bims-ginsta Biomed News
on Genome instability
Issue of 2024–06–23
nineteen papers selected by
Jinrong Hu, National University of Singapore
  1. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis.
  2. Quantifying DNA replication speeds in single cells by scEdU-seq.
  3. Wnt signaling couples G2 phase control with differentiation during hematopoiesis in Drosophila.
  4. Mechanics of spindle orientation in human mitotic cells is determined by pulling forces on astral microtubules and clustering of cortical dynein.
  5. Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.
  6. Strand-resolved mutagenicity of DNA damage and repair.
  7. Bidirectional activation of stem-like programs between metastatic cancer and alveolar type 2 cells within the niche.
  8. How germ granules promote germ cell fate.
  9. Filamin protects myofibrils from contractile damage through changes in its mechanosensory region.
  10. Multiscale topology classifies cells in subcellular spatial transcriptomics.
  11. The maintenance of oocytes in the mammalian ovary involves extreme protein longevity.
  12. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons.
  13. Short-term cold exposure induces persistent epigenomic memory in brown fat.
  14. Cardiac Development at a Single-Cell Resolution.
  15. YAP dysregulation triggers hypertrophy by CCN2 secretion and TGFβ uptake in human pluripotent stem cell-derived cardiomyocytes.
  16. Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule.
  17. Dynamic models of human development and concepts of the individual.
  18. DYRK1A signalling synchronizes the mitochondrial import pathways for metabolic rewiring.
  19. KLF4 in smooth muscle cell-derived progenitor cells is essential for angiotensin II-induced cardiac inflammation and fibrosis.
  1. Genes Dev. 2024 Jun 12.
    Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis.
    Noor M Kotb, Gulay Ulukaya, Ankita Chavan, Son C Nguyen, Lydia Proskauer, Eric F Joyce, Dan Hasson, Madhav Jagannathan, Prashanth Rangan.
      Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ cell genes during differentiation, and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we found that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ cell genes into a silenced state and activating a group of oocyte genes and nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, cross-talk between genome architecture and NPCs is essential for successful cell fate transitions.
    Keywords:  LAD; NPC; TAD; differentiation; genome organization; heterochromatin; lamin; nucleoporins
    DOI:  https://doi.org/10.1101/gad.351402.123
  2. Nat Methods. 2024 Jun 17.
    Quantifying DNA replication speeds in single cells by scEdU-seq.
    Jeroen van den Berg, Vincent van Batenburg, Christoph Geisenberger, Rinskje B Tjeerdsma, Anchel de Jaime-Soguero, Sergio P Acebrón, Marcel A T M van Vugt, Alexander van Oudenaarden.
      In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.
    DOI:  https://doi.org/10.1038/s41592-024-02308-4
  3. Dev Cell. 2024 Jun 06. pii: S1534-5807(24)00341-1. [Epub ahead of print]
    Wnt signaling couples G2 phase control with differentiation during hematopoiesis in Drosophila.
    Lauren M Goins, Juliet R Girard, Bama Charan Mondal, Sausan Buran, Chloe C Su, Ruby Tang, Titash Biswas, Jessica A Kissi, Utpal Banerjee.
      During homeostasis, a critical balance is maintained between myeloid-like progenitors and their differentiated progeny, which function to mitigate stress and innate immune challenges. The molecular mechanisms that help achieve this balance are not fully understood. Using genetic dissection in Drosophila, we show that a Wnt6/EGFR-signaling network simultaneously controls progenitor growth, proliferation, and differentiation. Unlike G1-quiescence of stem cells, hematopoietic progenitors are blocked in G2 phase by a β-catenin-independent (Wnt/STOP) Wnt6 pathway that restricts Cdc25 nuclear entry and promotes cell growth. Canonical β-catenin-dependent Wnt6 signaling is spatially confined to mature progenitors through localized activation of the tyrosine kinases EGFR and Abelson kinase (Abl), which promote nuclear entry of β-catenin and facilitate exit from G2. This strategy combines transcription-dependent and -independent forms of both Wnt6 and EGFR pathways to create a direct link between cell-cycle control and differentiation. This unique combinatorial strategy employing conserved components may underlie homeostatic balance and stress response in mammalian hematopoiesis.
