bims-ginsta Biomed News
on Genome instability
Issue of 2024–07–28
thirty papers selected by
Jinrong Hu, National University of Singapore
  1. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells.
  2. Plasticity of the mitotic spindle in response to karyotype variation.
  3. Rigidity percolation and active advection synergize in the actomyosin cortex to drive amoeboid cell motility.
  4. Sex-specific DNA-replication in the early mammalian embryo.
  5. Aging-associated reduction of chromosomal histones in mammalian oocytes.
  6. Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
  7. Condensin I folds the Caenorhabditis elegans genome.
  8. mTOR links nutrients, inflammaging and lifespan.
  9. Structural anisotropy results in mechano-directional transport of proteins across nuclear pores.
  10. Mst1-mediated phosphorylation of FoxO1 and C/EBP-β stimulates cell-protective mechanisms in cardiomyocytes.
  11. Cohesin prevents cross-domain gene coactivation.
  12. Competition shapes the landscape of X-chromosome-linked genetic diversity.
  13. Autocrine glutamate signaling drives cell competition in Drosophila.
  14. Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.
  15. Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression.
  16. Embryonic stem cells maintain high origin activity and slow forks to coordinate replication with cell cycle progression.
  17. Hepatic lipopolysaccharide binding protein partially uncouples inflammation from fibrosis in MAFLD.
  18. Polysome collapse and RNA condensation fluidize the cytoplasm.
  19. Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs.
  20. The structure and mechanics of the cell cortex depend on the location and adhesion state.
  21. Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain.
  22. Generation and Characterization of hiPSC-Derived Vascularized-, Perfusable Cardiac Microtissues-on-Chip.
  23. An NAD+-dependent metabolic checkpoint regulates hematopoietic stem cell activation and aging.
  24. Germline regulation of the somatic mitochondrial stress response.
  25. 3D chromatin structures associated with ncRNA roX2 for hyperactivation and coactivation across the entire X chromosome.
  26. Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity.
  27. Transient formation of collaterals contributes to the restoration of the arterial tree during cardiac regeneration in neonatal mice.
  28. Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration.
  29. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes.
  30. Temporally resolved early bone morphogenetic protein-driven transcriptional cascade during human amnion specification.
  1. Nat Struct Mol Biol. 2024 Jul 24.
    Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells.
    Michael C Lanz, Shuyuan Zhang, Matthew P Swaffer, Inbal Ziv, Luisa Hernández Götz, Jacob Kim, Frank McCarthy, Daniel F Jarosz, Joshua E Elias, Jan M Skotheim.
      Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.
    DOI:  https://doi.org/10.1038/s41594-024-01353-z
  2. Curr Biol. 2024 Jul 17. pii: S0960-9822(24)00842-X. [Epub ahead of print]
    Plasticity of the mitotic spindle in response to karyotype variation.
    Preethi Kunchala, Joseph M Varberg, Eileen O'Toole, Jennifer Gardner, Sarah E Smith, Melainia McClain, Sue L Jaspersen, R Scott Hawley, Jennifer L Gerton.
      Karyotypes, composed of chromosomes, must be accurately partitioned by the mitotic spindle for optimal cell health. However, it is unknown how underlying characteristics of karyotypes, such as chromosome number and size, govern the scaling of the mitotic spindle to ensure accurate chromosome segregation and cell proliferation. We utilize budding yeast strains engineered with fewer chromosomes, including just two "mega chromosomes," to study how spindle size and function are responsive to, and scaled by, karyotype. We determined that deletion and overexpression of spindle-related genes are detrimental to the growth of strains with two chromosomes, suggesting that mega chromosomes exert altered demands on the spindle. Using confocal microscopy, we demonstrate that cells with fewer but longer chromosomes have smaller spindle pole bodies, fewer microtubules, and longer spindles. Moreover, using electron tomography and confocal imaging, we observe elongated, bent anaphase spindles with fewer core microtubules in strains with mega chromosomes. Cells harboring mega chromosomes grow more slowly, are delayed in mitosis, and a subset struggle to complete chromosome segregation. We propose that the karyotype of the cell dictates the microtubule number, type, spindle pole body size, and spindle length, subsequently influencing the dynamics of mitosis, such as the rate of spindle elongation and the velocity of pole separation. Taken together, our results suggest that mitotic spindles are highly plastic ultrastructures that can accommodate and adjust to a variety of karyotypes, even within a species.
    Keywords:  anaphase; centromere; chromosome; chromosome segregation; chromosome size; karyotype; metaphase; microtubule; mitosis; spindle; spindle pole body; tomography
    DOI:  https://doi.org/10.1016/j.cub.2024.06.058
  3. Dev Cell. 2024 Jul 20. pii: S1534-5807(24)00401-5. [Epub ahead of print]
    Rigidity percolation and active advection synergize in the actomyosin cortex to drive amoeboid cell motility.
