Journal article
Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
Respiratory research, Vol.23(1), pp.97-97
04/21/2022
DOI: 10.1186/s12931-022-02013-w
PMCID: PMC9026726
PMID: 35449067
Abstract
Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF.
We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets.
We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts.
We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF.
Details
- Title: Subtitle
- Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
- Creators
- Auyon J Ghosh - Brigham and Women's HospitalBrian D Hobbs - Brigham and Women's HospitalJeong H Yun - Brigham and Women's HospitalAabida Saferali - Brigham and Women's HospitalMatthew Moll - Brigham and Women's HospitalZhonghui Xu - Brigham and Women's HospitalRobert P Chase - Brigham and Women's HospitalJarrett Morrow - Brigham and Women's HospitalJohn Ziniti - Brigham and Women's HospitalFrank Sciurba - University of PittsburghLucas Barwick - Emmes (United States)Andrew H Limper - Mayo ClinicKevin Flaherty - University of MichiganGerard Criner - Temple UniversityKevin K Brown - National Jewish HealthRobert Wise - Johns Hopkins School of MedicineFernando J Martinez - Weill Cornell MedicineDaniel McGoldrick - University of WashingtonMichael H Cho - Harvard UniversityDawn L DeMeo - Brigham and Women's HospitalEdwin K Silverman - Brigham and Women's HospitalPeter J Castaldi - Brigham and Women's HospitalCraig P Hersh - Brigham and Women's HospitalNHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Contributors
- Karin F Hoth (Contributor) - University of Iowa, Psychiatry
- Resource Type
- Journal article
- Publication Details
- Respiratory research, Vol.23(1), pp.97-97
- DOI
- 10.1186/s12931-022-02013-w
- PMID
- 35449067
- PMCID
- PMC9026726
- NLM abbreviation
- Respir Res
- ISSN
- 1465-993X
- eISSN
- 1465-993X
- Grant note
- P01HL114501 / NIH HHS R01HL130512 / NIH HHS T32HL007427 / NIH HHS R01HL125583 / NIH HHS U01HL089856 / NIH HHS
- Language
- English
- Date published
- 04/21/2022
- Academic Unit
- Psychiatry; Iowa Neuroscience Institute
- Record Identifier
- 9984293755502771
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