bims-ginsta Biomed News
on Genome instability
Issue of 2023–12–17
twenty-six papers selected by
Jinrong Hu, National University of Singapore
  1. Phase-separated CCER1 coordinates the histone-to-protamine transition and male fertility.
  2. CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline.
  3. Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules.
  4. CENP-A and CENP-B collaborate to create an open centromeric chromatin state.
  5. Two-phase kinetics and cell cortex elastic behavior in Xenopus gastrula cell-cell adhesion.
  6. Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy.
  7. Single-cell analysis of chromatin accessibility in the adult mouse brain.
  8. GRAF1 integrates PINK1-Parkin signaling and actin dynamics to mediate cardiac mitochondrial homeostasis.
  9. Regulation of condensin II by self-suppression and release mechanisms.
  10. Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos.
  11. Eif4enif1 haploinsufficiency disrupts oocyte mitochondrial dynamics and leads to subfertility.
  12. cGAS-STING signalling regulates microglial chemotaxis in genome instability.
  13. Multi-level 3D genome organization deteriorates during breast cancer progression.
  14. CKAP5 enables formation of persistent actin bundles templated by dynamically instable microtubules.
  15. Modeling cardiac fibroblast heterogeneity from human pluripotent stem cell-derived epicardial cells.
  16. Length control emerges from cytoskeletal network geometry.
  17. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.
  18. CRISPR loss of function screening to identify genes involved in human primordial germ cell-like cell development.
  19. Cell stretching activates an ATM mechano-transduction pathway that remodels cytoskeleton and chromatin.
  20. Robust small molecule-aided cardiac reprogramming systems selective to cardiac fibroblasts.
  21. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors.
  22. ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging.
  23. Phenotypic profiling of solute carriers characterizes serine transport in cancer.
  24. Actin contraction controls nuclear blebbing and rupture independent of actin confinement.
  25. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes.
  26. FANCD2-dependent mitotic DNA synthesis relies on PCNA K164 ubiquitination.
  1. Nat Commun. 2023 Dec 11. 14(1): 8209
    Phase-separated CCER1 coordinates the histone-to-protamine transition and male fertility.
    Dongdong Qin, Yayun Gu, Yu Zhang, Shu Wang, Tao Jiang, Yao Wang, Cheng Wang, Chang Chen, Tao Zhang, Weiya Xu, Hanben Wang, Ke Zhang, Liangjun Hu, Lufan Li, Wei Xie, Xin Wu, Zhibin Hu.
      Idiopathic fertility disorders are associated with mutations in various genes. Here, we report that coiled-coil glutamate-rich protein 1 (CCER1), a germline-specific and intrinsically disordered protein (IDP), mediates postmeiotic spermatid differentiation. In contrast, CCER1 deficiency results in defective sperm chromatin compaction and infertility in mice. CCER1 increases transition protein (Tnp1/2) and protamine (Prm1/2) transcription and mediates multiple histone epigenetic modifications during the histone-to-protamine (HTP) transition. Immiscible with heterochromatin in the nucleus, CCER1 self-assembles into a polymer droplet and forms a liquid-liquid phase-separated condensate in the nucleus. Notably, we identified loss-of-function (LoF) variants of human CCER1 (hCCER1) in five patients with nonobstructive azoospermia (NOA) that were absent in 2713 fertile controls. The mutants led to premature termination or frameshift in CCER1 translation, and disrupted condensates in vitro. In conclusion, we propose that nuclear CCER1 is a phase-separated condensate that links histone epigenetic modifications, HTP transitions, chromatin condensation, and male fertility.
    DOI:  https://doi.org/10.1038/s41467-023-43480-z
  2. bioRxiv. 2023 Dec 02. pii: 2023.11.30.569508. [Epub ahead of print]
    CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline.
    Yuka Kitamura, Kazuki Takahashi, So Maezawa, Yasuhisa Munakata, Akihiko Sakashita, Noam Kaplan, Satoshi H Namekawa.
      Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.
    DOI:  https://doi.org/10.1101/2023.11.30.569508
  3. Science. 2023 Dec 08. 382(6675): 1184-1190
    Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules.
    Kyle W Muir, Christopher Batters, Tom Dendooven, Jing Yang, Ziguo Zhang, Alister Burt, David Barford.
      Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
    DOI:  https://doi.org/10.1126/science.adj8736
  4. Nat Commun. 2023 Dec 12. 14(1): 8227
    CENP-A and CENP-B collaborate to create an open centromeric chromatin state.
    Harsh Nagpal, Ahmad Ali-Ahmad, Yasuhiro Hirano, Wei Cai, Mario Halic, Tatsuo Fukagawa, Nikolina Sekulić, Beat Fierz.
      Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore assemble, connecting the centromere to spindle microtubules during cell division. The DNA-binding centromeric protein CENP-B is involved in maintaining centromere stability and, together with CENP-A, shapes the centromeric chromatin state. The nanoscale organization of centromeric chromatin is not well understood. Here, we use single-molecule fluorescence and cryoelectron microscopy (cryoEM) to show that CENP-A incorporation establishes a dynamic and open chromatin state. The increased dynamics of CENP-A chromatin create an opening for CENP-B DNA access. In turn, bound CENP-B further opens the chromatin fiber structure and induces nucleosomal DNA unwrapping. Finally, removal of CENP-A increases CENP-B mobility in cells. Together, our studies show that the two centromere-specific proteins collaborate to reshape chromatin structure, enabling the binding of centromeric factors and establishing a centromeric chromatin state.
    DOI:  https://doi.org/10.1038/s41467-023-43739-5
  5. Dev Cell. 2023 Dec 05. pii: S1534-5807(23)00612-3. [Epub ahead of print]
    Two-phase kinetics and cell cortex elastic behavior in Xenopus gastrula cell-cell adhesion.
    Serge E Parent, Olivia Luu, Ashley E E Bruce, Rudolf Winklbauer.
      Morphogenetic movements during animal development involve repeated making and breaking of cell-cell contacts. Recent biophysical models of cell-cell adhesion integrate adhesion molecule interactions and cortical cytoskeletal tension modulation, describing equilibrium states for established contacts. We extend this emerging unified concept of adhesion to contact formation kinetics, showing that aggregating Xenopus embryonic cells rapidly achieve Ca2+-independent low-contact states. Subsequent transitions to cadherin-dependent high-contact states show rapid decreases in contact cortical F-actin levels but slow contact area growth. We developed a biophysical model that predicted contact growth quantitatively from known cellular and cytoskeletal parameters, revealing that elastic resistance to deformation and cytoskeletal network turnover are essential determinants of adhesion kinetics. Characteristic time scales of contact growth to low and high states differ by an order of magnitude, being at a few minutes and tens of minutes, respectively, thus providing insight into the timescales of cell-rearrangement-dependent tissue movements.
    Keywords:  F-actin; Xenopus; adhesion; cadherin; cytoskeleton; dynamics; gastrula; modeling; viscoelasticity
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.014
  6. Cell. 2023 Nov 28. pii: S0092-8674(23)01228-X. [Epub ahead of print]
    Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy.
    Cesar A Perez-Ramirez, Haruko Nakano, Richard C Law, Nedas Matulionis, Jennifer Thompson, Andrew Pfeiffer, Junyoung O Park, Atsushi Nakano, Heather R Christofk.
      Mounting evidence suggests metabolism instructs stem cell fate decisions. However, how fetal metabolism changes during development and how altered maternal metabolism shapes fetal metabolism remain unexplored. We present a descriptive atlas of in vivo fetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using 13C-glucose and liquid chromatography-mass spectrometry (LC-MS), we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Our analysis revealed metabolic features specific to a hyperglycemic environment and signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from hyperglycemic dams. Tracing 13C-glucose revealed disparate fetal nutrient sourcing depending on maternal glycemic states. Regardless of glycemic state, histidine-derived metabolites accumulated in late-stage fetal tissues. Our rich dataset presents a comprehensive overview of in vivo fetal tissue metabolism and alterations due to maternal hyperglycemia.
    Keywords:  development; diabetes; fetal metabolism; isotope tracing; metabolism; metabolomics; pregnancy
    DOI:  https://doi.org/10.1016/j.cell.2023.11.011
  7. Nature. 2023 Dec;624(7991): 378-389
    Single-cell analysis of chromatin accessibility in the adult mouse brain.
    Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren.
      Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs-specifically, those identified from a subset of cortical excitatory neurons-are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.
    DOI:  https://doi.org/10.1038/s41586-023-06824-9
  8. Nat Commun. 2023 Dec 11. 14(1): 8187
    GRAF1 integrates PINK1-Parkin signaling and actin dynamics to mediate cardiac mitochondrial homeostasis.
    Qiang Zhu, Matthew E Combs, Juan Liu, Xue Bai, Wenbo B Wang, Laura E Herring, Jiandong Liu, Jason W Locasale, Dawn E Bowles, Ryan T Gross, Michelle Mendiola Pla, Christopher P Mack, Joan M Taylor.
