bims-ginsta Biomed News
on Genome instability
Issue of 2026–08–23
28 papers selected by
Jinrong Hu, National University of Singapore



  1. Nat Aging. 2026 Aug 20.
      Cellular senescence contributes to aging and age-related diseases by driving chronic inflammation through the senescence-associated secretory phenotype (SASP), including interferon-stimulated genes (ISGs). Here we confirm and extend previous observations that cyclin D1 (CCND1), a key cell cycle regulator, is paradoxically upregulated across models of nonproliferating senescent cells. We show that CCND1 and its kinase partner CDK6 drive SASP and ISG expression in senescent cells by promoting DNA damage accumulation. This leads to the formation of cytoplasmic chromatin fragments that activate pro-inflammatory cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling. In aged mouse livers, senescent hepatocytes show increased Ccnd1 expression. Hepatocyte-specific Ccnd1 knockout or treatment with the clinical grade CDK4/6 inhibitor palbociclib reduces DNA damage and ISGs in aged mouse liver. Further, palbociclib suppresses frailty and improves physical performance of aged mice. These findings demonstrate a role for CCND1/CDK6 in regulating DNA damage and inflammation in senescence and aging, highlighting it as a promising target for therapeutic repurposing.
    DOI:  https://doi.org/10.1038/s43587-026-01196-x
  2. Nat Struct Mol Biol. 2026 Aug 18.
      Nuclear envelope (NE) reformation after mitosis is essential for daughter cell viability and requires tightly coordinated nuclear pore complex (NPC) assembly and nuclear membrane reformation. Here we combined acute molecular perturbations in live cells with correlative three-dimensional electron tomography or MINFLUX super-resolution microscopy to show that degrading Nup62 during mitosis arrests NPC assembly at an intermediate step with smaller membrane pores and removes the whole central transport channel. Molecular dynamics simulations predicted that 32 copies of the central channel subcomplex, recruited into the previously unoccupied pore center, can self-associate through hydrophobic interactions to occupy and expand pore volume, exerting an outward-pushing force; indeed, disrupting these interactions during NPC assembly blocked pore dilation. Later in mitotic exit, perturbed cells exhibited impaired nuclear import, smaller nuclei and looser NE spacing. Acute inhibition of nuclear import recapitulated these NE defects without affecting NPC assembly. Together, our findings reveal a two-step molecular mechanism linking NPC assembly and NE reformation. First, hydrophobic FG-nucleoporins dilate the assembling nuclear pore by forming the central transport channel, which then allows nuclear-import-driven nuclear expansion, leading to tight, regular NE membrane spacing.
    DOI:  https://doi.org/10.1038/s41594-026-01865-w
  3. Proc Natl Acad Sci U S A. 2026 Aug 25. 123(34): e2528342123
      Collective migration of epithelial cells drives diverse tissue remodeling processes. In many cases, a free tissue edge works alone or in combination with other external cues to align the cells for collective movement, but how edge-free or closed epithelia become polarized for directed migration without these cues is unclear. Here, we use the rotational migration of the follicular epithelial cells in the Drosophila egg chamber to explore how cells in an edgeless epithelium initiate rotational collective migration, and how the rotational axis is specified. By employing methods for long-term live imaging and delaying the onset of rotation, we show that symmetry breaking can occur at multiple developmental stages and that the atypical cadherin Fat2 promotes local motility at the basal epithelial surface before rotation begins. We then combine experiments with theoretical modeling to identify a positive feedback loop in which planar polarization of Fat2 aligns the front-rear axes of the individual cells in a common direction and the resulting tissue motion leads to the planar polarization of Fat2. This mechanosensitive feedback, coupled with rigid-body dynamics of the egg chamber, can break chiral symmetry and produce sustained rotation in silico. We further propose that mechanical constraints arising from intertissue interactions and tissue geometry ensure that rotation occurs around the anterior-posterior axis. Our findings suggest a biophysical mechanism-combining Fat2-mediated velocity-polarity alignment, rigid-body dynamics, and tissue geometry-by which a closed epithelial tissue can self-organize into persistent, large-scale rotational migration in vivo, expanding current flocking theories.
    Keywords:  chiral symmetry breaking; collective cell migration; epithelium; mathematical modeling; self-organization
    DOI:  https://doi.org/10.1073/pnas.2528342123
  4. Cell Rep. 2026 Aug 16. pii: S2211-1247(26)00938-1. [Epub ahead of print]45(8): 117860
      At the onset of eukaryotic DNA replication, double hexamers of MCM2-7 are assembled into inactive pre-replication complexes (pre-RCs) at replication origins. An excess of pre-RCs is loaded onto DNA, but only a fraction becomes activated to form CMG helicases when origins fire. The replisome, built around CMG, must navigate past dormant origins harboring inactive pre-RCs, but the mechanism by which this is achieved is unclear. Here, we used single-molecule imaging to visualize collisions between replisomes and pre-RCs during DNA replication in Xenopus laevis egg extracts. We show that pre-RCs are frequently removed from DNA upon collision and that efficient pre-RC removal requires the accessory helicases FANCJ and RTEL1. Furthermore, simultaneous depletion of both FANCJ and RTEL1 in human cells leads to pre-RC accumulation on chromatin and DNA damage. Together, our findings reveal a role for FANCJ and RTEL1 in pre-RC removal, ensuring efficient replication fork progression and maintaining genome stability.
