bims-ginsta Biomed News
on Genome instability
Issue of 2024–09–01
28 papers selected by
Jinrong Hu, National University of Singapore
  1. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress.
  2. The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.
  3. A conserved germline-specific Dsn1 alternative splice isoform supports oocyte and embryo development.
  4. Incompatibility in cell adhesion constitutes a barrier to interspecies chimerism.
  5. Embryonic genome instability upon DNA replication timing program emergence.
  6. Non-apical mitoses contribute to cell delamination during mouse gastrulation.
  7. Microtubules Sequester Acetylated YAP in the Cytoplasm and Inhibit Heart Regeneration.
  8. INF2-mediated actin polymerization at ER-organelle contacts regulates organelle size and movement.
  9. Adaptive microtubule reinforcement enables cell migration through 3D environments.
  10. Egr1 regulates regenerative senescence and cardiac repair.
  11. A transcriptional enhancer regulates cardiac maturation.
  12. Myosin forces elicit an F-actin structural landscape that mediates mechanosensitive protein recognition.
  13. Context-dependent roles of mitochondrial LONP1 in orchestrating the balance between airway progenitor versus progeny cells.
  14. Single-cell multiomic analysis identifies macrophage subpopulations in promoting cardiac repair.
  15. Fate induction in CD8 CAR T cells through asymmetric cell division.
  16. Spatially clustered type I interferon responses at injury borderzones.
  17. Neuroepithelial bodies and terminal bronchioles are niches for distinctive club cells that repair the airways following acute notch inhibition.
  18. RAD51 protects abasic sites to prevent replication fork breakage.
  19. Recent advances and future prospects in direct cardiac reprogramming.
  20. Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas.
  21. Release of mitochondrial dsRNA into the cytosol is a key driver of the inflammatory phenotype of senescent cells.
  22. Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair.
  23. Cardiac troponin I directly binds and inhibits mitochondrial ATP synthase with a noncanonical role in the post-ischemic heart.
  24. The VE-cadherin/AmotL2 mechanosensory pathway suppresses aortic inflammation and the formation of abdominal aortic aneurysms.
  25. A cardiac dyad component controls cardiomyocytes maturation in regenerative hearts.
  26. Titin governs myocardial passive stiffness with major support from microtubules and actin and the extracellular matrix.
  27. Villification of the intestinal epithelium is driven by Foxl1.
  28. Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts.
  1. Nat Commun. 2024 Aug 28. 15(1): 7404
    Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress.
    Anchel de Jaime-Soguero, Janina Hattemer, Anja Bufe, Alexander Haas, Jeroen van den Berg, Vincent van Batenburg, Biswajit Das, Barbara di Marco, Stefania Androulaki, Nicolas Böhly, Jonathan J M Landry, Brigitte Schoell, Viviane S Rosa, Laura Villacorta, Yagmur Baskan, Marleen Trapp, Vladimir Benes, Andrei Chabes, Marta Shahbazi, Anna Jauch, Ulrike Engel, Annarita Patrizi, Rocio Sotillo, Alexander van Oudenaarden, Josephine Bageritz, Julieta Alfonso, Holger Bastians, Sergio P Acebrón.
      Human development relies on the correct replication, maintenance and segregation of our genetic blueprints. How these processes are monitored across embryonic lineages, and why genomic mosaicism varies during development remain unknown. Using pluripotent stem cells, we identify that several patterning signals-including WNT, BMP, and FGF-converge into the modulation of DNA replication stress and damage during S-phase, which in turn controls chromosome segregation fidelity in mitosis. We show that the WNT and BMP signals protect from excessive origin firing, DNA damage and chromosome missegregation derived from stalled forks in pluripotency. Cell signalling control of chromosome segregation declines during lineage specification into the three germ layers, but re-emerges in neural progenitors. In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation during the onset of neurogenesis, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight roles for morphogens and cellular identity in genome maintenance that contribute to somatic mosaicism during mammalian development.
    DOI:  https://doi.org/10.1038/s41467-024-51821-9
  2. Cell. 2024 Aug 20. pii: S0092-8674(24)00892-4. [Epub ahead of print]
    The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.
    Justin L Engel, Xiao Zhang, Mingming Wu, Yan Wang, Jose Espejo Valle-Inclán, Qing Hu, Kidist S Woldehawariat, Mathijs A Sanders, Agata Smogorzewska, Jin Chen, Isidro Cortés-Ciriano, Roger S Lo, Peter Ly.
      Chromothripsis describes the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei. Although micronuclei accumulate DNA double-strand breaks and replication defects throughout interphase, how chromosomes undergo shattering remains unresolved. Using CRISPR-Cas9 screens, we identify a non-canonical role of the Fanconi anemia (FA) pathway as a driver of chromothripsis. Inactivation of the FA pathway suppresses chromosome shattering during mitosis without impacting interphase-associated defects within micronuclei. Mono-ubiquitination of FANCI-FANCD2 by the FA core complex promotes its mitotic engagement with under-replicated micronuclear chromosomes. The structure-selective SLX4-XPF-ERCC1 endonuclease subsequently induces large-scale nucleolytic cleavage of persistent DNA replication intermediates, which stimulates POLD3-dependent mitotic DNA synthesis to prime shattered fragments for reassembly in the ensuing cell cycle. Notably, FA-pathway-induced chromothripsis generates complex genomic rearrangements and extrachromosomal DNA that confer acquired resistance to anti-cancer therapies. Our findings demonstrate how pathological activation of a central DNA repair mechanism paradoxically triggers cancer genome evolution through chromothripsis.
