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Xia J, Li Y, Zhu H, Xue F, Shi F, Li N. A Bayesian Change Point Model for Dynamic Alternative Transcription Start Site Usage During Cellular Differentiation. J Comput Biol 2024; 31:445-457. [PMID: 38752891 DOI: 10.1089/cmb.2023.0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024] Open
Abstract
ABSTRACT An alternative transcription start site (ATSS) is a major driving force for increasing the complexity of transcripts in human tissues. As a transcriptional regulatory mechanism, ATSS has biological significance. Many studies have confirmed that ATSS plays an important role in diseases and cell development and differentiation. However, exploration of its dynamic mechanisms remains insufficient. Identifying ATSS change points during cell differentiation is critical for elucidating potential dynamic mechanisms. For relative ATSS usage as percentage data, the existing methods lack sensitivity to detect the change point for ATSS longitudinal data. In addition, some methods have strict requirements for data distribution and cannot be applied to deal with this problem. In this study, the Bayesian change point detection model was first constructed using reparameterization techniques for two parameters of a beta distribution for the percentage data type, and the posterior distributions of parameters and change points were obtained using Markov Chain Monte Carlo (MCMC) sampling. With comprehensive simulation studies, the performance of the Bayesian change point detection model is found to be consistently powerful and robust across most scenarios with different sample sizes and beta distributions. Second, differential ATSS events in the real data, whose change points were identified using our method, were clustered according to their change points. Last, for each change point, pathway and transcription factor motif analyses were performed on its differential ATSS events. The results of our analyses demonstrated the effectiveness of the Bayesian change point detection model and provided biological insights into cell differentiation.
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Affiliation(s)
- Juan Xia
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yuxia Li
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Haotian Zhu
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Feiyang Xue
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Feng Shi
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
| | - Nana Li
- Department of Mathematics, College of Informatics, Huazhong Agricultural University, Wuhan, P.R. China
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Pepe G, Appierdo R, Ausiello G, Helmer-Citterich M, Gherardini PF. A Meta-Analysis Approach to Gene Regulatory Network Inference Identifies Key Regulators of Cardiovascular Diseases. Int J Mol Sci 2024; 25:4224. [PMID: 38673810 PMCID: PMC11049946 DOI: 10.3390/ijms25084224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), encompassing dilated cardiomyopathy (DC), ischemic cardiomyopathy (ICM), and hypertrophic cardiomyopathy (HCM), is a topic of substantial interest in basic and clinical research. Here, we used a Partial Correlation Coefficient-based algorithm (PCC) within the context of a meta-analysis framework to construct a Gene Regulatory Network (GRN) that identifies key regulators whose activity is perturbed in Heart Failure. By integrating data from multiple independent studies, our approach unveiled crucial regulatory associations between transcription factors (TFs) and structural genes, emphasizing their pivotal roles in regulating metabolic pathways, such as fatty acid metabolism, oxidative stress response, epithelial-to-mesenchymal transition, and coagulation. In addition to known associations, our analysis also identified novel regulators, including the identification of TFs FPM315 and OVOL2, which are implicated in dilated cardiomyopathies, and TEAD1 and TEAD2 in both dilated and ischemic cardiomyopathies. Moreover, we uncovered alterations in adipogenesis and oxidative phosphorylation pathways in hypertrophic cardiomyopathy and discovered a role for IL2 STAT5 signaling in heart failure. Our findings underscore the importance of TF activity in the initiation and progression of cardiac disease, highlighting their potential as pharmacological targets.