    Keywords:  CP: molecular biology; FANCJ; MCM2-7; RTEL1; eukaryotic DNA replication; single-molecule imaging
    DOI:  https://doi.org/10.1016/j.celrep.2026.117860
  5. Cell. 2026 Aug 20. pii: S0092-8674(26)00639-2. [Epub ahead of print]189(17): 5449-5465.e5
      A recent study reported the existence of lymphatic vessels in normal bone and suggested their involvement in bone regeneration after injury. However, this conclusion was based on approaches that do not allow unequivocal identification of the spatial localization of lymphatic endothelial cells (LECs). Here, we employed a Prox1-based genetic tool and a dual-recombinase-mediated LEC-specific labeling system to trace lymphatic vessels with high specificity. We found that LECs are present in the connective tissues, including the periosteum surrounding the bone. However, they do not reside within the bone itself, nor do they penetrate the periosteum to facilitate bone regeneration after injury. By contrast, hyperplastic LECs on the bone surface breach the periosteum and invade bone tissue in mouse models of generalized lymphatic anomaly and Gorham-Stout disease. These data demonstrate that lymphatic vessels are absent from bone during homeostasis and regeneration after injury but invade bone during disease. This Matters Arising paper is in response to Biswas et al. (2023), published in Cell. See also the response by Yang et al. (2026), published in this issue.
    Keywords:  bone; disease; dual recombinase; lineage tracing; lymphatic endothelial cells; lymphatic vessels; repair
    DOI:  https://doi.org/10.1016/j.cell.2026.05.039
  6. Dev Cell. 2026 Aug 21. pii: S1534-5807(26)00288-1. [Epub ahead of print]
      Organs comprise diverse cell types originating from shared or distinct lineages. During embryogenesis, mesodermal Pax7+ progenitors give rise to skeletal muscle as well as non-muscle lineages like dermis and adipocytes. Here, we asked whether Pax7+ cells retain multipotency during early postnatal limb muscle growth. Lineage tracing in neonatal mice revealed unexpected early postnatal plasticity, yielding multiple non-myogenic lineages, including a previously unrecognized subpopulation of fibro-adipogenic progenitors, termed Pax7FAPs. Using mouse models, we demonstrated that Notch signaling primes neonatal Pax7+ cells toward a fibrogenic molecular identity, biasing their trajectory away from myogenesis. Long-term tracing confirmed that neonatally generated Pax7FAPs persist into adulthood. Furthermore, adult muscle injury triggered de novo generation of Pax7FAPs, which exhibited higher proliferative capacity than resident stromal cells. This postnatal Pax7+ multipotency reveals an additional cellular contribution to muscle development and regeneration.
    Keywords:  FAPs; Notch signaling; lineage tracing; multipotency; muscle; plasticity; postnatal development; progenitors; stem cells
    DOI:  https://doi.org/10.1016/j.devcel.2026.07.019
  7. Cell. 2026 Aug 19. pii: S0092-8674(26)00923-2. [Epub ahead of print]
      Human protein-coding genes evolved via rearrangement of domains from ancestral genes. We develop a scalable, evolutionarily guided method to assemble novel genes from constituent domains within a protein family, termed DESynR (domain engineered via synthesis and recombination) genes. In primary human T cells, DESynR activator protein-1 (AP-1) transcription factors (TFs) significantly outperform natural AP-1 TFs across in vitro and in vivo antitumor assays. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming and establish non-natural T cell states that optimize features of exhaustion, effector and cytotoxic function, and persistence-sometimes co-opting gene modules from disparate cell types. Reprogramming is primarily driven by differential regulation of established AP-1-bound regulatory elements rather than unique binding. Finally, we screen DESynR erythroblast transformation-specific (ETS) and forkhead box (FOX) TFs to support generalizability across protein families. Overall, we demonstrate that reconfiguring existing protein domains may uncover non-evolved genes that program therapeutically relevant cell states.
    Keywords:  CAR T cells; genome engineering; synthetic biology; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.cell.2026.07.054
  8. Science. 2026 Aug 20. 393(6813): eady3027
      Coronary collateral arteries have been proposed to form de novo through artery reassembly, a process in which arterial endothelial cells (ECs) migrate away from preexisting arteries and reassemble into new arteries. Using genetic tools that trace arterial ECs, we found that their contribution to collaterals is modest. Dual genetic lineage tracing revealed that capillary ECs, rather than arterial ECs, serve as the major building blocks for de novo collaterals. The capillary-to-collateral conversion is functionally crucial for cardiac repair. In addition, transient Vegfa expression through modified messenger RNA markedly promoted collateral formation. Mechanistically, vascular endothelial growth factor (VEGF) drives arterialization by regulating HES1 transcription through YY1/SETD1A-mediated H3K4 trimethylation. Collectively, these findings redefine the cellular origin and mechanism of coronary collateral formation and highlight its role in facilitating efficient cardiac repair.