      The serine/threonine kinase, PINK1, and the E3 ubiquitin ligase, Parkin, are known to facilitate LC3-dependent autophagosomal encasement and lysosomal clearance of dysfunctional mitochondria, and defects in this process contribute to a variety of cardiometabolic and neurological diseases. Although recent evidence indicates that dynamic actin remodeling plays an important role in PINK1/Parkin-mediated mitochondrial autophagy (mitophagy), the underlying signaling mechanisms remain unknown. Here, we identify the RhoGAP GRAF1 (Arhgap26) as a PINK1 substrate that regulates mitophagy. GRAF1 promotes the release of damaged mitochondria from F-actin anchors, regulates mitochondrial-associated Arp2/3-mediated actin remodeling and facilitates Parkin-LC3 interactions to enhance mitochondria capture by autophagosomes. Graf1 phosphorylation on PINK1-dependent sites is dysregulated in human heart failure, and cardiomyocyte-restricted Graf1 depletion in mice blunts mitochondrial clearance and attenuates compensatory metabolic adaptations to stress. Overall, we identify GRAF1 as an enzyme that coordinates cytoskeletal and metabolic remodeling to promote cardioprotection.
    DOI:  https://doi.org/10.1038/s41467-023-43889-6
  9. Mol Biol Cell. 2023 Dec 13. mbcE23100392
    Regulation of condensin II by self-suppression and release mechanisms.
    Makoto M Yoshida, Kazuhisa Kinoshita, Keishi Shintomi, Yuuki Aizawa, Tatsuya Hirano.
      In vertebrates, two distinct condensin complexes, condensin I and condensin II, cooperate to drive mitotic chromosome assembly. It remains largely unknown how the two complexes differentially contribute to this process at a mechanistic level. We have previously dissected the role of individual subunits of condensin II by introducing recombinant complexes into Xenopus egg extracts. Here we extend these efforts by introducing a modified functional assay using extracts depleted of topoisomerase IIα (topo IIα), which allows us to further elucidate the functional similarities and differences between condensin I and condensin II. The intrinsically disordered C-terminal region of the CAP-D3 subunit (the D3 C-tail) is a major target of Cdk1 phosphorylation, and phosphorylation-deficient mutations in this region impair condensin II functions. We also identify a unique helical structure in CAP-D3 (the D3 HEAT docker) that is predicted to directly interact with CAP-G2. Deletion of the D3 HEAT docker, along with the D3 C-tail, enhances the ability of condensin II to assemble mitotic chromosomes. Taken together, we propose a self-suppression mechanism unique to condensin II that is released by mitotic phosphorylation. Evolutionary implications of our findings are also discussed.
    DOI:  https://doi.org/10.1091/mbc.E23-10-0392
  10. Science. 2023 Dec 15. 382(6676): eadi5516
    Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos.
    Lijia Li, Fangnong Lai, Xiaoyu Hu, Bofeng Liu, Xukun Lu, Zili Lin, Ling Liu, Yunlong Xiang, Tristan Frum, Michael A Halbisen, Fengling Chen, Qiang Fan, Amy Ralston, Wei Xie.
      Pioneer transcription factors (TFs), such as OCT4 and SOX2, play crucial roles in pluripotency regulation. However, the master TF-governed pluripotency regulatory circuitry was largely inferred from cultured cells. In this work, we investigated SOX2 binding from embryonic day 3.5 (E3.5) to E7.5 in the mouse. In E3.5 inner cell mass (ICM), SOX2 regulates the ICM-trophectoderm program but is dispensable for opening global enhancers. Instead, SOX2 occupies preaccessible enhancers in part opened by early-stage expressing TFs TFAP2C and NR5A2. SOX2 then widely redistributes when cells adopt naive and formative pluripotency by opening enhancers or poising them for rapid future activation. Hence, multifaceted pioneer TF-enhancer interaction underpins pluripotency progression in embryos, including a distinctive state in E3.5 ICM that bridges totipotency and pluripotency.
    DOI:  https://doi.org/10.1126/science.adi5516
  11. Development. 2023 Dec 01. pii: dev202151. [Epub ahead of print]150(23):
    Eif4enif1 haploinsufficiency disrupts oocyte mitochondrial dynamics and leads to subfertility.
    Yuxi Ding, Zequn He, Yanwei Sha, Kehkooi Kee, Lin Li.
      Infertility affects couples worldwide. Premature ovarian insufficiency (POI) refers to loss of ovarian function before 40 years of age and is a contributing factor to infertility. Several case studies have reported dominant-inherited POI symptoms in families with heterozygous EIF4ENIF1 (4E-T) mutations. However, the effects of EIF4ENIF1 haploinsufficiency have rarely been studied in animal models to reveal the underlying molecular changes related to infertility. Here, we demonstrate that Eif4enif1 haploinsufficiency causes mouse subfertility, impairs oocyte maturation and partially arrests early embryonic development. Using dual-omic sequencing, we observed that Eif4enif1 haploinsufficiency significantly altered both transcriptome and translatome in mouse oocytes, by which we further revealed oocyte mitochondrial hyperfusion and mitochondria-associated ribonucleoprotein domain distribution alteration in Eif4enif1-deficient oocytes. This study provides new insights into the molecular mechanisms underlying clinical fertility failure and new avenues to pursue new therapeutic targets to address infertility.
