1
|
Wang Z, Miao QR, Xu S, Pillai ICL, Rau CD. Editorial: Community series in epigenetic regulation in cardiovascular diseases, volume III. Front Cardiovasc Med 2024; 11:1406370. [PMID: 38689860 PMCID: PMC11059069 DOI: 10.3389/fcvm.2024.1406370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Affiliation(s)
- Zhihua Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Robert Miao
- Grossman Long Island School of Medicine, New York University, Mineola, NY, United States
| | - Suowen Xu
- Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Indulekha C. L. Pillai
- Stem Cells and Regenerative Biology Laboratory, School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Christoph D. Rau
- Computational Medicine Program and Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| |
Collapse
|
2
|
Liu J, Liu T, Ren S(V, Zhu C, Bouso E, Mamlouk S, Rau CD, Wang Y, Gao C. Metabolic status differentiates Trp53inp2 function in pressure-overload induced heart failure. Front Cardiovasc Med 2023; 10:1226586. [PMID: 38188257 PMCID: PMC10766701 DOI: 10.3389/fcvm.2023.1226586] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Cardiometabolic disorders encompass a broad range of cardiovascular complications associated with metabolic dysfunction. These conditions have an increasing share in the health burden worldwide due to worsening endemic of hypertension, obesity, and diabetes. Previous studies have identified Tumor Protein p53-inducible Nuclear Protein 2 (Trp53inp2) as a molecular link between hyperglycemia and cardiac hypertrophy. However, its role in cardiac pathology has never been determined in vivo. In this study, we generated a cardiac specific knockout model of Trp53inp2 (Trp53inp2-cKO) and investigated the impact of Trp53inp2 inactivation on the pathogenesis of heart failure under mechanic or/and metabolic stresses. Based on echocardiography assessment, inactivation of Trp53inp2 in heart led to accelerated onset of HFrEF in response to pressure-overload, with significantly reduced ejection fraction and elevated heart failure marker genes comparing to the control mice. In contrast, inactivation of Trp53inp2 ameliorated cardiac dysfunction induced by combined stresses of high fat diet and moderate pressure overload (Cardiometabolic Disorder Model). Moreover, Trp53inp2 inactivation led to reduced expression of glucose metabolism genes in lean, pressure-overloaded hearts. However, the same set of genes were significantly induced in the Trp53inp2-cKO hearts under both mechanical and metabolic stresses. In summary, we have demonstrated for the first time that cardiomyocyte Trp53inp2 has diametrically differential roles in the pathogenesis of heart failure and glucose regulation under mechanical vs. mechanical plus metabolic stresses. This insight suggests that Trp53inp2 may exacerbate the cardiac dysfunction during pressure overload injury but have a protective effect in cardiac diastolic function in cardiometabolic disease.
Collapse
Affiliation(s)
- Jianfang Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tian Liu
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, United States
| | - Shuxun (Vincent) Ren
- Signature Research Program in Cardiovascular and Metabolic Diseases, DukeNUS Medical School, Singapore, Singapore
| | - Cansheng Zhu
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, United States
| | - Eyad Bouso
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, United States
| | - Samir Mamlouk
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, United States
| | - Christoph D. Rau
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Yibin Wang
- Signature Research Program in Cardiovascular and Metabolic Diseases, DukeNUS Medical School, Singapore, Singapore
| | - Chen Gao
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, United States
| |
Collapse
|
3
|
Huang J, Lee JZ, Rau CD, Pezhouman A, Yokota T, Miwa H, Feldman M, Kong TK, Yang Z, Tay WT, Pushkarsky I, Kim K, Parikh SS, Udani S, Soh BS, Gao C, Stiles L, Shirihai OS, Knollmann BC, Ardehali R, Di Carlo D, Wang Y. Regulation of Postnatal Cardiomyocyte Maturation by an RNA Splicing Regulator RBFox1. Circulation 2023; 148:1263-1266. [PMID: 37844148 PMCID: PMC10593507 DOI: 10.1161/circulationaha.122.061602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/18/2023]
Affiliation(s)
- Jijun Huang
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Josh Z. Lee
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
| | - Christoph D. Rau
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Department of Genetics and Computational Medicine, University of North Carolina, Chapel Hill, NC
| | - Arash Pezhouman
- Division of Cardiology, Department of Medicine, UCLA
- Section of Cardiology, Department of Internal Medicine, Baylor College of Medicine, Houston, Texas
| | - Tomohiro Yokota
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Division of Cardiology, Department of Medicine, UCLA
- Greater Los Angeles VA Healthcare System, Department of Medicine, Los Angeles, California, USA
| | - Hiromi Miwa
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | | | - Tsz Kin Kong
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
| | - Ziyue Yang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Woan Ting Tay
- Signature Research Program of Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore
| | | | - Kyungsoo Kim
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Shan S. Parikh
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Shreya Udani
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | - Boon Seng Soh
- Institute of Molecular and Cell Biology, The Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chen Gao
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Department of Pharmacology and System Physiology, University of Cincinnati, Cincinnati, OH
| | - Linsey Stiles
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Orian S. Shirihai
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Bjorn C. Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Reza Ardehali
- Division of Cardiology, Department of Medicine, UCLA
- Section of Cardiology, Department of Internal Medicine, Baylor College of Medicine, Houston, Texas
| | - Dino Di Carlo
- Department of Bioengineering, Samueli School of Engineering, UCLA
| | - Yibin Wang
- Cardiovascular laboratory, Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine
- Signature Research Program of Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore
| |
Collapse
|
4
|
Swift SK, Purdy AL, Kolell ME, Andresen KG, Lahue C, Buddell T, Akins KA, Rau CD, O'Meara CC, Patterson M. Cardiomyocyte ploidy is dynamic during postnatal development and varies across genetic backgrounds. Development 2023; 150:dev201318. [PMID: 36912240 PMCID: PMC10113957 DOI: 10.1242/dev.201318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
Abstract
Somatic polyploidization, an adaptation by which cells increase their DNA content to support growth, is observed in many cell types, including cardiomyocytes. Although polyploidization is believed to be beneficial, progression to a polyploid state is often accompanied by loss of proliferative capacity. Recent work suggests that genetics heavily influence cardiomyocyte ploidy. However, the developmental course by which cardiomyocytes reach their final ploidy state has only been investigated in select backgrounds. Here, we assessed cardiomyocyte number, cell cycle activity, and ploidy dynamics across two divergent mouse strains: C57BL/6J and A/J. Both strains are born and reach adulthood with comparable numbers of cardiomyocytes; however, the end composition of ploidy classes and developmental progression to reach the final state differ substantially. We expand on previous findings that identified Tnni3k as a mediator of cardiomyocyte ploidy and uncover a role for Runx1 in ploidy dynamics and cardiomyocyte cell division, in both developmental and injury contexts. These data provide novel insights into the developmental path to cardiomyocyte polyploidization and challenge the paradigm that hypertrophy is the sole mechanism for growth in the postnatal heart.
Collapse
Affiliation(s)
- Samantha K. Swift
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Alexandra L. Purdy
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Mary E. Kolell
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Kaitlyn G. Andresen
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Caitlin Lahue
- University of North Carolina School of Medicine, Department of Genetics, Chapel Hill, NC 27599, USA
| | - Tyler Buddell
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
- Medical College of Wisconsin, Cardiovascular Center, Milwaukee, WI 53226, USA
| | - Kaelin A. Akins
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
| | - Christoph D. Rau
- University of North Carolina School of Medicine, Department of Genetics, Chapel Hill, NC 27599, USA
| | - Caitlin C. O'Meara
- Medical College of Wisconsin, Cardiovascular Center, Milwaukee, WI 53226, USA
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI 53226, USA
| | - Michaela Patterson
- Medical College of Wisconsin, Department of Cell Biology, Neurobiology, and Anatomy, Milwaukee, WI 53226, USA
- Medical College of Wisconsin, Cardiovascular Center, Milwaukee, WI 53226, USA
| |
Collapse
|
5
|
Yu JY, Cao N, Rau CD, Lee RP, Yang J, Flach RJR, Petersen L, Zhu C, Pak YL, Miller RA, Liu Y, Wang Y, Li Z, Sun H, Gao C. Cell-autonomous effect of cardiomyocyte branched-chain amino acid catabolism in heart failure in mice. Acta Pharmacol Sin 2023:10.1038/s41401-023-01076-9. [PMID: 36991098 DOI: 10.1038/s41401-023-01076-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 02/03/2023] [Accepted: 03/12/2023] [Indexed: 03/31/2023] Open
Abstract
Parallel to major changes in fatty acid and glucose metabolism, defect in branched-chain amino acid (BCAA) catabolism has also been recognized as a metabolic hallmark and potential therapeutic target for heart failure. However, BCAA catabolic enzymes are ubiquitously expressed in all cell types and a systemic BCAA catabolic defect is also manifested in metabolic disorder associated with obesity and diabetes. Therefore, it remains to be determined the cell-autonomous impact of BCAA catabolic defect in cardiomyocytes in intact hearts independent from its potential global effects. In this study, we developed two mouse models. One is cardiomyocyte and temporal-specific inactivation of the E1α subunit (BCKDHA-cKO) of the branched-chain α-ketoacid dehydrogenase (BCKDH) complex, which blocks BCAA catabolism. Another model is cardiomyocyte specific inactivation of the BCKDH kinase (BCKDK-cKO), which promotes BCAA catabolism by constitutively activating BCKDH activity in adult cardiomyocytes. Functional and molecular characterizations showed E1α inactivation in cardiomyocytes was sufficient to induce loss of cardiac function, systolic chamber dilation and pathological transcriptome reprogramming. On the other hand, inactivation of BCKDK in intact heart does not have an impact on baseline cardiac function or cardiac dysfunction under pressure overload. Our results for the first time established the cardiomyocyte cell autonomous role of BCAA catabolism in cardiac physiology. These mouse lines will serve as valuable model systems to investigate the underlying mechanisms of BCAA catabolic defect induced heart failure and to provide potential insights for BCAA targeted therapy.
