Lymphocyte type determines the effect of single nucleotide polymorphisms on Lymphotoxin Alpha expression. (51.9)

Abstract

Abstract The lymphotoxin alpha (LTA) gene contains many single nucleotide polymorphisms (SNPs); some influence expression levels and are associated with disease. The impact of SNPs on LTA expression primarily has been analyzed in B cells, yet T cells contribute the most to LTA levels. Thus, we investigated the cell type-specific effects of the LTA +81C/A and +369G/C SNPs on expression. The LTA +81A SNP significantly increased expression relative to +81C in T cells; opposite of its impact in B cells. Conversely, the LTA +369G SNP was found to significantly decrease expression only in T cells under basal conditions. The impact of this SNP was partly due to stronger binding to and repression of LTA +369G by Sp1. ChIP assays showed Sp1 binding to this region of the LTA locus in vivo, but the two Sp1 sites in close proximity could not be distinguished. However, mutation of the LTA +369 SNP-associated Sp1 site did result in an expected increase in expression further implicating that Sp1 binding to this site suppresses expression. Numerous studies associate SNPs with disease and mechanisms are proposed to explain these associations based on the known impact of the SNP on expression. We show that LTA SNPs can differentially impact expression levels depending on stimulation status and cell type. Thus, it is critical to consider the cell type-specific impact of a SNP and the pertinence of different cell types to disease pathogenesis when proposing a mechanism behind a disease association.