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Yin T, Wang G, Wang L, Mudgal P, Wang E, Pan CC, Alexander PB, Wu H, Cao C, Liang Y, Tan L, Huang D, Chong M, Chen R, Lim BJW, Xiang K, Xue W, Wan L, Hu H, Loh YH, Wang XF, Li QJ. Breaking NGF-TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection. Nat Immunol 2024; 25:268-281. [PMID: 38195702 DOI: 10.1038/s41590-023-01723-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Melanoma cells, deriving from neuroectodermal melanocytes, may exploit the nervous system's immune privilege for growth. Here we show that nerve growth factor (NGF) has both melanoma cell intrinsic and extrinsic immunosuppressive functions. Autocrine NGF engages tropomyosin receptor kinase A (TrkA) on melanoma cells to desensitize interferon γ signaling, leading to T and natural killer cell exclusion. In effector T cells that upregulate surface TrkA expression upon T cell receptor activation, paracrine NGF dampens T cell receptor signaling and effector function. Inhibiting NGF, either through genetic modification or with the tropomyosin receptor kinase inhibitor larotrectinib, renders melanomas susceptible to immune checkpoint blockade therapy and fosters long-term immunity by activating memory T cells with low affinity. These results identify the NGF-TrkA axis as an important suppressor of anti-tumor immunity and suggest larotrectinib might be repurposed for immune sensitization. Moreover, by enlisting low-affinity T cells, anti-NGF reduces acquired resistance to immune checkpoint blockade and prevents melanoma recurrence.
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Affiliation(s)
- Tao Yin
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Guoping Wang
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Ergang Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Christopher C Pan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | | | | | | | - Yaosi Liang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - De Huang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Mengyang Chong
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Rui Chen
- Hervor Therapeutics, Hangzhou, China
| | - Bryan Jian Wei Lim
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Kun Xiang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Wei Xue
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lixin Wan
- Department of Molecular Oncology and Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Hailan Hu
- Zhejiang University School of Brain Science and Brain Medicine, Hangzhou, China
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xiao-Fan Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
| | - Qi-Jing Li
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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2
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Bao Q, Tay NL, Lim CY, Chua DHH, Kee SK, Choolani M, Loh YH, Ng SC, Chai C. Integration-free induced pluripotent stem cells from three endangered Southeast Asian non-human primate species. Sci Rep 2024; 14:2391. [PMID: 38287040 PMCID: PMC10825216 DOI: 10.1038/s41598-023-50510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024] Open
Abstract
Advanced molecular and cellular technologies provide promising tools for wildlife and biodiversity conservation. Induced pluripotent stem cell (iPSC) technology offers an easily accessible and infinite source of pluripotent stem cells, and have been derived from many threatened wildlife species. This paper describes the first successful integration-free reprogramming of adult somatic cells to iPSCs, and their differentiation, from three endangered Southeast Asian primates: the Celebes Crested Macaque (Macaca nigra), the Lar Gibbon (Hylobates lar), and the Siamang (Symphalangus syndactylus). iPSCs were also generated from the Proboscis Monkey (Nasalis larvatus). Differences in mechanisms could elicit new discoveries regarding primate evolution and development. iPSCs from endangered species provides a safety net in conservation efforts and allows for sustainable sampling for research and conservation, all while providing a platform for the development of further in vitro models of disease.
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Affiliation(s)
- Qiuye Bao
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Nicole Liling Tay
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Christina Yingyan Lim
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | | | - Su Keyau Kee
- Cytogenetics Laboratory, Department of Pathology, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Soon Chye Ng
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.
- Sincere Healthcare Group, 8 Sinaran Drive, Singapore, 307470, Singapore.
| | - Chou Chai
- Institute of Molecular and Cell Biology-Endangered Species Conservation By Assisted Reproduction (IMCB-ESCAR) Joint Laboratory, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
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3
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Ng MSF, Kwok I, Tan L, Shi C, Cerezo-Wallis D, Tan Y, Leong K, Calvo GF, Yang K, Zhang Y, Jin J, Liong KH, Wu D, He R, Liu D, Teh YC, Bleriot C, Caronni N, Liu Z, Duan K, Narang V, Ballesteros I, Moalli F, Li M, Chen J, Liu Y, Liu L, Qi J, Liu Y, Jiang L, Shen B, Cheng H, Cheng T, Angeli V, Sharma A, Loh YH, Tey HL, Chong SZ, Iannacone M, Ostuni R, Hidalgo A, Ginhoux F, Ng LG. Deterministic reprogramming of neutrophils within tumors. Science 2024; 383:eadf6493. [PMID: 38207030 DOI: 10.1126/science.adf6493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Neutrophils are increasingly recognized as key players in the tumor immune response and are associated with poor clinical outcomes. Despite recent advances characterizing the diversity of neutrophil states in cancer, common trajectories and mechanisms governing the ontogeny and relationship between these neutrophil states remain undefined. Here, we demonstrate that immature and mature neutrophils that enter tumors undergo irreversible epigenetic, transcriptional, and proteomic modifications to converge into a distinct, terminally differentiated dcTRAIL-R1+ state. Reprogrammed dcTRAIL-R1+ neutrophils predominantly localize to a glycolytic and hypoxic niche at the tumor core and exert pro-angiogenic function that favors tumor growth. We found similar trajectories in neutrophils across multiple tumor types and in humans, suggesting that targeting this program may provide a means of enhancing certain cancer immunotherapies.
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Affiliation(s)
- Melissa S F Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Changming Shi
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daniela Cerezo-Wallis
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- National Skin Centre, National Healthcare Group, Singapore
| | - Keith Leong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Gabriel F Calvo
- Department of Mathematics & MOLAB-Mathematical Oncology Laboratory, University of Castilla-La Mancha, Ciudad Real, Spain
| | - Katharine Yang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yuning Zhang
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology Program, Life Science Institute, National University of Singapore, Singapore
| | - Jingsi Jin
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ka Hang Liong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Dandan Wu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui He
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dehua Liu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Camille Bleriot
- INSERM U1015, Institut Gustave Roussy, Villejuif, France
- CNRS UMR8253, Institut Necker des Enfants Malades, Paris, France
| | - Nicoletta Caronni
- Genomics of the Innate Immune System Unit, San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Vipin Narang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Iván Ballesteros
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Federica Moalli
- Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mengwei Li
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yao Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Jingjing Qi
- Department of Biliary and Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Cancer Biology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingbin Liu
- Department of Biliary and Pancreatic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Cancer Biology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Veronique Angeli
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology Program, Life Science Institute, National University of Singapore, Singapore
| | - Ankur Sharma
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore
| | - Hong Liang Tey
- National Skin Centre, National Healthcare Group, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Renato Ostuni
- Genomics of the Innate Immune System Unit, San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- INSERM U1015, Institut Gustave Roussy, Villejuif, France
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, National University of Singapore, Singapore
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4
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Viswanathan R, Cheruba E, Wong PM, Yi Y, Ngang S, Chong DQ, Loh YH, Tan IB, Cheow LF. DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA. Sci Adv 2023; 9:eadi0197. [PMID: 37713482 PMCID: PMC10881072 DOI: 10.1126/sciadv.adi0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the most abundant DNA modifications that have important roles in gene regulation. Detailed studies of these different epigenetic marks aimed at understanding their combined effects and dynamic interconversion are, however, hampered by the inability of current methods to simultaneously measure both modifications, particularly in samples with limited quantities. We present DNA analysis by restriction enzyme for simultaneous detection of multiple epigenomic states (DARESOME), an assay based on modification-sensitive restriction digest and sequential tag ligation that can concurrently perform quantitative profiling of unmodified cytosine, 5mC, and 5hmC in CCGG sites genome-wide. DARESOME reveals the opposing roles of 5mC and 5hmC in gene expression regulation as well as their interconversion during aging in mouse brain. Implementation of DARESOME in single cells demonstrates pronounced 5hmC strand bias that reflects the semiconservative replication of DNA. Last, we showed that DARESOME enables integrative genomic, 5mC, and 5hmC profiling of cell-free DNA that uncovered multiomics cancer signatures in liquid biopsy.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yao Yi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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5
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Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH. Single-nucleus multiomic mapping of m 6A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. Mol Cell 2023; 83:S1097-2765(23)00649-4. [PMID: 37657444 PMCID: PMC10895704 DOI: 10.1016/j.molcel.2023.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/21/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, single-cell technologies for analyzing m6A heterogeneity are not extensively established. Here, we developed single-nucleus m6A-CUT&Tag (sn-m6A-CT) for simultaneous profiling of m6A methylomes and transcriptomes within a single nucleus using mouse embryonic stem cells (mESCs). m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high-throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and insights into epitranscriptomic landscape in defining cell fate identity and states.
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Affiliation(s)
- Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
| | - Ka Wai Wong
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Jia Hao Jackie Teo
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Minh T N Le
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Department of Surgery, Immunology Program, Cancer Program, and Nanomedicine Translational Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Graduate School's Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore, Singapore.
