights into the cellular processes underlying primitive streak formation and the emergence of germ layers.
    Keywords:  Actomyosin dynamics; Avians; Epithelial remodeling; Epithelial-to-mesenchymal transition; Gastrulation; primitive streak
    DOI:  https://doi.org/10.1242/dev.205461
  9. Science. 2026 Sep 10. eaei5957
      The ciliary transition zone (TZ) regulates ciliary proteome composition, yet its molecular architecture, protein content, and contribution to motile ciliopathies remain poorly defined. We applied in situ cryo-electron tomography and subtomogram averaging to human multiciliated epithelial cells. This approach resolved TZ-specific doublet microtubules at subnanometer resolution and identified nine constituent proteins. We identified that ECT2L and DZANK1 form the major linker complexes between adjacent TZ doublet microtubules. Biallelic loss-of-function variants in either gene cause primary ciliary dyskinesia. ECT2L and DZANK1 deficiency disrupted TZ architecture, caused microtubular abnormalities and abnormal bulbous ciliary tips, and impaired mucociliary clearance. These findings establish a direct genetic link between TZ defects and human motile ciliopathy, and illustrate how in situ structural biology can uncover mechanisms of human disease.
    DOI:  https://doi.org/10.1126/science.aei5957
  10. Genes Dev. 2026 Sep 10.
      Classic models of the French flag problem depict sharp cell type boundaries emerging from threshold responses to morphogen gradients. How discrete cell type boundaries arise from morphogen signals that vary continuously across developing tissues remains incompletely understood. We use hair follicle dermal condensate (DC) formation to study a sharp developmental transition in which proliferative progenitors undergo cell cycle exit concurrent with molecular differentiation. Using genetic and genomic approaches, we show that Wnt and Hedgehog signaling coordinate separable cellular events during DC commitment. Elevated Wnt signaling promotes cell cycle exit through reduced chromatin binding of the Hedgehog mediator GLI3, while Hedgehog signaling induces differentiation genes in a Wnt-dependent manner and simultaneously elevates Wnt activity. When these responses coincide, differentiation and cell cycle exit occur together, limiting the duration and abundance of intermediate states and producing a sharp boundary. When they do not, intermediate states persist and expand, producing a graded boundary. Thus, a sharp boundary can emerge from a continuous transition that is compressed in time and space.
    Keywords:  Hedgehog; Wnt; dermis; morphogen; patterning; scRNA sequencing
    DOI:  https://doi.org/10.1101/gad.353815.126
  11. Nat Commun. 2026 08 11. pii: 9633. [Epub ahead of print]17(1):
      The spindle assembly checkpoint (SAC) promotes faithful chromosome segregation by delaying mitosis until all kinetochores attach to spindle microtubules. However, unusually prolonged mitoses block daughter cell proliferation through a p53-dependent memory mechanism-the "mitotic stopwatch"-suggesting a selective pressure to avoid significant mitotic delays. Here, we show that microtubule occupancy at kinetochores is a cornerstone linking SAC silencing with mitotic duration and memory. By combining live-cell with super-resolution microscopy, photobleaching and laser microsurgery in Indian muntjac fibroblasts, we demonstrate that SAC silencing is gradual and confined to microtubule attachments within kinetochores. Augmin promotes timely SAC silencing with high microtubule occupancy at kinetochores, whereas MPS1/CDK1 inhibition silences the SAC irrespective of microtubule occupancy. Conversely, low microtubule occupancy delays SAC silencing, increases segregation errors and blocks daughter cell proliferation due to mitotic stopwatch surveillance. Thus, timely SAC silencing with high microtubule occupancy avoids "bad memories" of mitosis to allow daughter cell proliferation.
    DOI:  https://doi.org/10.1038/s41467-026-76654-6
  12. Science. 2026 Sep 10. eaek5696
      The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the sequential transcription of ncRNAs emanating from distinct regulatory elements underlies gene activation in Drosophila embryos. Single-allele co-visualization uncovers that optimal gene activation is achieved by only moderate levels of enhancer activity. Disrupting enhancer-associated ncRNAs causes precocious gene activation, providing evidence that ncRNAs control the timing of gene expression in development. We further show that enhancer transcription can regulate long-range interactions within complex regulatory landscapes. We propose that ncRNAs locally modulate regulatory element activity in cis to shape genome organization and orchestrate the temporal control of gene expression in development.
    DOI:  https://doi.org/10.1126/science.aek5696
  13. J Cell Biol. 2026 Nov 02. pii: e202605096. [Epub ahead of print]225(11):
      Ribosome biogenesis occurs in the nucleolus, a biomolecular condensate whose material properties are thought to be important for function. However, the molecular basis of nucleolar dynamics and their relationship to ribosome assembly remain incompletely understood. We present a platform for high-throughput FRAP (HiT-FRAP) and use it to screen hundreds of genes for their impact on dynamics of the nucleolar scaffold nucleophosmin (NPM1). We find that NPM1 dynamics and nucleolar morphology are sensitive to ribosome assembly state: accumulation of early pre-ribosomal intermediates slows NPM1 dynamics and compacts the condensate, while accumulation of abortive late precursors accelerates dynamics and disrupts condensate integrity. These opposing biophysical states correlate with the strength of NPM1-pre-ribosome interactions. Importantly, mutations in the NPM1 intrinsically disordered region that alter pre-ribosome binding directly tune nucleolar dynamics. These results establish that ribosomal precursor assembly state determines nucleolar material properties through the strength of scaffold-pre-ribosome interactions and introduce HiT-FRAP as a platform for interrogating condensate dynamics broadly.
