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Pamuk S, Ertugrul B, Kasarci G, Bireller S, Ergen A, Cakmakoglu B, Ulusan M. Focusing on tumor and it's microenvironmental immune members for head and neck cancer patients. Pathol Res Pract 2024; 263:155575. [PMID: 39236499 DOI: 10.1016/j.prp.2024.155575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/09/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024]
Abstract
OBJECTIVE Immune-related gene expression levels in the tumor microenvironment (TM) of head and neck squamous cell carcinoma (HNSCC) patients was compared. MATERIALS AND METHODS The CD163, CD274, CD86, FUT4, FOXP3, and ITGAX levels of HNSCC patients in their tumor tissues (n =76) and surrounding tissues adjacent to the tumor (n =76) were determined using quantitative real-time PCR (qRT-PCR). Changes in these genes were also evaluated by associating with demographical data of the patients. RESULTS CD163, CD274, FUT4, and FOXP3 gene expression levels were significantly higher in tumor tissue than in surrounding tissue. FUT4 fold change was statistically higher in patients with lymph node involvement. CD86 expression was statistically lower in smokers of 50 boxes per year or more. CD163, CD274, and FUT4 expressions were increased in response to the presence of extranodal extension (ENE). CONCLUSIONS These preliminary results demonstrate the alterations in expression levels of immunologic markers are associated with the clinical presentations of HNSCC. AVAILABILITY OF DATA AND MATERIALS The datasets used and/or analysed during the current study available from the corresponding author on reasonable request.
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Affiliation(s)
- Saim Pamuk
- Department of Otorhinolaryngology & Head and Neck Surgery, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Baris Ertugrul
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Goksu Kasarci
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey; Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Sinem Bireller
- Department of Biochemistry, Faculty of Pharmacy, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Arzu Ergen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Bedia Cakmakoglu
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
| | - Murat Ulusan
- Department of Otorhinolaryngology & Head and Neck Surgery, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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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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Ahmed FF, Das AD, Sumi MJ, Islam MZ, Rahman MS, Rashid MH, Alyami SA, Alotaibi N, Azad AKM, Moni MA. Identification of genetic biomarkers, drug targets and agents for respiratory diseases utilising integrated bioinformatics approaches. Sci Rep 2023; 13:19072. [PMID: 37925496 PMCID: PMC10625598 DOI: 10.1038/s41598-023-46455-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common differential genes and potential hub genes (HubGs), emphasizing their actions, signaling pathways, regulatory biomarkers for diagnosing RD and candidate drugs for treating RD. In this paper we used integrated bioinformatics approaches (such as, gene ontology (GO) and KEGG pathway enrichment analysis, molecular docking, molecular dynamic simulation and network-based molecular interaction analysis). We discovered 73 common DEGs (CDEGs) and ten HubGs (ATAD2B, PPP1CB, FOXO1, AKT3, BCR, PDE4D, ITGB1, PCBP2, CD44 and SMARCA2). Several significant functions and signaling pathways were strongly related to RD. We recognized six transcription factor (TF) proteins (FOXC1, GATA2, FOXL1, YY1, POU2F2 and HINFP) and five microRNAs (hsa-mir-218-5p, hsa-mir-335-5p, hsa-mir-16-5p, hsa-mir-106b-5p and hsa-mir-15b-5p) as the important transcription and post-transcription regulators of RD. Ten HubGs and six major TF proteins were considered drug-specific receptors. Their binding energy analysis study was carried out with the 63 drug agents detected from network analysis. Finally, the five complexes (the PDE4D-benzo[a]pyrene, SMARCA2-benzo[a]pyrene, HINFP-benzo[a]pyrene, CD44-ketotifen and ATAD2B-ponatinib) were selected for RD based on their strong binding affinity scores and stable performance as the most probable repurposable protein-drug complexes. We believe our findings will give readers, wet-lab scientists, and pharmaceuticals a thorough grasp of the biology behind RD.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| | - Arnob Dip Das
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mst Joynab Sumi
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Zohurul Islam