    Keywords:  DNA repair; DNA replication; Fanconi anemia; chromothripsis; ecDNA; fragile sites; genome rearrangements; genomic instability; micronuclei; mitosis
    DOI:  https://doi.org/10.1016/j.cell.2024.08.001
  3. Curr Biol. 2024 Aug 17. pii: S0960-9822(24)01028-5. [Epub ahead of print]
    A conserved germline-specific Dsn1 alternative splice isoform supports oocyte and embryo development.
    Jimmy Ly, Cecilia S Blengini, Sarah L Cady, Karen Schindler, Iain M Cheeseman.
      The chromosome segregation and cell division programs associated with somatic mitosis and germline meiosis display dramatic differences such as kinetochore orientation, cohesin removal, or the presence of a gap phase.1,2,3,4,5,6 These changes in chromosome segregation require alterations to the established cell division machinery.5,6 It remains unclear what aspects of kinetochore function and its regulatory control differ between the mitotic and meiotic cell divisions to rewire these core processes. Alternative RNA splicing can generate distinct protein isoforms to allow for the differential control of cell processes across cell types. However, alternative splice isoforms that differentially modulate distinct cell division programs have remained elusive. Here, we demonstrate that mammalian germ cells express an alternative mRNA splice isoform for the kinetochore component, DSN1, a subunit of the MIS12 complex that links the centromeres to spindle microtubules during chromosome segregation. This germline DSN1 isoform bypasses the requirement for Aurora kinase phosphorylation for its centromere localization due to the absence of a key regulatory region allowing DSN1 to display persistent centromere localization. Expression of the germline DSN1 isoform in somatic cells results in constitutive kinetochore localization, chromosome segregation errors, and growth defects, providing an explanation for its tight cell-type-specific expression. Reciprocally, precisely eliminating expression of the germline-specific DSN1 splice isoform in mouse models disrupts oocyte maturation and early embryonic divisions coupled with a reduction in fertility. Together, this work identifies a germline-specific splice isoform for a chromosome segregation component and implicates its role in mammalian fertility.
    Keywords:  alternative splicing; fertility; kinetochore; meiosis; mitosis
    DOI:  https://doi.org/10.1016/j.cub.2024.07.089
  4. Cell Stem Cell. 2024 Aug 18. pii: S1934-5909(24)00286-8. [Epub ahead of print]
    Incompatibility in cell adhesion constitutes a barrier to interspecies chimerism.
    Emily Ballard, Masahiro Sakurai, Leqian Yu, Lizhong Liu, Seiya Oura, Jia Huang, Jun Wu.
      Interspecies blastocyst complementation holds great potential to address the global shortage of transplantable organs by growing human organs in animals. However, a major challenge in this approach is the limited chimerism of human cells in evolutionarily distant animal hosts due to various xenogeneic barriers. Here, we reveal that human pluripotent stem cells (PSCs) struggle to adhere to animal PSCs. To overcome this barrier, we developed a synthetic biology strategy that leverages nanobody-antigen interactions to enhance interspecies cell adhesion. We engineered cells to express nanobodies and their corresponding antigens on their outer membranes, significantly improving adhesion between different species' PSCs during in vitro assays and increasing the chimerism of human PSCs in mouse embryos. Studying and manipulating interspecies pluripotent cell adhesion will provide valuable insights into cell interaction dynamics during chimera formation and early embryogenesis.
    Keywords:  blastocyst complementation; cell adhesion; early embryogenesis; interspecies chimeras; interspecies organogenesis; nanobody; pluripotent stem cells; primed pluripotency; synthetic biology; xenogeneic barrier
    DOI:  https://doi.org/10.1016/j.stem.2024.07.010
  5. Nature. 2024 Aug 28.
    Embryonic genome instability upon DNA replication timing program emergence.
    Saori Takahashi, Hirohisa Kyogoku, Takuya Hayakawa, Hisashi Miura, Asami Oji, Yoshiko Kondo, Shin-Ichiro Takebayashi, Tomoya S Kitajima, Ichiro Hiratani.
      Faithful DNA replication is essential for genome integrity1-4. Under-replicated DNA leads to defects in chromosome segregation, which are common during embryogenesis5-8. However, the regulation of DNA replication remains poorly understood in early mammalian embryos. Here we constructed a single-cell genome-wide DNA replication atlas of pre-implantation mouse embryos and identified an abrupt replication program switch accompanied by a transient period of genomic instability. In 1- and 2-cell embryos, we observed the complete absence of a replication timing program, and the entire genome replicated gradually and uniformly using extremely slow-moving replication forks. In 4-cell embryos, a somatic-cell-like replication timing program commenced abruptly. However, the fork speed was still slow, S phase was extended, and markers of replication stress, DNA damage and repair increased. This was followed by an increase in break-type chromosome segregation errors specifically during the 4-to-8-cell division with breakpoints enriched in late-replicating regions. These errors were rescued by nucleoside supplementation, which accelerated fork speed and reduced the replication stress. By the 8-cell stage, forks gained speed, S phase was no longer extended and chromosome aberrations decreased. Thus, a transient period of genomic instability exists during normal mouse development, preceded by an S phase lacking coordination between replisome-level regulation and megabase-scale replication timing regulation, implicating a link between their coordination and genome stability.
    DOI:  https://doi.org/10.1038/s41586-024-07841-y
  6. Nat Commun. 2024 Aug 28. 15(1): 7364
    Non-apical mitoses contribute to cell delamination during mouse gastrulation.
    Evangéline Despin-Guitard, Viviane S Rosa, Steffen Plunder, Navrita Mathiah, Kristof Van Schoor, Eliana Nehme, Sara Merino-Aceituno, Joaquim Egea, Marta N Shahbazi, Eric Theveneau, Isabelle Migeotte.
