bims-ginsta Biomed News
on Genome instability
Issue of 2024–01–21
fourteen papers selected by
Jinrong Hu, National University of Singapore
  1. Regulation of centrosome size by the cell-cycle oscillator in Drosophila embryos.
  2. Acinar-ductal cell rearrangement drives branching morphogenesis of the murine pancreas in an IGF/PI3K-dependent manner.
  3. Coupling Cell Size Regulation and Proliferation Dynamics of C. glutamicum Reveals Cell Division Based on Surface Area.
  4. Evidence for novel mechanisms that control cell cycle entry and cell size.
  5. Inherited blood cancer predisposition through altered transcription elongation.
  6. ERK-mediated curvature feedback regulates branching morphogenesis in lung epithelial tissue.
  7. A quick restart: RNA polymerase jumping onto post-replicative chromatin.
  8. Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation.
  9. Live-cell imaging defines a threshold in CDK activity at the G2/M transition.
  10. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.
  11. Distinguishing between driver and passenger mechanisms of aging.
  12. A mechanical wave travels along a genetic guide to drive the formation of an epithelial furrow during Drosophila gastrulation.
  13. Loss of the WDR23 proteostasis impacts mitochondrial homeostasis in the mouse brain.
  14. VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification.
  1. EMBO J. 2024 Jan 17.
    Regulation of centrosome size by the cell-cycle oscillator in Drosophila embryos.
    Siu-Shing Wong, Alan Wainman, Saroj Saurya, Jordan W Raff.
      Mitotic centrosomes assemble when centrioles recruit large amounts of pericentriolar material (PCM) around themselves. In early C. elegans embryos, mitotic centrosome size appears to be set by the limiting amount of a key component. In Drosophila syncytial embryos, thousands of mitotic centrosomes are assembled as the embryo proceeds through 13 rounds of rapid nuclear division, driven by a core cell cycle oscillator. These divisions slow during nuclear cycles 11-13, and we find that centrosomes respond by reciprocally decreasing their growth rate, but increasing their growth period-so that they grow to a relatively consistent size at each cycle. At the start of each cycle, moderate CCO activity initially promotes centrosome growth, in part by stimulating Polo/PLK1 recruitment to centrosomes. Later in each cycle, high CCO activity inhibits centrosome growth by suppressing the centrosomal recruitment and/or maintenance of centrosome proteins. Thus, in fly embryos, mitotic centrosome size appears to be regulated predominantly by the core cell cycle oscillator, rather than by the depletion of a limiting component.
    Keywords:  Cell Cycle; Centriole; Centrosome; Organelle Size; PCM
    DOI:  https://doi.org/10.1038/s44318-023-00022-z
  2. Dev Cell. 2024 Jan 13. pii: S1534-5807(23)00691-3. [Epub ahead of print]
    Acinar-ductal cell rearrangement drives branching morphogenesis of the murine pancreas in an IGF/PI3K-dependent manner.
    Jean-Francois Darrigrand, Anna Salowka, Alejo Torres-Cano, Rafael Tapia-Rojo, Tong Zhu, Sergi Garcia-Manyes, Francesca M Spagnoli.
      During organ formation, progenitor cells need to acquire different cell identities and organize themselves into distinct structural units. How these processes are coordinated and how tissue architecture(s) is preserved despite the dramatic cell rearrangements occurring in developing organs remain unclear. Here, we identified cellular rearrangements between acinar and ductal progenitors as a mechanism to drive branching morphogenesis in the pancreas while preserving the integrity of the acinar-ductal functional unit. Using ex vivo and in vivo mouse models, we found that pancreatic ductal cells form clefts by protruding and pulling on the acinar basement membrane, which leads to acini splitting. Newly formed acini remain connected to the bifurcated branches generated by ductal cell rearrangement. Insulin growth factor (IGF)/phosphatidylinositol 3-kinase (PI3K) pathway finely regulates this process by controlling pancreatic ductal tissue fluidity, with a simultaneous impact on branching and cell fate acquisition. Together, our results explain how acinar structure multiplication and branch bifurcation are synchronized during pancreas organogenesis.