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- High Performance Computing (HPC) Laboratory, Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Harun Rashid
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Salem A Alyami
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Naif Alotaibi
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Data Science, School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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Zhang C, Lin Q, Li C, Chen Z, Deng M, Weng H, Zhu X. Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma. Sci Rep 2023; 13:13894. [PMID: 37626099 PMCID: PMC10457392 DOI: 10.1038/s41598-023-38568-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. This study aimed to determine the prognostic significance of endoplasmic reticulum (ER) stress-related genes in DLBCL. ER stress-related genes were obtained from the molecular signatures database. Gene expression data and clinical outcomes from the gene expression omnibus and TCGA datasets were collected, and differentially expressed genes (DEGs) were screened out. Gene ontology enrichment analysis, the kyoto encyclopaedia of genes and genomes pathway analysis, and geneset enrichment analysis were used to analyse the possible biological function of ER stress-related DEGs in DLBCL. Protein-protein interaction network construction using the STRING online and hub genes were identified by cytoHubba on Cytoscape software. The significant prognosis-related genes were screened, and the differential expression was validated. The immune microenvironment assessment of significant genes were evaluated. Next, the nomogram was built using univariate and multivariate Cox regression analysis. 26 ER stress-related DEGs were screened. Functional enrichment analysis showed them to be involved in the regulation of the endoplasmic reticulum mainly. NUPR1 and TRIB3 were identified as the most significant prognostic-related genes by comparison with the GSE10846, GSE11318, and TCGA datasets. NUPR1 was correlated with a good prognosis and immune infiltration in DLBCL; on the other hand, high expression of TRIB3 significantly correlated with a poor prognosis, which was an independent prognostic factor for DLBCL. In summary, we identified NUPR1 and TRIB3 as critical ER stress-related genes in DLBCL. NUPR1 might be involved in immune infiltration in DLBCL, and TRIB3 might serve as a potential therapeutic target and prognostic factor in DLBCL.
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Affiliation(s)
- Chaofeng Zhang
- Department of Hematology and Rheumatology, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Qi Lin
- Department of Pharmacy, The Affiliated Hospital of Putian University, Putian, Fujian Province, China
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Chaoqi Li
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Zhimin Chen
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Mengmeng Deng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Huixin Weng
- Pharmaceutical and Medical Technology College, Putian University, Putian, Fujian Province, China
| | - Xiongpeng Zhu
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian Province, China.
- Department of Haematology, Quanzhou First Hospital of Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China.
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Shirvaliloo M. LncRNA H19 promotes tumor angiogenesis in smokers by targeting anti-angiogenic miRNAs. Epigenomics 2023; 15:61-73. [PMID: 36802727 DOI: 10.2217/epi-2022-0145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
A key concept in drug discovery is the identification of candidate therapeutic targets such as long noncoding RNAs (lncRNAs) because of their extensive involvement in neoplasms, and impressionability by smoking. Induced by exposure to cigarette smoke, lncRNA H19 targets and inactivates miR-29, miR-30a, miR-107, miR-140, miR-148b, miR-199a and miR-200, which control the rate of angiogenesis by inhibiting BiP, DLL4, FGF7, HIF1A, HIF1B, HIF2A, PDGFB, PDGFRA, VEGFA, VEGFB, VEGFC, VEGFR1, VEGFR2 and VEGFR3. Nevertheless, these miRNAs are often dysregulated in bladder cancer, breast cancer, colorectal cancer, glioma, gastric adenocarcinoma, hepatocellular carcinoma, meningioma, non-small-cell lung carcinoma, oral squamous cell carcinoma, ovarian cancer, prostate adenocarcinoma and renal cell carcinoma. As such, the present perspective article seeks to establish an evidence-based hypothetical model of how a smoking-related lncRNA known as H19 might aggravate angiogenesis by interfering with miRNAs that would otherwise regulate angiogenesis in a nonsmoking individual.