    Keywords:   Eif4enif1 ; Fertility; Mitochondrial dynamics; Mouse; Oocyte; RBP; Translation
    DOI:  https://doi.org/10.1242/dev.202151
  12. Nucleic Acids Res. 2023 Dec 12. pii: gkad1184. [Epub ahead of print]
    cGAS-STING signalling regulates microglial chemotaxis in genome instability.
    Emily J Talbot, Lisha Joshi, Peter Thornton, Mahya Dezfouli, Kalliopi Tsafou, Michael Perkinton, Svetlana V Khoronenkova.
      Defective DNA damage signalling and repair is a hallmark of age-related and genetic neurodegenerative disease. One mechanism implicated in disease progression is DNA damage-driven neuroinflammation, which is largely mediated by tissue-resident immune cells, microglia. Here, we utilise human microglia-like cell models of persistent DNA damage and ATM kinase deficiency to investigate how genome instability shapes microglial function. We demonstrate that upon DNA damage the cytosolic DNA sensing cGAS-STING axis drives chronic inflammation and a robust chemokine response, exemplified by production of CCL5 and CXCL10. Transcriptomic analyses revealed that cell migratory pathways were highly enriched upon IFN-β treatment of human iPSC-derived microglia, indicating that the chemokine response to DNA damage mirrors type I interferon signalling. Furthermore, we find that STING deletion leads to a defect in microglial chemotaxis under basal conditions and upon ATM kinase loss. Overall, this work provides mechanistic insights into cGAS-STING-dependent neuroinflammatory mechanisms and consequences of genome instability in the central nervous system.
    DOI:  https://doi.org/10.1093/nar/gkad1184
  13. bioRxiv. 2023 Nov 27. pii: 2023.11.26.568711. [Epub ahead of print]
    Multi-level 3D genome organization deteriorates during breast cancer progression.
    Roberto Rossini, Mohammadsaleh Oshaghi, Maxim Nekrasov, Aurélie Bellanger, Renae Domaschenz, Yasmin Dijkwel, Mohamed Abdelhalim, Philippe Collas, David Tremethick, Jonas Paulsen.
      Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.
    DOI:  https://doi.org/10.1101/2023.11.26.568711
  14. Curr Biol. 2023 Dec 06. pii: S0960-9822(23)01581-6. [Epub ahead of print]
    CKAP5 enables formation of persistent actin bundles templated by dynamically instable microtubules.
    Jan Sabo, Michaela Dujava Zdimalova, Paula G Slater, Vojtech Dostal, Stepan Herynek, Lenka Libusova, Laura A Lowery, Marcus Braun, Zdenek Lansky.
      Cytoskeletal rearrangements and crosstalk between microtubules and actin filaments are vital for living organisms. Recently, an abundantly present microtubule polymerase, CKAP5 (XMAP215 homolog), has been reported to play a role in mediating crosstalk between microtubules and actin filaments in the neuronal growth cones. However, the molecular mechanism of this process is unknown. Here, we demonstrate, in a reconstituted system, that CKAP5 enables the formation of persistent actin bundles templated by dynamically instable microtubules. We explain the templating by the difference in CKAP5 binding to microtubules and actin filaments. Binding to the microtubule lattice with higher affinity, CKAP5 enables the formation of actin bundles exclusively on the microtubule lattice, at CKAP5 concentrations insufficient to support any actin bundling in the absence of microtubules. Strikingly, when the microtubules depolymerize, actin bundles prevail at the positions predetermined by the microtubules. We propose that the local abundance of available CKAP5-binding sites in actin bundles allows the retention of CKAP5, resulting in persisting actin bundles. In line with our observations, we found that reducing CKAP5 levels in vivo results in a decrease in actin-microtubule co-localization in growth cones and specifically decreases actin intensity at microtubule plus ends. This readily suggests a mechanism explaining how exploratory microtubules set the positions of actin bundles, for example, in cytoskeleton-rich neuronal growth cones.
    Keywords:  CKAP5; XMAP215; actin filaments; cytoskeleton; cytoskeleton-associated proteins; filament crosslinkers; in vitro reconstitution; microtubules; neuronal growth cones
    DOI:  https://doi.org/10.1016/j.cub.2023.11.031
  15. Nat Commun. 2023 Dec 11. 14(1): 8183
    Modeling cardiac fibroblast heterogeneity from human pluripotent stem cell-derived epicardial cells.
