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Huang T, Liu D, Wang X, Kuang J, Wu M, Wang B, Liang Z, Fan Y, Chen B, Ma Z, Fu Y, Zhang W, Ming J, Qin Y, Zhao C, Wang B, Pei D. Engineering mouse cell fate controller by rational design. Nat Commun 2024; 15:6200. [PMID: 39043686 PMCID: PMC11266670 DOI: 10.1038/s41467-024-50551-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
Cell fate is likely regulated by a common machinery, while components of this machine remain to be identified. Here we report the design and testing of engineered cell fate controller NanogBiD, fusing BiD or BRG1 interacting domain of SS18 with Nanog. NanogBiD promotes mouse somatic cell reprogramming efficiently in contrast to the ineffective native protein under multiple testing conditions. Mechanistic studies further reveal that it facilitates cell fate transition by recruiting the intended Brg/Brahma-associated factor (BAF) complex to modulate chromatin accessibility and reorganize cell state specific enhancers known to be occupied by canonical Nanog, resulting in precocious activation of multiple genes including Sall4, miR-302, Dppa5a and Sox15 towards pluripotency. Although we have yet to test our approach in other species, our findings suggest that engineered chromatin regulators may provide much needed tools to engineer cell fate in the cells as drugs era.
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Affiliation(s)
- Tao Huang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Dong Liu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaomin Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Manqi Wu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Beibei Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zechuan Liang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yixin Fan
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Chen
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zhaoyi Ma
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yu Fu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wenhui Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yue Qin
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province, Hangzhou, China.
| | - Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province, Hangzhou, China.
- Zhejiang University of Science and Technology School of Information and Electronic Engineering, Hangzhou, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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2
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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3
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Hu X, Huang X, Yang Y, Sun Y, Zhao Y, Zhang Z, Qiu D, Wu Y, Wu G, Lei L. Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader. Nucleic Acids Res 2024; 52:5529-5548. [PMID: 38512058 PMCID: PMC11162783 DOI: 10.1093/nar/gkae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 02/24/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial junction. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.
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Affiliation(s)
- Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Xingwei Huang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Yue Yang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanhua Zhao
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Yanshuang Wu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
| | - Guangming Wu
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 Guangdong Province, China
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province 150081, China
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4
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Orsetti A, van Oosten D, Vasarhelyi RG, Dănescu TM, Huertas J, van Ingen H, Cojocaru V. Structural dynamics in chromatin unraveling by pioneer transcription factors. Biophys Rev 2024; 16:365-382. [PMID: 39099839 PMCID: PMC11297019 DOI: 10.1007/s12551-024-01205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Pioneer transcription factors are proteins with a dual function. First, they regulate transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to DNA while wrapped around histone proteins in the chromatin and mediate chromatin opening. The molecular mechanisms that connect the two functions are yet to be discovered. In recent years, pioneer factors received increased attention mainly because of their crucial role in promoting cell fate transitions that could be used for regenerative therapies. For example, the three factors required to induce pluripotency in somatic cells, Oct4, Sox2, and Klf4 were classified as pioneer factors and studied extensively. With this increased attention, several structures of complexes between pioneer factors and chromatin structural units (nucleosomes) have been resolved experimentally. Furthermore, experimental and computational approaches have been designed to study two unresolved, key scientific questions: First, do pioneer factors induce directly local opening of nucleosomes and chromatin fibers upon binding? And second, how do the unstructured tails of the histones impact the structural dynamics involved in such conformational transitions? Here we review the current knowledge about transcription factor-induced nucleosome dynamics and the role of the histone tails in this process. We discuss what is needed to bridge the gap between the static views obtained from the experimental structures and the key structural dynamic events in chromatin opening. Finally, we propose that integrating nuclear magnetic resonance spectroscopy with molecular dynamics simulations is a powerful approach to studying pioneer factor-mediated dynamics of nucleosomes and perhaps small chromatin fibers using native DNA sequences.
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Affiliation(s)
- Andrea Orsetti
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Daphne van Oosten
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | | | - Theodor-Marian Dănescu
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Vlad Cojocaru
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
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5
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Martinez-Sarmiento JA, Cosma MP, Lakadamyali M. Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Rep 2024; 43:114170. [PMID: 38700983 PMCID: PMC11195307 DOI: 10.1016/j.celrep.2024.114170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent.
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Affiliation(s)
- Jose A Martinez-Sarmiento
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080 Guangzhou, China.
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Kunitomi A, Hirohata R, Osawa M, Washizu K, Arreola V, Saiki N, Kato TM, Nomura M, Kunitomi H, Ohkame T, Ohkame Y, Kawaguchi J, Hara H, Kusano K, Yamamoto T, Takashima Y, Tohyama S, Yuasa S, Fukuda K, Takasu N, Yamanaka S. H1FOO-DD promotes efficiency and uniformity in reprogramming to naive pluripotency. Stem Cell Reports 2024; 19:710-728. [PMID: 38701780 PMCID: PMC11103934 DOI: 10.1016/j.stemcr.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Heterogeneity among both primed and naive pluripotent stem cell lines remains a major unresolved problem. Here we show that expressing the maternal-specific linker histone H1FOO fused to a destabilizing domain (H1FOO-DD), together with OCT4, SOX2, KLF4, and LMYC, in human somatic cells improves the quality of reprogramming to both primed and naive pluripotency. H1FOO-DD expression was associated with altered chromatin accessibility around pluripotency genes and with suppression of the innate immune response. Notably, H1FOO-DD generates naive induced pluripotent stem cells with lower variation in transcriptome and methylome among clones and a more uniform and superior differentiation potency. Furthermore, we elucidated that upregulation of FKBP1A, driven by these five factors, plays a key role in H1FOO-DD-mediated reprogramming.
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Affiliation(s)
- Akira Kunitomi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
| | - Ryoko Hirohata
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; CiRA Foundation, Kyoto 606-8397, Japan
| | - Mitsujiro Osawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Kaho Washizu
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Vanessa Arreola
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Norikazu Saiki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Tomoaki M Kato
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; CiRA Foundation, Kyoto 606-8397, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; CiRA Foundation, Kyoto 606-8397, Japan
| | - Haruko Kunitomi
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Tokiko Ohkame
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yusuke Ohkame
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | | | | | | | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Yasuhiro Takashima
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shinsuke Yuasa
- Department of Cardiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Naoko Takasu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; CiRA Foundation, Kyoto 606-8397, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; CiRA Foundation, Kyoto 606-8397, Japan; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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7
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Zhu F, Yan N, Lu X, Xu J, Gu H, Liang J, Cheng K, Wang X, Ma X, Ma N, Zhao X, Chen C, Nie G. Cell-Reprogramming-Inspired Dynamically Responsive Hydrogel Boosts the Induction of Pluripotency via Phase-Separated Biomolecular Condensates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211609. [PMID: 36989141 DOI: 10.1002/adma.202211609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/23/2023] [Indexed: 05/16/2023]
Abstract
Induced pluripotent stem cells (iPSCs) have wide applications in disease modeling, personalized medicine, and tissue engineering. The generation of iPSCs from somatic cells via transcriptional-factor- or chemical molecule-based approaches are time-consuming and inefficient. Here, a cell-reprogramming-inspired dynamically responsive hydrogel is fabricated via a synthetic-biology-based strategy. Human and mouse somatic cells (including senescent cells) are efficiently reprogrammed into iPSCs that exhibit key features of embryonic stem cells. The cell-reprogramming-responsive hydrogel possesses dynamic bioresponsiveness, and it faithfully senses metabolic remodeling and extracellular acidification during cell reprogramming, responding by changing its mechanical properties accordingly. Mechanistic study demonstrates that the autonomous change of the mechanical properties of the cell-reprogramming-responsive hydrogel elicits the formation of Yes-associated protein (YAP) biomolecular condensates with the appropriate timing during cell reprogramming, ensuring a faster and more efficient generation of iPSCs than conventional cell reprogramming approach. Taken together, this study reveals the robust induction of pluripotency by coordination of cell-reprogramming-inspired dynamically responsive hydrogel and phase-separated biomolecular condensates.
