LIPA rSNPs (rs1412444 and rs2246833), Transcriptional Factor Binding Sites and Disease

Background: The lysosomal acid lipase A (LIPA) gene transcribes the lysosomal acid lipase (LAL) which hydrolyzes cholesteryl esters and triglycerides in the cell lysosome thereby generating free cholesterol and fatty acids. Two LIPA single nucleotide polymorphisms (SNPs, rs1412444 and rs2246833) found to be associated with coronary artery disease (CAD) and myocardial infarction (MI) were analyzed with respect to alterations in transcriptional factor binding sites (TFBS) created by the SNP alleles. Materials & Methods: The JASPAR CORE and ConSite databases were used to identify the TFBS. The Vector NTI Advance 11.5 computer program (Invitrogen, Life Technologies) was used to identify TFBS in the LIPA gene. Results: These regulatory (r) SNPs in intron one (rs2246833) and intron two (rs141244) which are in linkage disequilibrium were found to alter TFBS resulting in potential changes in LIPA regulation. The rs2246833 common LIPA-C allele creates three unique punitive TFBS for the FOXC1, SP2 and ZNF143 transcriptional factors (TFs), while the minor LIPA-T allele creates one unique punitive TFBS for the MZF1 TF. The rs1412444 common LIPA-C allele creates five unique punitive TFBS for the ELF1, ETS1, GABPA, HOXA5 and SPI1 TFs, while the minor LIPA-T allele creates twelve unique punitive TFBS for the FOXA1, FOXL1, FOXO3, HNF1B, MEF2A, NFIC, NFKB1, PAX2, SOX6, SOX9, SRY and THAP1 TFs. Conclusion: The changes created by LIPArs1412444 and rs2246833 SNP alleles provide alternative TFBS for TFs that would affect LIPA regulation which in turn can be associated with human disease. Between the two LIPA rs141244 alleles there are a total of 43 potential TFBS which suggests that this is prominent binding site for TFs involved with LIPA gene regulation