    Juan Manuel García-Arcos, Johannes Ziegler, Silvia Grigolon, Loïc Reymond, Gaurav Shajepal, Cédric J Cattin, Alexis Lomakin, Daniel J Müller, Verena Ruprecht, Stefan Wieser, Raphael Voituriez, Matthieu Piel.
      Spontaneous locomotion is a common feature of most metazoan cells, generally attributed to the properties of actomyosin networks. This force-producing machinery has been studied down to the most minute molecular details, especially in lamellipodium-driven migration. Nevertheless, how actomyosin networks work inside contraction-driven amoeboid cells still lacks unifying principles. Here, using stable motile blebs from HeLa cells as a model amoeboid motile system, we imaged the dynamics of the actin cortex at the single filament level and revealed the co-existence of three distinct rheological phases. We introduce "advected percolation," a process where rigidity percolation and active advection synergize, spatially organizing the actin network's mechanical properties into a minimal and generic locomotion mechanism. Expanding from our observations on simplified systems, we speculate that this model could explain, down to the single actin filament level, how amoeboid cells, such as cancer or immune cells, can propel efficiently through complex 3D environments.
    Keywords:  actomyosin; amoeboid migration; biophysics; bleb; cancer; cytoplast; extracellular vesicles; percolation; polymer physics; rheology
    DOI:  https://doi.org/10.1016/j.devcel.2024.06.023
  4. Nat Commun. 2024 Jul 27. 15(1): 6323
    Sex-specific DNA-replication in the early mammalian embryo.
    Jason Alexander Halliwell, Javier Martin-Gonzalez, Adnan Hashim, John Arne Dahl, Eva R Hoffmann, Mads Lerdrup.
      The timing of DNA replication in mammals is crucial for minimizing errors and influenced by genome usage and chromatin states. Replication timing in the newly formed mammalian embryo remains poorly understood. Here, we have investigated replication timing in mouse zygotes and 2-cell embryos, revealing that zygotes lack a conventional replication timing program, which then emerges in 2-cell embryos. This program differs from embryonic stem cells and generally correlates with transcription and genome compartmentalization of both parental genomes. However, consistent and systematic differences existed between the replication timing of the two parental genomes, including considerably later replication of maternal pericentromeric regions compared to paternal counterparts. Moreover, maternal chromatin modified by Polycomb Repressive Complexes in the oocyte, undergoes early replication, despite belonging to the typically late-replicating B-compartment of the genome. This atypical and asynchronous replication of the two parental genomes may advance our understanding of replication stress in early human embryos and trigger strategies to reduce errors and aneuploidies.
    DOI:  https://doi.org/10.1038/s41467-024-50727-w
  5. Genes Cells. 2024 Jul 23.
    Aging-associated reduction of chromosomal histones in mammalian oocytes.
    Masashi Mori, Manami Koshiguchi, Osamu Takenouchi, Mei A Mukose, Hinako M Takase, Tappei Mishina, Hailiang Mei, Miho Kihara, Takaya Abe, Azusa Inoue, Tomoya S Kitajima.
      Mammalian oocytes undergo a long-term meiotic arrest that can last for almost the entire reproductive lifespan. This arrest occurs after DNA replication and is prolonged with age, which poses a challenge to oocytes in maintaining replication-dependent chromosomal proteins required for the completion of meiosis. In this study, we show that chromosomal histones are reduced with age in mouse oocytes. Both types of histone H3 variants, replication-dependent H3.1/H3.2 and replication-independent H3.3, decrease with age. Aging-associated histone reduction is associated with transcriptomic features that are caused by genetic depletion of histone H3.3. Neither the genetic reduction of chromosomal H3.1/H3.2 nor H3.3 accelerates the aging-associated increase in premature chromosome separation that causes meiotic segregation errors. We suggest that aging-associated reduction of chromosomal histones is linked to several transcriptomic abnormalities but does not significantly contribute to errors in meiotic chromosome segregation during the reproductive lifespan of mice.
    Keywords:  aging; chromosome; meiosis; oocyte
    DOI:  https://doi.org/10.1111/gtc.13146
  6. Cell Stem Cell. 2024 Jul 18. pii: S1934-5909(24)00250-9. [Epub ahead of print]
    Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
    Rui Chen, Rui Fan, Fei Chen, Niraimathi Govindasamy, Heike Brinkmann, Martin Stehling, Ralf H Adams, Hyun-Woo Jeong, Ivan Bedzhov.
      Embryonic diapause is a reproductive adaptation that enables some mammalian species to halt the otherwise continuous pace of embryonic development. In this dormant state, the embryo exploits poorly understood regulatory mechanisms to preserve its developmental potential for prolonged periods of time. Here, using mouse embryos and single-cell RNA sequencing, we molecularly defined embryonic diapause at single-cell resolution, revealing transcriptional dynamics while the embryo seemingly resides in a state of suspended animation. Additionally, we found that the dormant pluripotent cells rely on integrin receptors to sense their microenvironment and preserve their viability via Yap/Taz-mediated prosurvival signaling.
