bims-ginsta Biomed News
on Genome instability
Issue of 2024‒03‒24
23 papers selected by
Jinrong Hu, National University of Singapore
  1. Subscaling of a cytosolic RNA binding protein governs cell size homeostasis in the multiple fission alga Chlamydomonas.
  2. A kinetic dichotomy between mitochondrial and nuclear gene expression processes.
  3. Fascin-induced bundling protects actin filaments from disassembly by cofilin.
  4. Competence for neural crest induction is controlled by hydrostatic pressure through Yap.
  5. FOXL2 interaction with different binding partners regulates the dynamics of ovarian development.
  6. Focal adhesions contain three specialized actin nanoscale layers.
  7. Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes.
  8. A fast-acting lipid checkpoint in G1 prevents mitotic defects.
  9. Mitotic bookmarking by transcription factors: be aware of redundancy.
  10. Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient.
  11. Precise and scalable self-organization in mammalian pseudo-embryos.
  12. Efficient formation of single-copy human artificial chromosomes.
  13. Caveolin-1 protects endothelial cells from extensive expansion of transcellular tunnel by stiffening the plasma membrane.
  14. Cell proliferation and Notch signaling coordinate the formation of epithelial folds in the Drosophila leg.
  15. YAP induces a neonatal-like pro-renewal niche in the adult heart.
  16. Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing.
  17. TOR regulates variability of protein synthesis rates.
  18. Single-cell omics identifies inflammatory signaling as a trans-differentiation trigger in mouse embryos.
  19. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
  20. Communication between the stem cell niche and an adjacent differentiation niche through miRNA and EGFR signaling orchestrates exit from the stem cell state in the Drosophila ovary.
  21. Determination of single-molecule loading rate during mechanotransduction in cell adhesion.
  22. The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue.
  23. Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells.
  1. PLoS Genet. 2024 Mar 18. 20(3): e1010503
    Subscaling of a cytosolic RNA binding protein governs cell size homeostasis in the multiple fission alga Chlamydomonas.
    Dianyi Liu, Cristina Lopez-Paz, Yubing Li, Xiaohong Zhuang, James Umen.
      Coordination of growth and division in eukaryotic cells is essential for populations of proliferating cells to maintain size homeostasis, but the underlying mechanisms that govern cell size have only been investigated in a few taxa. The green alga Chlamydomonas reinhardtii (Chlamydomonas) proliferates using a multiple fission cell cycle that involves a long G1 phase followed by a rapid series of successive S and M phases (S/M) that produces 2n daughter cells. Two control points show cell-size dependence: the Commitment control point in mid-G1 phase requires the attainment of a minimum size to enable at least one mitotic division during S/M, and the S/M control point where mother cell size governs cell division number (n), ensuring that daughter distributions are uniform. tny1 mutants pass Commitment at a smaller size than wild type and undergo extra divisions during S/M phase to produce small daughters, indicating that TNY1 functions to inhibit size-dependent cell cycle progression. TNY1 encodes a cytosolic hnRNP A-related RNA binding protein and is produced once per cell cycle during S/M phase where it is apportioned to daughter cells, and then remains at constant absolute abundance as cells grow, a property known as subscaling. Altering the dosage of TNY1 in heterozygous diploids or through mis-expression increased Commitment cell size and daughter cell size, indicating that TNY1 is a limiting factor for both size control points. Epistasis placed TNY1 function upstream of the retinoblastoma tumor suppressor complex (RBC) and one of its regulators, Cyclin-Dependent Kinase G1 (CDKG1). Moreover, CDKG1 protein and mRNA were found to over-accumulate in tny1 cells suggesting that CDKG1 may be a direct target of repression by TNY1. Our data expand the potential roles of subscaling proteins outside the nucleus and imply a control mechanism that ties TNY1 accumulation to pre-division mother cell size.
    DOI:  https://doi.org/10.1371/journal.pgen.1010503
  2. Mol Cell. 2024 Mar 14. pii: S1097-2765(24)00170-9. [Epub ahead of print]
    A kinetic dichotomy between mitochondrial and nuclear gene expression processes.
