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Cordero J, Elsherbiny A, Wang Y, Jürgensen L, Constanty F, Günther S, Boerries M, Heineke J, Beisaw A, Leuschner F, Hassel D, Dobreva G. Leveraging chromatin state transitions for the identification of regulatory networks orchestrating heart regeneration. Nucleic Acids Res 2024; 52:4215-4233. [PMID: 38364861 PMCID: PMC11077086 DOI: 10.1093/nar/gkae085] [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: 05/26/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
The limited regenerative capacity of the human heart contributes to high morbidity and mortality worldwide. In contrast, zebrafish exhibit robust regenerative capacity, providing a powerful model for studying how to overcome intrinsic epigenetic barriers maintaining cardiac homeostasis and initiate regeneration. Here, we present a comprehensive analysis of the histone modifications H3K4me1, H3K4me3, H3K27me3 and H3K27ac during various stages of zebrafish heart regeneration. We found a vast gain of repressive chromatin marks one day after myocardial injury, followed by the acquisition of active chromatin characteristics on day four and a transition to a repressive state on day 14, and identified distinct transcription factor ensembles associated with these events. The rapid transcriptional response involves the engagement of super-enhancers at genes implicated in extracellular matrix reorganization and TOR signaling, while H3K4me3 breadth highly correlates with transcriptional activity and dynamic changes at genes involved in proteolysis, cell cycle activity, and cell differentiation. Using loss- and gain-of-function approaches, we identified transcription factors in cardiomyocytes and endothelial cells influencing cardiomyocyte dedifferentiation or proliferation. Finally, we detected significant evolutionary conservation between regulatory regions that drive zebrafish and neonatal mouse heart regeneration, suggesting that reactivating transcriptional and epigenetic networks converging on these regulatory elements might unlock the regenerative potential of adult human hearts.
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Affiliation(s)
- Julio Cordero
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Adel Elsherbiny
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yinuo Wang
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lonny Jürgensen
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Florian Constanty
- Institute of Experimental Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, 69110 Heidelberg, Germany
| | - Joerg Heineke
- Department of Cardiovascular Physiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Arica Beisaw
- Institute of Experimental Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Florian Leuschner
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - David Hassel
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Gergana Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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Chen S, Lu K, Hou Y, You Z, Shu C, Wei X, Wu T, Shi N, Zhang G, Wu J, Chen S, Zhang L, Li W, Zhang D, Ju S, Chen M, Xu B. YY1 complex in M2 macrophage promotes prostate cancer progression by upregulating IL-6. J Immunother Cancer 2023; 11:jitc-2022-006020. [PMID: 37094986 PMCID: PMC10152059 DOI: 10.1136/jitc-2022-006020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Tumor-associated macrophages are mainly polarized into the M2 phenotype, remodeling the tumor microenvironment and promoting tumor progression by secreting various cytokines. METHODS Tissue microarray consisting of prostate cancer (PCa), normal prostate, and lymph node metastatic samples from patients with PCa were stained with Yin Yang 1 (YY1) and CD163. Transgenic mice overexpressing YY1 were constructed to observe PCa tumorigenesis. Furthermore, in vivo and in vitro experiments, including CRISPR-Cas9 knock-out, RNA sequencing, chromatin immunoprecipitation (ChIP) sequencing, and liquid-liquid phase separation (LLPS) assays, were performed to investigate the role and mechanism of YY1 in M2 macrophages and PCa tumor microenvironment. RESULTS YY1 was highly expressed in M2 macrophages in PCa and was associated with poorer clinical outcomes. The proportion of tumor-infiltrated M2 macrophages increased in transgenic mice overexpressing YY1. In contrast, the proliferation and activity of anti-tumoral T lymphocytes were suppressed. Treatment targeting YY1 on M2 macrophages using an M2-targeting peptide-modified liposome carrier suppressed PCa cell lung metastasis and generated synergistic anti-tumoral effects with PD-1 blockade. IL-4/STAT6 pathway regulated YY1, and YY1 increased the macrophage-induced PCa progression by upregulating IL-6. Furthermore, by conducting H3K27ac-ChIP-seq in M2 macrophages and THP-1, we found that thousands of enhancers were gained during M2 macrophage polarization, and these M2-specific enhancers were enriched in YY1 ChIP-seq signals. In addition, an M2-specific IL-6 enhancer upregulated IL-6 expression through long-range chromatin interaction with IL-6 promoter in M2 macrophages. During M2 macrophage polarization, YY1 formed an LLPS, in which p300, p65, and CEBPB acted as transcriptional cofactors. CONCLUSIONS Phase separation of the YY1 complex in M2 macrophages upregulated IL-6 by promoting IL-6 enhancer-promoter interactions, thereby increasing PCa progression.
