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Xu C, Huang KK, Law JH, Chua JS, Sheng T, Flores NM, Pizzi MP, Okabe A, Tan ALK, Zhu F, Kumar V, Lu X, Benitez AM, Lian BSX, Ma H, Ho SWT, Ramnarayanan K, Anene-Nzelu CG, Razavi-Mohseni M, Abdul Ghani SAB, Tay ST, Ong X, Lee MH, Guo YA, Ashktorab H, Smoot D, Li S, Skanderup AJ, Beer MA, Foo RSY, Wong JSH, Sanghvi K, Yong WP, Sundar R, Kaneda A, Prabhakar S, Mazur PK, Ajani JA, Yeoh KG, So JBY, Tan P. Comprehensive molecular phenotyping of ARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities. Gut 2023; 72:1651-1663. [PMID: 36918265 DOI: 10.1136/gutjnl-2022-328332] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVE Gastric cancer (GC) is a leading cause of cancer mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising from ARID1A loss. DESIGN Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of ARID1A inactivation across molecular subtypes. Single-cell transcriptomic profiles of ARID1A-mutated GCs were analysed to examine tumour microenvironmental changes arising from ARID1A loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of ARID1A-mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS We observed prevalent ARID1A inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. ARID1A-depletion caused loss of H3K27ac activation signals at ARID1A-occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as NFKB1 and NFKB2. Promoter activation in ARID1A-mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to ARID1A-genomic status. CONCLUSION Our results suggest a therapeutic strategy for ARID1A-mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.
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Affiliation(s)
- Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jia Hao Law
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joy Shijia Chua
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Taotao Sheng
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Melissa Pool Pizzi
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xiaoyin Lu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana Morales Benitez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Haoran Ma
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Shamaine Wei Ting Ho
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Montreal Heart Institute, Quebec, Québec, Canada
- Department of Medicine, University of Montreal, Quebec, Québec, Canada
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | | | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Duane Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Kaushal Sanghvi
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Health System, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pawel Karol Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Jimmy Bok-Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Division of Surgical Oncology, National University Cancer Institute, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
- Cellular and Molecular Research, National Cancer Centre, Singapore
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2
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Jeon AJ, Anene-Nzelu CG, Teo YY, Chong SL, Sekar K, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Chung AYF, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Bee-Lan Ong D, Lim J, de Villa VH, dela Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BK, Foo RSY, Chow PKH. A genomic enhancer signature associates with hepatocellular carcinoma prognosis. JHEP Rep 2023; 5:100715. [PMID: 37168287 PMCID: PMC10165154 DOI: 10.1016/j.jhepr.2023.100715] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 05/13/2023] Open
Abstract
Background & Aims Lifestyle and environmental-related exposures are important risk factors for hepatocellular carcinoma (HCC), suggesting that epigenetic dysregulation significantly underpins HCC. We profiled 30 surgically resected tumours and the matched adjacent normal tissues to understand the aberrant epigenetic events associated with HCC. Methods We identified tumour differential enhancers and the associated genes by analysing H3K27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) and Hi-C/HiChIP data from the resected tumour samples of 30 patients with early-stage HCC. This epigenome dataset was analysed with previously reported genome and transcriptome data of the overlapping group of patients from the same cohort. We performed patient-specific differential expression testing using multiregion sequencing data to identify genes that undergo both enhancer and gene expression changes. Based on the genes selected, we identified two patient groups and performed a recurrence-free survival analysis. Results We observed large-scale changes in the enhancer distribution between HCC tumours and the adjacent normal samples. Many of the gain-in-tumour enhancers showed corresponding upregulation of the associated genes and vice versa, but much of the enhancer and gene expression changes were patient-specific. A subset of the upregulated genes was activated in a subgroup of patients' tumours. Recurrence-free survival analysis revealed that the patients with a more robust upregulation of those genes showed a worse prognosis. Conclusions We report the genomic enhancer signature associated with differential prognosis in HCC. Findings that cohere with oncofoetal reprogramming in HCC were underpinned by genome-wide enhancer rewiring. Our results present the epigenetic changes in HCC that offer the rational selection of epigenetic-driven gene targets for therapeutic intervention or disease prognostication in HCC. Impact and Implications Lifestyle and environmental-related exposures are the important risk factors of hepatocellular carcinoma (HCC), suggesting that tumour-associated epigenetic dysregulations may significantly underpin HCC. We profiled tumour tissues and their matched normal from 30 patients with early-stage HCC to study the dysregulated epigenetic changes associated with HCC. By also analysing the patients' RNA-seq and clinical data, we found the signature genes - with epigenetic and transcriptomic dysregulation - associated with worse prognosis. Our findings suggest that systemic approaches are needed to consider the surrounding cellular environmental and epigenetic changes in HCC tumours.
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Affiliation(s)
- Ah-Jung Jeon
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Quebec, Canada
| | - Yue-Yang Teo
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Shay Lee Chong
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Karthik Sekar
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Lingyan Wu
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Sin-Chi Chew
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Raden Indah Kendarsari
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Hannah Lai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Neslihan Arife Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Alexander Yaw Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Peng-Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Juinn Huar Kam
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Krishnakumar Madhavan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Alfred Kow
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Iyer Shridhar Ganpathi
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Shihleone Loong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Tracy Jiezhen Loh
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei Keat Wan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | | | - Yin Huei Pang
- Department of Pathology, National University Hospital, Singapore
| | - Boon Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H. de Villa
- Department of Surgery and Center for Liver Health and Transplantation, The Medical City, Pasig City, Philippines
| | - Rouchelle D. dela Cruz
- Department of Laboratory Medicine and Pathology, The Medical City, Pasig City, Philippines
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | | | - Glenn K. Bonney
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Brian K.P. Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Roger Sik Yin Foo
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
- Corresponding author. Address: National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore 168583, Singapore. Tel.: +65-63065424.
