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Mao M, Song S, Li X, Lu J, Li J, Zhao W, Liu H, Liu J, Zeng B. Advances in epigenetic modifications of autophagic process in pulmonary hypertension. Front Immunol 2023; 14:1206406. [PMID: 37398657 PMCID: PMC10313199 DOI: 10.3389/fimmu.2023.1206406] [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: 04/15/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Pulmonary hypertension is characterized by pulmonary arterial remodeling that results in increased pulmonary vascular resistance, right ventricular failure, and premature death. It is a threat to public health globally. Autophagy, as a highly conserved self-digestion process, plays crucial roles with autophagy-related (ATG) proteins in various diseases. The components of autophagy in the cytoplasm have been studied for decades and multiple studies have provided evidence of the importance of autophagic dysfunction in pulmonary hypertension. The status of autophagy plays a dynamic suppressive or promotive role in different contexts and stages of pulmonary hypertension development. Although the components of autophagy have been well studied, the molecular basis for the epigenetic regulation of autophagy is less understood and has drawn increasing attention in recent years. Epigenetic mechanisms include histone modifications, chromatin modifications, DNA methylation, RNA alternative splicing, and non-coding RNAs, which control gene activity and the development of an organism. In this review, we summarize the current research progress on epigenetic modifications in the autophagic process, which have the potential to be crucial and powerful therapeutic targets against the autophagic process in pulmonary hypertension development.
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Affiliation(s)
- Min Mao
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Shasha Song
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xin Li
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jiayao Lu
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Jie Li
- Marketing Department, Shenzhen Reyson Biotechnology Co., Ltd, Shenzhen, China
- Nanjing Evertop Electronics Ltd., Nanjing, China
| | - Weifang Zhao
- Quality Management Department International Registration, North China Pharmaceutical Co., Ltd. (NCPC), Hebei Huamin Pharmaceutical Co., Ltd., Shijiazhuang, China
| | - Hanmin Liu
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- National Health Commission (NHC) Key Laboratory of Chronobiology (Sichuan University), Chengdu, China
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan University, Chengdu, China
- Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jingxin Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Bin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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Tan R, You Q, Yu D, Xiao C, Adu-Amankwaah J, Cui J, Zhang T. Novel hub genes associated with pulmonary artery remodeling in pulmonary hypertension. Front Cardiovasc Med 2022; 9:945854. [PMID: 36531719 PMCID: PMC9748075 DOI: 10.3389/fcvm.2022.945854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
Pulmonary hypertension (PH) is a life-threatening disease with complex pathogenesis. According to etiology, PH is divided into five major groups in clinical classification. However, pulmonary artery (PA) remodeling is their common feature, in addition to bone morphogenetic protein receptor type 2; it is elusive whether there are other novel common genes and similar underlying mechanisms. To identify novel common hub genes involved in PA remodeling at different PH groups, we analyzed mRNA-Seq data located in the general gene expression profile GSE130391 utilizing bioinformatics technology. This database contains PA samples from different PH groups of hospitalized patients with chronic thromboembolic pulmonary hypertension (CTEPH), idiopathic pulmonary artery hypertension (IPAH), and PA samples from organ donors without known pulmonary vascular diseases as control. We screened 22 hub genes that affect PA remodeling, most of which have not been reported in PH. We verified the top 10 common hub genes in hypoxia with Sugen-induced PAH rat models by qRT-PCR. The three upregulated candidate genes are WASF1, ARHGEF1 and RB1 and the seven downregulated candidate genes are IL1R1, RHOB, DAPK1, TNFAIP6, PKN1, PLOD2, and MYOF. WASF1, ARHGEF1, and RB1 were upregulated significantly in hypoxia with Sugen-induced PAH, while IL1R1, DAPK1, and TNFA1P6 were upregulated significantly in hypoxia with Sugen-induced PAH. The DEGs detected by mRNA-Seq in hospitalized patients with PH are different from those in animal models. This study will provide some novel target genes to further study PH mechanisms and treatment.