    Keywords:  ECM remodeling; IGF/PI3K; acinar-ductal architecture; branching morphogenesis; pancreas; pancreatic acinar cells; pancreatic ducts; tissue fluidity
    DOI:  https://doi.org/10.1016/j.devcel.2023.12.011
  3. bioRxiv. 2023 Dec 28. pii: 2023.12.26.573217. [Epub ahead of print]
    Coupling Cell Size Regulation and Proliferation Dynamics of C. glutamicum Reveals Cell Division Based on Surface Area.
    César Nieto, Sarah Täuber, Luisa Blöbaum, Zahra Vahdat, Alexander Grünberger, Abhyudai Singh.
      Single cells actively coordinate growth and division to regulate their size, yet how this size homeostasis at the single-cell level propagates over multiple generations to impact clonal expansion remains fundamentally unexplored. Classical timer models for cell proliferation (where the duration of the cell cycle is an independent variable) predict that the stochastic variation in colony size will increase monotonically over time. In stark contrast, implementing size control according to adder strategy (where on average a fixed size added from cell birth to division) leads to colony size variations that eventually decay to zero. While these results assume a fixed size of the colony-initiating progenitor cell, further analysis reveals that the magnitude of the intercolony variation in population number is sensitive to heterogeneity in the initial cell size. We validate these predictions by tracking the growth of isogenic microcolonies of Corynebacterium glutamicum in microfluidic chambers. Approximating their cell shape to a capsule, we observe that the degree of random variability in cell size is different depending on whether the cell size is quantified as per length, surface area, or volume, but size control remains an adder regardless of these size metrics. A comparison of the observed variability in the colony population with the predictions suggests that proliferation matches better with a cell division based on the cell surface. In summary, our integrated mathematical-experimental approach bridges the paradigms of single-cell size regulation and clonal expansion at the population levels. This innovative approach provides elucidation of the mechanisms of size homeostasis from the stochastic dynamics of colony size for rod-shaped microbes.
    DOI:  https://doi.org/10.1101/2023.12.26.573217
  4. Mol Biol Cell. 2024 Jan 17. mbcE23050174
    Evidence for novel mechanisms that control cell cycle entry and cell size.
    Amanda Brambila, Beth E Prichard, Jerry T DeWitt, Douglas R Kellogg.
      Entry into the cell cycle in late G1 phase occurs only when sufficient growth has occurred. In budding yeast, a cyclin called Cln3 is thought to link cell cycle entry to cell growth. Cln3 accumulates during growth in early G1 phase and eventually helps trigger expression of late G1 phase cyclins that drive cell cycle entry. All current models for cell cycle entry assume that expression of late G1 phase cyclins is initiated at the transcriptional level. Current models also assume that the sole function of Cln3 in cell cycle entry is to promote transcription of late G1 phase cyclins, and that Cln3 works solely in G1 phase. Here, we show that cell cycle-dependent expression of the late G1 phase cyclin Cln2 does not require any functions of the CLN2 promoter. Moreover, Cln3 can influence accumulation of Cln2 protein via post-transcriptional mechanisms. Finally, we show that Cln3 has functions in mitosis that strongly influence cell size. Together, these discoveries reveal the existence of surprising new mechanisms that challenge current models for control of cell cycle entry and cell size.
    DOI:  https://doi.org/10.1091/mbc.E23-05-0174
  5. Cell. 2024 Jan 04. pii: S0092-8674(23)01348-X. [Epub ahead of print]
    Inherited blood cancer predisposition through altered transcription elongation.
    Jiawei Zhao, Liam D Cato, Uma P Arora, Erik L Bao, Samuel C Bryant, Nicholas Williams, Yuemeng Jia, Seth R Goldman, Jyoti Nangalia, Michael A Erb, Seychelle M Vos, Scott A Armstrong, Vijay G Sankaran.
      Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies in a large population cohort to identify inherited predisposition genes for these blood cancers. CTR9, which encodes a key component of the PAF1 transcription elongation complex, is among the significant genes identified. The risk variants found in the cases cause loss of function and result in a ∼10-fold increased odds of acquiring a myeloid malignancy. Partial CTR9 loss of function expands human hematopoietic stem cells (HSCs) by increased super elongation complex-mediated transcriptional activity, which thereby increases the expression of key regulators of HSC self-renewal. By following up on insights from a human genetic study examining inherited predisposition to the myeloid malignancies, we define a previously unknown antagonistic interaction between the PAF1 and super elongation complexes. These insights could enable targeted approaches for blood cancer prevention.
    Keywords:  CTR9; PAF1 complex; cancer predisposition; hematopoiesis; hematopoietic stem cells; myeloid malignancies; self-renewal; super elongation complex; transcription elongation
    DOI:  https://doi.org/10.1016/j.cell.2023.12.016
  6. Curr Biol. 2024 Jan 09. pii: S0960-9822(23)01749-9. [Epub ahead of print]
    ERK-mediated curvature feedback regulates branching morphogenesis in lung epithelial tissue.
    Tsuyoshi Hirashima, Michiyuki Matsuda.
      Intricate branching patterns emerge in internal organs due to the recurrent occurrence of simple deformations in epithelial tissues. During murine lung development, epithelial cells in distal tips of the single tube require fibroblast growth factor (FGF) signals emanating from their surrounding mesenchyme to form repetitive tip bifurcations. However, it remains unknown how the cells employ FGF signaling to convert their behaviors to achieve the recursive branching processes. Here, we show a mechano-chemical regulatory system underlying lung branching morphogenesis, orchestrated by extracellular signal-regulated kinase (ERK) as a downstream driver of FGF signaling. We found that tissue-scale curvature regulated ERK activity in the lung epithelium using two-photon live cell imaging and mechanical perturbations. ERK activation occurs specifically in epithelial tissues exhibiting positive curvature, regardless of whether the change in curvature was attributable to morphogenesis or perturbations. Moreover, ERK activation accelerates actin polymerization preferentially at the apical side of cells, mechanically contributing to the extension of the apical membrane, culminating in a reduction of epithelial tissue curvature. These results indicate the existence of a negative feedback loop between tissue curvature and ERK activity that transcends spatial scales. Our mathematical model confirms that this regulatory mechanism is sufficient to generate the recursive branching processes. Taken together, we propose that ERK orchestrates a curvature feedback loop pivotal to the self-organized patterning of tissues.
    Keywords:  ERK; FRET biosensor; curvature; live-cell imaging; lung development; mathematical model; mechano-chemical feedback; mechanobiology; self-organization; tissue morphogenesis
    DOI:  https://doi.org/10.1016/j.cub.2023.12.049
  7. Mol Cell. 2024 Jan 18. pii: S1097-2765(23)01075-4. [Epub ahead of print]84(2): 186-188
    A quick restart: RNA polymerase jumping onto post-replicative chromatin.
    Marcel Werner, Stephan Hamperl.
      Two recent studies in Molecular Cell1 and Nature2 show that evicted RNA polymerases reassociate rapidly with post-replicative chromatin and proceed into an unusual transcription cycle, bypassing regular controls and creating a temporary window for altered gene expression.
    DOI:  https://doi.org/10.1016/j.molcel.2023.12.029
  8. bioRxiv. 2023 Dec 30. pii: 2023.12.30.573688. [Epub ahead of print]
    Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation.
    Karen G Cornejo, Andie Venegas, Morgan H Sono, Madeline Door, Brenda Gutierrez-Ruiz, Lucy B Karabedian, Supratik G Nandi, Emily C Dykhuizen, Ramendra N Saha.
      Signal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, including Arc . The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.
    DOI:  https://doi.org/10.1101/2023.12.30.573688
  9. Dev Cell. 2024 Jan 08. pii: S1534-5807(23)00695-0. [Epub ahead of print]
    Live-cell imaging defines a threshold in CDK activity at the G2/M transition.
    Hironori Sugiyama, Yuhei Goto, Yohei Kondo, Damien Coudreuse, Kazuhiro Aoki.