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6
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Murray A, Gough G, Cindrić A, Vučković F, Koschut D, Borelli V, Petrović DJ, Bekavac A, Plećaš A, Hribljan V, Brunmeir R, Jurić J, Pučić-Baković M, Slana A, Deriš H, Frkatović A, Groet J, O'Brien NL, Chen HY, Yeap YJ, Delom F, Havlicek S, Gammon L, Hamburg S, Startin C, D'Souza H, Mitrečić D, Kero M, Odak L, Krušlin B, Krsnik Ž, Kostović I, Foo JN, Loh YH, Dunn NR, de la Luna S, Spector T, Barišić I, Thomas MSC, Strydom A, Franceschi C, Lauc G, Krištić J, Alić I, Nižetić D. Dose imbalance of DYRK1A kinase causes systemic progeroid status in Down syndrome by increasing the un-repaired DNA damage and reducing LaminB1 levels. EBioMedicine 2023; 94:104692. [PMID: 37451904 PMCID: PMC10435767 DOI: 10.1016/j.ebiom.2023.104692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND People with Down syndrome (DS) show clinical signs of accelerated ageing. Causative mechanisms remain unknown and hypotheses range from the (essentially untreatable) amplified-chromosomal-instability explanation, to potential actions of individual supernumerary chromosome-21 genes. The latter explanation could open a route to therapeutic amelioration if the specific over-acting genes could be identified and their action toned-down. METHODS Biological age was estimated through patterns of sugar molecules attached to plasma immunoglobulin-G (IgG-glycans, an established "biological-ageing-clock") in n = 246 individuals with DS from three European populations, clinically characterised for the presence of co-morbidities, and compared to n = 256 age-, sex- and demography-matched healthy controls. Isogenic human induced pluripotent stem cell (hiPSCs) models of full and partial trisomy-21 with CRISPR-Cas9 gene editing and two kinase inhibitors were studied prior and after differentiation to cerebral organoids. FINDINGS Biological age in adults with DS is (on average) 18.4-19.1 years older than in chronological-age-matched controls independent of co-morbidities, and this shift remains constant throughout lifespan. Changes are detectable from early childhood, and do not require a supernumerary chromosome, but are seen in segmental duplication of only 31 genes, along with increased DNA damage and decreased levels of LaminB1 in nucleated blood cells. We demonstrate that these cell-autonomous phenotypes can be gene-dose-modelled and pharmacologically corrected in hiPSCs and derived cerebral organoids. Using isogenic hiPSC models we show that chromosome-21 gene DYRK1A overdose is sufficient and necessary to cause excess unrepaired DNA damage. INTERPRETATION Explanation of hitherto observed accelerated ageing in DS as a developmental progeroid syndrome driven by DYRK1A overdose provides a target for early pharmacological preventative intervention strategies. FUNDING Main funding came from the "Research Cooperability" Program of the Croatian Science Foundation funded by the European Union from the European Social Fund under the Operational Programme Efficient Human Resources 2014-2020, Project PZS-2019-02-4277, and the Wellcome Trust Grants 098330/Z/12/Z and 217199/Z/19/Z (UK). All other funding is described in details in the "Acknowledgements".
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Affiliation(s)
- Aoife Murray
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK.
| | - Gillian Gough
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ana Cindrić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Frano Vučković
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - David Koschut
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Disease Intervention Technology Laboratory (DITL), Institute of Molecular and Cellular Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Vincenzo Borelli
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Italy
| | - Dražen J Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia; Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Bekavac
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ante Plećaš
- Faculty of Veterinary Medicine, Department of Anatomy, Histology and Embryology, University of Zagreb, Zagreb, Croatia
| | - Valentina Hribljan
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Reinhard Brunmeir
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Julija Jurić
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Anita Slana
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Helena Deriš
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Azra Frkatović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jűrgen Groet
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK
| | - Niamh L O'Brien
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK
| | - Hong Yu Chen
- Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Yee Jie Yeap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Frederic Delom
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Steven Havlicek
- Laboratory of Neurogenetics, Genome Institute of Singapore, A∗STAR, Singapore
| | - Luke Gammon
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Sarah Hamburg
- The London Down Syndrome Consortium (LonDownS), London, UK
| | - Carla Startin
- The London Down Syndrome Consortium (LonDownS), London, UK; Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Division of Psychiatry, University College London, London, UK; School of Psychology, University of Roehampton, London, UK
| | - Hana D'Souza
- The London Down Syndrome Consortium (LonDownS), London, UK; Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK
| | - Dinko Mitrečić
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Mijana Kero
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ljubica Odak
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Božo Krušlin
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ivica Kostović
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Laboratory of Neurogenetics, Genome Institute of Singapore, A∗STAR, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Norris Ray Dunn
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Institute of Molecular and Cell Biology (IMCB), A∗STAR, Singapore
| | - Susana de la Luna
- ICREA, Genome Biology Programme (CRG), Universitat Pompeu Fabra (UPF), CIBER of Rare Diseases, Barcelona, Spain
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ingeborg Barišić
- Department of Medical Genetics, Children's Hospital Zagreb, Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael S C Thomas
- The London Down Syndrome Consortium (LonDownS), London, UK; Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK
| | - Andre Strydom
- The London Down Syndrome Consortium (LonDownS), London, UK; Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Division of Psychiatry, University College London, London, UK
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Italy; Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia; Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Alić
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; Faculty of Veterinary Medicine, Department of Anatomy, Histology and Embryology, University of Zagreb, Zagreb, Croatia.
| | - Dean Nižetić
- Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK; The London Down Syndrome Consortium (LonDownS), London, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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7
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Yi Y, Zeng Y, Sam TW, Hamashima K, Tan RJR, Warrier T, Phua JX, Taneja R, Liou YC, Li H, Xu J, Loh YH. Ribosomal proteins regulate 2-cell-stage transcriptome in mouse embryonic stem cells. Stem Cell Reports 2023; 18:463-474. [PMID: 36638791 PMCID: PMC9968990 DOI: 10.1016/j.stemcr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
A rare sub-population of mouse embryonic stem cells (mESCs), the 2-cell-like cell, is defined by the expression of MERVL and 2-cell-stage-specific transcript (2C transcript). Here, we report that the ribosomal proteins (RPs) RPL14, RPL18, and RPL23 maintain the identity of mESCs and regulate the expression of 2C transcripts. Disregulation of the RPs induces DUX-dependent expression of 2C transcripts and alters the chromatin landscape. Mechanically, knockdown (KD) of RPs triggers the binding of RPL11 to MDM2, an interaction known to prevent P53 protein degradation. Increased P53 protein upon RP KD further activates its downstream pathways, including DUX. Our study delineates the critical roles of RPs in 2C transcript activation, ascribing a novel function to these essential proteins.
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Affiliation(s)
- Yao Yi
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Rachel Jun Rou Tan
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jun Xiang Phua
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore; Joint Center for Single Cell Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore.
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8
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Perlin JR, Anderson WJ, Bartfeld S, Couturier A, de Soysa Y, Hawley RS, Hu P, Loh YH, Mandal L, Master Z, Muotri AR, Piddini E, Polo JM, Mazzoni EO. ISSCR Education Committee syllabus and learning guide for enhancing stem cell literacy. Stem Cell Reports 2023; 18:417-419. [PMID: 36638789 PMCID: PMC9968981 DOI: 10.1016/j.stemcr.2022.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/15/2023] Open
Abstract
The rapidly evolving stem cell field puts much stress on developing educational resources. The ISSCR Education Committee has created a flexible stem cell syllabus rooted in core concepts to facilitate stem cell literacy. The free syllabus will be updated regularly to maintain accuracy and relevance.
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Affiliation(s)
- Julie R Perlin
- International Society for Stem Cell Research, Skokie, IL, USA.
| | | | | | | | | | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ping Hu
- Guangzhou Laboratory, Guangzhou, China
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Lolitika Mandal
- Indian Institute of Science Education and Research Mohali (IISERMohali), Punjab, India
| | | | | | | | - Jose M Polo
- Monash University, Melbourne, VIC, Australia
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9
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Ho BX, Pang JKS, Chen Y, Loh YH, An O, Yang HH, Seshachalam VP, Koh JLY, Chan WK, Ng SY, Soh BS. Robust generation of human-chambered cardiac organoids from pluripotent stem cells for improved modelling of cardiovascular diseases. Stem Cell Res Ther 2022; 13:529. [PMID: 36544188 PMCID: PMC9773542 DOI: 10.1186/s13287-022-03215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tissue organoids generated from human pluripotent stem cells are valuable tools for disease modelling and to understand developmental processes. While recent progress in human cardiac organoids revealed the ability of these stem cell-derived organoids to self-organize and intrinsically formed chamber-like structure containing a central cavity, it remained unclear the processes involved that enabled such chamber formation. METHODS Chambered cardiac organoids (CCOs) differentiated from human embryonic stem cells (H7) were generated by modulation of Wnt/ß-catenin signalling under fully defined conditions, and several growth factors essential for cardiac progenitor expansion. Transcriptomic profiling of day 8, day 14 and day 21 CCOs was performed by quantitative PCR and single-cell RNA sequencing. Endothelin-1 (EDN1) known to induce oxidative stress in cardiomyocytes was used to induce cardiac hypertrophy in CCOs in vitro. Functional characterization of cardiomyocyte contractile machinery was performed by immunofluorescence staining and analysis of brightfield and fluorescent video recordings. Quantitative PCR values between groups were compared using two-tailed Student's t tests. Cardiac organoid parameters comparison between groups was performed using two-tailed Mann-Whitney U test when sample size is small; otherwise, Welch's t test was used. Comparison of calcium kinetics parameters derived from the fluorescent data was performed using two-tailed Student's t tests. RESULTS Importantly, we demonstrated that a threshold number of cardiac progenitor was essential to line the circumference of the inner cavity to ensure proper formation of a chamber within the organoid. Single-cell RNA sequencing revealed improved maturation over a time course, as evidenced from increased mRNA expression of cardiomyocyte maturation genes, ion channel genes and a metabolic shift from glycolysis to fatty acid ß-oxidation. Functionally, CCOs recapitulated clinical cardiac hypertrophy by exhibiting thickened chamber walls, reduced fractional shortening, and increased myofibrillar disarray upon treatment with EDN1. Furthermore, electrophysiological assessment of calcium transients displayed tachyarrhythmic phenotype observed as a consequence of rapid depolarization occurring prior to a complete repolarization. CONCLUSIONS Our findings shed novel insights into the role of progenitors in CCO formation and pave the way for the robust generation of cardiac organoids, as a platform for future applications in disease modelling and drug screening in vitro.
