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Sánchez Carretero L, Cardeñosa Pérez ÀC, Peces-Barba G, Pérez-Rial S. Differential lung gene expression identified Zscan2 and Bag6 as novel tissue repair players in an experimental COPD model. PLoS One 2024; 19:e0309166. [PMID: 39172905 PMCID: PMC11340952 DOI: 10.1371/journal.pone.0309166] [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: 02/28/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024] Open
Abstract
Chronic obstructive pulmonary disease is a common chronic lung disease with an ever-increasing incidence. Despite years of drug research and approvals, we are still not able to halt progress or restore normal lung function. Our previous studies have demonstrated that liver growth factor-LGF has an effect on the repair of the affected tissue in a mouse model of cigarette smoke exposure, but by what pathways it achieves this is unknown. The present study aimed to identify differentially expressed genes between emphysematous mice treated with LGF to identify potential therapeutic targets for the treatment of pulmonary emphysema. The emphysema mouse model was induced by prolonged exposure to cigarette smoke. To determine the gene expression profile of the lung in smokers treated or not with LGF, lung messenger RNA gene expression was assessed with the Agilent Array platform. We carried out differentially expressed gene analysis, functional enrichment and validated in treated mouse lung samples. The treated group significantly improved lung function (~35%) and emphysema level (~20%), consistent with our previous published studies. Microarray analysis demonstrated 290 differentially expressed genes in total (2.0-fold over or lower expressed). Injury repair-associated genes and pathways were further enhanced in the lung of LGF treated mice. The expression trends of two genes (Zscan2 and Bag6) were different in emphysematous lungs treated with LGF compared to untreated lungs. Therefore, Zscan2 and Bag6 genes could play a role in regulating inflammation and the immune response in the lung that undergoes partial lung regeneration. However, further studies are necessary to demonstrate this causal relationship.
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Affiliation(s)
- Laura Sánchez Carretero
- Respiratory Research Unit, Health Research Institute–Fundación Jimenez Diaz University Hospital, Madrid, Spain
| | - Àdele Chole Cardeñosa Pérez
- Respiratory Research Unit, Health Research Institute–Fundación Jimenez Diaz University Hospital, Madrid, Spain
| | - Germán Peces-Barba
- Respiratory Research Unit, Health Research Institute–Fundación Jimenez Diaz University Hospital, Madrid, Spain
| | - Sandra Pérez-Rial
- Molecular Genetics Department, Ramón y Cajal University Hospital–IRYCIS, Madrid, Spain
- Network Biomedical Research Center for Rare Diseases, Carlos III Health Institute (CIBERER, ISCIII), Madrid, Spain
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Jiang C, Peng M, Dai Z, Chen Q. Screening of Lipid Metabolism-Related Genes as Diagnostic Indicators in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:2739-2754. [PMID: 38046983 PMCID: PMC10693249 DOI: 10.2147/copd.s428984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/11/2023] [Indexed: 12/05/2023] Open
Abstract
Objective It has been observed that local and systemic disorders of lipid metabolism occur during the development of chronic obstructive pulmonary disease (COPD), but no specific mechanism has yet been identified. Methods The mRNA microarray dataset GSE76925 of COPD patients was downloaded from the Gene Expression Omnibus database and screened for differentially expressed genes (DEGs). Lipid metabolism-related genes (LMRGs) were extracted from the Kyoto Encyclopedia of Genes and Genomes database and Molecular Signature Database. The DEGs were intersected with LMRGs to obtain differentially expressed lipid metabolism-related genes (DeLMRGs). GO enrichment analysis and KEGG pathway analysis were performed on DeLMRGs, and protein-protein interaction networks were constructed and screened to identify hub genes. The GSE8581 validation set and further ELISA experiments were used to validate key DeLMRG expression. Results Differential analysis of dataset GSE76925 identified 587 DEGs, of which 62 genes were up-regulated and 525 were down-regulated. Taking the intersection of 587 DEGs with 1102 LMRGs, 20 DeLMRGs were obtained, including 1 up-regulated gene and 19 down-regulated genes. 10 hub genes were screened by cytohubba plugin, including 9 down-regulated genes PLA2G4A, HPGDS, LEP, PTGES3, LEPR, PLA2G2D, MED21, SPTLC1 and BCHE, as well as the only up-regulated gene PLA2G7. Validation of the identified 10 DeLMRGs using the validation set GSE8581 revealed that BCHE and PLA2G7 expression levels differed between the two groups. We further constructed the ceRNA network of BCHE and PLA2G7. Cell experiments also showed that PLA2G7 expression was up-regulated and BCHE expression was down-regulated in CSE-treated RAW264.7 and THP-1 cells. Conclusion Based on a comprehensive bioinformatic analysis of lipid metabolism genes, we identified BCHE and PLA2G7 as potentially significant biomarkers of COPD. These biomarkers may represent promising targets for COPD diagnosis and treatment.