    Erik McShane, Mary Couvillion, Robert Ietswaart, Gyan Prakash, Brendan M Smalec, Iliana Soto, Autum R Baxter-Koenigs, Karine Choquet, L Stirling Churchman.
      Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared with nuclear mRNAs, mt-mRNAs were produced 1,100-fold more, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors LRPPRC and FASTKD5 identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
    Keywords:  LRPPRC; Leighs disease; RNA life cycle; gene regulation; genetic conflict; metabolic regulation; mitochondrial gene expression; mitochondrial translation; mitonuclear balance; organellular biogenesis; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.028
  3. J Cell Biol. 2024 Jun 03. pii: e202312106. [Epub ahead of print]223(6):
    Fascin-induced bundling protects actin filaments from disassembly by cofilin.
    Jahnavi Chikireddy, Léana Lengagne, Rémi Le Borgne, Catherine Durieu, Hugo Wioland, Guillaume Romet-Lemonne, Antoine Jégou.
      Actin filament turnover plays a central role in shaping actin networks, yet the feedback mechanism between network architecture and filament assembly dynamics remains unclear. The activity of ADF/cofilin, the main protein family responsible for filament disassembly, has been mainly studied at the single filament level. This study unveils that fascin, by crosslinking filaments into bundles, strongly slows down filament disassembly by cofilin. We show that this is due to a markedly slower initiation of the first cofilin clusters, which occurs up to 100-fold slower on large bundles compared with single filaments. In contrast, severing at cofilin cluster boundaries is unaffected by fascin bundling. After the formation of an initial cofilin cluster on a filament within a bundle, we observed the local removal of fascin. Notably, the formation of cofilin clusters on adjacent filaments is highly enhanced, locally. We propose that this interfilament cooperativity arises from the local propagation of the cofilin-induced change in helicity from one filament to the other filaments of the bundle. Overall, taking into account all the above reactions, we reveal that fascin crosslinking slows down the disassembly of actin filaments by cofilin. These findings highlight the important role played by crosslinkers in tuning actin network turnover by modulating the activity of other regulatory proteins.
    DOI:  https://doi.org/10.1083/jcb.202312106
  4. Nat Cell Biol. 2024 Mar 18.
    Competence for neural crest induction is controlled by hydrostatic pressure through Yap.
    Delan N Alasaadi, Lucas Alvizi, Jonas Hartmann, Namid Stillman, Prachiti Moghe, Takashi Hiiragi, Roberto Mayor.
      Embryonic induction is a key mechanism in development that corresponds to an interaction between a signalling and a responding tissue, causing a change in the direction of differentiation by the responding tissue. Considerable progress has been achieved in identifying inductive signals, yet how tissues control their responsiveness to these signals, known as competence, remains poorly understood. While the role of molecular signals in competence has been studied, how tissue mechanics influence competence remains unexplored. Here we investigate the role of hydrostatic pressure in controlling competence in neural crest cells, an embryonic cell population. We show that neural crest competence decreases concomitantly with an increase in the hydrostatic pressure of the blastocoel, an embryonic cavity in contact with the prospective neural crest. By manipulating hydrostatic pressure in vivo, we show that this increase leads to the inhibition of Yap signalling and impairs Wnt activation in the responding tissue, which would be required for neural crest induction. We further show that hydrostatic pressure controls neural crest induction in amphibian and mouse embryos and in human cells, suggesting a conserved mechanism across vertebrates. Our work sets out how tissue mechanics can interplay with signalling pathways to regulate embryonic competence.
    DOI:  https://doi.org/10.1038/s41556-024-01378-y
  5. Sci Adv. 2024 Mar 22. 10(12): eadl0788
    FOXL2 interaction with different binding partners regulates the dynamics of ovarian development.
    Roberta Migale, Michelle Neumann, Richard Mitter, Mahmoud-Reza Rafiee, Sophie Wood, Jessica Olsen, Robin Lovell-Badge.
      The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2's role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (Usp7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
    DOI:  https://doi.org/10.1126/sciadv.adl0788
  6. Nat Commun. 2024 Mar 21. 15(1): 2547
    Focal adhesions contain three specialized actin nanoscale layers.
