bims-ginsta Biomed News
on Genome instability
Issue of 2024–04–21
24 papers selected by
Jinrong Hu, National University of Singapore
  1. Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication.
  2. Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.
  3. Mechanical stress combines with planar polarised patterning during metaphase to orient embryonic epithelial cell divisions.
  4. Detection of newly synthesized RNA reveals transcriptional reprogramming during ZGA and a role of Obox3 in totipotency acquisition.
  5. Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells.
  6. Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions.
  7. CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
  8. Human skeletal muscle aging atlas.
  9. Identification of signaling pathways that specify a subset of migrating enteric neural crest cells at the wavefront in mouse embryos.
  10. Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids.
  11. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence.
  12. RAD52-dependent mitotic DNA synthesis is required for genome stability in Cyclin E1-overexpressing cells.
  13. Control of neuronal excitation-inhibition balance by BMP-SMAD1 signalling.
  14. The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression.
  15. Local environment in biomolecular condensates modulates enzymatic activity across length scales.
  16. Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties.
  17. A spatiotemporal atlas of mouse liver homeostasis and regeneration.
  18. FOXP1 is a gatekeeper of cellular senescence with ovarian aging.
  19. Buffering Mechanism in Aortic Arch Artery Formation and Congenital Heart Disease.
  20. Endo-reduplication in mouse liver after conditional mutation of ORC2 and combined mutation of ORC1 and ORC2.
  21. A spatiotemporal atlas of cholestatic injury and repair in mice.
  22. EGFR-dependent endocytosis of Wnt9a and Fzd9b promotes β-catenin signaling during hematopoietic stem cell development in zebrafish.
  23. Placental senescence pathophysiology is shared between peripartum cardiomyopathy and preeclampsia in mouse and human.
  24. Neural crest origin of sympathetic neurons at the dawn of vertebrates.
  1. Dev Cell. 2024 Apr 11. pii: S1534-5807(24)00200-4. [Epub ahead of print]
    Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication.
    Adler Guerrero Zuniga, Timothy J Aikin, Connor McKenney, Yovel Lendner, Alain Phung, Paul W Hook, Amy Meltzer, Winston Timp, Sergi Regot.
      Whole-genome duplication (WGD) is a frequent event in cancer evolution that fuels chromosomal instability. WGD can result from mitotic errors or endoreduplication, yet the molecular mechanisms that drive WGD remain unclear. Here, we use live single-cell analysis to characterize cell-cycle dynamics upon aberrant Ras-ERK signaling. We find that sustained ERK signaling in human cells leads to reactivation of the APC/C in G2, resulting in tetraploid G0-like cells that are primed for WGD. This process is independent of DNA damage or p53 but dependent on p21. Transcriptomics analysis and live-cell imaging showed that constitutive ERK activity promotes p21 expression, which is necessary and sufficient to inhibit CDK activity and which prematurely activates the anaphase-promoting complex (APC/C). Finally, either loss of p53 or reduced ERK signaling allowed for endoreduplication, completing a WGD event. Thus, sustained ERK signaling-induced G2 cell cycle exit represents an alternative path to WGD.
    Keywords:  cell cycle dynamics; oncogenesis; signaling dynamics; whole-genome duplication
    DOI:  https://doi.org/10.1016/j.devcel.2024.03.032
  2. Development. 2024 Apr 15. pii: dev.202362. [Epub ahead of print]
    Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.
    Vanessa Barone, Antonio Tagua, Jesus Á Andrés-San Román, Amro Hamdoun, Juan Garrido-García, Deirdre C Lyons, Luis M Escudero.
      Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes adopting a shape named "scutoid" that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here we use live-imaging of the sea star embryo coupled with deep learning-based segmentation, to dissect the relative contributions of cell density, tissue compaction, and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing just after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.
    Keywords:  3D epithelial packing; AB-T1; Computational modelling; Deep-learning; Echinoderm embryo; Morphogenesis; Scutoid; Sea star
    DOI:  https://doi.org/10.1242/dev.202362
  3. Development. 2024 Apr 19. pii: dev.202862. [Epub ahead of print]
    Mechanical stress combines with planar polarised patterning during metaphase to orient embryonic epithelial cell divisions.
    Guy B Blanchard, Elena Scarpa, Leila Muresan, Bénédicte Sanson.