    DOI:  https://doi.org/10.1083/jcb.202605096
  14. Cell Metab. 2026 Sep 10. pii: S1550-4131(26)00339-6. [Epub ahead of print]
      Senescent cells, which are normally cleared by the immune system but accumulate with age, contribute to multiple disorders including metabolic dysfunction and impaired fitness. While immune checkpoint inhibitors have been well studied in cancer, the role of programmed cell death ligand 2 (PD-L2) in non-cancerous, age-associated cellular senescence remains unclear. We found that PD-L2 is upregulated in isolated senescent human cells and during aging, and senolytics can remove age-associated, highly PD-L2-expressing senescent cells. Old PD-L2 knockout mice accumulate fewer senescent cells than old wild-type mice, and their insulin sensitivity and grip strength are greater. Anti-PD-L2 therapy restored insulin sensitivity in aged wild-type mice. PD-L2 acts as an immune checkpoint on senescent cells, allowing them to evade immune clearance and promoting their persistence during aging. Targeting PD-L2 in senescent cells may be a strategy for alleviating the age-related dysfunction associated with cellular senescence.
    Keywords:  PD-1; PD-L1; PD-L2; aging; cellular senescence; immune-related adverse events; immunotherapy; irAE; sPD-L2; senolytics
    DOI:  https://doi.org/10.1016/j.cmet.2026.08.014
  15. Nat Phys. 2026 ;22(9): 1436-1445
      There is broad consensus that intermediate filaments, such as keratin, play a key role in protecting cells and tissues from large deformations. However, little is known about how they fulfil this function. Here we show that epithelial cells slowly adapt to stretching through a coupling of a star-bundling transition of keratin filaments with the escape of the nucleus from its keratin cage. The bundling transition begins with a depletion of keratin filaments at tricellular junctions followed by a progressive accumulation in thick bundles that bisect cell-cell junctions. Bundling is a cooperative process that initiates in a few scattered cells and propagates to their neighbours, leading to the growth of multicellular clusters that contain a percolated network of thick keratin bundles. Bundling dynamics are slow and strongly influenced by the interaction between actin and keratin. Informed by a computational model, we provide evidence that keratin bundling generates a compressive stress on the nucleus, which is relaxed by nuclear escape from the keratin cage. The topological transitions identified here provide epithelia with a multiscale mechanism to adapt to sustained stretching.
    Keywords:  Biological physics; Biopolymers in vivo; Computational biophysics
    DOI:  https://doi.org/10.1038/s41567-026-03371-8
  16. Cell. 2026 Sep 08. pii: S0092-8674(26)00947-5. [Epub ahead of print]
      The mating type switching/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex removes and repositions nucleosomes at promoters for the initiation of transcription. Though long thought to function independently, we find that SWI/SNF is an integral component of the transcription machinery. SWI/SNF associates with an RNA polymerase II pre-initiation complex (PIC), Mediator, and a nucleosome, and the entire assembly dimerizes to form a giant 7-megadalton complex. We present high-resolution cryo-electron microscopy (cryo-EM) structures of both PIC-Mediator-SWI/SNF and PIC-Mediator-SWI/SNF-nucleosome complexes, together with results of cross-linking and mass spectrometry. The structures reveal how SWI/SNF enhances the initiation of transcription through stabilization of PIC organization and concerted remodeling of the so-called +1 nucleosome. The structural model suggests the coordinated actions of two DNA translocases, Snf2 of SWI/SNF and Ssl2 of TFIIH, for the initiation of transcription.
    Keywords:  +1 nucleosome; SWI/SNF chromatin remodeling complex; cross-linking and mass spectrometry; cryo-electron microscopy; intrinsically disordered region; transcription pre-initiation complex
    DOI:  https://doi.org/10.1016/j.cell.2026.08.020
  17. Nat Chem Biol. 2026 Sep 07.
      In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum (ER), mitochondria and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that N6-methyladenosine-rich RNAs are recruited to SGs within 10 minutes of stress induction, and ER‑proximal RNAs associate with G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell surface tagging (CAP-CELL), enabling spatially resolved cell typing and identifying cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.
    DOI:  https://doi.org/10.1038/s41589-026-02313-y
  18. Sci Adv. 2026 Sep 11. 12(37): eaef1579
      Centromeres, defined by CENP-A-containing nucleosomes, direct kinetochore assembly for spindle attachment. In mitosis, CENP-A and the constitutive centromere-associated network (CCAN) of the inner kinetochore are arranged into bipartite subdomains within clearings of chromatin. However, less is known about their architecture during interphase. We report here an unrecognized structural role for the CENP-A chaperone machinery in establishing interphase centromere architecture. In interphase, CENP-A and the CCAN assemble conserved shell-like structures that enclose a chromatin-poor central cavity. This cavity is occupied by the interphase-specific CENP-A chaperone complex, which promotes CENP-A assembly once per cell cycle. The presence of the chaperone complex, but not its CENP-A-incorporating activity, is required to generate both the shell architecture and chromatin clearing. The CCAN scaffold CENP-C exhibits radial organization throughout the structure and is essential for its formation, primarily by recruiting the HJURP chaperone. Our findings broaden the role of the CENP-A chaperone machinery to include the structural organization of interphase vertebrate centromeres, independent of CENP-A deposition.
