1
|
Guan Q, Zhang Z, Zhao P, Huang L, Lu R, Liu C, Zhao Y, Shao X, Tian Y, Li J. Identification of idiopathic pulmonary fibrosis hub genes and exploration of the mechanisms of action of Jinshui Huanxian formula. Int Immunopharmacol 2024; 132:112048. [PMID: 38593509 DOI: 10.1016/j.intimp.2024.112048] [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: 02/19/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a common and heterogeneous chronic disease, and the mechanism of Jinshui Huanxian formula (JHF) on IPF remains unclear. For a total of 385 lung normal tissue samples from the Gene Expression Omnibus database, 37,777,639 gene pairs were identified through microarray and RNA-seq platforms. Using the individualized differentially expressed gene (DEG) analysis algorithm RankComp (FDR < 0.01), we identified 344 genes as DEGs in at least 95 % (n = 81) of the IPF samples. Of these genes, IGF1, IFNGR1, GLI2, HMGCR, DNM1, KIF4A, and TNFRSF11A were identified as hub genes. These genes were verified using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in mice with pulmonary fibrosis (PF) and MRC-5 cells, and they were highly effective at classifying IPF samples in the independent dataset GSE134692 (AUC = 0.587-0.788) and mice with PF (AUC = 0.806-1.000). Moreover, JHF ameliorated the pathological changes in mice with PF and significantly reversed the changes in hub gene expression (KIF4A, IFNGR1, and HMGCR). In conclusion, a series of IPF hub genes was identified, and validated in an independent dataset, mice with PF, and MRC-5 cells. Moreover, the abnormal gene expression was normalized by JHF. These findings provide guidance for further exploration of the pathogenesis and treatment of IPF.
Collapse
Affiliation(s)
- Qingzhou Guan
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Zhenzhen Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Peng Zhao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Lidong Huang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Ruilong Lu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Chunlei Liu
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yakun Zhao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xuejie Shao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yange Tian
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China.
| | - Jiansheng Li
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province and Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou 450046, China; Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou 450000, China.
| |
Collapse
|
2
|
Zhang J, Jiang P, Tu Y, Li N, Huang Y, Jiang S, Kong W, Yuan R. Identification and validation of long non-coding RNA associated ceRNAs in intrauterine adhesion. Bioengineered 2021; 13:1039-1048. [PMID: 34968168 PMCID: PMC8805920 DOI: 10.1080/21655979.2021.2017578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrauterine adhesion (IUA) is an endometrial fibrotic disease with unclear pathogenesis. Increasing evidence suggested the important role of competitive endogenous RNA (ceRNA) in diseases. This study aimed to identify and verify the key long non-coding RNA (lncRNA) associated-ceRNAs in IUA. The lncRNA/mRNA expression file was obtained by transcriptome sequencing of IUA and normal samples. The microRNAs expression date was downloaded from the Gene Expression Omnibus database. Differential expressions of mRNAs, lncRNAs and miRNAs were analyzed using the DESeq2 (2010) R package. Protein interaction network was constructed to explore hub genes. TargetScan and miRanda databases were used to predicate the interaction. Enrichment analysis in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were performed to identify the biological functions of ceRNAs. Regression analysis of ceRNAs’ expression level was performed. There were 915 mRNAs and 418 lncRNAs differentially expressed. AURKA, CDC20, IL6, ASPM, CDCA8, BIRC5, UBE2C, H2AFX, RRM2 and CENPE were identified as hub genes. The ceRNAs network, including 28 lncRNAs, 28 miRNAs, and 299 mRNAs, was constructed. Regression analysis showed a good positive correlation between ceRNAs expression levels (r > 0.700, p < 0.001). The enriched functions include ion transmembrane transport, focal adhesion, cAMP signaling pathway and cGMP-PKG signaling pathway. The novel lncRNA-miRNA-mRNA network in IUA was excavated. Crucial lncRNAs such as ADIRF-AS1, LINC00632, DIO3OS, MBNL1-AS1, MIR1-1HG-AS1, AC100803.2 was involved in the development of IUA. cGMP-PKG signaling pathway and ion transport might be new directions for IUA pathogenesis research.
Collapse
Affiliation(s)
- Jingni Zhang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Jiang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Tu
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ning Li
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuzhen Huang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shan Jiang
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Kong
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Rui Yuan
- Department of Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|