      The planar orientation of cell division (OCD) is important for epithelial morphogenesis and homeostasis. We ask how mechanics and antero-posterior (AP) patterning combine to influence the first divisions after gastrulation in the Drosophila embryonic epithelium. We analyse hundreds of cell divisions and show that stress anisotropy, notably from compressive forces, can reorient division directly in metaphase. Stress anisotropy influences the OCD by imposing cell elongation, despite mitotic rounding and over-riding interphase cell elongation. In strongly elongated cells, the mitotic spindle adapts its length to, and hence its orientation is constrained by, the cell long axis. Alongside mechanical cues, there is a tissue-wide bias of the mitotic spindle orientation towards AP-patterned planar polarised Myosin-II. This spindle bias is lost in an AP-patterning mutant. Thus, a patterning-induced mitotic spindle orientation bias over-rides mechanical cues in mildly elongated cells but the spindle is constrained to the high stress axis in strongly elongated cells.
    Keywords:   Drosophila ; Axis extension; Cell division orientation; Mechanics; Morphogenesis; Myosin-II; Neighbour compression; Planar polarity; Steric hindrance; Stress anisotropy
    DOI:  https://doi.org/10.1242/dev.202862
  4. Cell Rep. 2024 Apr 14. pii: S2211-1247(24)00446-7. [Epub ahead of print]43(4): 114118
    Detection of newly synthesized RNA reveals transcriptional reprogramming during ZGA and a role of Obox3 in totipotency acquisition.
    Mizuki Sakamoto, Aoi Ito, Sayaka Wakayama, Hiroyuki Sasaki, Teruhiko Wakayama, Takashi Ishiuchi.
      Zygotic genome activation (ZGA) after fertilization enables the maternal-to-zygotic transition. However, the global view of ZGA, particularly at initiation, is incompletely understood. Here, we develop a method to capture and sequence newly synthesized RNA in early mouse embryos, providing a view of transcriptional reprogramming during ZGA. Our data demonstrate that major ZGA gene activation begins earlier than previously thought. Furthermore, we identify a set of genes activated during minor ZGA, the promoters of which show enrichment of the Obox factor motif, and find that Obox3 or Obox5 overexpression in mouse embryonic stem cells activates ZGA genes. Notably, the expression of Obox factors is severely impaired in somatic cell nuclear transfer (SCNT) embryos, and restoration of Obox3 expression corrects the ZGA profile and greatly improves SCNT embryo development. Hence, our study reveals dynamic transcriptional reprogramming during ZGA and underscores the crucial role of Obox3 in facilitating totipotency acquisition.
    Keywords:  CP: Developmental biology; CP: Molecular biology; Obox3; mouse early development; newly synthesized RNA; somatic cell nuclear transfer; zygotic genome activation
    DOI:  https://doi.org/10.1016/j.celrep.2024.114118
  5. J Cell Biol. 2024 Jul 01. pii: e202309027. [Epub ahead of print]223(7):
    Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells.
    Yung-Li Chen, Alisha N Jones, Amy Crawford, Michael Sattler, Andreas Ettinger, Maria-Elena Torres-Padilla.
      The centromere is a fundamental higher-order structure in chromosomes ensuring their faithful segregation upon cell division. Centromeric transcripts have been described in several species and suggested to participate in centromere function. However, low sequence conservation of centromeric repeats appears inconsistent with a role in recruiting highly conserved centromeric proteins. Here, we hypothesized that centromeric transcripts may function through a secondary structure rather than sequence conservation. Using mouse embryonic stem cells (ESCs), we show that an imbalance in the levels of forward or reverse minor satellite (MinSat) transcripts leads to severe chromosome segregation defects. We further show that MinSat RNA adopts a stem-loop secondary structure, which is conserved in human α-satellite transcripts. We identify an RNA binding region in CENPC and demonstrate that MinSat transcripts function through the structured region of the RNA. Importantly, mutants that disrupt MinSat secondary structure do not cause segregation defects. We propose that the conserved role of centromeric transcripts relies on their secondary RNA structure.
    DOI:  https://doi.org/10.1083/jcb.202309027
  6. Nat Commun. 2024 Apr 15. 15(1): 3216
    Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions.
    Min Lee, Hyungseok C Moon, Hyeonjeong Jeong, Dong Wook Kim, Hye Yoon Park, Yongdae Shin.
      Biomolecular condensates, often assembled through phase transition mechanisms, play key roles in organizing diverse cellular activities. The material properties of condensates, ranging from liquid droplets to solid-like glasses or gels, are key features impacting the way resident components associate with one another. However, it remains unclear whether and how different material properties would influence specific cellular functions of condensates. Here, we combine optogenetic control of phase separation with single-molecule mRNA imaging to study relations between phase behaviors and functional performance of condensates. Using light-activated condensation, we show that sequestering target mRNAs into condensates causes translation inhibition. Orthogonal mRNA imaging reveals highly transient nature of interactions between individual mRNAs and condensates. Tuning condensate composition and material property towards more solid-like states leads to stronger translational repression, concomitant with a decrease in molecular mobility. We further demonstrate that β-actin mRNA sequestration in neurons suppresses spine enlargement during chemically induced long-term potentiation. Our work highlights how the material properties of condensates can modulate functions, a mechanism that may play a role in fine-tuning the output of condensate-driven cellular activities.
