Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels

Abstract

Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly assumed that mRNA expression changes will lead to consequent changes in protein levels, methodological challenges have limited our ability to test the degree to which this assumption holds true. Here, we further developed the micro-western array approach and globally examined relationships between human genetic variation and cellular protein levels. We collected more than 250,000 protein level measurements comprising 441 transcription factor and signaling protein isoforms across 68 Yoruba (YRI) HapMap lymphoblastoid cell lines (LCLs) and identified 12 cis and 160 trans protein level QTLs (pQTLs) at a false discovery rate (FDR) of 20%. Whereas up to two thirds of cis mRNA expression QTLs (eQTLs) were also pQTLs, many pQTLs were not associated with mRNA expression. Notably, we replicated and functionally validated a trans pQTL relationship between the KARS lysyl-tRNA synthetase locus and levels of the DIDO1 protein. This study demonstrates proof of concept in applying an antibody-based microarray approach to iteratively measure the levels of human proteins and relate these levels to human genome variation and other genomic data sets. Our results suggest that protein-based mechanisms might functionally buffer genetic alterations that influence mRNA expression levels and that pQTLs might contribute phenotypic diversity to a human population independently of influences on mRNA expression.

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

“…Genetic variants can affect transcript levels or mRNA stability 181 , which in turn could alter protein levels 182–186 . Alternatively, missense variants can change a protein's stability and influence protein-binding partners 187 .…”

Pharmacoethnicity in Paclitaxel-Induced Sensory Peripheral Neuropathy

“…The samples also have gene expression (41), miRNA (42), modified cytosine (43) and protein data (44) that allow for the elucidation of potential function of the genetic variants associated with pharmacologic phenotypes. Our observation of a lack of population difference in paclitaxel-induced cytotoxicity is in contrast to population differences observed for platinating agents (45), and antimetabolites (46).…”

Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach

“…Using a protein dataset composed of 441 human signaling and transcription factor proteins that were quantified in these cell lines using a microwestern and/or reverse phase protein array [23,39], we evaluated for the enrichment of protein quantitative trait loci (pQTLs); genotype correlated to protein expression at p ≤ 0.0001). Of the 2711 dQTLs, 271 were associated with baseline expression of 130 unique proteins (Supplementary Table S2).…”

“…HapMap LCLs were purchased from Coriell Institute for Medical Research (Camden, NJ, USA). The 68 LCLs of Yoruban ancestry (YRI 1 and YRI 3) were used in previous experiments evaluating protein levels [23,39]. Table S4 lists the cell lines.…”

“…For this purpose, the LCL model from the International HapMap Consortium [21] has several advantages including publically available genetic information [21], gene expression [22], and protein expression data [23] to correlate with cytotoxicity (cell growth inhibition following drug exposure) phenotypes. Furthermore, associations between genetic variants and drug responses in LCLs have been replicated in patient samples [24,25,26,27].…”