MRNA Sequencing to identify transcriptional changes in early and late stages of lung in human Idiopathic Pulmonary Fibrosis
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE124685 | GEO | 2019/10/11
REPOSITORIES: GEO
Similar Datasets
Project description:Purpose: The goal of this study is to compare transcriptome profiling (RNA-seq) of lung tissue biopsies derived from patients with idiopathic pulmonary fibrosis (IPF or IPF-UIP), or rheumatoid arthritis-associated interstitial diseases (RA-ILD or RA-UIP), or non-usual interstitial pneumonia (non-UIP) controls. Methods: Total RNA was extracted using the RNeasy kit (Qiagen) from fresh frozen lung tissue obtained from the Lung Tissue Repository Consortium (LTRC). RNA samples were then sent to the Genome Analysis Core at Mayo Clinic for sequencing using conventional Illumina mRNA-Seq protocols. A total of 23,295 genes were probed using this platform. Results: RNA-seq data revealed considerable transcriptomic differences between the groups. A heat map generated with the most differentially expressed genes (P<0.05) revealed two distinct gene expression profiles among the three groups. The heat map for the 3 RA-UIP and 20 IPF patients showed a similar gene expression pattern, which contrasted significantly from the non-UIP control group. Conclusions: The RNA-Seq data analysis shows similarities and differences between gene expression profiles of RA-UIP and IPF, suggesting both shared and differential disease-causing mechanistic pathways. Transcriptomic data distinguishes the RA-UIP group from IPF via JAK2-related JAK/STAT signaling pathways.
2022-05-31 | GSE199152 | GEO
Project description:The mechanisms and molecular pathways underlying interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches were used to identify perturbed networks in these disease states to gain a better understanding of the underlying mechanisms of disease. Through profiling genes and miRNAs, we found subsets of genes and miRNAs that distinguish different disease stages, ILDs from controls, and idiopathic pulmonary fibrosis (IPF) from non-specific interstitial pneumonitis (NSIP). Traditional pathway analysis revealed several disease-associated modules involving genes from the TGF-beta, Wnt, focal adhesion and smooth muscle actin pathways that may be involved in advancing fibrosis. A comprehensively integrative approach was used to construct a global gene regulatory network based on the perturbation of key regulatory elements, transcriptional factors and miRNAs. The data also demonstrated that several subnetworks were significantly associated with key molecules involved in the diseases. We present a broad overview of the disease at a molecular level and discuss several possibly key regulatory molecular circuits that could play central roles in facilitating the progression of ILDs. Lung tissue samples from 23 patients with IPF or related disorders were obtained from the Lung Tissue Research Consortium (www.ltrcpublic.org). 11 samples came from patients who had been diagnosed with usual interstitial pneumonia/ idiopathic pulmonary fibrosis (UIP/IPF), 5 samples came from patients with non-specific interstitial pneumonia (NSIP), the remaining from patients with uncharacterized fibrosis and from patients with other ILD variants. B. Biopsies from uninvolved lung tissue from lung cancer patients (5 samples) and from one lung transplant patient were used as controls for comparison with the ILD samples.
2011-03-24 | E-GEOD-21369 | biostudies-arrayexpress
Project description:The mechanisms and molecular pathways underlying interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches were used to identify perturbed networks in these disease states to gain a better understanding of the underlying mechanisms of disease. Through profiling genes and miRNAs, we found subsets of genes and miRNAs that distinguish different disease stages, ILDs from controls, and idiopathic pulmonary fibrosis (IPF) from non-specific interstitial pneumonitis (NSIP). Traditional pathway analysis revealed several disease-associated modules involving genes from the TGF-beta, Wnt, focal adhesion and smooth muscle actin pathways that may be involved in advancing fibrosis. A comprehensively integrative approach was used to construct a global gene regulatory network based on the perturbation of key regulatory elements, transcriptional factors and miRNAs. The data also demonstrated that several subnetworks were significantly associated with key molecules involved in the diseases. We present a broad overview of the disease at a molecular level and discuss several possibly key regulatory molecular circuits that could play central roles in facilitating the progression of ILDs. Lung tissue samples from thirty patients with IPF or related disorders were obtained from the Lung Tissue Research Consortium (www.ltrcpublic.org). Ten samples came from patients who had been diagnosed with usual interstitial pneumonia/ idiopathic pulmonary fibrosis (UIP/IPF), nine samples came from patients with non-specific interstitial pneumonia (NSIP), four from patients with uncharacterized fibrosis, and the remaining samples came from patients with other ILD variants. Biopsies from uninvolved lung tissue from lung cancer patients (5 samples) and from one lung transplant patient were used as controls for comparison with the ILD samples.