Collapse
Affiliation(s)
- Jia-Yu Yu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University of Medicine, Shanghai, 200025, China
| | - Nancy Cao
- School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Christoph D Rau
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ro-Po Lee
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Jieping Yang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Lauren Petersen
- Health Science Center, University of Utah, Salt Lake City, UT, USA
| | - Cansheng Zhu
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, USA
| | - Yea-Lyn Pak
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Yunxia Liu
- Signature Research Program in Cardiovascular and Metabolic Diseases, DukeNUS School of Medicine and National Heart Center of Singapore, Singapore, Singapore
| | - Yibin Wang
- Signature Research Program in Cardiovascular and Metabolic Diseases, DukeNUS School of Medicine and National Heart Center of Singapore, Singapore, Singapore
| | - Zhaoping Li
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Haipeng Sun
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University of Medicine, Shanghai, 200025, China
| | - Chen Gao
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, USA.
| |
Collapse
|
6
|
Xu S, Pillai ICL, Rau CD, Wang Z. Editorial: Epigenetic regulation in cardiovascular diseases, volume II. Front Cardiovasc Med 2023; 10:1166268. [PMID: 36950284 PMCID: PMC10025521 DOI: 10.3389/fcvm.2023.1166268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Affiliation(s)
- Suowen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, China
- Correspondence: Suowen Xu Indulekha C. L. Pillai Christoph D. Rau Zhihua Wang
| | - Indulekha C. L. Pillai
- Stem Cells and Regenerative Biology Laboratory, School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Correspondence: Suowen Xu Indulekha C. L. Pillai Christoph D. Rau Zhihua Wang
| | - Christoph D. Rau
- Department of Genetics and Computational Medicine Program, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Correspondence: Suowen Xu Indulekha C. L. Pillai Christoph D. Rau Zhihua Wang
| | - Zhihua Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Correspondence: Suowen Xu Indulekha C. L. Pillai Christoph D. Rau Zhihua Wang
| |
Collapse
|
7
|
Swift SK, Kolell ME, Purdy AL, Flinn MA, O'Meara CC, Rau CD, Patterson M. Abstract P1113: Ploidy Reversal As A Postnatal Developmental Program In Murine Hearts. Circ Res 2022. [DOI: 10.1161/res.131.suppl_1.p1113] [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
Polyploidization is a normal cellular adaptation for a variety of cell types in mammals, including cardiomyocytes (CMs); however, the development of polyploidization understudied. Recent work suggests that genetics contribute to diverse displays of ploidy in the adult murine heart. Therefore, we hypothesized that the developmental progression to reach differing end-states may similarly be affected. Here, we assessed CM endowment, cell cycle, and ploidy temporally across two diverse inbred mouse strains, A/J and C57Bl/6J. Consistent with previous work, C57Bl/6J hearts displayed rapid cell cycle activation in the first postnatal week largely coinciding with the first round of endomitosis. Total CM numbers are relatively unchanged after P7, while final ploidy states are generally constant from P14 on. In contrast, A/J mice displayed depressed cell cycle activation in the first week of life. Polyploidy in A/Js reaches its peak at P21, whereby only ~3.5% of CMs remained mononuclear and diploid. Interestingly, from 3-6 weeks of age, we observed a dramatic expansion of total CM numbers and of the 1x2N subpopulation to ~8%, which could not be explained by proliferation of the residual diploid population. Instead, the expanded diploid population appears to come from a polyploid CM. This finding was confirmed by analysis identifying a population of CMs which had definitively completed cytokinesis by 6 weeks which was not present at 3 weeks. We believe this is the first report of ploidy reversal by a mammalian CM, a phenomenon first observed by the hepatocyte field. Ongoing single nuclear RNA seq is examining the transcriptomic differences between A/J and C57Bl/6J CMs at P21 to identify this unique “primed” population competent to undergo ploidy reversal. Preliminary results from this study suggest that AJ CM nuclei, regardless of their ploidy, are more likely to be in the cell cycle in comparison to C57. Understanding the developmental paths to end state CM endowment and ploidy states can help us understand the biology of organ size and reciprocally can be applied to stimulating regeneration.
Collapse
|
8
|
Cao Y, Vergnes L, Wang YC, Pan C, Chella Krishnan K, Moore TM, Rosa-Garrido M, Kimball TH, Zhou Z, Charugundla S, Rau CD, Seldin MM, Wang J, Wang Y, Vondriska TM, Reue K, Lusis AJ. Sex differences in heart mitochondria regulate diastolic dysfunction. Nat Commun 2022; 13:3850. [PMID: 35787630 PMCID: PMC9253085 DOI: 10.1038/s41467-022-31544-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 07/27/2021] [Accepted: 06/15/2022] [Indexed: 01/10/2023] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) exhibits a sex bias, being more common in women than men, and we hypothesize that mitochondrial sex differences might underlie this bias. As part of genetic studies of heart failure in mice, we observe that heart mitochondrial DNA levels and function tend to be reduced in females as compared to males. We also observe that expression of genes encoding mitochondrial proteins are higher in males than females in human cohorts. We test our hypothesis in a panel of genetically diverse inbred strains of mice, termed the Hybrid Mouse Diversity Panel (HMDP). Indeed, we find that mitochondrial gene expression is highly correlated with diastolic function, a key trait in HFpEF. Consistent with this, studies of a "two-hit" mouse model of HFpEF confirm that mitochondrial function differs between sexes and is strongly associated with a number of HFpEF traits. By integrating data from human heart failure and the mouse HMDP cohort, we identify the mitochondrial gene Acsl6 as a genetic determinant of diastolic function. We validate its role in HFpEF using adenoviral over-expression in the heart. We conclude that sex differences in mitochondrial function underlie, in part, the sex bias in diastolic function.
Collapse
Affiliation(s)
- Yang Cao
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Laurent Vergnes
- Metabolism Theme, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA
| | - Yu-Chen Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Calvin Pan
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Karthickeyan Chella Krishnan
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
- Department of Pharmacology and Physiology, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Timothy M Moore
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Todd H Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Zhiqiang Zhou
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Sarada Charugundla
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Christoph D Rau
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marcus M Seldin
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Jessica Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Yibin Wang
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Karen Reue
- Metabolism Theme, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA
- Molecular Biology Institute at UCLA, Los Angeles, CA, 90095, USA
| | - Aldons J Lusis
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90024, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
| |
Collapse
|
9
|
Pillai ICL, Xu S, Rau CD, Wang Z. Editorial: Epigenetic Regulation in Cardiovascular Diseases. Front Cardiovasc Med 2022; 8:831851. [PMID: 35087888 PMCID: PMC8787130 DOI: 10.3389/fcvm.2021.831851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Indulekha C. L. Pillai
- Stem Cells and Regenerative Biology Laboratory, School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Suowen Xu
- Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Christoph D. Rau
- Computational Medicine Program and Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zhihua Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Zhihua Wang
| |
Collapse
|
10
|
Baranowski BJ, Allen MD, Nyarko JN, Rector RS, Padilla J, Mousseau DD, Rau CD, Wang Y, Laughlin MH, Emter CA, MacPherson RE, Olver TD. Cerebrovascular insufficiency and amyloidogenic signaling in Ossabaw swine with cardiometabolic heart failure. JCI Insight 2021; 6:143141. [PMID: 34027891 PMCID: PMC8262360 DOI: 10.1172/jci.insight.143141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Individuals with heart failure (HF) frequently present with comorbidities, including obesity, insulin resistance, hypertension, and dyslipidemia. Many patients with HF experience cardiogenic dementia, yet the pathophysiology of this disease remains poorly understood. Using a swine model of cardiometabolic HF (Western diet+aortic banding; WD-AB), we tested the hypothesis that WD-AB would promote a multidementia phenotype involving cerebrovascular dysfunction alongside evidence of Alzheimer’s disease (AD) pathology. The results provide evidence of cerebrovascular insufficiency coupled with neuroinflammation and amyloidosis in swine with experimental cardiometabolic HF. Although cardiac ejection fraction was normal, indices of arterial compliance and cerebral blood flow were reduced, and cerebrovascular regulation was impaired in the WD-AB group. Cerebrovascular dysfunction occurred concomitantly with increased MAPK signaling and amyloidogenic processing (i.e., increased APP, BACE1, CTF, and Aβ40 in the prefrontal cortex and hippocampus) in the WD-AB group. Transcriptomic profiles of the stellate ganglia revealed the WD-AB group displayed an enrichment of gene networks associated with MAPK/ERK signaling, AD, frontotemporal dementia, and a number of behavioral phenotypes implicated in cognitive impairment. These provide potentially novel evidence from a swine model that cerebrovascular and neuronal pathologies likely both contribute to the dementia profile in a setting of cardiometabolic HF.
Collapse
Affiliation(s)
- Bradley J Baranowski
- Department of Health Sciences and.,Centre for Neuroscience, Brock University, St. Catharines, Ontario, Canada
| | - Matti D Allen
- Department of Physical Medicine and Rehabilitation, School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Jennifer Nk Nyarko
- Department of Psychiatry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - R Scott Rector
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, USA.,Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, Missouri, USA
| | - Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Darrell D Mousseau
- Department of Psychiatry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph D Rau
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yibin Wang
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - M Harold Laughlin
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, USA
| | - Craig A Emter
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, USA
| | - Rebecca Ek MacPherson
- Department of Health Sciences and.,Centre for Neuroscience, Brock University, St. Catharines, Ontario, Canada
| | - T Dylan Olver
- Department of Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
11
|
Kelly SC, Rau CD, Ouyang A, Thorne PK, Olver TD, Edwards JC, Domeier TL, Padilla J, Grisanti LA, Fleenor BS, Wang Y, Rector RS, Emter CA. The right ventricular transcriptome signature in Ossabaw swine with cardiometabolic heart failure: implications for the coronary vasculature. Physiol Genomics 2021; 53:99-115. [PMID: 33491589 PMCID: PMC7988741 DOI: 10.1152/physiolgenomics.00093.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 11/22/2022] Open
Abstract
Heart failure (HF) patients with deteriorating right ventricular (RV) structure and function have a nearly twofold increased risk of death compared with those without. Despite the well-established clinical risk, few studies have examined the molecular signature associated with this HF condition. The purpose of this study was to integrate morphological, molecular, and functional data with the transcriptome data set in the RV of a preclinical model of cardiometabolic HF. Ossabaw swine were fed either normal diet without surgery (lean control, n = 5) or Western diet and aortic-banding (WD-AB; n = 4). Postmortem RV weight was increased and positively correlated with lung weight in the WD-AB group compared with CON. Total RNA-seq was performed and gene expression profiles were compared and analyzed using principal component analysis, weighted gene co-expression network analysis, module enrichment analysis, and ingenuity pathway analysis. Gene networks specifically associated with RV hypertrophic remodeling identified a hub gene in MAPK8 (or JNK1) that was associated with the selective induction of the extracellular matrix (ECM) component fibronectin. JNK1 and fibronectin protein were increased in the right coronary artery (RCA) of WD-AB animals and associated with a decrease in matrix metalloproteinase 14 protein, which specifically degrades fibronectin. RCA fibronectin content was correlated with increased vascular stiffness evident as a decreased elastin elastic modulus in WD-AB animals. In conclusion, this study establishes a molecular and transcriptome signature in the RV using Ossabaw swine with cardiometabolic HF. This signature was associated with altered ECM regulation and increased vascular stiffness in the RCA, with selective dysregulation of fibronectin.