    Reena Kumari, Katharina Ven, Megan Chastney, Shrikant B Kokate, Johan Peränen, Jesse Aaron, Konstantin Kogan, Leonardo Almeida-Souza, Elena Kremneva, Renaud Poincloux, Teng-Leong Chew, Peter W Gunning, Johanna Ivaska, Pekka Lappalainen.
      Focal adhesions (FAs) connect inner workings of cell to the extracellular matrix to control cell adhesion, migration and mechanosensing. Previous studies demonstrated that FAs contain three vertical layers, which connect extracellular matrix to the cytoskeleton. By using super-resolution iPALM microscopy, we identify two additional nanoscale layers within FAs, specified by actin filaments bound to tropomyosin isoforms Tpm1.6 and Tpm3.2. The Tpm1.6-actin filaments, beneath the previously identified α-actinin cross-linked actin filaments, appear critical for adhesion maturation and controlled cell motility, whereas the adjacent Tpm3.2-actin filament layer beneath seems to facilitate adhesion disassembly. Mechanistically, Tpm3.2 stabilizes ACF-7/MACF1 and KANK-family proteins at adhesions, and hence targets microtubule plus-ends to FAs to catalyse their disassembly. Tpm3.2 depletion leads to disorganized microtubule network, abnormally stable FAs, and defects in tail retraction during migration. Thus, FAs are composed of distinct actin filament layers, and each may have specific roles in coupling adhesions to the cytoskeleton, or in controlling adhesion dynamics.
    DOI:  https://doi.org/10.1038/s41467-024-46868-7
  7. Cell. 2024 Mar 11. pii: S0092-8674(24)00227-7. [Epub ahead of print]
    Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes.
    Javier Ganz, Lovelace J Luquette, Sara Bizzotto, Michael B Miller, Zinan Zhou, Craig L Bohrson, Hu Jin, Antuan V Tran, Vinayak V Viswanadham, Gannon McDonough, Katherine Brown, Yasmine Chahine, Brian Chhouk, Alon Galor, Peter J Park, Christopher A Walsh.
      Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
    Keywords:  aging; brain cancer; brain disorders; glial cells; glioma; gliomagenesis; oligodendrocyte precursor cells; oligodendrocytes; somatic mutations
    DOI:  https://doi.org/10.1016/j.cell.2024.02.025
  8. Nat Commun. 2024 Mar 18. 15(1): 2441
    A fast-acting lipid checkpoint in G1 prevents mitotic defects.
    Marielle S Köberlin, Yilin Fan, Chad Liu, Mingyu Chung, Antonio F M Pinto, Peter K Jackson, Alan Saghatelian, Tobias Meyer.
      Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
    DOI:  https://doi.org/10.1038/s41467-024-46696-9
  9. Trends Biochem Sci. 2024 Mar 18. pii: S0968-0004(24)00064-1. [Epub ahead of print]
    Mitotic bookmarking by transcription factors: be aware of redundancy.
    Miguel V Silva, Diogo S Castro.
      A recent report by Chervova, Molliex, et al. shows redundant functions for the transcription factors (TFs) ESRRB and NR5A2 as mitotic bookmarkers in mouse embryonic stem (ES) cells. These occupy some of their target sites in mitotic chromatin, ensuring their robust reactivation after cell division, including markers and regulators of pluripotency.
    Keywords:  cell identity; mitotic bookmarking by transcription factors; nuclear receptors; pluripotency network; transcription
    DOI:  https://doi.org/10.1016/j.tibs.2024.03.003
  10. Cell. 2024 Mar 13. pii: S0092-8674(24)00232-0. [Epub ahead of print]
    Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient.
    Matthew R King, Kiersten M Ruff, Andrew Z Lin, Avnika Pant, Mina Farag, Jared M Lalmansingh, Tingting Wu, Martin J Fossat, Wei Ouyang, Matthew D Lew, Emma Lundberg, Michael D Vahey, Rohit V Pappu.
      Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.
    Keywords:  Cajal bodies; biomolecular condensates; condensation; emergent property; evolution; interphase; nuclear speckles; nucleolus; pH; phase separation; proton motive force; reconstitution
    DOI:  https://doi.org/10.1016/j.cell.2024.02.029
  11. Nat Struct Mol Biol. 2024 Mar 15.
    Precise and scalable self-organization in mammalian pseudo-embryos.