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Affiliation(s)
- Beatrice Xuan Ho
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Jeremy Kah Sheng Pang
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Ying Chen
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore ,grid.4280.e0000 0001 2180 6431Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077 Singapore ,grid.418812.60000 0004 0620 9243Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore
| | - Yuin-Han Loh
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore ,grid.418812.60000 0004 0620 9243Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore
| | - Omer An
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599 Singapore
| | - Henry He Yang
- grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599 Singapore
| | - Veerabrahma Pratap Seshachalam
- grid.510300.7Computational Phenomics Group, Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670 Singapore
| | - Judice L. Y. Koh
- grid.510300.7Computational Phenomics Group, Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670 Singapore
| | - Woon-Khiong Chan
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
| | - Shi Yan Ng
- grid.418812.60000 0004 0620 9243Neurotherapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117456 Singapore ,grid.276809.20000 0004 0636 696XNational Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433 Singapore
| | - Boon Seng Soh
- grid.418812.60000 0004 0620 9243Disease Modelling and Therapeutics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117543 Singapore
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10
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De Los Angeles A, Regenberg A, Mascetti V, Benvenisty N, Church G, Deng H, Izpisua Belmonte JC, Ji W, Koplin J, Loh YH, Niu Y, Pei D, Pera M, Pho N, Pinzon-Arteaga C, Saitou M, Silva JCR, Tao T, Trounson A, Warrier T, Zambidis ET. Why it is important to study human-monkey embryonic chimeras in a dish. Nat Methods 2022; 19:914-919. [PMID: 35879609 PMCID: PMC9780756 DOI: 10.1038/s41592-022-01571-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The study of human–animal chimeras is fraught with technical and ethical challenges. In this Comment, we discuss the importance and future of human–monkey chimera research within the context of current scientific and regulatory obstacles.
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Affiliation(s)
| | - Alan Regenberg
- Johns Hopkins Berman Institute of Bioethics, Johns Hopkins University, Baltimore, MD, USA
| | - Victoria Mascetti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hongkui Deng
- College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | | | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Julian Koplin
- Melbourne Law School, University of Melbourne, Melbourne, Victoria, Australia
- Biomedical Ethics Research Group, Mudoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | | | - Nam Pho
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Carlos Pinzon-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Jose C R Silva
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Tan Tao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Alan Trounson
- Monash University, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Clayton, Victoria, Australia
| | - Tushar Warrier
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Elias T Zambidis
- Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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11
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Warrier T, El Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood MJ, Collins J, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res 2022; 50:7326-7349. [PMID: 35776115 PMCID: PMC9303280 DOI: 10.1093/nar/gkac531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene 'islands' that drive differentiation to other lineages. The 'unearthing' of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
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Affiliation(s)
- Tushar Warrier
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi El Farran
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Benedict Shao Quan Ho
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiuye Bao
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xuezhi Bi
- Proteomics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Infectious Disease Translational Research Programme, National University of Singapore, Singapore 117597, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - James J Collins
- Howard Hughes Medical Institute, Boston, MA 02114, USA
- Institute for Medical Engineering and Science Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 MedicalDrive, Singapore 117456, Singapore
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12
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Goh CJH, Wong JH, El Farran C, Tan BX, Coffill CR, Loh YH, Lane D, Arumugam P. Correction to: Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen. G3 Genes|Genomes|Genetics 2022; 12:6529170. [PMID: 35169844 PMCID: PMC8895985 DOI: 10.1093/g3journal/jkac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Gautam P, Hamashima K, Chen Y, Zeng Y, Makovoz B, Parikh BH, Lee HY, Lau KA, Su X, Wong RCB, Chan WK, Li H, Blenkinsop TA, Loh YH. Multi-species single-cell transcriptomic analysis of ocular compartment regulons. Nat Commun 2021; 12:5675. [PMID: 34584087 PMCID: PMC8478974 DOI: 10.1038/s41467-021-25968-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 09/07/2021] [Indexed: 11/23/2022] Open
Abstract
The retina is a widely profiled tissue in multiple species by single-cell RNA sequencing studies. However, integrative research of the retina across species is lacking. Here, we construct the first single-cell atlas of the human and porcine ocular compartments and study inter-species differences in the retina. In addition to that, we identify putative adult stem cells present in the iris tissue. We also create a disease map of genes involved in eye disorders across compartments of the eye. Furthermore, we probe the regulons of different cell populations, which include transcription factors and receptor-ligand interactions and reveal unique directional signalling between ocular cell types. In addition, we study conservation of regulons across vertebrates and zebrafish to identify common core factors. Here, we show perturbation of KLF7 gene expression during retinal ganglion cells differentiation and conclude that it plays a significant role in the maturation of retinal ganglion cells. A comprehensive analysis of the ocular networks among various tissues is necessary to understand eye physiology in health and disease. Here the authors present a multi-species single-cell transcriptomic atlas consisting of cells of the cornea, iris, ciliary body, neural retina, retinal pigmented epithelium, and choroid.
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Affiliation(s)
- Pradeep Gautam
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Ying Chen
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.,Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Bar Makovoz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhav Harshad Parikh
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Translational Retinal Research Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Hsin Yee Lee
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Katherine Anne Lau
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Xinyi Su
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Translational Retinal Research Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.,Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Raymond C B Wong
- Centre for Eye Research Australia, Melbourne, Vic, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic, Australia.,Shenzhen Eye Hospital, Shenzhen University School of Medicine, Shenzhen, China
| | - Woon-Khiong Chan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.,Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore. .,Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
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14
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Sriram S, Kang NY, Subramanian S, Nandi T, Sudhagar S, Xing Q, Tong GJL, Chen AKL, Srijaya TC, Tan P, Loh YH, Chang YT, Sugii S. Novel live cell fluorescent probe for human-induced pluripotent stem cells highlights early reprogramming population. Stem Cell Res Ther 2021; 12:113. [PMID: 33546754 PMCID: PMC7866770 DOI: 10.1186/s13287-021-02171-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/15/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Despite recent rapid progress in method development and biological understanding of induced pluripotent stem (iPS) cells, there has been a relative shortage of tools that monitor the early reprogramming process into human iPS cells. METHODS We screened the in-house built fluorescent library compounds that specifically bind human iPS cells. After tertiary screening, the selected probe was analyzed for its ability to detect reprogramming cells in the time-dependent manner using high-content imaging analysis. The probe was compared with conventional dyes in different reprogramming methods, cell types, and cell culture conditions. Cell sorting was performed with the fluorescent probe to analyze the early reprogramming cells for their pluripotent characteristics and genome-wide gene expression signatures by RNA-seq. Finally, the candidate reprogramming factor identified was investigated for its ability to modulate reprogramming efficiency. RESULTS We identified a novel BODIPY-derived fluorescent probe, BDL-E5, which detects live human iPS cells at the early reprogramming stage. BDL-E5 can recognize authentic reprogramming cells around 7 days before iPS colonies are formed and stained positive with conventional pluripotent markers. Cell sorting of reprogrammed cells with BDL-E5 allowed generation of an increased number and higher quality of iPS cells. RNA sequencing analysis of BDL-E5-positive versus negative cells revealed early reprogramming patterns of gene expression, which notably included CREB1. Reprogramming efficiency was significantly increased by overexpression of CREB1 and decreased by knockdown of CREB1. CONCLUSION Collectively, BDL-E5 offers a valuable tool for delineating the early reprogramming pathway and clinically applicable commercial production of human iPS cells.
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Affiliation(s)
- Sandhya Sriram
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - Nam-Young Kang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore.,Department of Creative IT Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Subha Subramanian
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore
| | - Samydurai Sudhagar
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Qiaorui Xing
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Gerine Jin-Ling Tong
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Allen Kuan-Liang Chen
- Bioprocessing Technology Institute, A*STAR, 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore.,Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, Singapore, 168752, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Young-Tae Chang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, POSTECH, Pohang, Gyeongbuk, 37673, Republic of Korea.,Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea
| | - Shigeki Sugii
- Fat Metabolism and Stem Cell Group, Singapore Bioimaging Consortium, A*STAR, 11 Biopolis Way, Singapore, 138667, Singapore. .,Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, Singapore, 138669, Singapore.