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Affiliation(s)
- Milad Shirvaliloo
- Infectious & Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran.,Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
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Zhang Y, Xia R, Lv M, Li Z, Jin L, Chen X, Han Y, Shi C, Jiang Y, Jin S. Machine-Learning Algorithm-Based Prediction of Diagnostic Gene Biomarkers Related to Immune Infiltration in Patients With Chronic Obstructive Pulmonary Disease. Front Immunol 2022; 13:740513. [PMID: 35350787 PMCID: PMC8957805 DOI: 10.3389/fimmu.2022.740513] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/11/2022] [Indexed: 01/15/2023] Open
Abstract
Objective This study aims to identify clinically relevant diagnostic biomarkers in chronic obstructive pulmonary disease (COPD) while exploring how immune cell infiltration contributes towards COPD pathogenesis. Methods The GEO database provided two human COPD gene expression datasets (GSE38974 and GSE76925; n=134) along with the relevant controls (n=49) for differentially expressed gene (DEG) analyses. Candidate biomarkers were identified using the support vector machine recursive feature elimination (SVM-RFE) analysis and the LASSO regression model. The discriminatory ability was determined using the area under the receiver operating characteristic curve (AUC) values. These candidate biomarkers were characterized in the GSE106986 dataset (14 COPD patients and 5 controls) in terms of their respective diagnostic values and expression levels. The CIBERSORT program was used to estimate patterns of tissue infiltration of 22 types of immune cells. Furthermore, the in vivo and in vitro model of COPD was established using cigarette smoke extract (CSE) to validated the bioinformatics results. Results 80 genes were identified via DEG analysis that were primarily involved in cellular amino acid and metabolic processes, regulation of telomerase activity and phagocytosis, antigen processing and MHC class I-mediated peptide antigen presentation, and other biological processes. LASSO and SVM-RFE were used to further characterize the candidate diagnostic markers for COPD, SLC27A3, and STAU1. SLC27A3 and STAU1 were found to be diagnostic markers of COPD in the metadata cohort (AUC=0.734, AUC=0.745). Their relevance in COPD were validated in the GSE106986 dataset (AUC=0.900 AUC=0.971). Subsequent analysis of immune cell infiltration discovered an association between SLC27A3 and STAU1 with resting NK cells, plasma cells, eosinophils, activated mast cells, memory B cells, CD8+, CD4+, and helper follicular T-cells. The expressions of SLC27A3 and STAU1 were upregulated in COPD models both in vivo and in vitro. Immune infiltration activation was observed in COPD models, accompanied by the enhanced expression of SLC27A3 and STAU1. Whereas, the knockdown of SLC27A3 or STAU1 attenuated the effect of CSE on BEAS-2B cells. Conclusion STUA1 and SLC27A3 are valuable diagnostic biomarkers of COPD. COPD pathogenesis is heavily influenced by patterns of immune cell infiltration. This study provides a molecular biology insight into COPD occurrence and in exploring new therapeutic means useful in COPD.
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Affiliation(s)
- Yuepeng Zhang
- Department of Respiratory Medicine, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Rongyao Xia
- Department of Respiratory Medicine, The Second Hospital of Harbin Medical University, Harbin, China
| | - Meiyu Lv
- Department of Respiratory Medicine, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Zhiheng Li
- Department of Medical Oncology, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Lingling Jin
- Department of Respiratory Medicine, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Xueda Chen
- Department of Respiratory Medicine, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Yaqian Han
- School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Chunpeng Shi
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yanan Jiang
- Department of Pharmacology, State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shoude Jin
- Department of Respiratory Medicine, The Fourth Hospital of Harbin Medical University, Harbin, China
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Lin J, Xue Y, Su W, Zhang Z, Wei Q, Huang T. Identification of Dysregulated Mechanisms and Candidate Gene Markers in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2022; 17:475-487. [PMID: 35281477 PMCID: PMC8904782 DOI: 10.2147/copd.s349694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/27/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to identify candidate gene markers that may facilitate chronic obstructive pulmonary disease (COPD) diagnosis and treatment. Methods The GSE47460 and GSE151052 datasets were analyzed to identify differentially expressed mRNAs (DEmRs) between COPD patients and controls. DEmRs that were differentially expressed in the same direction in both datasets were analyzed for functional enrichment and for coexpression. Genes from the largest three modules were tested for their ability to diagnose COPD based on the area under the receiver operating characteristic curve (AUC). Genes with AUC > 0.7 in both datasets were used to perform regression based on the "least absolute shrinkage and selection operator" in order to identify feature genes. We also identified differentially expressed miRNAs (DEmiRs) between COPD patients and controls using the GSE38974 dataset, then constructed a regulatory network. We also examined associations between feature genes and immune cell infiltration in COPD, and we identified methylation markers of COPD using the GSE63704 dataset. Results A total of 1350 genes differentially regulated in the same direction in the GSE47460 and GSE151052 datasets were found. The genes were significantly enriched in immune-related biological functions. Of 186 modules identified using MEGENA, the largest were C1_ 6, C1_ 3, and C1_ 2. Of the 22 candidate genes screened based on AUC, 11 feature genes emerged from analysis of a subset of GSE47460 data, which we validated using another subset of GSE47460 data as well as the independent GSE151052 dataset. Feature genes correlated significantly with infiltration by immune cells. The feature genes GPC4 and RS1 were predicted to be regulated by miR-374a-3p. We identified 117 candidate methylation markers of COPD, including PRRG4. Conclusion The feature genes we identified may be potential diagnostic markers and therapeutic targets in COPD. These findings provide new leads for exploring disease mechanisms and targeted treatments.