    Keywords:  Cdc25; Drosophila; EGFR; G2 phase; Wnt6; blood development; cell cycle; hematopoiesis; lymph gland; β-catenin
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.023
  4. Dev Cell. 2024 Jun 04. pii: S1534-5807(24)00340-X. [Epub ahead of print]
    Mechanics of spindle orientation in human mitotic cells is determined by pulling forces on astral microtubules and clustering of cortical dynein.
    Maya I Anjur-Dietrich, Vicente Gomez Hererra, Reza Farhadifar, Haiyin Wu, Holly Merta, Shirin Bahmanyar, Michael J Shelley, Daniel J Needleman.
      The forces that orient the spindle in human cells remain poorly understood due to a lack of direct mechanical measurements in mammalian systems. We use magnetic tweezers to measure the force on human mitotic spindles. Combining the spindle's measured resistance to rotation, the speed at which it rotates after laser ablating astral microtubules, and estimates of the number of ablated microtubules reveals that each microtubule contacting the cell cortex is subject to ∼5 pN of pulling force, suggesting that each is pulled on by an individual dynein motor. We find that the concentration of dynein at the cell cortex and extent of dynein clustering are key determinants of the spindle's resistance to rotation, with little contribution from cytoplasmic viscosity, which we explain using a biophysically based mathematical model. This work reveals how pulling forces on astral microtubules determine the mechanics of spindle orientation and demonstrates the central role of cortical dynein clustering.
    Keywords:  clustering; dynein; forces; mechanics; metaphase; microtubules; mitosis; orientation; spindle
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.022
  5. bioRxiv. 2024 May 24. pii: 2024.05.23.595547. [Epub ahead of print]
    Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.
    S Galatidou, A Petelski, A Pujol, K Lattes, L B Latorraca, T Fair, M Popovic, R Vassena, N Slavov, M Barragan.
      Advanced maternal age is associated with a decline in oocyte quality, which often leads to reproductive failure in humans. However, the mechanisms behind this age-related decline remain unclear. To gain insights into this phenomenon, we applied plexDIA, a multiplexed, single-cell mass spectrometry method, to analyze the proteome of oocytes from both young women and women of advanced maternal age. Our findings primarily revealed distinct proteomic profiles between immature fully grown germinal vesicle and mature metaphase II oocytes. Importantly, we further show that a woman's age is associated with changes in her oocyte proteome. Specifically, when compared to oocytes obtained from young women, advanced maternal age oocytes exhibited lower levels of the proteasome and TRiC complex, as well as other key regulators of proteostasis and meiosis. This suggests that aging adversely affects the proteostasis and meiosis networks in human oocytes. The proteins identified in this study hold potential as targets for improving oocyte quality and may guide future studies into the molecular processes underlying oocyte aging.
    DOI:  https://doi.org/10.1101/2024.05.23.595547
  6. Nature. 2024 Jun;630(8017): 744-751
    Strand-resolved mutagenicity of DNA damage and repair.
    Liver Cancer Evolution Consortium
      DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.
    DOI:  https://doi.org/10.1038/s41586-024-07490-1
  7. Dev Cell. 2024 May 31. pii: S1534-5807(24)00338-1. [Epub ahead of print]
    Bidirectional activation of stem-like programs between metastatic cancer and alveolar type 2 cells within the niche.
    Felipe S Rodrigues, Adam Karoutas, Stefanie Ruhland, Nicolas Rabas, Tatiana Rizou, Stefania Di Blasio, Rute M M Ferreira, Victoria L Bridgeman, Robert Goldstone, Miriam L Sopena, Joo-Hyeon Lee, Luigi Ombrato, Ilaria Malanchi.