      During the epithelial-mesenchymal transition driving mouse embryo gastrulation, cells divide more frequently at the primitive streak, and half of those divisions happen away from the apical pole. These observations suggest that non-apical mitoses might play a role in cell delamination. We aim to uncover and challenge the molecular determinants of mitosis position in different regions of the epiblast through computational modeling and pharmacological treatments of embryos and stem cell-based epiblast spheroids. Blocking basement membrane degradation at the streak has no impact on the asymmetry in mitosis frequency and position. By contrast, disturbance of the actomyosin cytoskeleton or cell cycle dynamics elicits ectopic non-apical mitosis and shows that the streak region is characterized by local relaxation of the actomyosin cytoskeleton and less stringent regulation of cell division. These factors are essential for normal dynamics at the streak and favor cell delamination from the epiblast.
    DOI:  https://doi.org/10.1038/s41467-024-51638-6
  7. Circulation. 2024 Aug 26.
    Microtubules Sequester Acetylated YAP in the Cytoplasm and Inhibit Heart Regeneration.
    Shijie Liu, Vaibhav Deshmukh, Fansen Meng, Yidan Wang, Yuka Morikawa, Jeffery D Steimle, Rich Gang Li, Jun Wang, James F Martin.
       BACKGROUND: The Hippo pathway effector YAP (Yes-associated protein) plays an essential role in cardiomyocyte proliferation and heart regeneration. In response to physiological changes, YAP moves in and out of the nucleus. The pathophysiological mechanisms regulating YAP subcellular localization after myocardial infarction remain poorly defined.
    METHODS: We identified YAP acetylation at site K265 by in vitro acetylation followed by mass spectrometry analysis. We used adeno-associated virus to express YAP-containing mutations that either abolished acetylation (YAP-K265R) or mimicked acetylation (YAP-K265Q) and studied how acetylation regulates YAP subcellular localization in mouse hearts. We generated a cell line with YAP-K265R mutation and investigated the protein-protein interactors by YAP immunoprecipitation followed by mass spectrometry, then validated the YAP interaction in neonatal rat ventricular myocytes. We examined colocalization of YAP and TUBA4A (tubulin α 4A) by superresolution imaging. Furthermore, we developed YAP-K265R and αMHC-MerCreMer (MCM); Yap-loxP/K265R mutant mice to examine the pathophysiological role of YAP acetylation in cardiomyocytes during cardiac regeneration.
    RESULTS: We found that YAP is acetylated at K265 by CBP (CREB-binding protein)/P300 (E1A-binding protein P300) and is deacetylated by nicotinamide phosphoribosyltransferase/nicotinamide adenine dinucleotide/sirtuins axis in cardiomyocytes. After myocardial infarction, YAP acetylation is increased, which promotes YAP cytoplasmic localization. Compared with controls, mice that were genetically engineered to express a K265R mutation that prevents YAP K256 acetylation showed improved cardiac regenerative ability and increased YAP nuclear localization. Mechanistically, YAP acetylation facilitates its interaction with TUBA4A, a component of the microtubule network that sequesters acetylated YAP in the cytoplasm. After myocardial infarction, the microtubule network increased in cardiomyocytes, resulting in the accumulation of YAP in the cytoplasm.
    CONCLUSIONS: After myocardial infarction, decreased sirtuin activity enriches YAP acetylation at K265. The growing TUBA4A network sequesters acetylated YAP within the cytoplasm, which is detrimental to cardiac regeneration.
    Keywords:  Hippo pathway; NAD+; Sirt1/2; acetylation; microtubules; myocardial infarction
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.067646
  8. Res Sq. 2024 Aug 16. pii: rs.3.rs-4720604. [Epub ahead of print]
    INF2-mediated actin polymerization at ER-organelle contacts regulates organelle size and movement.
    Cara R Schiavon, Yuning Wang, Jasmine W Feng, Stephanie Garrett, Tsung-Chang Sung, Yelena Dayn, Chunxin Wang, Richard J Youle, Omar A Quintero-Carmona, Gerald S Shadel, Uri Manor.
      Proper regulation of organelle dynamics and inter-organelle contacts is critical for cellular health and function. Both the endoplasmic reticulum (ER) and actin cytoskeleton are known to regulate organelle dynamics, but how, when, and where these two subcellular components are coordinated to control organelle dynamics remains unclear. Here, we show that ER-associated actin consistently marks mitochondrial, endosomal, and lysosomal fission sites. We also show that actin polymerization by the ER-anchored isoform of the formin protein INF2 is a key regulator of the morphology and mobility of these organelles. Together, our findings establish a mechanism by which INF2-mediated polymerization of ER-associated actin at ER-organelle contacts regulates organelle dynamics.
    DOI:  https://doi.org/10.21203/rs.3.rs-4720604/v1
  9. Nat Cell Biol. 2024 Aug 23.
    Adaptive microtubule reinforcement enables cell migration through 3D environments.
      
    DOI:  https://doi.org/10.1038/s41556-024-01477-w
  10. Nat Cardiovasc Res. 2024 Aug;3(8): 915-932
    Egr1 regulates regenerative senescence and cardiac repair.
    Lingling Zhang, Jacob Elkahal, Tianzhen Wang, Racheli Rimmer, Alexander Genzelinakh, Elad Bassat, Jingkui Wang, Dahlia Perez, David Kain, Daria Lendengolts, Roni Winkler, Hanna Bueno-Levy, Kfir Baruch Umansky, David Mishaly, Avraham Shakked, Shoval Miyara, Avital Sarusi-Portuguez, Naomi Goldfinger, Amir Prior, David Morgenstern, Yishai Levin, Yoseph Addadi, Baoguo Li, Varda Rotter, Uriel Katz, Elly M Tanaka, Valery Krizhanovsky, Rachel Sarig, Eldad Tzahor.