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Affiliation(s)
- Rubin Tan
- Department of Physiology, Basic Medical School, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Rubin Tan
| | - Qiang You
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Dongdong Yu
- Department of Tumor Radiotherapy, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chushu Xiao
- Department of Pathophysiology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Joseph Adu-Amankwaah
- Department of Physiology, Basic Medical School, Xuzhou Medical University, Xuzhou, China
| | - Jie Cui
- Department of Physiology, Basic Medical School, Xuzhou Medical University, Xuzhou, China
| | - Ting Zhang
- Department of Pathophysiology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Hu J, Zhou S, Guo W. Construction of the coexpression network involved in the pathogenesis of thyroid eye disease via bioinformatics analysis. Hum Genomics 2022; 16:38. [PMID: 36076300 PMCID: PMC9461120 DOI: 10.1186/s40246-022-00412-0] [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: 09/05/2021] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
Background Thyroid eye disease (TED) is the most common orbital pathology that occurs in up to 50% of patients with Graves’ disease. Herein, we aimed at discovering the possible hub genes and pathways involved in TED based on bioinformatical approaches. Results The GSE105149 and GSE58331 datasets were downloaded from the Gene Expression Omnibus (GEO) database and merged for identifying TED-associated modules by weighted gene coexpression network analysis (WGCNA) and local maximal quasi-clique merger (lmQCM) analysis. EdgeR was run to screen differentially expressed genes (DEGs). Transcription factor (TF), microRNA (miR) and drug prediction analyses were performed using ToppGene suite. Function enrichment analysis was used to investigate the biological function of genes. Protein–protein interaction (PPI) analysis was performed based on the intersection between the list of genes obtained by WGCNA, lmQCM and DEGs, and hub genes were identified using the MCODE plugin. Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes. Key TFs regulating genes in the TED-associated coexpression network, including NFRKB, ZNF711, ZNF407 and MORC2, and miRs including hsa-miR-144, hsa-miR-3662, hsa-miR-12136 and hsa-miR-3646, were identified. Genes in the coexpression network were enriched in the biological processes including proteasomal protein catabolic process and proteasome-mediated ubiquitin-dependent protein catabolic process and the pathways of endocytosis and ubiquitin-mediated proteolysis. Drugs perturbing genes in the coexpression network were also predicted and included enzyme inhibitors, chlorodiphenyl and finasteride. Conclusions For the first time, TED-associated coexpression network was constructed and key genes and their functions, as well as TFs, miRs and drugs, were predicted. The results of the present work may be relevant in the treatment and diagnosis of TED and may boost molecular studies regarding TED. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00412-0.
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Affiliation(s)
- Jinxing Hu
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Shan Zhou
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China. .,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Weiying Guo
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
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Bai Z, Xu L, Dai Y, Yuan Q, Zhou Z. ECM2 and GLT8D2 in human pulmonary artery hypertension: fruits from weighted gene co-expression network analysis. J Thorac Dis 2021; 13:2242-2254. [PMID: 34012575 PMCID: PMC8107565 DOI: 10.21037/jtd-20-3069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Pulmonary artery hypertension (PAH) is an incurable disease with a high mortality rate. Current medications ameliorate symptoms but cannot target adverse vascular remodeling. New therapeutic strategies for PAH need to be established. Methods Using the weighted gene coexpression network analysis (WGCNA) algorithm, we constructed a coexpression network of dataset GSE117261 from the Gene Expression Omnibus (GEO) database. Key modules were identified by the relationship between module eigengenes and clinical traits. Hub genes were screened out based on gene significance (GS), module membership (MM), and mean pulmonary artery pressure (mPAP). External validations were conducted in GSE48149 and GSE113439. Functional enrichment and immune cell infiltration were analyzed using Metascape and CIBERSORTx. Results The WGCNA analysis revealed 13 coexpression modules. The pink module had the highest correlation with PAH in terms of module eigengene (r=0.79; P=2e-18) and module significance (MS =0.43). Functional enrichment indicated genes in the pink module contributed to the immune system process and extracellular matrix (ECM). In the pink module, ECM2 (GS =0.65, MM =0.86, ρ=0.407, P=0.0019) and GLT8D2 (GS =0.63, MM =0.85, ρ=0.443, P=0.006) were identified as hub genes. For immune cells infiltration in PAH lung tissue, hub genes were positively correlated with M2 macrophages and resting mast cells, and were negatively correlated with monocytes, neutrophils, and CD4-naïve T cells. Conclusions Our research identified 2 hub genes ECM2 and GLT8D2 related to PAH. The functions of these hub genes were involved in the immune process and ECM, indicating that they might serve as candidate therapeutic targets for PAH.
