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Pan D, Di X, Yan B, Su X. Advances in the Study of Non-Coding RNA in the Signaling Pathway of Pulmonary Fibrosis. Int J Gen Med 2024; 17:1419-1431. [PMID: 38617054 PMCID: PMC11016256 DOI: 10.2147/ijgm.s455707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/24/2024] [Indexed: 04/16/2024] Open
Abstract
Pulmonary fibrosis is a group of chronic, progressive, and irreversible interstitial lung diseases, which are common to most end-stage lung diseases and are one of the most difficult diseases of the respiratory system. In recent years, due to the frequent occurrence of air pollution and smog, the incidence of pulmonary fibrosis in China has increased year by year, the morbidity and mortality rates of pulmonary fibrosis have gradually increased and the age of the disease tends to be younger. However, the pathogenesis of pulmonary fibrosis is not yet fully understood and is needed to further explore new drug targets. Studies have shown that non-coding RNAs play an important role in regulating the process of pulmonary fibrosis, non-coding RNAs and their specifically expressed can promote or inhibit the process. Here, we review the role of some in the regulation of pulmonary fibrosis signaling pathways and provide new ideas for the clinical diagnosis and treatment of pulmonary fibrosis.
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Affiliation(s)
- Dengyun Pan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xin Di
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - Bingdi Yan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - Xiaomin Su
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, People’s Republic of China
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Zhou S, Li Y, Sun W, Ma D, Liu Y, Cheng D, Li G, Ni C. circPVT1 promotes silica-induced epithelial-mesenchymal transition by modulating the miR-497-5p/TCF3 axis. J Biomed Res 2024; 38:163-174. [PMID: 38529638 PMCID: PMC11001589 DOI: 10.7555/jbr.37.20220249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 03/27/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a vital pathological feature of silica-induced pulmonary fibrosis. However, whether circRNA is involved in the process remains unclear. The present study aimed to investigate the role of circPVT1 in the silica-induced EMT and the underlying mechanisms. We found that an elevated expression of circPVT1 promoted EMT and enhanced the migratory capacity of silica-treated epithelial cells. The isolation of cytoplasmic and nuclear separation assay showed that circPVT1 was predominantly expressed in the cytoplasm. RNA immunoprecipitation assay and RNA pull-down experiment indicated that cytoplasmic-localized circPVT1 was capable of binding to miR-497-5p. Furthermore, we found that miR-497-5p attenuated the silica-induced EMT process by targeting transcription factor 3 (TCF3), an E-cadherin transcriptional repressor, in the silica-treated epithelial cells. Collectively, these results reveal a novel role of the circPVT1/miR-497-5p/TCF3 axis in the silica-induced EMT process in lung epithelial cells. Once validated, this finding may provide a potential theoretical basis for the development of interventions and treatments for pulmonary fibrosis.
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Affiliation(s)
- Siyun Zhou
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yan Li
- Biomedical Publications Center, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Wenqing Sun
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dongyu Ma
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yi Liu
- Gusu School, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Demin Cheng
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Guanru Li
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Chunhui Ni
- Department of Occupational Medical and Environmental Health, Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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Surendran A, Huang C, Liu L. Circular RNAs and their roles in idiopathic pulmonary fibrosis. Respir Res 2024; 25:77. [PMID: 38321530 PMCID: PMC10848557 DOI: 10.1186/s12931-024-02716-2] [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: 10/11/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited treatment options. Circular RNAs (circRNAs) have emerged as a novel class of non-coding RNAs with diverse functions in cellular processes. This review paper aims to explore the potential involvement of circRNAs in the pathogenesis of IPF and their diagnostic and therapeutic implications. We begin by providing an overview of the epidemiology and risk factors associated with IPF, followed by a discussion of the pathophysiology underlying this complex disease. Subsequently, we delve into the history, types, biogenesis, and functions of circRNAs and then emphasize their regulatory roles in the pathogenesis of IPF. Furthermore, we examine the current methodologies for detecting circRNAs and explore their diagnostic applications in IPF. Finally, we discuss the potential utility of circRNAs in the treatment of IPF. In conclusion, circRNAs hold great promise as novel biomarkers and therapeutic targets in the management of IPF.
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Affiliation(s)
- Akshaya Surendran
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lin Liu
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA.
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.