Collapse
Affiliation(s)
- Shannon C Kelly
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Christoph D Rau
- Department of Computational Medicine and Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - An Ouyang
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Pamela K Thorne
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - T Dylan Olver
- Department of Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jenna C Edwards
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Timothy L Domeier
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri
| | - Jaume Padilla
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Laurel A Grisanti
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Bradley S Fleenor
- Human Performance Laboratory, School of Kinesiology, Ball State University, Muncie, Indiana
| | - Yibin Wang
- David Geffen School of Medicine, University of California, Los Angeles, California
| | - R Scott Rector
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri
- Department of Medicine-Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri
- Research Service, Harry S. Truman Memorial VA Hospital, University of Missouri, Columbia, Missouri
| | - Craig A Emter
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri
| |
Collapse
|
12
|
Rau CD, Gonzales NM, Bloom JS, Park D, Ayroles J, Palmer AA, Lusis AJ, Zaitlen N. Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for "polygenic epistasis". PLoS Genet 2020; 16:e1009165. [PMID: 33104702 PMCID: PMC7644088 DOI: 10.1371/journal.pgen.1009165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/21/2020] [Revised: 11/05/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background The majority of quantitative genetic models used to map complex traits assume that alleles have similar effects across all individuals. Significant evidence suggests, however, that epistatic interactions modulate the impact of many alleles. Nevertheless, identifying epistatic interactions remains computationally and statistically challenging. In this work, we address some of these challenges by developing a statistical test for polygenic epistasis that determines whether the effect of an allele is altered by the global genetic ancestry proportion from distinct progenitors. Results We applied our method to data from mice and yeast. For the mice, we observed 49 significant genotype-by-ancestry interaction associations across 14 phenotypes as well as over 1,400 Bonferroni-corrected genotype-by-ancestry interaction associations for mouse gene expression data. For the yeast, we observed 92 significant genotype-by-ancestry interactions across 38 phenotypes. Given this evidence of epistasis, we test for and observe evidence of rapid selection pressure on ancestry specific polymorphisms within one of the cohorts, consistent with epistatic selection. Conclusions Unlike our prior work in human populations, we observe widespread evidence of ancestry-modified SNP effects, perhaps reflecting the greater divergence present in crosses using mice and yeast. Many statistical tests which link genetic markers in the genome to differences in traits rely on the assumption that the same polymorphism will have identical effects in different individuals. However, there is substantial evidence indicating that this is not the case. Epistasis is the phenomenon in which multiple polymorphisms interact with one another to amplify or negate each other’s effects on a trait. We hypothesized that individual SNP effects could be changed in a polygenic manner, such that the proportion of as genetic ancestry, rather than specific markers, might be used to capture epistatic interactions. Motivated by this possibility, we develop a new statistical test that allowed us to examine the genome to identify polymorphisms which have different effects depending on the ancestral makeup of each individual. We use our test in two different populations of inbred mice and a yeast panel and demonstrate that these sorts of variable effect polymorphisms exist in 14 different physical traits in mice and 38 phenotypes in yeast as well as in murine gene expression. We use the term “polygenic epistasis” to distinguish these interactions from the more conventional two- or multi-locus interactions.
Collapse
Affiliation(s)
- Christoph D. Rau
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Natalia M. Gonzales
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Joshua S. Bloom
- Department of Human Genetics, UCLA, Los Angeles, CA, United States of America
| | - Danny Park
- Department of Medicine, UCSF, San Francisco, CA, United States of America
| | - Julien Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States of America
| | - Abraham A. Palmer
- Department of Psychiatry, and Institute for Genomic Medicine, UCSD, San Diego, CA, United States of America
| | - Aldons J. Lusis
- Department of Human Genetics, UCLA, Los Angeles, CA, United States of America
| | - Noah Zaitlen
- Department of Neurology, UCLA, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
13
|
Krebber MM, van Dijk CGM, Vernooij RWM, Brandt MM, Emter CA, Rau CD, Fledderus JO, Duncker DJ, Verhaar MC, Cheng C, Joles JA. Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Extracellular Matrix Remodeling during Left Ventricular Diastolic Dysfunction and Heart Failure with Preserved Ejection Fraction: A Systematic Review and Meta-Analysis. Int J Mol Sci 2020; 21:ijms21186742. [PMID: 32937927 PMCID: PMC7555240 DOI: 10.3390/ijms21186742] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/01/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are pivotal regulators of extracellular matrix (ECM) composition and could, due to their dynamic activity, function as prognostic tools for fibrosis and cardiac function in left ventricular diastolic dysfunction (LVDD) and heart failure with preserved ejection fraction (HFpEF). We conducted a systematic review on experimental animal models of LVDD and HFpEF published in MEDLINE or Embase. Twenty-three studies were included with a total of 36 comparisons that reported established LVDD, quantification of cardiac fibrosis and cardiac MMP or TIMP expression or activity. LVDD/HFpEF models were divided based on underlying pathology: hemodynamic overload (17 comparisons), metabolic alteration (16 comparisons) or ageing (3 comparisons). Meta-analysis showed that echocardiographic parameters were not consistently altered in LVDD/HFpEF with invasive hemodynamic measurements better representing LVDD. Increased myocardial fibrotic area indicated comparable characteristics between hemodynamic and metabolic models. Regarding MMPs and TIMPs; MMP2 and MMP9 activity and protein and TIMP1 protein levels were mainly enhanced in hemodynamic models. In most cases only mRNA was assessed and there were no correlations between cardiac tissue and plasma levels. Female gender, a known risk factor for LVDD and HFpEF, was underrepresented. Novel studies should detail relevant model characteristics and focus on MMP and TIMP protein expression and activity to identify predictive circulating markers in cardiac ECM remodeling.
Collapse
Affiliation(s)
- Merle M. Krebber
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
| | - Christian G. M. van Dijk
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
| | - Robin W. M. Vernooij
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, P.O. Box 85500, 3508 GA Utrecht, The Netherlands
| | - Maarten M. Brandt
- Experimental Cardiology, Department of Cardiology, Thorax center, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.M.B.); (D.J.D.)
| | - Craig A. Emter
- Department of Biomedical Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA;
| | - Christoph D. Rau
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Joost O. Fledderus
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
| | - Dirk J. Duncker
- Experimental Cardiology, Department of Cardiology, Thorax center, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.M.B.); (D.J.D.)
| | - Marianne C. Verhaar
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
| | - Caroline Cheng
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
| | - Jaap A. Joles
- Department Nephrology and Hypertension, University Medical Center Utrecht, P.O. Box 8599, 3508 GA Utrecht, The Netherlands; (M.M.K.); (C.G.M.v.D.); (R.W.M.V.); (J.O.F.); (M.C.V.); (C.C.)
- Correspondence:
| |
Collapse
|
14
|
Rau CD, Romay M, Wong E, Tan W, Lusis AJ, Foo R, Wang Y. Abstract MP144: Identification of Epigenetic Regulators of Cardiac Hypertrophy by an Epigenome-wide Association Study in Mice. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.mp144] [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
We previously reported a study of heart failure in a large cohort of inbred mouse strains, the Hybrid Mouse Diversity Panel (HMDP), treated with the beta-adrenergic agonist isoproterenol, which identified over 30 genome-wide significant loci for heart failure-related traits. Our approach combined systems-level tools with the benefits of a curated model organism population to identify genetic variations that drive heart failure.
We now expand this study into the epigenome. Recent research has demonstrated that DNA methylation affects the progression of cardiovascular phenotypes. This research suggests that DNA methylation may serve as an additional marker of genes involved in heart failure-associated phenotypes. Using Reduced Representational Bisulfite Sequencing, we profiled left ventricular tissue samples from 88 strains of the HMDP both before and after isoproterenol challenge (30 mg/kg/day for 21 days). We identified approximately 168,000 CpGs that vary across the panel and associated them with a set of phenotypes in both control and treated animals using the epigenome-wide association study (EWAS) algorithm MACAU. 179 significant associations were recovered at an FDR of 5%, including loci that associated pre-treatment CpG methylation with 19 different post-treatment phenotypes.
By combining these EWAS loci with information from the Wellcome Trust Mouse Genomes Resource and prior work done in the heart failure HMDP, we identify several high-confidence candidate genes, including
Coro1a
, a gene whose pre-treatment promoter methylation status predicts post-treatment wall thickening and
Eprs
, which predicts right ventricular weight post-treatment.
Mospd3
, a gene that was associated with right ventricular weight post-treatment in both EWAS and GWAS analyses was studied further using neonatal rat ventricular myocytes. This
in vitro
work demonstrates that
Mospd3
knockdown results in reduced cellular hypertrophy and changes to hypertrophy-related gene expression. Further analysis of the EWAS loci using
in vitro
and
in
vivo techniques will likely validate additional genes and elucidate how DNA methylation acts to regulate pathways underlying heart failure.
Collapse
Affiliation(s)
| | | | - Eleanor Wong
- Genome Institute of Singapore, Singapore, Singapore
| | - Wilson Tan
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Roger Foo
- Cardiovascular Rsch Institute, Singapore
| | | |
Collapse
|
15
|
Abstract
Cardiovascular diseases are the leading cause of death worldwide. Complex diseases with highly heterogenous disease progression among patient populations, cardiovascular diseases feature multifactorial contributions from both genetic and environmental stressors. Despite significant effort utilizing multiple approaches from molecular biology to genome-wide association studies, the genetic landscape of cardiovascular diseases, particularly for the nonfamilial forms of heart failure, is still poorly understood. In the past decade, systems-level approaches based on omics technologies have become an important approach for the study of complex traits in large populations. These advances create opportunities to integrate genetic variation with other biological layers to identify and prioritize candidate genes, understand pathogenic pathways, and elucidate gene-gene and gene-environment interactions. In this review, we will highlight some of the recent progress made using systems genetics approaches to uncover novel mechanisms and molecular bases of cardiovascular pathophysiological manifestations. The key technology and data analysis platforms necessary to implement systems genetics will be described, and the current major challenges and future directions will also be discussed. For complex cardiovascular diseases, such as heart failure, systems genetics represents a powerful strategy to obtain mechanistic insights and to develop individualized diagnostic and therapeutic regiments, paving the way for precision cardiovascular medicine.
Collapse
Affiliation(s)
- Christoph D. Rau
- Departments of Anesthesiology, Medicine, Physiology
- Current address: Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Aldons J. Lusis
- Department of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, Physiology
| |
Collapse
|
16
|
Wen WTL, Wong E, Vondriska TM, Yibin W, Rau CD, Foo R. Abstract 944: Differential Dna Methylation Co-segregates With the Severity of Heart Failure. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.944] [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
Heart failure (HF) is a leading cause of morbidity and mortality worldwide. As a potential epigenetic biomarker, DNA methylation differs between healthy and diseased hearts. However, its association according to disease severity has not yet been studied. Here, we sought to investigate how DNA methylation (DNAm) differs across HF disease severity, and study the use of a DNMT methyltransferase inhibitor RG108 on DNAm and its effect on heart function. A fixed dose of Isoprenaline (ISO), or saline control (SAL), administered to a hybrid mouse diversity panel (HMDP) consisting of 85 classical and recombinant inbred mouse strains produced a range of cardiac hypertrophy and/or LV dilatation. Left ventricles were harvested and subjected to genome-wide cardiac DNAm profiling by Reduced Representation Bisulfite Sequencing (RRBS). Unsupervised clustering of the top 1% most variable CpG methylation segregated strains to their genetic origin. Disregarding strain-specific methylation differences, differential methylation between ISO and SAL unexpectedly categorised mice into mild and severe disease responders. In the severe-responder strain BTBRT, the pharmacological DNMT methyltransferase inhibitor, RG108, rescued disease from ISO-response, with accompanying evidence of gene expression recovery. This work establishes the range of cardiac differential DNAm correlating according to disease severity. It displays the involvement of DNA methylation-dependent gene expression changes that turns out to be unique, despite different mouse strain backgrounds. This gives further proof of principle that cardiac DNAm changes represent novel biomarkers for disease stratification and consequent targeted therapy.