    DOI:  https://doi.org/10.1038/s41467-024-47442-x
  7. Development. 2024 Apr 15. pii: dev.202505. [Epub ahead of print]
    CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
    Wei Shi, Lauren K Wasson, Kerry M Dorr, Zachary L Robbe, Caralynn M Wilczewski, Austin J Hepperla, Ian J Davis, Christine E Seidman, Jonathan G Seidman, Frank L Conlon.
      Regulation of chromatin states is essential for proper temporal and spatial gene expression. Chromatin states are modulated by remodeling complexes composed of components that have enzymatic activities. CHD4 is the catalytic core of the Nucleosome Remodeling and Deacetylase (NuRD) complex that represses gene transcription. However, it remains to be determined how CHD4, a ubiquitous enzyme that remodels chromatin structure, functions in cardiomyocytes to maintain heart development. Particularly, there exists controversy as to whether other proteins besides the NuRD components interact with CHD4 in the heart. Using quantitative proteomics, we identified that CHD4 interacts with SMYD1, a striated muscle-restricted histone methyltransferase that is essential for cardiomyocyte differentiation and cardiac morphogenesis. Comprehensive transcriptomic and chromatin accessibility studies of Smyd1 and Chd4 null embryonic hearts revealed that SMYD1 and CHD4 repress a group of common genes and pathways that included glycolysis, response to hypoxia, and angiogenesis. Our study reveals a novel mechanism by which CHD4 functions during heart development, and we have revealed an uncharacterized mechanism regarding how SMYD1 represses cardiac transcription in the developing heart.
    Keywords:  CHD4; Chromatin accessibility; SMYD1; Transcription
    DOI:  https://doi.org/10.1242/dev.202505
  8. Nat Aging. 2024 Apr 15.
    Human skeletal muscle aging atlas.
    Veronika R Kedlian, Yaning Wang, Tianliang Liu, Xiaoping Chen, Liam Bolt, Catherine Tudor, Zhuojian Shen, Eirini S Fasouli, Elena Prigmore, Vitalii Kleshchevnikov, Jan Patrick Pett, Tong Li, John E G Lawrence, Shani Perera, Martin Prete, Ni Huang, Qin Guo, Xinrui Zeng, Lu Yang, Krzysztof Polański, Nana-Jane Chipampe, Monika Dabrowska, Xiaobo Li, Omer Ali Bayraktar, Minal Patel, Natsuhiko Kumasaka, Krishnaa T Mahbubani, Andy Peng Xiang, Kerstin B Meyer, Kourosh Saeb-Parsy, Sarah A Teichmann, Hongbo Zhang.
      Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
    DOI:  https://doi.org/10.1038/s43587-024-00613-3
  9. Dev Cell. 2024 Apr 15. pii: S1534-5807(24)00202-8. [Epub ahead of print]
    Identification of signaling pathways that specify a subset of migrating enteric neural crest cells at the wavefront in mouse embryos.
    Bingyan Zhou, Chenzhao Feng, Song Sun, Xuyong Chen, Didi Zhuansun, Di Wang, Xiaosi Yu, Xinyao Meng, Jun Xiao, Luyao Wu, Jing Wang, Jing Wang, Ke Chen, Zejian Li, Jingyi You, Handan Mao, Shimin Yang, Jiaxin Zhang, Chunlei Jiao, Zhi Li, Donghai Yu, Xiaojuan Wu, Tianqi Zhu, Jixin Yang, Lei Xiang, Jiazhe Liu, Tailiang Chai, Juan Shen, Chuan-Xi Mao, Juncheng Hu, Xingjie Hao, Bo Xiong, Shan Zheng, Zhihua Liu, Jiexiong Feng.
