Date of Award
Open Access Honors Thesis
Background: The natriuretic peptide (NP) system is a critical physiologic pathway in heart failure, but there is marked individual variability in its functioning which may be genetic in origin. We investigated how genetic variations in NP pathway genes correlate with gene expression and protein abundance.
Methods: DNA, RNA, and tissue from human kidney (n=77) were obtained. Kidney was chosen as target tissue because each of the four candidate genes and proteins (natriuretic peptide receptor 1 (NPR1), NPR2, NPR3 and membrane metallo-endopeptidase (MME)) are expressed there. DNA samples were genotyped for 120 single nucleotide polymorphisms (SNP) in these four genes using a custom Illumina array. mRNA levels were quantified using real-time reverse transcriptase polymerase chain reaction. Protein concentration was determined in tissue lysates using commercially available assays for each target. The association of SNPs with RNA and protein quantity was tested with ANOVA adjusted for gender and race. A principal components (PC) based method was also used to test the association of overall gene variation with RNA and protein quantity. Findings with false discovery rate (FDR) <0.05 were considered significant.
Results: Eleven SNPs in NPR2 were significantly associated with protein expression after controlling for FDR at 0.05, but none of these were associated with RNA quantity. Several genotypes in MME and NPR3 showed crude associations (unadjusted p<0.05) for protein and RNA quantity, but not after controlling for FDR. There were no SNPs associated with RNA or protein expression in NPR1. RNA and Protein quantity poorly correlated with each other; NPR1 and MME showed weak but significant positive correlations (p = 0.04 and 0.03, respectively). The PC analysis yielded similar overall results, with PC1 of NPR2 (accounting for 71% of variability) being the only significant association with protein (p=0.04), and no associations for RNA.
Conclusions: Genetic variation NPR2 is associated with altered protein expression, but this is not explained via gene expression. There were crude associations for MME and NPR3 variants but these did not reach adjusted significance in this small study. Additional studies are needed to assess the clinical impact, if any, of NPR2 genetic variation.
Sunkara, Bipin, "Association of genetic variation, gene expression, and protein abundance within the natriuretic peptide pathway" (2012). Honors College Theses. 8.