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Wu T, Wu S, Jiao H, Feng J, Zeng X. Overexpression of hsa_circ_0001861 inhibits pulmonary fibrosis through targeting miR-296-5p/BCL-2 binding component 3 axis. Eur J Histochem 2023; 67:3839. [PMID: 37781863 PMCID: PMC10614724 DOI: 10.4081/ejh.2023.3839] [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] [Received: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Pulmonary fibrosis is a progressive lung disorder. Evidence has shown that hsa_circular (circ)RNA_0001861 is dysregulated in pulmonary fibrosis. However, the detailed function of hsa_circRNA_0001861 in pulmonary fibrosis remains unexplored. To investigate the function of hsa_circRNA_0001861 in pulmonary fibrosis, human pulmonary fibroblasts in vitro were used, and cell counting kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) staining were performed to assess cell viability and proliferation, respectively. Western blot analysis and reverse transcription-quantitative PCR (RT-qPCR) were used to evaluate protein and mRNA levels. Meanwhile, the relationship among hsa_circRNA_0001861, miR-296-5p and BCL-2 binding component 3 (BBC3) was investigated by RNA pull-down assays. Furthermore, an in vivo model of lung fibrosis was constructed to assess the function of hsa_circRNA_0001861 in lung fibrosis. The data revealed that TGF‑β1 significantly increased the proliferation of pulmonary fibroblasts, while this phenomenon was markedly abolished by hsa_circRNA_0001861 overexpression. hsa_circRNA_0001861 overexpression markedly inhibited TGF‑β1‑induced fibrosis in pulmonary fibroblasts through the mediation of α-smooth muscle actin, E-cadherin, collagen III and fibronectin 1. Meanwhile, hsa_circRNA_0001861 could bind with miR-296-5p, and BBC3 was identified to be the downstream mRNA of miR-296-5p. In addition, the upregulation of hsa_circRNA_0001861 clearly reversed TGF‑β1‑induced fibrosis and proliferation in pulmonary fibroblasts through the upregulation of BBC3. Furthermore, hsa_circRNA_0001861 upregulation markedly alleviated pulmonary fibrosis in vivo. Hsa_circRNA_0001861 upregulation attenuated pulmonary fibrosis by modulating the miR-296-5p/BBC3 axis. Hence, the present study may provide some insights for the discovery of new methods against pulmonary fibrosis.
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Affiliation(s)
- Tao Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Hunan Provincial College of Traditional Chinese Medicine, Zhuzhou, Hunan.
| | - Shikui Wu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Hunan Provincial College of Traditional Chinese Medicine, Zhuzhou, Hunan.
| | - Hailu Jiao
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Hunan Provincial College of Traditional Chinese Medicine, Zhuzhou, Hunan.
| | - Jun Feng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Hunan Provincial College of Traditional Chinese Medicine, Zhuzhou, Hunan.
| | - Xiang Zeng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Hunan Provincial College of Traditional Chinese Medicine, Zhuzhou, Hunan.
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Wong R, Zhang Y, Zhao H, Ma D. Circular RNAs in organ injury: recent development. J Transl Med 2022; 20:533. [PMID: 36401311 PMCID: PMC9673305 DOI: 10.1186/s12967-022-03725-9] [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: 08/05/2022] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
Circular ribonucleic acids (circRNAs) are a class of long non-coding RNA that were once regarded as non-functional transcription byproducts. However, recent studies suggested that circRNAs may exhibit important regulatory roles in many critical biological pathways and disease pathologies. These studies have identified significantly differential expression profiles of circRNAs upon changes in physiological and pathological conditions of eukaryotic cells. Importantly, a substantial number of studies have suggested that circRNAs may play critical roles in organ injuries. This review aims to provide a summary of recent studies on circRNAs in organ injuries with respect to (1) changes in circRNAs expression patterns, (2) main mechanism axi(e)s, (3) therapeutic implications and (4) future study prospective. With the increasing attention to this research area and the advancement in high-throughput nucleic acid sequencing techniques, our knowledge of circRNAs may bring fruitful outcomes from basic and clinical research.