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Affiliation(s)
- Jie Lin
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China
| | - Yanlong Xue
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China
| | - Wenyan Su
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China
| | - Zan Zhang
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China
| | - Qiu Wei
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China,Correspondence: Qiu Wei; Tianxia Huang, Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, 89 Qixing Road, Nanning, Guangxi, 530022, People’s Republic of China, Tel +86 7712636163, Fax +86 7712617892, Email ;
| | - Tianxia Huang
- Department of Respiratory and Critical Care, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People’s Republic of China,Department of Respiratory and Critical Care, The First People’s Hospital of Nanning, Nanning, Guangxi, 530022, People’s Republic of China
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Chen L, Zhu D, Huang J, Zhang H, Zhou G, Zhong X. Identification of Hub Genes Associated with COPD Through Integrated Bioinformatics Analysis. Int J Chron Obstruct Pulmon Dis 2022; 17:439-456. [PMID: 35273447 PMCID: PMC8901430 DOI: 10.2147/copd.s353765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/20/2022] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lin Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, LiuZhou, Guangxi, People’s Republic of China
| | - Donglan Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Jinfu Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Hui Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Guang Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Xiaoning Zhong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
- Correspondence: Xiaoning Zhong, Tel +86 13607881203, Fax +86 771-5356702, Email
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Zhang J, Liu J, Xu S, Yu X, Zhang Y, Li X, Zhang L, Yang J, Xing X. Bioinformatics analyses of the pathogenesis and new biomarkers of chronic obstructive pulmonary disease. Medicine (Baltimore) 2021; 100:e27737. [PMID: 34797299 PMCID: PMC8601278 DOI: 10.1097/md.0000000000027737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/21/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is one of the major cause of global death. The purpose of our analysis was to detect a more reliable biomarker and small-molecule drug candidates and to identify the precise mechanisms involved in COPD. METHODS Three data sets were downloaded from the Gene Expression Omnibus database and analysed by Gene Expression Omnibus 2R. Functional enrichment analyses were performed by Metascape. We use the STRING data to build a protein-protein interaction network. The targets of differentially expressed microRNA (DE miRNA) were predicted by the miRWalk database. Small-molecule drugs were predicted on connectivity map. RESULTS A total of 181 differentially expressed genes and 35 DE miRNAs were confirmed. The protein-protein interaction network including all integrated differentially expressed genes was constructed, and 4 modules were filtrated. The module genes were relative to immune, inflammatory and oxidative stress functions according to a pathway analysis. The top 20 key genes were screened. Among the DE miRNAs found to be regulating key genes, miR-194-3p, MiR-502-5p, MiR-5088-5p, MiR-3127-5p, and miR-23a-5p might be the most significant due to their high number of connecting nodes in COPD. In addition, cephaeline, emetine, gabapentin, and amrinone were found to be potential drugs to treat COPD patients. CONCLUSION Our study suggests that miR-194-3p, miR-502-5p, and miR-23a-5p might participate in the nosogenesis of COPD. In addition, 4 potential small-molecule drugs were considered potentially useful for treating COPD patients.