      Senescence plays a key role in various physiological and pathological processes. We reported that injury-induced transient senescence correlates with heart regeneration, yet the multi-omics profile and molecular underpinnings of regenerative senescence remain obscure. Using proteomics and single-cell RNA sequencing, here we report the regenerative senescence multi-omic signature in the adult mouse heart and establish its role in neonatal heart regeneration and agrin-mediated cardiac repair in adult mice. We identified early growth response protein 1 (Egr1) as a regulator of regenerative senescence in both models. In the neonatal heart, Egr1 facilitates angiogenesis and cardiomyocyte proliferation. In adult hearts, agrin-induced senescence and repair require Egr1, activated by the integrin-FAK-ERK-Akt1 axis in cardiac fibroblasts. We also identified cathepsins as injury-induced senescence-associated secretory phenotype components that promote extracellular matrix degradation and potentially assist in reducing fibrosis. Altogether, we uncovered the molecular signature and functional benefits of regenerative senescence during heart regeneration, with Egr1 orchestrating the process.
    DOI:  https://doi.org/10.1038/s44161-024-00493-1
  11. Nat Cardiovasc Res. 2024 Jun;3(6): 666-684
    A transcriptional enhancer regulates cardiac maturation.
    Myo Htet, Shunyao Lei, Sheetal Bajpayi, Harshi Gangrade, Marios Arvanitis, Asimina Zoitou, Sean Murphy, Elaine Zhelan Chen, Navid Koleini, Brian Leei Lin, Chulan Kwon, Emmanouil Tampakakis.
      Cardiomyocyte maturation is crucial for generating adult cardiomyocytes and the application of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs). However, regulation at the cis-regulatory element level and its role in heart disease remain unclear. Alpha-actinin 2 (ACTN2) levels increase during CM maturation. In this study, we investigated a clinically relevant, conserved ACTN2 enhancer's effects on CM maturation using hPSC and mouse models. Heterozygous ACTN2 enhancer deletion led to abnormal CM morphology, reduced function and mitochondrial respiration. Transcriptomic analyses in vitro and in vivo showed disrupted CM maturation and upregulated anabolic mammalian target for rapamycin (mTOR) signaling, promoting senescence and hindering maturation. As confirmation, ACTN2 enhancer deletion induced heat shock protein 90A expression, a chaperone mediating mTOR activation. Conversely, targeting the ACTN2 enhancer via enhancer CRISPR activation (enCRISPRa) promoted hPSC-CM maturation. Our studies reveal the transcriptional enhancer's role in cardiac maturation and disease, offering insights into potentially fine-tuning gene expression to modulate cardiomyocyte physiology.
    DOI:  https://doi.org/10.1038/s44161-024-00484-2
  12. bioRxiv. 2024 Aug 17. pii: 2024.08.15.608188. [Epub ahead of print]
    Myosin forces elicit an F-actin structural landscape that mediates mechanosensitive protein recognition.
    Ayala G Carl, Matthew J Reynolds, Pinar S Gurel, Donovan Y Z Phua, Xiaoyu Sun, Lin Mei, Keith Hamilton, Yasuharu Takagi, Alex J Noble, James R Sellers, Gregory M Alushin.
      Cells mechanically interface with their surroundings through cytoskeleton-linked adhesions, allowing them to sense physical cues that instruct development and drive diseases such as cancer. Contractile forces generated by myosin motor proteins mediate these mechanical signal transduction processes through unclear protein structural mechanisms. Here, we show that myosin forces elicit structural changes in actin filaments (F-actin) that modulate binding by the mechanosensitive adhesion protein α-catenin. Using correlative cryo-fluorescence microscopy and cryo-electron tomography, we identify F-actin featuring domains of nanoscale oscillating curvature at cytoskeleton-adhesion interfaces enriched in zyxin, a marker of actin-myosin generated traction forces. We next introduce a reconstitution system for visualizing F-actin in the presence of myosin forces with cryo-electron microscopy, which reveals morphologically similar superhelical F-actin spirals. In simulations, transient forces mimicking tugging and release of filaments by motors produce spirals, supporting a mechanistic link to myosin's ATPase mechanochemical cycle. Three-dimensional reconstruction of spirals uncovers extensive asymmetric remodeling of F-actin's helical lattice. This is recognized by α-catenin, which cooperatively binds along individual strands, preferentially engaging interfaces featuring extended inter-subunit distances while simultaneously suppressing rotational deviations to regularize the lattice. Collectively, we find that myosin forces can deform F-actin, generating a conformational landscape that is detected and reciprocally modulated by a mechanosensitive protein, providing a direct structural glimpse at active force transduction through the cytoskeleton.
    DOI:  https://doi.org/10.1101/2024.08.15.608188
  13. Cell Stem Cell. 2024 Aug 16. pii: S1934-5909(24)00287-X. [Epub ahead of print]
    Context-dependent roles of mitochondrial LONP1 in orchestrating the balance between airway progenitor versus progeny cells.
    Le Xu, Chunting Tan, Justinn Barr, Nicole Talaba, Jamie Verheyden, Ji Sun Chin, Samvel Gaboyan, Nikita Kasaraneni, Ruth M Elgamal, Kyle J Gaulton, Grace Lin, Kamyar Afshar, Eugene Golts, Angela Meier, Laura E Crotty Alexander, Zea Borok, Yufeng Shen, Wendy K Chung, David J McCulley, Xin Sun.