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15
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Wang HF, Warrier T, Farran CA, Zheng ZH, Xing QR, Fullwood MJ, Zhang LF, Li H, Xu J, Lim TM, Loh YH. Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen. Cell Rep 2020; 33:108309. [PMID: 33113365 DOI: 10.1016/j.celrep.2020.108309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/23/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
cis-regulatory elements (CREs) regulate the expression of genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of their target genes in the cellular native environment. In this study, we perform a features-oriented CRISPR-utilized systematic (FOCUS) screen of OCT4-bound CREs using CRISPR-Cas9 to identify functional enhancers important for pluripotency maintenance in mESCs. From the initial 235 candidates tested, 16 CREs are identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncover a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.
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Affiliation(s)
- Hao Fei Wang
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Tushar Warrier
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi A Farran
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiao Rui Xing
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Melissa J Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore; Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Tit-Meng Lim
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Yuin-Han Loh
- Laboratory for Epigenetics, Stem Cells and Cell Therapy, Programme in Stem Cell, Regenerative Medicine and Aging, A(∗)STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore 117593, Singapore.
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16
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Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CXD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF, Loh YH. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Sci Adv 2020; 6:6/37/eaba1190. [PMID: 32917699 PMCID: PMC7486102 DOI: 10.1126/sciadv.aba1190] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/30/2020] [Indexed: 05/16/2023]
Abstract
Cellular reprogramming suffers from low efficiency especially for the human cells. To deconstruct the heterogeneity and unravel the mechanisms for successful reprogramming, we adopted single-cell RNA sequencing (scRNA-Seq) and single-cell assay for transposase-accessible chromatin (scATAC-Seq) to profile reprogramming cells across various time points. Our analysis revealed that reprogramming cells proceed in an asynchronous trajectory and diversify into heterogeneous subpopulations. We identified fluorescent probes and surface markers to enrich for the early reprogrammed human cells. Furthermore, combinatory usage of the surface markers enabled the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 and a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Together, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part list of the reprogramming machinery.
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Affiliation(s)
- Q R Xing
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chadi A El Farran
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Pradeep Gautam
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yu Song Chuah
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Cheng-Xu Delon Toh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Nam-Young Kang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Singapore 138667, Singapore
- Department of Creative IT Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Shigeki Sugii
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore 138669, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Young-Tae Chang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Singapore 138667, Singapore
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - James J Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Division of Pediatric Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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17
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Xing QR, Farran CAE, Zeng YY, Yi Y, Warrier T, Gautam P, Collins JJ, Xu J, Dröge P, Koh CG, Li H, Zhang LF, Loh YH. Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Res 2020; 30:1027-1039. [PMID: 32699019 PMCID: PMC7397874 DOI: 10.1101/gr.257840.119] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human cells of various lineage origins (BJ, K562, JK1, and Jurkat), and 480 primary cord blood cells undergoing erythroblast differentiation. With the joint profiles, we configured the transcriptional and chromatin accessibility landscapes of discrete cell states, uncovered linked sets of cis-regulatory elements and target genes unique to each state, and constructed interactome and transcription factor (TF)–centered upstream regulatory networks for various cell states.
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Affiliation(s)
- Qiao Rui Xing
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chadi A El Farran
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Ying Ying Zeng
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yao Yi
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Tushar Warrier
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Pradeep Gautam
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - James J Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Cheng-Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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18
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Xing QR, Cipta NO, Hamashima K, Liou YC, Koh CG, Loh YH. Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies. Front Genet 2020; 11:662. [PMID: 32765578 PMCID: PMC7380244 DOI: 10.3389/fgene.2020.00662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/01/2020] [Indexed: 12/30/2022] Open
Abstract
Cellular heterogeneity plays a pivotal role in tissue homeostasis and the disease development of multicellular organisms. To deconstruct the heterogeneity, a multitude of single-cell toolkits measuring various cellular contents, including genome, transcriptome, epigenome, and proteome, have been developed. More recently, multi-omics single-cell techniques enable the capture of molecular footprints with a higher resolution by simultaneously profiling various cellular contents within an individual cell. Integrative analysis of multi-omics datasets unravels the relationships between cellular modalities, builds sophisticated regulatory networks, and provides a holistic view of the cell state. In this review, we summarize the major developments in the single-cell field and review the current state-of-the-art single-cell multi-omic techniques and the bioinformatic tools for integrative analysis.
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Affiliation(s)
- Qiao Rui Xing
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nadia Omega Cipta
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kiyofumi Hamashima
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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19
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Chen Y, Yi Y, Xu J, Chan WK, Loh YH. Re-entering the pluripotent state from blood lineage: promises and pitfalls of blood reprogramming. FEBS Lett 2019; 593:3244-3252. [PMID: 31691960 DOI: 10.1002/1873-3468.13659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022]
Abstract
Blood reprogramming, in which induced pluripotent stem cells (iPSCs) are derived from haematopoietic lineages, has rapidly advanced over the past decade. Since the first report using human blood, haematopoietic cell types from various sources, such as the peripheral bone marrow and cord blood, have been successfully reprogrammed. The volume of blood required has also decreased, from around tens of millilitres to a single finger-prick drop. Besides, while early studies were limited to reprogramming methods relying on viral integration, nonintegrating reprogramming systems for blood lineages have been subsequently established. Together, these improvements have made feasible the future clinical applications of blood-derived iPSCs. Here, we review the progress in blood reprogramming from various perspectives, including the starting materials and subsequent reprogramming strategies. We also discuss the downstream applications of blood-derived iPSCs, highlighting their clinical value in terms of disease modelling and therapeutic development.
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Affiliation(s)
- Ying Chen
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Yao Yi
- Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Woon-Khiong Chan
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Yuin-Han Loh
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, A*STAR Institute of Molecular and Cell Biology, Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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20
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Lee E, Sivalingam J, Lim ZR, Chia G, Shi LG, Roberts M, Loh YH, Reuveny S, Oh SKW. Review: In vitro generation of red blood cells for transfusion medicine: Progress, prospects and challenges. Biotechnol Adv 2018; 36:2118-2128. [PMID: 30273713 DOI: 10.1016/j.biotechadv.2018.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/19/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
In vitro generation of red blood cells (RBCs) has the potential to circumvent the shortfalls in global demand for blood for transfusion applications. The conventional approach for RBC generation has been from differentiation of hematopoietic stem cells (HSCs) derived from cord blood, adult bone marrow or peripheral blood. More recently, RBCs have been generated from human induced pluripotent stem cells (hiPSCs) as well as from immortalized adult erythroid progenitors. In this review, we highlight the recent advances to RBC generation from these different approaches and discuss the challenges and new strategies that can potentially make large-scale in vitro generation of RBCs a feasible approach.
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Affiliation(s)
- Esmond Lee
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Palo Alto, CA 94305, USA.
| | - Jaichandran Sivalingam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore.
| | - Zhong Ri Lim
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore
| | - Gloryn Chia
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore
| | - Low Gin Shi
- Brilliant Research Pte. Ltd, Singapore 139955, Republic of Singapore
| | - Mackenna Roberts
- Oxford-University College London Centre for the Advancement of Sustainable Medical Innovation, University of Oxford, UK
| | - Yuin-Han Loh
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Shaul Reuveny
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore
| | - Steve Kah-Weng Oh
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668, Republic of Singapore
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21
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Fang HT, El Farran CA, Xing QR, Zhang LF, Li H, Lim B, Loh YH. Global H3.3 dynamic deposition defines its bimodal role in cell fate transition. Nat Commun 2018; 9:1537. [PMID: 29670118 PMCID: PMC5906632 DOI: 10.1038/s41467-018-03904-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 03/21/2018] [Indexed: 01/19/2023] Open
Abstract
H3.3 is a histone variant, which is deposited on genebodies and regulatory elements, by Hira, marking active transcription. Moreover, H3.3 is deposited on heterochromatin by Atrx/Daxx complex. The exact role of H3.3 in cell fate transition remains elusive. Here, we investigate the dynamic changes in the deposition of the histone variant H3.3 during cellular reprogramming. H3.3 maintains the identities of the parental cells during reprogramming as its removal at early time-point enhances the efficiency of the process. We find that H3.3 plays a similar role in transdifferentiation to hematopoietic progenitors and neuronal differentiation from embryonic stem cells. Contrastingly, H3.3 deposition on genes associated with the newly reprogrammed lineage is essential as its depletion at the later phase abolishes the process. Mechanistically, H3.3 deposition by Hira, and its K4 and K36 modifications are central to the role of H3.3 in cell fate conversion. Finally, H3.3 safeguards fibroblast lineage by regulating Mapk cascade and collagen synthesis.
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Affiliation(s)
- Hai-Tong Fang
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Chadi A El Farran
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Qiao Rui Xing
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Bing Lim
- Stem Cell and Regenerative Biology Group, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117456, Singapore.