    DOI:  https://doi.org/10.1126/sciadv.aef1579
  19. Nat Commun. 2026 Aug 13. pii: 9729. [Epub ahead of print]17(1):
      Certain forms of mitochondrial impairment confer longevity, while disease-associated mitochondrial dysfunction triggers pathogenesis. The adaptive pathways that distinguish benefit from pathology remain unclear. Here we reveal that longevity induced by mitochondrial Complex I/nuo-6 mutation in C. elegans is dependent on the endoplasmic reticulum (ER) Ca2+ channel, InsP3R. To explain this connection, we test multiple candidate links between Ca2+ and mitochondrial homeostasis previously established in vitro, including mitochondrial calcium uniporter (MCU)-dependent stimulation of respiration and cytosolic pathways regulating mitochondrial dynamics. We find that MCU is dispensable for both respiration and longevity in Complex I mutants. Conversely, transcriptomic profiling and imaging reveal InsP3R impairment results in maladaptive expansion of compromised mitochondrial networks. We provide evidence that this aberrant mitochondrial expansion results from disruption of a conserved, InsP3R-dependent actin remodeling network centered on Arp2/3. Disruption of actin remodeling or autophagy mimics the mitochondrial expansion and longevity suppression of InsP3R mutants. Conversely, driving mitochondrial fragmentation ameliorates mitochondrial expansion and rescues longevity in InsP3R mutants, supporting a model in which InsP3R-dependent actin remodeling is required for segregation and clearance of mitochondria. These findings identify an inter-organelle signaling axis linking ER calcium release and cytoskeletal remodeling to adaptive mitochondrial responses associated with longevity.
    DOI:  https://doi.org/10.1038/s41467-026-76514-3
  20. Cell. 2026 Sep 11. pii: S0092-8674(26)00996-7. [Epub ahead of print]
      Immune elimination of chronic infection or cancer requires cytotoxic CD8+ T cells that adopt and maintain an effector phenotype. Cytotoxic T cell function is a bioenergetically demanding process. Here, we report the ability of D-α-hydroxybutyrate (DAHB) to act as a signaling molecule that increases mitochondrial ATP production and drives the conversion of proliferating T cells into cytotoxic effector cells. DAHB signaling switches ATP production from glycolysis to oxidative phosphorylation supported by fatty acid oxidation. This conversion elevates the level of a phosphagen, phosphocreatine (PCr). Both the PCr bioenergetic reserve and oxidative phosphorylation were required for T cell effector differentiation. DAHB-induced CD8 effector gene transcription was coupled to bioenergetics by BAF-complex-dependent remodeling of chromatin at effector loci. DAHB-enhanced CD8+ T cell antitumor activity both in vitro and in vivo. Together, these findings link cellular bioenergetics to the regulation of chromatin accessibility and gene expression required to support effector function.
    Keywords:  BAF; CD8 T cell effector function; D-alpha-hydroxybutyrate; OXPHOS; chromatin remodeling; creatine; phosphocreatine; tumor immunology
    DOI:  https://doi.org/10.1016/j.cell.2026.08.023
  21. Elife. 2026 Sep 08. pii: RP101088. [Epub ahead of print]13
      Polarization is crucial for the proper functioning of epithelial cells. Early hallmarks include the trafficking and enrichment of polarity molecules to form the apical membrane (AM) or cell-cell junctions, and the apical positioning of the centrosome. However, the dependencies among polarity molecules, AM formation, and centrosome positioning remain poorly understood. When cultured in Matrigel, de novo polarization of a single epithelial cell is often coupled with cytokinesis. During mitotic exit, centrosomes move to the future AM site, raising questions about their role in polarization. We perturbed centrosomes and polarity regulators in Matrigel-cultured cells and manipulated polarity direction using suspension culture to examine the relationships among polarization features. Surprisingly, centrosomal microtubules may not be necessary for centrosome positioning or AM formation, but their absence reduces the efficiency of AM formation. The polarity regulator Par3, rather than AM component trafficking, influences centrosome positioning. In suspension culture, centrosomes migrate in the direction opposite to AM formation. Taken together, our findings define the hierarchical relationships among several polarization features and show that centrosome-based polarity is not universal in epithelial cells, providing new insights into the mechanisms of epithelial polarization.
