Pneumonia: host susceptibility and shared genetics with pulmonary function and other traits

Clin Exp Immunol. 2019 Dec;198(3):367-380. doi: 10.1111/cei.13367. Epub 2019 Oct 1.


Pneumonia is a common and severe infectious lung disease. Host genetics, together with underlying medical and lifestyle conditions, determine pneumonia susceptibility. We performed a secondary analysis of the results of two genome-wide studies for pneumonia in 23andMe participants (40 600 cases/90 039 controls) (Tian et al., 2017) and UK Biobank (BB) participants (12 614 cases/324 585 controls) (via the Global Biobank Engine) and used the GTEx database to correlate the results with expression quantitative trait loci (eQTLs) data in lung and whole blood. In the 23andMe pneumonia single nucleotide polymorphism (SNP) set, 177 genotyped SNPs in the human leukocyte antigen (HLA) region satisfied the genome-wide significance level, P ≤ 5·0E-08. Several target genes (e.g. C4A, VARS2, SFTA2, HLA-C, HLA-DQA2) were unidirectionally regulated by many HLA eSNPs associated with a higher risk of pneumonia. In lung, C4A transcript was up-regulated by 291 pneumonia risk alleles spanning the half the HLA region. Among SNPs correlated with the expression levels of SFTA2 and VARS2, approximately 75% overlapped: all risk alleles were associated with VARS2 up-regulation and SFTA2 down-regulation. To find shared gene loci between pneumonia and pulmonary function (PF), we used data from the Global Biobank Engine and literature on genome-wide association studies (GWAS) of PF in general populations. Numerous gene loci overlapped between pneumonia and PF: 28·8% in the BB data set and 49·2% in the 23andMe data set. Enrichment analysis within the database of Genotypes and Phenotypes (dbGaP) and National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) Catalog of pneumonia and pneumonia/PF gene sets identified significant overlap between these gene sets and genes related to inflammatory, developmental, neuropsychiatric and cardiovascular and obesity-related traits.

Keywords: C4A; eQTLs; genetic susceptibility; pneumonia; pulmonary function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Gene Expression
  • Genetic Association Studies
  • Genetic Predisposition to Disease / genetics*
  • Genome-Wide Association Study / methods*
  • Genotype
  • HLA Antigens / genetics
  • Humans
  • Lung / metabolism*
  • Lung / pathology
  • Phenotype
  • Pneumonia / genetics*
  • Polymorphism, Single Nucleotide*
  • Quantitative Trait Loci / genetics
  • Valine-tRNA Ligase / genetics


  • HLA Antigens
  • VARS2 protein, human
  • Valine-tRNA Ligase