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Expression analysis of stable chronic obstructive pulmonary disease and acute exacerbation of chronic obstructive pulmonary disease

ABSTRACT: Investigation of whole genome gene expression level changes of the dynamic gene profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD) on day1, 3 and 10, compared to the normal people and stable COPD patients. A five chip study using total RNA recovered from Peripheral Blood Mononuclear Cell of Peripheral Blood.Evaluating the dynamic gene profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD) on day1, 3 and 10 after the hospital admission, to compared with healthy controls or patients with stable COPD. Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

ORGANISM(S): Homo sapiens

SUBMITTER: Wang Xiangdong

PROVIDER: E-GEOD-60399 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of stable chronic obstructive pulmonary disease and acute exacerbation of chronic obstructive pulmonary disease

Project description:Investigation of whole genome gene expression level changes of the dynamic gene profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD) on day1, 3 and 10, compared to the normal people and stable COPD patients.

2014-08-14 | GSE60399 | GEO

Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease

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2024-10-01 | GSE249584 | GEO

Epigenome‑wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes

Project description:Genome wide DNA methylation profiling of Chronic Obstructive Pulmonary Disease (COPD) patients and healthy subjects. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across in peripheral blood mononuclear cell samples. Samples included 6 normal subjects and 12 COPD patients among which 3 of them have 2nd samples from follow-up examination.

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Different Transcriptome Features of Peripheral Blood Mononuclear Cells in Non-Emphysematous Chronic Obstructive Pulmonary Disease [COPD_PBMC]

Project description:Non-emphysematous COPD, which is defined based on chest computed tomography (CT) findings, may present different transcriptome features of peripheral blood mononuclear cells (PBMCs) derived from bone marrow (BM). In obstructive disorder-fixed COPD, including the airway-dominant phenotype, the upregulated differentially expressed genes (DEGs) were mainly related to Th2 inflammation, suppression of pulmonary vascular remodeling, and the function of BM-derived progenitor cells. Airway-dominant phenotypes are associated with less obstructive impairment. The upregulated DEGs in emphysematous COPD could be associated with airway inflammation and remodeling, suggesting an asthmatic component. Upregulated XCL1, PRKCZ, TMEM102, CD200R1, and AQP1 levels are associated with the activation of T lymphocytes and eosinophils. The upregulation of keratan sulfate biosynthesis and metabolic processes is associated with protection against destruction of the distal airways. The upregulation of ITGA3 could augment interactions with extracellular matrix proteins. COL6A1 may augment the profibrotic mast cell phenotype during the deposition of alveolar collagen VI. The upregulated HSPG2, PDGFRB and PAK4 may contribute to airway wall thickening. The upregulated SERPINF1 could explain the better preserved vascular bed, and the upregulation of SERPINF1 and ISM1 seem to protect against emphysema formation. These patterns in PBMCs may be related to the pathogenesis of nonemphysematous COPD.

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Project description:Background. Circular RNAs (circRNAs) play an important role in the occurrence and development of diseases. However, the role of circRNAs in male smokers with chronic obstructive pulmonary disease (COPD) remains unclear. Methods. Stable COPD patients and healthy controls were recruited. Peripheral blood mononuclear cells (PBMCs) were extracted. After high-throughput RNA sequencing (RNA-Seq) of PBMCs, a bioinformatics method was used to analyse differentially expressed (DE) circRNAs (DEcircRNAs) and mRNAs (DEmRNAs). Results. Total of 114 DEcircRNAs and 58 DEmRNAs were identified. Functional enrichment analysis showed that processes related to COPD include the regulation of interleukin (IL)-18, IL-5 and the NLRP3 inflammasome; differentiation of T helper type 1 (Th1), Th2, and Th17 cells, and the AMPK, Wnt, JAK-STAT, and PI3K-Akt signalling pathways. In the protein–protein interaction (PPI) network, the core genes were MYO16, MYL4, SCN4A, NRCAM, HMCN1, MYOM2, and IQSEC3. Small-molecule prediction results revealed potential drugs for the COPD treatment. Additionally, the circRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) regulatory network was constructed. Conclusion. This study identified a set of dysregulated circRNAs and mRNAs and revealed potentially important genes, pathways, new small-molecule drugs and ceRNA regulatory networks in male smokers with COPD. These circRNAs might be prospective biomarkers or potential molecular targets of the ceRNA mechanism for COPD.