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22
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Sivalingam J, Chen HY, Yang BX, Lim ZR, Lam ATL, Woo TL, Chen AKL, Reuveny S, Loh YH, Oh SKW. Improved erythroid differentiation of multiple human pluripotent stem cell lines in microcarrier culture by modulation of Wnt/β-Catenin signaling. Haematologica 2018. [PMID: 29519863 DOI: 10.3324/haematol.2017.180919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Jaichandran Sivalingam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Hong Yu Chen
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Republic of Singapore
| | - Bin-Xia Yang
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Republic of Singapore
| | - Zhong Ri Lim
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Alan Tin Lun Lam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Tsung Liang Woo
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Allen Kuan-Liang Chen
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Shaul Reuveny
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Steve Kah-Weng Oh
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Republic of Singapore
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23
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Lee E, Lim ZR, Chen HY, Yang BX, Lam ATL, Chen AKL, Sivalingam J, Reuveny S, Loh YH, Oh SKW. Defined Serum-Free Medium for Bioreactor Culture of an Immortalized Human Erythroblast Cell Line. Biotechnol J 2018; 13:e1700567. [PMID: 29330927 DOI: 10.1002/biot.201700567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Anticipated shortages in donated blood supply have prompted investigation of alternative approaches for in vitro production of red blood cells (RBCs), such as expansion of conditional immortalization erythroid progenitors. However, there is a bioprocessing challenge wherein factors promoting maximal cell expansion and growth-limiting inhibitory factors are yet to be investigated. The authors use an erythroblast cell line (ImEry) derived from immortalizing CD71+CD235a+ erythroblast from adult peripheral blood for optimization of expansion culture conditions. Design of experiments (DOE) is used in media formulation to explore relationships and interactive effects between factors which affect cell expansion. Our in-house optimized medium formulation produced significantly higher cell densities (3.62 ± 0.055) × 106 cells mL-1 , n = 3) compared to commercial formulations (2.07 ± 0.055) × 106 cells mL-1 , n = 3; at 209 h culture). Culture media costs per unit of blood is shown to have a 2.96-3.09 times cost reduction. As a proof of principle for scale up, ImEry are expanded in a half-liter stirred-bioreactor under controlled settings. Growth characteristics, metabolic, and molecular profile of the cells are evaluated. ImEry has identical O2 binding capacity to adult erythroblasts. Amino acid supplementation results in further yield improvements. The study serves as a first step for scaling up erythroblast expansion in controlled bioreactors.
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Affiliation(s)
- Esmond Lee
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 265 Campus Drive, Palo Alto, CA, 94305, USA
| | - Zhong Ri Lim
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
| | - Hong-Yu Chen
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138668, Republic of Singapore
| | - Bin Xia Yang
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138668, Republic of Singapore
| | - Alan Tin-Lun Lam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
| | - Allen Kuan-Liang Chen
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
| | - Jaichandran Sivalingam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
| | - Shaul Reuveny
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138668, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
| | - Steve Kah-Weng Oh
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, Centros, Level 4, Singapore, 138668, Republic of Singapore
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24
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Gautam P, Yu T, Loh YH. Regulation of ERVs in pluripotent stem cells and reprogramming. Curr Opin Genet Dev 2017; 46:194-201. [PMID: 28866476 DOI: 10.1016/j.gde.2017.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/28/2017] [Accepted: 07/27/2017] [Indexed: 01/22/2023]
Abstract
Recent advances in our understanding of endogenous retroviruses (ERVs) regulation and its functional aspects have provided us with vast power to unravel its role in the host's genome. Co-evolutionary model of ERVs and Kruppel associated box-Zinc Finger Proteins (KRAB-ZFPs) provides a deeper knowledge of how the genome is shaped during the course of evolution. However, the role of ERVs in normal cellular function still remains an enigma. Here we review studies in recent years with a focus on the role of ERVs in maintaining stemness and cell fate reprogramming, along with the recent discoveries of novel regulatory factors which have been shown to mediate ERV expression in both canonical and non-canonical pathways.
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Affiliation(s)
- Pradeep Gautam
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Tao Yu
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Ageing, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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25
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Mzoughi S, Zhang J, Hequet D, Teo SX, Fang H, Xing QR, Bezzi M, Seah MKY, Ong SLM, Shin EM, Wollmann H, Wong ESM, Al-Haddawi M, Stewart CL, Tergaonkar V, Loh YH, Dunn NR, Messerschmidt DM, Guccione E. PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling. Nat Genet 2017; 49:1354-1363. [PMID: 28740264 DOI: 10.1038/ng.3922] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 06/30/2017] [Indexed: 12/11/2022]
Abstract
The transcriptional network acting downstream of LIF, WNT and MAPK-ERK to stabilize mouse embryonic stem cells (ESCs) in their naive state has been extensively characterized. However, the upstream factors regulating these three signaling pathways remain largely uncharted. PR-domain-containing proteins (PRDMs) are zinc-finger sequence-specific chromatin factors that have essential roles in embryonic development and cell fate decisions. Here we characterize the transcriptional regulator PRDM15, which acts independently of PRDM14 to regulate the naive state of mouse ESCs. Mechanistically, PRDM15 modulates WNT and MAPK-ERK signaling by directly promoting the expression of Rspo1 (R-spondin1) and Spry1 (Sprouty1). Consistent with these findings, CRISPR-Cas9-mediated disruption of PRDM15-binding sites in the Rspo1 and Spry1 promoters recapitulates PRDM15 depletion, both in terms of local chromatin organization and the transcriptional modulation of these genes. Collectively, our findings uncover an essential role for PRDM15 as a chromatin factor that modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency.
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Affiliation(s)
- Slim Mzoughi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jingxian Zhang
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Delphine Hequet
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shun Xie Teo
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Haitong Fang
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Qiao Rui Xing
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Marco Bezzi
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michelle Kay Yi Seah
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Sheena L M Ong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Eun Myoung Shin
- Cancer Science Institute of Singapore (CSI), National University of Singapore, Singapore.,NF-κB Signaling in Human Ailments, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Heike Wollmann
- DNA Sequencing Facility NGS Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Esther S M Wong
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Colin L Stewart
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Vinay Tergaonkar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NF-κB Signaling in Human Ailments, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,National Cancer Centre Singapore, Singapore.,Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - N Ray Dunn
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Daniel M Messerschmidt
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore (CSI), National University of Singapore, Singapore.,National Cancer Centre Singapore, Singapore.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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26
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Chen HY, Tan HK, Loh YH. Derivation of Transgene-Free Induced Pluripotent Stem Cells from a Single Drop of Blood. Curr Protoc Stem Cell Biol 2016; 38:4A.9.1-4A.9.10. [PMID: 27532818 DOI: 10.1002/cpsc.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Human-induced pluripotent stem cells (hiPSCs) have great potential for future use in therapeutic regenerative medicine. Based on the current protocol for deriving hiPSCs, invasive procedures such as skin biopsies and venipuncture are required for obtaining donor samples. Herein, we present a detailed protocol for deriving hiPSCs from human finger-prick (FP) blood. In this method, the transgene-free hiPSCs can be easily generated from only 10 µl of FP blood. The finger-pricked iPSCs (FPiPSCs) show all the pluripotency markers and can be easily differentiated into various cell lineages. The time required for deriving the FPiPSCs is relatively short-10 to 15 days for FP blood expansion and 20 to 30 days for reprogramming. This method can be easily adapted for setting up a large scale iPSC bank as it requires only 10 µl of the donor FP blood, which can be easily collected. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hong Yu Chen
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell, Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Hong-Kee Tan
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell, Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell, Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, 117543, Singapore
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27
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Sivalingam J, Lam ATL, Chen HY, Yang BX, Chen AKL, Reuveny S, Loh YH, Oh SKW. Superior Red Blood Cell Generation from Human Pluripotent Stem Cells Through a Novel Microcarrier-Based Embryoid Body Platform. Tissue Eng Part C Methods 2016; 22:765-80. [PMID: 27392822 DOI: 10.1089/ten.tec.2015.0579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In vitro generation of red blood cells (RBCs) from human embryonic stem cells and human induced pluripotent stem cells appears to be a promising alternate approach to circumvent shortages in donor-derived blood supplies for clinical applications. Conventional methods for hematopoietic differentiation of human pluripotent stem cells (hPSC) rely on embryoid body (EB) formation and/or coculture with xenogeneic cell lines. However, most current methods for hPSC expansion and EB formation are not amenable for scale-up to levels required for large-scale RBC generation. Moreover, differentiation methods that rely on xenogenic cell lines would face obstacles for future clinical translation. In this study, we report the development of a serum-free and chemically defined microcarrier-based suspension culture platform for scalable hPSC expansion and EB formation. Improved survival and better quality EBs generated with the microcarrier-based method resulted in significantly improved mesoderm induction and, when combined with hematopoietic differentiation, resulted in at least a 6-fold improvement in hematopoietic precursor expansion, potentially culminating in a 80-fold improvement in the yield of RBC generation compared to a conventional EB-based differentiation method. In addition, we report efficient terminal maturation and generation of mature enucleated RBCs using a coculture system that comprised primary human mesenchymal stromal cells. The microcarrier-based platform could prove to be an appealing strategy for future scale-up of hPSC culture, EB generation, and large-scale generation of RBCs under defined and xeno-free conditions.