    Keywords:  3D culture; Madin–Darby canine kidney cells; cell biology; centrosome migration; cytokinesis; epithelial polarity; microtubule
    DOI:  https://doi.org/10.7554/eLife.101088
  22. Nat Phys. 2026 Aug 24.
      Amputated salamander limbs or fish fins precisely regenerate to their pre-injury size, providing a paradigm for positional memory. Although this phenomenon has been appreciated for centuries, how position-dependent cues control tissue growth remains unresolved. Here we quantify extracellular signal-regulated kinase (Erk) activity in whole populations of osteoblasts during zebrafish fin regeneration. We show that Erk activity scales with the amount of amputated tissue, predicts the likelihood of osteoblast cycling, and predicts the size of regenerated skeletal structures. We find that osteoblast Erk activity depends on fibroblast growth factors receptor signalling and organizes into millimetre-long gradients spanning from the distal tip to the amputation site. Mathematical modelling suggests gradients are established by acute, distally restricted deposition of ligand, whose activity is long-lived and transported by tissue growth. This mechanism is supported by the observed scaling of expression of the essential epidermal ligand Fgf20a with extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signalling and cycling to control size in regenerating appendages.
    DOI:  https://doi.org/10.1038/s41567-026-03426-w
  23. PLoS Genet. 2026 Sep;22(9): e1012301
      Disruption of endoplasmic reticulum (ER) homeostasis activates the unfolded protein response (UPR) to restore proteostasis. Although defects in the secretory machinery can induce ER stress, whether specific trafficking components actively couple cargo handling to UPR signaling remains unclear. Here, using Caenorhabditis elegans genetics, imaging, and biochemical assays, we show that neuronal overexpression of the gap junction protein UNC-9 cell-autonomously activates the IRE-1-XBP-1 branch of the ER UPR. Loss of the early secretory pathway proteins ERGI-2 or ERGI-3 suppresses this response and disrupts UNC-9 localization, revealing functions for these proteins that extend beyond cargo trafficking. ERGI-2 and ERGI-3 interact with both UNC-9 and the ER chaperone HSP-4/BiP, suggesting that they couple the handling of excessive UNC-9 to UPR activation. This requirement is cargo-selective: ERGI-2 and ERGI-3 are dispensable for UPR activation induced by overexpression of another innexin, UNC-7, or unrelated proteins. Moreover, activation of the IRE-1-XBP-1 pathway reduces abnormal UNC-9 accumulation in ergi-2 and ergi-3 mutants. Together, our findings identify ER-to-Golgi trafficking proteins as cargo-selective regulators that link secretory-pathway demand to adaptive UPR.
    DOI:  https://doi.org/10.1371/journal.pgen.1012301
  24. Nat Commun. 2026 Aug 07. pii: 9520. [Epub ahead of print]17(1):
      During de novo lumenogenesis, epithelial cells establish luminal identity by directing apical cargo to an apical membrane initiation site (AMIS). Although this process has been widely studied, the mechanisms governing AMIS formation and its progression into a luminal precursor remain poorly understood. Here we combine quantitative light and electron microscopy with proximity proteomics to demonstrate that apical cargo is delivered to the AMIS in large apical precursor organelles, termed vacuolar apical compartments (VACs). VACs possess a microvilli-rich cortex and undergo exocytic fusion at the AMIS to generate a nascent lumen. Lumen initiation is tightly coordinated with the assembly and rearrangement of apical cell junctions and requires the Crumbs complex protein PatJ. Together, our results show that PatJ is a key structural determinant of the apical-lateral interface and indicate that VACs act as specialized transport organelles that deliver a preassembled apical surface to the AMIS, enabling rapid and efficient lumen initiation.
    DOI:  https://doi.org/10.1038/s41467-026-75503-w
  25. Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2533876123
      Obstacles to translation elongation stall ribosomes and allow deleterious proteins to accumulate, which threatens cellular health. Cells recognize and clear stalled ribosomes via several interrelated pathways, although the mechanisms by which cells distinguish stalled from normally elongating ribosomes and mount an appropriate response are incompletely understood. While recent work highlights how ribosome collisions help cells to recognize stalled ribosomes, how other factors contribute to detection remains unclear. Here, we report a requirement for the translational factor eIF5A in the mRNA decay response to ribosomal stalling, i.e., No-Go mRNA Decay (NGD). We identified the Caenorhabditis elegans polyamine transporter, catp-6, via a forward genetic screen as a factor required for NGD. During our mechanistic dissection of the catp-6 phenotype, we uncovered a role for cellular polyamines and the translation elongation factor eIF5A in NGD, and we show this requirement is conserved from C. elegans to Saccharomyces cerevisiae. Our analyses support the idea that cells use eIF5A to identify ribosomal stalls and execute NGD and uncover a molecular function for a core protein synthesis factor in limiting expression from stall-inducing mRNAs. Our work offers insight into how cells identify and remove problematic mRNAs from the translational pool. Our work also raises the possibility that dysregulated mRNA decay is an unrecognized pathophysiology associated with polyaminopathies and eIF5A disorders, of relevance to varied neurodegenerative and aging phenotypes and efforts to pharmacologically inhibit eIF5A.
