Diversity and impact of rare variants in genes encoding the platelet G protein-coupled receptors.

Gillian C. Lowe,Stuart J. Mundell,Neil V. Morgan,Martina E. Daly,Steve P. Watson,Matthew L. Jones,Andrew D. Mumford,Michael A. Simpson,Marie Lordkipanidzé,Jane E. Norman,Sian Drake

doi:10.1160/th14-08-0679

Abstract

SummaryPlatelet responses to activating agonists are influenced by common population variants within or near G protein-coupled receptor (GPCR) genes that affect receptor activity. However, the impact of rare GPCR gene variants is unknown. We describe the rare single nucleotide variants (SNVs) in the coding and splice regions of 18 GPCR genes in 7,595 exomes from the 1,000-genomes and Exome Sequencing Project databases and in 31 cases with inherited platelet function disorders (IPFDs). In the population databases, the GPCR gene target regions contained 740 SNVs (318 synonymous, 410 missense, 7 stop gain and 6 splice region) of which 70% had global minor allele frequency (MAF) < 0.05%. Functional annotation using six computational algorithms, experimental evidence and structural data identified 156/740 (21%) SNVs as potentially damaging to GPCR function, most commonly in regions encoding the transmembrane and C-terminal intracellular receptor domains. In 31 index cases with IPFDs (Gi-pathway defect n=15; secretion defect n=11; thromboxane pathway defect n=3 and complex defect n=2) there were 256 SNVs in the target regions of 15 stimulatory platelet GPCRs (34 unique; 12 with MAF<1% and 22 with MAF ≥ 1%). These included rare variants predicting R122H, P258T and V207A substitutions in the P2Y12 receptor that were annotated as potentially damaging, but only partially explained the platelet function defects in each case. Our data highlight that potentially damaging variants in platelet GPCR genes have low individual frequencies, but are collectively abundant in the population. Potentially damaging variants are also present in pedigrees with IPFDs and may contribute to complex laboratory phenotypes.

Highlights

G protein-coupled receptors (GPCRs) are seven transmembrane domain proteins that mediate signal transduction from a wide range of extracellular stimuli
Using the International Union of Basic and Clinical Pharmacology (IUPHAR) database, we identified 18 Class A GPCRs with robust evidence of expression in human platelets at transcript and protein levels
In order to assess the allelic diversity of the platelet GPCR genes, we surveyed the 1,000 genomes (1,092 subjects) and Exome Sequencing Project (ESP) (6,503 subjects) datasets for coding and splice region single nucleotide variants (SNVs) in the 18 selected GPCR genes

Summary

Introduction

G protein-coupled receptors (GPCRs) are seven transmembrane domain proteins that mediate signal transduction from a wide range of extracellular stimuli. GPCRs are expressed widely in haematopoietic and vascular tissues, including platelets, in which they mediate activation signals from agonists such as thrombin (protease activated receptors [PAR] 1 and 4), thromboxane A2 (thromboxane A2 receptor [TP]), epinephrine (α2A-adrenoreceptor) and ADP (P2Y12 and P2Y1 receptors). Platelets express Gscoupled GPCRs such as the prostacyclin (IP1), adenosine 2A (A2A) and prostaglandin D2 (DP1) receptors, which mediate inhibitory signals from prostacyclin, adenosine and PGD2 respectively, to suppress platelet activation. Similar associations have been demonstrated between common variants in the PAR1 (F2R), PAR4 (F2RL3) and the TP receptor (TBXA2R) genes and function of the corresponding GPCRs [3,4,5]. Since the common GPCR gene variants lie exclusively in noncoding regions, these effects are most likely caused by changes in receptor expression, and not altered receptor function [4, 7]

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Conclusion