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Affiliation(s)
- Jaichandran Sivalingam
- 1 Stem Cell Group, Bioprocessing Technology Institute , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Alan Tin-Lun Lam
- 1 Stem Cell Group, Bioprocessing Technology Institute , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Hong Yu Chen
- 2 Institute of Molecular and Cellular Biology , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Bin Xia Yang
- 2 Institute of Molecular and Cellular Biology , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Allen Kuan-Liang Chen
- 1 Stem Cell Group, Bioprocessing Technology Institute , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Shaul Reuveny
- 1 Stem Cell Group, Bioprocessing Technology Institute , Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Yuin-Han Loh
- 2 Institute of Molecular and Cellular Biology , Agency for Science, Technology and Research, Singapore, Republic of Singapore .,3 Department of Biological Sciences, National University of Singapore , Singapore, Republic of Singapore
| | - Steve Kah-Weng Oh
- 1 Stem Cell Group, Bioprocessing Technology Institute , Agency for Science, Technology and Research, Singapore, Republic of Singapore
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28
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Toh CX, Chan JW, Chong ZS, Wang H, Guo H, Satapathy S, Ma D, Goh G, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins J, Daley G, Wee K, Farran CEL, Li H, Lim YP, Bard F, Loh YH. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell Rep 2016; 15:2597-607. [DOI: 10.1016/j.celrep.2016.05.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/03/2016] [Accepted: 05/11/2016] [Indexed: 01/02/2023] Open
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29
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Zhang W, Ni P, Mou C, Zhang Y, Guo H, Zhao T, Loh YH, Chen L. Cops2 promotes pluripotency maintenance by Stabilizing Nanog Protein and Repressing Transcription. Sci Rep 2016; 6:26804. [PMID: 27226076 PMCID: PMC4881025 DOI: 10.1038/srep26804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 12/02/2022] Open
Abstract
The COP9 signalosome has been implicated in pluripotency maintenance of human embryonic stem cells. Yet, the mechanism for the COP9 signalosome to regulate pluripotency remains elusive. Through knocking down individual COP9 subunits, we demonstrate that Cops2, but not the whole COP9 signalosome, is essential for pluripotency maintenance in mouse embryonic stem cells. Down-regulation of Cops2 leads to reduced expression of pluripotency genes, slower proliferation rate, G2/M cell cycle arrest, and compromised embryoid differentiation of embryonic stem cells. Cops2 also facilitates somatic cell reprogramming. We further show that Cops2 binds to Nanog protein and prevent the degradation of Nanog by proteasome. Moreover, Cops2 functions as transcriptional corepressor to facilitate pluripotency maintenance. Altogether, our data reveal the essential role and novel mechanisms of Cops2 in pluripotency maintenance.
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Affiliation(s)
- Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Peiling Ni
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chunlin Mou
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yanqin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hongchao Guo
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China.,State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China.,Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Tong Zhao
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Lingyi Chen
- State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China.,State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences, Beijing 100021, China
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Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YFS, Goh GYL, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell 2015; 163:230-45. [PMID: 26365490 DOI: 10.1016/j.cell.2015.08.037] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 07/07/2015] [Accepted: 08/13/2015] [Indexed: 12/25/2022]
Abstract
Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome.
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Affiliation(s)
- Bin Xia Yang
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Chadi A El Farran
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hong Chao Guo
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tao Yu
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hai Tong Fang
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Hao Fei Wang
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sharon Schlesinger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Yu Fen Samantha Seah
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Germaine Yen Lin Goh
- Membrane Traffic Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Suat Peng Neo
- Quantitative Proteomics Group, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Yinghui Li
- Division of Cancer Genetics and Therapeutics, Laboratory of NF-κB Signaling, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vinay Tergaonkar
- Division of Cancer Genetics and Therapeutics, Laboratory of NF-κB Signaling, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Tit-Meng Lim
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Lingyi Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - James J Collins
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, New York, NY 10032, USA
| | - George Q Daley
- Howard Hughes Medical Institute, Boston, MA 02115, USA; Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Frederic A Bard
- Membrane Traffic Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, A(∗)STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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Maury JJP, EL Farran CA, Ng D, Loh YH, Bi X, Bardor M, Choo ABH. RING1B O-GlcNAcylation regulates gene targeting of polycomb repressive complex 1 in human embryonic stem cells. Stem Cell Res 2015; 15:182-9. [DOI: 10.1016/j.scr.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/25/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022] Open
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Faucon PC, Pardee K, Kumar RM, Li H, Loh YH, Wang X. Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions. PLoS One 2014; 9:e102873. [PMID: 25057990 PMCID: PMC4109943 DOI: 10.1371/journal.pone.0102873] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 06/24/2014] [Indexed: 02/04/2023] Open
Abstract
Fully-connected triads (FCTs), such as the Oct4-Sox2-Nanog triad, have been implicated as recurring transcriptional motifs embedded within the regulatory networks that specify and maintain cellular states. To explore the possible connections between FCT topologies and cell fate determinations, we employed computational network screening to search all possible FCT topologies for multistability, a dynamic property that allows the rise of alternate regulatory states from the same transcriptional network. The search yielded a hierarchy of FCTs with various potentials for multistability, including several topologies capable of reaching eight distinct stable states. Our analyses suggested that complete auto-activation is an effective indicator for multistability, and, when gene expression noise was incorporated into the model, the networks were able to transit multiple states spontaneously. Different levels of stochasticity were found to either induce or disrupt random state transitioning with some transitions requiring layovers at one or more intermediate states. Using this framework we simulated a simplified model of induced pluripotency by including constitutive overexpression terms. The corresponding FCT showed random state transitioning from a terminal state to the pluripotent state, with the temporal distribution of this transition matching published experimental data. This work establishes a potential theoretical framework for understanding cell fate determinations by connecting conserved regulatory modules with network dynamics. Our results could also be employed experimentally, using established developmental transcription factors as seeds, to locate cell lineage specification networks by using auto-activation as a cipher.
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Affiliation(s)
- Philippe C. Faucon
- School of Computing, Informatics, Decision Systems Engineering, Arizona State University, Tempe, Arizona, United States of America
| | - Keith Pardee
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, Massachusetts, United States of America
| | - Roshan M. Kumar
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, Massachusetts, United States of America
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CXD, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 2014; 15:92-101. [PMID: 24813856 PMCID: PMC4082735 DOI: 10.1016/j.stem.2014.04.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/28/2014] [Accepted: 04/02/2014] [Indexed: 12/20/2022]
Abstract
Alternative RNA splicing (AS) regulates proteome diversity, including isoform-specific expression of several pluripotency genes. Here, we integrated global gene expression and proteomic analyses and identified a molecular signature suggesting a central role for AS in maintaining human pluripotent stem cell (hPSC) self-renewal. We demonstrate that the splicing factor SFRS2 is an OCT4 target gene required for pluripotency. SFRS2 regulates AS of the methyl-CpG binding protein MBD2, whose isoforms play opposing roles in maintenance of and reprogramming to pluripotency. Although both MDB2a and MBD2c are enriched at the OCT4 and NANOG promoters, MBD2a preferentially interacts with repressive NuRD chromatin remodeling factors and promotes hPSC differentiation, whereas overexpression of MBD2c enhances reprogramming of fibroblasts to pluripotency. The miR-301 and miR-302 families provide additional regulation by targeting SFRS2 and MDB2a. These data suggest that OCT4, SFRS2, and MBD2 participate in a positive feedback loop, regulating proteome diversity in support of hPSC self-renewal and reprogramming.
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Affiliation(s)
- Yu Lu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yuin-Han Loh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA; A(∗)STAR Institute of Molecular and Cell Biology and Department of Biological Sciences, National University of Singapore, Singapore 138673, Singapore
| | - Hu Li
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcella Cesana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jignesh R Parikh
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bioinformatics Program, Boston University, Boston, MA 02115, USA
| | - Nathan Salomonis
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Cheng-Xu Delon Toh
- A(∗)STAR Institute of Molecular and Cell Biology and Department of Biological Sciences, National University of Singapore, Singapore 138673, Singapore
| | - Stelios T Andreadis
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - C John Luckey
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James J Collins
- Howard Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George Q Daley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Pediatric Hematology Oncology, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, MA 02115, USA.
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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Tan HK, Toh CXD, Ma D, Yang B, Liu TM, Lu J, Wong CW, Tan TK, Li H, Syn C, Tan EL, Lim B, Lim YP, Cook SA, Loh YH. Human finger-prick induced pluripotent stem cells facilitate the development of stem cell banking. Stem Cells Transl Med 2014; 3:586-98. [PMID: 24646489 DOI: 10.5966/sctm.2013-0195] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients can be a good model for studying human diseases and for future therapeutic regenerative medicine. Current initiatives to establish human iPSC (hiPSC) banking face challenges in recruiting large numbers of donors with diverse diseased, genetic, and phenotypic representations. In this study, we describe the efficient derivation of transgene-free hiPSCs from human finger-prick blood. Finger-prick sample collection can be performed on a "do-it-yourself" basis by donors and sent to the hiPSC facility for reprogramming. We show that single-drop volumes of finger-prick samples are sufficient for performing cellular reprogramming, DNA sequencing, and blood serotyping in parallel. Our novel strategy has the potential to facilitate the development of large-scale hiPSC banking worldwide.