    DOI:  https://doi.org/10.1126/science.ady3027
  9. Nat Aging. 2026 Aug 19.
      Aging is characterized by persistent low-grade inflammation linked to impaired tissue homeostasis, yet the underlying molecular mechanisms remain poorly understood. The mammalian skin is a clinically relevant site of aging-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress and DNA damage accumulation. Here we show that, in the murine epidermis, aging engages a previously uncharacterized BMAL1-YAP functional cooperation with enhanced binding at inflammation-related enhancers, amplifying target gene transcription. Independent of its circadian clock role, BMAL1 partners with the mechanosensitive cofactor YAP at enhancer regions to regulate epidermal identity genes. However, in aged skin, this cooperative binding undergoes a functional shift, enhancing the expression of inflammation-related genes, partially coregulated by NF-κB. In addition, aged pro-inflammatory IL-17 signaling activates YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal aging, linking chromatin dynamics to inflammatory programs through rewiring of BMAL1-YAP-occupied enhancers, highlighting potential strategies to counteract chronic inflammation and restore tissue homeostasis during aging.
    DOI:  https://doi.org/10.1038/s43587-026-01192-1
  10. Cell Genom. 2026 Aug 17. pii: S2666-979X(26)00193-X. [Epub ahead of print] 101331
      Super-enhancer (SE) hubs have been proposed to coordinate gene expression through 3D genome organization and transcriptional condensates. Using multiplexed imaging, we mapped hundreds of SEs in thousands of mouse embryonic stem cells and also paired SE position with nascent transcription measurements. We found that most SEs are spatially isolated, with multiway SE hubs occurring in only a small fraction of cells. Rare hubs were largely promiscuous, cooperative aggregates shaped by genomic proximity, nuclear speckle association, and general transcription machinery occupancy. Perturbing cohesin, CTCF, BET proteins, or RNA polymerase II showed that normal genome organization generally suppresses SE clustering. Combined RNA and DNA imaging demonstrated that SE hubs were neither necessary nor sufficient for transcriptional bursting, although larger hubs weakly increased burst probability. These results challenge models in which SE hubs are a dominant mechanism of enhancer function and instead suggest rare transcriptional crosstalk.
    Keywords:  3D genome organization; clustering; enhancer hub; enhancers; multiplexed imaging; single-cell gene expression; super-enhancers
    DOI:  https://doi.org/10.1016/j.xgen.2026.101331
  11. Cell Syst. 2026 Aug 19. pii: S2405-4712(26)00190-0. [Epub ahead of print] 101708
      The ability to follow transcription in individual cells with live imaging has revealed key dynamical mechanisms of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light-sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of the transcriptional dynamics of the segmentation clock. Our measurements reveal that smooth clock protein oscillations arise from discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.
    Keywords:  light sheet fluorescence microscopy; somitogenesis; transcription; zebrafish
    DOI:  https://doi.org/10.1016/j.cels.2026.101708
  12. bioRxiv. 2026 Aug 06. pii: 2026.08.02.741928. [Epub ahead of print]
      Mosaic chromosomal alterations (mCAs) increase with age and are associated with multiple diseases, yet the cell types and states that harbor these alterations remain largely unknown. Because mCAs arise in individual cells prior to clonal expansion, they are typically rare and obscured in bulk data. We develop CHASM, a method for detecting chromosomal copy number alterations (CNA) from single-cell chromatin accessibility (scATAC-seq) data, a scalable modality that captures both cell state and chromosomal alterations. CHASM estimates a CNA-null background for each cell, providing an individualized expectation for chromosomal accessibility, which is critical in non-neoplastic tissues where alteration-carrying cells are not readily distinguishable from normal. By comparing each cell against its expected background, CHASM distinguishes chromosomal alterations from background variation and achieves more stringent control of false positives. We validate CHASM using in silico spike-in experiments, cross-modality comparisons with matched single-cell DNA and RNA data, and established genome-instability contrasts, including p53 deficiency and chromosome Y loss. Applied to multiple aging data sets, CHASM consistently recovers mCA burden in age-susceptible cell populations and reveals aging-associated signatures not detected by existing methods. In a cohort of 99 human kidney samples spanning age and disease conditions, CHASM identifies enrichment of mCAs in injury-associated cell states (VCAM1-high proximal tubule cells). Notably, CHASM detects the age-associated emergence of mCAs in cancer-relevant genomic regions, including chromosomes 3 gains and losses and chromosome 7 gain, in ostensibly normal cell populations. Cells harboring mCAs exhibit activation of injury-response regulatory programs and reduced epithelial identity programs, while elevated mCA burden in specific epithelial populations are associated with increased immune and stromal infiltration. Overall, we develop CHASM for high-specificity detection of CNA at single cell resolution. Applied across tissues, CHASM reveals aging-patterns of genome instability within cell types and implicates mCAs in early, pre-disease cellular states.
