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Brochet P, Ianni BM, Laugier L, Frade AF, Silva Nunes JP, Teixeira PC, Mady C, Ferreira LRP, Ferré Q, Santos RHB, Kuramoto A, Cabantous S, Steffen S, Stolf AN, Pomerantzeff P, Fiorelli AI, Bocchi EA, Pissetti CW, Saba B, Cândido DDS, Dias FC, Sampaio MF, Gaiotto FA, Marin-Neto JA, Fragata A, Zaniratto RCF, Siqueira S, Peixoto GDL, Rigaud VOC, Bacal F, Buck P, Almeida RR, Lin-Wang HT, Schmidt A, Martinelli M, Hirata MH, Donadi EA, Costa Pereira A, Rodrigues Junior V, Puthier D, Kalil J, Spinelli L, Cunha-Neto E, Chevillard C. Epigenetic regulation of transcription factor binding motifs promotes Th1 response in Chagas disease cardiomyopathy. Front Immunol 2022; 13:958200. [PMID: 36072583 PMCID: PMC9441916 DOI: 10.3389/fimmu.2022.958200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 01/03/2023] Open
Abstract
Chagas disease, caused by the protozoan Trypanosoma cruzi, is an endemic parasitic disease of Latin America, affecting 7 million people. Although most patients are asymptomatic, 30% develop complications, including the often-fatal Chronic Chagasic Cardiomyopathy (CCC). Although previous studies have demonstrated some genetic deregulations associated with CCCs, the causes of their deregulations remain poorly described. Based on bulk RNA-seq and whole genome DNA methylation data, we investigated the genetic and epigenetic deregulations present in the moderate and severe stages of CCC. Analysis of heart tissue gene expression profile allowed us to identify 1407 differentially expressed transcripts (DEGs) specific from CCC patients. A tissue DNA methylation analysis done on the same tissue has permitted the identification of 92 regulatory Differentially Methylated Regions (DMR) localized in the promoter of DEGs. An in-depth study of the transcription factors binding sites (TFBS) in the DMRs corroborated the importance of TFBS’s DNA methylation for gene expression in CCC myocardium. TBX21, RUNX3 and EBF1 are the transcription factors whose binding motif appears to be affected by DNA methylation in the largest number of genes. By combining both transcriptomic and methylomic analysis on heart tissue, and methylomic analysis on blood, 4 biological processes affected by severe CCC have been identified, including immune response, ion transport, cardiac muscle processes and nervous system. An additional study on blood methylation of moderate CCC samples put forward the importance of ion transport and nervous system in the development of the disease.
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Affiliation(s)
- Pauline Brochet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Barbara Maria Ianni
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Laurie Laugier
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Inserm, UMR_906, Marseille, France
| | - Amanda Farage Frade
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - João Paulo Silva Nunes
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Priscila Camillo Teixeira
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Charles Mady
- Myocardiopathies and Aortic Diseases Unit, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ludmila Rodrigues Pinto Ferreira
- RNA Systems Biology Laboratory (RSBL), Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Quentin Ferré
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Ronaldo Honorato Barros Santos
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Andreia Kuramoto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Sandrine Cabantous
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Inserm, UMR_906, Marseille, France
| | - Samuel Steffen
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Antonio Noedir Stolf
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Pablo Pomerantzeff
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Alfredo Inacio Fiorelli
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Edimar Alcides Bocchi
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Cristina Wide Pissetti
- Laboratory of Immunology, Universidade Federal Do Triângulo Mineiro (UFTM), Uberaba, Brazil
| | - Bruno Saba
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Darlan da Silva Cândido
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Fabrício C. Dias
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Marcelo Ferraz Sampaio
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Fabio Antônio Gaiotto
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - José Antonio Marin-Neto
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Abílio Fragata
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Ricardo Costa Fernandes Zaniratto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Sergio Siqueira
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Giselle De Lima Peixoto
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Vagner Oliveira-Carvalho Rigaud
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Heart Failure Unit, Heart Institute Instituto do Coração (InCor) School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Fernando Bacal
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Paula Buck
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Rafael Ribeiro Almeida
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Hui Tzu Lin-Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - André Schmidt
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Martino Martinelli
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Eduardo Antonio Donadi
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Alexandre Costa Pereira
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Denis Puthier
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Jorge Kalil
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Lionel Spinelli
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
| | - Christophe Chevillard
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
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Yang Y, Qian F, Li X, Li Y, Zhou L, Wang Q, Zhou X, Zhang J, Song C, Yu Z, Cui T, Feng C, Zhu J, Shang D, Liu J, Sun M, Zhang Y, Tang H, Li C. GREAP: a comprehensive enrichment analysis software for human genomic regions. Brief Bioinform 2022; 23:6663640. [PMID: 35959979 DOI: 10.1093/bib/bbac329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 12/12/2022] Open
Abstract
The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing >400 000 000 customizable tracks for visualization. The platform is freely available at http://www.liclab.net/Greap/view/index.
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Affiliation(s)
- Yongsan Yang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.,West China Biomedical Big Data Center, West China Hospital, Sichuan University, China
| | - Fengcui Qian
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yanyu Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Liwei Zhou
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Xinyuan Zhou
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Chao Song
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhengmin Yu
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Cui
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Desi Shang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Jiaqi Liu
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Mengfei Sun
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yuexin Zhang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Huifang Tang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China.,School of Computer, University of South China, Hengyang, Hunan, 421001, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan, 421001, China.,The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
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