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Affiliation(s)
- Fei Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Na Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xukun Lu
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Junchao Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keman Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Xiaona Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaotu Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Nana Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Xiao Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong, 510700, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- The GBA National Institute for Nanotechnology Innovation, Guangdong, 510700, China
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8
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Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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9
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Guo X, Wang C, Zhang Y, Wei R, Xi R. Cell-fate conversion of intestinal cells in adult Drosophila midgut by depleting a single transcription factor. Nat Commun 2024; 15:2656. [PMID: 38531872 DOI: 10.1038/s41467-024-46956-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
The manipulation of cell identity by reprograming holds immense potential in regenerative medicine, but is often limited by the inefficient acquisition of fully functional cells. This problem can potentially be resolved by better understanding the reprogramming process using in vivo genetic models, which are currently scarce. Here we report that both enterocytes (ECs) and enteroendocrine cells (EEs) in adult Drosophila midgut show a surprising degree of cell plasticity. Depleting the transcription factor Tramtrack in the differentiated ECs can initiate Prospero-mediated cell transdifferentiation, leading to EE-like cells. On the other hand, depletion of Prospero in the differentiated EEs can lead to the loss of EE-specific transcription programs and the gain of intestinal progenitor cell identity, allowing cell cycle re-entry or differentiation into ECs. We find that intestinal progenitor cells, ECs, and EEs have a similar chromatin accessibility profile, supporting the concept that cell plasticity is enabled by pre-existing chromatin accessibility with switchable transcription programs. Further genetic analysis with this system reveals that the NuRD chromatin remodeling complex, cell lineage confliction, and age act as barriers to EC-to-EE transdifferentiation. The establishment of this genetically tractable in vivo model should facilitate mechanistic investigation of cell plasticity at the molecular and genetic level.
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Affiliation(s)
- Xingting Guo
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Chenhui Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Yongchao Zhang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Ruxue Wei
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Rongwen Xi
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.
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10
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Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet 2024; 56:473-482. [PMID: 38361031 DOI: 10.1038/s41588-024-01658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
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Affiliation(s)
- Satoko Ishii
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taishi Kakizuka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Tagawa
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Chiaki Sanbo
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Miyanari
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
- Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
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11
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Choi W, Choe MS, Kim SM, Kim SJ, Lee J, Lee Y, Lee SM, Dho SH, Lee MY, Kim LK. RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1. Cell Mol Life Sci 2024; 81:99. [PMID: 38386071 PMCID: PMC10884155 DOI: 10.1007/s00018-024-05129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/27/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Proneural genes play a crucial role in neuronal differentiation. However, our understanding of the regulatory mechanisms governing proneural genes during neuronal differentiation remains limited. RFX4, identified as a candidate regulator of proneural genes, has been reported to be associated with the development of neuropsychiatric disorders. To uncover the regulatory relationship, we utilized a combination of multi-omics data, including ATAC-seq, ChIP-seq, Hi-C, and RNA-seq, to identify RFX4 as an upstream regulator of proneural genes. We further validated the role of RFX4 using an in vitro model of neuronal differentiation with RFX4 knock-in and a CRISPR-Cas9 knock-out system. As a result, we found that RFX4 directly interacts with the promoters of POU3F2 and NEUROD1. Transcriptomic analysis revealed a set of genes associated with neuronal development, which are highly implicated in the development of neuropsychiatric disorders, including schizophrenia. Notably, ectopic expression of RFX4 can drive human embryonic stem cells toward a neuronal fate. Our results strongly indicate that RFX4 serves as a direct upstream regulator of proneural genes, a role that is essential for normal neuronal development. Impairments in RFX4 function could potentially be related to the development of various neuropsychiatric disorders. However, understanding the precise mechanisms by which the RFX4 gene influences the onset of neuropsychiatric disorders requires further investigation through human genetic studies.
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Affiliation(s)
- Wonyoung Choi
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul, Korea
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Mu Seog Choe
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Su Min Kim
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea
| | - So Jin Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jiyeon Lee
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea
| | - Yeongun Lee
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea
| | - Sun-Min Lee
- Department of Physics, Konkuk University, Seoul, Republic of Korea
| | - So Hee Dho
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea
| | - Min-Young Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea.
| | - Lark Kyun Kim
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06230, Republic of Korea.
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12
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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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13
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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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14
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MacCarthy CM, Wu G, Malik V, Menuchin-Lasowski Y, Velychko T, Keshet G, Fan R, Bedzhov I, Church GM, Jauch R, Cojocaru V, Schöler HR, Velychko S. Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell 2024; 31:127-147.e9. [PMID: 38141611 DOI: 10.1016/j.stem.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/02/2023] [Accepted: 11/20/2023] [Indexed: 12/25/2023]
Abstract
Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission has only been demonstrated for mice and rats. By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a gain of function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-quality OSKM iPSCs capable of supporting the development of healthy all-iPSC mice. Sox2/Oct4 dimerization emerged as the core driver of naive pluripotency with its levels diminished upon priming. Transient overexpression of the SK cocktail (Sox+Klf4) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naive reset in mammals.
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Affiliation(s)
| | - Guangming Wu
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; International Bio Island, Guangzhou, China; MingCeler Biotech, Guangzhou, China
| | - Vikas Malik
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Taras Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gal Keshet
- Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rui Fan
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ivan Bedzhov
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard University, Boston, MA, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Vlad Cojocaru
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; University of Utrecht, Utrecht, the Netherlands; STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard University, Boston, MA, USA.
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15
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Cipriano A, Moqri M, Maybury-Lewis SY, Rogers-Hammond R, de Jong TA, Parker A, Rasouli S, Schöler HR, Sinclair DA, Sebastiano V. Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming. NATURE AGING 2024; 4:14-26. [PMID: 38102454 PMCID: PMC11058000 DOI: 10.1038/s43587-023-00539-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Over the past decade, there has been a dramatic increase in efforts to ameliorate aging and the diseases it causes, with transient expression of nuclear reprogramming factors recently emerging as an intriguing approach. Expression of these factors, either systemically or in a tissue-specific manner, has been shown to combat age-related deterioration in mouse and human model systems at the cellular, tissue and organismal level. Here we discuss the current state of epigenetic rejuvenation strategies via partial reprogramming in both mouse and human models. For each classical reprogramming factor, we provide a brief description of its contribution to reprogramming and discuss additional factors or chemical strategies. We discuss what is known regarding chromatin remodeling and the molecular dynamics underlying rejuvenation, and, finally, we consider strategies to improve the practical uses of epigenetic reprogramming to treat aging and age-related diseases, focusing on the open questions and remaining challenges in this emerging field.
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Affiliation(s)
- Andrea Cipriano
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Mahdi Moqri
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tineke Anna de Jong
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Alexander Parker
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Sajede Rasouli
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Hans Robert Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - David A Sinclair
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA.
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.
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16
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Zhu W, Bu G, Hu R, Zhang J, Qiao L, Zhou K, Wang T, Li Q, Zhang J, Wu L, Xie Y, Hu T, Yang S, Guan J, Chu X, Shi J, Zhang X, Lu F, Liu X, Miao YL. KLF4 facilitates chromatin accessibility remodeling in porcine early embryos. SCIENCE CHINA. LIFE SCIENCES 2024; 67:96-112. [PMID: 37698691 DOI: 10.1007/s11427-022-2349-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/20/2023] [Indexed: 09/13/2023]
Abstract
Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos. Current studies have illustrated several pioneer factors as being important for agricultural animals, but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear. By employing low-input DNase-seq (liDNase-seq), we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development. Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos. Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos, whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts. Furthermore, KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos. In addition, we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation, whereas knockdown of KLF4 disrupted this process. Taken together, our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.
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Affiliation(s)
- Wei Zhu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Guowei Bu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lianyong Qiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Qiao Li
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taotao Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Shichun Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Jiaqi Guan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xiaoyu Chu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Juanjuan Shi
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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17
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Tu Z, Bi Y, Mao T, Wang H, Gao S, Wang Y. Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:35. [PMID: 37938437 PMCID: PMC10632355 DOI: 10.1186/s13619-023-00179-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Naïve pluripotent state can be obtained by several strategies from various types of cells, in which the cell fate roadmap as well as key biological events involved in the journey have been described in detail. Here, we carefully explored the chromatin accessibility dynamics during the primed-to-naïve transition by adopting a dual fluorescent reporter system and the assay for transposase-accessible chromatin (ATAC)-seq. Our results revealed critical chromatin remodeling events and highlight the discordance between chromatin accessibility and transcriptional activity. We further demonstrate that the differential epigenetic modifications and transcription factor (TF) activities may play a critical role in regulating gene expression, and account for the observed variations in gene expression despite similar chromatin landscapes.