    Keywords:  Taz; Yap; embryo dormancy; embryonic diapause; embryonic stem cells; epiblast; extracellular matrix; integrin; pluripotency; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.stem.2024.06.015
  7. Nat Genet. 2024 Jul 22.
    Condensin I folds the Caenorhabditis elegans genome.
    Moushumi Das, Jennifer I Semple, Anja Haemmerli, Valeriia Volodkina, Janik Scotton, Todor Gitchev, Ahrmad Annan, Julie Campos, Cyril Statzer, Alexander Dakhovnik, Collin Y Ewald, Julien Mozziconacci, Peter Meister.
      The structural maintenance of chromosome (SMC) complexes-cohesin and condensins-are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans, a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin IDC, leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/IDC inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin IDC. C. elegans condensin I/IDC thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression.
    DOI:  https://doi.org/10.1038/s41588-024-01832-5
  8. Nat Aging. 2024 Jul 26.
    mTOR links nutrients, inflammaging and lifespan.
    Helena M Cochemé, Jesús Gil.
      
    DOI:  https://doi.org/10.1038/s43587-024-00681-5
  9. Nat Phys. 2024 ;20(7): 1180-1193
    Structural anisotropy results in mechano-directional transport of proteins across nuclear pores.
    Fani Panagaki, Rafael Tapia-Rojo, Tong Zhu, Natalie Milmoe, Patricia Paracuellos, Stephanie Board, Marc Mora, Jane Walker, Elena Rostkova, Andrew Stannard, Elvira Infante, Sergi Garcia-Manyes.
      The nuclear pore complex regulates nucleocytoplasmic transport by means of a tightly synchronized suite of biochemical reactions. The physicochemical properties of the translocating cargos are emerging as master regulators of their shuttling dynamics. As well as being affected by molecular weight and surface-exposed amino acids, the kinetics of the nuclear translocation of protein cargos also depend on their nanomechanical properties, yet the mechanisms underpinning the mechanoselectivity of the nuclear pore complex are unclear. Here we show that proteins with locally soft regions in the vicinity of the nuclear-localization sequence exhibit higher nuclear-import rates, and that such mechanoselectivity is specifically impaired upon knocking down nucleoporin 153, a key protein in the nuclear pore complex. This allows us to design a short, easy-to-express and chemically inert unstructured peptide tag that accelerates the nuclear-import rate of stiff protein cargos. We also show that U2OS osteosarcoma cells expressing the peptide-tagged myocardin-related transcription factor import this mechanosensitive protein to the nucleus at higher rates and display faster motility. Locally unstructured regions lower the free-energy barrier of protein translocation and might offer a control mechanism for nuclear mechanotransduction.
    Keywords:  Biological physics; Single-molecule biophysics
    DOI:  https://doi.org/10.1038/s41567-024-02438-8
  10. Nat Commun. 2024 Jul 25. 15(1): 6279
    Mst1-mediated phosphorylation of FoxO1 and C/EBP-β stimulates cell-protective mechanisms in cardiomyocytes.
    Yasuhiro Maejima, Jihoon Nah, Zahra Aryan, Peiyong Zhai, Eun-Ah Sung, Tong Liu, Koichiro Takayama, Siavash Moghadami, Tetsuo Sasano, Hong Li, Junichi Sadoshima.
      The molecular mechanisms by which FoxO transcription factors mediate diametrically opposite cellular responses, namely death and survival, remain unknown. Here we show that Mst1 phosphorylates FoxO1 Ser209/Ser215/Ser218/Thr228/Ser232/Ser243, thereby inhibiting FoxO1-mediated transcription of proapoptotic genes. On the other hand, Mst1 increases FoxO1-C/EBP-β interaction and activates C/EBP-β by phosphorylating it at Thr299, thereby promoting transcription of prosurvival genes. Myocardial ischemia/reperfusion injury is larger in cardiac-specific FoxO1 knockout mice than in control mice. However, the concurrent presence of a C/EBP-β T299E phospho-mimetic mutation reduces infarct size in cardiac-specific FoxO1 knockout mice. The C/EBP-β phospho-mimetic mutant exhibits greater binding to the promoter of prosurvival genes than wild type C/EBP-β. In conclusion, phosphorylation of FoxO1 by Mst1 inhibits binding of FoxO1 to pro-apoptotic gene promoters but enhances its binding to C/EBP-β, phosphorylation of C/EBP-β, and transcription of prosurvival genes, which stimulate protective mechanisms in the heart.
    DOI:  https://doi.org/10.1038/s41467-024-50393-y
  11. Nat Genet. 2024 Jul 24.
    Cohesin prevents cross-domain gene coactivation.
    Peng Dong, Shu Zhang, Valentina Gandin, Liangqi Xie, Lihua Wang, Andrew L Lemire, Wenhong Li, Hideo Otsuna, Takashi Kawase, Arthur D Lander, Howard Y Chang, Zhe J Liu.
      The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.
    DOI:  https://doi.org/10.1038/s41588-024-01852-1
  12. Nat Genet. 2024 Jul 26.
    Competition shapes the landscape of X-chromosome-linked genetic diversity.
