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Li B, Zhang J, Dong H, Feng X, Yu L, Zhu J, Zhang J. Systematic analysis of various RNA transcripts and construction of biological regulatory networks at the post-transcriptional level for chronic obstructive pulmonary disease. J Transl Med 2023; 21:790. [PMID: 37936118 PMCID: PMC10631086 DOI: 10.1186/s12967-023-04674-7] [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: 05/26/2023] [Accepted: 10/29/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Although chronic inflammation, oxidative stress, airway remodeling, and protease-antiprotease imbalance have been implicated in chronic obstructive pulmonary disease (COPD), the exact pathogenesis is still obscure. Gene transcription and post-transcriptional regulation have been taken into account as key regulators of COPD occurrence and development. Identifying the hub genes and constructing biological regulatory networks at the post-transcriptional level will help extend current knowledge on COPD pathogenesis and develop potential drugs. METHODS All lung tissues from non-smokers (n = 6), smokers without COPD (smokers, n = 7), and smokers with COPD (COPD, n = 7) were collected to detect messenger RNA (mRNA), microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNA) expression and identify the hub genes. Biological regulatory networks were constructed at the post-transcriptional level, including the RNA-binding protein (RBP)-hub gene interaction network and the competitive endogenous RNA (ceRNA) network. In addition, we assessed the composition and abundance of immune cells in COPD lung tissue and predicted potential therapeutic drugs for COPD. Finally, the hub genes were confirmed at both the RNA and protein levels. RESULTS Among the 20 participants, a total of 121169 mRNA transcripts, 1871 miRNA transcripts, 4244 circRNA transcripts, and 122130 lncRNA transcripts were detected. There were differences in the expression of 1561 mRNAs, 48 miRNAs, 33 circRNAs, and 545 lncRNAs between smokers and non-smokers, as well as 1289 mRNAs, 69 miRNAs, 32 circRNAs, and 433 lncRNAs between smokers and COPD patients. 18 hub genes were identified in COPD. TGF-β signaling and Wnt/β-catenin signaling may be involved in the development of COPD. Furthermore, the circRNA/lncRNA-miRNA-mRNA ceRNA networks and the RBP-hub gene interaction network were also constructed. Analysis of the immune cell infiltration level revealed that M2 macrophages and activated NK cells were increased in COPD lung tissues. Finally, we identified that the ITK inhibitor and oxybutynin chloride may be effective in treating COPD. CONCLUSIONS We identified several novel hub genes involved in COPD pathogenesis. TGF-β signaling and Wnt/β-catenin signaling were the most dysregulated pathways in COPD patients. Our study constructed post-transcriptional biological regulatory networks and predicted small-molecule drugs for the treatment of COPD, which enhanced the existing understanding of COPD pathogenesis and suggested an innovative direction for the therapeutic intervention of the disease.
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Affiliation(s)
- Beibei Li
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Jiajun Zhang
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Hui Dong
- Center of Research Equipment Management, General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Xueyan Feng
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Liang Yu
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Jinyuan Zhu
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Jin Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, 804 Shengli South Street, Xingqing District, Yinchuan, 750004, China.
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Hsieh MJ, Lo YS, Tsai YJ, Ho HY, Lin CC, Chuang YC, Lin SH, Chen MK. FAM13A polymorphisms are associated with a specific susceptibility to clinical progression of oral cancer in alcohol drinkers. BMC Cancer 2023; 23:607. [PMID: 37391706 DOI: 10.1186/s12885-023-11052-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/09/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) is a genetic variation that occurs when a single nucleotide base in the DNA sequence varies between individuals and is present in at least 1% of the population. Genetic variants in FAM13A are associated with different types of chronic respiratory diseases, including chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and lung cancer. However, there is little literature on the association of FAM13A genotypes with oral cancer. Therefore, this project will explore the correlation between the FAM13A genotype and the formation of oral cancer. METHODS In this project, we will examine the presence of gene polymorphisms gene polymorphisms of rs1059122, rs3017895, rs3756050, and rs7657817 in the FAM13A gene exon, and combine the expression of these genes to try to clarify the impact of the FAM13A gene polymorphism on oral cancer. First, four loci (rs1059122, rs3017895, rs3756050, and rs7657817) of the FAM13A SNP were genotyped using TaqMan allelic discrimination. RESULTS By estimating OR and AOR, FAM13A exhibited different genotypic variables in four SNPs that were not statistically significant between controls and patients with oral cancer. The results of the general analysis showed that different distributions of allelic types did not affect clinical stage, tumour size, lymph node invasion, distant metastasis, and pathological differentiation status. However, in the alcohol drinking group specifically, patients with the rs3017895 SNP G genotype had a 3.17-fold (95% CI, 1.102-9.116; p = 0.032) increase in the well differentiated state of cells compared to patients with the A allele. CONCLUSIONS Our results suggested that the SNP rs3017895 FAM13A could contribute to oral cancer. More sample studies are needed in the future to confirm our results and more functional studies are needed to investigate their relevant roles in the development of oral cancer.