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Affiliation(s)
- Zhifen Tu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yan Bi
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tengyan Mao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hong Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Yixuan Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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18
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Liao R, Wu Y, Qin L, Jiang Z, Gou S, Zhou L, Hong Q, Li Y, Shi J, Yao Y, Lai L, Li Y, Liu P, Thiery JP, Qin D, Graf T, Liu X, Li P. BCL11B and the NuRD complex cooperatively guard T-cell fate and inhibit OPA1-mediated mitochondrial fusion in T cells. EMBO J 2023; 42:e113448. [PMID: 37737560 PMCID: PMC10620766 DOI: 10.15252/embj.2023113448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
The nucleosome remodeling and histone deacetylase (NuRD) complex physically associates with BCL11B to regulate murine T-cell development. However, the function of NuRD complex in mature T cells remains unclear. Here, we characterize the fate and metabolism of human T cells in which key subunits of the NuRD complex or BCL11B are ablated. BCL11B and the NuRD complex bind to each other and repress natural killer (NK)-cell fate in T cells. In addition, T cells upregulate the NK cell-associated receptors and transcription factors, lyse NK-cell targets, and are reprogrammed into NK-like cells (ITNKs) upon deletion of MTA2, MBD2, CHD4, or BCL11B. ITNKs increase OPA1 expression and exhibit characteristically elongated mitochondria with augmented oxidative phosphorylation (OXPHOS) activity. OPA1-mediated elevated OXPHOS enhances cellular acetyl-CoA levels, thereby promoting the reprogramming efficiency and antitumor effects of ITNKs via regulating H3K27 acetylation at specific targets. In conclusion, our findings demonstrate that the NuRD complex and BCL11B cooperatively maintain T-cell fate directly by repressing NK cell-associated transcription and indirectly through a metabolic-epigenetic axis, providing strategies to improve the reprogramming efficiency and antitumor effects of ITNKs.
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Affiliation(s)
- Rui Liao
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yi Wu
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Le Qin
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Zhiwu Jiang
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Shixue Gou
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Linfu Zhou
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Qilan Hong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
- Centre for Genomic RegulationThe Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Yao Li
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Jingxuan Shi
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yao Yao
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Liangxue Lai
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
| | - Yangqiu Li
- Institute of HematologyMedical College, Jinan UniversityGuangzhouChina
| | - Pentao Liu
- School of Biomedical Sciences, Stem Cell and Regenerative Medicine Consortium, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | | | - Dajiang Qin
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Thomas Graf
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
- Centre for Genomic RegulationThe Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Xingguo Liu
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & InnovationChinese Academy of SciencesHong Kong SARChina
| | - Peng Li
- China‐New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, GIBH‐HKU Guangdong‐Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH‐CUHK Joint Research Laboratory on Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouChina
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & InnovationChinese Academy of SciencesHong Kong SARChina
- Department of SurgeryThe Chinese University of Hong KongHong Kong SARChina
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19
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Zhong H, Zhang R, Li G, Huang P, Zhang Y, Zhu J, Kuang J, Hutchins AP, Qin D, Zhu P, Pei D, Li D. c-JUN is a barrier in hESC to cardiomyocyte transition. Life Sci Alliance 2023; 6:e202302121. [PMID: 37604584 PMCID: PMC10442936 DOI: 10.26508/lsa.202302121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
Loss of c-JUN leads to early mouse embryonic death, possibly because of a failure to develop a normal cardiac system. How c-JUN regulates human cardiomyocyte cell fate remains unknown. Here, we used the in vitro differentiation of human pluripotent stem cells into cardiomyocytes to study the role of c-JUN. Surprisingly, the knockout of c-JUN improved cardiomyocyte generation, as determined by the number of TNNT2+ cells. ATAC-seq data showed that the c-JUN defect led to increased chromatin accessibility on critical regulatory elements related to cardiomyocyte development. ChIP-seq data showed that the knockout c-JUN increased RBBP5 and SETD1B expression, leading to improved H3K4me3 deposition on key genes that regulate cardiogenesis. The c-JUN KO phenotype could be copied using the histone demethylase inhibitor CPI-455, which also up-regulated H3K4me3 levels and increased cardiomyocyte generation. Single-cell RNA-seq data defined three cell branches, and knockout c-JUN activated more regulons that are related to cardiogenesis. In summary, our data demonstrated that c-JUN could regulate cardiomyocyte cell fate by modulating H3K4me3 modification and chromatin accessibility and shed light on how c-JUN regulates heart development in humans.
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Affiliation(s)
- Hui Zhong
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ran Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Guihuan Li
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Yudan Zhang
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jieying Zhu
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Dajiang Qin
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences; Hong Kong, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease and Guangzhou Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Dongwei Li
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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20
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Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560808. [PMID: 37873116 PMCID: PMC10592962 DOI: 10.1101/2023.10.04.560808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ectopic expression of OCT4, SOX2, KLF4 and MYC (OSKM) transforms differentiated cells into induced pluripotent stem cells. To refine our mechanistic understanding of reprogramming, especially during the early stages, we profiled chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of human fibroblast reprogramming. Using neural networks that map DNA sequence to ATAC-seq profiles at base-resolution, we annotated cell-state-specific predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of Tn5-bias corrected TF footprints, linked peaks to putative target genes, and elucidated rewiring of TF-to-gene cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution, connect TF stoichiometry and motif syntax to diversification of cell fate trajectories, and provide new perspectives on the dynamics and role of transient regulatory elements in somatic silencing.
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Affiliation(s)
- Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jacob Schreiber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - David Burns
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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21
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Maresca M, van den Brand T, Li H, Teunissen H, Davies J, de Wit E. Pioneer activity distinguishes activating from non-activating SOX2 binding sites. EMBO J 2023; 42:e113150. [PMID: 37691488 PMCID: PMC10577566 DOI: 10.15252/embj.2022113150] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 09/12/2023] Open
Abstract
Genome-wide transcriptional activity involves the binding of many transcription factors (TFs) to thousands of sites in the genome. Pioneer TFs are a class of TFs that maintain open chromatin and allow non-pioneer TFs access to their target sites. Determining which TF binding sites directly drive transcription remains a challenge. Here, we use acute protein depletion of the pioneer TF SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of the pioneer factor. To understand the relationship with transcription, we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted mainly at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
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Affiliation(s)
- Michela Maresca
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Teun van den Brand
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hangpeng Li
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Hans Teunissen
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Elzo de Wit
- Division of Gene RegulationThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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22
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Li D, Luo L, Guo L, Wu C, Zhang R, Peng Y, Wu M, Kuang J, Li Y, Zhang Y, Xie J, Xie W, Mao R, Ma G, Fu X, Chen J, Hutchins AP, Pei D. c-Jun as a one-way valve at the naive to primed interface. Cell Biosci 2023; 13:191. [PMID: 37838693 PMCID: PMC10576270 DOI: 10.1186/s13578-023-01141-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND c-Jun is a proto-oncogene functioning as a transcription factor to activate gene expression under many physiological and pathological conditions, particularly in somatic cells. However, its role in early embryonic development remains unknown. RESULTS Here, we show that c-Jun acts as a one-way valve to preserve the primed state and impair reversion to the naïve state. c-Jun is induced during the naive to primed transition, and it works to stabilize the chromatin structure and inhibit the reverse transition. Loss of c-Jun has surprisingly little effect on the naïve to primed transition, and no phenotypic effect on primed cells, however, in primed cells the loss of c-Jun leads to a failure to correctly close naïve-specific enhancers. When the primed cells are induced to reprogram to a naïve state, these enhancers are more rapidly activated when c-Jun is lost or impaired, and the conversion is more efficient. CONCLUSIONS The results of this study indicate that c-Jun can function as a chromatin stabilizer in primed EpiSCs, to maintain the epigenetic cell type state and act as a one-way valve for cell fate conversions.