Collapse
Affiliation(s)
| | - Eleanor Wong
- Cardiovascular Institute of Singapore, Singapore, Singapore
| | | | - Wang Yibin
- Dept of Anesthesiology and Medicine, UCLA, Los Angeles, CA
| | | | - Roger Foo
- Cardiovascular Institute of Singapore, Singapore, Singapore
| |
Collapse
|
17
|
Tzimas C, Rau CD, Buergisser PE, Jean-Louis G, Lee K, Chukwuneke J, Dun W, Wang Y, Tsai EJ. WIPI1 is a conserved mediator of right ventricular failure. JCI Insight 2019; 5:122929. [PMID: 31021818 DOI: 10.1172/jci.insight.122929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Right ventricular dysfunction is highly prevalent across cardiopulmonary diseases and independently predicts death in both heart failure (HF) and pulmonary hypertension (PH). Progression towards right ventricular failure (RVF) can occur in spite of optimal medical treatment of HF or PH, highlighting current insufficient understanding of RVF molecular pathophysiology. To identify molecular mechanisms that may distinctly underlie RVF, we investigated the cardiac ventricular transcriptome of advanced HF patients, with and without RVF. Using an integrated systems genomic and functional biology approach, we identified an RVF-specific gene module, for which WIPI1 served as a hub and HSPB6 and MAP4 as drivers, and confirmed the ventricular specificity of Wipi1, Hspb6, and Map4 transcriptional changes in adult murine models of pressure overload induced RV- versus LV- failure. We uncovered a shift towards non-canonical autophagy in the failing RV that correlated with RV-specific Wipi1 upregulation. In vitro siRNA silencing of Wipi1 in neonatal rat ventricular myocytes limited non-canonical autophagy and blunted aldosterone-induced mitochondrial superoxide levels. Our findings suggest that Wipi1 regulates mitochondrial oxidative signaling and non-canonical autophagy in cardiac myocytes. Together with our human transcriptomic analysis and corroborating studies in an RVF mouse model, these data render Wipi1 a potential target for RV-directed HF therapy.
Collapse
Affiliation(s)
- Christos Tzimas
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Christoph D Rau
- Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Petra E Buergisser
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Gaston Jean-Louis
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Katherine Lee
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute of Human Nutrition, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jeffrey Chukwuneke
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Wen Dun
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Yibin Wang
- Division of Molecular Medicine, Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Emily J Tsai
- Division of Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
18
|
Affiliation(s)
- Christoph D Rau
- From Departments of Anesthesiology and Perioperative Medicine (C.D.R., T.M.V.), Medicine (T.M.V.), and Physiology (T.M.V.), David Geffen School of Medicine at the University of California, Los Angeles.
| | - Thomas M Vondriska
- From Departments of Anesthesiology and Perioperative Medicine (C.D.R., T.M.V.), Medicine (T.M.V.), and Physiology (T.M.V.), David Geffen School of Medicine at the University of California, Los Angeles.
| |
Collapse
|
19
|
Rau CD, Wang J, Ohearn J, Avetisyan R, Lusis AJ, Wang Y. Abstract 372: Master Transcriptional Regulators of Cardiac Gene Expression in Heart Failure. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.372] [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
Background:
Heart failure (HF) is characterized by complex transcriptional networks that direct the heart from a healthy to diseased state. Although some contributing genes have been identified through molecular biology and GWAS, heritability studies suggest that many genes have resisted discovery through these approaches. Identifying connective regulatory loci, especially master transcriptional regulators that affect the expression of many genes, offers a promising means of discovering novel relevant genes that have not been detected with other methods.
Methods and Results:
Transcriptional regulators of HF were identified using nine-week-old female mice from 93 lines of the Hybrid Mouse Diversity Panel. Mice received 30 ug/g/day of isoproterenol (ISO) for 3 weeks to induce cardiac dysfunction. Transcriptomes were generated from left ventricles of these mice along with age-matched controls. Expression Quantitative Trait Loci (eQTLs) for 13,156 transcripts were identified using a mixed model in three conditions (control, treated, delta). Suggestive (P<1E-4) eQTLs were sorted into 500kb bins tiled across the genome to identify loci that regulate a significant number of transcripts. Ten hotspot loci that regulate over 5% (658 of 13156) of expressed genes were identified, several of which contain genes with known roles in HF, including
Drosha
,
Akap5
and
Dicer1
. Several novel regulators were also identified, including the Serine Proteinase Inhibitor,
Serpina3n
,
which resides in a locus that regulates the change in expression of 9.7% (1276 of 13156) of all genes and is strongly correlated with changes in heart weight after ISO treatment. In subsequent
in vitro
work,
Serpina3n
knockdown resulted in reduced cellular hypertrophy, changes to hypertrophy-related gene expression, and modulation of the expression of several genes linked to its locus.
Conclusion:
GWAS performed on over 20,000 transcripts in control and ISO-treated hearts identified 10 genomic loci that regulate over 5% of the expressed genes in the heart.
Serpina3n
is a novel master regulator of HF. Further analysis of other master regulatory loci will reveal additional genes and improve our understanding of the transcriptional networks that direct the progression towards heart failure.
Collapse
|
20
|
Gao C, Hsiao YH(E, Wang M, Xiong Z, Ren S, Rau CD, Li K, Xiao X, Wang Y, Xing Y. Abstract 263: Cytosolic RBFox1 in Cardiac Pathological Remodeling. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.263] [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
Background:
RBFox1 is known to be an RNA splicing regulator with enriched expression in cardiac muscle. Loss of RBFox1 expression is a molecular hallmark associated with heart failure in mouse and human. Genetic manipulation of RBFox1 reveals a major function of RBFox1 in the pathogenesis of cardiac hypertrophy, fibrosis and dysfunction under pathological stresses. However, much of our current knowledge about RBFox1 focuses on the nuclear RBFox1 with a major impact on global alternative splicing changes. Yet, RBFox1 gene also generates a cytosolic isoform-RBFox1c through alternative splicing, and the specific function of RBFox1c has not been characterized.
Goal and Methods:
This study investigated the functional impact and the underlying mechanism of the RBFox1c in cardiac pathological remodeling and targeted gene regulation.
Results:
RBFox1c expression is significantly repressed in stressed cardiomyocytes in vivo and in vitro. RNA-Seq combined with IPA analyses from cardiomyocytes revealed RBFox1c but not the nucleus RBFox1 specifically suppressed pro-inflammatory genes. In the cardiac specific RBFox1 knockout mice, enhanced cardiac fibrosis is observed following I/R injury associated with elevated expression of pro-inflammatory genes. In contrast, cardiac specific expression of RBFox1c reduced cardiac fibrosis and inflammatory gene expression following pressure-overload and myocardial infarct injury associated with improved ejection fraction. Motif enrichment analysis identified significant enrichment of the RBFox1 binding motif in the 3’UTR of the RBFox1c regulated genes. We performed CLIP analysis followed by RT-PCR and observed RBFox1c interacted with inflammatory gene 3’UTR. Lastly, we explored the interactome of RBFox1c and found RBFox1c specifically interacted with a component of RNA decay machinery-Upf1. Indeed, while expression of RBFox1c repressed inflammatory gene expression, inactivation of Upf1 abolished this effect in cardiomyocytes.
Conclusion:
RBFox1 regulates cardiac transcriptome reprogramming at two post-transcriptional steps. The RBFox1 nuclei isoform regulates RNA splicing reprogramming, and the RBFox1c represses proinflammatory genes via recruitment of Upf1 mediated RNA degradation.
Collapse
Affiliation(s)
- Chen Gao
- UCLA-Los Angeles, Los Angeles, CA
| | | | | | | | | | | | | | | | | | - Yi Xing
- UCLA-Los Angeles, Los Angeles, CA
| |
Collapse
|
21
|
Abstract
Isoproterenol is used widely for inducing heart failure in mice. Isoproterenol is a nonselective beta-adrenergic agonist. The acute model mimics stress-induced cardiomyopathy. The chronic model mimics advanced heart failure in humans. In this chapter, we describe a protocol that we used to induce heart failure in 100+ strains of inbred mice. Techniques on surgical pump implantation and echocardiography are described in detail. We also discuss the impact of drug dosage, duration, mortality, age, gender, and strain on cardiac remodeling responses. The success of model creation may be assessed by echocardiogram or molecular markers. This chapter may be relevant to those who are interested in using this heart failure model.
Collapse
Affiliation(s)
- Sunny C Chang
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Shuxun Ren
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Christoph D Rau
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jessica J Wang
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
| |
Collapse
|
22
|
Patterson M, Barske L, Van Handel B, Rau CD, Gan P, Sharma A, Parikh S, Denholtz M, Huang Y, Yamaguchi Y, Shen H, Allayee H, Crump JG, Force TI, Lien CL, Makita T, Lusis AJ, Kumar SR, Sucov HM. Frequency of mononuclear diploid cardiomyocytes underlies natural variation in heart regeneration. Nat Genet 2017; 49:1346-1353. [PMID: 28783163 DOI: 10.1038/ng.3929] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
Adult mammalian cardiomyocyte regeneration after injury is thought to be minimal. Mononuclear diploid cardiomyocytes (MNDCMs), a relatively small subpopulation in the adult heart, may account for the observed degree of regeneration, but this has not been tested. We surveyed 120 inbred mouse strains and found that the frequency of adult mononuclear cardiomyocytes was surprisingly variable (>7-fold). Cardiomyocyte proliferation and heart functional recovery after coronary artery ligation both correlated with pre-injury MNDCM content. Using genome-wide association, we identified Tnni3k as one gene that influences variation in this composition and demonstrated that Tnni3k knockout resulted in elevated MNDCM content and increased cardiomyocyte proliferation after injury. Reciprocally, overexpression of Tnni3k in zebrafish promoted cardiomyocyte polyploidization and compromised heart regeneration. Our results corroborate the relevance of MNDCMs in heart regeneration. Moreover, they imply that intrinsic heart regeneration is not limited nor uniform in all individuals, but rather is a variable trait influenced by multiple genes.
Collapse
Affiliation(s)
- Michaela Patterson
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Lindsey Barske
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ben Van Handel
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Christoph D Rau
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Peiheng Gan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Avneesh Sharma
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Shan Parikh
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matt Denholtz
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Ying Huang
- Program of Developmental Biology and Regenerative Medicine, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Yukiko Yamaguchi
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hua Shen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Thomas I Force
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ching-Ling Lien
- Program of Developmental Biology and Regenerative Medicine, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Takako Makita
- Developmental Neuroscience Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - S Ram Kumar
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Henry M Sucov
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
23
|
Rau CD, Romay M, Wong E, Tan W, Lusis AJ, Foo R, Wang Y. Abstract 324: Identification of Regulators of Cardiac DNA Methylation Using a Systems Genetics Approach in Mice. Circ Res 2017. [DOI: 10.1161/res.121.suppl_1.324] [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
Systems biology approaches to studying heart failure in humans are hampered by numerous environmental factors and inciting incidents which combine to complicate the application of standard population-based tools and algorithms to the syndrome. We recently reported a study of heart failure in a large cohort of inbred mouse strains (the Hybrid Mouse Diversity Panel; HMDP) treated with the beta-adrenergic agonist isoproterenol. We demonstrated that it was possible to combine systems-level tools with the benefits of an animal model to capture and identify numerous genetic variations which drive heart failure.
Recent research on the epigenome has identified changes to DNA methylation which affect the progression of cardiovascular diseases and suggests that DNA methylation may serve as an important additional marker or even driver of genes involved in heart failure-associated phenotypes. We have supplemented our prior study by completing reduced representational bisulfite sequencing on 88 strains from our panel both with and without catecholamine challenge.
We have identified 75,000 CpGs which vary among the strains of the HMDP across the genome. Each CpG was mapped to the genome using GWAS to identify methylation quantitative trait loci (mQTLs). These mQTLs were then grouped together to identify mQTL hotspots, regions on the genome which regulate a sizable fractions of all observed CpGs. We then overlapped these hotspots with hotspots which regulate the expression of gene transcripts.