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3
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McKinsey TA, Foo R, Anene-Nzelu CG, Travers JG, Vagnozzi RJ, Weber N, Thum T. Emerging epigenetic therapies of cardiac fibrosis and remodelling in heart failure: from basic mechanisms to early clinical development. Cardiovasc Res 2023; 118:3482-3498. [PMID: 36004821 DOI: 10.1093/cvr/cvac142] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/02/2022] [Accepted: 08/21/2022] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular diseases and specifically heart failure (HF) impact global health and impose a significant economic burden on society. Despite current advances in standard of care, the risks for death and readmission of HF patients remain unacceptably high and new therapeutic strategies to limit HF progression are highly sought. In disease settings, persistent mechanical or neurohormonal stress to the myocardium triggers maladaptive cardiac remodelling, which alters cardiac function and structure at both the molecular and cellular levels. The progression and magnitude of maladaptive cardiac remodelling ultimately leads to the development of HF. Classical therapies for HF are largely protein-based and mostly are targeted to ameliorate the dysregulation of neuroendocrine pathways and halt adverse remodelling. More recently, investigation of novel molecular targets and the application of cellular therapies, epigenetic modifications, and regulatory RNAs has uncovered promising new avenues to address HF. In this review, we summarize the current knowledge on novel cellular and epigenetic therapies and focus on two non-coding RNA-based strategies that reached the phase of early clinical development to counteract cardiac remodelling and HF. The current status of the development of translating those novel therapies to clinical practice, limitations, and future perspectives are additionally discussed.
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Affiliation(s)
- Timothy A McKinsey
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Roger Foo
- NUHS Cardiovascular Disease Translational Research Programme, NUS Yong Loo Lin School of Medicine, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Cardiovascular Research Institute, National University Heart Centre, 14 Medical Drive, Level 8, 117599 Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- NUHS Cardiovascular Disease Translational Research Programme, NUS Yong Loo Lin School of Medicine, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Cardiovascular Research Institute, National University Heart Centre, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Montreal Heart Institute, 5000 Rue Belanger, H1T 1C8, Montreal, Canada
| | - Joshua G Travers
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Ronald J Vagnozzi
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Natalie Weber
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.,REBIRTH Center for Translational Regenerative Therapies, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.,Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Straße 1, 30625 Hannover, Germany
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4
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Ho SWT, Sheng T, Xing M, Ooi WF, Xu C, Sundar R, Huang KK, Li Z, Kumar V, Ramnarayanan K, Zhu F, Srivastava S, Isa ZFBA, Anene-Nzelu CG, Razavi-Mohseni M, Shigaki D, Ma H, Tan ALK, Ong X, Lee MH, Tay ST, Guo YA, Huang W, Li S, Beer MA, Foo RSY, Teh M, Skanderup AJ, Teh BT, Tan P. Regulatory enhancer profiling of mesenchymal-type gastric cancer reveals subtype-specific epigenomic landscapes and targetable vulnerabilities. Gut 2023; 72:226-241. [PMID: 35817555 DOI: 10.1136/gutjnl-2021-326483] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/03/2022] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Gastric cancer (GC) comprises multiple molecular subtypes. Recent studies have highlighted mesenchymal-subtype GC (Mes-GC) as a clinically aggressive subtype with few treatment options. Combining multiple studies, we derived and applied a consensus Mes-GC classifier to define the Mes-GC enhancer landscape revealing disease vulnerabilities. DESIGN Transcriptomic profiles of ~1000 primary GCs and cell lines were analysed to derive a consensus Mes-GC classifier. Clinical and genomic associations were performed across >1200 patients with GC. Genome-wide epigenomic profiles (H3K27ac, H3K4me1 and assay for transposase-accessible chromatin with sequencing (ATAC-seq)) of 49 primary GCs and GC cell lines were generated to identify Mes-GC-specific enhancer landscapes. Upstream regulators and downstream targets of Mes-GC enhancers were interrogated using chromatin immunoprecipitation followed by sequencing (ChIP-seq), RNA sequencing, CRISPR/Cas9 editing, functional assays and pharmacological inhibition. RESULTS We identified and validated a 993-gene cancer-cell intrinsic Mes-GC classifier applicable to retrospective cohorts or prospective single samples. Multicohort analysis of Mes-GCs confirmed associations with poor patient survival, therapy resistance and few targetable genomic alterations. Analysis of enhancer profiles revealed a distinctive Mes-GC epigenomic landscape, with TEAD1 as a master regulator of Mes-GC enhancers and Mes-GCs exhibiting preferential sensitivity to TEAD1 pharmacological inhibition. Analysis of Mes-GC super-enhancers also highlighted NUAK1 kinase as a downstream target, with synergistic effects observed between NUAK1 inhibition and cisplatin treatment. CONCLUSION Our results establish a consensus Mes-GC classifier applicable to multiple transcriptomic scenarios. Mes-GCs exhibit a distinct epigenomic landscape, and TEAD1 inhibition and combinatorial NUAK1 inhibition/cisplatin may represent potential targetable options.
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Affiliation(s)
- Shamaine Wei Ting Ho
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Taotao Sheng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Manjie Xing
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Wen Fong Ooi
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore.,Singapore Gastric Cancer Consortium, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | | | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.,Montreal Heart Institute, Quebec, Quebec, Canada.,Department of Medicine, University of Montreal, Quebec, Quebec, Canada
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Dustin Shigaki
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Haoran Ma
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Weitai Huang
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Singapore Gastric Cancer Consortium, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
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5
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Sheng T, Ho SWT, Ooi WF, Xu C, Xing M, Padmanabhan N, Huang KK, Ma L, Ray M, Guo YA, Sim NL, Anene-Nzelu CG, Chang MM, Razavi-Mohseni M, Beer MA, Foo RSY, Sundar R, Chan YH, Tan ALK, Ong X, Skanderup AJ, White KP, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Med 2021; 13:158. [PMID: 34635154 PMCID: PMC8504099 DOI: 10.1186/s13073-021-00970-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity-however, most predicted enhancer regions remain to be functionally tested. METHODS We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology. We applied Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to assess functional enhancer activity. An Activity-by-contact (ABC) model was employed to explore the effects of histone acetylation and CapSTARR-seq levels on enhancer-promoter interactions. RESULTS We report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are GC-associated in vivo (> 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying CapSTARR-seq to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers, even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. We identified cancer-relevant genes (ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4α as a master trans-acting factor associated with GC enhancer heterogeneity. CONCLUSIONS Our results indicate that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, providing insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.