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Affiliation(s)
- Dongwei Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, 190 Kaiyuan Dadao, Huangpu District, Guangzhou, 510799, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Ling Luo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Lin Guo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chuman Wu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ran Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510100, Guangdong, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Yuling Peng
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, 190 Kaiyuan Dadao, Huangpu District, Guangzhou, 510799, China
| | - Menghua Wu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, 190 Kaiyuan Dadao, Huangpu District, Guangzhou, 510799, China
| | - Junqi Kuang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yan Li
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yudan Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jun Xie
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Wenxiu Xie
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Rui Mao
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiekai Chen
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Yunqi Town, No.18 Longshan Street, Xihu District, Hangzhou, 310024, China.
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23
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Phan QM, Salz L, Kindl SS, Lopez JS, Thompson SM, Makkar J, Driskell IM, Driskell RR. Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation. EMBO J 2023; 42:e113880. [PMID: 37602956 PMCID: PMC10548174 DOI: 10.15252/embj.2023113880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the epigenetic mechanisms that regulate DFP differentiation are not known. Our objective was to use multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanism that governs its differentiation potential. Our initial results indicated that the overall transcription profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage-specific genes. Surprisingly, the repressive chromatin profile of DFPs renders them unable to reform the skin in allograft assays despite their multipotent potential. We hypothesized that chromatin derepression was modulated by the H3K27me3 demethylase, Kdm6b/Jmjd3. Dermal fibroblast-specific deletion of Kdm6b/Jmjd3 in mice resulted in adipocyte compartment ablation and inhibition of mature dermal papilla functions, confirmed by additional single-cell RNA-seq, ChIP-seq, and allografting assays. We conclude that DFPs are functionally derepressed during murine skin development by Kdm6b/Jmjd3. Our studies therefore reveal a multimodal understanding of how DFPs differentiate into distinct fibroblast lineages and provide a novel publicly available multiomics search tool.
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Affiliation(s)
- Quan M Phan
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Lucia Salz
- North Rhine‐Westphalia Technical University of AachenAachenGermany
| | - Sam S Kindl
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Jayden S Lopez
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Sean M Thompson
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Jasson Makkar
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Iwona M Driskell
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Ryan R Driskell
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
- Center for Reproductive BiologyWashington State UniversityPullmanWAUSA
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24
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Hu H, Ho D, Tan DS, MacCarthy C, Yu CH, Weng M, Schöler H, Jauch R. Evaluation of the determinants for improved pluripotency induction and maintenance by engineered SOX17. Nucleic Acids Res 2023; 51:8934-8956. [PMID: 37607832 PMCID: PMC10516664 DOI: 10.1093/nar/gkad597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023] Open
Abstract
An engineered SOX17 variant with point mutations within its DNA binding domain termed SOX17FNV is a more potent pluripotency inducer than SOX2, yet the underlying mechanism remains unclear. Although wild-type SOX17 was incapable of inducing pluripotency, SOX17FNV outperformed SOX2 in mouse and human pluripotency reprogramming. In embryonic stem cells, SOX17FNV could replace SOX2 to maintain pluripotency despite considerable sequence differences and upregulated genes expressed in cleavage-stage embryos. Mechanistically, SOX17FNV co-bound OCT4 more cooperatively than SOX2 in the context of the canonical SoxOct DNA element. SOX2, SOX17, and SOX17FNV were all able to bind nucleosome core particles in vitro, which is a prerequisite for pioneer transcription factors. Experiments using purified proteins and in cellular contexts showed that SOX17 variants phase-separated more efficiently than SOX2, suggesting an enhanced ability to self-organise. Systematic deletion analyses showed that the N-terminus of SOX17FNV was dispensable for its reprogramming activity. However, the C-terminus encodes essential domains indicating multivalent interactions that drive transactivation and reprogramming. We defined a minimal SOX17FNV (miniSOX) that can support reprogramming with high activity, reducing the payload of reprogramming cassettes. This study uncovers the mechanisms behind SOX17FNV-induced pluripotency and establishes engineered SOX factors as powerful cell engineering tools.
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Affiliation(s)
- Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Cheng-han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
| | | | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong
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25
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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26
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Weng M, Hu H, Graus MS, Tan DS, Gao Y, Ren S, Ho DHH, Langer J, Holzner M, Huang Y, Ling GS, Lai CSW, Francois M, Jauch R. An engineered Sox17 induces somatic to neural stem cell fate transitions independently from pluripotency reprogramming. SCIENCE ADVANCES 2023; 9:eadh2501. [PMID: 37611093 PMCID: PMC10446497 DOI: 10.1126/sciadv.adh2501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Advanced strategies to interconvert cell types provide promising avenues to model cellular pathologies and to develop therapies for neurological disorders. Yet, methods to directly transdifferentiate somatic cells into multipotent induced neural stem cells (iNSCs) are slow and inefficient, and it is unclear whether cells pass through a pluripotent state with full epigenetic reset. We report iNSC reprogramming from embryonic and aged mouse fibroblasts as well as from human blood using an engineered Sox17 (eSox17FNV). eSox17FNV efficiently drives iNSC reprogramming while Sox2 or Sox17 fail. eSox17FNV acquires the capacity to bind different protein partners on regulatory DNA to scan the genome more efficiently and has a more potent transactivation domain than Sox2. Lineage tracing and time-resolved transcriptomics show that emerging iNSCs do not transit through a pluripotent state. Our work distinguishes lineage from pluripotency reprogramming with the potential to generate more authentic cell models for aging-associated neurodegenerative diseases.
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Affiliation(s)
- Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthew S. Graus
- The David Richmond Laboratory for Cardiovascular Development: Gene Regulation and Editing Program, The Centenary Institute, Camperdown, NSW 2006, Australia
- Genome Imaging Centre, The Centenary Institute, Camperdown, NSW 2006, Australia
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shimiao Ren
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Jakob Langer
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Markus Holzner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhua Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Guang Sheng Ling
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cora Sau Wan Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Cognitive and Brain Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mathias Francois
- The David Richmond Laboratory for Cardiovascular Development: Gene Regulation and Editing Program, The Centenary Institute, Camperdown, NSW 2006, Australia
- Genome Imaging Centre, The Centenary Institute, Camperdown, NSW 2006, Australia
- The University of Sydney, School of Medical Sciences, Camperdown, NSW 2006, Australia
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
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27
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Chen X, Lu Y, Wang L, Ma X, Pu J, Lin L, Deng Q, Li Y, Wang W, Jin Y, Hu Z, Zhou Z, Chen G, Jiang L, Wang H, Zhao X, He X, Fu J, Russ HA, Li W, Zhu S. A fast chemical reprogramming system promotes cell identity transition through a diapause-like state. Nat Cell Biol 2023; 25:1146-1156. [PMID: 37550515 DOI: 10.1038/s41556-023-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
Cellular reprogramming by only small molecules holds enormous potentials for regenerative medicine. However, chemical reprogramming remains a slow process and labour intensive, hindering its broad applications and the investigation of underlying molecular mechanisms. Here, through screening of over 21,000 conditions, we develop a fast chemical reprogramming (FCR) system, which significantly improves the kinetics of cell identity rewiring. We find that FCR rapidly goes through an interesting route for pluripotent reprogramming, uniquely transitioning through a developmentally diapause-like state. Furthermore, FCR critically enables comprehensive characterizations using multi-omics technologies, and has revealed unexpected important features including key regulatory factors and epigenetic dynamics. Particularly, activation of pluripotency-related endogenous retroviruses via inhibition of heterochromatin significantly enhances reprogramming. Our studies provide critical insights into how only environmental cues are sufficient to rapidly reinstate pluripotency in somatic cells, and make notable technical and conceptual advances for solving the puzzle of regeneration.
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Affiliation(s)
- Xi Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yunkun Lu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Ma
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Jiaqi Pu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Lianyu Lin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Qian Deng
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yuhan Li
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Weiyun Wang
- Institute of Regenerative Medicine and Orthopedics, Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Yan Jin
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Zhensheng Hu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Ziyu Zhou
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Guo Chen
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Liling Jiang
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hao Wang
- Hangzhou Women's Hospital, Prenatal Diagnosis Center, Hangzhou, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiangwei He
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junfen Fu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Childhealth, Hangzhou, China
| | - Holger A Russ
- Department of Pharmacology and Therapeutics, School of Medicine, University of Florida, Gainesville, FL, USA
- Diabetes Institute, School of Medicine, University of Florida, Gainesville, FL, USA
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Saiyong Zhu
- The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China.