    DOI:  https://doi.org/10.64898/2026.08.02.741928
  13. Biophys J. 2026 Aug 21. pii: S0006-3495(26)00582-5. [Epub ahead of print]
      Integrins are bidirectional mechanochemical receptors that transmit signals upon ligand binding to the cytoskeleton (outside-in) and cytoskeletal forces back across the membrane (inside-out) to the integrin-ligand bond. Integrins are activated prior to ligand binding, which involves large conformational rearrangements across the extracellular, transmembrane, and cytoplasmic regions. While the conformational and energetic basis of outside-in activation is increasingly well defined, the mechanical forces required for separating the tightly packed αβ transmembrane (TM) helices during inside-out signaling remain largely unknown. Here, we directly quantify the forces required to dissociate integrin TM domains (TMDs) in a lipid environment. Engineered α5β1 polypeptides consisting of TMDs and cytoplasmic tails were reconstituted into lipid nanodiscs and probed using single-molecule optical tweezers. Mechanical marker domains on each cytoplasmic tail verified correct vectorial force application, and fluorescent lipids confirmed nanodisc integrity. We find that the heterodimeric TM complex is a mechanically robust unit. In wild-type constructs, no TMD separation was observed in repeated pulls up to ∼35 pN. Point mutations in the β1-TMD (G744L, L748R) that weaken TMD interactions revealed discrete splitting events. The high mechanical forces necessary for TMD separation support a "ratchet-like" role for mechanical forces in inside-out signaling: rather than actively opening closed TMDs they prevent re-closing of spontaneously split TMDs thus keeping them open and activated.
    DOI:  https://doi.org/10.1016/j.bpj.2026.08.017
  14. Nature. 2026 Aug 19.
      The human brain develops and matures over an exceptionally prolonged period of time that spans nearly two decades of life. Processes that govern species-specific aspects of human postnatal brain development are difficult to study in animal models1. While human brain organoids offer a promising in vitro model, they have thus far been shown to largely mimic early stages of brain development. Here we develop human brain organoids for 5 years in culture, optimizing growth conditions to extend excitatory neuron viability beyond previous limits. Using maturation-associated modules derived from endogenous human brain, we show that brain organoids transcriptionally age with cell type specificity over years in culture. Whole-genome methylation profiling reveals that the predicted epigenomic age of organoids correlates precisely with time spent in vitro, and parallels epigenomic ageing in vivo. Notably, we show that in chimeric organoids generated by mixing neural progenitors of different ages, old progenitors rapidly produce late neuronal fates, skipping the production of earlier neuronal progeny, therefore showing that progenitors that age in organoids retain a memory of the time spent in vitro. The data indicate that human brain organoids can continue to mature and record the passage of time over many years in culture.
    DOI:  https://doi.org/10.1038/s41586-026-10877-x
  15. bioRxiv. 2026 Aug 03. pii: 2026.07.31.742119. [Epub ahead of print]
      Spatial patterning of mRNA translation is a fundamental process in early embryogenesis. Existing RNA translation profiling methods lack subcellular spatial resolution at the single-molecule level, limiting our understanding of spatial RNA biology in embryogenesis. To address this, we profiled the spatial translatome of intact mouse embryos at near-genomic scale by adapting RIBOmap and incorporating multiplexed organelle staining. In oocytes, 2-cell and 4-cell embryos, we systematically analyzed RNA translation across three spatial scales: organelle, subcellular, and intercellular. We found that functionally related genes exhibit spatially and temporally controlled translation patterns near distinct organelles. Using Harmonics, a graph signal processing framework, we demonstrate that embryo asymmetry emerges at the first cell division and is amplified at later stages. This work paves the way for comprehensively investigating the fundamental spatial post-transcriptional regulation at the earliest moments of mammalian life.
    DOI:  https://doi.org/10.64898/2026.07.31.742119
  16. Mol Cell. 2026 Aug 18. pii: S1097-2765(26)00511-3. [Epub ahead of print]
      A small fraction of the genome reproducibly positions near nuclear speckles (NSs), increasing the expression and/or splicing efficiency of NS-associated genes. How specific genomic regions in mammalian cells are targeted to NSs remains unclear. Here, we demonstrate the establishment of genome-wide NS association without active transcription. We show that DNA sequences derived from NS-associated regions, when integrated as transgenes, are autonomously targeted to NSs. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis-regulatory elements, including an ∼600-bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS targeting, properties that appear to be common among several other tested AADs. A subset of acidic activator TFs contains an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at the NS periphery for context-specific transcriptional responses.
