Purinergic receptor P2RX7 (P2RX7, NCBI Gene ID: 5027) is a protein coding gene that produces an inotropic class of ligand-gated ion channels and is expressed in many tissues throughout the human body; though mostly expressed in brain and skin cells (NCBI 2020). The protein encoded from P2RX7 differs from other P2X receptor genes, as well as other ligand-gated channels, since it can transport molecules up to 900 Da (Benzaquen et al 2019). The P2RX7 protein has been shown to be associated with many biological processes, and is a potential target for anti-inflammatory therapy (Peng et al 2019). As P2RX7 is expressed in many cell lines, including immune and non-immune cells, and is involved with genetic expression signaling, macrophage immune response, and membrane voltage potential of both the cell plasma membrane and the nuclear membrane (Fuller et al 2009). Numerous splicing variants of this gene have been identified, many of which seem to be involved with nonsense-mediated decay (NCBI 2020). Furthermore, single nucleotide polymorphisms in P2RX7 have been shown to play a role in a myriad of diseases, ranging from mood disorders, bipolar disorder, and unipolar depression (McQuillin et al 2009) to tuberculosis susceptibility (Peng et al 2019).
Previous research has been performed on many different SNPs within P2RX7. One of the most highly researched SNPs is rs3751143, which was also associated with multiple phenotypes including IL-8 level in serum, a chronic obstructive pulmonary disease biomarker, Toxoplasma gondii killing, and mineral density (Peng et al 2019). ASE results from the lung tissue of 48 donors in China found the rs3751143 wild-type A allele to be overexpressed over the mutant C allele in heterozygous individuals. The expression ratio (C/A) had a mean ± SD of 0.84 ± 0.16 with 95% confidence interval 0.76–0.92; P = 0.001 (Peng et al 2019). This presented the possibility that SNPs in linkage disequilibrium with rs3751143 play a role in the regulation of the expression of P2RX7. Peng et al (2019) focused their study on Chinese populations, performing computational LD analysis on Han Chinese in Beijing (CHB) and Southern Han Chinese (CHS) populations.
By analyzing variants in linkage disequilibrium with rs3751143, Peng et al (2019) uncovered SNP rs11615992. This variant became the focus of many subsequent investigations. Peng et al (2019) deployed a long-distance gene interaction model that inserted the SNP rs116155992 into a region upstream from the luciferase gene in a pGL3-promoter vector. Their results demonstrated an increase in expression of luciferase when spliced with both SNP alleles, specifically the A allele of rs11615992 and the A allele of rs3751143 (Peng et al, 2019). This resulted in a more than 40% increased luciferase activity when compared with the rs11615992 G allele (Peng et al 2019). To test whether the SNP rs11615992 may interact with the P2RX7 transcription factor (TF), Peng et al (2019) computationally predicted a TF binding to the area surrounding rs11615992 by using the TRANSFAC database. The results indicated that the TF POU2F1 (POU class 2 homeobox 1) also binds to the region surrounding rs11615992 (Peng et al 2019). Subsequently, this related transcription factor, POU2F1, was used in a ChIP-seq experiment which showed the region associated with rs11615992 displayed significantly higher levels of immunoprecipitation of the antibody for POU2F1 than IgG (Peng et al 2019). This validated that, despite being found downstream of the P2RX7 gene, rs11615992 has the potential to play an important regulatory role in the transcription of P2RX7 (Peng et al 2019).
This current study aims to computationally investigate the region surrounding P2RX7 for other SNPs in linkage disequilibrium with rs3751143 in more geographically diverse populations. It is important to note that Peng et al’s (2019) chromosome conformation capture assay verified that the region surrounding rs11615992, a position 5 kb downstream of rs3751143, could interact with the P2RX7 promoter as an enhancer. This leaves open the possibility for both upstream and downstream SNPs in LD with rs3751143 to affect P2RX7 expression as shown with rs11615992.