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28
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Louis TL, Wong WH, Yao P, Kurd NS, Tysl T, Indralingam CS, Ma S, Huang WJM, Chang JT. Regulation of CD8 T Cell Differentiation by the RNA-Binding Protein DDX5. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:241-251. [PMID: 37265401 PMCID: PMC10373580 DOI: 10.4049/jimmunol.2200778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
The RNA-binding protein DEAD-box protein 5 (DDX5) is a polyfunctional regulator of gene expression, but its role in CD8+ T cell biology has not been extensively investigated. In this study, we demonstrate that deletion of DDX5 in murine CD8+ T cells reduced the differentiation of terminal effector, effector memory T, and terminal effector memory cells while increasing the generation of central memory T cells, whereas forced expression of DDX5 elicited the opposite phenotype. DDX5-deficient CD8+ T cells exhibited increased expression of genes that promote central memory T cell differentiation, including Tcf7 and Eomes. Taken together, these findings reveal a role for DDX5 in regulating the differentiation of effector and memory CD8+ T cell subsets in response to microbial infection.
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Affiliation(s)
- Tiani L. Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - William H. Wong
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, USA
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29
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Fu X, Zhuang Q, Babarinde IA, Shi L, Ma G, Hu H, Li Y, Chen J, Xiao Z, Deng B, Sun L, Jauch R, Hutchins AP. Restricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner. Cell Death Discov 2023; 9:245. [PMID: 37452056 PMCID: PMC10349098 DOI: 10.1038/s41420-023-01533-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Somatic cell reprogramming and oncogenic transformation share surprisingly similar features, yet transformed cells are resistant to reprogramming. Epigenetic barriers must block transformed cells from reprogramming, but the nature of those barriers is unclear. In this study, we generated a systematic panel of transformed mouse embryonic fibroblasts (MEFs) using oncogenic transgenes and discovered transformed cell lines compatible with reprogramming when transfected with Oct4/Sox2/Klf4/Myc. By comparing the reprogramming-capable and incapable transformed lines we identified multiple stages of failure in the reprogramming process. Some transformed lines failed at an early stage, whilst other lines seemed to progress through a conventional reprogramming process. Finally, we show that MEK inhibition overcomes one critical reprogramming barrier by indirectly suppressing a hyperacetylated active epigenetic state. This study reveals that diverse epigenetic barriers underly resistance to reprogramming of transformed cells.
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Affiliation(s)
- Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiang Zhuang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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30
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Lv T, Jiang S, Wang X, Hou Y. Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level. Heliyon 2023; 9:e18133. [PMID: 37519753 PMCID: PMC10375800 DOI: 10.1016/j.heliyon.2023.e18133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Mouse somatic cells can be reprogrammed into induced pluripotent stem cells through a highly heterogeneous process regulated by numerous biological factors, including adenosine-to-inosine (A-to-I) RNA editing. In this study, we analyzed A-to-I RNA editing sites using a single-cell RNA sequencing (scRNA-seq) dataset with high-depth and full-length coverage. Our method revealed that A-to-I RNA editing frequency varied widely at the single-cell level and underwent dynamic changes. We also found that A-to-I RNA editing level was correlated with the expression of the RNA editing enzyme ADAR1. The analysis combined with gene ontology (GO) enrichment revealed that ADAR1-dependent A-to-I editing may downregulate the expression levels of Igtp, Irgm2, Mndal, Ifi202b, and Tapbp in the early stage, to inhibit the pathways of cellular response to interferon-beta and regulation of protein complex stability to promote mesenchymal-epithelial transition (MET). Notably, we identified a negative correlation between A-to-I RNA editing frequency and the expression of certain genes, such as Nras, Ube2l6, Zfp987, and Adsl.
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Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
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31
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Yu X, Wang Y, Song Y, Gao X, Deng H. AP-1 is a regulatory transcription factor of inflammaging in the murine kidney and liver. Aging Cell 2023; 22:e13858. [PMID: 37154113 PMCID: PMC10352569 DOI: 10.1111/acel.13858] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
Aging is characterized by chronic low-grade inflammation in multiple tissues, also termed "inflammaging", which represents a significant risk factor for many aging-related chronic diseases. However, the mechanisms and regulatory networks underlying inflammaging across different tissues have not yet been fully elucidated. Here, we profiled the transcriptomes and epigenomes of the kidney and liver from young and aged mice and found that activation of the inflammatory response is a conserved signature in both tissues. Moreover, we revealed links between transcriptome changes and chromatin dynamics through integrative analysis and identified AP-1 and ETS family transcription factors (TFs) as potential regulators of inflammaging. Further in situ validation showed that c-JUN (a member of the AP-1 family) was mainly activated in aged renal and hepatic cells, while increased SPI1 (a member of the ETS family) was mostly induced by elevated infiltration of macrophages, indicating that these TFs have different mechanisms in inflammaging. Functional data demonstrated that genetic knockdown of Fos, a major member of the AP-1 family, significantly attenuated the inflammatory response in aged kidneys and livers. Taken together, our results revealed conserved signatures and regulatory TFs of inflammaging in the kidney and liver, providing novel targets for the development of anti-aging interventions.
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Affiliation(s)
- Xiaojie Yu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yuting Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yifan Song
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Xianda Gao
- School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingChina
| | - Hongkui Deng
- The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
- School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingChina
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32
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Gong W, Dsouza N, Garry DJ. SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors. Genome Biol 2023; 24:125. [PMID: 37218013 DOI: 10.1186/s13059-023-02954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
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Affiliation(s)
- Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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33
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Wang B, Li C, Ming J, Wu L, Fang S, Huang Y, Lin L, Liu H, Kuang J, Zhao C, Huang X, Feng H, Guo J, Yang X, Guo L, Zhang X, Chen J, Liu J, Zhu P, Pei D. The NuRD complex cooperates with SALL4 to orchestrate reprogramming. Nat Commun 2023; 14:2846. [PMID: 37208322 DOI: 10.1038/s41467-023-38543-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. Here, we report that chromatin remodeling complex NuRD participates in closing open chromatin in the early phase of somatic reprogramming. Sall4, Jdp2, Glis1 and Esrrb can reprogram MEFs to iPSCs efficiently, but only Sall4 is indispensable capable of recruiting endogenous components of NuRD. Yet knocking down NuRD components only reduces reprogramming modestly, in contrast to disrupting the known Sall4-NuRD interaction by mutating or deleting the NuRD interacting motif at its N-terminus that renders Sall4 inept to reprogram. Remarkably, these defects can be partially rescured by grafting NuRD interacting motif onto Jdp2. Further analysis of chromatin accessibility dynamics demonstrates that the Sall4-NuRD axis plays a critical role in closing the open chromatin in the early phase of reprogramming. Among the chromatin loci closed by Sall4-NuRD encode genes resistant to reprogramming. These results identify a previously unrecognized role of NuRD in reprogramming, and may further illuminate chromatin closing as a critical step in cell fate control.
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Affiliation(s)
- Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chen Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Wu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shicai Fang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Joint School of Life Science, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yi Huang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Joint School of Life Science, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lihui Lin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences, Guangzhou, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences, Guangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xingnan Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huijian Feng
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Guo
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Xuejie Yang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Liman Guo
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Xiaofei Zhang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Jing Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
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Missinato MA, Murphy S, Lynott M, Yu MS, Kervadec A, Chang YL, Kannan S, Loreti M, Lee C, Amatya P, Tanaka H, Huang CT, Puri PL, Kwon C, Adams PD, Qian L, Sacco A, Andersen P, Colas AR. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells. Nat Commun 2023; 14:1709. [PMID: 36973293 PMCID: PMC10043290 DOI: 10.1038/s41467-023-37256-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury.