    Mélody Merle, Leah Friedman, Corinne Chureau, Armin Shoushtarizadeh, Thomas Gregor.
      Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. Here we investigate this phenomenon using gastruloids, a three-dimensional in vitro model for early mammalian development. Our study reveals intrinsic reproducibility in the self-organization of gastruloids, encompassing growth dynamics and gene expression patterns. We observe a remarkable degree of control over gene expression along the main body axis, with pattern boundaries positioned with single-cell precision. Furthermore, as gastruloids grow, both their physical proportions and gene expression patterns scale proportionally with system size. Notably, these properties emerge spontaneously in self-organizing cell aggregates, distinct from many in vivo systems constrained by fixed boundary conditions. Our findings shed light on the intricacies of developmental precision, reproducibility and size scaling within a mammalian system, suggesting that these phenomena might constitute fundamental features of multicellularity.
    DOI:  https://doi.org/10.1038/s41594-024-01251-4
  12. Science. 2024 Mar 22. 383(6689): 1344-1349
    Efficient formation of single-copy human artificial chromosomes.
    Craig W Gambogi, Gabriel J Birchak, Elie Mer, David M Brown, George Yankson, Kathryn Kixmoeller, Janardan N Gavade, Josh L Espinoza, Prakriti Kashyap, Chris L Dupont, Glennis A Logsdon, Patrick Heun, John I Glass, Ben E Black.
      Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
    DOI:  https://doi.org/10.1126/science.adj3566
  13. Elife. 2024 Mar 22. pii: RP92078. [Epub ahead of print]12
    Caveolin-1 protects endothelial cells from extensive expansion of transcellular tunnel by stiffening the plasma membrane.
    Camille Morel, Eline Lemerle, Feng-Ching Tsai, Thomas Obadia, Nishit Srivastava, Maud Marechal, Audrey Salles, Marvin Albert, Caroline Stefani, Yvonne Benito, François Vandenesch, Christophe Lamaze, Stéphane Vassilopoulos, Matthieu Piel, Patricia Bassereau, David Gonzalez-Rodriguez, Cecile Leduc, Emmanuel Lemichez.
      Large transcellular pores elicited by bacterial mono-ADP-ribosyltransferase (mART) exotoxins inhibiting the small RhoA GTPase compromise the endothelial barrier. Recent advances in biophysical modeling point toward membrane tension and bending rigidity as the minimal set of mechanical parameters determining the nucleation and maximal size of transendothelial cell macroaperture (TEM) tunnels induced by bacterial RhoA-targeting mART exotoxins. We report that cellular depletion of caveolin-1, the membrane-embedded building block of caveolae, and depletion of cavin-1, the master regulator of caveolae invaginations, increase the number of TEMs per cell. The enhanced occurrence of TEM nucleation events correlates with a reduction in cell height due to the increase in cell spreading and decrease in cell volume, which, together with the disruption of RhoA-driven F-actin meshwork, favor membrane apposition for TEM nucleation. Strikingly, caveolin-1 specifically controls the opening speed of TEMs, leading to their dramatic 5.4-fold larger widening. Consistent with the increase in TEM density and width in siCAV1 cells, we record a higher lethality in CAV1 KO mice subjected to a catalytically active mART exotoxin targeting RhoA during staphylococcal bloodstream infection. Combined theoretical modeling with independent biophysical measurements of plasma membrane bending rigidity points toward a specific contribution of caveolin-1 to membrane stiffening in addition to the role of cavin-1/caveolin-1-dependent caveolae in the control of membrane tension homeostasis.
    Keywords:  bacterial toxin; caveolin-1; cell biology; human; mouse; physics of living systems; plasma membrane mechanics; transendothelial cell macroaperture
    DOI:  https://doi.org/10.7554/eLife.92078
  14. Development. 2024 Mar 21. pii: dev.202384. [Epub ahead of print]
    Cell proliferation and Notch signaling coordinate the formation of epithelial folds in the Drosophila leg.