    Keywords:  NGD; PARK9; eIF5A; polyamine; ribosome
    DOI:  https://doi.org/10.1073/pnas.2533876123
  26. Nat Commun. 2026 09 08. pii: 9358. [Epub ahead of print]17(1):
      A major gap in our understanding of animal development is how adult body plans arise in animals with indirect development, where adults emerge from the transformation of a distinct larval form during metamorphosis. We address this question by examining cellular changes in the enteropneust hemichordate Schizocardium californicum, a species with a complex lifecycle and dramatic metamorphosis. Employing whole-body single-cell RNA sequencing, we chart the cellular composition and transcriptional dynamics of larval, metamorphic, and adult stages. Our tissue-level atlas reveals that ectodermal and endodermal cell types in larvae and adults occupy distinct transcriptional spaces, showing greater similarity to other cell types within the same life stage than to their counterparts in the opposite stage. In contrast, mesodermal cell types from both larvae and adults cluster closely together, indicating conserved transcriptional profiles. These findings demonstrate that the extensive morphological reorganization during metamorphosis is accompanied by broad shifts in transcriptional identity and reveal life-history stage as a major organizing axis of cellular state during the larva-to-adult transition.
    DOI:  https://doi.org/10.1038/s41467-026-77191-y
  27. Nat Metab. 2026 Sep 07.
      Metabolic remodelling underlies tumour progression. However, how metabolites act as signalling molecules to support cancer cell proliferation remains unclear. Here we show that argininosuccinate (ASA), a key intermediate of the urea cycle, promotes purine nucleoside biosynthesis in tyrosine kinase-driven haematological malignancies. Mechanistically, BCR-ABL phosphorylates argininosuccinate synthase 1 (ASS1), which increases ASA production from citrulline. ASA directly binds cytosolic 5'-nucleotidase II (NT5C2) and enhances its nucleosidase activity. The resulting purine nucleosides serve as a carbon source for glycolysis and the tricarboxylic acid cycle, which supports leukaemia cell proliferation under glucose-replete conditions. Loss of ASS1 or NT5C2 disrupts central carbon metabolism and inhibits leukaemia progression in vivo, which can be rescued with inosine or adenosine supplementation. Collectively, our findings uncover an ASA-NT5C2 signalling axis linking urea cycle dysregulation to purine metabolism, and identify purine nucleosides as a carbon source in tyrosine kinase-driven haematological malignancies.
    DOI:  https://doi.org/10.1038/s42255-026-01586-w
  28. Sci Adv. 2026 Sep 11. 12(37): eaef4578
      Hedgehog family morphogens present an interesting paradox: Despite being hydrophobic because of dual-lipid modifications, they form spatial concentration gradients that are highly conserved and essential for many aspects of metazoan development. Using live-cell single-molecule tracking and engineered synthetic signaling ligands, we isolated the distinct contribution of each lipid modification to Hedgehog diffusion and signaling potency. We found that although both lipid modifications enhance signaling potency, they do so through different mechanisms. Palmitate directly promotes receptor engagement, whereas cholesterol topologically confines secreted morphogens on the cell surface, effectively using the lipid membrane as a nonsignaling co-receptor that enriches ligands locally at the cost of restricting long-range diffusion. Our results on the function of cholesterol point to an intrinsic trade-off between signaling potency and gradient formation, with implications for the evolution and mechanism of nonsignaling co-receptors.
    DOI:  https://doi.org/10.1126/sciadv.aef4578
  29. Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2538135123
      Biological ducts must transport fluids while preserving structural integrity, yet how mechano-signaling coordinates wall deformation with luminal flow in vivo remains unclear. Here, we combine intravital two-photon excitation microscopy, light-sheet imaging, and Förster resonance energy transfer-based kinase biosensors to resolve ejaculation-like events in the mouse vas deferens. Acute phenylephrine stimulation elicits a sequence of luminal dynamics: an initial retrograde pressure-redistribution wave followed by a ballistic antegrade flow that propels dense sperm suspensions from the proximal to the distal duct. This contraction-driven flow opens a normally collapsed, wrinkled distal segment, driving progressive lumen expansion and unfolding of epithelial wrinkles. We show that the vas deferens actively modulates luminal geometry in response to these flow dynamics: ROCK activity in smooth muscle is required for global contraction and cAMP-associated signaling modulates this contractile response. By contrast, extracellular signal-regulated kinase activity in circumferential smooth muscle is dispensable for the ductal contraction but essential for active, flow-dependent remodeling of the distal lumen, forming the core of the mechano-signaling module that couples sperm flow to valve opening. These findings establish the vas deferens as an experimentally tractable model of ductal tissue hydraulics and reveal a mechano-signaling framework by which a tubular organ converts transient muscular input into robust, directional luminal transport.
    Keywords:  intravital imaging; male reproduction; mechano-signaling coupling; sperm transport; vas deferens
    DOI:  https://doi.org/10.1073/pnas.2538135123
  30. Nat Commun. 2026 Aug 11. pii: 9634. [Epub ahead of print]17(1):
      Wound closure is an essential aspect of regeneration, often serving as the first morphogenetic step preceding downstream events. Animals capable of whole-body regeneration can heal virtually any wound, but how the process of re-epithelialization compares across injury types remains understudied. Here, we investigate wound closure in the acoel Hofstenia miamia. We find that H. miamia deploy two distinct modes of closure, depending on which epithelial layers are injured. Regardless of geometry, wounds that injure the outer epidermis close by constriction. In contrast, damage to both the outer epidermis and pharyngeal epithelium induces long, actin-rich protrusions that form transient bridges across the wound prior to re-epithelialization. Muscle contraction is differentially required across conditions, and pharmacological inhibition of actomyosin contractility is sufficient to shift closure dynamics across epithelia. This work compares wound closure within the same animal, identifying a wide toolkit of repair strategies that appears independent of subsequent regenerative processes.