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Affiliation(s)
- Saisai Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Kai Lu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zonghao You
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Chuanjun Shu
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoying Wei
- Department of Pathology, Southeast University Zhongda Hospital, Nanjing, China
| | - Tiange Wu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Naipeng Shi
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Guangyuan Zhang
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Jianping Wu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Shuqiu Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Lihua Zhang
- Department of Pathology, Southeast University Zhongda Hospital, Nanjing, China
| | - Wenchao Li
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Dingxiao Zhang
- School of Biomedical Sciences, Hunan University, Changsha, Hunan, China
| | - Shenghong Ju
- Department of Radiology, Southeast University Zhongda Hospital, Nanjing, China
| | - Ming Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Bin Xu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Institute of Medical Phenomics Research, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
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Yang X, Zhang M, Xie B, Peng Z, Manning JR, Zimmerman R, Wang Q, Wei AC, Khalifa M, Reynolds M, Jin J, Om M, Zhu G, Bedja D, Jiang H, Jurczak M, Shiva S, Scott I, O’Rourke B, Kass DA, Paolocci N, Feng N. Myocardial brain-derived neurotrophic factor regulates cardiac bioenergetics through the transcription factor Yin Yang 1. Cardiovasc Res 2023; 119:571-586. [PMID: 35704040 PMCID: PMC10226756 DOI: 10.1093/cvr/cvac096] [Citation(s) in RCA: 3] [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] [Received: 01/04/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/21/2023] Open
Abstract
AIMS Brain-derived neurotrophic factor (BDNF) is markedly decreased in heart failure patients. Both BDNF and its receptor, tropomyosin-related kinase receptor (TrkB), are expressed in cardiomyocytes; however, the role of myocardial BDNF signalling in cardiac pathophysiology is poorly understood. Here, we investigated the role of BDNF/TrkB signalling in cardiac stress response to exercise and pathological stress. METHODS AND RESULTS We found that myocardial BDNF expression was increased in mice with swimming exercise but decreased in a mouse heart failure model and human failing hearts. Cardiac-specific TrkB knockout (cTrkB KO) mice displayed a blunted adaptive cardiac response to exercise, with attenuated upregulation of transcription factor networks controlling mitochondrial biogenesis/metabolism, including peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α). In response to pathological stress (transaortic constriction, TAC), cTrkB KO mice showed an exacerbated heart failure progression. The downregulation of PGC-1α in cTrkB KO mice exposed to exercise or TAC resulted in decreased cardiac energetics. We further unravelled that BDNF induces PGC-1α upregulation and bioenergetics through a novel signalling pathway, the pleiotropic transcription factor Yin Yang 1. CONCLUSION Taken together, our findings suggest that myocardial BDNF plays a critical role in regulating cellular energetics in the cardiac stress response.