      While all eukaryotic cells are dependent on mitochondria for function, in a complex tissue, which cell type and which cell behavior are more sensitive to mitochondrial deficiency remain unpredictable. Here, we show that in the mouse airway, compromising mitochondrial function by inactivating mitochondrial protease gene Lonp1 led to reduced progenitor proliferation and differentiation during development, apoptosis of terminally differentiated ciliated cells and their replacement by basal progenitors and goblet cells during homeostasis, and failed airway progenitor migration into damaged alveoli following influenza infection. ATF4 and the integrated stress response (ISR) pathway are elevated and responsible for the airway phenotypes. Such context-dependent sensitivities are predicted by the selective expression of Bok, which is required for ISR activation. Reduced LONP1 expression is found in chronic obstructive pulmonary disease (COPD) airways with squamous metaplasia. These findings illustrate a cellular energy landscape whereby compromised mitochondrial function could favor the emergence of pathological cell types.
    Keywords:  ATF4; BOK; COPD; airway homeostasis; differentiated progeny cells; influenza infection; integrated stress response; lung epithelial cells; mitochondria; progenitor basal cells
    DOI:  https://doi.org/10.1016/j.stem.2024.08.001
  14. J Clin Invest. 2024 Aug 27. pii: e175297. [Epub ahead of print]
    Single-cell multiomic analysis identifies macrophage subpopulations in promoting cardiac repair.
    Mingzhu Fu, Shengtao Jia, Longhui Xu, Xin Li, Yufang Lv, Yulong Zhong, Shanshan Ai.
      Cardiac macrophages/monocytes participate in maintaining homeostasis and orchestrating cardiac responses upon injury. However, the function of specific macrophage/monocyte subtypes and the related cell fate commitment mechanisms remain elusive in regenerative and nonregenerative hearts due to their cellular heterogeneities. Using spatiotemporal single-cell epigenomic analysis of cardiac macrophages/monocytes in regenerative (P1) and nonregenerative (P10) mouse hearts post injury, we found that P1 hearts accumulate reparative Arg1+ macrophages, while proinflammatory S100a9+Ly6c+ monocytes are uniquely abundant during nonregenerative remodeling. Moreover, blocking chemokine CXCR2 to inhibit the specification of the S100a9+Ly6c+-biased inflammatory fate in P10 hearts resulted in elevated wound repair responses and marked improvements in cardiac function after injury. Single-cell RNA-seq further confirmed an increased Arg1+ macrophage subpopulation after CXCR2 blockade, which was accomplished by increased expression of wound repair-related genes and reduced expression of proinflammatory genes. Collectively, our findings provide instructive insights into the molecular mechanisms underlying the function and fate specification of heterogeneous macrophages/monocytes during cardiac repair and identify potential therapeutic targets for myocardial infarction.
    Keywords:  Cardiology; Cardiovascular disease; Epigenetics; Macrophages
    DOI:  https://doi.org/10.1172/JCI175297
  15. Nature. 2024 Aug 28.
    Fate induction in CD8 CAR T cells through asymmetric cell division.
    Casey S Lee, Sisi Chen, Corbett T Berry, Andre R Kelly, Patrick J Herman, Sangwook Oh, Roddy S O'Connor, Aimee S Payne, Christoph T Ellebrecht.
      Early expansion and long-term persistence predict efficacy of chimeric antigen receptor T cells (CARTs)1-7, but mechanisms governing effector versus memory CART differentiation and whether asymmetric cell division induces differential fates in human CARTs remain unclear. Here we show that target-induced proximity labelling enables isolation of first-division proximal-daughter and distal-daughter CD8 CARTs that asymmetrically distribute their surface proteome and transcriptome, resulting in divergent fates. Target-engaged CARs remain on proximal daughters, which inherit a surface proteome resembling activated-undivided CARTs, whereas the endogenous T cell receptor and CD8 enrich on distal daughters, whose surface proteome resembles resting CARTs, correlating with glycolytic and oxidative metabolism, respectively. Despite memory-precursor phenotype and in vivo longevity, distal daughters demonstrate transient potent cytolytic activity similar to proximal daughters, uncovering an effector-like state in distal daughters destined to become memory CARTs. Both partitioning of pre-existing transcripts and changes in RNA velocity contribute to asymmetry of fate-determining factors, resulting in diametrically opposed transcriptional trajectories. Independent of naive, memory or effector surface immunophenotype, proximal-daughter CARTs use core sets of transcription factors known to support proliferation and effector function. Conversely, transcription factors enriched in distal daughters restrain differentiation and promote longevity, evidenced by diminished long-term in vivo persistence and function of distal-daughter CARTs after IKZF1 disruption. These studies establish asymmetric cell division as a framework for understanding mechanisms of CART differentiation and improving therapeutic outcomes.
    DOI:  https://doi.org/10.1038/s41586-024-07862-7
  16. Nature. 2024 Aug 28.
    Spatially clustered type I interferon responses at injury borderzones.
    V K Ninh, D M Calcagno, J D Yu, B Zhang, N Taghdiri, R Sehgal, J M Mesfin, C J Chen, K Kalhor, A Toomu, J M Duran, E Adler, J Hu, K Zhang, K L Christman, Z Fu, B Bintu, K R King.