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Affiliation(s)
- Taotao Sheng
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Lijia Ma
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Mohana Ray
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Yu Amanda Guo
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Ngak Leng Sim
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
- Montreal Heart Institute, Montreal, Canada
- Department of Medicine, University of Montreal, Montreal, Canada
| | - Mei Mei Chang
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Hospital, Singapore, 119074, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Anders Jacobsen Skanderup
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Kevin P White
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA.
- Tempus Labs, Chicago, USA.
| | - Sudhakar Jha
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA.
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 168752, Singapore.
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
- Singapore Gastric Cancer Consortium, Singapore, 119228, Singapore.
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6
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Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Poon PSY, Lam YN, Lin JS, Tay ST, Lee MH, Tan ALK, Ong X, White K, Rozen SG, Beer M, Foo RSY, Grabsch HI, Skanderup AJ, Li S, Teh BT, Tan P. Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. J Clin Invest 2021; 130:3005-3020. [PMID: 32364535 DOI: 10.1172/jci126726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/10/2018] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Transcriptional reactivation of telomerase catalytic subunit (TERT) is a frequent hallmark of cancer, occurring in 90% of human malignancies. However, specific mechanisms driving TERT reactivation remain obscure for many tumor types and in particular gastric cancer (GC), a leading cause of global cancer mortality. Here, through comprehensive genomic and epigenomic analysis of primary GCs and GC cell lines, we identified the transcription factor early B cell factor 1 (EBF1) as a TERT transcriptional repressor and inactivation of EBF1 function as a major cause of TERT upregulation. Abolishment of EBF1 function occurs through 3 distinct (epi)genomic mechanisms. First, EBF1 is epigenetically silenced via DNA methyltransferase, polycomb-repressive complex 2 (PRC2), and histone deacetylase activity in GCs. Second, recurrent, somatic, and heterozygous EBF1 DNA-binding domain mutations result in the production of dominant-negative EBF1 isoforms. Third, more rarely, genomic deletions and rearrangements proximal to the TERT promoter remobilize or abolish EBF1-binding sites, derepressing TERT and leading to high TERT expression. EBF1 is also functionally required for various malignant phenotypes in vitro and in vivo, highlighting its importance for GC development. These results indicate that multimodal genomic and epigenomic alterations underpin TERT reactivation in GC, converging on transcriptional repressors such as EBF1.
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Affiliation(s)
- Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Po-Hsien Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Zhimei Li
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Xiaosai Yao
- Institute of Molecular and Cell Biology, Singapore
| | - Mandoli Amit
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ley Moy Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Taotao Sheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Jing Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Mohana Ray
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Gregorio Fazzi
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Kevin Junliang Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Giovani Claresta Wijaya
- Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Tingdong Yan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Mei Mei Chang
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Kakoli Das
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Zul Fazreen Adam Isa
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jeanie Wu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Polly Suk Yean Poon
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Yue Ning Lam
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Joyce Suling Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kevin White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.,Tempus Labs, Chicago, Illinois, USA
| | - Steven George Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
| | - Michael Beer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Medicine, and.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore.,Human Genetics, Genome Institute of Singapore, Singapore
| | - Heike Irmgard Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands.,Pathology and Data Analyticis, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, United Kingdom
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Laboratory of Cancer Epigenome, Department of Medical Sciences, National Cancer Centre, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore.,Cellular and Molecular Research, National Cancer Centre, Singapore.,Singapore Gastric Cancer Consortium, Singapore.,Biomedical Research Council, Agency for Science, Technology and Research, Singapore
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7
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Robinson EL, Anene-Nzelu CG, Rosa-Garrido M, Foo RSY. Cardiac epigenetics: Driving signals to the cardiac epigenome in development and disease. J Mol Cell Cardiol 2020; 151:88. [PMID: 33232681 DOI: 10.1016/j.yjmcc.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Conrad Waddington's famous illustration of a ball poised at the top of an undulating epigenetic landscape is often evoked when one thinks of epigenetics. Although the original figure was a metaphor for gene regulation during cell fate determination, we now know that epigenetic regulation is important for the homeostasis of every tissue and organ in the body. This is evident in the cardiovascular system, one of the first organs to develop and one whose function is vital to human life. Epigenetic mechanisms are central in regulating transcription and signaling programs that drive cardiovascular disease and development. The epigenome not only instructs cell and context specific gene expression signatures, but also retains "memory" of past events and can pass it down to subsequent generations. Understanding the various input and output signals from the cardiac epigenome is crucial for unraveling the molecular underpinnings of cardiovascular disease and development. This knowledge is useful for patient risk stratification, understanding disease pathophysiology, and identifying novel approaches for cardiac regeneration and therapy. In this special issue, a series of high-quality reviews and original research articles examining the field of cardiac epigenetics will broaden our insights into this fundamental aspect of molecular and cellular cardiology. Topics include DNA methylation, histone modifications, chromatin architecture, transcription factors, and long non-coding RNA biology in the diverse cell types that comprise the cardiovascular system. We hope that our readers will expand their horizons and be challenged to envision innovative strategies to further probe the epigenome and develop diagnostic and therapeutic solutions for cardiovascular pathologies.