      During enteric nervous system (ENS) development, pioneering wavefront enteric neural crest cells (ENCCs) initiate gut colonization. However, the molecular mechanisms guiding their specification and niche interaction are not fully understood. We used single-cell RNA sequencing and spatial transcriptomics to map the spatiotemporal dynamics and molecular landscape of wavefront ENCCs in mouse embryos. Our analysis shows a progressive decline in wavefront ENCC potency during migration and identifies transcription factors governing their specification and differentiation. We further delineate key signaling pathways (ephrin-Eph, Wnt-Frizzled, and Sema3a-Nrp1) utilized by wavefront ENCCs to interact with their surrounding cells. Disruptions in these pathways are observed in human Hirschsprung's disease gut tissue, linking them to ENS malformations. Additionally, we observed region-specific and cell-type-specific transcriptional changes in surrounding gut tissues upon wavefront ENCC arrival, suggesting their role in shaping the gut microenvironment. This work offers a roadmap of ENS development, with implications for understanding ENS disorders.
    Keywords:  Hirschsprung's disease; enteric nervous system; enteric neural crest cells; single-cell transcriptomics; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.devcel.2024.03.034
  10. Dev Cell. 2024 Apr 09. pii: S1534-5807(24)00198-9. [Epub ahead of print]
    Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids.
    Chaitanya Dingare, Dominica Cao, Jenny Jingni Yang, Berna Sozen, Benjamin Steventon.
      Patterning and growth are fundamental features of embryonic development that must be tightly coordinated. To understand how metabolism impacts early mesoderm development, we used mouse embryonic stem-cell-derived gastruloids, that co-expressed glucose transporters with the mesodermal marker T/Bra. We found that the glucose mimic, 2-deoxy-D-glucose (2-DG), blocked T/Bra expression and abolished axial elongation in gastruloids. However, glucose removal did not phenocopy 2-DG treatment despite a decline in glycolytic intermediates. As 2-DG can also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification both in vivo and in vitro. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. Proteomics analysis demonstrated that mannose reversed glycosylation of the Wnt pathway regulator, secreted frizzled receptor Frzb. Our study showed how mannose controls mesoderm specification in mouse gastruloids.
    Keywords:  FGF; Wnt; gastrulation; gastruloids; glycosylation; metabolomics; self-organisation
    DOI:  https://doi.org/10.1016/j.devcel.2024.03.031
  11. Cell Stem Cell. 2024 Apr 12. pii: S1934-5909(24)00096-1. [Epub ahead of print]
    Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence.
    Xue Han, Linqing Xing, Yantao Hong, Xuechun Zhang, Bo Hao, J Yuyang Lu, Mengyuan Huang, Zuhui Wang, Shaoqian Ma, Ge Zhan, Tong Li, Xiaowen Hao, Yibing Tao, Guanwen Li, Shuqin Zhou, Zheng Zheng, Wen Shao, Yitian Zeng, Dacheng Ma, Wenhao Zhang, Zhen Xie, Haiteng Deng, Jiangwei Yan, Wulan Deng, Xiaohua Shen.
      Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
    Keywords:  RNA exosome; RNP mesh; chromatin organization; nuclear RNA homeostasis; pluripotency; senescence; transcription; translation
    DOI:  https://doi.org/10.1016/j.stem.2024.03.015
  12. Cell Rep. 2024 Apr 15. pii: S2211-1247(24)00444-3. [Epub ahead of print]43(4): 114116
    RAD52-dependent mitotic DNA synthesis is required for genome stability in Cyclin E1-overexpressing cells.
    Anastasia Audrey, Yannick P Kok, Shibo Yu, Lauren de Haan, Bert van de Kooij, Nathalie van den Tempel, Mengting Chen, H Rudolf de Boer, Bert van der Vegt, Marcel A T M van Vugt.
      Overexpression of Cyclin E1 perturbs DNA replication, resulting in DNA lesions and genomic instability. Consequently, Cyclin E1-overexpressing cancer cells increasingly rely on DNA repair, including RAD52-mediated break-induced replication during interphase. We show that not all DNA lesions induced by Cyclin E1 overexpression are resolved during interphase. While DNA lesions upon Cyclin E1 overexpression are induced in S phase, a significant fraction of these lesions is transmitted into mitosis. Cyclin E1 overexpression triggers mitotic DNA synthesis (MiDAS) in a RAD52-dependent fashion. Chemical or genetic inactivation of MiDAS enhances mitotic aberrations and persistent DNA damage. Mitosis-specific degradation of RAD52 prevents Cyclin E1-induced MiDAS and reduces the viability of Cyclin E1-overexpressing cells, underscoring the relevance of RAD52 during mitosis to maintain genomic integrity. Finally, analysis of breast cancer samples reveals a positive correlation between Cyclin E1 amplification and RAD52 expression. These findings demonstrate the importance of suppressing mitotic defects in Cyclin E1-overexpressing cells through RAD52.