      A key step for metastatic outgrowth involves the generation of a deeply altered microenvironment (niche) that supports the malignant behavior of cancer cells. The complexity of the metastatic niche has posed a significant challenge in elucidating the underlying programs driving its origin. Here, by focusing on early stages of breast cancer metastasis to the lung in mice, we describe a cancer-dependent chromatin remodeling and activation of developmental programs in alveolar type 2 (AT2) cells within the niche. We show that metastatic cells can prime AT2 cells into a reprogrammed multilineage state. In turn, this cancer-induced reprogramming of AT2 cells promoted stem-like features in cancer cells and enhanced their initiation capacity. In conclusion, we propose the concept of "reflected stemness" as an early phenomenon during metastatic niche initiation, wherein metastatic cells reprogram the local tissue into a stem-like state that enhances intrinsic cancer-initiating potential, creating a positive feedback loop where tumorigenic programs are amplified.
    Keywords:  Metastasis; Sox9; alveolar type 2 cells; breast cancer; lung stem cells; metastasis-initiating cells; metastatic niche; multilineage state; tissue reprogramming
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.020
  8. Nat Rev Genet. 2024 Jun 18.
    How germ granules promote germ cell fate.
    Melissa C Pamula, Ruth Lehmann.
      Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
    DOI:  https://doi.org/10.1038/s41576-024-00744-8
  9. PLoS Genet. 2024 Jun 21. 20(6): e1011101
    Filamin protects myofibrils from contractile damage through changes in its mechanosensory region.
    Lucas A B Fisher, Belén Carriquí-Madroñal, Tiara Mulder, Sven Huelsmann, Frieder Schöck, Nicanor González-Morales.
      Filamins are mechanosensitive actin crosslinking proteins that organize the actin cytoskeleton in a variety of shapes and tissues. In muscles, filamin crosslinks actin filaments from opposing sarcomeres, the smallest contractile units of muscles. This happens at the Z-disc, the actin-organizing center of sarcomeres. In flies and vertebrates, filamin mutations lead to fragile muscles that appear ruptured, suggesting filamin helps counteract muscle rupturing during muscle contractions by providing elastic support and/or through signaling. An elastic region at the C-terminus of filamin is called the mechanosensitive region and has been proposed to sense and counteract contractile damage. Here we use molecularly defined mutants and microscopy analysis of the Drosophila indirect flight muscles to investigate the molecular details by which filamin provides cohesion to the Z-disc. We made novel filamin mutations affecting the C-terminal region to interrogate the mechanosensitive region and detected three Z-disc phenotypes: dissociation of actin filaments, Z-disc rupture, and Z-disc enlargement. We tested a constitutively closed filamin mutant, which prevents the elastic changes in the mechanosensitive region and results in ruptured Z-discs, and a constitutively open mutant which has the opposite elastic effect on the mechanosensitive region and gives rise to enlarged Z-discs. Finally, we show that muscle contraction is required for Z-disc rupture. We propose that filamin senses myofibril damage by elastic changes in its mechanosensory region, stabilizes the Z-disc, and counteracts contractile damage at the Z-disc.
    DOI:  https://doi.org/10.1371/journal.pgen.1011101
  10. Nature. 2024 Jun 19.
    Multiscale topology classifies cells in subcellular spatial transcriptomics.
    Katherine Benjamin, Aneesha Bhandari, Jessica D Kepple, Rui Qi, Zhouchun Shang, Yanan Xing, Yanru An, Nannan Zhang, Yong Hou, Tanya L Crockford, Oliver McCallion, Fadi Issa, Joanna Hester, Ulrike Tillmann, Heather A Harrington, Katherine R Bull.
      Spatial transcriptomics measures in situ gene expression at millions of locations within a tissue1, hitherto with some trade-off between transcriptome depth, spatial resolution and sample size2. Although integration of image-based segmentation has enabled impactful work in this context, it is limited by imaging quality and tissue heterogeneity. By contrast, recent array-based technologies offer the ability to measure the entire transcriptome at subcellular resolution across large samples3-6. Presently, there exist no approaches for cell type identification that directly leverage this information to annotate individual cells. Here we propose a multiscale approach to automatically classify cell types at this subcellular level, using both transcriptomic information and spatial context. We showcase this on both targeted and whole-transcriptome spatial platforms, improving cell classification and morphology for human kidney tissue and pinpointing individual sparsely distributed renal mouse immune cells without reliance on image data. By integrating these predictions into a topological pipeline based on multiparameter persistent homology7-9, we identify cell spatial relationships characteristic of a mouse model of lupus nephritis, which we validate experimentally by immunofluorescence. The proposed framework readily generalizes to new platforms, providing a comprehensive pipeline bridging different levels of biological organization from genes through to tissues.