    Alonso Rodríguez, David Foronda, Sergio Córdoba, Daniel Felipe-Cordero, Antonio Baonza, David Miguez, Carlos Estella.
      The formation of complex three-dimensional organs during development requires the precise coordination between patterning networks and mechanical forces. In particular, tissue folding is a crucial process that relies on a combination of local and tissue-wide mechanical forces. Here, we investigate the contribution of cell proliferation to epithelial morphogenesis using the Drosophila leg tarsal folds as a model. We reveal that tissue-wide compression forces generated by cell proliferation, in coordination with Notch signaling pathway, are essential for the formation of epithelial folds in precise locations along the proximo-distal axis of the leg. As cell numbers increase, compressive stresses arise, promoting the folding of the epithelium and reinforcing the apical constriction of invaginating cells. Additionally, the Notch target dysfusion (dysf) plays a key function specifying the location of the folds, through the apical accumulation of F-actin and the apico-basal shortening of invaginating cells. These findings provide new insights into the intricate mechanisms involved in epithelial morphogenesis, highlighting the critical role of tissue-wide forces in shaping a three-dimensional organ in a reproducible manner.
    Keywords:  Cell proliferation; Drosophila; Epithelial folding; Morphogenesis; Notch; Tissue compression
    DOI:  https://doi.org/10.1242/dev.202384
  15. Nat Cardiovasc Res. 2024 Mar;3(3): 283-300
    YAP induces a neonatal-like pro-renewal niche in the adult heart.
    Rich Gang Li, Xiao Li, Yuka Morikawa, Francisco J Grisanti-Canozo, Fansen Meng, Chang-Ru Tsai, Yi Zhao, Lin Liu, Jong Kim, Bing Xie, Elzbieta Klysik, Shijie Liu, Md Abul Hassan Samee, James F Martin.
      After myocardial infarction (MI), mammalian hearts do not regenerate, and the microenvironment is disrupted. Hippo signaling loss of function with activation of transcriptional co-factor YAP induces heart renewal and rebuilds the post-MI microenvironment. In this study, we investigated adult renewal-competent mouse hearts expressing an active version of YAP, called YAP5SA, in cardiomyocytes (CMs). Spatial transcriptomics and single-cell RNA sequencing revealed a conserved, renewal-competent CM cell state called adult (a)CM2 with high YAP activity. aCM2 co-localized with cardiac fibroblasts (CFs) expressing complement pathway component C3 and macrophages (MPs) expressing C3ar1 receptor to form a cellular triad in YAP5SA hearts and renewal-competent neonatal hearts. Although aCM2 was detected in adult mouse and human hearts, the cellular triad failed to co-localize in these non-renewing hearts. C3 and C3ar1 loss-of-function experiments indicated that C3a signaling between MPs and CFs was required to assemble the pro-renewal aCM2, C3+ CF and C3ar1+ MP cellular triad.
    DOI:  https://doi.org/10.1038/s44161-024-00428-w
  16. bioRxiv. 2024 Mar 10. pii: 2024.03.05.583597. [Epub ahead of print]
    Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing.
    Gerrald A Lodewijk, Sayaka Kozuki, Clara Han, Benjamin R Topacio, Abolfazl Zargari, Seungho Lee, Gavin Knight, Randolph Ashton, Lei S Qi, S Ali Shariati.
      Embryonic stem cells (ESCs) can self-organize in vitro into developmental patterns with spatial organization and molecular similarity to that of early embryonic stages. This self-organization of ESCs requires transmission of signaling cues, via addition of small molecule chemicals or recombinant proteins, to induce distinct embryonic cellular fates and subsequent assembly into structures that can mimic aspects of early embryonic development. During natural embryonic development, different embryonic cell types co-develop together, where each cell type expresses specific fate-inducing transcription factors through activation of non-coding regulatory elements and interactions with neighboring cells. However, previous studies have not fully explored the possibility of engineering endogenous regulatory elements to shape self-organization of ESCs into spatially-ordered embryo models. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize ESCs into early embryonic models. Our results show that CRISPR-based activation (CRISPRa) of only two endogenous regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that the emergence of spatially-ordered embryonic patterns happens through the intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-Programmed Embryo Models (CPEMs) show highly consistent composition of major embryonic cell types that are spatially-organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CPEMs with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings offer a programmable embryo model and demonstrate that minimum intrinsic epigenome editing is sufficient to self-organize ESCs into highly consistent pre-gastrulation embryo models.