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Affiliation(s)
- Jihua Zhang
- Department of Respiratory Medicine, The People's Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Jie Liu
- The graduate School, Kunming Medical University, Kunming, Yunnan, China
| | - Shuanglan Xu
- The graduate School, Kunming Medical University, Kunming, Yunnan, China
| | - Xiaochao Yu
- The graduate School, Kunming Medical University, Kunming, Yunnan, China
| | - Yi Zhang
- Department of Respiratory Medicine, The People's Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Xiao Li
- Department of Respiratory Medicine, The People's Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Liqiong Zhang
- Department of Respiratory Medicine, The People's Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Jiao Yang
- First Department of Respiratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiqian Xing
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming, Yunnan, China
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An J, Yang T, Dong J, Liao Z, Wan C, Shen Y, Chen L. Identifying miRNA Modules and Related Pathways of Chronic Obstructive Pulmonary Disease Associated Emphysema by Weighted Gene Co-Expression Network Analysis. Int J Chron Obstruct Pulmon Dis 2021; 16:3119-3130. [PMID: 34815668 PMCID: PMC8605490 DOI: 10.2147/copd.s325300] [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: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a heterogeneous chronic inflammatory disease characterized by progressive airflow limitation that causes high morbidity and mortality. MicroRNA, a short-chain noncoding RNA, regulates gene expression at the transcriptional level. microRNA modules with a role in the pathogenesis of COPD may serve as COPD biomarkers. METHODS We downloaded the GSE33336 microarray data set from the Gene Expression Omnibus (GEO) database, the data are derived from 29 lung samples of patients with emphysema undergoing curative resection for lung cancer. We used weighted gene co-expression network analysis (WGCNA) to construct co-expression modules and detect trait-related microRNA modules. We used the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to predict the biological function of the interest modules, and we screened out candidate hub microRNAs based on their module membership (MM) value and top proteins on the results of the protein-protein interaction (PPI) network. RESULTS Three microRNA modules (royal blue, light yellow and grey60) were highly associated with COPD. Axon guidance, proteoglycans in cancer and mitogen-activated protein kinases (MAPK) signaling pathway were common pathways in these three modules. Keratin18 (KRT18) was the top protein in our study. miR-452, miR-149, miR-133a, miR-181a and miR-421 in hub microRNAs may play a role in COPD. CONCLUSION These findings provide evidence for the role of miRNAs in COPD and identify biomarker candidates.
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Affiliation(s)
- Jing An
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Ting Yang
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Jiajia Dong
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Zenglin Liao
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Chun Wan
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Yongchun Shen
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
| | - Lei Chen
- Department of Respiratory and Critical Care Medicine, Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People’s Republic of China
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Zhu D, Ma N, Chen L, Huang J, Zhong X. Verification of the role of spiperone in the treatment of COPD through bioinformatics analysis. Int Immunopharmacol 2021; 101:108308. [PMID: 34741870 DOI: 10.1016/j.intimp.2021.108308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Aim of this study is investigates the influence of spiperone on hydrolase activity pathway in chronic obstructive pulmonary disease (COPD). PATIENTS AND METHODS Differentially expressed genes (DEGs) were calculated by the limma package from microarray data GSE20257, and analysed via gene set enrichment analysis (GSEA) for identifying COPD related pathways. The regulation of hydrolase activity pathway related drugs was predicted by connectivity Map analysis (CMap). Western blotting and reverse transcription quantitative polymerase chain reaction (RT-qPCR) were used to investigate the effect of spiperone on regulation of hydrolase activity pathway in vitro experiment. RESULTS A total of 378 DEGs were identified by the limma package. GSEA suggested that the regulation of hydrolase activity pathway was involved in the development of COPD. CMap of hub genes of regulation of hydrolase activity pathwayshown the most significant compound was spiperone. Results of vitro experiment verify that cigarette smoke extract (CSE) can increase the expression of fibronectin 1 (FN1) and epidermal growth factor (EGF), coinsided with decrease the expression of chemokine (C-X3-C motif) ligand 1 (CX3CL1), chemokoine (C-C motif) ligand 20 (CCL20), complement component 3 (C3) and slithomolog 2 (SLIT2) in BESA-2B cells and U937 cells. Spiperone can reverse the effect of CSE in BESA-2B cells and U937 cells. CONCLUSION Regulation of hydrolase activity pathway was involved in the occurrence of COPD, spiperone was a potential drug for the treatment of COPD by affecting the regulation of hydrolase activity pathway. This study had provided new insights into the potential pathogenesis and treatment of COPD.
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Affiliation(s)
- Donglan Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Nan Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Lin Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Jinfu Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, Guangxi 530021, China
| | - Xiaoning Zhong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No 6 Shuangyong Road, Nanning, Guangxi 530021, China.