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Role of Circular RNAs in Pulmonary Fibrosis. Int J Mol Sci 2022; 23:ijms231810493. [PMID: 36142402 PMCID: PMC9504269 DOI: 10.3390/ijms231810493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 12/19/2022] Open
Abstract
Pulmonary fibrosis is a chronic progressive form of interstitial lung disease, characterized by the histopathological pattern of usual interstitial pneumonia. Apart from aberrant alterations of protein-coding genes, dysregulation of non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs (circRNAs), is crucial to the initiation and progression of pulmonary fibrosis. CircRNAs are single-stranded RNAs that form covalently closed loops without 5′ caps and 3′ tails. Different from canonical splicing of mRNA, they are produced from the back-splicing of precursor mRNAs and have unique biological functions, as well as potential biomedical implications. They function as important gene regulators through multiple actions, including sponging microRNAs and proteins, regulating transcription, and splicing, as well as protein-coding and translation in a cap-independent manner. This review comprehensively summarizes the alteration and functional role of circRNAs in pulmonary fibrosis, with a focus on the involvement of the circRNA in the context of cell-specific pathophysiology. In addition, we discuss the diagnostic and therapeutic potential of targeting circRNA and their regulatory pathway mediators, which may facilitate the translation of recent advances from bench to bedside in the future.
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Jinlian Xiaodu Decoction Protects against Bleomycin-Induced Pulmonary Fibrosis in Rats. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4206364. [PMID: 35783517 PMCID: PMC9246571 DOI: 10.1155/2022/4206364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/17/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
Background Jinlian Xiaodu Decoction (JXD) was reported to have anti-inflammatory and lung protection effects. This study aimed to explore the role and mechanism of JXD on bleomycin (BLM)-induced pulmonary fibrosis (PF). Methods The UHPLC-Q/TOF-MS system was applied to analyze JXD composition. The PF model was established by BLM intratracheal administration in Wistar rats. Subsequently, BLM-treated rats were intragastrically administered with dexamethasone (DXM, 1 g/kg/d) or JXD (3.5, 7 or 14 g/kg/d). Next, the lung coefficient was calculated; H&E, Masson, and TUNEL staining were used for lung morphological analysis and apoptosis assessment. Bronchoalveolar lavage fluid (BALF) biochemical analysis was conducted to count the inflammatory cell number. The expression of inflammatory factors mRNA in the lung tissue and BALF were measured by qRT-PCR. The content and activity of oxidative stress-related proteins were detected. The expression of PF-related, apoptosis-related, and TGF-β1 pathway-related protein were assessed by immunohistochemistry or Western blot. Results Twenty-six compounds were identified from JXD in both negative and positive ion modes. In BLM-induced rats, JXD reduced the lung coefficient and alleviated PF injury. JXD decreased inflammatory cell count and TNF-α, IL-1β, IL-6, and MCP-1 content. Meanwhile, JXD blunted BLM-induced oxidative stress and a high level of HYP. Furthermore, TUNEL analysis found that JXD inhibited cell apoptosis and increased Bcl-2/Bax ratio in BLM-induced lung. Moreover, JXD relieved the role of BLM on α-SMA, TGF-β1, collagen I, fibronectin, E-cadherin protein expression, and the phosphorylation of Smad2/3 in PF rat. Conclusion This study revealed the protective effect and possible element of JXD on BLM-caused PF.
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Qi F, Li Y, Yang X, Wu Y, Lin L, Liu X. Hsa_circ_0044226 knockdown attenuates progression of pulmonary fibrosis by inhibiting CDC27. Aging (Albany NY) 2020; 12:14808-14818. [PMID: 32710728 PMCID: PMC7425454 DOI: 10.18632/aging.103543] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disorder. Here, we performed a bioinformatics analysis using the GSE102660 dataset from the Gene Expression Omnibus database to identify differentially expressed circRNAs (DEcircRNAs) in tissues from IPF patients and healthy controls. The results identified 45 DEcircRNAs, among which expression of hsa_circ_0044226 was markedly higher in lung tissues from IPF patients than from healthy controls. Knocking down hsa_circ_0044226 expression using a targeted shRNA inhibited TGF-β1-induced fibrosis in RLE-6TN cells and in a bleomycin-induced mouse model of IPA. The diminished TGF-β1-induced fibrosis was associated with upregulated expression of E-cadherin and downregulated expression of α-SMA, collagen III and fibronectin 1, as well as with reduced expression of CDC27, suggesting inhibition of epithelial-to-mesenchymal transition (EMT). All of those effects were reversed by overexpression of CDC27. This suggests CDC27 overexpression abolishes the antifibrotic effect of hsa_circ_0044226 knockdown through activation of EMT. Furthermore, hsa_circ_0044226 knockdown decreased the expression of CDC27 in BLM-induced pulmonary fibrosis mouse model. Collectively then, these findings indicate that downregulation of hsa_circ_0044226 attenuates pulmonary fibrosis in vitro and in vivo by inhibiting CDC27, which in turn suppresses EMT. This suggests hsa_circ_0044226 may be a useful therapeutic target for the treatment of IPF.