    Keywords:  BAC; COL1A1; acidic activation domains; bacterial artificial chromosome; cis-regulatory elements; nuclear genome positioning; nuclear speckle; transcription independent
    DOI:  https://doi.org/10.1016/j.molcel.2026.07.025
  17. Nat Cell Biol. 2026 Aug 21.
      cGAS is the primary innate immune DNA sensor. On binding DNA, cGAS generates cGAMP, ultimately driving inflammation. Although normally silenced on self-DNA, genotoxic stress can activate cGAS, proposed to be mediated by micronuclei, chromosome bridges and DNA:RNA hybrids. However, mechanistically, this is poorly understood due to a lack of sensitive and selective single-cell cGAS activation assays. Here we solve this with an improved cGAMP reporter for microscopy, flow cytometry and biochemical assays. Strikingly, we find that genotoxic stress-mediated cGAS activation is a rare event that is not driven by enrichment on micronuclei and occurs by mechanisms that vary in dependence on the genotoxic stress. Following chromosome mis-segregation, cGAS activation correlates with bridge association but, notably, ionizing radiation activates cGAS independently of bridges. Whereas simple DNA:RNA hybrids are inert, more complex structures such as R-loops activate cGAS. Our work revises the cGAS signalling framework and introduces a flexible tool to examine it.
    DOI:  https://doi.org/10.1038/s41556-026-02037-0
  18. bioRxiv. 2026 Aug 05. pii: 2026.08.04.742839. [Epub ahead of print]
      Changes in the number of chromosomes or their spatial organization within the nucleus have critical consequences for cell fate. Yet capturing the karyotype or three-dimensional architecture of chromatin in living cells remains limited by the difficulty in labeling endogenous loci non-invasively. The most widely used tools rely on dCas9, a bulky protein whose persistent DNA binding interferes with DNA and RNA metabolism, causes DNA damage, and is hard to multiplex. We developed ZATELLITE , an AI-enabled tool to target endogenous repetitive sequences with fluorescently-tagged synthetic zinc fingers. ZATELLITE probes have key advantages over dCas9: they are smaller, easier to multiplex and, critically, they do not cause DNA damage or chromosomal abnormalities, even after long-term labeling. We generated a collection of ZATELLITE probes to label the centromeres of nearly all human chromosomes, enabling the capture of genome organization and karyotype alterations in real time in living cells. Finally, we show that ZATELLITE can be used for simultaneous labeling and epigenetic editing of centromeres. Thus, ZATELLITE is a non-toxic, versatile tool for genome visualization and manipulation.
    DOI:  https://doi.org/10.64898/2026.08.04.742839
  19. Circ Res. 2026 Aug 19.
       BACKGROUND: Pathological fibrosis is a major finding in cardiovascular diseases and can result in arrhythmia and heart failure. Desmosome gene mutations can lead to arrhythmogenic cardiomyopathy. Among arrhythmogenic cardiomyopathies, pathogenic DSP (desmoplakin) variants cause a distinctive cardiomyopathy with excessive cardiac fibrosis that could precede ventricular dysfunction. DSP variants are also linked to other fibrotic diseases. Whether DSP plays any role in pathological fibrosis remains unknown.
    METHODS: Mesenchymal stromal cells (MSCs) are resident fibroblast-like cells that are responsible for fibrogenesis in most organs, including the heart. We first used RNA-seq genome-wide analyses to generate cardiac fibroblast-like, induced pluripotent stem cell-derived MSCs from normal donors and patients with arrhythmogenic cardiomyopathy with DSP mutations. We then studied the fibrogenic responses of cardiac MSCs to TGFβ1 (transforming growth factor β1) using Western/Co-IP, autophagy assays, gene knockdowns/over-expressions, genomic analyses, mouse DSP knockdown models, immunostaining, and qPCR.
    RESULTS: TGFβ1 induced excessive accumulation of VIM (vimentin)/fibrillar collagens and over-activated fibrotic genes in DSP-mutant MSCs when compared with normal MSCs. In normal MSCs, VIMs bind to wild-type DSP during normal fibrogenesis after TGFβ1. DSP-mutant MSCs exhibited a haplo-insufficient phenotype with increased DSP-unbound VIMs that sequestered BECN1 (beclin-1) from activating autophagy and CAV1 (caveolin-1)-mediated endocytosis. Decreased autophagy caused collagen accumulation, and diminished CAV1 endocytosis resulted in abnormal CAV1 plaque formation that over-activated fibrotic genes (COL1A1, COL3A1, and fibronectin [FN]) via heightened p38 activity after TGFβ1. Genome-wide analysis and DSP knockdown in mouse fibroblasts confirmed this novel role of DSP mutations in pathological fibrosis. Overexpression of VIM-binding domains of DSP could suppress pathological fibrosis by increasing collagen autophagic degradation and decreasing fibrotic gene expression.
