Integrated gene-based and pathway analyses using UK Biobank data identify novel genes for chronic respiratory diseases.

Abstract

BACKGROUND:

Chronic respiratory diseases have become a non-negligible cause of death globally. Although smoking and environmental exposures are primary risk factors for chronic respiratory diseases, genetic factors also play an important role in determining individual's susceptibility to diseases. Here we performed integrated gene-based and pathway analyses to systematically illuminate the heritable characteristics of chronic respiratory diseases.

METHODS:

UK (United Kingdom) Biobank is a very large, population-based prospective study with over 500,000 participants, established to allow detailed investigations of the genetic and nongenetic determinants of the diseases. Utilizing the GWAS-summarized data downloaded from UK Biobank, we conducted gene-based analysis to obtain associations of susceptibility genes with asthma, chronic obstructive pulmonary disease(COPD) and pneumonia using FUSION and MAGMA software. Across the identified susceptibility regions, functional annotation integrating multiple functional data sources was performed to explore potential regulatory mechanisms with INQUISIT algorithm. To further detect the biological process involved in the development of chronic respiratory diseases, we undertook pathway enrichment analysis with the R package (clusterProfiler).

RESULTS:

A total of 195 susceptibility genes were identified significantly associated with chronic respiratory diseases (Pbonferroni < 0.05), and 24/195 located out of known susceptibility regions (e.g. WDPCP in 2p15). Within the identified susceptibility regions, functional annotation revealed an aggregation of credible variants in promoter-like and enhancer-like histone modification regions and such regulatory mechanisms were specific to lung tissues. Furthermore, 110 genes with INQUISIT score ≥1 may influence diseases susceptibility through exerting effects on coding sequences, proximal promoter and distal enhancer regulations. Pathway enrichment results showed that these genes were enriched in immune-related processes and nicotinic acetylcholine receptors pathways.

CONCLUSIONS:

This study implemented an integrated gene-based and pathway strategy to explore the underlying biological mechanisms and our findings may serve as promising targets for future clinical treatments of chronic respiratory diseases.

• Authors: Lijuan Wang, Rui Fang, Meng Zhu, Na Qin, Yuzhuo Wang, Jingyi Fan, Qi Sun, Mengmeng Ji, Xikang Fan, Junxing Xie, Hongxia Ma, Juncheng Dai
• Journal: Gene (Gene) Vol. 767 Pg. 145287 (Jan 30 2021) ISSN: 1879-0038 [Electronic] Netherlands
• PMID: 33181258 (Publication Type: Journal Article)
• Copyright: Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.

Topics

• Asthma (genetics)
• Biological Specimen Banks
• Chronic Disease (epidemiology)
• Databases, Genetic
• Female
• Genetic Predisposition to Disease (genetics)
• Genome-Wide Association Study (methods)
• Humans
• Lung (physiopathology)
• Male
• Polymorphism, Single Nucleotide (genetics)
• Prospective Studies
• Pulmonary Disease, Chronic Obstructive (genetics)
• Respiration Disorders (genetics)
• Smoking (genetics)
• United Kingdom