A Dataset of 26 Candidate Gene and Pro-Inflammatory Cytokine Variants for Association Studies in Idiopathic Pulmonary Fibrosis: Frequency Distribution in Normal Czech Population

Idiopathic pulmonary fibrosis (IPF) is a specific form of chronic, progressive fibrosing interstitial pneumonia with poor diagnosis and a median survival of 2–3 years from initial diagnosis (1, 2). The cellular inflammation drives the fibrotic response in lung and plays a major role in IPF pathogenesis (3). Inflammatory cells (majorly, type 2 alveolar epithelial cells) release TGF-β, the key mediator of pulmonary fibrosis, that regulates several profibrotic cytokines/chemokines, their receptors, receptor subunits, and growth factors inducing process of epithelial–mesenchymal transition (EMT) (3, 4). Among the pro-inflammatory and profibrotic cytokines involved in IPF pathogenesis, interleukin (IL)-1 (4), IL-1β (5), IL-4, IL-5 (6), IL-6Rα (4), angiogenic IL-8/CXCL-8 (7), IL-13, its receptor IL-13 Rα2 (8), and IL-33 (9) have been implicated in accelerated inflammation and irreversible damage to lung architecture with loss of alveolar-capillary barrier basal membrane leading to persistent fibrosis. Genes encoding these factors exhibit nucleotide variation that could affect the severity of immune/inflammatory reactions and extent of any subsequent dysregulated fibroproliferative activity in disease development. Furthermore, variants in mucin-encoding genes (10–13) and in genes for pathogen-associated molecular patterns (PAMPs) receptors of innate immunity known as toll-like receptors (TLRs) (14, 15) have been also implicated in IPF immunopathogenesis and related to rapid progression of the disease. Investigations of these “candidate” gene variant(s) e.g., in case-control association studies may, therefore, provide novel insight into underlying mechanism of IPF susceptibility/disease outcome and, further, may aid to develop novel diagnostic approaches and eventually therapeutic interventions based on genetic information (16). A candidate gene study typically involves genotyping 5–50 single nucleotide polymorphisms (SNPs) within gene(s) for its coding and non-coding/regulatory regions (17). Irrespective of the number of tested gene variants; for a standard conductance, data collection, and transparent reporting of a genetic association study, the recommendations of STrengthening the REporting of Genetic Association studies (STREGA) and STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) should be considered (16). In case-control studies, knowledge of frequency distribution of candidate gene loci/variants among normal (healthy control) population(s) is necessary and could be useful also for genetically related population(s) to determine the gene variants associated with disease and/or its clinical course. The role of inflammatory and profibrotic mechanisms involving gene variation has been investigated in IPF and spectrum of susceptible polymorphic gene variants, including those in genes of immune reactions and signaling processes, have been recently reported from both genome-wide association studies (GWAS) and population-based case-control studies (14, 18, 19) performed mostly in US Caucasians, and also in some other ethnicities. The nominated gene variants, summarized in Table ​Table1,1, are of different functions and implicate some yet-unanticipated pathways in IPF pathogenesis, including endoplasmic reticulum stress and unfolded protein response, cellular senescence, DNA-damage response, and already known Wnt–β-catenin signaling (20). The distribution of SNPs may greatly differ with populations (ethnicities), for example, a high frequency of MUC5B rs35705950*T allele in IPF cases is observed among European-Americans (14–34%) (21, 22), while its low frequency is characteristic for Asians, such as Chinese (3.3%) (23), Japanese (3.4%) (24), and Korean (1.0%) cohorts (11). Similarly, MUC2 rs7934606*A allele exhibit frequency of 41% in Europeans and 1% in Asians (1000 Genomes Project Phase 3 allele frequencies). Furthermore, in context of participation of more than one gene in IPF pathogenesis, it will be important to analyze multiple susceptible gene variants. The approach of analyzing common and rare genetic factors in IPF susceptibility may provide novel insights into IPF and it could also be helpful in identifying population-specific rare variants, predominant panel of candidate gene variants for IPF risk and in understanding the basis of variable disease severity or progression among different populations. Table 1 List of candidate SNPs investigated in the study. No complex data have been yet reported on IPF-related variants in Slavonic populations, including Czechs. Starting our investigations of plausible multiple IPF susceptibility polymorphisms primarily in Czech and also related populations, we adopted allele-specific MALDI-TOF mass spectrometry-based SNPs genotyping assay for determination of gene variation in the relevant targets. Several IPF susceptible SNPs in genes of various functional categories were multiplexed, and in the first phase genotyped in probands from normal (healthy) Czech population using Sequenom MassARRAY platform. In the current dataset manuscript, we, besides genotyping methodology, report the genotype, allele, and phenotype (carriage rate) frequencies for plausible IPF susceptibility variants among normal population of Czech Republic of Western Slavonic (Caucasian) ancestry.