    CONCLUSIONS: Our data reveal that DSP deficiency in MSCs/fibroblasts leads to exaggerated fibrogenesis in DSP-cardiomyopathy by decreasing BECN1 availability for autophagy and CAV1-endocytosis. Overexpression of VIM binding domains of DSP could be a new strategy to treat pathological fibrosis.
    Keywords:  collagen; endocytosis; fibrosis; mutations; phenotype
    DOI:  https://doi.org/10.1161/CIRCRESAHA.124.325512
  20. Circ Res. 2026 Aug 21.
       BACKGROUND: Translational control of gene expression is crucial in cardiomyocytes, particularly in response to hypertrophic stimuli. The ERK (extracellular signal-regulated kinase) pathway plays a key role in inducing cardiac hypertrophy and regulating specific protein translation. However, it remains unclear how this specificity is achieved, and the spatiotemporal regulation of protein translation is not fully understood.
    METHODS: We used SINAP (single-molecule imaging of nascent peptide) reporters to visualize and analyze the translation dynamics in single adult rat ventricular cardiomyocytes and tracked active translation sites at high spatiotemporal resolution. We also examined the effects of adrenergic stimulation and the role of the ERK pathway in translation localization.
    RESULTS: Our findings revealed that translation sites are primarily localized near Z-lines in cardiomyocytes, with some sites being highly dynamic and moving during translation. The 3' untranslated regions did not significantly change the localization of translation. Many translation sites colocalized with microtubules, and their movement predominantly occurred along microtubular tracks. Adrenergic stimulation led to a transient shift in translation activity toward the perinuclear region, peaking at 12 hours and requiring ERK pathway activity for this localization change. This shift is part of the hypertrophic response and is required for early translation of genes such as Nppa.
    CONCLUSIONS: Our high-resolution single-cell study demonstrates that protein translation in cardiomyocytes is dynamic and responsive to hypertrophic stimuli in an ERK-dependent manner. The localized translation mechanism allows cardiomyocytes to rapidly adapt to changing environments by preferentially translating mRNAs in the perinuclear region. These findings provide new insights into the spatial regulation of translation in cardiomyocytes and its role in cardiac hypertrophy.
    Keywords:  adult; myocytes, cardiac; neurons; phosphorylation; serotonin
    DOI:  https://doi.org/10.1161/CIRCRESAHA.126.329033
  21. Dev Cell. 2026 Aug 18. pii: S1534-5807(26)00287-X. [Epub ahead of print]
      Intratumoral heterogeneity fuels cancer progression and therapy resistance, yet the cooperative mechanisms between distinct subclones remain poorly defined. Here, we uncover a tumor-promoting form of cell competition wherein malignant clones hijack interclonal Hedgehog (Hh) and Wnt signaling to convert competitive pressure into a pro-tumorigenic force. In Drosophila, we find that Pp1-87B depleted, RAS-mutant "loser" cells undergo Hh-mediated apoptosis while secreting Wingless (Wg). This paracrine Wg signal hyperactivate β-catenin in neighboring RAS "winner" clones, reprogramming them into invasive super-competitors. This mechanism is conserved in human pancreatic ductal adenocarcinoma (PDAC), where PPP1CA loss in KRAS-mutant cells induces analogous Hh-Wnt synergy, accelerating tumor growth in mouse xenograft models and correlating with clonal selection in patient specimens. Our study elucidates a paradoxical role for cell competition in intratumoral heterogeneity, where distinct tumor clones across species exploit conserved developmental signaling pathways to fuel malignancy. These findings establish interclonal communication as a critical driver of tumor ecosystem dynamics and identify Hh-Wnt crosstalk as a promising therapeutic vulnerability in heterogeneous cancers.
    Keywords:  Drosophila; Hedgehog; PDAC; Pp1-87B/PPP1CA; Ras; WNT; interclonal communication; intratumoral heterogeneity; tumor-promoting cell competition
    DOI:  https://doi.org/10.1016/j.devcel.2026.07.018
  22. Mol Cell. 2026 Aug 20. pii: S1097-2765(26)00521-6. [Epub ahead of print]
      Eukaryotic transcription is a highly dynamic and adaptable process that underpins the gene expression programs regulating development, cellular identity, and responses to extracellular signals. Gene-specific regulation of transcription across different cell types and environmental conditions is therefore fundamental to both normal physiology and disease. This specificity is shaped by phosphorylation of the RNA polymerase II (RNAPII) C-terminal domain (CTD) and its associated transcription factors. While cyclin-dependent kinases (CDKs) have long been recognized as the regulators of RNAPII activity, emerging evidence points to a broader, more diverse network of transcriptional kinases. Here, we highlight non-canonical transcriptional kinases that could operate alongside and beyond CDKs to modulate transcription by RNAPII. We discuss how these kinases could introduce context-specific CTD modifications that enable transcriptional plasticity, facilitate rapid loci-specific activation, and integrate signaling and stress-responsive pathways, ultimately adding a layer of regulatory complexity with profound implications for dynamic transcriptional regulation in development, homeostasis, and disease.