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Affiliation(s)
- Emma Louise Robinson
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Chukwuemeka George Anene-Nzelu
- Genome Institute of Singapore, Biopolis, Singapore; Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Manuel Rosa-Garrido
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Roger S Y Foo
- Genome Institute of Singapore, Biopolis, Singapore; Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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8
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Madsen A, Höppner G, Krause J, Hirt MN, Laufer SD, Schweizer M, Tan WLW, Mosqueira D, Anene-Nzelu CG, Lim I, Foo RSY, Eschenhagen T, Stenzig J. An Important Role for DNMT3A-Mediated DNA Methylation in Cardiomyocyte Metabolism and Contractility. Circulation 2020; 142:1562-1578. [PMID: 32885664 PMCID: PMC7566310 DOI: 10.1161/circulationaha.119.044444] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Supplemental Digital Content is available in the text. Background: DNA methylation acts as a mechanism of gene transcription regulation. It has recently gained attention as a possible therapeutic target in cardiac hypertrophy and heart failure. However, its exact role in cardiomyocytes remains controversial. Thus, we knocked out the main de novo DNA methyltransferase in cardiomyocytes, DNMT3A, in human induced pluripotent stem cells. Functional consequences of DNA methylation-deficiency under control and stress conditions were then assessed in human engineered heart tissue from knockout human induced pluripotent stem cell–derived cardiomyocytes. Methods: DNMT3A was knocked out in human induced pluripotent stem cells by CRISPR/Cas9gene editing. Fibrin-based engineered heart tissue was generated from knockout and control human induced pluripotent stem cell–derived cardiomyocytes. Development and baseline contractility were analyzed by video-optical recording. Engineered heart tissue was subjected to different stress protocols, including serum starvation, serum variation, and restrictive feeding. Molecular, histological, and ultrastructural analyses were performed afterward. Results: Knockout of DNMT3A in human cardiomyocytes had three main consequences for cardiomyocyte morphology and function: (1) Gene expression changes of contractile proteins such as higher atrial gene expression and lower MYH7/MYH6 ratio correlated with different contraction kinetics in knockout versus wild-type; (2) Aberrant activation of the glucose/lipid metabolism regulator peroxisome proliferator-activated receptor gamma was associated with accumulation of lipid vacuoles within knockout cardiomyocytes; (3) Hypoxia-inducible factor 1α protein instability was associated with impaired glucose metabolism and lower glycolytic enzyme expression, rendering knockout-engineered heart tissue sensitive to metabolic stress such as serum withdrawal and restrictive feeding. Conclusion: The results suggest an important role of DNA methylation in the normal homeostasis of cardiomyocytes and during cardiac stress, which could make it an interesting target for cardiac therapy.
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Affiliation(s)
- Alexandra Madsen
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
| | - Grit Höppner
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
| | - Julia Krause
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.).,Department of Cardiology, University Heart and Vascular Center Hamburg, Germany (J.K.)
| | - Marc N Hirt
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
| | - Sandra D Laufer
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
| | - Michaela Schweizer
- Department of Morphology and Electron Microscopy, Center for Molecular Neurobiology (M.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Diogo Mosqueira
- Division of Cancer & Stem Cells, Biodiscovery Institute, University of Nottingham, United Kingdom (D.M.)
| | - Chukwuemeka George Anene-Nzelu
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., I.L., R.S.Y.F.).,Cardiovascular Research Institute, National University of Singapore (C.G.A.-N., I.L., R.S.Y.F.)
| | - Ives Lim
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., I.L., R.S.Y.F.)
| | - Roger S Y Foo
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., I.L., R.S.Y.F.).,Cardiovascular Research Institute, National University of Singapore (C.G.A.-N., I.L., R.S.Y.F.)
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
| | - Justus Stenzig
- Institute of Experimental Pharmacology and Toxicology (A.M., G.H., M.N.H., S.D.L., T.E., J.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany (A.M., G.H., J.K., M.N.H., S.D.L., T.E., J.S.)
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9
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Anene-Nzelu CG, Tan WLW, Lee CJM, Wenhao Z, Perrin A, Dashi A, Tiang Z, Autio MI, Lim B, Wong E, Tan HS, Pan B, Morley MP, Margulies KB, Cappola TP, Foo RSY. Assigning Distal Genomic Enhancers to Cardiac Disease-Causing Genes. Circulation 2020; 142:910-912. [PMID: 32866060 PMCID: PMC9136986 DOI: 10.1161/circulationaha.120.046040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Wilson Lek Wen Tan
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Chang Jie Mick Lee
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Zheng Wenhao
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Arnaud Perrin
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Albert Dashi
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Zenia Tiang
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Matias Ilmari Autio
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Bram Lim
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Eleanor Wong
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Hui San Tan
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Bangfen Pan
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
| | - Michael P Morley
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Kenneth B Margulies
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Thomas P Cappola
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Roger S-Y Foo
- Cardiovascular Research Institute, National University Health System, Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
- Genome Institute of Singapore (C.G.A.-N., W.L.W.T., C.J.M.L., Z.W., A.P., A.D., Z.T., M.I.A., B.L., E.W., H.S.T., B.P., R.S.-Y.F.)