    DOI:  https://doi.org/10.1038/s41586-024-07563-1
  11. Nat Cell Biol. 2024 Jun 20.
    The maintenance of oocytes in the mammalian ovary involves extreme protein longevity.
    Katarina Harasimov, Rebecca L Gorry, Luisa M Welp, Sarah Mae Penir, Yehor Horokhovskyi, Shiya Cheng, Katsuyoshi Takaoka, Alexandra Stützer, Ann-Sophie Frombach, Ana Lisa Taylor Tavares, Monika Raabe, Sara Haag, Debojit Saha, Katharina Grewe, Vera Schipper, Silvio O Rizzoli, Henning Urlaub, Juliane Liepe, Melina Schuh.
      Women are born with all of their oocytes. The oocyte proteome must be maintained with minimal damage throughout the woman's reproductive life, and hence for decades. Here we report that oocyte and ovarian proteostasis involves extreme protein longevity. Mouse ovaries had more extremely long-lived proteins than other tissues, including brain. These long-lived proteins had diverse functions, including in mitochondria, the cytoskeleton, chromatin and proteostasis. The stable proteins resided not only in oocytes but also in long-lived ovarian somatic cells. Our data suggest that mammals increase protein longevity and enhance proteostasis by chaperones and cellular antioxidants to maintain the female germline for long periods. Indeed, protein aggregation in oocytes did not increase with age and proteasome activity did not decay. However, increasing protein longevity cannot fully block female germline senescence. Large-scale proteome profiling of ~8,890 proteins revealed a decline in many long-lived proteins of the proteostasis network in the aging ovary, accompanied by massive proteome remodeling, which eventually leads to female fertility decline.
    DOI:  https://doi.org/10.1038/s41556-024-01442-7
  12. Cell. 2024 Jun 05. pii: S0092-8674(24)00575-0. [Epub ahead of print]
    TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons.
    Tae Wan Kim, So Yeon Koo, Markus Riessland, Fayzan Chaudhry, Benjamin Kolisnyk, Hyein S Cho, Marco Vincenzo Russo, Nathalie Saurat, Sanjoy Mehta, Ralph Garippa, Doron Betel, Lorenz Studer.
      Ongoing, early-stage clinical trials illustrate the translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, an unresolved challenge is the extensive cell death following transplantation. Here, we performed a pooled CRISPR-Cas9 screen to enhance postmitotic dopamine neuron survival in vivo. We identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of tumor necrosis factor alpha (TNF-α)-nuclear factor κB (NF-κB) signaling in limiting cell survival. As a translationally relevant strategy to purify postmitotic dopamine neurons, we identified cell surface markers that enable purification without the need for genetic reporters. Combining cell sorting and treatment with adalimumab, a clinically approved TNF-α inhibitor, enabled efficient engraftment of postmitotic dopamine neurons with extensive reinnervation and functional recovery in a preclinical PD mouse model. Thus, transient TNF-α inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic hPSC-derived dopamine neurons in PD.
    Keywords:  Parkinson’s disease; TNF-α inhibition; TP53; apoptosis; cell purification; cell survival; cell therapy; dopamine neurons; genetic screen; transplantation
    DOI:  https://doi.org/10.1016/j.cell.2024.05.030
  13. Cell Metab. 2024 Jun 12. pii: S1550-4131(24)00187-6. [Epub ahead of print]
    Short-term cold exposure induces persistent epigenomic memory in brown fat.
    Shin-Ichi Inoue, Matthew J Emmett, Hee-Woong Lim, Mohit Midha, Hannah J Richter, Isaac J Celwyn, Rashid Mehmood, Maria Chondronikola, Samuel Klein, Amy K Hauck, Mitchell A Lazar.