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Affiliation(s)
- Gerardo Pepe
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
| | - Romina Appierdo
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Gabriele Ausiello
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
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3
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Li J, Hua Y, Liu Y, Qu X, Zhang J, Ishida M, Yoshida N, Tabata A, Miyoshi H, Shiba M, Higo S, Sougawa N, Takeda M, Kawamura T, Matsuura R, Okuzaki D, Toyofuku T, Sawa Y, Liu L, Miyagawa S. Human induced pluripotent stem cell-derived closed-loop cardiac tissue for drug assessment. iScience 2024; 27:108992. [PMID: 38333703 PMCID: PMC10850789 DOI: 10.1016/j.isci.2024.108992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/16/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Human iPSC-derived cardiomyocytes (hiPSC-CMs) exhibit functional immaturity, potentially impacting their suitability for assessing drug proarrhythmic potential. We previously devised a traveling wave (TW) system to promote maturation in 3D cardiac tissue. To align with current drug assessment paradigms (CiPA and JiCSA), necessitating a 2D monolayer cardiac tissue, we integrated the TW system with a multi-electrode array. This gave rise to a hiPSC-derived closed-loop cardiac tissue (iCT), enabling spontaneous TW initiation and swift pacing of cardiomyocytes from various cell lines. The TW-paced cardiomyocytes demonstrated heightened sarcomeric and functional maturation, exhibiting enhanced response to isoproterenol. Moreover, these cells showcased diminished sensitivity to verapamil and maintained low arrhythmia rates with ranolazine-two drugs associated with a low risk of torsades de pointes (TdP). Notably, the TW group displayed increased arrhythmia rates with high and intermediate risk TdP drugs (quinidine and pimozide), underscoring the potential utility of this system in drug assessment applications.
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Affiliation(s)
- Junjun Li
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ying Hua
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yuting Liu
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Xiang Qu
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Jingbo Zhang
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Masako Ishida
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Noriko Yoshida
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Akiko Tabata
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hayato Miyoshi
- Fujifilm Corporation, Ashigarakami 258-8577, Kanagawa, Japan
| | - Mikio Shiba
- Cardiovascular Division, Osaka Police Hospital, Tennoji 543-0035, Osaka, Japan
| | - Shuichiro Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita 565-0871, Osaka, Japan
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Suita 565-0871, Osaka, Japan
| | - Nagako Sougawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Physiology, Osaka Dental University, 8-1 Kuzuha Hanazono-cho, Hirakata 573-1121, Osaka, Japan
| | - Maki Takeda
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Takuji Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ryohei Matsuura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toshihiko Toyofuku
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita 565-0871, Osaka, Japan
| | - Yoshiki Sawa
- Department of Future Medicine, Division of Health Science, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Li Liu
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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4
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Matthews ER, Johnson OD, Horn KJ, Gutiérrez JA, Powell SR, Ward MC. Anthracyclines induce cardiotoxicity through a shared gene expression response signature. PLoS Genet 2024; 20:e1011164. [PMID: 38416769 PMCID: PMC10927150 DOI: 10.1371/journal.pgen.1011164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/11/2024] [Accepted: 01/31/2024] [Indexed: 03/01/2024] Open
Abstract
TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.
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Affiliation(s)
- E. Renee Matthews
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Omar D. Johnson
- Biochemistry, Cellular and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kandace J. Horn
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - José A. Gutiérrez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Simon R. Powell
- Neuroscience Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle C. Ward
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases. Genes (Basel) 2023; 14:2051. [PMID: 38002994 PMCID: PMC10671453 DOI: 10.3390/genes14112051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Affiliation(s)
| | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620, USA; (S.A.C.); (J.J.M.)