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12
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Hernandez-Pacheco N, Gorenjak M, Li J, Repnik K, Vijverberg SJ, Berce V, Jorgensen A, Karimi L, Schieck M, Samedy-Bates LA, Tavendale R, Villar J, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Kabesch M, Hawcutt DB, Turner S, Palmer CN, Tantisira KG, Burchard EG, Maitland-van der Zee AH, Flores C, Potočnik U, Pino-Yanes M. Identification of ROBO2 as a Potential Locus Associated with Inhaled Corticosteroid Response in Childhood Asthma. J Pers Med 2021; 11:jpm11080733. [PMID: 34442380 PMCID: PMC8399629 DOI: 10.3390/jpm11080733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Inhaled corticosteroids (ICS) are the most common asthma controller medication. An important contribution of genetic factors in ICS response has been evidenced. Here, we aimed to identify novel genetic markers involved in ICS response in asthma. A genome-wide association study (GWAS) of the change in lung function after 6 weeks of ICS treatment was performed in 166 asthma patients from the SLOVENIA study. Patients with an improvement in lung function ≥8% were considered as ICS responders. Suggestively associated variants (p-value ≤ 5 × 10−6) were evaluated in an independent study (n = 175). Validation of the association with asthma exacerbations despite ICS use was attempted in European (n = 2681) and admixed (n = 1347) populations. Variants previously associated with ICS response were also assessed for replication. As a result, the SNP rs1166980 from the ROBO2 gene was suggestively associated with the change in lung function (OR for G allele: 7.01, 95% CI: 3.29–14.93, p = 4.61 × 10−7), although this was not validated in CAMP. ROBO2 showed gene-level evidence of replication with asthma exacerbations despite ICS use in Europeans (minimum p-value = 1.44 × 10−5), but not in admixed individuals. The association of PDE10A-T with ICS response described by a previous study was validated. This study suggests that ROBO2 could be a potential novel locus for ICS response in Europeans.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Department of Pediatrics, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Andrea Jorgensen
- Department of Biostatistics, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Lesly-Anne Samedy-Bates
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, Calle Barranco de la Ballena s/n, 35019 Las Palmas de Gran Canaria, Spain
- Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael’s Hospital, 30 Bond St, Toronto, ON M5B 1W8, Canada
| | - Somnath Mukhopadhyay
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children’s Hospital, 94 N-S Rd, Falmer, Brighton BN2 5BE, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, 200 London Rd, Liverpool L3 9TA, UK;
| | - Katia M. C. Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
| | - Daniel B. Hawcutt
- Department of Women’s and Children’s Health, University of Liverpool, Liverpool L69 3BX, UK;
- Alder Hey Children’s Hospital, E Prescot Rd, Liverpool L14 5AB, UK
| | - Steve Turner
- Child Health, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK;
| | - Colin N. Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Kelan G. Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Polígono Industrial de Granadilla, 38600 Granadilla, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
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Deng M, Yin Y, Zhang Q, Zhou X, Hou G. Identification of Inflammation-Related Biomarker Lp-PLA2 for Patients With COPD by Comprehensive Analysis. Front Immunol 2021; 12:670971. [PMID: 34093570 PMCID: PMC8176901 DOI: 10.3389/fimmu.2021.670971] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is a complex and persistent lung disease and lack of biomarkers. The aim of this study is to screen and verify effective biomarkers for medical practice. Methods Differential expressed genes analysis and weighted co-expression network analysis were used to explore potential biomarker. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA) analysis were used to explore potential mechanism. CIBERSORTx website was used to evaluate tissue-infiltrating immune cells. Enzyme-linked immunosorbent assay (ELISA) was used to assess the concentrations of the Lp-PLA2 in serum. Results Ten genes were selected via combined DEGs and WGCNA. Furthermore, PLA2G7 was choose based on validation from independent datasets. Immune infiltrate and enrichment analysis suggest PLA2G7 may regulate immune pathway via macrophages. Next, Lp-PLA2(coded by PLA2G7 gene) level was upregulated in COPD patients, increased along with The Global Average of COPD (GOLD) stage. In additional, Lp-PLA2 level was significant correlate with FEV1/FVC, BMI, FFMI, CAT score, mMRC score and 6MWD of COPD patients. Finally, the predictive efficiency of Lp-PLA2 level (AUC:0.796) and derived nomogram model (AUC:0.884) in exercise tolerance was notably superior to that of the sit-to-stand test and traditional clinical features. Conclusion Lp-PLA2 is a promising biomarker for COPD patients and is suitable for assessing exercise tolerance in clinical practice.