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Affiliation(s)
- Ming-Ju Hsieh
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
- Program in Tissue Engineering and Regenerative Medicine, College of Medicine, National Chung Hsing University, Taichung, 402, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404, Taiwan
| | - Yu-Sheng Lo
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Yun-Jung Tsai
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua, 500, Taiwan
- Translational Pathology Core Laboratory, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Hsin-Yu Ho
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Chia-Chieh Lin
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Yi-Ching Chuang
- Oral Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Shu-Hui Lin
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua, 500, Taiwan
- Translational Pathology Core Laboratory, Changhua Christian Hospital, Changhua, 500, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan
| | - Mu-Kuan Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Changhua Christian Hospital, No.135, Nanxiao St., Changhua City, Changhua County, 500, Taiwan.
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 402, Taiwan.
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Feng X, Dong H, Li B, Yu L, Zhu J, Lou C, Zhang J. Integrative analysis of the expression profiles of whole coding and non-coding RNA transcriptomes and construction of the competing endogenous RNA networks for chronic obstructive pulmonary disease. Front Genet 2023; 14:1050783. [PMID: 36793900 PMCID: PMC9923003 DOI: 10.3389/fgene.2023.1050783] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The pathogenesis of Chronic Obstructive Pulmonary Disease (COPD) is implicated in airway inflammation, oxidative stress, protease/anti-protease and emphysema. Abnormally expressed non-coding RNAs (ncRNAs) play a vital role in regulation of COPD occurrence and progression. The regulatory mechanisms of the circRNA/lncRNA-miRNA-mRNA (competing endogenous RNA, ceRNA) networks might facilitate our cognition of RNA interactions in COPD. This study aimed to identified novel RNA transcripts and constructed the potential ceRNA networks of COPD patients. Total transcriptome sequencing of the tissues from patients with COPD (COPD) (n = 7) and non-COPD control subjects (Normal) (n = 6) was performed, and the expression profiles of differentially expressed genes (DEGs), including mRNAs, lncRNAs, circRNAs, and miRNAs, were analyzed. The ceRNA network was established based on the miRcode and miRanda databases. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA), and Gene set variation analysis (GSVA) were implemented for functional enrichment analysis of DEGs. Finally, CIBERSORTx was extracted to analyze the relevance between hub genes and various immune cells.The Starbase and JASPAR databases were used to construct hub-RNA binding proteins (RBPs) and lncRNA-transcription factor (TF) interaction networks. A total of 1,796 mRNAs, 2,207 lncRNAs, and 11 miRNAs showed differentially expression between the lung tissue samples from the normal and COPD groups. Based on these DEGs, lncRNA/circRNA-miRNA-mRNA ceRNA networks were constructed respectively. In addition, ten hub genes were identified. Among them, RPS11, RPL32, RPL5, and RPL27A were associated with the proliferation, differentiation, and apoptosis of the lung tissue. The biological function revealed that TNF-α via NF-kB and IL6/JAK/STAT3 signaling pathways were involved in COPD. Our research constructed the lncRNA/circRNA-miRNA-mRNA ceRNA networks, filtrated ten hub genes may regulate the TNF-α/NF-κB, IL6/JAK/STAT3 signally pathways, which indirectly elucidated the post-transcriptional regulation mechanism of COPD and lay the foundation for excavating the novel targets of diagnosis and treatment in COPD.
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Affiliation(s)
- Xueyan Feng
- Clinical medical school, Ningxia Medical University, Yinchuan, China
| | - Hui Dong
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Beibei Li
- Clinical medical school, Ningxia Medical University, Yinchuan, China
| | - Liang Yu
- Department of Thoracic Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Jinyuan Zhu
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Caili Lou
- Clinical medical school, Ningxia Medical University, Yinchuan, China
| | - Jin Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan, China,*Correspondence: Jin Zhang,
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Su X, Wu W, Zhu Z, Lin X, Zeng Y. The effects of epithelial-mesenchymal transitions in COPD induced by cigarette smoke: an update. Respir Res 2022; 23:225. [PMID: 36045410 PMCID: PMC9429334 DOI: 10.1186/s12931-022-02153-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 12/15/2022] Open
Abstract
Cigarette smoke is a complex aerosol containing a large number of compounds with a variety of toxicity and carcinogenicity. Long-term exposure to cigarette smoke significantly increases the risk of a variety of diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. Epithelial–mesenchymal transition (EMT) is a unique biological process, that refers to epithelial cells losing their polarity and transforming into mobile mesenchymal cells, playing a crucial role in organ development, fibrosis, and cancer progression. Numerous recent studies have shown that EMT is an important pathophysiological process involved in airway fibrosis, airway remodeling, and malignant transformation of COPD. In this review, we summarized the effects of cigarette smoke on the development and progression of COPD and focus on the specific changes and underlying mechanisms of EMT in COPD induced by cigarette smoke. We spotlighted the signaling pathways involved in EMT induced by cigarette smoke and summarize the current research and treatment approaches for EMT in COPD, aiming to provide ideas for potential new treatment and research directions.