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Affiliation(s)
- Hong-Kee Tan
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore; Research and Development Unit, National Heart Centre Singapore, Singapore; Stem Cell and Developmental Biology, Genome Institute of Singapore, and Bioinformatics Institute, A*STAR, Singapore; Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA; Health Sciences Authority, Singapore; Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore; Department of Paediatrics, University Children's Medical Institute, National University Hospital, Singapore; Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA; Department of Biochemistry, Yong Loo Lin School of Medicine, Department of Biological Sciences, and NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Duke-NUS Graduate Medical School, Singapore; Royal Brompton Hospital, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom
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Bajpai VK, Mistriotis P, Loh YH, Daley GQ, Andreadis ST. Functional vascular smooth muscle cells derived from human induced pluripotent stem cells via mesenchymal stem cell intermediates. Cardiovasc Res 2012; 96:391-400. [PMID: 22941255 PMCID: PMC3584971 DOI: 10.1093/cvr/cvs253] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 12/12/2022] Open
Abstract
AIMS Smooth muscle cells (SMC) play an important role in vascular homeostasis and disease. Although adult mesenchymal stem cells (MSC) have been used as a source of contractile SMC, they suffer from limited proliferation potential and culture senescence, particularly when originating from older donors. By comparison, human induced pluripotent stem cells (hiPSC) can provide an unlimited source of functional SMC for autologous cell-based therapies and for creating models of vascular disease. Our goal was to develop an efficient strategy to derive functional, contractile SMC from hiPSC. METHODS AND RESULTS We developed a robust, stage-wise, feeder-free strategy for hiPSC differentiation into functional SMC through an intermediate stage of multipotent MSC, which could be coaxed to differentiate into fat, bone, cartilage, and muscle. At this stage, the cells were highly proliferative and displayed higher clonogenic potential and reduced senescence when compared with parental hair follicle mesenchymal stem cells. In addition, when exposed to differentiation medium, the myogenic proteins such as α-smooth muscle actin, calponin, and myosin heavy chain were significantly upregulated and displayed robust fibrillar organization, suggesting the development of a contractile phenotype. Indeed, tissue constructs prepared from these cells exhibited high levels of contractility in response to receptor- and non-receptor-mediated agonists. CONCLUSION We developed an efficient stage-wise strategy that enabled hiPSC differentiation into contractile SMC through an intermediate population of clonogenic and multipotent MSC. The high yield of MSC and SMC derivation suggests that our strategy may facilitate an acquisition of the large numbers of cells required for regenerative medicine or for studying vascular disease pathophysiology.
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MESH Headings
- Actins/metabolism
- Adipogenesis
- Animals
- Biomarkers/metabolism
- Calcium-Binding Proteins/metabolism
- Cell Differentiation/genetics
- Cell Lineage/genetics
- Cell Proliferation
- Cells, Cultured
- Cellular Senescence
- Chondrogenesis
- Coculture Techniques
- Gene Expression Regulation, Developmental
- Genotype
- Humans
- Induced Pluripotent Stem Cells/drug effects
- Induced Pluripotent Stem Cells/metabolism
- Induced Pluripotent Stem Cells/physiology
- Mesenchymal Stem Cells/drug effects
- Mesenchymal Stem Cells/metabolism
- Mesenchymal Stem Cells/physiology
- Mice
- Microfilament Proteins/metabolism
- Muscle Development/genetics
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/physiology
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/physiology
- Myosin Heavy Chains/metabolism
- Osteogenesis
- Phenotype
- Up-Regulation
- Vasoconstriction/drug effects
- Vasoconstrictor Agents/pharmacology
- Calponins
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Affiliation(s)
- Vivek K. Bajpai
- Bioengineering Laboratory, Department of Chemical and Biological Engineering,University of Buffalo, The State University of New York, 908 Furnas Hall, Amherst, NY 14260-4200, USA
| | - Panagiotis Mistriotis
- Bioengineering Laboratory, Department of Chemical and Biological Engineering,University of Buffalo, The State University of New York, 908 Furnas Hall, Amherst, NY 14260-4200, USA
| | - Yuin-Han Loh
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - George Q. Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stelios T. Andreadis
- Bioengineering Laboratory, Department of Chemical and Biological Engineering,University of Buffalo, The State University of New York, 908 Furnas Hall, Amherst, NY 14260-4200, USA
- Department of Biomedical Engineering, University of Buffalo, The State University of New York, Amherst, NY 14260-4200, USA
- Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
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Wen B, Wu H, Loh YH, Briem E, Daley GQ, Feinberg AP. Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions. BMC Genomics 2012; 13:566. [PMID: 23102236 PMCID: PMC3507770 DOI: 10.1186/1471-2164-13-566] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as Large Organized Chromatin K (lysine) modifications (LOCKs), of histone H3 lysine-9 dimethylation (H3K9me2) or other repressive histone posttranslational modifications. The microstructure of these regions has not previously been explored. RESULTS We analyzed the genome-wide distribution of H3K9me2 in two human pluripotent stem cell lines and three differentiated cells lines. We identified > 2,500 small regions with very low H3K9me2 signals in the body of LOCKs, which were termed as euchromatin islands (EIs). EIs are 6.5-fold enriched for DNase I Hypersensitive Sites and 8-fold enriched for the binding of CTCF, the major organizer of higher-order chromatin. Furthermore, EIs are 2-6 fold enriched for differentially DNA-methylated regions associated with tissue types (T-DMRs), reprogramming (R-DMRs) and cancer (C-DMRs). Gene ontology (GO) analysis suggests that EI-associated genes are functionally related to organ system development, cell adhesion and cell differentiation. CONCLUSIONS We identify the existence of EIs as a finer layer of epigenomic architecture within large heterochromatin domains. Their enrichment for CTCF sites and DNAse hypersensitive sites, as well as association with DMRs, suggest that EIs play an important role in normal epigenomic architecture and its disruption in disease.
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Affiliation(s)
- Bo Wen
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Loh YH, Yang JC, De Los Angeles A, Guo C, Cherry A, Rossi DJ, Park IH, Daley GQ. Excision of a viral reprogramming cassette by delivery of synthetic Cre mRNA. ACTA ACUST UNITED AC 2012; Chapter 4:Unit4A.5. [PMID: 22605648 DOI: 10.1002/9780470151808.sc04a05s21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The generation of patient-specific induced pluripotent stem (iPS) cells provides an invaluable resource for cell therapy, in vitro modeling of human disease, and drug screening. To date, most human iPS cells have been generated with integrating retro- and lenti-viruses and are limited in their potential utility because residual transgene expression may alter their differentiation potential or induce malignant transformation. Alternatively, transgene-free methods using adenovirus and protein transduction are limited by low efficiency. This unit describes a protocol for the generation of transgene-free human induced pluripotent stem cells using retroviral transfection of a single vector, which includes the coding sequences of human OCT4, SOX2, KLF4, and cMYC linked with picornaviral 2A plasmids. Moreover, after reprogramming has been achieved, this cassette can be removed using mRNA transfection of Cre recombinase. The method described herein to excise reprogramming factors with ease and efficiency facilitates the experimental generation and use of transgene-free human iPS cells.
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Affiliation(s)
- Yuin-Han Loh
- Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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De Los Angeles A, Loh YH, Tesar PJ, Daley GQ. Accessing naïve human pluripotency. Curr Opin Genet Dev 2012; 22:272-82. [PMID: 22463982 PMCID: PMC4171054 DOI: 10.1016/j.gde.2012.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/01/2012] [Accepted: 03/01/2012] [Indexed: 11/17/2022]
Abstract
Pluripotency manifests during mammalian development through formation of the epiblast, founder tissue of the embryo proper. Rodent pluripotent stem cells can be considered as two distinct states: naïve and primed. Naïve pluripotent stem cell lines are distinguished from primed cells by self-renewal in response to LIF signaling and MEK/GSK3 inhibition (LIF/2i conditions) and two active X chromosomes in female cells. In rodent cells, the naïve pluripotent state may be accessed through at least three routes: explantation of the inner cell mass, somatic cell reprogramming by ectopic Oct4, Sox2, Klf4, and C-myc, and direct reversion of primed post-implantation-associated epiblast stem cells (EpiSCs). In contrast to their rodent counterparts, human embryonic stem cells and induced pluripotent stem cells more closely resemble rodent primed EpiSCs. A critical question is whether naïve human pluripotent stem cells with bona fide features of both a pluripotent state and naïve-specific features can be obtained. In this review, we outline current understanding of the differences between these pluripotent states in mice, new perspectives on the origins of naïve pluripotency in rodents, and recent attempts to apply the rodent paradigm to capture naïve pluripotency in human cells. Unraveling how to stably induce naïve pluripotency in human cells will influence the full realization of human pluripotent stem cell biology and medicine.
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Affiliation(s)
- Alejandro De Los Angeles
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, MA 02115, USA
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Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Hongguang H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ. Erratum: Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 2012. [DOI: 10.1038/nbt0112-112b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Infertility is a problem faced by millions worldwide. In a recent paper published in Cell, Hayashi et al. (2011) provided a potential solution for male infertility through the generation of functional spermatozoa that can give rise to healthy offspring from embryonic stem cells and induced pluripotent stem cells.