      Sterile inflammation after myocardial infarction is classically credited to myeloid cells interacting with dead cell debris in the infarct zone1,2. Here we show that cardiomyocytes are the dominant initiators of a previously undescribed type I interferon response in the infarct borderzone. Using spatial transcriptomics analysis in mice and humans, we find that myocardial infarction induces colonies of interferon-induced cells (IFNICs) expressing interferon-stimulated genes decorating the borderzone, where cardiomyocytes experience mechanical stress, nuclear rupture and escape of chromosomal DNA. Cardiomyocyte-selective deletion of Irf3 abrogated IFNIC colonies, whereas mice lacking Irf3 in fibroblasts, macrophages, neutrophils or endothelial cells, Ccr2-deficient mice or plasmacytoid-dendritic-cell-depleted mice did not. Interferons blunted the protective matricellular programs and contractile function of borderzone fibroblasts, and increased vulnerability to pathological remodelling. In mice that died after myocardial infarction, IFNIC colonies were immediately adjacent to sites of ventricular rupture, while mice lacking IFNICs were protected from rupture and exhibited improved survival3. Together, these results reveal a pathological borderzone niche characterized by a cardiomyocyte-initiated innate immune response. We suggest that selective inhibition of IRF3 activation in non-immune cells could limit ischaemic cardiomyopathy while avoiding broad immunosuppression.
    DOI:  https://doi.org/10.1038/s41586-024-07806-1
  17. Cell Rep. 2024 Aug 23. pii: S2211-1247(24)01005-2. [Epub ahead of print]43(9): 114654
    Neuroepithelial bodies and terminal bronchioles are niches for distinctive club cells that repair the airways following acute notch inhibition.
    Sai Manoz Lingamallu, Aditya Deshpande, Neenu Joy, Kirthana Ganeshan, Neelanjana Ray, Rajesh Kumar Ladher, Makoto Mark Taketo, Daniel Lafkas, Arjun Guha.
      Lower airway club cells (CCs) serve the dual roles of a secretory cell and a stem cell. Here, we probe how the CC fate is regulated. We find that, in response to acute perturbation of Notch signaling, CCs adopt distinct fates. Although the vast majority transdifferentiate into multiciliated cells, a "variant" subpopulation (v-CCs), juxtaposed to neuroepithelial bodies (NEBs; 5%-10%) and located at bronchioalveolar duct junctions (>80%), does not. Instead, v-CCs transition into lineage-ambiguous states but can revert to a CC fate upon restoration of Notch signaling and repopulate the airways with CCs and multiciliated cells. The v-CC response to Notch inhibition is dependent on localized activation of β-catenin in v-CCs. We propose that the CC fate is stabilized by canonical Notch signaling, that airways are susceptible to perturbations to this pathway, and that NEBs/terminal bronchioles comprise niches that modulate CC plasticity via β-catenin activation to facilitate airway repair post Notch inhibition.
    Keywords:  CP: Developmental biology; Notch signaling; airways; club cells; lung; multiciliated cells; neuroepithelial body; plasticity; repair; terminal bronchioles; variant club cells
    DOI:  https://doi.org/10.1016/j.celrep.2024.114654
  18. Mol Cell. 2024 Aug 22. pii: S1097-2765(24)00580-X. [Epub ahead of print]84(16): 3026-3043.e11
    RAD51 protects abasic sites to prevent replication fork breakage.
    Yodhara Wijesekara Hanthi, Miguel Angel Ramirez-Otero, Robert Appleby, Anna De Antoni, Luay Joudeh, Vincenzo Sannino, Salli Waked, Alessandra Ardizzoia, Viviana Barra, Daniele Fachinetti, Luca Pellegrini, Vincenzo Costanzo.
      Abasic sites are DNA lesions repaired by base excision repair. Cleavage of unrepaired abasic sites in single-stranded DNA (ssDNA) can lead to chromosomal breakage during DNA replication. How rupture of abasic DNA is prevented remains poorly understood. Here, using cryoelectron microscopy (cryo-EM), Xenopus laevis egg extracts, and human cells, we show that RAD51 nucleofilaments specifically recognize and protect abasic sites, which increase RAD51 association rate to DNA. In the absence of BRCA2 or RAD51, abasic sites accumulate as a result of DNA base methylation, oxidation, and deamination, inducing abasic ssDNA gaps that make replicating DNA fibers sensitive to APE1. RAD51 assembled on abasic DNA prevents abasic site cleavage by the MRE11-RAD50 complex, suppressing replication fork breakage triggered by an excess of abasic sites or POLθ polymerase inhibition. Our study highlights the critical role of BRCA2 and RAD51 in safeguarding against unrepaired abasic sites in DNA templates stemming from base alterations, ensuring genomic stability.
    Keywords:  APOBEC3B; BRCA2; DNA recombination; DNA replication; DNMT1; RAD51; TET2; abasic sites; base excision repair; replication fork protection
    DOI:  https://doi.org/10.1016/j.molcel.2024.07.004
  19. Nat Cardiovasc Res. 2023 Dec;2(12): 1148-1158
    Recent advances and future prospects in direct cardiac reprogramming.
    Yifang Xie, Ben Van Handel, Li Qian, Reza Ardehali.
      Cardiovascular disease remains a leading cause of death worldwide despite important advances in modern medical and surgical therapies. As human adult cardiomyocytes have limited regenerative ability, cardiomyocytes lost after myocardial infarction are replaced by fibrotic scar tissue, leading to cardiac dysfunction and heart failure. To replace lost cardiomyocytes, a promising approach is direct cardiac reprogramming, in which cardiac fibroblasts are transdifferentiated into induced cardiomyocyte-like cells (iCMs). Here we review cardiac reprogramming cocktails (including transcription factors, microRNAs and small molecules) that mediate iCM generation. We also highlight mechanistic studies exploring the barriers to and facilitators of this process. We then review recent progress in iCM reprogramming, with a focus on single-cell '-omics' research. Finally, we discuss obstacles to clinical application.
    DOI:  https://doi.org/10.1038/s44161-023-00377-w
  20. Cell. 2024 Aug 22. pii: S0092-8674(24)00829-8. [Epub ahead of print]187(17): 4520-4545
    Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas.