    Teresa Buenaventura, Hakan Bagci, Ilinca Patrascan, Joshua J Graham, Kelsey D Hipwell, Roel Oldenkamp, James W D King, Jesus Urtasun, George Young, Daniel Mouzo, David Gomez-Cabrero, Benjamin D Rowland, Daniel Panne, Amanda G Fisher, Matthias Merkenschlager.
      X chromosome inactivation (XCI) generates clonal heterogeneity within XX individuals. Combined with sequence variation between human X chromosomes, XCI gives rise to intra-individual clonal diversity, whereby two sets of clones express mutually exclusive sequence variants present on one or the other X chromosome. Here we ask whether such clones merely co-exist or potentially interact with each other to modulate the contribution of X-linked diversity to organismal development. Focusing on X-linked coding variation in the human STAG2 gene, we show that Stag2variant clones contribute to most tissues at the expected frequencies but fail to form lymphocytes in Stag2WT Stag2variant mouse models. Unexpectedly, the absence of Stag2variant clones from the lymphoid compartment is due not solely to cell-intrinsic defects but requires continuous competition by Stag2WT clones. These findings show that interactions between epigenetically diverse clones can operate in an XX individual to shape the contribution of X-linked genetic diversity in a cell-type-specific manner.
    DOI:  https://doi.org/10.1038/s41588-024-01840-5
  13. Dev Cell. 2024 Jul 17. pii: S1534-5807(24)00400-3. [Epub ahead of print]
    Autocrine glutamate signaling drives cell competition in Drosophila.
    Carmo Castilho Soares, Alberto Rizzo, Marta Forés Maresma, Pascal Meier.
      Cell competition is an evolutionarily conserved quality control process that eliminates suboptimal or potentially dangerous cells. Although differential metabolic states act as direct drivers of competition, how these are measured across tissues is not understood. Here, we demonstrate that vesicular glutamate transporter (VGlut) and autocrine glutamate signaling are required for cell competition and Myc-driven super-competition in the Drosophila epithelia. We find that the loss of glutamate-stimulated VGlut>NMDAR>CaMKII>CrebB signaling triggers loser status and cell death under competitive settings via the autocrine induction of TNF. This in turn drives TNFR>JNK activation, triggering loser cell elimination and PDK/LDH-dependent metabolic reprogramming. Inhibiting caspases or preventing loser cells from transferring lactate to their neighbors nullifies cell competition. Further, in a Drosophila model for premalignancy, Myc-overexpressing clones co-opt this signaling circuit to acquire super-competitor status. Targeting glutamate signaling converts Myc "super-competitor" clones into "losers," highlighting new therapeutic opportunities to restrict the evolution of fitter clones.
    Keywords:  Myc; NMDAR; TNF-JNK; VGlut; cell competition; glutamate; lactate
    DOI:  https://doi.org/10.1016/j.devcel.2024.06.022
  14. Nucleic Acids Res. 2024 Jul 23. pii: gkae630. [Epub ahead of print]
    Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.
    Arka Banerjee, Meric Ataman, Maciej Jerzy Smialek, Debdatto Mookherjee, Julius Rabl, Aleksei Mironov, Lea Mues, Ludovic Enkler, Mairene Coto-Llerena, Alexander Schmidt, Daniel Boehringer, Salvatore Piscuoglio, Anne Spang, Nitish Mittal, Mihaela Zavolan.
      Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.
    DOI:  https://doi.org/10.1093/nar/gkae630
  15. Nat Genet. 2024 Jul 24.
    Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression.
    Amin Abedini, Jonathan Levinsohn, Konstantin A Klötzer, Bernhard Dumoulin, Ziyuan Ma, Julia Frederick, Poonam Dhillon, Michael S Balzer, Rojesh Shrestha, Hongbo Liu, Steven Vitale, Andi M Bergeson, Kishor Devalaraja-Narashimha, Paola Grandi, Tanmoy Bhattacharyya, Erding Hu, Steven S Pullen, Carine M Boustany-Kari, Paolo Guarnieri, Anil Karihaloo, Daniel Traum, Hanying Yan, Kyle Coleman, Matthew Palmer, Lea Sarov-Blat, Lori Morton, Christopher A Hunter, Klaus H Kaestner, Mingyao Li, Katalin Susztak.
      Kidneys are intricate three-dimensional structures in the body, yet the spatial and molecular principles of kidney health and disease remain inadequately understood. We generated high-quality datasets for 81 samples, including single-cell, single-nuclear, spot-level (Visium) and single-cell resolution (CosMx) spatial-RNA expression and single-nuclear open chromatin, capturing cells from healthy, diabetic and hypertensive diseased human kidneys. Combining these data, we identify cell types and map them to their locations within the tissue. Unbiased deconvolution of the spatial data identifies the following four distinct microenvironments: glomerular, immune, tubule and fibrotic. We describe the complex organization of microenvironments in health and disease and find that the fibrotic microenvironment is able to molecularly classify human kidneys and offers an improved prognosis compared to traditional histopathology. We provide a comprehensive spatially resolved molecular roadmap of the human kidney and the fibrotic process, demonstrating the clinical utility of spatial transcriptomics.