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Affiliation(s)
- Wei-Xia Ang
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Medical Biology, Singapore 138648, Singapore
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Abstract
Embryonic stem cells (ESCs) first derived from the inner cell mass of blastocyst-stage embryos have the unique capacity of indefinite self-renewal and potential to differentiate into all somatic cell types. Similar developmental potency can be achieved by reprogramming differentiated somatic cells into induced pluripotent stem cells (iPSCs). Both types of pluripotent stem cells provide great potential for fundamental studies of tissue differentiation, and hold promise for disease modeling, drug development, and regenerative medicine. Although much has been learned about the molecular mechanisms that underlie pluripotency in such cells, our understanding remains incomplete. A comprehensive understanding of ESCs and iPSCs requires the deconstruction of complex transcription regulatory networks, epigenetic mechanisms, and biochemical interactions critical for the maintenance of self-renewal and pluripotency. In this review, we will discuss recent advances gleaned from application of global "omics" techniques to dissect the molecular mechanisms that define the pluripotent state.
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Affiliation(s)
- Yuin-Han Loh
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Massachusetts 02115, USA
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43
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Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 2010; 42:1113-7. [PMID: 21057500 DOI: 10.1038/ng.710] [Citation(s) in RCA: 764] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 09/18/2010] [Indexed: 12/11/2022]
Abstract
The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome, resulting in altered patterns of gene expression. Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs) that occurs upon derivation of human iPSCs and identify numerous lincRNAs whose expression is linked to pluripotency. Among these, we defined ten lincRNAs whose expression was elevated in iPSCs compared with embryonic stem cells, suggesting that their activation may promote the emergence of iPSCs. Supporting this, our results indicate that these lincRNAs are direct targets of key pluripotency transcription factors. Using loss-of-function and gain-of-function approaches, we found that one such lincRNA (lincRNA-RoR) modulates reprogramming, thus providing a first demonstration for critical functions of lincRNAs in the derivation of pluripotent stem cells.
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Affiliation(s)
- Sabine Loewer
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Manton Center for Orphan Disease Research, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts, USA
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44
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Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ. Reprogramming of T cells from human peripheral blood. Cell Stem Cell 2010; 7:15-9. [PMID: 20621044 DOI: 10.1016/j.stem.2010.06.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 05/31/2010] [Accepted: 06/05/2010] [Indexed: 12/31/2022]
Affiliation(s)
- Yuin-Han Loh
- Division of Pediatric Hematology Oncology, Department of Biological Chemistry and Molecular Pharmacology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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45
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Yuan P, Han J, Guo G, Orlov YL, Huss M, Loh YH, Yaw LP, Robson P, Lim B, Ng HH. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev 2009; 23:2507-20. [PMID: 19884257 DOI: 10.1101/gad.1831909] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The histone H3 Lys 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression. Using chromatin immmunoprecipitation (ChIP) and sequencing (ChIP-seq) analyses, we identified Eset target genes with Eset-dependent H3K9 trimethylation. We confirmed that genes that are preferentially expressed in the TE (Tcfap2a and Cdx2) are bound and repressed by Eset. Single-cell PCR analysis shows that the expression of Cdx2 and Tcfap2a is also induced in Eset-depleted morula cells. Importantly, Eset-depleted cells can incorporate into the TE of a blastocyst and, subsequently, placental tissues. Coimmunoprecipitation and ChIP assays further demonstrate that Eset interacts with Oct4, which in turn recruits Eset to silence these trophoblast-associated genes. Our results suggest that Eset restricts the extraembryonic trophoblast lineage potential of pluripotent cells and links an epigenetic regulator to key cell fate decision through a pluripotency factor.
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Affiliation(s)
- Ping Yuan
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
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46
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Chan EM, Ratanasirintrawoot S, Park IH, Manos PD, Loh YH, Huo H, Miller JD, Hartung O, Rho J, Ince TA, Daley GQ, Schlaeger TM. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat Biotechnol 2009; 27:1033-7. [PMID: 19826408 DOI: 10.1038/nbt.1580] [Citation(s) in RCA: 411] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 09/19/2009] [Indexed: 12/28/2022]
Abstract
Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by enforced expression of transcription factors. Using serial live imaging of human fibroblasts undergoing reprogramming, we identified distinct colony types that morphologically resemble embryonic stem (ES) cells yet differ in molecular phenotype and differentiation potential. By analyzing expression of pluripotency markers, methylation at the OCT4 and NANOG promoters and differentiation into teratomas, we determined that only one colony type represents true iPS cells, whereas the others represent reprogramming intermediates. Proviral silencing and expression of TRA-1-60, DNMT3B and REX1 can be used to distinguish the fully reprogrammed state, whereas alkaline phosphatase, SSEA-4, GDF3, hTERT and NANOG are insufficient as markers. We also show that reprogramming using chemically defined medium favors formation of fully reprogrammed over partially reprogrammed colonies. Our data define molecular markers of the fully reprogrammed state and highlight the need for rigorous characterization and standardization of putative iPS cells.
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Affiliation(s)
- Elayne M Chan
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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47
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Feng B, Jiang J, Kraus P, Ng JH, Heng JCD, Chan YS, Yaw LP, Zhang W, Loh YH, Han J, Vega VB, Cacheux-Rataboul V, Lim B, Lufkin T, Ng HH. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat Cell Biol 2009; 11:197-203. [DOI: 10.1038/ncb1827] [Citation(s) in RCA: 371] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 10/22/2008] [Indexed: 02/04/2023]
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48
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Ng JH, Heng JCD, Loh YH, Ng HH. Transcriptional and epigenetic regulations of embryonic stem cells. Mutat Res 2008; 647:52-8. [PMID: 18778721 DOI: 10.1016/j.mrfmmm.2008.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/17/2008] [Accepted: 08/07/2008] [Indexed: 11/25/2022]
Abstract
Embryonic stem cells (ESCs) are characterized by their broad developmental potential and the capacity to self-renew. The advent of high-throughput technologies has facilitated genome-wide studies of transcriptional network, resulting in an ever-increasing repertoire of transcription factors implicated in the maintenance of the embryonic stem cell state. While the transcriptional circuitry continues to expand, epigenetic regulation has also gained attention as an important process in stem cell function. Herein, we discuss the recent advancements made in understanding the transcriptional and epigenetic regulations of embryonic stem cells.
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Affiliation(s)
- Jia-Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
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49
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Abstract
Embryonic stem (ES) cells are pluripotent cells with the ability to self-renew indefinitely. These unique properties are controlled by genetic factors and chromatin structure. The exit from the self-renewing state is accompanied by changes in epigenetic chromatin modifications such as an induction in the silencing-associated histone H3 Lys 9 dimethylation and trimethylation (H3K9Me2/Me3) marks. Here, we show that the H3K9Me2 and H3K9Me3 demethylase genes, Jmjd1a and Jmjd2c, are positively regulated by the ES cell transcription factor Oct4. Interestingly, Jmjd1a or Jmjd2c depletion leads to ES cell differentiation, which is accompanied by a reduction in the expression of ES cell-specific genes and an induction of lineage marker genes. Jmjd1a demethylates H3K9Me2 at the promoter regions of Tcl1, Tcfcp2l1, and Zfp57 and positively regulates the expression of these pluripotency-associated genes. Jmjd2c acts as a positive regulator for Nanog, which encodes for a key transcription factor for self-renewal in ES cells. We further demonstrate that Jmjd2c is required to reverse the H3K9Me3 marks at the Nanog promoter region and consequently prevents transcriptional repressors HP1 and KAP1 from binding. Our results connect the ES cell transcription circuitry to chromatin modulation through H3K9 demethylation in pluripotent cells.
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Affiliation(s)
- Yuin-Han Loh
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
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50
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Lim LS, Loh YH, Zhang W, Li Y, Chen X, Wang Y, Bakre M, Ng HH, Stanton LW. Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol Biol Cell 2007; 18:1348-58. [PMID: 17267691 PMCID: PMC1838990 DOI: 10.1091/mbc.e06-07-0624] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Embryonic stem (ES) cell pluripotency is dependent upon sustained expression of the key transcriptional regulators Oct4, Nanog, and Sox2. Dissection of the regulatory networks downstream of these transcription factors has provided critical insight into the molecular mechanisms that regulate ES cell pluripotency and early differentiation. Here we describe a role for Zic3, a member of the Gli family of zinc finger transcription factors, in the maintenance of pluripotency in ES cells. We show that Zic3 is expressed in ES cells and that this expression is repressed upon differentiation. The expression of Zic3 in pluripotent ES cells is also directly regulated by Oct4, Sox2, and Nanog. Targeted repression of Zic3 in human and mouse ES cells by RNA interference-induced expression of several markers of the endodermal lineage. Notably, the expression of Nanog, a key pluripotency regulator and repressor of extraembryonic endoderm specification in ES cells, was significantly reduced in Zic3 knockdown cells. This suggests that Zic3 may prevent endodermal marker expression through Nanog-regulated pathways. Thus our results extend the ES cell transcriptional network beyond Oct4, Nanog, and Sox2, and further establish that Zic3 plays an important role in the maintenance of pluripotency by preventing endodermal lineage specification in embryonic stem cells.
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Affiliation(s)
| | | | - Weiwei Zhang
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Yixun Li
- Information and Mathematical Sciences Group, Genome Institute of Singapore, Singapore 138672; and
| | - Xi Chen
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Yinan Wang
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | | | - Huck-Hui Ng
- Gene Regulation Laboratory, and
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Lawrence W. Stanton
- *Stem Cell and Developmental Biology Group
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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