    Keywords:  RNA synthesis; gene expression; kinase; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2026.07.035
  23. Angew Chem Int Ed Engl. 2026 Aug 19. e2990236
      Detecting and quantifying specific RNA-protein interaction pairs under diverse physiological conditions is crucial for elucidating disease mechanisms and exploring potential therapeutic targets. However, it still remains a major challenge to visualize specific intracellular RNA-protein interactions at near-single-molecule resolution. In this work, we introduce an RNA-protein interaction visualization method by antibody-guided proximal in situ reverse-transcription detection (RAPID), to enable spatial localization and quantification of specific RNA-protein interaction pairs within single cells at near-single-molecule resolution. We demonstrate the high specificity and robustness of RAPID by validating the interaction between the heterogeneous nuclear ribonucleoprotein hnRNPC and the long noncoding RNA (lncRNA) MALAT1 in HeLa cells. Using RAPID, we found that SFPQ-NEAT1 interactions exhibited distinct spatial organization and dynamic changes upon cellular stimulation, indicating that the SFPQ-NEAT1 axis is closely associated with nuclear reorganization and stimulus-responsive gene regulation. RAPID, providing a new perspective on RNA-protein interactions, represents a novel analytical tool that facilitates further investigation of their roles in biology and disease.
    Keywords:  RNA‐protein interactions; near‐single‐molecule resolution; quantification; single‐cell imaging; site‐specific
    DOI:  https://doi.org/10.1002/anie.2990236
  24. Proc Natl Acad Sci U S A. 2026 Aug 25. 123(34): e2534903123
      Hsp70 chaperones are central regulators of proteostasis, mediating folding, refolding, degradation, and aggregation-prevention. Their activity is tuned by the diverse J-domain proteins (JDPs), which both recruit client proteins and stimulate Hsp70 ATP hydrolysis via interaction with a conserved J-domain. The cytosol contains four Hsp70 paralogs-the stress-inducible HSPA1A/B and HSPA6, and the constitutively expressed HSPA8. Whether these act redundantly or carry distinct cellular functions has remained unresolved. Here, we systematically map the interactions of cytosolic Hsp70s with broad-specificity JDPs to elucidate how paralog identity shapes cellular function. We found that despite the high conservation of the JDP-Hsp70 interaction sites, the affinities of these interactions and their functionality varied greatly. HSPA8 behaves as a generalist, engaging all JDP classes with comparable affinity, consistent with its housekeeping role. By contrast, HSPA1 preferentially binds canonical Class A and B JDPs, while showing only weak binding to Class B'. Therefore, under stress, HSPA1 pairs only with Class A/B JDPs to support robust protein refolding, while freeing Class B' to suppress protein aggregation in an Hsp70-independent manner. Most unexpectedly, HSPA6, the most stress-inducible paralog, binds selectivity to Class B JDPs, losing interactions with both Class A and B'. Thus, under severe stress, HSPA6 works exclusively with Class B JDPs to ensure ATP-dependent protein repair, while freeing Class A and B' JDPs to act independently of Hsp70 to protect damaged/misfolded proteins. Our findings reveal an evolved hierarchy of paralog-specific JDP couplings that dynamically rewires the Hsp70 network from active repair to protection during stress.
    Keywords:  Hsp70 and J-domain proteins; NMR; molecular chaperones; protein folding and aggregation; protein homeostasis
    DOI:  https://doi.org/10.1073/pnas.2534903123
  25. Cell Rep. 2026 Aug 18. pii: S2211-1247(26)00813-2. [Epub ahead of print]45(8): 117735
      During environmental stress, cells form dynamic biomolecular condensates called stress granules (SGs) that can undergo a maturation process towards more solid-like material states. Deposition of SG proteins in insoluble aggregates is a hallmark of neurodegenerative pathologies, provoking inquiry into the pathological link and mechanisms underlying SG maturation. Here we show that yeast SGs mature into a solid-like state during long-term stationary phase driven by protein kinase A (PKA)-dependent phosphorylation of the SG proteome. Catalytic PKA subunits condense in SGs upon stationary phase where SG-localized PKA activity is maintained. PKA phosphorylates key SG components, including the pyruvate kinase Cdc19, which is necessary and sufficient for Cdc19 maturation into amyloid-like structures. Inhibiting PKA during long-term stationary phase prevents SG maturation, which alters metabolism and delays ordered re-start of cell growth after re-feeding. These results describe a SG maturation mechanism selectively activated during chronic stress that preserves SG integrity and promotes cell survival.