2011-04-19 | E-GEOD-21394 | biostudies-arrayexpress
Project description:Rationale: Idiopathic interstitial pneumonia (IIP) and its’ familial variants are progressive and largely untreatable disorders with poorly understood molecular mechanisms. Both the genetics and the histologic type of IIP play a role in understanding the etiology and pathogenesis of interstitial lung disease, but transcriptional signatures of these subtypes are unknown. Objectives: To evaluate gene expression in the lung tissue from patients with usual interstitial pneumonia (UIP) and non-specific interstitial pneumonia (NSIP) that were either familial or non-familial in origin and compare them to gene expression from normal lung parenchyma. Methods: We profiled RNA from lungs of 16 patients with sporadic IIP, 10 with familial IIP, and 9 normal controls on a whole human genome oligonucleotide microarray. Results: Significant transcriptional differences exist in familial and sporadic IIPs. The genes distinguishing the genetic subtypes belong to the same functional categories as transcripts that distinguish IIP from normal samples. Relevant categories include chemokines and growth factors and their receptors, complement components, genes associated with cell proliferation and death, and genes in the Wnt pathway. Keywords: disease state analysis
2006-10-01 | GSE5774 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease characterized by unknown causes and few treatment options We used microarray to determine the expression of miRNA and 17 miRNAs were differentially expressed in IPF lungs, including 10 upregulated and 7 downregulated miRNAs. Lung tissue was obtained from 4 IPF patients with histological evidence of usual interstitial pneumonia at the time of surgical lung biopsy or lung transplantation. The diagnosis of IPF was derived according to the standards accepted by the American Thoracic Society/European Respiratory Society. Histological normal lung tissues used as controls was obtained from 3 patients with primary spontaneous pneumothorax at the time of thoracoscopy with stapling of any air leak.The miRNA expression profile was determined by Affymetrix microarray, and transcriptome with Affymetrix array
2015-12-04 | E-GEOD-75647 | biostudies-arrayexpress
Project description:Idiopathic pulmonary fibrosis (IPF) is a specific form of chronic, progressive fibrosing interstitial disease of unknown cause. It remains impractical to conduct early diagnosis and predict IPF progression just based on gene expression information. Moreover, the relationship between gene expression and quantitative phenotypic value in IPF keeps controversial. To identify biomarkers to predict survival in IPF, we profiled protein-coding gene expression in peripheral blood mononuclear cells (PBMCs). We linked the gene expression level with the quantitative phenotypic variation in IPF, including diffusing capacity of the lung for carbon monoxide (DLCO) and forced vital capacity (FVC) percent predicted. In silico analyses on the expression profiles and quantitative phenotypic data allowed for the generation of a set of IPF molecular signature that predicted survival of IPF effectively. Total RNA was isolated from PBMCs using standard molecular biology protocols without DNA contamination or RNA degradation. Sample processing (e.g., cDNA generation, fragmentation, end labeling, hybridization to Affymetrix GeneChip Human Exon 1.0 ST arrays) was performed per manufacturer’s instructions. A total of 45 healthy controls and 70 IPF patients were included in the microarray analysis.