    DOI:  https://doi.org/10.1038/s41588-024-01802-x
  16. EMBO Rep. 2024 Jul 25.
    Embryonic stem cells maintain high origin activity and slow forks to coordinate replication with cell cycle progression.
    Kiminori Kurashima, Yasunao Kamikawa, Tomomi Tsubouchi.
      Embryonic stem (ES) cells are pluripotent stem cells that can produce all cell types of an organism. ES cells proliferate rapidly and are thought to experience high levels of intrinsic replication stress. Here, by investigating replication fork dynamics in substages of S phase, we show that mammalian pluripotent stem cells maintain a slow fork speed and high active origin density throughout the S phase, with little sign of fork pausing. In contrast, the fork speed of non-pluripotent cells is slow at the beginning of S phase, accompanied by increased fork pausing, but thereafter fork pausing rates decline and fork speed rates accelerate in an ATR-dependent manner. Thus, replication fork dynamics within the S phase are distinct between ES and non-ES cells. Nucleoside addition can accelerate fork speed and reduce origin density. However, this causes miscoordination between the completion of DNA replication and cell cycle progression, leading to genome instability. Our study indicates that fork slowing in the pluripotent stem cells is an integral aspect of DNA replication.
    Keywords:  Cell Cycle Regulation; Origin Density; Pluripotent Stem Cells; Replication Fork Speed
    DOI:  https://doi.org/10.1038/s44319-024-00207-5
  17. J Clin Invest. 2024 Jul 26. pii: e179752. [Epub ahead of print]
    Hepatic lipopolysaccharide binding protein partially uncouples inflammation from fibrosis in MAFLD.
    Dan Wang, Ania Baghoomian, Zhengyi Zhang, Ya Cui, Emily C Whang, Xiang Li, Josue Fraga, Rachel Spellman, Tien S Dong, We Li, Arpana Gupta, Jihane N Benhammou, Tamer Sallam.
      
    Keywords:  Cholesterol; Fibrosis; Genetics; Hepatitis; Hepatology
    DOI:  https://doi.org/10.1172/JCI179752
  18. Mol Cell. 2024 Jul 25. pii: S1097-2765(24)00531-8. [Epub ahead of print]84(14): 2698-2716.e9
    Polysome collapse and RNA condensation fluidize the cytoplasm.
    Ying Xie, Tong Shu, Tiewei Liu, Marie-Christin Spindler, Julia Mahamid, Glen M Hocky, David Gresham, Liam J Holt.
      The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
    Keywords:  P-bodies; Q-bodies; biomolecular condensates; biophysics; cryo-electron tomography; microrheology; polysome; stress granules
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.024
  19. Nat Commun. 2024 Jul 22. 15(1): 6160
    Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs.
    Loren Koçillari, Silvia Cattelan, Maria Berica Rasotto, Flavio Seno, Amos Maritan, Andrea Pilastro.
      Sperm length is highly variable across species and many questions about its variation remain open. Although variation in body mass may affect sperm length evolution through its influence on multiple factors, the extent to which sperm length variation is linked to body mass remains elusive. Here, we use the Pareto multi-task evolution framework to investigate the relationship between sperm length and body mass across tetrapods. We find that tetrapods occupy a triangular Pareto front, indicating that trade-offs shape the evolution of sperm length in relation to body mass. By exploring the factors predicted to influence sperm length evolution, we find that sperm length evolution is mainly driven by sperm competition and clutch size, rather than by genome size. Moreover, the triangular Pareto front is maintained within endotherms, internal fertilizers, mammals and birds, suggesting similar evolutionary trade-offs within tetrapods. Finally, we demonstrate that the Pareto front is robust to phylogenetic dependencies and finite sampling bias. Our findings provide insights into the evolutionary mechanisms driving interspecific sperm length variation and highlight the importance of considering multiple trade-offs in optimizing reproductive traits.
    DOI:  https://doi.org/10.1038/s41467-024-50391-0
  20. Proc Natl Acad Sci U S A. 2024 Jul 30. 121(31): e2320372121
    The structure and mechanics of the cell cortex depend on the location and adhesion state.
    D A D Flormann, L Kainka, G Montalvo, C Anton, J Rheinlaender, D Thalla, D Vesperini, M O Pohland, K H Kaub, M Schu, F Pezzano, V Ruprecht, E Terriac, R J Hawkins, F Lautenschläger.