Three genomic regions were identified as multi-omic master regulators which affect both DNA methylation and gene expression for over 5% of the expressed transcripts and varying CpGs. Closer examination of these loci identified the serine peptidase inhibitor
Serpina3n
as a likely candidate gene for the regulation of DNA methylation, gene expression and cardiac phenotypes. Subsequent
in vitro
and
in vivo
work demonstrate that
Serpina3n
knockdown results in reduced cellular hypertrophy and changes to hypertrophy-related gene expression. Further analysis of the other master regulatory regions will likely reveal additional genes which will improve our understanding of how DNA methylation acts to regulate pathways underlying heart failure.
Collapse
Affiliation(s)
| | | | - Eleanor Wong
- National Institute of Singapore, Singapore, Singapore
| | - Wilson Tan
- National Institute of Singapore, Singapore, Singapore
| | | | - Roger Foo
- National Institute of Singapore, Singapore, Singapore
| | | |
Collapse
|
24
|
Seldin MM, Kim ED, Romay MC, Li S, Rau CD, Wang JJ, Krishnan KC, Wang Y, Deb A, Lusis AJ. A systems genetics approach identifies Trp53inp2 as a link between cardiomyocyte glucose utilization and hypertrophic response. Am J Physiol Heart Circ Physiol 2017; 312:H728-H741. [PMID: 28235788 PMCID: PMC5407157 DOI: 10.1152/ajpheart.00068.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Cardiac failure has been widely associated with an increase in glucose utilization. The aim of our study was to identify factors that mechanistically bridge this link between hyperglycemia and heart failure. Here, we screened the Hybrid Mouse Diversity Panel (HMDP) for substrate-specific cardiomyocyte candidates based on heart transcriptional profile and circulating nutrients. Next, we utilized an in vitro model of rat cardiomyocytes to demonstrate that the gene expression changes were in direct response to substrate abundance. After overlaying candidates of interest with a separate HMDP study evaluating isoproterenol-induced heart failure, we chose to focus on the gene Trp53inp2 as a cardiomyocyte glucose utilization-specific factor. Trp53inp2 gene knockdown in rat cardiomyocytes reduced expression and protein abundance of key glycolytic enzymes. This resulted in reduction of both glucose uptake and glycogen content in cardiomyocytes stimulated with isoproterenol. Furthermore, this reduction effectively blunted the capacity of glucose and isoprotereonol to synergistically induce hypertrophic gene expression and cell size expansion. We conclude that Trp53inp2 serves as regulator of cardiomyocyte glycolytic activity and can consequently regulate hypertrophic response in the context of elevated glucose content.NEW & NOTEWORTHY Here, we apply a novel method for screening transcripts based on a substrate-specific expression pattern to identify Trp53inp2 as an induced cardiomyocyte glucose utilization factor. We further show that reducing expression of the gene could effectively blunt hypertrophic response in the context of elevated glucose content.
Collapse
Affiliation(s)
- Marcus M Seldin
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Eric D Kim
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Milagros C Romay
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Shen Li
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Christoph D Rau
- Department of Anesthesiology, University of California Los Angeles, Los Angeles, California
| | - Jessica J Wang
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Karthickeyan Chella Krishnan
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Yibin Wang
- Department of Anesthesiology, University of California Los Angeles, Los Angeles, California
| | - Arjun Deb
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| | - Aldons J Lusis
- Department of Medicine, Cardiology Division at the University of California Los Angeles, Los Angeles, California; and
| |
Collapse
|
25
|
Rau CD, Romay MC, Tuteryan M, Wang JJC, Santolini M, Ren S, Karma A, Weiss JN, Wang Y, Lusis AJ. Systems Genetics Approach Identifies Gene Pathways and Adamts2 as Drivers of Isoproterenol-Induced Cardiac Hypertrophy and Cardiomyopathy in Mice. Cell Syst 2017; 4:121-128.e4. [PMID: 27866946 PMCID: PMC5338604 DOI: 10.1016/j.cels.2016.10.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
We previously reported a genetic analysis of heart failure traits in a population of inbred mouse strains treated with isoproterenol to mimic catecholamine-driven cardiac hypertrophy. Here, we apply a co-expression network algorithm, wMICA, to perform a systems-level analysis of left ventricular transcriptomes from these mice. We describe the features of the overall network but focus on a module identified in treated hearts that is strongly related to cardiac hypertrophy and pathological remodeling. Using the causal modeling algorithm NEO, we identified the gene Adamts2 as a putative regulator of this module and validated the predictive value of NEO using small interfering RNA-mediated knockdown in neonatal rat ventricular myocytes. Adamts2 silencing regulated the expression of the genes residing within the module and impaired isoproterenol-induced cellular hypertrophy. Our results provide a view of higher order interactions in heart failure with potential for diagnostic and therapeutic insights.
Collapse
Affiliation(s)
- Christoph D Rau
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Milagros C Romay
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mary Tuteryan
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jessica J-C Wang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marc Santolini
- Center for Interdisciplinary Research on Complex Systems, Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Shuxun Ren
- Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alain Karma
- Center for Interdisciplinary Research on Complex Systems, Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - James N Weiss
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yibin Wang
- Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
26
|
Rau CD, Civelek M, Pan C, Lusis AJ. A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel. Methods Mol Biol 2017; 1488:153-188. [PMID: 27933524 DOI: 10.1007/978-1-4939-6427-7_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In this chapter we address the recent explosion in large multilevel population studies such as the METSIM study in humans as well as large panels of animal models such as the Hybrid Mouse Diversity Panel or the BXD set of recombinant inbred strains. These studies have harnessed the increasing affordability of large-scale high-throughput profiling to gather massive quantities of data. These datasets, spread across different -omics levels (genome, transcriptome, etc.), different tissues (e.g. heart, plasma, bone) and different environmental factors (e.g. diet, drugs) each individually have led to a number of novel findings relevant to a variety of complex diseases and other phenotypes. The analysis of these results, however, is often limited to individuals with a comprehensive understanding of database languages such as SQL. In this chapter, we describe the development of a GUI-based database analysis suite, using the Hybrid Mouse Diversity Panel as an example to lay out a series of methods for visualization and integration of large systems genetics datasets. The database is based on the Shiny suite of tools in R, and is transferrable to other SQL-based datasets.
Collapse
Affiliation(s)
- Christoph D Rau
- Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Calvin Pan
- Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, University of California, Campus - 167917, BH-307 CHS, 10833 Le Conte Ave., Los Angeles, CA, USA.
| |
Collapse
|
27
|
Abstract
A systems approach deconvolutes genes specific to and enriched in endothelium from whole-organ transcriptome data, with applications to other cell types and tissues.
Collapse
Affiliation(s)
- Christoph D Rau
- Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Gao
- Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yibin Wang
- Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
28
|
Rau CD, Romay M, Wang J, Lusis AJ, Wang Y. Abstract 133: A Systems Genetics Approach to Identify Genetic Pathways and Key Drivers of Isoproterenol-induced Cardiac Hypertrophy and Cardiomyopathy in Mice. Circ Res 2016. [DOI: 10.1161/res.119.suppl_1.133] [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
Heart Failure (HF) is a complex disease involving numerous environmental and genetic factors. We previously reported a genetic analysis of HF traits in a population of inbred mouse strains treated with isoproterenol, a β-adrenergic agonist used to mimic catecholamine-driven cardiac hypertrophy. We now present a systems genetics analysis in which we have used left ventricular transcript levels from these mice to perform co-expression network modeling. We constructed gene networks composed of 8,126 genes and 20 modules using the wMICA algorithm. In the wMICA network generated from treated hearts, we identified a module with significant correlations to several HF-related phenotypic traits. Further analysis of this module showed significant over-representation of genes known to contribute to the development of HF. Using the causal modeling algorithm NEO, we identified the gene
Adamts2
as a putative master regulator of the module. We then validated the role of this gene through siRNA-mediated knockdown in neonatal rat ventricular myocytes (NRVM). Consistent with our model,
Adamts2
silencing was able to regulate the expression of the genes residing within the module as well as impairing isoproterenol-induced cell size changes
.
Our results provide a view of higher order interactions in heart failure with potential to facilitate diagnostic and therapeutic approaches.
Collapse
|
29
|
Karbassi E, Monte E, Chapski DJ, Lopez R, Rosa Garrido M, Kim J, Wisniewski N, Rau CD, Wang JJ, Weiss JN, Wang Y, Lusis AJ, Vondriska TM. Relationship of disease-associated gene expression to cardiac phenotype is buffered by genetic diversity and chromatin regulation. Physiol Genomics 2016; 48:601-15. [PMID: 27287924 DOI: 10.1152/physiolgenomics.00035.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/04/2016] [Indexed: 12/11/2022] Open
Abstract
Expression of a cohort of disease-associated genes, some of which are active in fetal myocardium, is considered a hallmark of transcriptional change in cardiac hypertrophy models. How this transcriptome remodeling is affected by the common genetic variation present in populations is unknown. We examined the role of genetics, as well as contributions of chromatin proteins, to regulate cardiac gene expression and heart failure susceptibility. We examined gene expression in 84 genetically distinct inbred strains of control and isoproterenol-treated mice, which exhibited varying degrees of disease. Unexpectedly, fetal gene expression was not correlated with hypertrophic phenotypes. Unbiased modeling identified 74 predictors of heart mass after isoproterenol-induced stress, but these predictors did not enrich for any cardiac pathways. However, expanded analysis of fetal genes and chromatin remodelers as groups correlated significantly with individual systemic phenotypes. Yet, cardiac transcription factors and genes shown by gain-/loss-of-function studies to contribute to hypertrophic signaling did not correlate with cardiac mass or function in disease. Because the relationship between gene expression and phenotype was strain specific, we examined genetic contribution to expression. Strikingly, strains with similar transcriptomes in the basal heart did not cluster together in the isoproterenol state, providing comprehensive evidence that there are different genetic contributors to physiological and pathological gene expression. Furthermore, the divergence in transcriptome similarity versus genetic similarity between strains is organ specific and genome-wide, suggesting chromatin is a critical buffer between genetics and gene expression.