      Deficiency of the epigenome modulator histone deacetylase 3 (HDAC3) in brown adipose tissue (BAT) impairs the ability of mice to survive in near-freezing temperatures. Here, we report that short-term exposure to mild cold temperature (STEMCT: 15°C for 24 h) averted lethal hypothermia of mice lacking HDAC3 in BAT (HDAC3 BAT KO) exposed to 4°C. STEMCT restored the induction of the thermogenic coactivator PGC-1α along with UCP1 at 22°C, which is greatly impaired in HDAC3-deficient BAT, and deletion of either UCP1 or PGC-1α prevented the protective effect of STEMCT. Remarkably, this protection lasted for up to 7 days. Transcriptional activator C/EBPβ was induced by short-term cold exposure in mouse and human BAT and, uniquely, remained high for 7 days following STEMCT. Adeno-associated virus-mediated knockdown of BAT C/EBPβ in HDAC3 BAT KO mice erased the persistent memory of STEMCT, revealing the existence of a C/EBPβ-dependent and HDAC3-independent cold-adaptive epigenomic memory.
    Keywords:  C/EBPβ; ERRα; HDAC3; PGC-1α; UCP1; brown adipose tissue; cold memory; mitochondria; oxidative phosphorylation; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2024.05.011
  14. Adv Exp Med Biol. 2024 ;1441 253-268
    Cardiac Development at a Single-Cell Resolution.
    Nicholas Wei, Carissa Lee, Lauren Duan, Francisco X Galdos, Tahmina Samad, Alireza Raissadati, William R Goodyer, Sean M Wu.
      Mammalian cardiac development is a complex, multistage process. Though traditional lineage tracing studies have characterized the broad trajectories of cardiac progenitors, the advent and rapid optimization of single-cell RNA sequencing methods have yielded an ever-expanding toolkit for characterizing heterogeneous cell populations in the developing heart. Importantly, they have allowed for a robust profiling of the spatiotemporal transcriptomic landscape of the human and mouse heart, revealing the diversity of cardiac cells-myocyte and non-myocyte-over the course of development. These studies have yielded insights into novel cardiac progenitor populations, chamber-specific developmental signatures, the gene regulatory networks governing cardiac development, and, thus, the etiologies of congenital heart diseases. Furthermore, single-cell RNA sequencing has allowed for the exquisite characterization of distinct cardiac populations such as the hard-to-capture cardiac conduction system and the intracardiac immune population. Therefore, single-cell profiling has also resulted in new insights into the regulation of cardiac regeneration and injury repair. Single-cell multiomics approaches combining transcriptomics, genomics, and epigenomics may uncover an even more comprehensive atlas of human cardiac biology. Single-cell analyses of the developing and adult mammalian heart offer an unprecedented look into the fundamental mechanisms of cardiac development and the complex diseases that may arise from it.
    Keywords:  Bioinformatics; Chamber morphogenesis; Heart development; Myocardial trabeculation; Single-cell RNA sequencing
    DOI:  https://doi.org/10.1007/978-3-031-44087-8_14
  15. bioRxiv. 2024 Jun 05. pii: 2024.06.03.597045. [Epub ahead of print]
    YAP dysregulation triggers hypertrophy by CCN2 secretion and TGFβ uptake in human pluripotent stem cell-derived cardiomyocytes.
    Orlando Chirikian, Mohamed A Faynus, Markus Merk, Zachary Singh, Christopher Muray, Jeffrey Pham, Alex Chialastri, Alison Vander Roest, Alex Goldstein, Trevor Pyle, Kerry V Lane, Brock Roberts, Jacqueline E Smith, Ruwanthi N Gunawardane, Nathan J Sniadecki, David L Mack, Jennifer Davis, Daniel Bernstein, Sebastian J Streichan, Dennis O Clegg, Siddharth S Dey, Maxwell Z Wilson, Beth L Pruitt.