    Keywords:  CCNE1; CP: Molecular biology; MiDAS; RAD52; break-induced replication; breast cancer; cell cycle; cyclin E1; mitosis; oncogene; replication stress
    DOI:  https://doi.org/10.1016/j.celrep.2024.114116
  13. Nature. 2024 Apr 17.
    Control of neuronal excitation-inhibition balance by BMP-SMAD1 signalling.
    Zeynep Okur, Nadia Schlauri, Vassilis Bitsikas, Myrto Panopoulou, Raul Ortiz, Michaela Schwaiger, Kajari Karmakar, Dietmar Schreiner, Peter Scheiffele.
      Throughout life, neuronal networks in the mammalian neocortex maintain a balance of excitation and inhibition, which is essential for neuronal computation1,2. Deviations from a balanced state have been linked to neurodevelopmental disorders, and severe disruptions result in epilepsy3-5. To maintain balance, neuronal microcircuits composed of excitatory and inhibitory neurons sense alterations in neural activity and adjust neuronal connectivity and function. Here we identify a signalling pathway in the adult mouse neocortex that is activated in response to increased neuronal network activity. Overactivation of excitatory neurons is signalled to the network through an increase in the levels of BMP2, a growth factor that is well known for its role as a morphogen in embryonic development. BMP2 acts on parvalbumin-expressing (PV) interneurons through the transcription factor SMAD1, which controls an array of glutamatergic synapse proteins and components of perineuronal nets. PV-interneuron-specific disruption of BMP2-SMAD1 signalling is accompanied by a loss of glutamatergic innervation in PV cells, underdeveloped perineuronal nets and decreased excitability. Ultimately, this impairment of the functional recruitment of PV interneurons disrupts the cortical excitation-inhibition balance, with mice exhibiting spontaneous epileptic seizures. Our findings suggest that developmental morphogen signalling is repurposed to stabilize cortical networks in the adult mammalian brain.
    DOI:  https://doi.org/10.1038/s41586-024-07317-z
  14. bioRxiv. 2024 Apr 03. pii: 2024.04.03.587821. [Epub ahead of print]
    The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression.
    Juan Jesus Vicente, Michael Wagenbach, Justin Decarreau, Alex Zelter, Michael J MacCoss, Trisha N Davis, Linda Wordeman.
      Centrosomes are the principal microtubule-organizing centers of the cell and play an essential role in mitotic spindle function. Centrosome biogenesis is achieved by strict control of protein acquisition and phosphorylation prior to mitosis. Defects in this process promote fragmentation of pericentriolar material culminating in multipolar spindles and chromosome missegregation. Centriolar satellites, membrane-less aggrupations of proteins involved in the trafficking of proteins toward and away from the centrosome, are thought to contribute to centrosome biogenesis. Here we show that the microtubule plus-end directed kinesin motor Kif9 localizes to centriolar satellites and regulates their pericentrosomal localization during interphase. Lack of Kif9 leads to aggregation of satellites closer to the centrosome and increased centrosomal protein degradation that disrupts centrosome maturation and results in chromosome congression and segregation defects during mitosis. Our data reveal roles for Kif9 and centriolar satellites in the regulation of cellular proteostasis and mitosis.
    DOI:  https://doi.org/10.1101/2024.04.03.587821
  15. Nat Commun. 2024 Apr 18. 15(1): 3322
    Local environment in biomolecular condensates modulates enzymatic activity across length scales.
    Marcos Gil-Garcia, Ana I Benítez-Mateos, Marcell Papp, Florence Stoffel, Chiara Morelli, Karl Normak, Katarzyna Makasewicz, Lenka Faltova, Francesca Paradisi, Paolo Arosio.
      The mechanisms that underlie the regulation of enzymatic reactions by biomolecular condensates and how they scale with compartment size remain poorly understood. Here we use intrinsically disordered domains as building blocks to generate programmable enzymatic condensates of NADH-oxidase (NOX) with different sizes spanning from nanometers to microns. These disordered domains, derived from three distinct RNA-binding proteins, each possessing different net charge, result in the formation of condensates characterized by a comparable high local concentration of the enzyme yet within distinct environments. We show that only condensates with the highest recruitment of substrate and cofactor exhibit an increase in enzymatic activity. Notably, we observe an enhancement in enzymatic rate across a wide range of condensate sizes, from nanometers to microns, indicating that emergent properties of condensates can arise within assemblies as small as nanometers. Furthermore, we show a larger rate enhancement in smaller condensates. Our findings demonstrate the ability of condensates to modulate enzymatic reactions by creating distinct effective solvent environments compared to the surrounding solution, with implications for the design of protein-based heterogeneous biocatalysts.
