Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets

Clin Transl Sci. 2020 Jan;13(1):169-178. doi: 10.1111/cts.12698. Epub 2019 Dec 3.

Abstract

As an extremely prevalent disease worldwide, allergic rhinitis (AR) is a condition characterized by chronic inflammation of the nasal mucosa. To identify the finer molecular mechanisms associated with the AR susceptibility genes, differentially expressed genes (DEGs) in AR were investigated. The DEG expression and clinical data of the GSE19187 data set were used for weighted gene co-expression network analysis (WGCNA). After the modules related to AR had been screened, the genes in the module were extracted for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, whereby the genes enriched in the KEGG pathway were regarded as the pathway-genes. The DEGs in patients with AR were subsequently screened out from GSE19187, and the sensitive genes were identified in GSE18574 in connection with the allergen challenge. Two kinds of genes were compared with the pathway-genes in order to screen the AR susceptibility genes. Receiver operating characteristic (ROC) curve was plotted to evaluate the capability of the susceptibility genes to distinguish the AR state. Based on the WGCNA in the GSE19187 data set, 10 co-expression network modules were identified. The correlation analyses revealed that the yellow module was positively correlated with the disease state of AR. A total of 89 genes were found to be involved in the enrichment of the yellow module pathway. Four genes (CST1, SH2D1B, DPP4, and SLC5A5) were upregulated in AR and sensitive to allergen challenge, whose potentials were further confirmed by ROC curve. Taken together, CST1, SH2D1B, DPP4, and SLC5A5 are susceptibility genes to AR.

MeSH terms

  • Biomarkers / analysis
  • Computational Biology / methods
  • Datasets as Topic
  • Dipeptidyl Peptidase 4 / analysis
  • Dipeptidyl Peptidase 4 / genetics
  • Gene Expression Profiling / statistics & numerical data
  • Gene Expression Regulation / immunology
  • Gene Regulatory Networks / immunology*
  • Genetic Predisposition to Disease*
  • Humans
  • Nasal Mucosa / immunology
  • Nasal Mucosa / pathology
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Predictive Value of Tests
  • ROC Curve
  • Rhinitis, Allergic / epidemiology
  • Rhinitis, Allergic / genetics*
  • Rhinitis, Allergic / immunology
  • Rhinitis, Allergic / pathology
  • Risk Assessment / methods
  • Salivary Cystatins / analysis
  • Salivary Cystatins / genetics
  • Symporters / analysis
  • Symporters / genetics
  • Transcription Factors / analysis
  • Transcription Factors / genetics

Substances

  • Biomarkers
  • CST1 protein, human
  • SH2D1B protein, human
  • Salivary Cystatins
  • Symporters
  • Transcription Factors
  • sodium-iodide symporter
  • DPP4 protein, human
  • Dipeptidyl Peptidase 4