    Ian Fernandes, Shunsuke Funakoshi, Homaira Hamidzada, Slava Epelman, Gordon Keller.
      Cardiac fibroblasts play an essential role in the development of the heart and are implicated in disease progression in the context of fibrosis and regeneration. Here, we establish a simple organoid culture platform using human pluripotent stem cell-derived epicardial cells and ventricular cardiomyocytes to study the development, maturation, and heterogeneity of cardiac fibroblasts under normal conditions and following treatment with pathological stimuli. We demonstrate that this system models the early interactions between epicardial cells and cardiomyocytes to generate a population of fibroblasts that recapitulates many aspects of fibroblast behavior in vivo, including changes associated with maturation and in response to pathological stimuli associated with cardiac injury. Using single cell transcriptomics, we show that the hPSC-derived organoid fibroblast population displays a high degree of heterogeneity that approximates the heterogeneity of populations in both the normal and diseased human heart. Additionally, we identify a unique subpopulation of fibroblasts possessing reparative features previously characterized in the hearts of model organisms. Taken together, our system recapitulates many aspects of human cardiac fibroblast specification, development, and maturation, providing a platform to investigate the role of these cells in human cardiovascular development and disease.
    DOI:  https://doi.org/10.1038/s41467-023-43312-0
  16. bioRxiv. 2023 Nov 29. pii: 2023.11.28.569063. [Epub ahead of print]
    Length control emerges from cytoskeletal network geometry.
    Shane G McInally, Alexander J B Reading, Aldric Rosario, Predrag R Jelenkovic, Bruce L Goode, Jane Kondev.
      Many cytoskeletal networks consist of individual filaments that are organized into elaborate higher order structures. While it is appreciated that the size and architecture of these networks are critical for their biological functions, much of the work investigating control over their assembly has focused on mechanisms that regulate the turnover of individual filaments through size-dependent feedback. Here, we propose a very different, feedback-independent mechanism to explain how yeast cells control the length of their actin cables. Our findings, supported by quantitative cell imaging and mathematical modeling, indicate that actin cable length control is an emergent property that arises from the cross-linked and bundled organization of the filaments within the cable. Using this model, we further dissect the mechanisms that allow cables to grow longer in larger cells, and propose that cell length-dependent tuning of formin activity allows cells to scale cable length with cell length. This mechanism is a significant departure from prior models of cytoskeletal filament length control and presents a new paradigm to consider how cells control the size, shape, and dynamics of higher order cytoskeletal structures.
    Significance Statement: Cells control the sizes of their cytoskeletal networks to ensure that these structures can efficiently perform their cellular functions. Until now, this ability has been attributed to molecular feedback mechanisms that control the rates at which individual filaments are assembled and disassembled. We find that size control of cytoskeletal networks does not require this type of feedback and can instead be encoded through the physical arrangement of the filaments within that network. These findings have important implications for understanding how the underlying geometry of higher order cytoskeletal networks contributes to cellular control over these structures.
    DOI:  https://doi.org/10.1101/2023.11.28.569063
  17. Sci Adv. 2023 Dec 08. 9(49): eadj4884
    In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.
    Xuewen Chen, Augustinus G Haribowo, Alan H Baik, Andrea Fossati, Erica Stevenson, Yiwen R Chen, Nabora S Reyes, Tien Peng, Michael A Matthay, Michela Traglia, Alexander R Pico, Daniel F Jarosz, Abigail Buchwalter, Sina Ghaemmaghami, Danielle L Swaney, Isha H Jain.
      Oxygen deprivation and excess are both toxic. Thus, the body's ability to adapt to varying oxygen tensions is critical for survival. While the hypoxia transcriptional response has been well studied, the post-translational effects of oxygen have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to varying oxygen tensions. In particular, several extracellular matrix (ECM) proteins are stabilized in the lung under both hypoxia and hyperoxia. Furthermore, we show that complex 1 of the electron transport chain is destabilized in hyperoxia, in accordance with the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a hyperoxia transcriptional regulator, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of varying oxygen tensions on protein turnover rates and identifies tissue-specific mediators of oxygen-dependent responses.
    DOI:  https://doi.org/10.1126/sciadv.adj4884
  18. PLoS Genet. 2023 Dec 13. 19(12): e1011080
    CRISPR loss of function screening to identify genes involved in human primordial germ cell-like cell development.
    Young Sun Hwang, Yasunari Seita, M Andrés Blanco, Kotaro Sasaki.