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6
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Feng Y, Cai L, Hong W, Zhang C, Tan N, Wang M, Wang C, Liu F, Wang X, Ma J, Gao C, Kumar M, Mo Y, Geng Q, Luo C, Lin Y, Chen H, Wang SY, Watson MJ, Jegga AG, Pedersen RA, Fu JD, Wang ZV, Fan GC, Sadayappan S, Wang Y, Pauklin S, Huang F, Huang W, Jiang L. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation 2022; 145:1663-1683. [PMID: 35400201 PMCID: PMC9251830 DOI: 10.1161/circulationaha.121.055781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Transcriptional reconfiguration is central to heart failure, the most common cause of which is dilated cardiomyopathy (DCM). The effect of 3-dimensional chromatin topology on transcriptional dysregulation and pathogenesis in human DCM remains elusive. METHODS We generated a compendium of 3-dimensional epigenome and transcriptome maps from 101 biobanked human DCM and nonfailing heart tissues through highly integrative chromatin immunoprecipitation (H3K27ac [acetylation of lysine 27 on histone H3]), in situ high-throughput chromosome conformation capture, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and RNA sequencing. We used human induced pluripotent stem cell-derived cardiomyocytes and mouse models to interrogate the key transcription factor implicated in 3-dimensional chromatin organization and transcriptional regulation in DCM pathogenesis. RESULTS We discovered that the active regulatory elements (H3K27ac peaks) and their connectome (H3K27ac loops) were extensively reprogrammed in DCM hearts and contributed to transcriptional dysregulation implicated in DCM development. For example, we identified that nontranscribing NPPA-AS1 (natriuretic peptide A antisense RNA 1) promoter functions as an enhancer and physically interacts with the NPPA (natriuretic peptide A) and NPPB (natriuretic peptide B) promoters, leading to the cotranscription of NPPA and NPPB in DCM hearts. We revealed that DCM-enriched H3K27ac loops largely resided in conserved high-order chromatin architectures (compartments, topologically associating domains) and their anchors unexpectedly had equivalent chromatin accessibility. We discovered that the DCM-enriched H3K27ac loop anchors exhibited a strong enrichment for HAND1 (heart and neural crest derivatives expressed 1), a key transcription factor involved in early cardiogenesis. In line with this, its protein expression was upregulated in human DCM and mouse failing hearts. To further validate whether HAND1 is a causal driver for the reprogramming of enhancer-promoter connectome in DCM hearts, we performed comprehensive 3-dimensional epigenome mappings in human induced pluripotent stem cell-derived cardiomyocytes. We found that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced a distinct gain of enhancer-promoter connectivity and correspondingly increased the expression of their connected genes implicated in DCM pathogenesis, thus recapitulating the transcriptional signature in human DCM hearts. Electrophysiology analysis demonstrated that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced abnormal calcium handling. Furthermore, cardiomyocyte-specific overexpression of Hand1 in the mouse hearts resulted in dilated cardiac remodeling with impaired contractility/Ca2+ handling in cardiomyocytes, increased ratio of heart weight/body weight, and compromised cardiac function, which were ascribed to recapitulation of transcriptional reprogramming in DCM. CONCLUSIONS This study provided novel chromatin topology insights into DCM pathogenesis and illustrated a model whereby a single transcription factor (HAND1) reprograms the genome-wide enhancer-promoter connectome to drive DCM pathogenesis.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
- These authors contributed equally to this work
| | - Liuyang Cai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR 999077, China
- These authors contributed equally to this work
| | - Wanzi Hong
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- These authors contributed equally to this work
| | - Chunxiang Zhang
- Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
- These authors contributed equally to this work
| | - Ning Tan
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Mingyang Wang
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland D02 VF25
| | - Feng Liu
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Xiaohong Wang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jianyong Ma
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chen Gao
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mohit Kumar
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yuanxi Mo
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Qingshan Geng
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Changjun Luo
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yan Lin
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Haiyang Chen
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shuang-Yin Wang
- Department of Immunology, Weizmann Institute of Science, Rehovot WR35+R8, Israel
| | - Michael J. Watson
- Department of Surgery, Cardiovascular & Thoracic, Duke University, Durham, NC 27710, USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH 45221, USA
| | - Roger A. Pedersen
- Department of OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research, Stanford University, Stanford, California, USA
| | - Ji-dong Fu
- Departments of Physiology and Cell Biology, the Dorothy M. Davis Heart and Lung Research Institute, Frick Center for Heart Failure and Arrhythmia, the Ohio State University, Columbus, OH 43210, USA
| | - Zhao V. Wang
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA, 75390-8573
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Feng Huang
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lei Jiang
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- Lead contact
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Wei C, Niu Y, Chen B, Qin P, Wang Y, Hou D, Li T, Li R, Wang C, Yin H, Han R, Xu H, Tian Y, Liu X, Kang X, Li Z. Genetic effect of an InDel in the promoter region of the NUDT15 and its effect on myoblast proliferation in chickens. BMC Genomics 2022; 23:138. [PMID: 35168561 PMCID: PMC8848950 DOI: 10.1186/s12864-022-08362-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