    DOI:  https://doi.org/10.1038/s41467-026-76555-8
  31. Nat Struct Mol Biol. 2026 Sep 10.
      The Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactors Ufd1 and Npl4 to extract polyubiquitinated proteins from membranes or multisubunit complexes, promoting their proteasomal degradation. A ubiquitin molecule in the chain is unfolded in an ATP-independent manner and initiates substrate translocation through the central pore of the ATPase. How ubiquitin is unfolded remains unclear. Here we demonstrate that the UT3 domain of Ufd1 specifically interacts with two K48-linked ubiquitins and unfolds one of the ubiquitins by binding its C-terminal β-strand into a conserved hydrophobic cleft. Simultaneous binding of UT3 to two ubiquitin molecules is required to overcome the energy barrier of ubiquitin unfolding. Subsequently, the UT3-unfolded ubiquitin is captured by Npl4 and Cdc48/p97. Experiments in vitro and in cells show that unfolding-defective mutants of Ufd1 indeed compromise Cdc48/p97 function. Our results provide a reasonable explanation of how simple protein-protein interactions cause the unfolding of the remarkably stable ubiquitin.
    DOI:  https://doi.org/10.1038/s41594-026-01884-7
  32. Elife. 2026 Sep 08. pii: RP110172. [Epub ahead of print]15
      RNA-binding protein TAR DNA-binding protein 43 (TDP-43) can form liquid-like nuclear assemblies whose phase behavior is thought to influence its aggregation propensity and neurotoxic activity. The mechanisms that govern the liquid-to-solid phase transition of TDP-43 remain poorly defined. Here, we combined chemical and genome-wide genetic screens to identify cellular factors that modulate the phase behavior of an RNA-binding-defective TDP-43 mutant. Our screens uncovered multiple cellular processes, including RNA splicing, protein translation, proteostasis imbalance, and nuclear export as TDP-43 phase regulators. We also developed a semi-permeabilized cell system that partially recapitulates the TDP-43 phase transition in vitro, and showed that nuclear export inhibition reshapes the nuclear environment to favor RNA-dependent liquid-liquid phase separation (LLPS) of TDP-43, which mitigates its aggregation. Nuclear export inhibition in a brain organoid model bearing an ALS-associated mutation reduces pathogenic phospho-TDP-43 accumulation. These findings identify multiple modulators of TDP-43 phase transitions in a sensitized model system and establish a framework for further dissecting the link between nuclear transport and TDP-43 phase dynamics.
    Keywords:  TDP-43; XPO1; cell biology; human; liquid-liquid phase separation; protein aggregation
    DOI:  https://doi.org/10.7554/eLife.110172
  33. Genes Dev. 2026 Sep 11.
      How mammalian organ size is precisely regulated remains incompletely understood. This process depends on the coordinated balance between cell proliferation, differentiation, and apoptosis. In the heart, the epicardium plays a central role in embryonic cardiac growth as a source of multiple cardiac progenitor lineages. The transcription factor Wt1 is essential for epicardial development and maturation, and its loss disrupts epicardial maintenance and the generation of epicardial-derived cells (EPDCs). In addition, the epicardium produces mitogenic factors required for cardiomyocyte (CM) proliferation, including those of the insulin-like growth factor (IGF) signaling pathway. Consistently, functional inactivation of Igf1 or Igf2 in mice results in severe prenatal growth reduction, with mutant embryos ∼60% smaller than controls, underscoring the roles of these genes in organ and fetal growth. We recently identified the cardiac lymphatic vasculature as an unexpected regulator of heart size during embryonic development. Here, by combining single-cell RNA sequencing with loss-of-function mouse models, we uncover a critical regulatory network linking cardiac lymphatics, the epicardium, Wt1, and Igf1 signaling that controls the final stages of embryonic cardiac growth. Our findings suggest that cardiac lymphatics act as a physiological quality control system for heart growth. Furthermore, using gain-of-function approaches in human epicardial organoids, we demonstrate that Reelin promotes epicardial fate, suggesting that the beneficial roles of lymphatics in adult cardiac repair are likely mediated through Reelin-dependent epicardial reactivation.