    DOI:  https://doi.org/10.1038/s41467-024-47435-w
  16. Cell. 2024 Apr 08. pii: S0092-8674(24)00315-5. [Epub ahead of print]
    Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties.
    Gabriela Prus, Shankha Satpathy, Brian T Weinert, Takeo Narita, Chunaram Choudhary.
      Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.
    Keywords:  cell signaling; dynamics; mass spectrometry; occupancy; posttranslational modification; proteomics; turnover rate; ubiquitin signaling; ubiquitylation
    DOI:  https://doi.org/10.1016/j.cell.2024.03.024
  17. Nat Genet. 2024 Apr 16.
    A spatiotemporal atlas of mouse liver homeostasis and regeneration.
    Jiangshan Xu, Pengcheng Guo, Shijie Hao, Shuncheng Shangguan, Quan Shi, Giacomo Volpe, Keke Huang, Jing Zuo, Juan An, Yue Yuan, Mengnan Cheng, Qiuting Deng, Xiao Zhang, Guangyao Lai, Haitao Nan, Baihua Wu, Xinyi Shentu, Liang Wu, Xiaoyu Wei, Yujia Jiang, Xin Huang, Fengyu Pan, Yumo Song, Ronghai Li, Zhifeng Wang, Chuanyu Liu, Shiping Liu, Yuxiang Li, Tao Yang, Zhicheng Xu, Wensi Du, Ling Li, Tanveer Ahmed, Kai You, Zhen Dai, Li Li, Baoming Qin, Yinxiong Li, Liangxue Lai, Dajiang Qin, Junling Chen, Rong Fan, Yongyin Li, Jinlin Hou, Michael Ott, Amar Deep Sharma, Tobias Cantz, Axel Schambach, Karsten Kristiansen, Andrew P Hutchins, Berthold Göttgens, Patrick H Maxwell, Lijian Hui, Xun Xu, Longqi Liu, Ao Chen, Yiwei Lai, Miguel A Esteban.
      The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
    DOI:  https://doi.org/10.1038/s41588-024-01709-7
  18. Nat Aging. 2024 Apr;4(4): 451-452
    FOXP1 is a gatekeeper of cellular senescence with ovarian aging.
      
    DOI:  https://doi.org/10.1038/s43587-024-00608-0
  19. Circ Res. 2024 Apr 15.
    Buffering Mechanism in Aortic Arch Artery Formation and Congenital Heart Disease.
    AnnJosette Ramirez, Christina A Vyzas, Huaning Zhao, Kevin Eng, Karl Degenhardt, Sophie Astrof.
       BACKGROUND: The resiliency of embryonic development to genetic and environmental perturbations has been long appreciated; however, little is known about the mechanisms underlying the robustness of developmental processes. Aberrations resulting in neonatal lethality are exemplified by congenital heart disease arising from defective morphogenesis of pharyngeal arch arteries (PAAs) and their derivatives.
    OBJECTIVE: To uncover mechanisms underlying the robustness of PAA morphogenesis.
    METHODS AND RESULTS: The second heart field (SHF) gives rise to the PAA endothelium. Here, we show that the number of SHF-derived endothelial cells (ECs) is regulated by VEGFR2 (vascular endothelial growth factor receptor 2) and Tbx1. Remarkably, when the SHF-derived EC number is decreased, PAA development can be rescued by the compensatory endothelium. Blocking such compensatory response leads to embryonic demise. To determine the source of compensating ECs and mechanisms regulating their recruitment, we investigated 3-dimensional EC connectivity, EC fate, and gene expression. Our studies demonstrate that the expression of VEGFR2 by the SHF is required for the differentiation of SHF-derived cells into PAA ECs. The deletion of 1 VEGFR2 allele (VEGFR2SHF-HET) reduces SHF contribution to the PAA endothelium, while the deletion of both alleles (VEGFR2SHF-KO) abolishes it. The decrease in SHF-derived ECs in VEGFR2SHF-HET and VEGFR2SHF-KO embryos is complemented by the recruitment of ECs from the nearby veins. Compensatory ECs contribute to PAA derivatives, giving rise to the endothelium of the aortic arch and the ductus in VEGFR2SHF-KO mutants. Blocking the compensatory response in VEGFR2SHF-KO mutants results in embryonic lethality shortly after mid-gestation. The compensatory ECs are absent in Tbx1± embryos, a model for 22q11 deletion syndrome, leading to unpredictable arch artery morphogenesis and congenital heart disease. Tbx1 regulates the recruitment of the compensatory endothelium in an SHF-noncell-autonomous manner.
    CONCLUSIONS: Our studies uncover a novel buffering mechanism underlying the resiliency of PAA development and remodeling.