Collapse
Affiliation(s)
- Elaheh Karbassi
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Emma Monte
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Douglas J Chapski
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Rachel Lopez
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Manuel Rosa Garrido
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Joseph Kim
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Nicholas Wisniewski
- Department of Integrative Biology and Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Christoph D Rau
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Jessica J Wang
- Department of Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - James N Weiss
- Department of Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Yibin Wang
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Microbiology Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California; and
| | - Thomas M Vondriska
- Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California; Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California
| |
Collapse
|
30
|
Monte E, Rosa-Garrido M, Karbassi E, Chen H, Lopez R, Rau CD, Wang J, Nelson SF, Wu Y, Stefani E, Lusis AJ, Wang Y, Kurdistani SK, Franklin S, Vondriska TM. Reciprocal Regulation of the Cardiac Epigenome by Chromatin Structural Proteins Hmgb and Ctcf: IMPLICATIONS FOR TRANSCRIPTIONAL REGULATION. J Biol Chem 2016; 291:15428-46. [PMID: 27226577 DOI: 10.1074/jbc.m116.719633] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 02/05/2023] Open
Abstract
Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications, and other chromatin features at pathology-associated genes. The extent to which genome-wide chromatin reorganization also contributes to the resultant changes in gene expression remains unknown. We examined the roles of two chromatin structural proteins, Ctcf (CCCTC-binding factor) and Hmgb2 (high mobility group protein B2), in regulating pathologic transcription and chromatin remodeling. Our data demonstrate a reciprocal relationship between Hmgb2 and Ctcf in controlling aspects of chromatin structure and gene expression. Both proteins regulate each others' expression as well as transcription in cardiac myocytes; however, only Hmgb2 does so in a manner that involves global reprogramming of chromatin accessibility. We demonstrate that the actions of Hmgb2 on local chromatin accessibility are conserved across genomic loci, whereas the effects on transcription are loci-dependent and emerge in concert with histone modification and other chromatin features. Finally, although both proteins share gene targets, Hmgb2 and Ctcf, neither binds these genes simultaneously nor do they physically colocalize in myocyte nuclei. Our study uncovers a previously unknown relationship between these two ubiquitous chromatin proteins and provides a mechanistic explanation for how Hmgb2 regulates gene expression and cellular phenotype. Furthermore, we provide direct evidence for structural remodeling of chromatin on a genome-wide scale in the setting of cardiac disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Yong Wu
- From the Departments of Anesthesiology
| | | | - Aldons J Lusis
- Medicine, Human Genetics, Microbiology, Immunology and Molecular Genetics, and
| | - Yibin Wang
- From the Departments of Anesthesiology, Medicine, Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095 and
| | | | - Sarah Franklin
- the Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112
| | - Thomas M Vondriska
- From the Departments of Anesthesiology, Medicine, Physiology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095 and
| |
Collapse
|
31
|
Lusis AJ, Seldin MM, Allayee H, Bennett BJ, Civelek M, Davis RC, Eskin E, Farber CR, Hui S, Mehrabian M, Norheim F, Pan C, Parks B, Rau CD, Smith DJ, Vallim T, Wang Y, Wang J. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits. J Lipid Res 2016; 57:925-42. [PMID: 27099397 PMCID: PMC4878195 DOI: 10.1194/jlr.r066944] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 02/07/2023] Open
Abstract
The Hybrid Mouse Diversity Panel (HMDP) is a collection of approximately 100 well-characterized inbred strains of mice that can be used to analyze the genetic and environmental factors underlying complex traits. While not nearly as powerful for mapping genetic loci contributing to the traits as human genome-wide association studies, it has some important advantages. First, environmental factors can be controlled. Second, relevant tissues are accessible for global molecular phenotyping. Finally, because inbred strains are renewable, results from separate studies can be integrated. Thus far, the HMDP has been studied for traits relevant to obesity, diabetes, atherosclerosis, osteoporosis, heart failure, immune regulation, fatty liver disease, and host-gut microbiota interactions. High-throughput technologies have been used to examine the genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes of the mice under various environmental conditions. All of the published data are available and can be readily used to formulate hypotheses about genes, pathways and interactions.
Collapse
Affiliation(s)
- Aldons J Lusis
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA Microbiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Marcus M Seldin
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Hooman Allayee
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Brian J Bennett
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Mete Civelek
- Departments of Biomedical Engineering University of Virginia, Charlottesville, VA
| | - Richard C Davis
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Eleazar Eskin
- Departments of Computer Science, University of California-Los Angeles, Los Angeles, CA
| | - Charles R Farber
- Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Simon Hui
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Margarete Mehrabian
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Frode Norheim
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Calvin Pan
- Human Genetics, University of California-Los Angeles, Los Angeles, CA
| | - Brian Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI
| | - Christoph D Rau
- Anesthesiology, University of California-Los Angeles, Los Angeles, CA
| | - Desmond J Smith
- Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Thomas Vallim
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| | - Yibin Wang
- Anesthesiology, University of California-Los Angeles, Los Angeles, CA
| | - Jessica Wang
- Departments of Medicine, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA
| |
Collapse
|
32
|
Sun H, Olson KC, Gao C, Prosdocimo DA, Zhou M, Wang Z, Jeyaraj D, Youn JY, Ren S, Liu Y, Rau CD, Shah S, Ilkayeva O, Gui WJ, William NS, Wynn RM, Newgard CB, Cai H, Xiao X, Chuang DT, Schulze PC, Lynch C, Jain MK, Wang Y. Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure. Circulation 2016; 133:2038-49. [PMID: 27059949 DOI: 10.1161/circulationaha.115.020226] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [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: 06/29/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Although metabolic reprogramming is critical in the pathogenesis of heart failure, studies to date have focused principally on fatty acid and glucose metabolism. Contribution of amino acid metabolic regulation in the disease remains understudied. METHODS AND RESULTS Transcriptomic and metabolomic analyses were performed in mouse failing heart induced by pressure overload. Suppression of branched-chain amino acid (BCAA) catabolic gene expression along with concomitant tissue accumulation of branched-chain α-keto acids was identified as a significant signature of metabolic reprogramming in mouse failing hearts and validated to be shared in human cardiomyopathy hearts. Molecular and genetic evidence identified the transcription factor Krüppel-like factor 15 as a key upstream regulator of the BCAA catabolic regulation in the heart. Studies using a genetic mouse model revealed that BCAA catabolic defect promoted heart failure associated with induced oxidative stress and metabolic disturbance in response to mechanical overload. Mechanistically, elevated branched-chain α-keto acids directly suppressed respiration and induced superoxide production in isolated mitochondria. Finally, pharmacological enhancement of branched-chain α-keto acid dehydrogenase activity significantly blunted cardiac dysfunction after pressure overload. CONCLUSIONS BCAA catabolic defect is a metabolic hallmark of failing heart resulting from Krüppel-like factor 15-mediated transcriptional reprogramming. BCAA catabolic defect imposes a previously unappreciated significant contribution to heart failure.
Collapse
Affiliation(s)
- Haipeng Sun
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Kristine C Olson
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Chen Gao
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Domenick A Prosdocimo
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Meiyi Zhou
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Zhihua Wang
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Darwin Jeyaraj
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Ji-Youn Youn
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Shuxun Ren
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Yunxia Liu
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Christoph D Rau
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Svati Shah
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Olga Ilkayeva
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Wen-Jun Gui
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Noelle S William
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - R Max Wynn
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Christopher B Newgard
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Hua Cai
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Xinshu Xiao
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - David T Chuang
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Paul Christian Schulze
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Christopher Lynch
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Mukesh K Jain
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany
| | - Yibin Wang
- From Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (H.S., M.Z., Y.L., Y.W.); Division of Molecular Medicine, Departments of Anesthesiology, Medicine, and Physiology, Molecular Biology Institute, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California, Los Angeles (H.S., C.G., Z.W., J.-Y.Y., S.R., C.D.R., H.C., X.X., Y.W.); Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA (K.C.O., C.L.); Case Cardiovascular Research Institute, Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University, Cleveland, OH (D.A.P., D.J., M.K.J.); Division of Cardiology, Department of Medicine (S.S.) and Sarah W. Stedman Nutrition and Metabolism Center, Departments of Medicine and Pharmacology and Cancer Biology (O.I., C.B.N.), and Duke University School of Medicine, Durham, NC; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas (W.-J.G., N.S.W., R.M.W., D.T.C.); and Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY (P.C.S.). Dr Schulze is now at the Department of Internal Medicine, Division of Cardiology, Angiology, Pneumology and Intensive Medical Care, Friedrich-Schiller-University, Jena, Germany.
| |
Collapse
|
33
|
Chen H, Orozco LD, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States. Circ Res 2016; 118:786-97. [PMID: 26838786 DOI: 10.1161/circresaha.115.305298] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 09/01/2015] [Accepted: 01/08/2016] [Indexed: 02/04/2023]
Abstract
RATIONALE Only a small portion of the known heritability of cardiovascular diseases, such as heart failure, can be explained based on single-gene mutations. Chromatin structure and regulation provide a substrate through which genetic differences in noncoding regions may affect cellular function and response to disease, but the mechanisms are unknown. OBJECTIVE We conducted genome-wide measurements of DNA methylation in different strains of mice that are susceptible and resistant to isoproterenol-induced dysfunction to test the hypothesis that this epigenetic mark may play a causal role in the development of heart failure. METHODS AND RESULTS BALB/cJ and BUB/BnJ mice, determined to be susceptible and resistant to isoproterenol-induced heart failure, respectively, were administered the drug for 3 weeks via osmotic minipump. Reduced representational bisulfite sequencing was then used to compare the differences between the cardiac DNA methylomes in the basal state between strains and then after isoproterenol treatment. Single-base resolution DNA methylation measurements were obtained and revealed a bimodal distribution of methylation in the heart, enriched in lone intergenic CpGs and depleted from CpG islands around genes. Isoproterenol induced global decreases in methylation in both strains; however, the basal methylation pattern between strains shows striking differences that may be predictive of disease progression before environmental stress. The global correlation between promoter methylation and gene expression (as measured by microarray) was modest and revealed itself only with focused analyses of transcription start site and gene body regions (in contrast to when gene methylation was examined in toto). Modules of comethylated genes displayed correlation with other protein-based epigenetic marks, supporting the hypothesis that chromatin modifications act in a combinatorial manner to specify transcriptional phenotypes in the heart. CONCLUSIONS This study provides the first single-base resolution map of the mammalian cardiac DNA methylome and the first case-control analysis of the changes in DNA methylation with heart failure. The findings demonstrate marked genetic differences in DNA methylation that are associated with disease progression.
Collapse
Affiliation(s)
- Haodong Chen
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.).
| | - Luz D Orozco
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Jessica Wang
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Christoph D Rau
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Liudmilla Rubbi
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Shuxun Ren
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Yibin Wang
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Matteo Pellegrini
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Aldons J Lusis
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Thomas M Vondriska
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.).
| |
Collapse
|
34
|
Gao C, Ren S, Lee JH, Qiu J, Chapski DJ, Rau CD, Zhou Y, Abdellatif M, Nakano A, Vondriska TM, Xiao X, Fu XD, Chen JN, Wang Y. RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure. J Clin Invest 2015; 126:195-206. [PMID: 26619120 DOI: 10.1172/jci84015] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/13/2015] [Indexed: 12/13/2022] Open
Abstract
RNA splicing is a major contributor to total transcriptome complexity; however, the functional role and regulation of splicing in heart failure remain poorly understood. Here, we used a total transcriptome profiling and bioinformatic analysis approach and identified a muscle-specific isoform of an RNA splicing regulator, RBFox1 (also known as A2BP1), as a prominent regulator of alternative RNA splicing during heart failure. Evaluation of developing murine and zebrafish hearts revealed that RBFox1 is induced during postnatal cardiac maturation. However, we found that RBFox1 is markedly diminished in failing human and mouse hearts. In a mouse model, RBFox1 deficiency in the heart promoted pressure overload-induced heart failure. We determined that RBFox1 is a potent regulator of RNA splicing and is required for a conserved splicing process of transcription factor MEF2 family members that yields different MEF2 isoforms with differential effects on cardiac hypertrophic gene expression. Finally, induction of RBFox1 expression in murine pressure overload models substantially attenuated cardiac hypertrophy and pathological manifestations. Together, this study identifies regulation of RNA splicing by RBFox1 as an important player in transcriptome reprogramming during heart failure that influence pathogenesis of the disease.
