We found that TNFRSF13B rs34562254 was associated with HCV infection susceptibility. More specifically, compared to subjects with rs34562254-CC (the wild type), those with CT/TT have an increased risk of HCV infection. The T allele’s effect was stronger in subjects who were older (≥ 50 years old), female, PBDs, and those with lower ALT and AST levels (≤ 40 U/L). Moreover, our bioinformatics analysis found that rs34562254 was located at the highest peak of the H3K4Me1 histone marker and potentially regulates mRNA transcription by affecting TF binding.
TNFRSF13B is a lymphocyte-specific tumor necrosis factor receptor that interacts with the NF-κB pathway and regulates B-cell development [28, 29]. It has been reported to be associated with a variety of human immune-related diseases such as CVID [22], asthma [24], and SLE [23]. Furthermore, Rand et al. have found that the TNFRSF13B rs34562254 polymorphism was correlated with multiple myeloma and coronary artery lesions [30]. In this study, based on the analyses of four genetic markers, we found that subjects with rs34562254-T were associated with an elevated risk of HCV infection.
From the NCBIdbSNP browser (https://www.ncbi.nlm.nih.gov/snp/), we found that rs34562254 is a missense mutation located in the exon region of TNFRSF13B. According to RegulomeDB, its RegulomeDB score is 3a (https://www.regulomedb.org/regulome-search/?regions=rs34562254&genome=GRCh37). RegulomeDB is a database that links SNPs with known and predicted regulatory elements within the intergenic regions of the Homo sapiens genome. The RegulomeDB score represents a model integrating functional genomics features with continuous values such as the expression of quantitative trait loci, TF binding, TF motif, ChIP-seq signal, and DNase Footprint [31]. Therefore, the rs34562254 SNP might have transcriptional regulatory functions including TF binding and DNase peak. Through the RNAfold web server, we found that the wildtype C allele of the centroid secondary structure had a lower MFE than the mutant T allele (-45.60 versus − 38.90 kcal/mol). From the ENCODE project and the UCSC genome browser, we found that rs34562254 was located on the highest peak of the H3K4Me1 histone marker, a major histone modification around enhancer elements in nucleosomes. When enhancer regions are enriched with H3K4me1 modifications, the enhancer enters a state of equilibrium. In contrast, when enhancer regions become enriched with both H3K4me1 and H3K27ac modifications, the enhancer enters an activated state that promotes gene expression [32]. Consequently, we speculate that genetic variants in rs34562254 might affect TNFRSF13B expression by influencing TF binding.
The stratified analysis showed that the rs34562254-T allele was significantly associated with HCV susceptibility in subjects that were female, over 50 years old, PBDs, and that had reduced ALT and AST levels (≤ 40 U/L). In general, compared to men, women usually develop more intense innate, humoral, and cellular immune responses to viral infections and vaccinations [33], suggesting that the allele’s associated risk is more significant in females. ALT and AST level are major indicators of liver injury severity. In hepatitis C, ALT and AST levels become abnormal (> 40 U/L), which may confound the effects of the rs34562254-T allele [19]. HCV is a common infection among older adults in certain areas of China [34]. Generally, older people are less healthy and are more likely than younger people to be exposed to potentially contaminated needles or blood products [35]. Accordingly, our result showed that the risk effect of the allele was more significant in the over 50 years old subgroup. For PBDs, they may rely on blood donation as a source of income. Blood-borne diseases such as HCV and HIV were frequently detected among PBDs in China during the early 1980s [36]; HCV infection was very prevalent [37].
Several limitations exist in this study. First, we did not test other SNPs in TNFSF/TNFRSF that may associate with HCV infection. Therefore, additional studies with more extensive genomic coverage are required to increase understanding of the role of TNFRSF13B polymorphisms in HCV infection. Second, in the multivariate regression analysis of TNFRSF SNP distribution and HCV infection outcome, HCV genotypes were not included due to a lack of data. Instead, we used existing HCV genotype data to perform a logistic regression on rs34562254 and found that the P value did not change. In future studies, we will collect as much baseline data as possible to improve our reliability. Finally, the potential biological functions of TNFRSF13B rs34562254 were speculated in the in silico analysis. The exact mechanisms of rs34562254 in TNFRSF13B in HCV infection need to be further investigated.