Background Molecular breeding accelerates the speed of animal breeding. Screening molecular markers that can affect economic traits through genome-wide association studies (GWAS) can provide a theoretical basis for molecular breeding. At present, a large number of molecular markers have been screened in poultry research, but few reports on how molecular markers affect economic traits exist. It is particularly important to reveal the action mechanisms of molecular markers, which can provide more accurate information for molecular breeding. Results The aim of this study was to investigate the relationships between two indels (NUDT15-indel-2777 and NUDT15-indel-1673) in the promoter region of NUDT15 and growth and carcass traits in chickens and to explore the regulatory mechanism of NUDT15. Significant differences were found in genotype and allele frequencies among commercial broilers, commercial laying hens and dual-purpose chickens. The results of association analyses showed that these two indel loci could significantly affect growth traits, such as body weight, and carcass traits. Tissue expression profiling at E12 showed that the expression of NUDT15 was significantly higher in skeletal muscle, and time-expression profiling of leg muscle showed that the expression of NUDT15 in myoblasts was significantly higher in the E10 and E12 proliferation stages than in other stages. Promoter activity analysis showed that pro-1673-I and pro-1673-D significantly inhibited promoter activity, and the promoter activity of pro-1673-D was significantly lower than that of pro-1673-I. In addition, when NUDT15 was overexpressed or underwent interference in chicken primary myoblasts (CPMs), NUDT15 could inhibit the proliferation of CPMs. Conclusion The results suggest that the studied indels in the promoter region of NUDT15 may regulate the proliferation of CPMs by affecting NUDT15 expression, ultimately affecting the growth and carcass traits of chickens. These indel polymorphisms may be used together as molecular markers for improving economic traits in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08362-6.
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Affiliation(s)
- Chengjie Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Panpan Qin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Dan Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Tong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Chunxiu Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Huadong Yin
- Farm Animal genetic resources exploration and innovation key laboratory of sichuan province, sichuan agricultural university, Chengdu, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China. .,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China.
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8
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Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
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Gacita AM, Fullenkamp DE, Ohiri J, Pottinger T, Puckelwartz MJ, Nobrega MA, McNally EM. Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression. Circulation 2021; 143:1302-1316. [PMID: 33478249 PMCID: PMC8009836 DOI: 10.1161/circulationaha.120.050432] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Inherited cardiomyopathy associates with a range of phenotypes, mediated by genetic and nongenetic factors. Noninherited cardiomyopathy also displays varying progression and outcomes. Expression of cardiomyopathy genes is under the regulatory control of promoters and enhancers, and human genetic variation in promoters and enhancers may contribute to this variability. METHODS We superimposed epigenomic profiling from hearts and cardiomyocytes, including promoter-capture chromatin conformation information, to identify enhancers for 2 cardiomyopathy genes, MYH7 and LMNA. Enhancer function was validated in human cardiomyocytes derived from induced pluripotent stem cells. We also conducted a genome-wide search to ascertain genomic variation in enhancers positioned to alter cardiac expression and correlated one of these variants to cardiomyopathy progression using biobank data. RESULTS Multiple enhancers were identified and validated for LMNA and MYH7, including a key enhancer that regulates the switch from MYH6 expression to MYH7 expression. Deletion of this enhancer resulted in a dose-dependent increase in MYH6 and faster contractile rate in engineered heart tissues. We searched for genomic variation in enhancer sequences across the genome, with a focus on nucleotide changes that create or interrupt transcription factor binding sites. The sequence variant, rs875908, disrupts a T-Box Transcription Factor 5 binding motif and maps to an enhancer region 2 kilobases from the transcriptional start site of MYH7. Gene editing to remove the enhancer that harbors this variant markedly reduced MYH7 expression in human cardiomyocytes. Using biobank-derived data, rs875908 associated with longitudinal echocardiographic features of cardiomyopathy. CONCLUSIONS Enhancers regulate cardiomyopathy gene expression, and genomic variation within these enhancer regions associates with cardiomyopathic progression over time. This integrated approach identified noncoding modifiers of cardiomyopathy and is applicable to other cardiac genes.
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Affiliation(s)
- Anthony M. Gacita
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Dominic E. Fullenkamp
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Joyce Ohiri
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Tess Pottinger
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
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Cappola TP, Burke MF. Studying Heart Failure Through the Lens of Gene Regulation. Circ Heart Fail 2020; 13:e007647. [PMID: 32993370 DOI: 10.1161/circheartfailure.120.007647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Thomas P Cappola
- Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine
| | - Megan F Burke
- Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine
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