    Keywords:  22q11 deletion syndrome; aorta, thoracic; ductus arteriosus; endothelial cells; veins
    DOI:  https://doi.org/10.1161/CIRCRESAHA.123.322767
  20. bioRxiv. 2024 Apr 06. pii: 2024.04.04.588006. [Epub ahead of print]
    Endo-reduplication in mouse liver after conditional mutation of ORC2 and combined mutation of ORC1 and ORC2.
    Roza K Przanowska, Yuechuan Chen, Takayuki-Okano Uchida, Etsuko Shibata, Xiaoxiao Hao, Isaac Segura Rueda, Kate Jensen, Piotr Przanowski, Anthony Trimboli, Yoshiyuki Shibata, Gustavo Leone, Anindya Dutta.
      The six subunit Origin Recognition Complex (ORC) is essential for loading MCM2-7 at origins of DNA replication to promote initiation of DNA replication in organisms ranging from S. cerevisiae to humans. In rare instances, as in cancer cell-lines in culture with mutations in ORC1 , ORC2 or ORC5 , or in endo-reduplicating mouse hepatocytes in vivo without ORC1 , DNA replication has been observed in the virtual absence of individual ORC subunits. Although ORC1 is dispensable in the mouse liver for endo-reduplication, because of the homology of ORC1 with CDC6, it could be argued that CDC6 was substituting for ORC1 to restore functional ORC. Here, we have created mice with a conditional deletion of ORC2 , to demonstrate that mouse embryo fibroblasts require ORC2 for proliferation, but that the mouse hepatocytes can carry out DNA synthesis in vitro and endo-reduplicate in vivo , despite the deletion of ORC2 . Combining the conditional mutation of ORC1 and ORC2 revealed that the mouse liver can still carry out endo-reduplication despite the deletion of the two genes, both during normal development and after partial hepatectomy. Since endo-reduplication, like normal S phase replication, requires the presence of MCM2-7 on the chromatin, these results suggest that in primary hepatocytes there is a mechanism to load sufficient MCM2-7 to carry out effective DNA replication despite the virtual absence of two subunits of ORC.
    DOI:  https://doi.org/10.1101/2024.04.04.588006
  21. Nat Genet. 2024 Apr 16.
    A spatiotemporal atlas of cholestatic injury and repair in mice.
    Baihua Wu, Xinyi Shentu, Haitao Nan, Pengcheng Guo, Shijie Hao, Jiangshan Xu, Shuncheng Shangguan, Lei Cui, Jin Cen, Qiuting Deng, Yan Wu, Chang Liu, Yumo Song, Xiumei Lin, Zhifeng Wang, Yue Yuan, Wen Ma, Ronghai Li, Yikang Li, Qiwei Qian, Wensi Du, Tingting Lai, Tao Yang, Chuanyu Liu, Xiong Ma, Ao Chen, Xun Xu, Yiwei Lai, Longqi Liu, Miguel A Esteban, Lijian Hui.
      Cholestatic liver injuries, characterized by regional damage around the bile ductular region, lack curative therapies and cause considerable mortality. Here we generated a high-definition spatiotemporal atlas of gene expression during cholestatic injury and repair in mice by integrating spatial enhanced resolution omics sequencing and single-cell transcriptomics. Spatiotemporal analyses revealed a key role of cholangiocyte-driven signaling correlating with the periportal damage-repair response. Cholangiocytes express genes related to recruitment and differentiation of lipid-associated macrophages, which generate feedback signals enhancing ductular reaction. Moreover, cholangiocytes express high TGFβ in association with the conversion of liver progenitor-like cells into cholangiocytes during injury and the dampened proliferation of periportal hepatocytes during recovery. Notably, Atoh8 restricts hepatocyte proliferation during 3,5-diethoxycarbonyl-1,4-dihydro-collidin damage and is quickly downregulated after injury withdrawal, allowing hepatocytes to respond to growth signals. Our findings lay a keystone for in-depth studies of cellular dynamics and molecular mechanisms of cholestatic injuries, which may further develop into therapies for cholangiopathies.
    DOI:  https://doi.org/10.1038/s41588-024-01687-w
  22. Sci Signal. 2024 Apr 16. 17(832): eadf4299
    EGFR-dependent endocytosis of Wnt9a and Fzd9b promotes β-catenin signaling during hematopoietic stem cell development in zebrafish.
    Nicole Nguyen, Kelsey A Carpenter, Jessica Ensing, Carla Gilliland, Emma J Rudisel, Emily M Mu, Kate E Thurlow, Timothy J Triche, Stephanie Grainger.