Collapse
|
35
|
Rau CD, Romay MC, Wang J, Ren S, Wang Y, Lusis AJ. Abstract 128: Network-based Approaches to Identify Novel Regulators of Heart Failure. Circ Res 2015. [DOI: 10.1161/res.117.suppl_1.128] [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
Heart failure is a highly heterogeneous disorder characterized by the interactions of multiple environmental and genetic factors. While reductionistic approaches have made significant inroads into characterizing the pathophysiology of the syndrome, they are unable to properly dissect the complex interactions between sets of genes and pathways which result in the emergent phenotypes . Systems genetics offers a means by which these interactions may be identified and explored. We have developed a resource, the Hybrid Mouse Diversity Panel (HMDP) to perform systems-level analyses in mice. Nine week old female mice from 93 unique inbred lines of the HMDP were give 30 ug/g/day of isoproterenol through an abdominally implanted Alzet micropump. After three weeks, mice were sacrificed along with age-matched controls. A portion of the left ventricle was arrayed on an Illumina Mouse Ref 8.0 platform.
Maximal Information Component Analysis was used to construct gene networks, and a module of 41 genes was identified which shows strong correlation to a number of important phenotypic traits, including heart weight and cardiac fibrosis. This module contains a number of genes of interest, including Lgals3, a diagnostic marker for heart failure. Through the use of structural equation modeling, we identified several key genes within the module for further analysis, the most important of which is the metalloprotease Adamts2.
We have performed a series of in vitro analyses demonstrating the important role of Adamts2 in this module using neonatal rat ventricular myocytes. Knockout of Adamts2 results in an amelioration of the hypertrophic response to catecholamine stimulation as well as a reduction of hypertrophic markers such as Nppa and Nppb. Furthermore, we observe that other genes in the module no longer respond to catecholamine stimulation after knockdown of Adamts2.
Collapse
|
36
|
Parks BW, Sallam T, Mehrabian M, Psychogios N, Hui ST, Norheim F, Castellani LW, Rau CD, Pan C, Phun J, Zhou Z, Yang WP, Neuhaus I, Gargalovic PS, Kirchgessner TG, Graham M, Lee R, Tontonoz P, Gerszten RE, Hevener AL, Lusis AJ. Genetic architecture of insulin resistance in the mouse. Cell Metab 2015. [PMID: 25651185 DOI: 10.1016/j.cmet.2015.01.002.genetic] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Insulin resistance (IR) is a complex trait with multiple genetic and environmental components. Confounded by large differences between the sexes, environment, and disease pathology, the genetic basis of IR has been difficult to dissect. Here we examine IR and related traits in a diverse population of more than 100 unique male and female inbred mouse strains after feeding a diet rich in fat and refined carbohydrates. Our results show dramatic variation in IR among strains of mice and widespread differences between sexes that are dependent on genotype. We uncover more than 15 genome-wide significant loci and validate a gene, Agpat5, associated with IR. We also integrate plasma metabolite levels and global gene expression from liver and adipose tissue to identify metabolite quantitative trait loci (mQTL) and expression QTL (eQTL), respectively. Our results provide a resource for analysis of interactions between diet, sex, and genetic background in IR.
Collapse
Affiliation(s)
- Brian W Parks
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Margarete Mehrabian
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nikolas Psychogios
- Cardiovascular Research Center and Cardiology Division, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Simon T Hui
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Frode Norheim
- Department of Nutrition, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Lawrence W Castellani
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christoph D Rau
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer Phun
- Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhenqi Zhou
- Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen-Pin Yang
- Department of Applied Genomics, Bristol-Myers Squibb, Princeton, NJ 08543, USA
| | - Isaac Neuhaus
- Department of Applied Genomics, Bristol-Myers Squibb, Princeton, NJ 08543, USA
| | - Peter S Gargalovic
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, NJ 08543, USA
| | - Todd G Kirchgessner
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, NJ 08543, USA
| | - Mark Graham
- Isis Pharmaceuticals, Carlsbad, CA 92008, USA
| | - Richard Lee
- Isis Pharmaceuticals, Carlsbad, CA 92008, USA
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert E Gerszten
- Cardiovascular Research Center and Cardiology Division, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrea L Hevener
- Division of Endocrinology, Diabetes and Hypertension, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
37
|
Neelankavil J, Rau CD, Wang Y. The Genetic Basis of Coronary Artery Disease and Atrial Fibrillation: A Search for Disease Mechanisms and Therapeutic Targets. J Cardiothorac Vasc Anesth 2015; 29:1328-32. [PMID: 25976605 DOI: 10.1053/j.jvca.2015.01.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/05/2023]
Affiliation(s)
| | | | - Yibin Wang
- Department of Anesthesiology; Department of Medicine and Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA.
| |
Collapse
|
38
|
Rau CD, Wang J, Avetisyan R, Romay MC, Martin L, Ren S, Wang Y, Lusis AJ. Mapping genetic contributions to cardiac pathology induced by Beta-adrenergic stimulation in mice. ACTA ACUST UNITED AC 2014; 8:40-9. [PMID: 25480693 DOI: 10.1161/circgenetics.113.000732] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Chronic stress-induced cardiac pathology exhibits both a wide range in severity and a high degree of heterogeneity in clinical manifestation in human patients. This variability is contributed to by complex genetic and environmental etiologies within the human population. Genetic approaches to elucidate the genetics underlying the acquired forms of cardiomyopathies, including genome-wide association studies, have been largely unsuccessful, resulting in limited knowledge as to the contribution of genetic variations for this important disease. METHODS AND RESULTS Using the β-adrenergic agonist isoproterenol as a specific pathological stressor to circumvent the problem of etiologic heterogeneity, we performed a genome-wide association study for genes influencing cardiac hypertrophy and fibrosis in a large panel of inbred mice. Our analyses revealed 7 significant loci and 17 suggestive loci, containing an average of 14 genes, affecting cardiac hypertrophy, fibrosis, and surrogate traits relevant to heart failure. Several loci contained candidate genes which are known to contribute to Mendelian cardiomyopathies in humans or have established roles in cardiac pathology based on molecular or genetic studies in mouse models. In particular, we identify Abcc6 as a novel gene underlying a fibrosis locus by validating that an allele with a splice mutation of Abcc6 dramatically and rapidly promotes isoproterenol-induced cardiac fibrosis. CONCLUSIONS Genetic variants significantly contribute to the phenotypic heterogeneity of stress-induced cardiomyopathy. Systems genetics is an effective approach to identify genes and pathways underlying the specific pathological features of cardiomyopathies. Abcc6 is a previously unrecognized player in the development of stress-induced cardiac fibrosis.
Collapse
Affiliation(s)
- Christoph D Rau
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Jessica Wang
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Rozeta Avetisyan
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Milagros C Romay
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Lisa Martin
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Shuxun Ren
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA
| | - Yibin Wang
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA.
| | - Aldons J Lusis
- From the Department of Microbiology, Immunology and Molecular Genetics, Department of Human Genetics (C.D.R., R.A., M.R., A.J.L.), Department of Medicine, Division of Cardiology, David Geffen School of Medicine (J.W., L.M., A.J.L.), and Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine (S.R., Y.W.), University of California, Los Angeles, CA.
| |
Collapse
|
39
|
Rau CD, Avetisyan R, Stein D, Romay M, Wang J, Wang Y, Lusis AJ. Abstract 163: Genetic Basis of Isoproterenol-Induced Cardiac Fibrosis. Circ Res 2014. [DOI: 10.1161/res.115.suppl_1.163] [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
Background:
Cardiac fibrosis is a common pathology in the diseased heart, which can cause a loss of elasticity and contractile dysfunction. Cardiac fibrosis is a complex process driven by many pathological triggers which involve numerous genes, pathways and cell types. Despite its importance, the genetic basis for the development of cardiac fibrosis has not been systematically explored.
Methods and Results:
We have developed a resource, the Hybrid Mouse Diversity Panel (HMDP) for high resolution GWAS and systems genetics study of quantitative traits in mice. Eight week old female mice from 80 unique inbred strains of the HMDP were given 30 ug/g/day of isoproterenol (ISO) for three weeks and cardiac fibrosis was assessed by Masson Trichrome staining which revealed a wide spectrum in the degree of fibrosis among the HMDP strains both before and after treatment. Using the Efficient Mixed Model Algorithm, we identified 13 significant or suggestive loci contributing to cardiac fibrosis, many containing numerous gene candidates. Within one of these loci, Abcc6, an orphan ABC transporter linked to the human disease pseudoxanthoma elasticum, was identified as a possible candidate for ISO-induced cardiac fibrosis. A splice-site mutation present in 19 strains of the HMDP was significantly linked to a higher degree of ISO-induced cardiac fibrosis(P=1E-4) but was not linked to increased fibrosis in untreated animals(P=0.25). Targeted genetic knockout of Abcc6 promoted ISO-induced cardiac fibrosis while reintroducing the wildtype Abcc6 allele to an genetic strain homozygous for the Abcc6 splice site mutation significantly alleviated ISO-induced cardiac fibrosis.
Conclusion:
A GWAS performed on levels of cardiac fibrosis observed in ISO treated animals using HMDP mice as model system uncovered significant genetic contributions to stress-induced cardiac fibrosis. Abcc6 is a novel gene contributing to ISO-induced cardiac fibrosis in the heart.
Collapse
|
40
|
Chen H, Orozco LD, Rubbi L, Wang J, Rau CD, Chapski D, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. Abstract 346: Genome-wide Bisulfite Sequencing After Isoproterenol Identifies DNA Methylation Modules Influencing Heart Failure Susceptibility. Circ Res 2013. [DOI: 10.1161/res.113.suppl_1.a346] [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
DNA methylation is an epigenetic mechanism that controls gene expression. Recent studies of human samples linked dysregulation of DNA methylation to cardiovascular diseases. However, whether DNA methylation is mechanistically involved in disease pathogenesis is unknown. To determine how DNA methylation participates in the development of heart failure, we measured the DNA methylome in healthy and hypertrophic mouse hearts (and in isolated cardiac myocytes in parallel experiments) using reduced representational bisulfite sequencing. Isoproterenol (ISO) minipumps were implanted in two mouse strains with opposite phenotypes: BUB/BnJ, which is resistant to ISO-induced hypertrophy/failure, and BALB/cJ, which is susceptible. DNA and mRNA were isolated from hearts and myocytes and analyzed by bisulfite sequencing and microarrays, respectively. The results reveal three levels of information about the methylome: basal differences between the resistant and susceptible strains, loci affected in a disease-associated manner, and strain-specific changes in methylation following ISO treatment_which serve as novel targets to understand the genetic basis of differential incidence of heart failure. We observed 1,122 loci undergoing a >20% change in methylation after ISO in either strain (p<0.05). Our data also showed significant ISO-induced methylation differences in genes related to myofibril assembly (GO:0031032, p=6e-7) and increased heart weight (MP:0002833, p=2e-6). We selected the top 15,000 promoter-associated CpGs with high variation among samples and carried out an unbiased weighted correlation network analysis (WGCNA) of these methylation data. We identified a module of promoter-associated CpGs whose demethylation is highly correlated with ISO treatment in both strains (75 CpGs, Pearson correlation=0.898, p=0.001). We also identified modules with strain-specific responses to ISO treatment. Interestingly, we found a module of 109 CpGs whose methylation is increased in BALB/cJ strain after ISO treatment, but decreased in BUB/BnJ strain. Our data demonstrate global changes in DNA methylation in the adult heart during the development of disease and reveal networks of modified loci that influence heart failure susceptibility.