    Jennifer E Rood, Anna Hupalowska, Aviv Regev.
      Comprehensively charting the biologically causal circuits that govern the phenotypic space of human cells has often been viewed as an insurmountable challenge. However, in the last decade, a suite of interleaved experimental and computational technologies has arisen that is making this fundamental goal increasingly tractable. Pooled CRISPR-based perturbation screens with high-content molecular and/or image-based readouts are now enabling researchers to probe, map, and decipher genetically causal circuits at increasing scale. This scale is now eminently suitable for the deployment of artificial intelligence and machine learning (AI/ML) to both direct further experiments and to predict or generate information that was not-and sometimes cannot-be gathered experimentally. By combining and iterating those through experiments that are designed for inference, we now envision a Perturbation Cell Atlas as a generative causal foundation model to unify human cell biology.
    DOI:  https://doi.org/10.1016/j.cell.2024.07.035
  21. Nat Commun. 2024 Aug 27. 15(1): 7378
    Release of mitochondrial dsRNA into the cytosol is a key driver of the inflammatory phenotype of senescent cells.
    Vanessa López-Polo, Mate Maus, Emmanouil Zacharioudakis, Miguel Lafarga, Camille Stephan-Otto Attolini, Francisco D M Marques, Marta Kovatcheva, Evripidis Gavathiotis, Manuel Serrano.
      The escape of mitochondrial double-stranded dsRNA (mt-dsRNA) into the cytosol has been recently linked to a number of inflammatory diseases. Here, we report that the release of mt-dsRNA into the cytosol is a general feature of senescent cells and a critical driver of their inflammatory secretome, known as senescence-associated secretory phenotype (SASP). Inhibition of the mitochondrial RNA polymerase, the dsRNA sensors RIGI and MDA5, or the master inflammatory signaling protein MAVS, all result in reduced expression of the SASP, while broadly preserving other hallmarks of senescence. Moreover, senescent cells are hypersensitized to mt-dsRNA-driven inflammation due to their reduced levels of PNPT1 and ADAR1, two proteins critical for mitigating the accumulation of mt-dsRNA and the inflammatory potency of dsRNA, respectively. We find that mitofusin MFN1, but not MFN2, is important for the activation of the mt-dsRNA/MAVS/SASP axis and, accordingly, genetic or pharmacologic MFN1 inhibition attenuates the SASP. Finally, we report that senescent cells within fibrotic and aged tissues present dsRNA foci, and inhibition of mitochondrial RNA polymerase reduces systemic inflammation associated to senescence. In conclusion, we uncover the mt-dsRNA/MAVS/MFN1 axis as a key driver of the SASP and we identify novel therapeutic strategies for senescence-associated diseases.
    DOI:  https://doi.org/10.1038/s41467-024-51363-0
  22. Nucleic Acids Res. 2024 Aug 24. pii: gkae721. [Epub ahead of print]
    Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair.
    Erica Colicino-Murbach, Caitlin Hathaway, Huzefa Dungrawala.
      Eukaryotic chromosomal replication occurs in a segmented, temporal manner wherein open euchromatin and compact heterochromatin replicate during early and late S-phase respectively. Using single molecule DNA fiber analyses coupled with cell synchronization, we find that newly synthesized strands remain stable at perturbed forks in early S-phase. Unexpectedly, stalled forks are susceptible to nucleolytic digestion during late replication resulting in defective fork restart. This inherent vulnerability to nascent strand degradation is dependent on fork reversal enzymes and resection nucleases MRE11, DNA2 and EXO1. Inducing chromatin compaction elicits digestion of nascent DNA in response to fork stalling due to reduced association of RAD51 with nascent DNA. Furthermore, RAD51 occupancy at stalled forks in late S-phase is diminished indicating that densely packed chromatin limits RAD51 accessibility to mediate replication fork protection. Genetic analyses reveal that susceptibility of late replicating forks to nascent DNA digestion is dependent on EXO1 via DNA mismatch repair (MMR) and that the BRCA2-mediated replication fork protection blocks MMR from degrading nascent DNA. Overall, our findings illustrate differential regulation of fork protection between early and late replication and demonstrate nascent strand degradation as a critical determinant of heterochromatin instability in response to replication stress.
    DOI:  https://doi.org/10.1093/nar/gkae721
  23. Nat Cardiovasc Res. 2024 Aug;3(8): 987-1002
    Cardiac troponin I directly binds and inhibits mitochondrial ATP synthase with a noncanonical role in the post-ischemic heart.
    Aly Elezaby, Amanda J Lin, Vijith Vijayan, Suman Pokhrel, Benjamin R Kraemer, Luiz R G Bechara, Isabel Larus, Junhui Sun, Valentina Baena, Zulfeqhar A Syed, Elizabeth Murphy, Brian Glancy, Nicolai P Ostberg, Bruno B Queliconi, Juliane C Campos, Julio C B Ferreira, Bereketeab Haileselassie, Daria Mochly-Rosen.
      Cardiac troponin I (cTnI) is a key regulator of cardiomyocyte contraction. However, its role in mitochondria is unknown. Here we show that cTnI localized to mitochondria in the heart, inhibited mitochondrial functions when stably expressed in noncardiac cells and increased the opening of the mitochondrial permeability transition pore under oxidative stress. Direct, specific and saturable binding of cTnI to F1FO-ATP synthase was demonstrated in vitro using immune-captured ATP synthase and in cells using proximity ligation assay. cTnI binding doubled ATPase activity, whereas skeletal troponin I and several human pathogenic cTnI variants associated with familial hypertrophic cardiomyopathy did not. A rationally designed peptide, P888, inhibited cTnI binding to ATP synthase, inhibited cTnI-induced increase in ATPase activity in vitro and reduced cardiac injury following transient ischemia in vivo. We suggest that cTnI-bound ATP synthase results in lower ATP levels, and releasing this interaction during cardiac ischemia-reperfusion may increase the reservoir of functional mitochondria to reduce cardiac injury.