      Cells exist in different phenotypes and can transition between them. A phenotype may be characterized by many different aspects. Here, we focus on the example of whether the cell is adhered or suspended and choose particular parameters related to the structure and mechanics of the actin cortex. The cortex is essential to cell mechanics, morphology, and function, such as for adhesion, migration, and division of animal cells. To predict and control cellular functions and prevent malfunctioning, it is necessary to understand the actin cortex. The structure of the cortex governs cell mechanics; however, the relationship between the architecture and mechanics of the cortex is not yet well enough understood to be able to predict one from the other. Therefore, we quantitatively measured structural and mechanical cortex parameters, including cortical thickness, cortex mesh size, actin bundling, and cortex stiffness. These measurements required developing a combination of measurement techniques in scanning electron, expansion, confocal, and atomic force microscopy. We found that the structure and mechanics of the cortex of cells in interphase are different depending on whether the cell is suspended or adhered. We deduced general correlations between structural and mechanical properties and show how these findings can be explained within the framework of semiflexible polymer network theory. We tested the model predictions by perturbing the properties of the actin within the cortex using compounds. Our work provides an important step toward predictions of cell mechanics from cortical structures and suggests how cortex remodeling between different phenotypes impacts the mechanical properties of cells.
    Keywords:  actin; cells; cortex; cytoskeleton; suspended
    DOI:  https://doi.org/10.1073/pnas.2320372121
  21. Nature. 2024 Jul 24.
    Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain.
    Jennifer M Kefauver, Markku Hakala, Luoming Zou, Josephine Alba, Javier Espadas, Maria G Tettamanti, Jelena Gajić, Caroline Gabus, Pablo Campomanes, Leandro F Estrozi, Nesli E Sen, Stefano Vanni, Aurélien Roux, Ambroise Desfosses, Robbie Loewith.
      Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins1-3. The composition and organization of membrane microdomains remain controversial because few techniques are available that allow the visualization of lipids in situ without disrupting their native behaviour3,4. The yeast eisosome, composed of the BAR-domain proteins Pil1 and Lsp1 (hereafter, Pil1/Lsp1), scaffolds a membrane compartment that senses and responds to mechanical stress by flattening and releasing sequestered factors5-9. Here we isolated near-native eisosomes as helical tubules made up of a lattice of Pil1/Lsp1 bound to plasma membrane lipids, and solved their structures by helical reconstruction. Our structures reveal a striking organization of membrane lipids, and, using in vitro reconstitutions and molecular dynamics simulations, we confirmed the positioning of individual PI(4,5)P2, phosphatidylserine and sterol molecules sequestered beneath the Pil1/Lsp1 coat. Three-dimensional variability analysis of the native-source eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects the sequestration of these lipids. Collectively, our results support a mechanism in which stretching of the Pil1/Lsp1 lattice liberates lipids that would otherwise be anchored by the Pil1/Lsp1 coat, and thus provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain.
    DOI:  https://doi.org/10.1038/s41586-024-07720-6
  22. Curr Protoc. 2024 Jul;4(7): e1097
    Generation and Characterization of hiPSC-Derived Vascularized-, Perfusable Cardiac Microtissues-on-Chip.
    Ulgu Arslan, Francijna E van den Hil, Christine L Mummery, Valeria Orlova.
      In the heart in vivo, vasculature forms a semi-permeable endothelial barrier for selective nutrient and (immune) cell delivery to the myocardium and removal of waste products. Crosstalk between the vasculature and the heart cells regulates homeostasis in health and disease. To model heart development and disease in vitro it is important that essential features of this crosstalk are captured. Cardiac organoid and microtissue models often integrate endothelial cells (ECs) to form microvascular networks inside the 3D structure. However, in static culture without perfusion, these networks may fail to show essential functionality. Here, we describe a protocol to generate an in vitro model of human induced pluripotent stem cell (hiPSC)-derived vascularized cardiac microtissues on a microfluidic organ-on-chip platform (VMToC) in which the blood vessels are perfusable. First, prevascularized cardiac microtissues (MT) are formed by combining hiPSC-derived cardiomyocytes, ECs, and cardiac fibroblasts in a pre-defined ratio. Next, these prevascularized MTs are integrated in the chips in a fibrin hydrogel containing additional vascular cells, which self-organize into tubular structures. The MTs become vascularized through anastomosis between the pre-existing microvasculature in the MT and the external vascular network. The VMToCs are then ready for downstream structural and functional assays and basic characterization. Using this protocol, cardiac MTs can be efficiently and robustly vascularized and perfused within 7 days. In vitro vascularized organoid and MT models have the potential to transition current 3D cardiac models to more physiologically relevant organ models that allow the role of the endothelial barrier in drug and inflammatory response to be investigated. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Generation of VMToC Support Protocol 1: Functional Characterization of VMToC Support Protocol 2: Structural Characterization of VMToC.
    Keywords:  cardiac microtissues; human induced pluripotent stem cells; vascularization; vessels‐on‐a‐chip
    DOI:  https://doi.org/10.1002/cpz1.1097
  23. Nat Aging. 2024 Jul 23.
    An NAD+-dependent metabolic checkpoint regulates hematopoietic stem cell activation and aging.
    Zehan Song, Sang Hee Park, Wei-Chieh Mu, Yufan Feng, Chih-Ling Wang, Yifei Wang, Marine Barthez, Ayane Maruichi, Jiayue Guo, Fanghan Yang, Anita Wong Lin, Kartoosh Heydari, Claudia C S Chini, Eduardo N Chini, Cholsoon Jang, Danica Chen.