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10
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Tan WLW, Anene-Nzelu CG, Wong E, Lee CJM, Tan HS, Tang SJ, Perrin A, Wu KX, Zheng W, Ashburn RJ, Pan B, Lee MY, Autio MI, Morley MP, Tam WL, Cheung C, Margulies KB, Chen L, Cappola TP, Loh M, Chambers J, Prabhakar S, Foo RSY. Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype. Circ Res 2020; 127:761-777. [PMID: 32529949 DOI: 10.1161/circresaha.120.317254] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Indexed: 12/15/2022]
Abstract
RATIONALE Identifying genetic markers for heterogeneous complex diseases such as heart failure is challenging and requires prohibitively large cohort sizes in genome-wide association studies to meet the stringent threshold of genome-wide statistical significance. On the other hand, chromatin quantitative trait loci, elucidated by direct epigenetic profiling of specific human tissues, may contribute toward prioritizing subthreshold variants for disease association. OBJECTIVE Here, we captured noncoding genetic variants by performing epigenetic profiling for enhancer H3K27ac chromatin immunoprecipitation followed by sequencing in 70 human control and end-stage failing hearts. METHODS AND RESULTS We have mapped a comprehensive catalog of 47 321 putative human heart enhancers and promoters. Three thousand eight hundred ninety-seven differential acetylation peaks (FDR [false discovery rate], 5%) pointed to pathways altered in heart failure. To identify cardiac histone acetylation quantitative trait loci (haQTLs), we regressed out confounding factors including heart failure disease status and used the G-SCI (Genotype-independent Signal Correlation and Imbalance) test1 to call out 1680 haQTLs (FDR, 10%). RNA sequencing performed on the same heart samples proved a subset of haQTLs to have significant association also to gene expression (expression quantitative trait loci), either in cis (180) or through long-range interactions (81), identified by Hi-C (high-throughput chromatin conformation assay) and HiChIP (high-throughput protein centric chromatin) performed on a subset of hearts. Furthermore, a concordant relationship between the gain or disruption of TF (transcription factor)-binding motifs, inferred from alternative alleles at the haQTLs, implied a surprising direct association between these specific TF and local histone acetylation in human hearts. Finally, 62 unique loci were identified by colocalization of haQTLs with the subthreshold loci of heart-related genome-wide association studies datasets. CONCLUSIONS Disease and phenotype association for 62 unique loci are now implicated. These loci may indeed mediate their effect through modification of enhancer H3K27 acetylation enrichment and their corresponding gene expression differences (bioRxiv: https://doi.org/10.1101/536763). Graphical Abstract: A graphical abstract is available for this article.
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Affiliation(s)
- Wilson Lek Wen Tan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Chukwuemeka George Anene-Nzelu
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Eleanor Wong
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Chang Jie Mick Lee
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Hui San Tan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Arnaud Perrin
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Kan Xing Wu
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
| | - Wenhao Zheng
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Robert John Ashburn
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Bangfen Pan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - May Yin Lee
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Matias Ilmari Autio
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Michael P Morley
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Wai Leong Tam
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Institute of Molecular and Cell Biology, Singapore (C.C.)
| | - Kenneth B Margulies
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Thomas P Cappola
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Epidemiology and Biostatistics, Imperial College London (M.L., J.C.), United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom (M.L., J.C.)
| | - John Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Epidemiology and Biostatistics, Imperial College London (M.L., J.C.), United Kingdom
- Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, United Kingdom (J.C.)
- Imperial College Healthcare NHS Trust, London, United Kingdom (M.L., J.C.)
| | - Shyam Prabhakar
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Roger S Y Foo
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
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11
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Nguyen NUN, Canseco DC, Xiao F, Nakada Y, Li S, Lam NT, Muralidhar S, Savla JJ, Hill JA, Wang Z, Ahmed MS, Hubbi M, Menendez-Montes I, Moon J, Ali SR, Villalobos E, Elhelaly WM, Thet S, Tan WLW, Anene-Nzelu CG, Foo R, Jagoree R, Cyert MS, Rothermel BA, Sadek HA. Abstract MP161: A Calcineurin-hoxb13 Axis Regulates Growth Mode of Mammalian Cardiomyocytes. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.mp161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A major factor in the progression to heart failure in humans is the inability of the adult heart to repair itself after injury. Our group recently demonstrated that the early postnatal mammalian heart is capable of regeneration following injury through proliferation of preexisting cardiomyocytes1,2. We recently also showed that Meis1, a TALE family homeodomain transcription factor, translocates to cardiomyocyte nuclei shortly after birth and mediates postnatal cell cycle arrest3. Here we report that Hoxb13 acts as a Meis1 cofactor in postnatal cardiomyocytes. Cardiomyocyte-specific deletion of Hoxb13 can both extend the postnatal window of cardiomyocyte proliferation and reactivate cardiomyocyte cell cycle in the adult heart. Moreover, adult Meis1/Hoxb13 double knockout hearts display widespread cardiomyocyte mitosis, sarcomere disassembly and an improvement in left ventricular systolic function following myocardial infarction both by echocardiography and MRI. ChIP-seq analysis demonstrates that Meis1 and Hoxb13 act cooperatively to regulate cardiomyocyte maturation and cell cycle. Finally, we show that the calcium-activated protein phosphatase calcineurin dephosphorylates Hoxb13 at serine-204 (S204), resulting in its nuclear localization and cell cycle arrest. Collectively, these results demonstrate that Meis1 and Hoxb13 act cooperatively to regulate cardiomyocyte maturation and proliferation and provide mechanistic insights into the link between hyperplastic and hypertrophic growth of cardiomyocytes.