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Affiliation(s)
- Chen Jiang
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Meijuan Peng
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ziyu Dai
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qiong Chen
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
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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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Chen X, Yuan Q, Guan H, Shi X, Sun J, Wu Z, Ren J, Xia S, Shang D. Identification and characterization of interferon-γ signaling-based personalized heterogeneity and therapeutic strategies in patients with pancreatic cancer. Front Oncol 2023; 13:1227606. [PMID: 37941546 PMCID: PMC10628740 DOI: 10.3389/fonc.2023.1227606] [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: 05/23/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
Background Interferon-γ (IFN-γ) is a key cytokine with diverse biological functions, including antiviral defense, antitumor activity, immune regulation, and modulation of cellular processes. Nonetheless, its role in pancreatic cancer (PC) therapy remains debated. Therefore, it is worthwhile to explore the role of Interferon-γ related genes (IFN-γGs) in the progression of PC development. Methodology Transcriptomic data from 930 PC were sourced from TCGA, GEO, ICGC, and ArrayExpress, and 93 IFN-γGs were obtained from the MSigDB. We researched the characteristics of IFN-γGs in pan-cancer. Subsequently, the cohort of 930 PC was stratified into two distinct subgroups using the NMF algorithm. We then examined disparities in the activation of cancer-associated pathways within these subpopulations through GSVA analysis. We scrutinized immune infiltration in both subsets and probed classical molecular target drug sensitivity variations. Finally, we devised and validated a novel IFN-γ related prediction model using LASSO and Cox regression analyses. Furthermore, we conducted RT-qPCR and immunohistochemistry assays to validate the expression of seven target genes included in the prediction model. Results We demonstrated the CNV, SNV, methylation, expression levels, and prognostic characteristics of IFN-γGs in pan-cancers. Notably, Cluster 2 demonstrated superior prognostic outcomes and heightened immune cell infiltration compared to Clusters 1. We also assessed the IC50 values of classical molecular targeted drugs to establish links between IFN-γGs expression levels and drug responsiveness. Additionally, by applying our prediction model, we segregated PC patients into high-risk and low-risk groups, identifying potential benefits of cisplatin, docetaxel, pazopanib, midostaurin, epothilone.B, thapsigargin, bryostatin.1, and AICAR for high-risk PC patients, and metformin, roscovitine, salubrinal, and cyclopamine for those in the low-risk group. The expression levels of these model genes were further verified through HPA website data and qRT-PCR assays in PC cell lines and tissues. Conclusion This study unveils IFN-γGs related molecular subsets in pancreatic cancer for the first time, shedding light on the pivotal role of IFN-γGs in the progression of PC. Furthermore, we establish an IFN-γGs related prognostic model for predicting the survival of PC, offering a theoretical foundation for exploring the precise mechanisms of IFN-γGs in PC.
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Affiliation(s)
- Xu Chen
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hewen Guan
- Department of Dermatology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xueying Shi
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jiaao Sun
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhiqiang Wu
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jie Ren
- Department of Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Shilin Xia
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Dong Shang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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