      Cyclin-dependent kinase (CDK) determines the temporal ordering of the cell cycle phases. However, despite significant progress in studying regulators of CDK and phosphorylation patterns of CDK substrates at the population level, it remains elusive how CDK regulators coordinately affect CDK activity at the single-cell level and how CDK controls the temporal order of cell cycle events. Here, we elucidate the dynamics of CDK activity in fission yeast and mammalian cells by developing a CDK activity biosensor, Eevee-spCDK. We find that although CDK activity does not necessarily correlate with cyclin levels, it converges to the same level around mitotic onset in several mutant backgrounds, including pom1Δ cells and wee1 or cdc25 overexpressing cells. These data provide direct evidence that cells enter the M phase when CDK activity reaches a high threshold, consistent with the quantitative model of cell cycle progression in fission yeast.
    Keywords:  Cdc25; FRET; Pom1; Wee1; cell cycle; cell size; cyclin-dependent kinase; fission yeast; imaging; phosphatase
    DOI:  https://doi.org/10.1016/j.devcel.2023.12.014
  10. Cell. 2024 Jan 18. pii: S0092-8674(23)01345-4. [Epub ahead of print]187(2): 446-463.e16
    Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.
    Radhika Mathur, Qixuan Wang, Patrick G Schupp, Ana Nikolic, Stephanie Hilz, Chibo Hong, Nadia R Grishanina, Darwin Kwok, Nicholas O Stevers, Qiushi Jin, Mark W Youngblood, Lena Ann Stasiak, Ye Hou, Juan Wang, Takafumi N Yamaguchi, Marisa Lafontaine, Anny Shai, Ivan V Smirnov, David A Solomon, Susan M Chang, Shawn L Hervey-Jumper, Mitchel S Berger, Janine M Lupo, Hideho Okada, Joanna J Phillips, Paul C Boutros, Marco Gallo, Michael C Oldham, Feng Yue, Joseph F Costello.
      Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection to acquire samples representing the whole tumor mapped by 3D spatial coordinates. Integrative tissue and single-cell analysis revealed sources of genomic, epigenomic, and microenvironmental intratumoral heterogeneity and their spatial patterning. By distinguishing tumor-wide molecular features from those with regional specificity, we inferred GBM evolutionary trajectories from neurodevelopmental lineage origins and initiating events such as chromothripsis to emergence of genetic subclones and spatially restricted activation of differential tumor and microenvironmental programs in the core, periphery, and contrast-enhancing regions. Our work depicts GBM evolution and heterogeneity from a 3D whole-tumor perspective, highlights potential therapeutic targets that might circumvent heterogeneity-related failures, and establishes an interactive platform enabling 360° visualization and analysis of 3D spatial patterns for user-selected genes, programs, and other features across whole GBM tumors.
    Keywords:  brain tumors; chromatin accessibility; chromatin interactions; epigenomics; genomics; glioblastoma; intratumoral heterogeneity; microenvironment; spatial analysis; tumor evolution
    DOI:  https://doi.org/10.1016/j.cell.2023.12.013
  11. Nat Genet. 2024 Jan 19.
    Distinguishing between driver and passenger mechanisms of aging.
    João Pedro de Magalhães.
      Understanding why we age is a long-standing question, and many mechanistic theories of aging have been proposed. Owing to limitations in studying the aging process, including a lack of adequate quantitative measurements, its mechanistic basis remains a subject of debate. Here, I explore theories of aging from the perspective of causal relationships. Many aging-related changes have been observed and touted as drivers of aging, including molecular changes in the genome, telomeres, mitochondria, epigenome and proteins and cellular changes affecting stem cells, the immune system and senescent cell buildup. Determining which changes are drivers and not passengers of aging remains a challenge, however, and I discuss how animal models and human genetic studies have been used empirically to infer causality. Overall, our understanding of the drivers of human aging is still inadequate; yet with a global aging population, elucidating the causes of aging has the potential to revolutionize biomedical research.