Collapse
Affiliation(s)
- Haodong Chen
- Univ of California, Los Angeles, Los Angeles, CA
| | - Luz D Orozco
- Univ of California, Los Angeles, Los Angeles, CA
| | | | - Jessica Wang
- Univ of California, Los Angeles, Los Angeles, CA
| | | | | | - Shuxun Ren
- Univ of California, Los Angeles, Los Angeles, CA
| | - Yibin Wang
- Univ of California, Los Angeles, Los Angeles, CA
| | | | | | | |
Collapse
|
41
|
Rau CD, Wang J, Ren S, Wang Z, Ruan H, Wang Y, Lusis AJ. Abstract 233: Isoproterenol-induced Cardiac Hypertrophy And Failure In Mice: Gene Network Modeling. Circ Res 2013. [DOI: 10.1161/res.113.suppl_1.a233] [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
Heart failure is highly heterogeneous and as a result, relatively few insights into the pathways and drivers of heart failure have been identified using system-wide methods such as genome-wide association studies (GWAS). We have developed a resource, the Hybrid Mouse Diversity Panel (HMDP) for high resolution GWAS and systems genetics in mice. Eight week old female mice from 93 unique inbred strains of the HMDP were given 20 μg/g/day of isoproterenol through an abdominally implanted Alzet micropump. Three weeks post-implantation, all mice were sacrificed, along with age-matched controls. The mice exhibited widely varying degrees of hypertrophy and heart functioning. A portion of the left ventricle was processed and arrayed on an Illumina Mouse Ref 8.0 platform.
We used Maximal Information Component Analysis, a novel method of network construction which allows for non-linear relationships between genes as well as non-binary partitioning of genes into sub-networks to subdivide the expression data into a series of modules. In order to identify modules which may contribute to Isoproterenol-induced hypertrophy and failure, we examined the correlation of each module to clinically relevant cardiac traits traits such as organ weights and echocardiographic parameters.
We identified several modules with strong correlations to multiple heart failure-related clinical traits, including one module of 41 genes which contained several genes of interest, including Lgals3, a diagnostic marker for heart failure. Utilizing eQTL hotspot analysis, we have identified a locus which is involved in the regulation of this module. A gene within this locus, Magi2, regulates the turnover of the β-adrenergic receptor and represents a likely candidate for the response to isoproterenol.
Collapse
|
42
|
Rau CD, Wisniewski N, Orozco LD, Bennett B, Weiss J, Lusis AJ. Maximal information component analysis: a novel non-linear network analysis method. Front Genet 2013; 4:28. [PMID: 23487572 PMCID: PMC3594742 DOI: 10.3389/fgene.2013.00028] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 02/21/2013] [Indexed: 11/26/2022] Open
Abstract
Background: Network construction and analysis algorithms provide scientists with the ability to sift through high-throughput biological outputs, such as transcription microarrays, for small groups of genes (modules) that are relevant for further research. Most of these algorithms ignore the important role of non-linear interactions in the data, and the ability for genes to operate in multiple functional groups at once, despite clear evidence for both of these phenomena in observed biological systems. Results: We have created a novel co-expression network analysis algorithm that incorporates both of these principles by combining the information-theoretic association measure of the maximal information coefficient (MIC) with an Interaction Component Model. We evaluate the performance of this approach on two datasets collected from a large panel of mice, one from macrophages and the other from liver by comparing the two measures based on a measure of module entropy, Gene Ontology (GO) enrichment, and scale-free topology (SFT) fit. Our algorithm outperforms a widely used co-expression analysis method, weighted gene co-expression network analysis (WGCNA), in the macrophage data, while returning comparable results in the liver dataset when using these criteria. We demonstrate that the macrophage data has more non-linear interactions than the liver dataset, which may explain the increased performance of our method, termed Maximal Information Component Analysis (MICA) in that case. Conclusions: In making our network algorithm more accurately reflect known biological principles, we are able to generate modules with improved relevance, particularly in networks with confounding factors such as gene by environment interactions.
Collapse
Affiliation(s)
- Christoph D Rau
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, USA ; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, CA, USA
| | | | | | | | | | | |
Collapse
|
43
|
Davis RC, van Nas A, Bennett B, Orozco L, Pan C, Rau CD, Eskin E, Lusis AJ. Genome-wide association mapping of blood cell traits in mice. Mamm Genome 2013; 24:105-18. [PMID: 23417284 DOI: 10.1007/s00335-013-9448-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/11/2013] [Indexed: 12/13/2022]
Abstract
Genetic variations in blood cell parameters can impact clinical traits. We report here the mapping of blood cell traits in a panel of 100 inbred strains of mice of the Hybrid Mouse Diversity Panel (HMDP) using genome-wide association (GWA). We replicated a locus previously identified in using linkage analysis in several genetic crosses for mean corpuscular volume (MCV) and a number of other red blood cell traits on distal chromosome 7. Our peak for SNP association to MCV occurred in a linkage disequilibrium (LD) block spanning from 109.38 to 111.75 Mb that includes Hbb-b1, the likely causal gene. Altogether, we identified five loci controlling red blood cell traits (on chromosomes 1, 7, 11, 12, and 16), and four of these correspond to loci for red blood cell traits reported in a recent human GWA study. For white blood cells, including granulocytes, monocytes, and lymphocytes, a total of six significant loci were identified on chromosomes 1, 6, 8, 11, 12, and 15. An average of ten candidate genes were found at each locus and those were prioritized by examining functional variants in the HMDP such as missense and expression variants. These results provide intermediate phenotypes and candidate loci for genetic studies of atherosclerosis and cancer as well as inflammatory and immune disorders in mice.
Collapse
Affiliation(s)
- Richard C Davis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Parks BW, Nam E, Org E, Kostem E, Norheim F, Hui ST, Pan C, Civelek M, Rau CD, Bennett BJ, Mehrabian M, Ursell LK, He A, Castellani LW, Zinker B, Kirby M, Drake TA, Drevon CA, Knight R, Gargalovic P, Kirchgessner T, Eskin E, Lusis AJ. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab 2013; 17:141-52. [PMID: 23312289 PMCID: PMC3545283 DOI: 10.1016/j.cmet.2012.12.007] [Citation(s) in RCA: 386] [Impact Index Per Article: 35.1] [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] [Received: 07/24/2012] [Revised: 11/05/2012] [Accepted: 12/12/2012] [Indexed: 12/16/2022]
Abstract
Obesity is a highly heritable disease driven by complex interactions between genetic and environmental factors. Human genome-wide association studies (GWAS) have identified a number of loci contributing to obesity; however, a major limitation of these studies is the inability to assess environmental interactions common to obesity. Using a systems genetics approach, we measured obesity traits, global gene expression, and gut microbiota composition in response to a high-fat/high-sucrose (HF/HS) diet of more than 100 inbred strains of mice. Here we show that HF/HS feeding promotes robust, strain-specific changes in obesity that are not accounted for by food intake and provide evidence for a genetically determined set point for obesity. GWAS analysis identified 11 genome-wide significant loci associated with obesity traits, several of which overlap with loci identified in human studies. We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity.
Collapse
Affiliation(s)
- Brian W Parks
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Weiss JN, Karma A, MacLellan WR, Deng M, Rau CD, Rees CM, Wang J, Wisniewski N, Eskin E, Horvath S, Qu Z, Wang Y, Lusis AJ. "Good enough solutions" and the genetics of complex diseases. Circ Res 2012; 111:493-504. [PMID: 22859671 DOI: 10.1161/circresaha.112.269084] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this Emerging Science Review, we discuss a systems genetics strategy, which we call gene module association study (GMAS), as a novel approach complementing genome-wide association studies (GWAS), to understand complex diseases by focusing on how genes work together in groups rather than singly. The first step is to characterize phenotypic differences among a genetically diverse population. The second step is to use gene expression microarray (or other high-throughput) data from the population to construct gene coexpression networks. Coexpression analysis typically groups 20 000 genes into 20 to 30 modules containing tens to hundreds of genes, whose aggregate behavior can be represented by the module's "eigengene." The third step is to correlate expression patterns with phenotype, as in GWAS, only applied to eigengenes instead of single nucleotide polymorphisms. The goal of the GMAS approach is to identify groups of coregulated genes that explain complex traits from a systems perspective. From an evolutionary standpoint, we hypothesize that variability in eigengene patterns reflects the "good enough solution" concept, that biological systems are sufficiently complex so that many possible combinations of the same elements (in this case eigengenes) can produce an equivalent output, that is, a "good enough solution" to accomplish normal biological functions. However, when faced with environmental stresses, some "good enough solutions" adapt better than others, explaining individual variability to disease and drug susceptibility. If validated, GMAS may imply that common polygenic diseases are related as much to group interactions between normal genes, as to multiple gene mutations.
Collapse
Affiliation(s)
- James N Weiss
- Cardiovascular Research Laboratory and Atherosclerosis Research Unit, Department of Medicine (Cardiology), David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC. Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome 2012; 23:680-92. [PMID: 22892838 DOI: 10.1007/s00335-012-9411-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/04/2012] [Indexed: 11/28/2022]
Abstract
We have developed an association-based approach using classical inbred strains of mice in which we correct for population structure, which is very extensive in mice, using an efficient mixed-model algorithm. Our approach includes inbred parental strains as well as recombinant inbred strains in order to capture loci with effect sizes typical of complex traits in mice (in the range of 5% of total trait variance). Over the last few years, we have typed the hybrid mouse diversity panel (HMDP) strains for a variety of clinical traits as well as intermediate phenotypes and have shown that the HMDP has sufficient power to map genes for highly complex traits with resolution that is in most cases less than a megabase. In this essay, we review our experience with the HMDP, describe various ongoing projects, and discuss how the HMDP may fit into the larger picture of common diseases and different approaches.
Collapse
Affiliation(s)
- Anatole Ghazalpour
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Rau CD, Wang JJ, Ren S, Wang Y, Lusis AJ. Abstract 16: Genomewide Association Study of Isoproterenol-Induced Heart Failure in a Large Mouse Panel. Circ Res 2012. [DOI: 10.1161/res.111.suppl_1.a16] [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
Heart failure is highly heterogeneous and association studies in humans have yielded few insights into its genetic basis. We have developed a resource, the Hybrid Mouse Diversity Panel, to efficiently perform association studies on complex diseases in a mouse model. Each strain within the panel has been densely genotyped and the panel displays significant baseline inter-strain variation. We used the panel to explore isoproterenol (a β-adrenergic agonist) induced heart failure.
Eight week old females from 105 unique inbred strains (average N = 6.7) were divided into control (average N = 2.5) and treated (average N = 4.1) cohorts. Treated mice received 20 μg/g/day of drug through an abdominally implanted Alzet micropump. All mice underwent echocardiography to assess left ventricular function both before and at weekly timepoints after treatment. At three weeks, all mice were sacrificed. Hearts (sectioned by chamber) lungs, liver and adrenal glands were weighed before storage for further analysis. Phenotypes were analyzed using the Efficient Mixed-Model Association (EMMA) algorithm to correct for population substructure. Promising gene candidates were tested on zebrafish morpholino models to assess any phenotypic effects.
Here we report initial findings from the panel. Chronic β-adrenergic stimulation results in marked variations in both weight and echocardiographic measurements. EMMA analysis of the data revealed several dozen putative peaks, including several repeated peaks in correlated phenotypes as well as replication of previously reported loci in both human and mouse studies. Further analysis of these peaks will shed light on the genetics underlying heart failure.
Collapse
|