      Hypertrophy Cardiomyopathy (HCM) is the most prevalent hereditary cardiovascular disease - affecting >1:500 individuals. Advanced forms of HCM clinically present with hypercontractility, hypertrophy and fibrosis. Several single-point mutations in b-myosin heavy chain (MYH7) have been associated with HCM and increased contractility at the organ level. Different MYH7 mutations have resulted in increased, decreased, or unchanged force production at the molecular level. Yet, how these molecular kinetics link to cell and tissue pathogenesis remains unclear. The Hippo Pathway, specifically its effector molecule YAP, has been demonstrated to be reactivated in pathological hypertrophic growth. We hypothesized that changes in force production (intrinsically or extrinsically) directly alter the homeostatic mechano-signaling of the Hippo pathway through changes in stresses on the nucleus. Using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we asked whether homeostatic mechanical signaling through the canonical growth regulator, YAP, is altered 1) by changes in the biomechanics of HCM mutant cardiomyocytes and 2) by alterations in the mechanical environment. We use genetically edited hiPSC-CM with point mutations in MYH7 associated with HCM, and their matched controls, combined with micropatterned traction force microscopy substrates to confirm the hypercontractile phenotype in MYH7 mutants. We next modulate contractility in healthy and disease hiPSC-CMs by treatment with positive and negative inotropic drugs and demonstrate a correlative relationship between contractility and YAP activity. We further demonstrate the activation of YAP in both HCM mutants and healthy hiPSC-CMs treated with contractility modulators is through enhanced nuclear deformation. We conclude that the overactivation of YAP, possibly initiated and driven by hypercontractility, correlates with excessive CCN2 secretion (connective tissue growth factor), enhancing cardiac fibroblast/myofibroblast transition and production of known hypertrophic signaling molecule TGFβ. Our study suggests YAP being an indirect player in the initiation of hypertrophic growth and fibrosis in HCM. Our results provide new insights into HCM progression and bring forth a testbed for therapeutic options in treating HCM.
    DOI:  https://doi.org/10.1101/2024.06.03.597045
  16. Dev Cell. 2024 May 20. pii: S1534-5807(24)00295-8. [Epub ahead of print]
    Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule.
    George Kelly, Tetsushi Kataura, Johan Panek, Gailing Ma, Hanna Salmonowicz, Ashley Davis, Hannah Kendall, Charlotte Brookes, Daniel Moscoh Ayine-Tora, Peter Banks, Glyn Nelson, Laura Dobby, Patricia R Pitrez, Laura Booth, Lydia Costello, Gavin D Richardson, Penny Lovat, Stefan Przyborski, Lino Ferreira, Laura Greaves, Karolina Szczepanowska, Thomas von Zglinicki, Satomi Miwa, Max Brown, Michael Flagler, John E Oblong, Charles C Bascom, Bernadette Carroll, Jóhannes Reynisson, Viktor I Korolchuk.
      Selective degradation of damaged mitochondria by autophagy (mitophagy) is proposed to play an important role in cellular homeostasis. However, the molecular mechanisms and the requirement of mitochondrial quality control by mitophagy for cellular physiology are poorly understood. Here, we demonstrated that primary human cells maintain highly active basal mitophagy initiated by mitochondrial superoxide signaling. Mitophagy was found to be mediated by PINK1/Parkin-dependent pathway involving p62 as a selective autophagy receptor (SAR). Importantly, this pathway was suppressed upon the induction of cellular senescence and in naturally aged cells, leading to a robust shutdown of mitophagy. Inhibition of mitophagy in proliferating cells was sufficient to trigger the senescence program, while reactivation of mitophagy was necessary for the anti-senescence effects of NAD precursors or rapamycin. Furthermore, reactivation of mitophagy by a p62-targeting small molecule rescued markers of cellular aging, which establishes mitochondrial quality control as a promising target for anti-aging interventions.
    Keywords:  PINK1; Parkin; aging; autophagy; mitophagy; nicotinamide; nicotinamide riboside; p62; rapamycin; redox; senescence
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.020
  17. Cell. 2024 Jun 20. pii: S0092-8674(24)00537-3. [Epub ahead of print]187(13): 3220-3223
    Dynamic models of human development and concepts of the individual.
    Insoo Hyun.
      Stem cells can be coaxed to self-organize into dynamic models of human development and early embryo formation. Despite their scientific promise, might widespread use of these technologies alter people's beliefs about what it means to be a human individual? Attention to some important philosophical distinctions may help navigate our thinking.
    DOI:  https://doi.org/10.1016/j.cell.2024.05.028
  18. Nat Commun. 2024 Jun 20. 15(1): 5265
    DYRK1A signalling synchronizes the mitochondrial import pathways for metabolic rewiring.