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Affiliation(s)
- Fei Qi
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
| | - Yong Li
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
| | - Xue Yang
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
| | - Yanping Wu
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
| | - Lianjun Lin
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
| | - Xinmin Liu
- Department of Geriatrics, Peking University First Hospital, Beijing 100034, China
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Duan R, Niu H, Yu T, Cui H, Yang T, Hao K, Wang C. Identification and Bioinformatic Analysis of Circular RNA Expression in Peripheral Blood Mononuclear Cells from Patients with Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2020; 15:1391-1401. [PMID: 32606648 PMCID: PMC7305829 DOI: 10.2147/copd.s252896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Circular RNAs (circRNAs) regulate other RNA transcripts by competing for shared microRNAs, which play roles in the pathogenesis of many diseases, including chronic obstructive pulmonary disease (COPD). However, the role of circRNAs in COPD remains unknown. This study aimed to investigate the expression profile and the role of circRNAs in COPD. Patients and Methods Twenty-one COPD patients and twenty-one normal controls were recruited. Total RNAs were collected from peripheral blood mononuclear cells (PBMCs) of each participant. CircRNAs and protein-coding mRNAs were profiled by microarray and systematically compared between patients with COPD and control subjects. The top differentially expressed circRNAs and mRNAs were validated by quantitative real-time PCR (RT-qPCR). Functional analysis identified pathways relevant to the pathogenesis of COPD. Next, the circRNA target pathway network, the circRNA-miRNA-mRNA network (ceRNA network) and functional ceRNA regulatory modules were constructed. Results In total, 2132 circRNAs and 2734 protein-coding mRNAs were differentially expressed (|fold change| >1.5 and P-value <0.05) in COPD patients. Six out of nine selected RNAs were confirmed by RT-qPCR validation. Our functional analysis suggested that immune imbalances and inflammatory responses play roles in the pathogenesis of COPD. The ceRNA network highlighted the differentially expressed circRNAs and their related miRNAs and mRNAs in COPD. In the circRNA target pathway network and functional ceRNA regulatory modules, hsa_circRNA_0008672 appeared in the top three KEGG pathways (NOD-like receptor signaling pathway, natural killer cell mediated cytotoxicity and Th17 cell differentiation) and may act as the miRNA sponge regulating the hsa_circRNA_0008672/miR-1265/MAPK1 axis. Conclusion Our findings demonstrate critical roles of the circRNAs in COPD molecular etiology. The data support a plausible mechanism that circRNAs may be involved in the development of COPD by affecting the immune balance. Moreover, the hsa_circRNA_0008672/miR-1265/MAPK1 axis may contribute to the pathogenesis of COPD, warranting further investigation.
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Affiliation(s)
- Ruirui Duan
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Hongtao Niu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Tao Yu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Han Cui
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Ting Yang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chen Wang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China.,National Clinical Research Center for Respiratory Diseases, Beijing, People's Republic of China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
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Chen Z, Pan X, Kong Y, Jiang Y, Zhong Y, Zhang H, Zhang Z, Yuan X, Li J. Pituitary-Derived Circular RNAs Expression and Regulatory Network Prediction During the Onset of Puberty in Landrace × Yorkshire Crossbred Pigs. Front Genet 2020; 11:135. [PMID: 32180798 PMCID: PMC7059797 DOI: 10.3389/fgene.2020.00135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/04/2020] [Indexed: 01/25/2023] Open
Abstract
Being the center of the hypothalamus-pituitary-ovary (HPO) axis, the pituitary plays a key role in the onset of puberty. Recent studies show that circular RNAs (circRNAs) can perform as miRNA sponges to regulate development in animals. However, the function of pituitary-derived circRNAs in first estrus remains unclear in pigs. In this study, we performed a genome-wide identification and characterization of circRNAs using pituitaries from Landrace × Yorkshire crossbred pigs at three stages: pre-, in-, and post-puberty, to describe such pituitary-derived circRNAs in pigs. A total of 5148 circRNAs were found in the gilts' pituitaries, averaging 18 682 bp in genomic distance, which consisted of approximately 91% exonic, 6% intergenic, and 3% intronic circRNAs. Furthermore, 158 novel circRNAs were identified for the first time and classified as putative pituitary-specific circRNAs. Their expression levels during the onset of puberty, significantly exceeded those of the other circRNAs, and the parental genes of these putative pituitary-specific circRNAs were enriched in "ssc04917: prolactin signaling pathway," "ssc04080: neuroactive ligand-receptor interaction," and "ssc04728: dopaminergic synapse" pathways, all of which were consistent with pituitary functioning. Additionally, 17 differentially regulated circRNAs were found and investigated for their potential interaction with miRNAs, along with genes, by constructing a circRNA-targeted miRNA-gene network. Taken together, these results provide new insight into the circRNA-mediated timing of puberty in gilts at the pituitary level.