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Affiliation(s)
- Xue Yang
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Manling Zhang
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Cardiology, Veteran Affair Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Bingxian Xie
- Department of Medicine, Division of Endocrinology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zishan Peng
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Janet R Manning
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Raymond Zimmerman
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qin Wang
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Echocardiography lab at Heart Center, Ningxia General Hospital, Ningxia Medical University, Ningxia, China
| | - An-chi Wei
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Graduate Institute of Biomedical and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Moustafa Khalifa
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Reynolds
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jenny Jin
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Om
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Guangshuo Zhu
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Djahida Bedja
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Hong Jiang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Michael Jurczak
- Department of Medicine, Division of Endocrinology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sruti Shiva
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Iain Scott
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian O’Rourke
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nazareno Paolocci
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ning Feng
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Cardiology, Veteran Affair Pittsburgh Healthcare System, Pittsburgh, PA, USA
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Yin X, Yin X, Pan X, Zhang J, Fan X, Li J, Zhai X, Jiang L, Hao P, Wang J, Chen Y. Post-myocardial infarction fibrosis: Pathophysiology, examination, and intervention. Front Pharmacol 2023; 14:1070973. [PMID: 37056987 PMCID: PMC10086160 DOI: 10.3389/fphar.2023.1070973] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Cardiac fibrosis plays an indispensable role in cardiac tissue homeostasis and repair after myocardial infarction (MI). The cardiac fibroblast-to-myofibroblast differentiation and extracellular matrix collagen deposition are the hallmarks of cardiac fibrosis, which are modulated by multiple signaling pathways and various types of cells in time-dependent manners. Our understanding of the development of cardiac fibrosis after MI has evolved in basic and clinical researches, and the regulation of fibrotic remodeling may facilitate novel diagnostic and therapeutic strategies, and finally improve outcomes. Here, we aim to elaborate pathophysiology, examination and intervention of cardiac fibrosis after MI.
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Affiliation(s)
- Xiaoying Yin
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xinxin Yin
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Pan
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jingyu Zhang
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xinhui Fan
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jiaxin Li
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaoxuan Zhai
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Lijun Jiang
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Panpan Hao
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jiali Wang
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Jiali Wang, ; Yuguo Chen,
| | - Yuguo Chen
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center for Emergency and Critical Care Medicine of Shandong Province, Institute of Emergency and Critical Care Medicine of Shandong University, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Jiali Wang, ; Yuguo Chen,
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Huang J, Wang Y, Zha Y, Zeng X, Li W, Zhou M. Transcriptome Analysis Reveals Hub Genes Regulating Autophagy in Patients With Severe COVID-19. Front Genet 2022; 13:908826. [PMID: 35923698 PMCID: PMC9340158 DOI: 10.3389/fgene.2022.908826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Background: The COVID-19 pandemic has currently developed into a worldwide threat to humankind. Importantly, patients with severe COVID-19 are believed to have a higher mortality risk than those with mild conditions. However, despite the urgent need to develop novel therapeutic strategies, the biological features and pathogenic mechanisms of severe COVID-19 are poorly understood. Methods: Here, peripheral blood mononuclear cells (PBMCs) from four patients with severe COVID-19, four patients with mild COVID-19, and four healthy controls were examined by RNA sequencing (RNA-Seq). We conducted gene expression analysis and Venn diagrams to detect specific differentially expressed genes (DEGs) in patients with severe disease compared with those with mild conditions. Gene Ontology (GO) enrichment analysis was performed to identify the significant biological processes, and protein–protein interaction networks were constructed to extract hub genes. These hub genes were then subjected to regulatory signatures and protein–chemical interaction analysis for certain regulatory checkpoints and identification of potent chemical agents. Finally, to demonstrate the cell type-specific expression of these genes, we performed single-cell RNA-Seq analyses using an online platform. Results: A total of 144 DEGs were specifically expressed in severe COVID-19, and GO enrichment analysis revealed a significant association of these specific DEGs with autophagy. Hub genes such as MVB12A, CHMP6, STAM, and VPS37B were then found to be most significantly involved in the biological processes of autophagy at the transcriptome level. In addition, six transcription factors, including SRF, YY1, CREB1, PPARG, NFIC, and GATA2, as well as miRNAs, namely, hsa-mir-1-3p, and potent chemical agents such as copper sulfate and cobalt chloride, may cooperate in regulating the autophagy hub genes. Furthermore, classical monocytes may play a central role in severe COVID-19. Conclusion: We suggest that autophagy plays a crucial role in severe COVID-19. This study might facilitate a more profound knowledge of the biological characteristics and progression of COVID-19 and the development of novel therapeutic approaches to achieve a breakthrough in the current COVID-19 pandemic.
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Affiliation(s)
- Jinfeng Huang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Yimeng Wang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yawen Zha
- Department of Radiation Oncology Ⅱ, Zhongshan People’s Hospital, Zhongshan, China
| | - Xin Zeng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wenxing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Southern Medical University, Guangzhou, China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
- *Correspondence: Meijuan Zhou,
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