    Adinarayana Marada, Corvin Walter, Tamara Suhm, Sahana Shankar, Arpita Nandy, Tilman Brummer, Ines Dhaouadi, F-Nora Vögtle, Chris Meisinger.
      Mitochondria require an extensive proteome to maintain a variety of metabolic reactions, and changes in cellular demand depend on rapid adaptation of the mitochondrial protein composition. The TOM complex, the organellar entry gate for mitochondrial precursors in the outer membrane, is a target for cytosolic kinases to modulate protein influx. DYRK1A phosphorylation of the carrier import receptor TOM70 at Ser91 enables its efficient docking and thus transfer of precursor proteins to the TOM complex. Here, we probe TOM70 phosphorylation in molecular detail and find that TOM70 is not a CK2 target nor import receptor for MIC19 as previously suggested. Instead, we identify TOM20 as a MIC19 import receptor and show off-target inhibition of the DYRK1A-TOM70 axis with the clinically used CK2 inhibitor CX4945 which activates TOM20-dependent import pathways. Taken together, modulation of DYRK1A signalling adapts the central mitochondrial protein entry gate via synchronization of TOM70- and TOM20-dependent import pathways for metabolic rewiring. Thus, DYRK1A emerges as a cytosolic surveillance kinase to regulate and fine-tune mitochondrial protein biogenesis.
    DOI:  https://doi.org/10.1038/s41467-024-49611-4
  19. bioRxiv. 2024 Jun 06. pii: 2024.06.04.597485. [Epub ahead of print]
    KLF4 in smooth muscle cell-derived progenitor cells is essential for angiotensin II-induced cardiac inflammation and fibrosis.
    Sizhao Lu, Austin J Jolly, Allison M Dubner, Keith A Strand, Marie F Mutryn, Tyler Hinthorn, Tysen Noble, Raphael A Nemenoff, Karen S Moulton, Mark W Majesky, Mary Cm Weiser-Evans.
      Cardiac fibrosis is defined by the excessive accumulation of extracellular matrix (ECM) material resulting in cardiac tissue scarring and dysfunction. While it is commonly accepted that myofibroblasts are the major contributors to ECM deposition in cardiac fibrosis, their origin remains debated. By combining lineage tracing and RNA sequencing, our group made the paradigm-shifting discovery that a subpopulation of resident vascular stem cells residing within the aortic, carotid artery, and femoral aartery adventitia (termed AdvSca1-SM cells) originate from mature vascular smooth muscle cells (SMCs) through an in situ reprogramming process. SMC-to-AdvSca1-SM reprogramming and AdvSca1-SM cell maintenance is dependent on induction and activity of the transcription factor, KLF4. However, the molecular mechanism whereby KLF4 regulates AdvSca1-SM phenotype remains unclear. In the current study, leveraging a highly specific AdvSca1-SM cell reporter system, single-cell RNA-sequencing (scRNA-seq), and spatial transcriptomic approaches, we demonstrate the profibrotic differentiation trajectory of coronary artery-associated AdvSca1-SM cells in the setting of Angiotensin II (AngII)-induced cardiac fibrosis. Differentiation was characterized by loss of stemness-related genes, including Klf4 , but gain of expression of a profibrotic phenotype. Importantly, these changes were recapitulated in human cardiac hypertrophic tissue, supporting the translational significance of profibrotic transition of AdvSca1-SM-like cells in human cardiomyopathy. Surprisingly and paradoxically, AdvSca1-SM-specific genetic knockout of Klf4 prior to AngII treatment protected against cardiac inflammation and fibrosis, indicating that Klf4 is essential for the profibrotic response of AdvSca1-SM cells. Overall, our data reveal the contribution of AdvSca1-SM cells to myofibroblasts in the setting of AngII-induced cardiac fibrosis. KLF4 not only maintains the stemness of AdvSca1-SM cells, but also orchestrates their response to profibrotic stimuli, and may serve as a therapeutic target in cardiac fibrosis.
    DOI:  https://doi.org/10.1101/2024.06.04.597485
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