2014-06-30 | E-GEOD-38958 | biostudies-arrayexpress
Project description:Pulmonary fibrosis is a chronic, progressive, and lethal interstitial lung disease. It is characterized by extracellular matrix deposition, fibroblast proliferation, and accumulation. Fibroblasts from normal or UIP histology were cultured and analyzed. Keywords: Fibroblasts from normal histology lung tissue or UIP histology lung tissue Five samples of primary human lung fibroblasts were obtained from explanted lungs of patients with Usual Interstitial Pneumonia (UIP) at the University of Pittsburgh Medical Center (Pittsburgh, PA, USA) and three samples of primary normal human lung fibroblasts were acquired from normal histololgy lung tissues of organ donors. The experimental protocol was approved by the University of Pittsburgh Institutional Reviews Board (IRB). Total RNA was extracted and used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays. Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647. The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.
2010-06-21 | E-GEOD-10921 | biostudies-arrayexpress
Project description:Chronic hypersensitivity pneumonitis (CHP) is caused by an immune response to antigen inhalation and is characterized by variable histopathological and clinical features. A subset of CHP subjects have usual interstitial pneumonia and appear to be clinically similar to subjects with idiopathic pulmonary fibrosis (IPF). However, the molecular relationship between CHP and IPF is not well understood. We report an RNA-seq based transcriptomic analysis for whole lung tissues from CHP, IPF and control subjects.
2020-07-01 | GSE150910 | GEO
Project description:Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses. Methods: We collected transcriptional and miRNA profiles on lung tissue from 167 subjects with IIP and 50 non-diseased controls. Differential expression of individual transcripts and miRNAs was identified using an ANCOVA model incorporating the clinical diagnosis of each subject as well as age, gender, and smoking status. Validation was performed in an independent cohort of 131 IIPs and 39 non-diseased controls. Results: Our results demonstrate a substantial degree of overlap in mRNA and miRNA signatures of clinical subtypes of IIP. However, we identify two subtypes of IPF/UIP based on a strong molecular signature associated with expression of cilium genes. We demonstrate that elevated expression of cilium genes is associated with more extensive microscopic honeycombing, more fibroblastic foci, higher expression of the airway mucin gene MUC5B, and better survival in an independent cohort of IPF/UIP patients. Moreover, we identify miRNAs involved in the regulation of cilium-associated gene expression that contribute to novel molecular subphenotypes of IPF. Conclusions: While subtypes of IIP are related biologically with similar transcriptional profiles, expression of cilium genes appear to identify two unique clinical presentations of IPF/UIP. 167 subjects with IIP and 50 non-diseased controls with no replicates
2013-06-21 | E-GEOD-32538 | biostudies-arrayexpress
Project description:Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses. Methods: We collected transcriptional and miRNA profiles on lung tissue from 167 subjects with IIP and 50 non-diseased controls. Differential expression of individual transcripts and miRNAs was identified using an ANCOVA model incorporating the clinical diagnosis of each subject as well as age, gender, and smoking status. Validation was performed in an independent cohort of 131 IIPs and 39 non-diseased controls. Results: Our results demonstrate a substantial degree of overlap in mRNA and miRNA signatures of clinical subtypes of IIP. However, we identify two subtypes of IPF/UIP based on a strong molecular signature associated with expression of cilium genes. We demonstrate that elevated expression of cilium genes is associated with more extensive microscopic honeycombing, more fibroblastic foci, higher expression of the airway mucin gene MUC5B, and better survival in an independent cohort of IPF/UIP patients. Moreover, we identify miRNAs involved in the regulation of cilium-associated gene expression that contribute to novel molecular subphenotypes of IPF. Conclusions: While subtypes of IIP are related biologically with similar transcriptional profiles, expression of cilium genes appear to identify two unique clinical presentations of IPF/UIP. 167 subjects with IIP and 50 non-diseased controls with no replicates
2013-06-21 | E-GEOD-32537 | biostudies-arrayexpress