      How hematopoietic stem cells (HSCs) maintain metabolic homeostasis to support tissue repair and regeneration throughout the lifespan is elusive. Here, we show that CD38, an NAD+-dependent metabolic enzyme, promotes HSC proliferation by inducing mitochondrial Ca2+ influx and mitochondrial metabolism in young mice. Conversely, aberrant CD38 upregulation during aging is a driver of HSC deterioration in aged mice due to dysregulated NAD+ metabolism and compromised mitochondrial stress management. The mitochondrial calcium uniporter, a mediator of mitochondrial Ca2+ influx, also supports HSC proliferation in young mice yet drives HSC decline in aged mice. Pharmacological inactivation of CD38 reverses HSC aging and the pathophysiological changes of the aging hematopoietic system in aged mice. Together, our study highlights an NAD+ metabolic checkpoint that balances mitochondrial activation to support HSC proliferation and mitochondrial stress management to enhance HSC self-renewal throughout the lifespan, and links aberrant Ca2+ signaling to HSC aging.
    DOI:  https://doi.org/10.1038/s43587-024-00670-8
  24. Trends Cell Biol. 2024 Jul 20. pii: S0962-8924(24)00142-9. [Epub ahead of print]
    Germline regulation of the somatic mitochondrial stress response.
    Liankui Zhou, Ying Liu.
      Mitochondria are pivotal organelles for cellular energy production and the regulation of stress responses. Recent research has elucidated complex mechanisms through which mitochondrial stress in one tissue can impact distant tissues, thereby promoting overall organismal health. Two recent studies by Shen et al. and Charmpilas et al. have demonstrated that an intact germline serves as a crucial signaling hub for the activation of the somatic mitochondrial unfolded protein response (UPRmt) in Caenorhabditis elegans.
    Keywords:  UPR(mt); cell-nonautonomous; germline; mitochondria; stress response
    DOI:  https://doi.org/10.1016/j.tcb.2024.07.004
  25. Sci Adv. 2024 Jul 26. 10(30): eado5716
    3D chromatin structures associated with ncRNA roX2 for hyperactivation and coactivation across the entire X chromosome.
    Simon Zhongyuan Tian, Yang Yang, Duo Ning, Ke Fang, Kai Jing, Guangyu Huang, Yewen Xu, Pengfei Yin, Haibo Huang, Gengzhan Chen, Yuqing Deng, Shaohong Zhang, Zhimin Zhang, Zhenxia Chen, Tong Gao, Wei Chen, Guoliang Li, Ruilin Tian, Yijun Ruan, Yiming Li, Meizhen Zheng.
      The three-dimensional (3D) organization of chromatin within the nucleus is crucial for gene regulation. However, the 3D architectural features that coordinate the activation of an entire chromosome remain largely unknown. We introduce an omics method, RNA-associated chromatin DNA-DNA interactions, that integrates RNA polymerase II (RNAPII)-mediated regulome with stochastic optical reconstruction microscopy to investigate the landscape of noncoding RNA roX2-associated chromatin topology for gene equalization to achieve dosage compensation. Our findings reveal that roX2 anchors to the target gene transcription end sites (TESs) and spreads in a distinctive boot-shaped configuration, promoting a more open chromatin state for hyperactivation. Furthermore, roX2 arches TES to transcription start sites to enhance transcriptional loops, potentially facilitating RNAPII convoying and connecting proximal promoter-promoter transcriptional hubs for synergistic gene regulation. These TESs cluster as roX2 compartments, surrounded by inactive domains for coactivation of multiple genes within the roX2 territory. In addition, roX2 structures gradually form and scaffold for stepwise coactivation in dosage compensation.
    DOI:  https://doi.org/10.1126/sciadv.ado5716
  26. Cell Rep. 2024 Jul 23. pii: S2211-1247(24)00874-X. [Epub ahead of print]43(8): 114545
    Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity.
    Martin A Michel, Simon Scutts, David Komander.
      Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.
    Keywords:  CP: Molecular biology; IKK; autophagy; mono-ubiquitination; optineurin; ubiquitin binding domain; ubiquitin chain linkage; ubiquitin code
    DOI:  https://doi.org/10.1016/j.celrep.2024.114545
  27. J Mol Cell Cardiol. 2024 Jul 20. pii: S0022-2828(24)00121-4. [Epub ahead of print]195 1-13
    Transient formation of collaterals contributes to the restoration of the arterial tree during cardiac regeneration in neonatal mice.
    Rachel Sturny, Lucie Boulgakoff, Robert G Kelly, Lucile Miquerol.