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Affiliation(s)
| | | | - Feng Xiao
- UT Southwestern Med Cntr, Dallas, TX
| | - Yuji Nakada
- Univ of Alabama at Birmingham, Birmingham, AL
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Roger Foo
- Cardiovascular Rsch Institute, Singapore
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12
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Nguyen NUN, Canseco DC, Xiao F, Nakada Y, Li S, Lam NT, Muralidhar SA, Savla JJ, Hill JA, Le V, Zidan KA, El-Feky HW, Wang Z, Ahmed MS, Hubbi ME, Menendez-Montes I, Moon J, Ali SR, Le V, Villalobos E, Mohamed MS, Elhelaly WM, Thet S, Anene-Nzelu CG, Tan WLW, Foo RS, Meng X, Kanchwala M, Xing C, Roy J, Cyert MS, Rothermel BA, Sadek HA. A calcineurin-Hoxb13 axis regulates growth mode of mammalian cardiomyocytes. Nature 2020; 582:271-276. [PMID: 32499640 PMCID: PMC7670845 DOI: 10.1038/s41586-020-2228-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [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: 12/02/2018] [Accepted: 02/24/2020] [Indexed: 11/08/2022]
Abstract
A major factor in the progression to heart failure in humans is the inability of the adult heart to repair itself after injury. We recently demonstrated that the early postnatal mammalian heart is capable of regeneration following injury through proliferation of preexisting cardiomyocytes1,2 and that Meis1, a three amino acid loop extension (TALE) family homeodomain transcription factor, translocates to cardiomyocyte nuclei shortly after birth and mediates postnatal cell cycle arrest3. Here we report that Hoxb13 acts as a cofactor of Meis1 in postnatal cardiomyocytes. Cardiomyocyte-specific deletion of Hoxb13 can extend the postnatal window of cardiomyocyte proliferation and reactivate the cardiomyocyte cell cycle in the adult heart. Moreover, adult Meis1-Hoxb13 double-knockout hearts display widespread cardiomyocyte mitosis, sarcomere disassembly and improved left ventricular systolic function following myocardial infarction, as demonstrated by echocardiography and magnetic resonance imaging. Chromatin immunoprecipitation with sequencing demonstrates that Meis1 and Hoxb13 act cooperatively to regulate cardiomyocyte maturation and cell cycle. Finally, we show that the calcium-activated protein phosphatase calcineurin dephosphorylates Hoxb13 at serine-204, resulting in its nuclear localization and cell cycle arrest. These results demonstrate that Meis1 and Hoxb13 act cooperatively to regulate cardiomyocyte maturation and proliferation and provide mechanistic insights into the link between hyperplastic and hypertrophic growth of cardiomyocytes.
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Affiliation(s)
- Ngoc Uyen Nhi Nguyen
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana C Canseco
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Feng Xiao
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuji Nakada
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shujuan Li
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicholas T Lam
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shalini A Muralidhar
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jainy J Savla
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph A Hill
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Victor Le
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kareem A Zidan
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hamed W El-Feky
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhaoning Wang
- Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mahmoud Salama Ahmed
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maimon E Hubbi
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Menendez-Montes
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jesung Moon
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shah R Ali
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Victoria Le
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elisa Villalobos
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Magid S Mohamed
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Waleed M Elhelaly
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Suwannee Thet
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
| | - Wilson Lek Wen Tan
- Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
| | - Roger S Foo
- Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
| | - Xun Meng
- The College of Life Sciences, Northwest University, Xi'an, China
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development/Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development/Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jagoree Roy
- Department of Biology, Stanford University, Stanford, California, USA
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, California, USA
| | - Beverly A Rothermel
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hesham A Sadek
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Li S, Nguyen NUN, Xiao F, Menendez-Montes I, Nakada Y, Tan WLW, Anene-Nzelu CG, Foo RS, Thet S, Cardoso AC, Wang P, Elhelaly WM, Lam NT, Pereira AHM, Hill JA, Sadek HA. Mechanism of Eccentric Cardiomyocyte Hypertrophy Secondary to Severe Mitral Regurgitation. Circulation 2020; 141:1787-1799. [PMID: 32272846 DOI: 10.1161/circulationaha.119.043939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Primary valvular heart disease is a prevalent cause of morbidity and mortality in both industrialized and developing countries. Although the primary consequence of valvular heart disease is myocardial dysfunction, treatment of valvular heart diseases centers around valve repair or replacement rather than prevention or reversal of myocardial dysfunction. This is particularly evident in primary mitral regurgitation (MR), which invariably results in eccentric hypertrophy and left ventricular (LV) failure in the absence of timely valve repair or replacement. The mechanism of LV dysfunction in primary severe MR is entirely unknown. METHODS Here, we developed the first mouse model of severe MR. Valvular damage was achieved by severing the mitral valve leaflets and chords with iridectomy scissors, and MR was confirmed by echocardiography. Serial echocardiography was performed to follow up LV morphology and systolic function. Analysis of cardiac tissues was subsequently performed to evaluate valve deformation, cardiomyocyte morphology, LV fibrosis, and cell death. Finally, dysregulated pathways were assessed by RNA-sequencing analysis and immunofluorescence. RESULTS In the ensuing 15 weeks after the induction of MR, gradual LV dilatation and dysfunction occurred, resulting in severe systolic dysfunction. Further analysis revealed that severe MR resulted in a marked increase in cardiac mass and increased cardiomyocyte length but not width, with electron microscopic evidence of sarcomere disarray and the development of sarcomere disruption. From a mechanistic standpoint, severe MR resulted in activation of multiple components of both the mammalian target of rapamycin and calcineurin pathways. Inhibition of mammalian target of rapamycin signaling preserved sarcomeric structure and prevented LV remodeling and systolic dysfunction. Immunohistochemical analysis uncovered a differential pattern of expression of the cell polarity regulator Crb2 (crumbs homolog 2) along the longitudinal axis of cardiomyocytes and close to the intercalated disks in the MR hearts. Electron microscopy images demonstrated a significant increase in polysome localization in close proximity to the intercalated disks and some areas along the longitudinal axis in the MR hearts. CONCLUSIONS These results indicate that LV dysfunction in response to severe MR is a form of maladaptive eccentric cardiomyocyte hypertrophy and outline the link between cell polarity regulation and spatial localization protein synthesis as a pathway for directional cardiomyocyte growth.
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Affiliation(s)
- Shujuan Li
- Department of Pediatric Cardiology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China (S.L.).,NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, China (S.L.).,Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ngoc Uyen Nhi Nguyen
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Feng Xiao
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ivan Menendez-Montes
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Yuji Nakada
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Wilson Lek Wen Tan
- Cardiovascular Research Institute, National University of Singapore (W.L.W.T., C.G.A.-N., R.S.F.).,Genome Institute of Singapore (W.L.W.T., C.G.A.-N., R.S.F.)
