In this study, SNPs located within expressed miRNA regions and their associations with PTB risk were analyzed. After stratification of results according to sex, we observed a significant association between rs895819 and overall TB risk of the female population. Several haplotypes of five SNPs were found to be significantly associated with PTB incidence.
MiRNAs, a class of micro-molecules, play key roles in gene expression regulation and in multiple biological and pathological processes, including embryonic development, tumorigenesis, immunoregulation and inflammation (Dai and Ahmed, 2011). When considered together, SNPs located within expressed miRNA regions and binding sites may be useful for predicting an individual’s future risk of contracting infectious and non-infectious diseases. To date, SNPs and miRNA sequence-based variations have been applied to the prediction of tumor-associated diseases, asthma, TB, cardiovascular and cerebrovascular diseases (among others) in recent decades (Chen et al., 2018b; Smits et al., 2011). For example, the SNP located within the 3' untranslated region (3' UTR) of the phosphatase and tensin homolog (PTEN) gene has been found to be associated with cervical cancer risk (Yu et al., 2020). Another miRNA, miR-27a, has also been found to play key roles in regulating gene expression and proliferation of ovarian cancer and breast cancer cells (Ljepoja et al., 2019; Zhang et al., 2019). In the present study, one SNP located within the expressed sequence of miR-27a was found to be associated with decreased PTB incidence in the female population, but not in the male population. Intriguingly, Wang et al. found that downregulation of miR-27a expression in MTB-infected THP-1 cells led to enhanced expression of interferon-γ (IFN-γ), interleukin-beta (IL-β), IL-6 and tumor necrosis factor-alpha (TNF-α); this enhanced cytokine expression was abolished by cell transfection with miR-27a mimics that also led to downregulated target gene IRAK4 expression (Wang et al., 2017). Taken together, these findings offer clues that will likely enhance our understanding of potential molecular mechanisms associated with TB disease incidence. Indeed, progress has already been made toward this goal in another study that verified that ER-located Ca(2+) transporter CACNA2D3 was another miR-27a target gene. When miR-27a activity was suppressed, downregulation of Ca(2+) signaling and subsequent inhibition of autophagosome formation occurred that promoted greater intracellular MTB survival (Liu et al., 2018). Meanwhile, another SNP located within the expressed region of miR-27a was found to be associated with increased colorectal cancer (CRC) risk and reduced breast cancer risk (Mashayekhi et al., 2018; Zhang et al., 2013; Zhang et al., 2020). These studies indicate that SNPs located within the expressed region of miR-27a were functional SNPs with putative roles in gene regulation that consequently influenced the occurrences of certain diseases.
Other miRNAs have been linked to human diseases as well. For example, results of one study implicated involvement of both miR-146 and miR-29 in post-transcriptional regulation of the renalase gene, a gene which contributes to observed inter-individual variations of cardiometabolic traits (Kalyani et al., 2015). In other studies, the SNP located within miR-146a (rs2910164) was confirmed to be associated with increased coronary artery disease (CAD) risk (Xiong et al., 2014) and reduced gastric cancer risk (Jiang et al., 2016). Although these studies also indicated that the SNP located within miR-146a was a functional SNP, this SNP did not appear to be associated with PTB incidence in the current study and thus was not found to affect TB risk. Similarly, other studies have shown that SNPs located within miR-196a-2 were associated with oral squamous cell carcinoma (OSCC) survival (Liu et al., 2013), but not with breast cancer risk (Mashayekhi et al., 2018) or colorectal cancer (CRC) risk (Hezova et al., 2012), aligning with results of this study showing no association of miR-196a-2 with PTB risk.
Another miRNA linked to huma disease, miR-423, was shown in one study to activate NF-κβ and promote breast cancer invasion (Dai et al., 2020) while miR-423-5p was shown in another study to be upregulated during active TB, highlighting its potential as a PTB biomarker (Tu et al., 2019). Meanwhile, the SNP (rs6505162) located within the expressed miR-423 region was associated with lower risks of gastrointestinal cancer, CRC and lung cancer, but was not associated with higher risks of esophageal cancer, breast cancer or gastric cancer (Moazeni-Roodi et al., 2019). Moreover, previous studies had identified miR-423 as a key factor associated with TB incidence that exerted its functional effects via gene regulation, although here this SNP was not found to be significantly associated with PTB incidence.
Yet another miRNA liked to human disease, miR-618, has been reported to suppress gastric cancer metastasis by downregulating transforming-growth factor beta 2 (TGF-2β) expression (Shi et al., 2019), and to inhibit prostate cancer cell migration and invasion by targeting FOXP2 and downregulating TGF-β (Song et al., 2017). Meanwhile, results of a meta-analysis study revealed that SNP rs2682818, located within the expressed sequence region of miR-618, was not associated with overall cancer risk, but was specifically associated with breast cancer risk (Feng et al., 2019). However, in another study rs2682818 was linked to reduced CRC risk (Chen et al., 2018a).
Haplotype analysis is a method that evaluates various combinations of multiple genetic variants to find haplotypes that are useful for predicting disease risk. In the present study, combinations of various haplotypes were evaluated to determine their associations with PTB risk. Ultimately, a strategy for predicting future disease incidence that was based on multiple SNPs was found to be superior to one based on a single SNP.
In order to discover potential SNP-disease associations for different age groups, stratification by age was conducted. Notably, SNPs with marginal levels of statistical significance were detected within expressed sequences of miR-423 and miR-27a for subjects aged ≥ 60 years, but not for subjects aged < 60 years. Thus, we speculate that significant SNP correlations with PTB disease may were not detected for some age groups, due to their statistically inadequate sample sizes. As a result, although the present study provided some useful information, further studies based on larger sample sizes are needed to verify the conclusions of this study and to discover SNPs with statistically stronger correlations with PTB risk.