      Revascularization of ischemic myocardium following cardiac damage is an important step in cardiac regeneration. However, the mechanism of arteriogenesis has not been well described during cardiac regeneration. Here we investigated coronary artery remodeling and collateral growth during cardiac regeneration. Neonatal MI was induced by ligature of the left descending artery (LAD) in postnatal day (P) 1 or P7 pups from the Cx40-GFP mouse line and the arterial tree was reconstructed in 3D from images of cleared hearts collected at 1, 2, 4, 7 and 14 days after infarction. We show a rapid remodeling of the left coronary arterial tree induced by neonatal MI and the formation of numerous collateral arteries, which are transient in regenerating hearts after MI at P1 and persistent in non-regenerating hearts after MI at P7. This difference is accompanied by restoration of a perfused or a non-perfused LAD following MI at P1 or P7 respectively. Interestingly, collaterals ameliorate cardiac perfusion and drive LAD repair, and lineage tracing analysis demonstrates that the restoration of the LAD occurs by remodeling of pre-existing arterial cells independently of whether they originate in large arteries or arterioles. These results demonstrate that the restoration of the LAD artery during cardiac regeneration occurs by pruning as the rapidly forming collaterals that support perfusion of the disconnected lower LAD subsequently disappear on restoration of a unique LAD. These results highlight a rapid phase of arterial remodeling that plays an important role in vascular repair during cardiac regeneration.
    Keywords:  3D imaging; Arterial tree; Cardiac regeneration; Collaterals
    DOI:  https://doi.org/10.1016/j.yjmcc.2024.07.005
  28. Curr Opin Cell Biol. 2024 Jul 19. pii: S0955-0674(24)00079-6. [Epub ahead of print]89 102400
    Post-transcriptional regulation as a conserved driver of neural crest and cancer-cell migration.
    Arvind Arul Nambi Rajan, Erica J Hutchins.
      Cells have evolved mechanisms to migrate for diverse biological functions. A process frequently deployed during metazoan cell migration is the epithelial-mesenchymal transition (EMT). During EMT, adherent epithelial cells undergo coordinated cellular transitions to mesenchymalize and reduce their intercellular attachments. This is achieved via tightly regulated changes in gene expression, which modulates cell-cell and cell-matrix adhesion to allow movement. The acquisition of motility and invasive properties following EMT allows some mesenchymal cells to migrate through complex environments to form tissues during embryogenesis; however, these processes may also be leveraged by cancer cells, which often co-opt these endogenous programs to metastasize. Post-transcriptional regulation is now emerging as a major conserved mechanism by which cells modulate EMT and migration, which we discuss here in the context of vertebrate development and cancer.
    DOI:  https://doi.org/10.1016/j.ceb.2024.102400
  29. Cell. 2024 Jul 16. pii: S0092-8674(24)00712-8. [Epub ahead of print]
    Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes.
    Yu Yang, Xueyan Chen, Jieying Pan, Huiheng Ning, Yaojun Zhang, Yufei Bo, Xianwen Ren, Jiesheng Li, Shishang Qin, Dongfang Wang, Min-Min Chen, Zemin Zhang.
      Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
    Keywords:  atypical B cell; pan-cancer analysis; single-cell RNA sequencing; tumor-infiltrating B cell
    DOI:  https://doi.org/10.1016/j.cell.2024.06.038
  30. Elife. 2024 Jul 25. pii: RP89367. [Epub ahead of print]12
    Temporally resolved early bone morphogenetic protein-driven transcriptional cascade during human amnion specification.
    Nikola Sekulovski, Jenna C Wettstein, Amber E Carleton, Lauren N Juga, Linnea E Taniguchi, Xiaolong Ma, Sridhar Rao, Jenna K Schmidt, Thaddeus G Golos, Chien-Wei Lin, Kenichiro Taniguchi.
      Amniogenesis, a process critical for continuation of healthy pregnancy, is triggered in a collection of pluripotent epiblast cells as the human embryo implants. Previous studies have established that bone morphogenetic protein (BMP) signaling is a major driver of this lineage specifying process, but the downstream BMP-dependent transcriptional networks that lead to successful amniogenesis remain to be identified. This is, in part, due to the current lack of a robust and reproducible model system that enables mechanistic investigations exclusively into amniogenesis. Here, we developed an improved model of early amnion specification, using a human pluripotent stem cell-based platform in which the activation of BMP signaling is controlled and synchronous. Uniform amniogenesis is seen within 48 hr after BMP activation, and the resulting cells share transcriptomic characteristics with amnion cells of a gastrulating human embryo. Using detailed time-course transcriptomic analyses, we established a previously uncharacterized BMP-dependent amniotic transcriptional cascade, and identified markers that represent five distinct stages of amnion fate specification; the expression of selected markers was validated in early post-implantation macaque embryos. Moreover, a cohort of factors that could potentially control specific stages of amniogenesis was identified, including the transcription factor TFAP2A. Functionally, we determined that, once amniogenesis is triggered by the BMP pathway, TFAP2A controls the progression of amniogenesis. This work presents a temporally resolved transcriptomic resource for several previously uncharacterized amniogenesis states and demonstrates a critical intermediate role for TFAP2A during amnion fate specification.
    Keywords:  amnion; developmental biology; epiblast; human; human embryonic stem cell; human pluripotent stem cell; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.89367
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