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University of Singapore (W.L.W.T., C.G.A.-N., R.S.F.).,Genome Institute of Singapore (W.L.W.T., C.G.A.-N., R.S.F.)
| | - Roger S Foo
- Cardiovascular Research Institute, National University of Singapore (W.L.W.T., C.G.A.-N., R.S.F.).,Genome Institute of Singapore (W.L.W.T., C.G.A.-N., R.S.F.)
| | - Suwannee Thet
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Alisson Campos Cardoso
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas.,Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo (A.C.C., A.H.M.P.)
| | - Ping Wang
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Waleed M Elhelaly
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Nicholas T Lam
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Ana Helena Macedo Pereira
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas.,Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo (A.C.C., A.H.M.P.)
| | - Joseph A Hill
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas.,Department of Molecular Biology (J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
| | - Hesham A Sadek
- Department of Internal Medicine, Division of Cardiology (S.L., N.U.N.N., F.X., I.M.-M., Y.N., S.T., A.C.C., P.W., W.M.E., N.T.L., A.H.M.P., J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas.,Center for Regenerative Science and Medicine (H.A.S.), University of Texas Southwestern Medical Center, Dallas.,Department of Molecular Biology (J.A.H., H.A.S.), University of Texas Southwestern Medical Center, Dallas
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14
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Lee DP, Tan WLW, Anene-Nzelu CG, Lee CJM, Li PY, Luu TDA, Chan CX, Tiang Z, Ng SL, Huang X, Efthymios M, Autio MI, Jiang J, Fullwood MJ, Prabhakar S, Lieberman Aiden E, Foo RSY. Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response. Circulation 2020; 139:1937-1956. [PMID: 30717603 DOI: 10.1161/circulationaha.118.036726] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The human genome folds in 3 dimensions to form thousands of chromatin loops inside the nucleus, encasing genes and cis-regulatory elements for accurate gene expression control. Physical tethers of loops are anchored by the DNA-binding protein CTCF and the cohesin ring complex. Because heart failure is characterized by hallmark gene expression changes, it was recently reported that substantial CTCF-related chromatin reorganization underpins the myocardial stress-gene response, paralleled by chromatin domain boundary changes observed in CTCF knockout. METHODS We undertook an independent and orthogonal analysis of chromatin organization with mouse pressure-overload model of myocardial stress (transverse aortic constriction) and cardiomyocyte-specific knockout of Ctcf. We also downloaded published data sets of similar cardiac mouse models and subjected them to independent reanalysis. RESULTS We found that the cardiomyocyte chromatin architecture remains broadly stable in transverse aortic constriction hearts, whereas Ctcf knockout resulted in ≈99% abolition of global chromatin loops. Disease gene expression changes correlated instead with differential histone H3K27-acetylation enrichment at their respective proximal and distal interacting genomic enhancers confined within these static chromatin structures. Moreover, coregulated genes were mapped out as interconnected gene sets on the basis of their multigene 3D interactions. CONCLUSIONS This work reveals a more stable genome-wide chromatin framework than previously described. Myocardial stress-gene transcription responds instead through H3K27-acetylation enhancer enrichment dynamics and gene networks of coregulation. Robust and intact CTCF looping is required for the induction of a rapid and accurate stress response.
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Affiliation(s)
- Dominic Paul Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Wilson Lek Wen Tan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chukwuemeka George Anene-Nzelu
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chang Jie Mick Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Peter Yiqing Li
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Tuan Danh Anh Luu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Cheryl Xueli Chan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Zenia Tiang
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Shi Ling Ng
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Xingfan Huang
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Motakis Efthymios
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Matias I Autio
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Jianming Jiang
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
- Department of Biochemistry, School of Medicine (J.J.), National University of Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute (M.J.F.), National University of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore (M.J.F.)
| | - Shyam Prabhakar
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
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15
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Cardoso AC, Lam NT, Savla JJ, Nakada Y, Pereira AHM, Elnwasany A, Menendez-Montes I, Ensley EL, Petric UB, Sharma G, Sherry AD, Malloy CR, Khemtong C, Kinter MT, Tan WLW, Anene-Nzelu CG, Foo RSY, Nguyen NUN, Li S, Ahmed MS, Elhelaly WM, Abdisalaam S, Asaithamby A, Xing C, Kanchwala M, Vale G, Eckert KM, Mitsche MA, McDonald JG, Hill JA, Huang L, Shaul PW, Szweda LI, Sadek HA. Mitochondrial Substrate Utilization Regulates Cardiomyocyte Cell Cycle Progression. Nat Metab 2020; 2:167-178. [PMID: 32617517 PMCID: PMC7331943] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The neonatal mammalian heart is capable of regeneration for a brief window of time after birth. However, this regenerative capacity is lost within the first week of life, which coincides with a postnatal shift from anaerobic glycolysis to mitochondrial oxidative phosphorylation, particularly towards fatty-acid utilization. Despite the energy advantage of fatty-acid beta-oxidation, cardiac mitochondria produce elevated rates of reactive oxygen species when utilizing fatty acids, which is thought to play a role in cardiomyocyte cell-cycle arrest through induction of DNA damage and activation of DNA-damage response (DDR) pathway. Here we show that inhibiting fatty-acid utilization promotes cardiomyocyte proliferation in the postnatatal heart. First, neonatal mice fed fatty-acid deficient milk showed prolongation of the postnatal cardiomyocyte proliferative window, however cell cycle arrest eventually ensued. Next, we generated a tamoxifen-inducible cardiomyocyte-specific, pyruvate dehydrogenase kinase 4 (PDK4) knockout mouse model to selectively enhance oxidation of glycolytically derived pyruvate in cardiomyocytes. Conditional PDK4 deletion resulted in an increase in pyruvate dehydrogenase activity and consequently an increase in glucose relative to fatty-acid oxidation. Loss of PDK4 also resulted in decreased cardiomyocyte size, decreased DNA damage and expression of DDR markers and an increase in cardiomyocyte proliferation. Following myocardial infarction, inducible deletion of PDK4 improved left ventricular function and decreased remodelling. Collectively, inhibition of fatty-acid utilization in cardiomyocytes promotes proliferation, and may be a viable target for cardiac regenerative therapies.