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Affiliation(s)
- Mingming Deng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Yan Yin
- Department of Pulmonary and Critical Care Medicine, First Hospital of China Medical University, Shenyang, China
| | - Qin Zhang
- Department of Pulmonary and Critical Care Medicine, First Hospital of China Medical University, Shenyang, China
| | - Xiaoming Zhou
- Department of Pulmonary and Critical Care Medicine, Fourth Hospital of China Medical University, Shenyang, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
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Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples. Sci Rep 2021; 11:10258. [PMID: 33986404 PMCID: PMC8119951 DOI: 10.1038/s41598-021-89762-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/23/2021] [Indexed: 11/08/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) kills over three million people worldwide every year. Despite its high global impact, the knowledge about the underlying molecular mechanisms is still limited. In this study, we aimed to extend the available knowledge by identifying a small set of COPD-associated genes. We analysed different publicly available gene expression datasets containing whole lung tissue (WLT) and airway epithelium (AE) samples from over 400 human subjects for differentially expressed genes (DEGs). We reduced the resulting sets of 436 and 663 DEGs using a novel computational approach that utilises a random depth-first search to identify genes which improve the distinction between COPD patients and controls along the first principle component of the data. Our method identified small sets of 10 and 15 genes in the WLT and AE, respectively. These sets of genes significantly (p < 10–20) distinguish COPD patients from controls with high fidelity. The final sets revealed novel genes like cysteine rich protein 1 (CRIP1) or secretoglobin family 3A member 2 (SCGB3A2) that may underlie fundamental molecular mechanisms of COPD in these tissues.
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Sunny SK, Zhang H, Mzayek F, Relton CL, Ring S, Henderson AJ, Ewart S, Holloway JW, Arshad SH. Pre-adolescence DNA methylation is associated with lung function trajectories from pre-adolescence to adulthood. Clin Epigenetics 2021; 13:5. [PMID: 33407823 PMCID: PMC7789734 DOI: 10.1186/s13148-020-00992-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The pattern of lung function development from pre-adolescence to adulthood plays a significant role in the pathogenesis of respiratory diseases. Inconsistent findings in genetic studies on lung function trajectories, the importance of DNA methylation (DNA-M), and the critical role of adolescence in lung function development motivated the present study of pre-adolescent DNA-M with lung function trajectories. This study investigated epigenome-wide associations of DNA-M at cytosine-phosphate-guanine dinucleotide sites (CpGs) at childhood with lung function trajectories from childhood to young adulthood. METHODS DNA-M was measured in peripheral blood at age 10 years in the Isle of Wight (IOW) birth cohort. Spirometry was conducted at ages 10, 18, and 26 years. A training/testing-based method was used to screen CpGs. Multivariable logistic regressions were applied to assess the association of DNA-M with lung function trajectories from pre-adolescence to adulthood. To detect differentially methylated regions (DMRs) among CpGs, DMR enrichment analysis was conducted. Findings were further tested in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Pathway analyses were performed on the mapped genes of the identified CpGs and DMRs. Biological relevance of the identified CpGs was assessed with gene expression. All analyses were stratified by sex. RESULTS High and low trajectories of FVC, FEV1, and FEV1/FVC in each sex were identified. At PBonferroni < 0.05, DNA-M at 96 distinct CpGs (41 in males) showed associations with FVC, FEV1, and FEV1/FVC trajectories in IOW cohort. These 95 CpGs (cg24000797 was disqualified) were further tested in ALSPAC; 44 CpGs (19 in males) of these 95 showed the same directions of association as in the IOW cohort; and three CpGs (two in males) were replicated. DNA-M at two and four CpGs showed significant associations with the corresponding gene expression in males and females, respectively. At PFDR < 0.05, 23 and 10 DMRs were identified in males and females, respectively. Pathways were identified; some of those were linked to lung function and chronic obstructive lung diseases. CONCLUSION The identified CpGs at pre-adolescence have the potential to serve as candidate markers for lung function trajectory prediction and chronic lung diseases.