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Lung proteomic biomarkers associated with chronic obstructive pulmonary disease

Project description:Identifying protein biomarkers for chronic obstructive pulmonary disease (COPD) has been challenging. Most previous studies have utilized individual proteins or pre-selected protein panels measured in blood samples. To identify COPD protein biomarkers by applying comprehensive mass spectrometry proteomics in lung tissue samples. We utilized mass spectrometry proteomic approaches to identify protein biomarkers from 152 lung tissue samples representing COPD cases and controls.

2022-01-07 | PXD024124 | Pride

Chronic obstructive pulmonary disease

Project description:Diaphragm muscles in Chronic Obstructive Pulmonary Disease (COPD) patients undergo an adaptive fast to slow transformation that includes cellular adaptations. This project studies the signaling mechanisms responsible for this transformation. Keywords: other

2003-07-16 | GSE475 | GEO

Pulmonary microRNA changes alter angiogenesis in chronic obstructive pulmonary disease and lung cancer

Project description:This experiment was carried out to see if there were any miRNA expression differences in pulmonary endothelial cells between patients with and without COPD. COPD is an inflammatory condition and although much work has previously been performed to investigate the inflammatory cells in COPD there has not been as much research looking at the endothelium through which inflammatory cells must pass through to reach the lung tissue. In this experiment pulmonary endothelial cells were extracted from whole lung tissue removed at the time of cardiothoracic surgery. This was performed for patients with and without COPD. RNA was extracted using the Qiagen microRNeasy kits prior to transferring to the University of Birmingham Biosciences department who performed RNA labelling and ran the microarrays. Once the microarrays were performed quality was checked using ArrayQualityMetrics and the COPD group was compared to the non-COPD group using SAM. The experiment was then repeated using another patient group. MiRNAs of interest were validated with qPCR initially before moving on to functional work.

2021-08-01 | E-MTAB-10311 | biostudies-arrayexpress

Comprehensive identification of RNA transcripts and construction of RNA networks in chronic obstructive pulmonary disease

Project description:Here, we report a comprehensive analysis of dysregulated mRNAs, lncRNAs, miRNAs and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. We mapped about 50~80 million sequence reads per sample to the human genome. GSEA analysis showed that these dysregulated RNAs correlate with several critical biological processes such as RNA modification, and RNA metabolism. RT-qPCR (SYBR Green assays) with more clinical COPD samples were used for the validation of some dysregulated RNAs. We have also constructed the co-expression network between lncRNA and mRNA, and established the circRNA-miRNA-mRNA in CAC based on this data. This study provides valuable insights to understand the RNA involvement and regulation in COPD, assisting future COPD investigations.

2022-06-15 | GSE198740 | GEO

Characterization of IL-6R-expressing monocytes in the lung of patients with chronic obstructive pulmonary disease [THP1]

Project description:Background: Monocytes play a crucial role in innate immune responses for host defense, yet their involvement in chronic obstructive pulmonary disease (COPD) remains poorly understood. We previously identified a subset of monocytes in COPD lung tissues characterized by high interleukin-6 receptor (IL-6R) expression. This study aimed to characterize the phenotypes of IL-6Rhi monocytes in the lung of COPD patients. Methods: Using flow cytometry, we assessed the abundance of pulmonary CD14+IL-6Rhi cells in never smokers (CNS), control ex-smokers (CES) and COPD patients. IL-6 expression in CD14+ monocytes from peripheral blood of patients with COPD was also examined. CD45+CD206–CD14+IL-6Rhi and CD45+CD206–CD14+IL-6R– cells were isolated from COPD lung tissues for transcriptome analysis. A monocyte line THP1 cell with constitutive IL-6R expression was stimulated with recombinant IL-6, followed by RNA sequencing to evaluate IL-6 responsiveness of IL-6R+ monocytes. Results: The number of pulmonary CD14+IL-6Rhi monocytes was elevated in COPD patients compared to CNS, while CD14+ monocytes in the peripheral blood of COPD patients did not express IL-6R. Upregulated mRNA expression in CD14+IL-6Rhi monocytes was associated with chemotaxis, monocyte differentiation, fatty acid metabolism and integrin-mediated signaling pathway. Stimulation of THP1 cells with recombinant IL-6 induced gene expression changes linked to chemotaxis and organism development. Conclusion: In patients with COPD, CD14+IL-6Rhi monocytes increase in lung tissues compared to CNS and exhibit a different transcriptome profile from CD14+IL-6R– monocytes.

2024-08-21 | GSE265855 | GEO

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