    DOI:  https://doi.org/10.1101/2024.03.05.583597
  17. EMBO J. 2024 Mar 18.
    TOR regulates variability of protein synthesis rates.
    Clovis Basier, Paul Nurse.
      Cellular processes are subject to inherent variability, but the extent to which cells can regulate this variability has received little investigation. Here, we explore the characteristics of the rate of cellular protein synthesis in single cells of the eukaryote fission yeast. Strikingly, this rate is highly variable despite protein synthesis being dependent on hundreds of reactions which might be expected to average out at the overall cellular level. The rate is variable over short time scales, and exhibits homoeostatic behaviour at the population level. Cells can regulate the level of variability through processes involving the TOR pathway, suggesting there is an optimal level of variability conferring a selective advantage. While this could be an example of bet-hedging, but we propose an alternative explanation: regulated 'loose' control of complex processes of overall cellular metabolism such as protein synthesis, may lead to this variability. This could ensure cells are fluid in control and agile in response to changing conditions, and may constitute a novel organisational principle of complex metabolic cellular systems.
    Keywords:  Control; Protein Synthesis; Single-Cell; TOR Pathway; Variability
    DOI:  https://doi.org/10.1038/s44318-024-00075-8
  18. Dev Cell. 2024 Mar 18. pii: S1534-5807(24)00109-6. [Epub ahead of print]
    Single-cell omics identifies inflammatory signaling as a trans-differentiation trigger in mouse embryos.
    Yifan Zhang, Zhixin Kang, Mengyao Liu, Lu Wang, Feng Liu.
      Trans-differentiation represents a direct lineage conversion; however, insufficient characterization of this process hinders its potential applications. Here, to explore a potential universal principal for trans-differentiation, we performed single-cell transcriptomic analysis of endothelial-to-hematopoietic transition (EHT), endothelial-to-mesenchymal transition, and epithelial-to-mesenchymal transition in mouse embryos. We applied three scoring indexes of entropies, cell-type signature transcription factor expression, and critical transition signals to show common features underpinning the fate plasticity of transition states. Cross-model comparison identified inflammatory-featured transition states and a common trigger role of interleukin-33 in promoting fate conversions. Multimodal profiling (integrative transcriptomic and chromatin accessibility analysis) demonstrated the inflammatory regulation of hematopoietic specification. Furthermore, multimodal omics and fate-mapping analyses showed that endothelium-specific Spi1, as an inflammatory effector, governs appropriate chromatin accessibility and transcriptional programs to safeguard EHT. Overall, our study employs single-cell omics to identify critical transition states/signals and the common trigger role of inflammatory signaling in developmental-stress-induced fate conversions.
    Keywords:  endothelial-to-hematopoietic transition; endothelial-to-mesenchymal transition; epithelial-to-mesenchymal transition; inflammatory signaling; single-cell omics; spi1; trans-differentiation
    DOI:  https://doi.org/10.1016/j.devcel.2024.02.010
  19. Elife. 2024 Mar 22. pii: RP90579. [Epub ahead of print]12
    Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
    Wayne Mitchell, Ludger J E Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Y Chen, Joao A Paulo, Kerry A Pierce, Angelina H Choy, Clary B Clish, Steven P Gygi, Vadim N Gladyshev.
      Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
    Keywords:  aging; biological age; cell biology; mitochondria; mouse; oxidative phosphorylation; reprogramming
    DOI:  https://doi.org/10.7554/eLife.90579
  20. PLoS Biol. 2024 Mar 21. 22(3): e3002515
    Communication between the stem cell niche and an adjacent differentiation niche through miRNA and EGFR signaling orchestrates exit from the stem cell state in the Drosophila ovary.
    Jiani Chen, Chaoqun Li, Yifeng Sheng, Junwei Zhang, Lan Pang, Zhi Dong, Zhiwei Wu, Yueqi Lu, Zhiguo Liu, Qichao Zhang, Xueying Guan, Xuexin Chen, Jianhua Huang.