      Cell-to-cell communication through secreted Wnt ligands that bind to members of the Frizzled (Fzd) family of transmembrane receptors is critical for development and homeostasis. Wnt9a signals through Fzd9b, the co-receptor LRP5 or LRP6 (LRP5/6), and the epidermal growth factor receptor (EGFR) to promote early proliferation of zebrafish and human hematopoietic stem cells during development. Here, we developed fluorescently labeled, biologically active Wnt9a and Fzd9b fusion proteins to demonstrate that EGFR-dependent endocytosis of the ligand-receptor complex was required for signaling. In human cells, the Wnt9a-Fzd9b complex was rapidly endocytosed and trafficked through early and late endosomes, lysosomes, and the endoplasmic reticulum. Using small-molecule inhibitors and genetic and knockdown approaches, we found that Wnt9a-Fzd9b endocytosis required EGFR-mediated phosphorylation of the Fzd9b tail, caveolin, and the scaffolding protein EGFR protein substrate 15 (EPS15). LRP5/6 and the downstream signaling component AXIN were required for Wnt9a-Fzd9b signaling but not for endocytosis. Knockdown or loss of EPS15 impaired hematopoietic stem cell development in zebrafish. Other Wnt ligands do not require endocytosis for signaling activity, implying that specific modes of endocytosis and trafficking may represent a method by which Wnt-Fzd specificity is established.
    DOI:  https://doi.org/10.1126/scisignal.adf4299
  23. Sci Transl Med. 2024 Apr 17. 16(743): eadi0077
    Placental senescence pathophysiology is shared between peripartum cardiomyopathy and preeclampsia in mouse and human.
    IPAC Investigators
      Peripartum cardiomyopathy (PPCM) is an idiopathic form of pregnancy-induced heart failure associated with preeclampsia. Circulating factors in late pregnancy are thought to contribute to both diseases, suggesting a common underlying pathophysiological process. However, what drives this process remains unclear. Using serum proteomics, we identified the senescence-associated secretory phenotype (SASP), a marker of cellular senescence associated with biological aging, as the most highly up-regulated pathway in young women with PPCM or preeclampsia. Placentas from women with preeclampsia displayed multiple markers of amplified senescence and tissue aging, as well as overall increased gene expression of 28 circulating proteins that contributed to SASP pathway enrichment in serum samples from patients with preeclampsia or PPCM. The most highly expressed placental SASP factor, activin A, was associated with cardiac dysfunction or heart failure severity in women with preeclampsia or PPCM. In a murine model of PPCM induced by cardiomyocyte-specific deletion of the gene encoding peroxisome proliferator-activated receptor γ coactivator-1α, inhibiting activin A signaling in the early postpartum period with a monoclonal antibody to the activin type II receptor improved heart function. In addition, attenuating placental senescence with the senolytic compound fisetin in late pregnancy improved cardiac function in these animals. These findings link senescence biology to cardiac dysfunction in pregnancy and help to elucidate the pathogenesis underlying cardiovascular diseases of pregnancy.
    DOI:  https://doi.org/10.1126/scitranslmed.adi0077
  24. Nature. 2024 Apr 17.
    Neural crest origin of sympathetic neurons at the dawn of vertebrates.
    Brittany M Edens, Jan Stundl, Hugo A Urrutia, Marianne E Bronner.
      The neural crest is an embryonic stem cell population unique to vertebrates1 whose expansion and diversification are thought to have promoted vertebrate evolution by enabling emergence of new cell types and structures such as jaws and peripheral ganglia2. Although jawless vertebrates have sensory ganglia, convention has it that trunk sympathetic chain ganglia arose only in jawed vertebrates3-8. Here, by contrast, we report the presence of trunk sympathetic neurons in the sea lamprey, Petromyzon marinus, an extant jawless vertebrate. These neurons arise from sympathoblasts near the dorsal aorta that undergo noradrenergic specification through a transcriptional program homologous to that described in gnathostomes. Lamprey sympathoblasts populate the extracardiac space and extend along the length of the trunk in bilateral streams, expressing the catecholamine biosynthetic pathway enzymes tyrosine hydroxylase and dopamine β-hydroxylase. CM-DiI lineage tracing analysis further confirmed that these cells derive from the trunk neural crest. RNA sequencing of isolated ammocoete trunk sympathoblasts revealed gene profiles characteristic of sympathetic neuron function. Our findings challenge the prevailing dogma that posits that sympathetic ganglia are a gnathostome innovation, instead suggesting that a late-developing rudimentary sympathetic nervous system may have been characteristic of the earliest vertebrates.
    DOI:  https://doi.org/10.1038/s41586-024-07297-0
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