    DOI:  https://doi.org/10.1038/s44161-024-00512-1
  24. Nat Cardiovasc Res. 2023 Jul;2(7): 629-644
    The VE-cadherin/AmotL2 mechanosensory pathway suppresses aortic inflammation and the formation of abdominal aortic aneurysms.
    Yuanyuan Zhang, Yumeng Zhang, Evelyn Hutterer, Sara Hultin, Otto Bergman, Solrun Kolbeinsdottir, Hong Jin, Maria J Forteza, Daniel F J Ketelhuth, Joy Roy, Ulf Hedin, Martin Enge, Ljubica Matic, Per Eriksson, Lars Holmgren.
      Endothelial cells respond to mechanical forces exerted by blood flow. Endothelial cell-cell junctions and the sites of endothelial adhesion to the matrix sense and transmit mechanical forces to the cellular cytoskeleton. Here we show that the scaffold protein AmotL2 connects junctional VE-cadherin and actin filaments to the nuclear lamina. AmotL2 is essential for the formation of radial actin filaments and the alignment of endothelial cells, and, in its absence, nuclear integrity and positioning are altered. Molecular analysis demonstrated that VE-cadherin binds to AmotL2 and actin, resulting in a cascade that transmits extracellular mechanical signals to the nuclear membrane. Furthermore, the endothelial deficit of AmotL2 in mice fed normal diet provoked a pro-inflammatory response and abdominal aortic aneurysms (AAAs). Transcriptome analysis of human AAA samples revealed a negative correlation between AmotL2 and inflammation of the aortic intima. These findings offer insight into the link between junctional mechanotransduction and vascular disease.
    DOI:  https://doi.org/10.1038/s44161-023-00298-8
  25. Nat Cardiovasc Res. 2023 Jun;2(6): 491
    A cardiac dyad component controls cardiomyocytes maturation in regenerative hearts.
    Elvira Forte.
      
    DOI:  https://doi.org/10.1038/s44161-023-00292-0
  26. Nat Cardiovasc Res. 2023 Nov;2(11): 991-1002
    Titin governs myocardial passive stiffness with major support from microtubules and actin and the extracellular matrix.
    Christine M Loescher, Johanna K Freundt, Andreas Unger, Anthony L Hessel, Michel Kühn, Franziska Koser, Wolfgang A Linke.
      Myocardial passive stiffness is crucial for the heart's pump function and is determined by mechanical elements, including the extracellular matrix and cytoskeletal filaments; however, their individual contributions are controversially discussed and difficult to quantify. In this study, we targeted the cytoskeletal filaments in a mouse model, which enables the specific, acute and complete cleavage of the sarcomeric titin springs. We show in vitro that each cytoskeletal filament's stiffness contribution varies depending on whether the elastic or the viscous forces are considered and on strain level. Titin governs myocardial elastic forces, with the largest contribution provided at both low and high strain. Viscous force contributions are more uniformly distributed among the microtubules, titin and actin. The extracellular matrix contributes at high strain. The remaining forces after total target element disruption are likely derived from desmin filaments. Our findings answer longstanding questions about cardiac mechanical architecture and allow better targeting of passive myocardial stiffness in heart failure.
    DOI:  https://doi.org/10.1038/s44161-023-00348-1
  27. Res Sq. 2024 Aug 16. pii: rs.3.rs-4882679. [Epub ahead of print]
    Villification of the intestinal epithelium is driven by Foxl1.
    Klaus Kaestner, Guoli Zhu, Deeksha Lahori, Jonathan Schug.
      The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRa as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed- forward loop with Foxo3. In the absence of Foxl1-dependent mesenchymal signaling, villus formation is delayed, the separation of epithelial cells into mitotic intervillus and postmitotic villus cells impaired, and the differentiation of secretory progenitors blocked. Thus, Foxl1 orchestrates key events during the epithelial transition of the fetal mammalian gut.
    DOI:  https://doi.org/10.21203/rs.3.rs-4882679/v1
  28. Nat Cell Biol. 2024 Aug 28.
    Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts.
    Daniel Ramsköld, Gert-Jan Hendriks, Anton J M Larsson, Juliane V Mayr, Christoph Ziegenhain, Michael Hagemann-Jensen, Leonard Hartmanis, Rickard Sandberg.
      Analyses of transcriptional bursting from single-cell RNA-sequencing data have revealed patterns of variation and regulation in the kinetic parameters that could be inferred. Here we profiled newly transcribed (4-thiouridine-labelled) RNA across 10,000 individual primary mouse fibroblasts to more broadly infer bursting kinetics and coordination. We demonstrate that inference from new RNA profiles could separate the kinetic parameters that together specify the burst size, and that the synthesis rate (and not the transcriptional off rate) controls the burst size. Importantly, transcriptome-wide inference of transcriptional on and off rates provided conclusive evidence that RNA polymerase II transcribes genes in bursts. Recent reports identified examples of transcriptional co-bursting, yet no global analyses have been performed. The deep new RNA profiles we generated with allelic resolution demonstrated that co-bursting rarely appears more frequently than expected by chance, except for certain gene pairs, notably paralogues located in close genomic proximity. Altogether, new RNA single-cell profiling critically improves the inference of transcriptional bursting and provides strong evidence for independent transcriptional bursting of mammalian genes.
    DOI:  https://doi.org/10.1038/s41556-024-01486-9
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