      The signaling environment, or niche, often governs the initial difference in behavior of an adult stem cell and a derivative that initiates a path towards differentiation. The transition between an instructive stem cell niche and differentiation niche must generally have single-cell resolution, suggesting that multiple mechanisms might be necessary to sharpen the transition. Here, we examined the Drosophila ovary and found that Cap cells, which are key constituents of the germline stem cell (GSC) niche, express a conserved microRNA (miR-124). Surprisingly, loss of miR-124 activity in Cap cells leads to a defect in differentiation of GSC derivatives. We present evidence that the direct functional target of miR-124 in Cap cells is the epidermal growth factor receptor (EGFR) and that failure to limit EGFR expression leads to the ectopic expression of a key anti-differentiation BMP signal in neighboring somatic escort cells (ECs), which constitute a differentiation niche. We further found that Notch signaling connects EFGR activity in Cap cells to BMP expression in ECs. We deduce that the stem cell niche communicates with the differentiation niche through a mechanism that begins with the selective expression of a specific microRNA and culminates in the suppression of the major anti-differentiation signal in neighboring cells, with the functionally important overall role of sharpening the spatial distinction between self-renewal and differentiation environments.
    DOI:  https://doi.org/10.1371/journal.pbio.3002515
  21. Science. 2024 Mar 22. 383(6689): 1374-1379
    Determination of single-molecule loading rate during mechanotransduction in cell adhesion.
    Myung Hyun Jo, Paul Meneses, Olivia Yang, Claudia C Carcamo, Sushil Pangeni, Taekjip Ha.
      Cells connect with their environment through surface receptors and use physical tension in receptor-ligand bonds for various cellular processes. Single-molecule techniques have revealed bond strength by measuring "rupture force," but it has long been recognized that rupture force is dependent on loading rate-how quickly force is ramped up. Thus, the physiological loading rate needs to be measured to reveal the mechanical strength of individual bonds in their functional context. We have developed an overstretching tension sensor (OTS) to allow more accurate force measurement in physiological conditions with single-molecule detection sensitivity even in mechanically active regions. We used serially connected OTSs to show that the integrin loading rate ranged from 0.5 to 4 piconewtons per second and was about three times higher in leukocytes than in epithelial cells.
    DOI:  https://doi.org/10.1126/science.adk6921
  22. Cell Rep. 2024 Mar 18. pii: S2211-1247(24)00283-3. [Epub ahead of print]43(3): 113955
    The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue.
    Paul-Andres Morocho-Jaramillo, Ilan Kotlar-Goldaper, Bhakti I Zakarauskas-Seth, Bettina Purfürst, Alessandro Filosa, Suphansa Sawamiphak.
      Epicardial adipose tissue (eAT) is a metabolically active fat depot that has been associated with a wide array of cardiac homeostatic functions and cardiometabolic diseases. A full understanding of its diverse physiological and pathological roles is hindered by the dearth of animal models. Here, we show, in the heart of an ectothermic teleost, the zebrafish, the existence of a fat depot localized underneath the epicardium, originating from the epicardium and exhibiting the molecular signature of beige adipocytes. Moreover, a subset of adipocytes within this cardiac fat tissue exhibits primitive thermogenic potential. Transcriptomic profiling and cross-species analysis revealed elevated glycolytic and cardiac homeostatic gene expression with downregulated obesity and inflammatory hallmarks in the teleost eAT compared to that of lean aged humans. Our findings unveil epicardium-derived beige fat in the heart of an ectotherm considered to possess solely white adipocytes for energy storage and identify pathways that may underlie age-driven remodeling of human eAT.
    Keywords:  CP: Developmental biology; CP: Metabolism; ectotherm; epicardial adipose tissue; thermogenic; transcriptome; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2024.113955
  23. Nat Commun. 2024 Mar 20. 15(1): 2482
    Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells.
    Hongyu Shi, Marc J Williams, Gryte Satas, Adam C Weiner, Andrew McPherson, Sohrab P Shah.
      Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.
    DOI:  https://doi.org/10.1038/s41467-024-46710-0
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