    Keywords:  Igf1; Reelin; Wt1; epicardioids; epicardium; heart; insulin-like growth factor; lymphangiocrine; lymphatics; mouse
    DOI:  https://doi.org/10.1101/gad.354151.126
  34. Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2530056123
      Pulsatile actomyosin networks emerge as a widespread mechanism driving tissue morphogenesis. Compared with myosin-II pulses, F-actin pulses are largely unexplored. By studying Drosophila oogenesis, we report that basal pulsatile actomyosin networks consist of F-actin bundle and meshwork architectures, implicating the existence of different F-actin microstructures and corresponding nucleators. Here, Rac1 and the Scar/WAVE-Arp2/3 complex (branched F-actin nucleator), exhibiting constant levels, are necessary to support F-actin pulsation, whereas pulses of Dia (unbranched F-actin nucleator) trigger F-actin pulsation. The pulsatile F-actin networks recruit the F-actin turnover regulator cofilin, thus generating cofilin pulses. Cofilin at relatively low concentration can cooperate with F-actin nucleators to amplify F-actin and enhance its pulsation, while cofilin at relatively high concentration might trigger the F-actin disassembly to attenuate its pulsation. These two different effects of cofilin on F-actin pulsation were confirmed by Zdk-cofilin optogenetics. Rac1 signaling, Dia, and cofilin are also crucial for F-actin pulses in border cell migration. Our findings thus reveal a coordinated regulation of F-actin pulses conferring actomyosin contractility in morphogenesis and cell migration.
    Keywords:  F-actin pulsation; Rac1–Rho1 signaling synergy; cell migration; cofilin; morphogenesis
    DOI:  https://doi.org/10.1073/pnas.2530056123
  35. Nature. 2026 Sep 09.
      An animal's ability to survive and thrive-whether fleeing from danger, eating a meal, or fighting an infection-arises from the collective moment-to-moment activity of many interacting cell types throughout the body. Physiology seeks to elucidate these cellular interactions that span organs, cell types and timescales, but has been limited by the inability to record this time-varying cellular activity simultaneously throughout the entire body. Here we develop WHOLISTIC (WHole-Organism Live-Imaging System for recording Tissue and IntraCellular activity), a method to image second-timescale activity of cells across the entire vertebrate body at cellular resolution. WHOLISTIC advances and integrates volumetric fluorescence microscopy, machine learning, and pancellular transgenic expression of calcium sensors1, demonstrated in larval zebrafish, with proof of concept in adult Danionella cerebrum. To access information about the molecular and ultrastructural substrates for the measured dynamics, we advanced whole-body expansion microscopy2. At the cellular scale, body-wide screening revealed unexpected responses, including chondrocyte reactions to cold and meningeal responses to ketamine. At the organ scale, WHOLISTIC identified rhythmic travelling waves along the renal nephron. At the multi-organ scale, it revealed unknown muscle synergies and muscle-organ interactions. At the whole-organism scale, the method captured brainstem-controlled redistribution of body-wide blood flow. Combining optogenetics with WHOLISTIC enabled all-optical causal dissection of brain-body interactions. These advances establish a paradigm for systems biology that bridges cellular and organismal physiology, enabling comprehensive discovery across scales-from fundamental mechanisms to therapeutic targets.
    DOI:  https://doi.org/10.1038/s41586-026-10979-6
  36. Dev Cell. 2026 Sep 09. pii: S1534-5807(26)00322-9. [Epub ahead of print]61(9): 1762-1763
      Embryonic diapause is a reversible dormant state that allows mammalian blastocysts to survive periods of environmental or metabolic stress. In this issue of Developmental Cell, Furlan et al.1 report that Nodal/Smad2 signaling sustains diapause by repressing Pparg-driven lipid storage in the blastocyst.
    DOI:  https://doi.org/10.1016/j.devcel.2026.08.011
  37. Cell Rep. 2026 Sep 07. pii: S2211-1247(26)01037-5. [Epub ahead of print]45(9): 117959
      There is growing evidence that mRNAs undergo intercellular transfer through cytoplasmic connections called tunneling nanotubes (TNTs), but whether transferred mRNAs are translated and affect cellular changes post-transfer is unknown. Using multiple lines of evidence, we show that transferred mRNAs undergo translation and can complement the phenotype of genetic mutations in vitro. For example, the human peroxisome biogenesis disorder, Zellweger Syndrome, results from mutations in genes such as PEX5 and PEX6. We demonstrate that the co-culture of patient-derived PEX6 mutant fibroblasts or PEX5 knockout cells with wild-type cells leads to de novo peroxisome biogenesis. We provide additional examples of genetic complementation via transfer of mRNAs encoding the HSF1 transcription factor or CRE recombinase. Complementation occurs by TNT-mediated mRNA transfer and translation in acceptor cells, but not by exosomes, nor by protein or peroxisome transfer. Our study provides evidence for the physiological significance of mRNA transfer and suggests another approach for mRNA therapeutics.
    Keywords:  CP: cell biology; CP: genomics; CRE; RNA trafficking; Zellweger syndrome; heat-shock; heat-shock factor 1; mRNA transfer; peroxisome; smFISH; tunneling nanotubes
    DOI:  https://doi.org/10.1016/j.celrep.2026.117959
  38. Nat Cardiovasc Res. 2026 Sep;5(9): 848-868
      Understanding how spatial organization and cell-cell interactions shape gene regulatory programs is central to decoding tissue development and function. The transition at birth, marked by increased circulatory demands and rapid tissue growth, requires precise spatiotemporal coordination of cardiac maturation. In this study, we generated a high-resolution spatial and temporal atlas of the postnatal mouse heart by integrating single-nucleus RNA sequencing with image-based spatial transcriptomics. This framework revealed dynamic cellular interactions, niche-specific signaling and transcriptional programs guiding cardiomyocyte maturation. To functionally test prioritized regulators in vivo and at scale, we developed PIP-seq (probe-based indel-detectable Perturb-seq), a high-throughput platform that detects single guide RNA identity, infers gene editing and profiles transcription from fixed nuclei. Applying PIP-seq to the developing postnatal heart, we identified 21 previously uncharacterized regulators of cardiomyocyte maturation, including genes essential for sarcomere assembly, metabolic reprogramming and electrophysiological transitions. Together, our findings define how microenvironmental signals and intrinsic gene programs cooperate to guide heart maturation and establish a broadly applicable framework for functional genomics in complex tissues.
