Association of variable number of tandem repeats in the coding region of the FAM46A gene, FAM46A rs11040 SNP and BAG6 rs3117582 SNP with susceptibility to tuberculosis

Abstract

We analyzed for association between the Family with sequence similarity 46, member A (FAM46A) gene (located on chromosome 6q14.1), BCL2-Associated Athanogene 6 (BAG6) gene (located on chromosome 6p21.3) and tuberculosis in Croatian Caucasian. We genotyped the FAM46A rs11040 SNP, FAM46A VNTR and BAG6 rs3117582 polymorphisms in a case-control study with 257 tuberculosis patients and 493 healthy individuals in a Croatian Caucasian population. We found that genotype FAM46A 3/3 (three VNTR repeats homozygote) was associated with susceptibility to tuberculosis (p<0.0015, Pcorr.<0.029, Odds ratio = 2.42, 95% Confidence Interval = 1.34-4.3). This association suggests that the protein domain encoded by the VNTR might be important for the function of the FAM46A protein, which, in turn, could be relevant in developing tuberculosis. In addition, we found that FAM46A rs11040 SNP:FAM46A VNTR:BAG6 haplotype 132 (G-3-C) is associated with susceptibility to tuberculosis (p<0.012, pcorr.<0.024, Odds ratio 3.45, 95% Confidence Interval = 1.26-9.74). This may suggests that the interaction between the FAM46A and BAG6 proteins may be involved in tuberculosis etiology. We found also that infection of human macrophages with heat-killed M. tuberculosis (H37Rv) led to over-expression of FAM46A (VNTR 3/4) transcript. This is the first study to show associations between the FAM46A gene VNTR polymorphisms, FAM46A rs11040 SNP:FAM46A VNTR:BAG6 haplotypes and any disease.

Figure 1. Schematic representation of FAM46A mRNA alleles in CCDS.

Cloning and sequencing of FAM46A mRNA from our studied population generated six variants of the FAM46A gene that were different at the VNTR site. FAM46A alleles 3, 4, 5, and 6 (UniProt identifiers: >sp|Q96IP4|29-33), (>sp|Q96IP4|24-28), (>sp|Q96IP4|34-38) and (>sp|Q96IP4|39-43, respectively) were previously reported. Our submission of the sequences for FAM46A allele 2 and 7 to the GenBank has recently (06.02.2014) been accepted for publication with accession numbers KF878392 and KF878393, respectively.

Figure 2. Mycobacterium tuberculosis (H37Rv) infection induces the over-expression of FAM46A RNA in macrophages.

Total RNA was extracted from macrophages that were infected with M. tuberculosis (H37Rv) for 12 hours and uninfected macrophages, respectively. Extracted RNAs were subjected to quantitative real-time PCR for FAM46A gene amplification. Copy number was normalized to that of uninfected macrophages.