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Affiliation(s)
- Maria A Missinato
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sean Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michael S Yu
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anaïs Kervadec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yu-Ling Chang
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mafalda Loreti
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Christopher Lee
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Prashila Amatya
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Hiroshi Tanaka
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chun-Teng Huang
- Viral Vector Core Facility Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peter D Adams
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Li Qian
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alessandra Sacco
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter Andersen
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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35
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Rani R, Nayak M, Nayak B. Exploring the reprogramming potential of B cells and comprehending its clinical and therapeutic perspective. Transpl Immunol 2023; 78:101804. [PMID: 36921730 DOI: 10.1016/j.trim.2023.101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023]
Abstract
Initiating from multipotent progenitors, the lineages extrapolated from hematopoietic stem cells are determined by transcription factors specific to each of them. The commitment factors assist in the differentiation of progenitor cells into terminally differentiated cells. B lymphocytes constitute a population of cells that expresses clonally diverse cell surface immunoglobulin (Ig) receptors specific to antigenic epitopes. B cells are a significant facet of the adaptive immune system. The secreted antibodies corresponding to the B cell recognize the antigens via the B cell receptor (BCR). Following antigen recognition, the B cell is activated and thereafter undergoes clonal expansion and proliferation to become memory B cells. The essence of 'cellular reprogramming' has aided in reliably altering the cells to desired tissue type. The potential of reprogramming has been harnessed to decipher and find solutions for various genetically inherited diseases and degenerative disorders. B lymphocytes can be reprogrammed to their initial naive state from where they get differentiated into any lineage or cell type similar to a pluripotent stem cell which can be accomplished by the deletion of master regulators of the B cell lineage. B cells can be reprogrammed into pluripotent stem cells and also can undergo transdifferentiation at the midway of cell differentiation to other cell types. Mandated expression of C/EBP in specialized B cells corresponds to their fast and effective reprogramming into macrophages, reversing the cell fate of these lymphocytes and allowing them to differentiate freshly into other types of cells. The co-expression of C/EBPα and OKSM (Oct4, Sox2, Klf4, c-Myc) amplified the reprogramming efficiency of B lymphocytes. Various human somatic cells including the immune cells are compliant to reprogramming which paves a path for opportunities like autologous tissue grafts, blood transfusion, and cancer immunotherapy. The ability to reprogram B cells offers an unprecedented opportunity for developing a therapeutic approach for several human diseases. Here, we will focus on all the proteins and transcription factors responsible for the developmental commitment of B lymphocytes and how it is harnessed in various applications.
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Affiliation(s)
- Reetika Rani
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha. 769008, India
| | - Madhusmita Nayak
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha. 769008, India
| | - Bismita Nayak
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha. 769008, India.
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36
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Phan QM, Salz L, Kindl SS, Lopez JS, Thompson SM, Makkar J, Driskell IM, Driskell RR. Lineage Commitment of Dermal Fibroblast Progenitors is Mediated by Chromatin De-repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531478. [PMID: 36945417 PMCID: PMC10028926 DOI: 10.1101/2023.03.07.531478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the mechanisms that regulate lineage commitment of naive dermal progenitors to form niches around the hair follicle, dermis, and hypodermis, are unknown. In our study, we used multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanisms that govern its differentiation potential. Our results indicate that the overall chromatin profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage specific genes. Surprisingly, the repressed chromatin profile of DFPs renders them unable to reform skin in allograft assays despite their multipotent potential. Distinct fibroblast lineages, such as the dermal papilla and adipocytes contained specific chromatin profiles that were de-repressed during late embryogenesis by the H3K27-me3 demethylase, Kdm6b/Jmjd3. Tissue-specific deletion of Kdm6b/Jmjd3 resulted in ablating the adipocyte compartment and inhibiting mature dermal papilla functions in single-cell-RNA-seq, ChIPseq, and allografting assays. Altogether our studies reveal a mechanistic multimodal understanding of how DFPs differentiate into distinct fibroblast lineages, and we provide a novel multiomic search-tool within skinregeneration.org.
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Affiliation(s)
- Quan M. Phan
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Lucia Salz
- North Rhine-Westphalia Technical University of Aachen, Aachen, Germany
| | - Sam S. Kindl
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Jayden S. Lopez
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Sean M. Thompson
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Jasson Makkar
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Iwona M. Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Ryan R. Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA
- Center for Reproductive Biology, Washington State University, Pullman, WA
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37
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Jin L, He J, Feng H, Li S, Liu H, Dong H, Hu M, Huang J, Wu H, Chen J, Qi L, Wu K. Transposable elements activation triggers necroptosis in mouse embryonic stem cells. Cell Death Dis 2023; 14:184. [PMID: 36882393 PMCID: PMC9992707 DOI: 10.1038/s41419-023-05705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
Deficiency of the histone H3K9 methyltransferase SETDB1 induces RIPK3-dependent necroptosis in mouse embryonic stem cells (mESCs). However, how necroptosis pathway is activated in this process remains elusive. Here we report that the reactivation of transposable elements (TEs) upon SETDB1 knockout is responsible for the RIPK3 regulation through both cis and trans mechanisms. IAPLTR2_Mm and MMERVK10c-int, both of which are suppressed by SETDB1-dependent H3K9me3, act as enhancer-like cis-regulatory elements and their RIPK3 nearby members enhance RIPK3 expression when SETDB1 is knockout. Moreover, reactivated endogenous retroviruses generate excessive viral mimicry, which promotes necroptosis mainly through Z-DNA-binding protein 1 (ZBP1). These results indicate TEs play an important role in regulating necroptosis.
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Affiliation(s)
- Lingmei Jin
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,Guangzhou Laboratory, Guangzhou, 510005, Guangdong Province, China
| | - Huijian Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sa Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Hongzhi Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - MingLi Hu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Junju Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Haoyu Wu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
| | - Ling Qi
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.
| | - Kaixin Wu
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
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38
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May D, Yun S, Gonzalez DG, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez LE, Cockburn K, Greco V. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. eLife 2023; 12:83444. [PMID: 36880644 PMCID: PMC10027315 DOI: 10.7554/elife.83444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/06/2023] [Indexed: 03/08/2023] Open
Abstract
Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of Keratin-10 (K10) nascent RNA, which marks the onset of stem cell differentiation, we find that Keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.
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Affiliation(s)
- Dennis May
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Sangwon Yun
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - David G Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Sangbum Park
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Institute for Quantitative Health Science & Engineering (IQ), Michigan State University, East Lansing, United States
- Division of Dermatology, Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, United States
- Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, United States
| | - Yanbo Chen
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Elizabeth Lathrop
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Biao Cai
- Department of Biostatistics, Yale University School of Public Health, New Haven, United States
| | - Tianchi Xin
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Department of Biostatistics, Yale University School of Public Health, New Haven, United States
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Deparment of Cell Biology, Yale University School of Medicine, New Haven, United States
| | - Lauren E Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, United States
| | - Katie Cockburn
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Valentina Greco
- Department of Genetics, Yale University School of Medicine, New Haven, United States
- Division of Dermatology, Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, United States
- Departments of Cell Biology and Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, United States
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39
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Li Z, Li Y, Zhang Q, Ge W, Zhang Y, Zhao X, Hu J, Yuan L, Zhang W. Establishment of Bactrian Camel Induced Pluripotent Stem Cells and Prediction of Their Unique Pluripotency Genes. Int J Mol Sci 2023; 24:ijms24031917. [PMID: 36768240 PMCID: PMC9916525 DOI: 10.3390/ijms24031917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) can differentiate into all types of cells and can be used in livestock for research on biological development, genetic breeding, and in vitro genetic resource conservation. The Bactrian camel is a large domestic animal that inhabits extreme environments and holds value in the treatment of various diseases and the development of the local economy. Therefore, we transferred four mouse genes (Oct4, Sox2, Klf4, and c-Myc) into Bactrian camel fetal fibroblasts (BCFFs) using retroviruses with a large host range to obtain Bactrian camel induced pluripotent stem cells (bciPSCs). They were comprehensively identified based on cell morphology, pluripotency gene and marker expression, chromosome number, transcriptome sequencing, and differentiation potential. The results showed the pluripotency of bciPSCs. However, unlike stem cells of other species, late formation of stem cell clones was observed; moreover, the immunofluorescence of SSEA1, SSEA3, and SSEA4 were positive, and teratoma formation took four months. These findings may be related to the extremely long gestation period and species specificity of Bactrian camels. By mining RNA sequence data, 85 potential unique pluripotent genes of Bactrian camels were predicted, which could be used as candidate genes for the production of bciPSC in the future. Among them, ASF1B, DTL, CDCA5, PROM1, CYTL1, NUP210, Epha3, and SYT13 are more attractive. In conclusion, we generated bciPSCs for the first time and obtained their transcriptome information, expanding the iPSC genetic information database and exploring the applicability of iPSCs in livestock. Our results can provide an experimental basis for Bactrian camel ESC establishment, developmental research, and genetic resource conservation.