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Affiliation(s)
- Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Fawaz Mzayek
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN UK
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN UK
- Population Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- Population Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Susan Ewart
- Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD UK
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Parkhurst Road, Newport, Isle of Wight, PO30 5TG UK
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Zhang Q, Song W, Ayidaerhan N, He Z. PTPLAD2 and USP49 Involved in the Pathogenesis of Smoke-Induced COPD by Integrative Bioinformatics Analysis. Int J Chron Obstruct Pulmon Dis 2020; 15:2515-2526. [PMID: 33116468 PMCID: PMC7571584 DOI: 10.2147/copd.s250576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is a typical chronic disease, but its molecular pathogenesis remains unclear. This study aimed to investigate the expression of biomarkers during COPD development. Methods Markers significantly associated with COPD were screened using bioinformatics tools. qRT-PCR and Western blot were used to explore the expression of PTPLAD2 and USP49 in BEAS-2B cells. CCK-8 assay was used to determine the influence of PTPLAD2 and USP49 in BEAS-2B on cell proliferation. Results In this study, 86 DEGs were identified in GSE76925. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that the phosphoinositide 3-kinase-Akt signaling pathway, ECM-receptor interaction, mRNA process, and viral transcription were all involved in the development of COPD. In addition, 14 hub genes were identified by WGCNA. PTPLAD2 and USP49 shared DEGs and hub genes and their expression levels were significantly reduced after CSE-treatment in BEAS-2B cells. Conclusion Our results suggest that PTPLAD2 and USP49 may be useful biomarkers of COPD.
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Affiliation(s)
- Qiang Zhang
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province110042, People’s Republic of China
| | - Wei Song
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province110042, People’s Republic of China
| | - Nahemuguli Ayidaerhan
- Department of Pulmonary and Critical Care Medicine, Tarbagatay Prefecture People’s Hospital, Tacheng, Xinjiang, People’s Republic of China
| | - Zheng He
- Department of Obstetrics and Gynecology Medicine, Shengjing Hospital of China Medical University, Shenyang, People’s Republic of China
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Wang J, Chen T, Yu X, OUYang N, Tan L, Jia B, Tong J, Li J. Identification and validation of smoking-related genes in lung adenocarcinoma using an in vitro carcinogenesis model and bioinformatics analysis. J Transl Med 2020; 18:313. [PMID: 32795291 PMCID: PMC7427766 DOI: 10.1186/s12967-020-02474-x] [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: 11/11/2019] [Accepted: 07/30/2020] [Indexed: 12/24/2022] Open
Abstract
Background Lung cancer is one of the most common carcinomas in the world, and lung adenocarcinoma (LUAD) is the most lethal and most common subtype of lung cancer. Cigarette smoking is the most leading risk factor of lung cancer, but it is still unclear how normal lung cells become cancerous in cigarette smokers. This study aims to identify potential smoking-related biomarkers associated with the progression and prognosis of LUAD, as well as their regulation mechanism using an in vitro carcinogenesis model and bioinformatics analysis. Results Based on the integration analysis of four Gene Expression Omnibus (GEO) datasets and our mRNA sequencing analysis, 2 up-regulated and 11 down-regulated genes were identified in both S30 cells and LUAD. By analyzing the LUAD dataset in The Cancer Gene Analysis (TCGA) database, 3 of the 13 genes, viz., glycophorin C (GYPC), NME/NM23 nucleoside diphosphate kinase 1 (NME1) and slit guidance ligand 2 (SLIT2), were found to be significantly correlated with LUAD patients’ smoking history. The expression levels of GYPC, NME1 and SLIT2 in S30 cells and lung cancer cell lines were validated by quantitative PCR, immunofluorescence, and western blot assays. Besides, these three genes are associated with tumor invasion depth, and elevated expression of NME1 was correlated with lymph node metastasis. The enrichment analysis suggested that these genes were highly correlated to tumorigenesis and metastasis-related biological processes and pathways. Moreover, the increased expression levels of GYPC and SLIT2, as well as decreased expression of NME1 were associated with a favorable prognosis in LUAD patients. Furthermore, based on the multi-omics data in the TCGA database, these genes were found to be regulated by DNA methylation. Conclusion In conclusion, our observations indicated that the differential expression of GYPC, NME1 and SLIT2 may be regulated by DNA methylation, and they are associated with cigarette smoke-induced LUAD, as well as serve as prognostic factors in LUAD patients.
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Affiliation(s)
- Jin Wang
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Tao Chen
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Xiaofan Yu
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Nan OUYang
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Lirong Tan
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Beibei Jia
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Jian Tong
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China
| | - Jianxiang Li
- Department of Toxicology, School of Public Health, Medical College of Soochow University, Renai Road, Suzhou, 215123, China. .,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Renai Road, Suzhou, 215123, China.
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