      Despite our increasing knowledge of molecular mechanisms guiding various aspects of human reproduction, those underlying human primordial germ cell (PGC) development remain largely unknown. Here, we conducted custom CRISPR screening in an in vitro system of hPGC-like cells (hPGCLCs) to identify genes required for acquisition and maintenance of PGC fate in humans. Amongst our candidates, we identified TCL1A, an AKT coactivator. Functional assessment in our in vitro hPGCLCs system revealed that TCL1A played a critical role in later stages of hPGCLC development. Moreover, we found that TCL1A loss reduced AKT-mTOR signaling, downregulated expression of genes related to translational control, and subsequently led to a reduction in global protein synthesis and proliferation. Together, our study highlights the utility of CRISPR screening for human in vitro-derived germ cells and identifies novel translational regulators critical for hPGCLC development.
    DOI:  https://doi.org/10.1371/journal.pgen.1011080
  19. Cell Rep. 2023 Dec 11. pii: S2211-1247(23)01567-X. [Epub ahead of print]42(12): 113555
    Cell stretching activates an ATM mechano-transduction pathway that remodels cytoskeleton and chromatin.
    Giulia Bastianello, Giancarlo Porcella, Galina V Beznoussenko, Gururaj Kidiyoor, Flora Ascione, Qingsen Li, Angela Cattaneo, Vittoria Matafora, Andrea Disanza, Micaela Quarto, Alexander A Mironov, Amanda Oldani, Sara Barozzi, Angela Bachi, Vincenzo Costanzo, Giorgio Scita, Marco Foiani.
      Ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) DNA damage response (DDR) kinases contain elastic domains. ATM also responds to reactive oxygen species (ROS) and ATR to nuclear mechanical stress. Mre11 mediates ATM activation following DNA damage; ATM mutations cause ataxia telangiectasia (A-T). Here, using in vivo imaging, electron microscopy, proteomic, and mechano-biology approaches, we study how ATM responds to mechanical stress. We report that cytoskeleton and ROS, but not Mre11, mediate ATM activation following cell deformation. ATM deficiency causes hyper-stiffness, stress fiber accumulation, Yes-associated protein (YAP) nuclear enrichment, plasma and nuclear membrane alterations during interstitial migration, and H3 hyper-methylation. ATM locates to the actin cytoskeleton and, following cytoskeleton stress, promotes phosphorylation of key cytoskeleton and chromatin regulators. Our data contribute to explain some clinical features of patients with A-T and pinpoint the existence of an integrated mechano-response in which ATM and ATR have distinct roles unrelated to their canonical DDR functions.
    Keywords:  ATM and ATR; CP: Cell biology; CP: Molecular biology; DNA damage response; ROS; ataxia telangiectasia; cell stretching; checkpoints; chromatin; cytoskeleton; interstitial migration; mechanical stress
    DOI:  https://doi.org/10.1016/j.celrep.2023.113555
  20. iScience. 2023 Dec 15. 26(12): 108466
    Robust small molecule-aided cardiac reprogramming systems selective to cardiac fibroblasts.
    Yanmeng Tao, Yang Yang, Zhenghao Yang, Lipeng Wang, Shi-Qiang Wang, Yang Zhao.
      Direct cardiac reprogramming to induce cardiomyocyte-like cells, e.g., by GMT (Gata4, Mef2c and Tbx5), is a promising route for regenerating damaged heart in vivo and disease modeling in vitro. Supplementation with additional factors and chemical agents can enhance efficiency but raises concerns regarding selectivity to cardiac fibroblasts and complicates delivery for in situ cardiac reprogramming. Here, we screened 2000 chemicals with known biological activities and found that a combination of 2C (SB431542 and Baricitinib) significantly enhances cardiac reprogramming by GMT. Without Gata4, MT (Mef2c and Tbx5) plus 2C could selectively reprogram cardiac fibroblasts with enhanced efficiency, kinetics, and cardiomyocyte function. Moreover, 2C significantly enhanced cardiac reprogramming in human cardiac fibroblasts. 2C synergistically enhances cardiac reprogramming by inhibiting Alk5, Tyk2 and downregulating Oas2, Oas3, Serpina3n and Tgfbi. 2C enables selective and robust cardiac reprogramming that can greatly facilitate disease modeling in vitro and advance clinical therapeutic heart regeneration in vivo.
    Keywords:  Cardiovascular medicine; Cell biology
    DOI:  https://doi.org/10.1016/j.isci.2023.108466
  21. Cell. 2023 Dec 07. pii: S0092-8674(23)01222-9. [Epub ahead of print]186(25): 5620-5637.e16
    Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors.