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Affiliation(s)
- Zeyang Bai
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lianyan Xu
- Department of Radiology, Peking Union Medical College Hospital, PUMC & CAMS, Beijing, China
| | - Yong Dai
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingchen Yuan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zihua Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Stifano G, De Palma R. Editorial: Etiopathogenesis of Systemic Sclerosis: An Update. Front Immunol 2021; 12:663381. [PMID: 33828566 PMCID: PMC8019788 DOI: 10.3389/fimmu.2021.663381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/08/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Giuseppina Stifano
- Arthritis Center, Boston University School of Medicine, Boston, MA, United States
| | - Raffaele De Palma
- Dipartimento di Medicina Interna e Specialità Mediche (DIMI), University of Genova, Genova, Italy.,Clinical Immunology, IRCCS Ospedale Policlinico San Martino-IST-Genova, Genova, Italy
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Shen W, Zhang Z, Ma J, Lu D, Lyu L. The Ubiquitin Proteasome System and Skin Fibrosis. Mol Diagn Ther 2021; 25:29-40. [PMID: 33433895 DOI: 10.1007/s40291-020-00509-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
The ubiquitin proteasome system (UPS) is a highly conserved way to regulate protein turnover in cells. The UPS hydrolyzes and destroys variant or misfolded proteins and finely regulates proteins involved in differentiation, apoptosis, and other biological processes. This system is a key regulatory factor in the proliferation, differentiation, and collagen secretion of skin fibroblasts. E3 ubiquitin protein ligases Parkin and NEDD4 regulate multiple signaling pathways in keloid. Tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) binding with deubiquitinase USP10 can induce p53 destabilization and promote keloid-derived fibroblast proliferation. The UPS participates in the occurrence and development of hypertrophic scars by regulating the transforming growth factor (TGF)-β/Smad signaling pathway. An initial study suggests that TNFα-induced protein 3 (TNFAIP3) polymorphisms may be significantly associated with scleroderma susceptibility in individuals of Caucasian descent. Sumoylation and multiple ubiquitin ligases, including Smurfs, UFD2, and KLHL42, play vital roles in scleroderma by targeting the TGF-β/Smad signaling pathway. In the future, drugs targeting E3 ligases and deubiquitinating enzymes have great potential for the treatment of skin fibrosis.
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Affiliation(s)
- Wanlu Shen
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Zhigang Zhang
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Jiaqing Ma
- School of Basic Medical Sciences, Kunming Medical University, Kunming, China
| | - Di Lu
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Lechun Lyu
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China.
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Xiao G, Zhuang W, Wang T, Lian G, Luo L, Ye C, Wang H, Xie L. Transcriptomic analysis identifies Toll-like and Nod-like pathways and necroptosis in pulmonary arterial hypertension. J Cell Mol Med 2020; 24:11409-11421. [PMID: 32860486 PMCID: PMC7576255 DOI: 10.1111/jcmm.15745] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammation and immunity play a causal role in the pathogenesis of pulmonary vascular remodelling and pulmonary arterial hypertension (PAH). However, the pathways and mechanisms by which inflammation and immunity contribute to pulmonary vascular remodelling remain unknown. RNA sequencing was used to analyse the transcriptome in control and rats injected with monocrotaline (MCT) for various weeks. Using the transcriptional profiling of MCT‐induced PAH coupled with bioinformatics analysis, we clustered the differentially expressed genes (DEGs) and chose the increased expression patterns associated with inflammatory and immune response. We found the enrichment of Toll‐like receptor (TLR) and Nod‐like receptor (NLR) pathways and identified NF‐κB‐mediated inflammatory and immune profiling in MCT‐induced PAH. Pathway‐based data integration and visualization showed the dysregulated TLR and NLR pathways, including increased expression of TLR2 and NLRP3, and their downstream molecules. Further analysis revealed that the activation of TLR and NLR pathways was associated with up‐regulation of damage‐associated molecular patterns (DAMPs) and RIPK3‐mediated necroptosis was involved in the generation of DAMPs in MCT‐induced PAH. Collectively, we identify RIPK3‐mediated necroptosis and its triggered TLR and NLR pathways in the progression of pulmonary vascular remodelling, thus providing novel insights into the mechanisms underlying inflammation and immunity in the pathogenesis of PAH.
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Affiliation(s)
- Genfa Xiao
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.,Department of General Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China.,Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Wei Zhuang
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Tingjun Wang
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.,Department of General Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China.,Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Guili Lian
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Li Luo
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.,Department of General Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China.,Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Chaoyi Ye
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Huajun Wang
- Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
| | - Liangdi Xie
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, People's Republic of China.,Department of General Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China.,Fujian Hypertension Research Institute, The First Affiliated Hospital of Fujian Medical University, People's Republic of China
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