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Affiliation(s)
- Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Weijing Wu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhixing Zhu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Xiaoping Lin
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China.
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Zhang DW, Ye JJ, Sun Y, Ji S, Kang JY, Wei YY, Fei GH. CD19 and POU2AF1 are Potential Immune-Related Biomarkers Involved in the Emphysema of COPD: On Multiple Microarray Analysis. J Inflamm Res 2022; 15:2491-2507. [PMID: 35479834 PMCID: PMC9035466 DOI: 10.2147/jir.s355764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/05/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Emphysema is the main cause of the progression of chronic obstructive pulmonary disease (COPD). This study aimed to identify the key genes involved in COPD-related emphysema. Patients and Methods GSE76925 was downloaded from Gene Expression Omnibus database. Protein–protein interaction networks of differentially expressed genes (DEGs) between control and COPD groups were constructed to identify hub genes using Cytoscape. Diagnostic performance of hub genes was evaluated using receiver operating characteristic analysis. Correlation analysis was performed to identify the key genes by analyzing the relationship between the hub genes and lung function and computed tomography (CT) indexes of emphysema. COPD patients were then divided into two groups based on the median expression of key genes and DEGs between these two groups were identified. Enrichment analysis of DEGs and correlation analysis between key genes and the infiltration of the immune cells were also analyzed. Finally, the role of key genes was evaluated in a lung tissues dataset (GSE47460) and a blood dataset (GSE76705). Additionally, the expression of key genes was validated by quantitative real-time polymerase chain reaction and immunohistochemistry. Results CD19 and POU2AF1 had diagnostic efficacy for COPD and were significantly correlated with lung function and CT indexes of emphysema. Enrichment and immune analyses revealed that CD19 and POU2AF1 were correlated with the B cells in COPD. These results were consistent in GSE47460. The expression of CD19 and POU2AF1 in blood was the opposite of that in lung tissues, and CD19 and POU2AF1 were both significantly upregulated in COPD lung tissues at both the mRNA and protein levels. Conclusion CD19 and POU2AF1 may serve as key regulators of emphysema and contribute to the progression of COPD by regulating the B-cell immunology. Targeting B cells may be a promising strategy for treating COPD.
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Affiliation(s)
- Da-Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jing-Jing Ye
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Ying Sun
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Shuang Ji
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jia-Ying Kang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Yuan-Yuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
- Correspondence: Guang-He Fei, Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China, Tel +86 551 6292 2013, Fax +86 551 6363 5578, Email
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Ning J, Du H, Zhang Y, Liu Q, Jiang T, Pang Y, Tian X, Yan L, Niu Y, Zhang R. N6-methyladenosine modification of CDH1 mRNA promotes PM2.5-induced pulmonary fibrosis via mediating epithelial mesenchymal transition. Toxicol Sci 2021; 185:143-157. [PMID: 34735003 DOI: 10.1093/toxsci/kfab133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The association between ambient airborne fine particulate matter (PM2.5) exposure and respiratory diseases has been investigated in epidemiological studies. To explore the potential mechanism of PM2.5-induced pulmonary fibrosis, sixty mice were divided into 3 groups to expose to different levels of PM2.5 for 8 and 16 weeks: filtered air (FA), unfiltered air (UA) and concentrated PM2.5 air (CA), respectively. BEAS-2B cells were treated with 0, 25, 50 and 100 μg/ml PM2.5 for 24 h. The biomarkers of pulmonary fibrosis, epithelial-mesenchymal transition (EMT), N6-methyladenosine (m6A) modification and metabolism of mRNAs were detected to characterize the effect of PM2.5 exposure. The results illustrated that PM2.5 exposure induced pathological alteration and pulmonary fibrosis in mice. The expression of E-cadherin (E-cad) was decreased whereas vimentin and N-cadherin (N-cad) expression were increased in a dose- and time-dependent manner after PM2.5 exposure. Mechanistically, PM2.5 exposure increased the levels of METTL3-mediated m6A modification of CDH1 mRNA. As a target gene of miR-494-3p, YTHDF2 was up-regulated by miR-494-3p down-regulation and then recognized m6A-modified CDH1 mRNA to inhibit the E-cad expression, consequently induced the EMT progression after PM2.5 exposure. Our study indicated that PM2.5 exposure triggered EMT progression to promote the pulmonary fibrosis via miR-494-3p/YTHDF2 recognized and METTL3 mediated m6A modification.
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Affiliation(s)
- Jie Ning
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Hairong Du
- Guangming District Center for Disease Control and Prevention, Shenzhen, 518016, China Guangdong PR
| | - Yaling Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Qingping Liu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Tao Jiang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yaxian Pang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xiaochen Tian
- Department of Orthopaedic Surgery, Shijiazhuang People's Hospital, Shijiazhuang, 050011, PR China
| | - Liqun Yan
- Departments of Radiology, Second Hospital of Hebei Medical University, Shijiazhuang, PR, 050000, China
| | - Yujie Niu
- Department of Occupation Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China.,Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China.,Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China
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