    Cody N Heiser, Alan J Simmons, Frank Revetta, Eliot T McKinley, Marisol A Ramirez-Solano, Jiawei Wang, Harsimran Kaur, Justin Shao, Gregory D Ayers, Yu Wang, Sarah E Glass, Naila Tasneem, Zhengyi Chen, Yan Qin, William Kim, Andrea Rolong, Bob Chen, Paige N Vega, Julia L Drewes, Nicholas O Markham, Nabil Saleh, Fotis Nikolos, Simon Vandekar, Angela L Jones, M Kay Washington, Joseph T Roland, Keith S Chan, Thomas Schürpf, Cynthia L Sears, Qi Liu, Martha J Shrubsole, Robert J Coffey, Ken S Lau.
      Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Analysis of spatial multi-omic data from 31 human colorectal specimens enabled phylogeographic mapping of tumor evolution that revealed individualized progression trajectories and accompanying microenvironmental and clonal alterations. Phylogeographic mapping ordered genetic events, classified tumors by their evolutionary dynamics, and placed clonal regions along global pseudotemporal progression trajectories encompassing the chromosomal instability (CIN+) and hypermutated (HM) pathways. Integrated single-cell and spatial transcriptomic data revealed recurring epithelial programs and infiltrating immune states along progression pseudotime. We discovered an immune exclusion signature (IEX), consisting of extracellular matrix regulators DDR1, TGFBI, PAK4, and DPEP1, that charts with CIN+ tumor progression, is associated with reduced cytotoxic cell infiltration, and shows prognostic value in independent cohorts. This spatial multi-omic atlas provides insights into colorectal tumor-microenvironment co-evolution, serving as a resource for stratification and targeted treatments.
    Keywords:  colorectal cancer; immune exclusion; microsatellite instability; multiplex imaging; mutations; spatial transcriptomics; stem cells; tumor evolution; tumor progression
    DOI:  https://doi.org/10.1016/j.cell.2023.11.006
  22. Science. 2023 Dec 08. 382(6675): eadf3208
    ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging.
    Goda Snieckute, Laura Ryder, Anna Constance Vind, Zhenzhen Wu, Frederic Schrøder Arendrup, Mark Stoneley, Sébastien Chamois, Ana Martinez-Val, Marion Leleu, René Dreos, Alexander Russell, David Michael Gay, Aitana Victoria Genzor, Beatrice So-Yun Choi, Astrid Linde Basse, Frederike Sass, Morten Dall, Lucile Chantal Marie Dollet, Melanie Blasius, Anne E Willis, Anders H Lund, Jonas T Treebak, Jesper Velgaard Olsen, Steen Seier Poulsen, Mary Elizabeth Pownall, Benjamin Anderschou Holbech Jensen, Christoffer Clemmensen, Zach Gerhart-Hines, David Gatfield, Simon Bekker-Jensen.
      The ribotoxic stress response (RSR) is a signaling pathway in which the p38- and c-Jun N-terminal kinase (JNK)-activating mitogen-activated protein kinase kinase kinase (MAP3K) ZAKα senses stalling and/or collision of ribosomes. Here, we show that reactive oxygen species (ROS)-generating agents trigger ribosomal impairment and ZAKα activation. Conversely, zebrafish larvae deficient for ZAKα are protected from ROS-induced pathology. Livers of mice fed a ROS-generating diet exhibit ZAKα-activating changes in ribosomal elongation dynamics. Highlighting a role for the RSR in metabolic regulation, ZAK-knockout mice are protected from developing high-fat high-sugar (HFHS) diet-induced blood glucose intolerance and liver steatosis. Finally, ZAK ablation slows animals from developing the hallmarks of metabolic aging. Our work highlights ROS-induced ribosomal impairment as a physiological activation signal for ZAKα that underlies metabolic adaptation in obesity and aging.
    DOI:  https://doi.org/10.1126/science.adf3208
  23. Nat Metab. 2023 Dec 08.
    Phenotypic profiling of solute carriers characterizes serine transport in cancer.
    Vasileios Papalazarou, Alice C Newman, Alejandro Huerta-Uribe, Nathalie M Legrave, Mattia Falcone, Tong Zhang, Lynn McGarry, Dimitris Athineos, Emma Shanks, Karen Blyth, Karen H Vousden, Oliver D K Maddocks.
      Serine is a vital amino acid in tumorigenesis. While cells can perform de novo serine synthesis, most transformed cells rely on serine uptake to meet their increased biosynthetic requirements. Solute carriers (SLCs), a family of transmembrane nutrient transport proteins, are the gatekeepers of amino acid acquisition and exchange in mammalian cells and are emerging as anticancer therapeutic targets; however, the SLCs that mediate serine transport in cancer cells remain unknown. Here we perform an arrayed RNAi screen of SLC-encoding genes while monitoring amino acid consumption and cell proliferation in colorectal cancer cells using metabolomics and high-throughput imaging. We identify SLC6A14 and SLC25A15 as major cytoplasmic and mitochondrial serine transporters, respectively. We also observe that SLC12A4 facilitates serine uptake. Dual targeting of SLC6A14 and either SLC25A15 or SLC12A4 diminishes serine uptake and growth of colorectal cancer cells in vitro and in vivo, particularly in cells with compromised de novo serine biosynthesis. Our results provide insight into the mechanisms that contribute to serine uptake and intracellular handling.