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Affiliation(s)
- Zitao Chen
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiangchun Pan
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yaru Kong
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yao Jiang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yuyi Zhong
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hao Zhang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhe Zhang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaolong Yuan
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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Yang L, Liu X, Zhang N, Chen L, Xu J, Tang W. Investigation of circular RNAs and related genes in pulmonary fibrosis based on bioinformatics analysis. J Cell Biochem 2019; 120:11022-11032. [PMID: 30767300 PMCID: PMC6593700 DOI: 10.1002/jcb.28380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023]
Abstract
Pulmonary fibrosis is a lethal inflammatory disease. In this study, we aimed to explore the potential-related circular RNAs (circRNAs) and genes that are associated with pulmonary fibrosis. Pulmonary fibrosis rat models were constructed and the fibrosis deposition was detected using hematoxylin and eosin and Masson staining. The differentially expressed circRNAs were obtained through RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were further performed to uncover the key function and pathways in pulmonary fibrosis. The interaction networks between circRNAs and their downstream micro RNAs (miRNAs) and genes were constructed by Cytoscape Software. The quantitative polymerase chain reaction was performed to validate the expression of 10 candidate circRNAs and five of them were performed ringwise sequencing in pulmonary fibrosis rats. We further selected five candidate circRNAs target miRNAs and messenger RNAs and validated by real-time polymerase chain reaction. The pulmonary fibrosis models were successfully constructed according to the pathological examination. circRNAs were differentially expressed between the pulmonary fibrosis and normal pulmonary tissues. GO analysis verified that the differentially expressed circRNAs were significantly clustered in the cellular component, molecular function, and biological process. In the KEGG analysis, circRNAs were enriched in the following pathways: antigen processing and presentation, phagosome, PI3K-AKt signaling pathway, HTLV-I infection, and Herpes simplex infection. After validation in pulmonary fibrosis rat models, it was found that five of those circRNAs (chr9:113534327|113546234 [down], chr1:200648164|200672411 [down], chr5:150850432|150865550 [up], chr20:14319170|14326640 [down], and chr10:57634023|57634588 [down]) showed a relatively consistent trend with predictions. Validation of these circRNAs target miRNAs and genes showed that chr9:113534327|113546234, chr20:14319170|14326640, and chr10:57634023|57634588 were implicated in Notch1 activated transforming growth factor-β (TGF-β) signaling pathway. The study demonstrated that a series of circRNAs are differentially expressed in pulmonary fibrosis rats. These circRNAs, especially TGF-β- and Notch1-related circRNAs might play an important role in regulating pulmonary fibrogenesis.
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Affiliation(s)
- Liteng Yang
- Department of Respiratory MedicineShenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen UniversityGuangdongShenzhenChina
| | - Xin Liu
- Department of Traditional Chinese Medicine, Zunyi Medical and Pharmaceutical CollegeGuizhouZunyiChina
| | - Ning Zhang
- Department of Respiratory MedicineShenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen UniversityGuangdongShenzhenChina
| | - Lifang Chen
- Department of Respiratory MedicineShenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen UniversityGuangdongShenzhenChina
| | - Jingyi Xu
- Department of Respiratory MedicineShenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen UniversityGuangdongShenzhenChina
| | - Wencheng Tang
- Department of Respiratory MedicineShenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen UniversityGuangdongShenzhenChina
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