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Affiliation(s)
- Alisson C. Cardoso
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Brazilian Biosciences National Laboratory, Brazilian Center
for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Nicholas T. Lam
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Jainy J. Savla
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Yuji Nakada
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Ana Helena M. Pereira
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Brazilian Biosciences National Laboratory, Brazilian Center
for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Abdallah Elnwasany
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Ivan Menendez-Montes
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Emily L. Ensley
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Ursa Bezan Petric
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Gaurav Sharma
- Advanced Imaging Research Center, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - A. Dean Sherry
- Advanced Imaging Research Center, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern
Medical Center, Dallas, Texas, USA
- Department of Chemistry, University of Texas in Dallas,
Dallas, Texas, USA
| | - Craig R. Malloy
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Advanced Imaging Research Center, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern
Medical Center, Dallas, Texas, USA
| | - Chalermchai Khemtong
- Advanced Imaging Research Center, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Department of Radiology, University of Texas Southwestern
Medical Center, Dallas, Texas, USA
| | - Michael T. Kinter
- Aging and Metabolism Research Program, Oklahoma Medical
Research Foundation, Oklahoma City, Oklahoma, USA
| | - Wilson Lek Wen Tan
- Cardiovascular Research Institute, National University
Health Systems, Singapore, Genome Institute of Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University
Health Systems, Singapore, Genome Institute of Singapore, Singapore
| | - Roger Sik-Yin Foo
- Cardiovascular Research Institute, National University
Health Systems, Singapore, Genome Institute of Singapore, Singapore
| | - Ngoc Uyen Nhi Nguyen
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Shujuan Li
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatric Cardiology, the First Affiliated
Hospital of Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen
University), Guangzhou, China
| | - Mahmoud Salama Ahmed
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Waleed M. Elhelaly
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Salim Abdisalaam
- Department of Radiation Oncology, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Aroumougame Asaithamby
- Department of Radiation Oncology, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Chao Xing
- McDermontt Center for Human Growth and Development,
University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mohammed Kanchwala
- McDermontt Center for Human Growth and Development,
University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Goncalo Vale
- Center for Human Nutrition, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Kaitlyn M. Eckert
- Center for Human Nutrition, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Matthew A Mitsche
- Center for Human Nutrition, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Jeffrey G. McDonald
- Center for Human Nutrition, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Department of Molecular Genetics, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph A. Hill
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Linzhang Huang
- Center for Pulmonary and Vascular Biology, Department of
Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas,
USA
| | - Philip W. Shaul
- Center for Pulmonary and Vascular Biology, Department of
Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas,
USA
| | - Luke I. Szweda
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
| | - Hesham A. Sadek
- Department of Internal Medicine, University of Texas
Southwestern Medical Center, Dallas, Texas, USA
- Center for Regenerative Science and Medicine, University
of Texas Southwestern Medical Center, Dallas, Texas, USA
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16
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Affiliation(s)
- Roger Sik-Yin Foo
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (R.S.-Y.F., C.G.A.-N.)
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (R.S.-Y.F., C.G.A.-N.).,Genome Institute of Singapore (C.G.A.-N.)
| | - Manuel Rosa-Garrido
- Departments of Anesthesiology, Medicine and Physiology, David Geffen School of Medicine at UCLA (M.R.-G., T.M.V.)
| | - Thomas M Vondriska
- Departments of Anesthesiology, Medicine and Physiology, David Geffen School of Medicine at UCLA (M.R.-G., T.M.V.)
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17
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Anene-Nzelu CG, Peh KY, Fraiszudeen A, Kuan YH, Ng SH, Toh YC, Leo HL, Yu H. Scalable alignment of three-dimensional cellular constructs in a microfluidic chip. Lab Chip 2013; 13:4124-4133. [PMID: 23969512 DOI: 10.1039/c3lc50730k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
There have been considerable efforts to engineer three-dimensional (3D) microfluidic environments to enhance cellular function over conventional two-dimensional (2D) cultures in microfluidic chips, but few involve topographical features, such as micro/nano-grooves, which are beneficial for cell types of cardiac, skeletal and neuronal lineages. Here we have developed a cost-effective and scalable method to incorporate micro-topographical cues into microfluidic chips to induce cell alignment. Using commercially available optical media as molds for replica molding, we produced large surface areas of polydimethylsiloxane (PDMS) micro-grooved substrates and plasma-bonded them to multiple microfluidic chips. Besides aligning a 2D monolayer of cells, the micro-grooved substrate can align 3D cellular constructs on chip. C2C12 mouse myoblasts were cultured three-dimensionally in a microfluidic chip with incorporated PDMS micro-grooved substrate remodeled into an aligned 3D cellular construct, where the actin cytoskeleton and nuclei were preferentially oriented along the micro-grooves. Cells within the 3D cellular constructs can align without being in direct contact with the micro-grooves due to synergism between topography and fluid shear stress. Aligned C2C12 3D cellular constructs showed enhanced differentiation into skeletal muscles as compared to randomly aligned ones. This novel method enables the routine inclusion of micro-topographical cues into 2D or 3D microfluidic cultures to generate relevant physiological models for studying tissue morphogenesis and drug screening applications.
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Affiliation(s)
- Chukwuemeka George Anene-Nzelu
- Department of Bioengineering, National University of Singapore, Block EA, #03-12, 9 Engineering Drive 1, Singapore 117576, Singapore
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