    DOI:  https://doi.org/10.1038/s42255-023-00936-2
  24. Mol Biol Cell. 2023 Dec 13. mbcE23070292
    Actin contraction controls nuclear blebbing and rupture independent of actin confinement.
    Mai Pho, Yasmin Berrada, Aachal Gunda, Anya Lavallee, Katherine Chiu, Arimita Padam, Marilena L Currey, Andrew D Stephens.
      The nucleus is a mechanically stable compartment of the cell that contains the genome and performs many essential functions. Nuclear mechanical components chromatin and lamins maintain nuclear shape, compartmentalization, and function by resisting antagonistic actin contraction and confinement. Studies have yet to compare chromatin and lamins perturbations side-by-side as well as modulated actin contraction while holding confinement constant. To accomplish this, we used NLS-GFP to measure nuclear shape and rupture in live cells with chromatin and lamin perturbations. We then modulated actin contraction while maintaining actin confinement measured by nuclear height. Wild type, chromatin decompaction, and lamin B1 null present bleb-based nuclear deformations and ruptures dependent on actin contraction and independent of actin confinement. Actin contraction inhibition by Y27632 decreased nuclear blebbing and ruptures while activation by CN03 increased rupture frequency. Lamin A/C null results in overall abnormal shape also reliant on actin contraction, but similar blebs and ruptures as wild type. Increased DNA damage is caused by nuclear blebbing or abnormal shape which can be relieved by inhibition of actin contraction which rescues nuclear shape and decreases DNA damage levels in all perturbations. Thus, actin contraction drives nuclear blebbing, bleb-based ruptures, and abnormal shape independent of changes in actin confinement. [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E23-07-0292
  25. Nat Commun. 2023 Dec 13. 14(1): 8272
    The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes.
    Federica Raguseo, Yiran Wang, Jessica Li, Marija Petrić Howe, Rubika Balendra, Anouk Huyghebaert, Devkee M Vadukul, Diana A Tanase, Thomas E Maher, Layla Malouf, Roger Rubio-Sánchez, Francesco A Aprile, Yuval Elani, Rickie Patani, Lorenzo Di Michele, Marco Di Antonio.
      Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
    DOI:  https://doi.org/10.1038/s41467-023-43872-1
  26. Cell Rep. 2023 Dec 05. pii: S2211-1247(23)01535-8. [Epub ahead of print]42(12): 113523
    FANCD2-dependent mitotic DNA synthesis relies on PCNA K164 ubiquitination.
    Wendy Leung, Ryan M Baxley, Emma Traband, Ya-Chu Chang, Colette B Rogers, Liangjun Wang, Wesley Durrett, Kendall S Bromley, Lidia Fiedorowicz, Tanay Thakar, Anika Tella, Alexandra Sobeck, Eric A Hendrickson, George-Lucian Moldovan, Naoko Shima, Anja-Katrin Bielinsky.
      Ubiquitination of proliferating cell nuclear antigen (PCNA) at lysine 164 (K164) activates DNA damage tolerance pathways. Currently, we lack a comprehensive understanding of how PCNA K164 ubiquitination promotes genome stability. To evaluate this, we generated stable cell lines expressing PCNAK164R from the endogenous PCNA locus. Our data reveal that the inability to ubiquitinate K164 causes perturbations in global DNA replication. Persistent replication stress generates under-replicated regions and is exacerbated by the DNA polymerase inhibitor aphidicolin. We show that these phenotypes are due, in part, to impaired Fanconi anemia group D2 protein (FANCD2)-dependent mitotic DNA synthesis (MiDAS) in PCNAK164R cells. FANCD2 mono-ubiquitination is significantly reduced in PCNAK164R mutants, leading to reduced chromatin association and foci formation, both prerequisites for FANCD2-dependent MiDAS. Furthermore, K164 ubiquitination coordinates direct PCNA/FANCD2 colocalization in mitotic nuclei. Here, we show that PCNA K164 ubiquitination maintains human genome stability by promoting FANCD2-dependent MiDAS to prevent the accumulation of under-replicated DNA.
    Keywords:  CP: Molecular biology; FANCD2; MiDAS; PCNA; replication stress; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2023.113523
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