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Affiliation(s)
- Zongshuai Li
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
| | - Yina Li
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
| | - Qiran Zhang
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenbo Ge
- Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Lanzhou 730070, China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence:
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
| | - Junjie Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Gansu Agricultural University, Lanzhou 730070, China
| | - Ligang Yuan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Wangdong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
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Peng J, Zhang WJ, Zhang Q, Su YH, Tang LP. The dynamics of chromatin states mediated by epigenetic modifications during somatic cell reprogramming. Front Cell Dev Biol 2023; 11:1097780. [PMID: 36727112 PMCID: PMC9884706 DOI: 10.3389/fcell.2023.1097780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Somatic cell reprogramming (SCR) is the conversion of differentiated somatic cells into totipotent or pluripotent cells through a variety of methods. Somatic cell reprogramming also provides a platform to investigate the role of chromatin-based factors in establishing and maintaining totipotency or pluripotency, since high expression of totipotency- or pluripotency-related genes usually require an active chromatin state. Several studies in plants or mammals have recently shed light on the molecular mechanisms by which epigenetic modifications regulate the expression of totipotency or pluripotency genes by altering their chromatin states. In this review, we present a comprehensive overview of the dynamic changes in epigenetic modifications and chromatin states during reprogramming from somatic cells to totipotent or pluripotent cells. In addition, we illustrate the potential role of DNA methylation, histone modifications, histone variants, and chromatin remodeling during somatic cell reprogramming, which will pave the way to developing reliable strategies for efficient cellular reprogramming.
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Affiliation(s)
| | | | | | - Ying Hua Su
- *Correspondence: Ying Hua Su, ; Li Ping Tang,
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41
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Sevinç K, Sevinç GG, Cavga AD, Philpott M, Kelekçi S, Can H, Cribbs AP, Yıldız AB, Yılmaz A, Ayar ES, Arabacı DH, Dunford JE, Ata D, Sigua LH, Qi J, Oppermann U, Onder TT. BRD9-containing non-canonical BAF complex maintains somatic cell transcriptome and acts as a barrier to human reprogramming. Stem Cell Reports 2022; 17:2629-2642. [PMID: 36332631 PMCID: PMC9768578 DOI: 10.1016/j.stemcr.2022.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Epigenetic reprogramming to pluripotency requires extensive remodeling of chromatin landscapes to silence existing cell-type-specific genes and activate pluripotency genes. ATP-dependent chromatin remodeling complexes are important regulators of chromatin structure and gene expression; however, the role of recently identified Bromodomain-containing protein 9 (BRD9) and the associated non-canonical BRG1-associated factors (ncBAF) complex in reprogramming remains unknown. Here, we show that genetic or chemical inhibition of BRD9, as well as ncBAF complex subunit GLTSCR1, but not the closely related BRD7, increase human somatic cell reprogramming efficiency and can replace KLF4 and c-MYC. We find that BRD9 is dispensable for human induced pluripotent stem cells under primed but not under naive conditions. Mechanistically, BRD9 inhibition downregulates fibroblast-related genes and decreases chromatin accessibility at somatic enhancers. BRD9 maintains the expression of transcriptional regulators MN1 and ZBTB38, both of which impede reprogramming. Collectively, these results establish BRD9 as an important safeguarding factor for somatic cell identity whose inhibition lowers chromatin-based barriers to reprogramming.
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Affiliation(s)
- Kenan Sevinç
- School of Medicine, Koç University, Istanbul, Turkey
| | | | - Ayşe Derya Cavga
- School of Medicine, Koç University, Istanbul, Turkey; Biostatistics, Bioinformatics and Data Management Core, KUTTAM, Koç University, Istanbul, Turkey
| | - Martin Philpott
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | - Simge Kelekçi
- School of Medicine, Koç University, Istanbul, Turkey
| | - Hazal Can
- School of Medicine, Koç University, Istanbul, Turkey
| | - Adam P Cribbs
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | | | | | | | | | - James E Dunford
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK
| | - Deniz Ata
- School of Medicine, Koç University, Istanbul, Turkey
| | - Logan H Sigua
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRU, University of Oxford, Oxford, UK; Centre for Medicine Discovery, University of Oxford, Oxford, UK; Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford OX3 7LD, UK
| | - Tamer T Onder
- School of Medicine, Koç University, Istanbul, Turkey.
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42
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The influence of high-order chromatin state in the regulation of stem cell fate. Biochem Soc Trans 2022; 50:1809-1822. [DOI: 10.1042/bst20220763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, genomic DNA is hierarchically compacted by histones into chromatin, which is initially assembled by the nucleosome and further folded into orderly and flexible structures that include chromatin fiber, chromatin looping, topologically associated domains (TADs), chromosome compartments, and chromosome territories. These distinct structures and motifs build the three-dimensional (3D) genome architecture, which precisely controls spatial and temporal gene expression in the nucleus. Given that each type of cell is characterized by its own unique gene expression profile, the state of high-order chromatin plays an essential role in the cell fate decision. Accumulating evidence suggests that the plasticity of high-order chromatin is closely associated with stem cell fate. In this review, we summarize the biological roles of the state of high-order chromatin in embryogenesis, stem cell differentiation, the maintenance of stem cell identity, and somatic cell reprogramming. In addition, we highlight the roles of epigenetic factors and pioneer transcription factors (TFs) involved in regulating the state of high-order chromatin during the determination of stem cell fate and discuss how H3K9me3-heterochromatin restricts stem cell fate. In summary, we review the most recent progress in research on the regulatory functions of high-order chromatin dynamics in the determination and maintenance of stem cell fate.
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Larcombe MR, Hsu S, Polo JM, Knaupp AS. Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200015. [PMID: 36911290 PMCID: PMC9993476 DOI: 10.1002/ggn2.202200015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 06/18/2023]
Abstract
Transcription factors (TFs) are the master regulators of cellular identity, capable of driving cell fate transitions including differentiations, reprogramming, and transdifferentiations. Pioneer TFs recognize partial motifs exposed on nucleosomal DNA, allowing for TF-mediated activation of repressed chromatin. Moreover, there is evidence suggesting that certain TFs can repress actively expressed genes either directly through interactions with accessible regulatory elements or indirectly through mechanisms that impact the expression, activity, or localization of other regulatory factors. Recent evidence suggests that during reprogramming, the reprogramming TFs initiate opening of chromatin regions rich in somatic TF motifs that are inaccessible in the initial and final cellular states. It is postulated that analogous to a sponge, these transiently accessible regions "soak up" somatic TFs, hence lowering the initial barriers to cell fate changes. This indirect TF-mediated gene regulation event, which is aptly named the "sponge effect," may play an essential role in the silencing of the somatic transcriptional network during different cellular conversions.
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Affiliation(s)
- Michael R. Larcombe
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Sheng Hsu
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
| | - Jose M. Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
- Adelaide Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth Australia5005Australia
| | - Anja S. Knaupp
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonVictoria3168Australia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoria3168Australia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoria3168Australia
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44
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Lin R, Zhai Z, Kuang J, Wu C, Yao Y, Shi R, He J, Xu S, Li P, Fan Y, Li W, Wu Z, Li X, Ming J, Guo J, Wang B, Li D, Cao S, Zhang X, Li Y, Pei D, Liu J. H3K27ac mediated SS18/BAFs relocation regulates JUN induced pluripotent-somatic transition. Cell Biosci 2022; 12:89. [PMID: 35710570 PMCID: PMC9204951 DOI: 10.1186/s13578-022-00827-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/05/2022] [Indexed: 12/16/2022] Open
Abstract
Background The exit from pluripotency or pluripotent-somatic transition (PST) landmarks an event of early mammalian embryonic development, representing a model for cell fate transition. Results In this study, using a robust JUN-induced PST within 8 h as a model, we investigate the chromatin accessibility dynamics (CAD) as well as the behaviors of corresponding chromatin remodeling complex SS18/BAFs, to probe the key events at the early stage of PST. Here, we report that, JUN triggers the open of 34661 chromatin sites within 4 h, accomplished with the activation of somatic genes, such as Anxa1, Fosl1. ChIP-seq data reveal a rapid relocation of SS18/BAFs from pluripotent loci to AP-1 associated ones. Consistently, the knockdown of Brg1, core component of BAF complexes, leads to failure in chromatin opening but not closing, resulting in delay for JUN induced PST. Notably, the direct interaction between SS18/BAFs and JUN-centric protein complexes is undetectable by IP-MS. Instead, we show that H3K27ac deposited by cJUN dependent process regulates SS18/BAFs complex to AP1-containing loci and facilitate chromatin opening and gene activation. Conclusions These results reveal a rapid transfer of chromatin remodeling complexes BAF from pluripotent to somatic loci during PST, revealing a simple mechanistic aspect of cell fate control. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00827-1.