    DOI:  https://doi.org/10.1038/s41588-023-01627-0
  12. Dev Cell. 2024 Jan 12. pii: S1534-5807(23)00694-9. [Epub ahead of print]
    A mechanical wave travels along a genetic guide to drive the formation of an epithelial furrow during Drosophila gastrulation.
    Anna Popkova, Urška Andrenšek, Sophie Pagnotta, Primož Ziherl, Matej Krajnc, Matteo Rauzi.
      Epithelial furrowing is a fundamental morphogenetic process during gastrulation, neurulation, and body shaping. A furrow often results from a fold that propagates along a line. How fold formation and propagation are controlled and driven is poorly understood. To shed light on this, we study the formation of the cephalic furrow, a fold that runs along the embryo dorsal-ventral axis during Drosophila gastrulation and the developmental role of which is still unknown. We provide evidence of its function and show that epithelial furrowing is initiated by a group of cells. This cellular cluster works as a pacemaker, triggering a bidirectional morphogenetic wave powered by actomyosin contractions and sustained by de novo medial apex-to-apex cell adhesion. The pacemaker's Cartesian position is under the crossed control of the anterior-posterior and dorsal-ventral gene patterning systems. Thus, furrow formation is driven by a mechanical trigger wave that travels under the control of a multidimensional genetic guide.
    Keywords:  actomyosin contractility; de novo adherens junction; epithelial folding; morphogenetic propagation; multidimensional genetic guide; pacemaker; trigger wave
    DOI:  https://doi.org/10.1016/j.devcel.2023.12.016
  13. Cell Signal. 2024 Jan 17. pii: S0898-6568(24)00029-9. [Epub ahead of print] 111061
    Loss of the WDR23 proteostasis impacts mitochondrial homeostasis in the mouse brain.
    Chatrawee Duangjan, Ronald W Irwin, Sean P Curran.
      Mitochondrial adaptation is important for stress resistance throughout life. Here we show that WDR23 loss results in an enrichment for genes regulated by nuclear respiratory factor 1 (NRF1), which coordinates mitochondrial biogenesis and respiratory functions, and an increased steady state level of several nuclear coded mitochondrial resident proteins in the brain. Wdr23KO also increases the endogenous levels of insulin degrading enzyme (IDE) and the relaxin-3 peptide (RLN3), both of which have established roles in mediating mitochondrial metabolic and oxidative stress responses. Taken together, these studies reveal an important role for WDR23 as a component of the mitochondrial homeostat in the murine brain.
    Keywords:  Complex I; Homeostasis; Mitochondria; Wdr23; hippocampus
    DOI:  https://doi.org/10.1016/j.cellsig.2024.111061
  14. Nat Commun. 2024 Jan 17. 15(1): 583
    VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification.
    Yueli Yang, Wenqi Jia, Zhiwei Luo, Yunpan Li, Hao Liu, Lixin Fu, Jinxiu Li, Yu Jiang, Junjian Lai, Haiwei Li, Babangida Jabir Saeed, Yi Zou, Yuan Lv, Liang Wu, Ting Zhou, Yongli Shan, Chuanyu Liu, Yiwei Lai, Longqi Liu, Andrew P Hutchins, Miguel A Esteban, Md Abdul Mazid, Wenjuan Li.
      In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due to ethical barriers and the scarcity of embryos. Recent reports have shown that human pluripotent stem cells (PSCs) can differentiate into trophectoderm (TE)-like cells (TELCs) and trophoblast stem cells (TSCs), offering a valuable in vitro model to study early placenta specification. Here, we demonstrate that the VGLL1 (vestigial-like family member 1), which is highly expressed during human and non-human primate TE specification in vivo but is negligibly expressed in mouse, is a critical regulator of cell fate determination and self-renewal in human TELCs and TSCs derived from naïve PSCs. Mechanistically, VGLL1 partners with the transcription factor TEAD4 (TEA domain transcription factor 4) to regulate chromatin accessibility at target gene loci through histone acetylation and acts in cooperation with GATA3 and TFAP2C. Our work is relevant to understand primate early embryogenesis and how it differs from other mammalian species.
    DOI:  https://doi.org/10.1038/s41467-024-44780-8
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