    DOI:  https://doi.org/10.1038/s44161-026-00861-z
  39. Cell. 2026 Sep 10. pii: S0092-8674(26)01001-9. [Epub ahead of print]
      Mitochondria are four-dimensional (4D: x, y, z, and time) organelles essential for cellular function. Characterizing their 4D phenotypic landscape across diverse cellular states requires both 4D imaging and analytical frameworks. We present MitoSpace, a self-supervised deep learning model trained without labels on terabytes of single-cell lattice light-sheet microscopy data of mitochondria under mechanistically distinct perturbations. MitoSpace learns latent representations that outperform predefined features in drug classification and capture interpretable variation in mitochondrial morphology and dynamics. Regression probes predict mitochondrial membrane potential from the learned representations (R2 = 0.91), establishing a quantitative mapping between form and function at the single-cell level. MitoSpace also generalizes zero-shot to unseen perturbations and human lung organoids. Dimensionality ablation reveals that representation quality improves monotonically from 2D to 3D to 4D, demonstrating the importance of volumetric and temporal information. The model, dataset, and interactive explorer are publicly available, providing a foundation for 4D phenotypic screening.
    Keywords:  contrastive learning; drug mechanism of action; foundation model; high-content phenotypic screening; lattice light-sheet microscopy; live-cell 4D imaging; mitochondria; mitochondrial dynamics; mitochondrial membrane potential; self-supervised learning
    DOI:  https://doi.org/10.1016/j.cell.2026.08.028
  40. Circulation. 2026 Sep 08.
       BACKGROUND: Direct reprogramming of cardiac fibroblasts (CFs) into induced cardiomyocytes (iCMs) holds promise as a therapeutic strategy for heart regeneration. After myocardial infarction (MI), resident quiescent CFs (QCFs) activate and differentiate into myofibroblasts (MFs) in the infarcted region that drive pathological cardiac fibrosis. Converting these injury-activated MFs into iCMs could simultaneously alleviate fibrosis and replenish lost cardiomyocytes. However, whether the marked heterogeneity of CFs in the infarcted heart, and in particular the activation of QCFs into MFs, creates an intrinsic barrier that limits the reprogramming of these injury-activated MFs remains unknown.
    METHODS: To define the molecular basis of this heterogeneity, we purified PDGFRα+ CFs and used Postn lineage tracing to distinguish injury-activated MFs from quiescent CFs, enabling matched comparison of their reprogramming competence and single-cell RNA sequencing (scRNA-seq) profiling of post-MI CF subpopulations. A targeted in vitro shRNA screen was conducted against 9 MF-enriched TFs as candidate molecular barriers for cardiac reprogramming. The lead candidate was validated in mouse MFs, human iPSC-derived MFs, primary human MFs, and in vivo using dual-recombinase-mediated lineage tracing. Mechanistic insights were gained through integrated bulk RNA-seq, scRNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag), together with functional assays including DNA-binding-deficient and domain-swap MEOX1 mutants.
    RESULTS: We identified the upregulated transcription factor MEOX1, a known fibrosis determinant downstream of the key post-MI cytokines transforming growth factor-beta 1 and interleukin-1 beta, as the principal molecular barrier responsible for the profound reprogramming resistance of MFs. MEOX1 knockdown markedly enhanced reprogramming efficiency in both mouse and human MFs and enabled GATA4-free reprogramming combinations. This inhibition depended on the transcriptional activation activity of MEOX1, as disrupting its DNA-binding domain or fusing it to a repressor domain rescued reprogramming. Integrated scRNA-seq and CUT&Tag analyses revealed that MEOX1 binds and stabilizes a fibrotic, MF-defining transcriptional program that antagonizes the cardiogenic program while also modulating the inflammatory response; its knockdown disrupted this fibrotic network to favor iCM fate acquisition. Using stringent dual-recombinase lineage tracing, we demonstrated that MEOX1 knockdown enables highly efficient in vivo MF-to-iCM conversion, leading to significant reductions in cardiac fibrosis and substantial improvement in cardiac function after MI.
    CONCLUSIONS: Our study identifies pathological MEOX1 upregulation as a key mechanism underlying the reprogramming resistance of post-MI mouse MFs and activated human MFs. Overcoming this barrier achieves unprecedented, lineage-confirmed in vivo reprogramming efficiency, thereby addressing a significant obstacle for the clinical translation of in situ reprogramming therapies.
    Keywords:  cellular reprogramming; fibrosis; myocardial infarction; myofibroblasts; regeneration
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.126.078415