    Keywords:  CP: cell biology; PKA; chronic stress; phase separation; phase transition; phosphorylation; protein kinase A; reversible amyloids; starvation; stress granule maturation; stress recovery; stress response
    DOI:  https://doi.org/10.1016/j.celrep.2026.117735
  26. Circ Res. 2026 Aug 21.
       BACKGROUND: Mutations in DSP, which encodes the protein desmoplakin, lead to cardiomyopathy with unusually high penetrance that presents with arrhythmias, fibro-fatty infiltration, and eventually heart failure. However, the precise mechanism of contractile dysfunction and dilation is incompletely understood. Here, we investigate the pathogenesis of DSP-R451G, a missense mutation that results in complete degradation of desmoplakin protein.
    METHODS: We use 3 complementary models to characterize desmoplakin-linked cardiomyopathy: induced pluripotent stem cell-derived engineered heart tissue expressing R451G desmoplakin, a heterozygous DspWT/R451G knock-in mouse, and left-ventricular biopsy specimens. Tissue-engineered constructs are used to characterize contractility, calcium handling, sarcomere length, and cell signaling. These results are corroborated in the R451G mouse. To expand the generalizability of the findings, we compare them to those from human heart biopsies bearing 3 different desmoplakin mutations.
    RESULTS: Using induced pluripotent stem cell-derived engineered heart tissue and isolated mouse ventricular cardiomyocytes, we recapitulate a disease phenotype consistent with desmoplakin cardiomyopathy and identify shortened resting sarcomere length as a pathogenic mechanism for contractile dysfunction. Phosphorylation of Src and protein kinase C underlies sarcomere shortening in mutant tissues, and pharmacological inhibition of these kinases rescues sarcomere length. Notably, these sarcomeric and biochemical hallmarks are also present in human hearts bearing 3 different desmoplakin mutations. We next identify redistribution of mechanical force at cardiomyocyte junctions as a proximal factor that may promote mechanoactivation of proto-oncogene tyrosine-protein kinase Src. Finally, we rescue sarcomere length and contractile function in DSP-mutant engineered heart tissue with dasatinib, a Food and Drug Administration-approved receptor tyrosine kinase inhibitor.
    CONCLUSIONS: Our study reveals a mechanism by which a desmosomal mutation affects cardiomyocyte function at the sarcomere level through activation of key signaling pathways that have not previously been implicated in desmoplakin cardiomyopathy.
    Keywords:  desmoplakin; heart failure; penetrance; phosphorylation; tyrosine
    DOI:  https://doi.org/10.1161/CIRCRESAHA.125.327676
  27. Mol Cell. 2026 Aug 17. pii: S1097-2765(26)00510-1. [Epub ahead of print]
      RNA splicing has historically been thought to be highly efficient and accurate, with little opportunity for deviation from regulated alternative splicing. This dogma has been challenged by recent observations that biological noise may contribute substantially to transcriptome diversity. However, quantitative understanding of stochastic splicing variation is challenging because these transcripts are likely subject to rapid degradation. Here, we use deep sequencing across RNA compartments to track splicing intermediates in human cells and see abundant cryptic splicing associated with genomic features that promote splicing noise. We observe pervasive usage of low-fidelity splice sites, likely due to stochasticity in recruitment or binding of the spliceosome. These sites are turned over quickly and show evidence for nuclear and cytoplasmic degradation, suggesting widespread surveillance and rapid quality control of non-productive transcripts. Our findings provide insights into the propensity for error in RNA processing mechanisms and regulation of alternative splice sites across a gene.
    Keywords:  RNA splicing; RNA-seq; genomics; systems biology
    DOI:  https://doi.org/10.1016/j.molcel.2026.07.024
  28. J Am Chem Soc. 2026 Aug 19. 148(32): 34311-34319
      In targeted protein degradation (TPD), specific subcellular proteins are removed by routing them to the ubiquitin-proteasome, autophagy, or lysosome machinery. For instance, proteolysis-targeting chimeras (PROTACs) are synthetic heterobifunctional small molecules that simultaneously bind the target and an E3 ubiquitin ligase to drive ubiquitination and degradation by the proteasome. Despite considerable success, designing such molecules is challenging, and the number of currently addressable ubiquitin E3 ligases is limited. Here, we design a heterobifunctional de novo protein to trigger the degradation of a common cancer target, resulting in a desired phenotypic output. First, we developed a highly stable and adaptable helix-turn-helix scaffold for presenting multiple binding sites. Next, we use computational protein design to incorporate and embellish hot-spot-binding sites to target the antiapoptotic mediators BCL-xL and MCL-1. We show a 75% success rate for creating submicromolar binders against these targets. Crystal structures of the complexes confirmed the designed binding poses. Then, we designed short linear motifs (SLiMs) into the loop of the scaffold to recruit KLHL20 and the ubiquitin ligase machinery. These designs have low micromolar affinity for KLHL20 comparable to that of the natural SLiMs. Moreover, the bifunctionalized proteins degrade BCL-xL in cells, leading to apoptosis.
    DOI:  https://doi.org/10.1021/jacs.6c07593