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Davis JL, Kennedy C, Clerkin S, Treacy NJ, Dodd T, Moss C, Murphy A, Brazil DP, Cagney G, Brougham DF, Murad R, Finlay D, Vuori K, Crean J. Single-cell multiomics reveals the complexity of TGFβ signalling to chromatin in iPSC-derived kidney organoids. Commun Biol 2022; 5:1301. [PMID: 36435939 PMCID: PMC9701233 DOI: 10.1038/s42003-022-04264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
TGFβ1 plays a regulatory role in the determination of renal cell fate and the progression of renal fibrosis. Here we show an association between SMAD3 and the histone methyltransferase, EZH2, during cell differentiation; ChIP-seq revealed that SMAD3 and EZH2 co-occupy the genome in iPSCs and in iPSC-derived nephron progenitors. Through integration of single cell gene expression and epigenome profiling, we identified de novo ACTA2+ve/POSTN+ve myofibroblasts in kidney organoids treated with TGFβ1, characterised by increased SMAD3-dependent cis chromatin accessibility and gene expression associated with fibroblast activation. We have identified fibrosis-associated regulons characterised by enrichment of SMAD3, AP1, the ETS family of transcription factors, and NUAK1, CREB3L1, and RARG, corresponding to enriched motifs at accessible loci identified by scATACseq. Treatment with the EZH2 specific inhibitor GSK343, blocked SMAD3-dependent cis co-accessibility and inhibited myofibroblast activation. This mechanism, through which TGFβ signals directly to chromatin, represents a critical determinant of fibrotic, differentiated states.
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Affiliation(s)
- Jessica L. Davis
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Ciaran Kennedy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Shane Clerkin
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Niall J. Treacy
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Thomas Dodd
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Catherine Moss
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Alison Murphy
- grid.7886.10000 0001 0768 2743UCD Genomics Core Facility, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Derek P. Brazil
- grid.4777.30000 0004 0374 7521Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, BT9 7BL Northern Ireland, UK
| | - Gerard Cagney
- grid.7886.10000 0001 0768 2743UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Dermot F. Brougham
- grid.7886.10000 0001 0768 2743UCD School of Chemistry, University College Dublin, Belfield, Dublin, 4 Ireland
| | - Rabi Murad
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Darren Finlay
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - Kristiina Vuori
- grid.479509.60000 0001 0163 8573Sanford Burnham Prebys Institute for Medical Discovery, La Jolla, CA 92037 USA
| | - John Crean
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, 4, Ireland.
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Zhang Y, He F, Zhang Y, Dai Q, Li Q, Nan J, Miao R, Cheng B. Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9. Mob DNA 2022; 13:25. [DOI: 10.1186/s13100-022-00279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Krüppel Associated Box-containing Zinc Finger Proteins (KRAB-ZFPs), representing the largest superfamily of transcription factors in mammals, are predicted to primarily target and repress transposable elements (TEs). It is challenging to dissect the distinct functions of these transcription regulators due to their sequence similarity and diversity, and also the complicated repetitiveness of their targeting TE sequences.
Results
Mouse KRAB-Zfps are mainly organized into clusters genomewide. In this study, we revealed that the intra-cluster members had a close evolutionary relationship, and a similar preference for zinc finger (ZnF) usage. KRAB-Zfps were expressed in a cell type- or tissue type specific manner and they tended to be actively transcribed together with other cluster members. Further sequence analyses pointed out the linker sequences in between ZnFs were conserved, and meanwhile had distinct cluster specificity. Based on these unique characteristics of KRAB-Zfp clusters, sgRNAs were designed to edit cluster-specific linkers to abolish the functions of the targeted cluster(s). Using mouse embryonic stem cells (mESC) as a model, we screened and obtained a series of sgRNAs targeting various highly expressed KRAB-Zfp clusters. The effectiveness of sgRNAs were verified in a reporter assay exclusively developed for multi-target sgRNAs and further confirmed by PCR-based analyses. Using mESC cell lines inducibly expressing Cas9 and these sgRNAs, we found that editing different KRAB-Zfp clusters resulted in the transcriptional changes of distinct categories of TEs.
Conclusions
Collectively, the intrinsic sequence correlations of intra-cluster KRAB-Zfp members discovered in this study suggest that the conserved cluster specific linkers played crucial roles in diversifying the tandem ZnF array and the related target specificity of KRAB-Zfps during clusters’ evolution. On this basis, an effective CRISPR-Cas9 based approach against the linker sequences is developed and verified for rapidly editing KRAB-Zfp clusters to identify the regulatory correlation between the cluster members and their potential TE targets.
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47
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Tomikawa J, Miyamoto K. Structural alteration of the nucleus for the reprogramming of gene expression. FEBS J 2022; 289:7221-7233. [PMID: 33891358 DOI: 10.1111/febs.15894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 01/13/2023]
Abstract
The regulation of gene expression is a critical process for establishing and maintaining cellular identity. Gene expression is controlled through a chromatin-based mechanism in the nucleus of eukaryotic cells. Recent studies suggest that chromatin accessibility and the higher-order structure of chromatin affect transcriptional outcome. This is especially evident when cells change their fate during development and nuclear reprogramming. Furthermore, non-chromosomal contents of the cell nucleus, namely nucleoskeleton proteins, can also affect chromatin and nuclear structures, resulting in transcriptional alterations. Here, we review our current mechanistic understanding about how chromatin and nuclear structures impact transcription in the course of embryonic development, cellular differentiation and nuclear reprogramming, and also discuss unresolved questions that remain to be addressed in the field.
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Affiliation(s)
- Junko Tomikawa
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kei Miyamoto
- Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
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48
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Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression. Mol Cell 2022; 82:3333-3349.e9. [PMID: 35981542 PMCID: PMC9481721 DOI: 10.1016/j.molcel.2022.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023]
Abstract
The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gaylor Boulay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gabriel Golczer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Marcelo Stanzione
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Soroush Hajizadeh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Meagan B Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity. Nat Cell Biol 2022; 24:1350-1363. [PMID: 36075976 PMCID: PMC9481462 DOI: 10.1038/s41556-022-00986-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/27/2022] [Indexed: 12/22/2022]
Abstract
Coordinated changes of cellular plasticity and identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvolute the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and reveal how the two processes intersect before they bifurcate. This approach led us to identify the transcription factor Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming and transformation. Multiomics characterization of these intermediates unveiled a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains reprogramming, transformation and transdifferentiation. Mechanistically, we found that Atoh8 restrains cellular plasticity, independent of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology. Huyghe, Furlan et al. compare pluripotent reprogramming with oncogenic transformation and identify Bcl11b and Atoh8 as regulators of cellular plasticity in both processes, thus offering a unifying theory on the factors constraining cell fate changes.
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50
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Kuang J, Huang T, Pei D. The Art of Reprogramming for Regenerative Medicine. Front Cell Dev Biol 2022; 10:927555. [PMID: 35846373 PMCID: PMC9280648 DOI: 10.3389/fcell.2022.927555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional pharmaceuticals in the forms of small chemical compounds or macromolecules such as proteins or RNAs have provided lifesaving solutions to many acute and chronic conditions to date. However, there are still many unmet medical needs, especially those of degenerative nature. The advent of cell-based therapy holds the promise to meet these challenges. In this review, we highlight a relatively new paradigm for generating or regenerating functional cells for replacement therapy against conditions such as type I diabetes, myocardial infarction, neurodegenerative diseases and liver fibrosis. We focus on the latest progresses in cellular reprogramming for generating diverse functional cell types. We will also discuss the mechanisms involved and conclude with likely general principles underlying reprogramming.
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Affiliation(s)
- Junqi Kuang
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tao Huang
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Duanqing Pei
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- *Correspondence: Duanqing Pei,
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