Genome-Wide Association Analysis of Soluble ICAM-1 Concentration Reveals Novel Associations at the NFKBIK, PNPLA3, RELA, and SH2B3 Loci

and SH2B3 Loci. PLoS Genet 7(4): e1001374. doi:10.1371/journal.pgen.1001374 Genome-Wide Association Analysis of Soluble ICAM-1 Concentration Reveals Novel Associations at the NFKBIK , PNPLA3 , RELA , and SH2B3 Loci Guillaume Pare Paul M Ridker Lynda Rose Maja Barbalic Jose e Dupuis Abbas Dehghan Joshua C. Bis Emelia J. Benjamin Dov Shiffman Alexander N. Parker Daniel I. Chasman Michel Georges, University of Lie`ge, Belgium Soluble ICAM-1 (sICAM-1) is an endothelium-derived inflammatory marker that has been associated with diverse conditions such as myocardial infarction, diabetes, stroke, and malaria. Despite evidence for a heritable component to sICAM-1 levels, few genetic loci have been identified so far. To comprehensively address this issue, we performed a genome-wide association analysis of sICAM-1 concentration in 22,435 apparently healthy women from the Women's Genome Health Study. While our results confirm the previously reported associations at the ABO and ICAM1 loci, four novel associations were identified in the vicinity of NFKBIK (rs3136642, P = 5.461029), PNPLA3 (rs738409, P = 5.861029), RELA (rs1049728, P = 2.7610216), and SH2B3 (rs3184504, P = 2.9610217). Two loci, NFKBIB and RELA, are involved in NFKB signaling pathway; PNPLA3 is known for its association with fatty liver disease; and SH3B2 has been associated with a multitude of traits and disease including myocardial infarction. These associations provide insights into the genetic regulation of sICAM-1 levels and implicate these loci in the regulation of endothelial function. - Funding: This study was supported by grants from the National Heart, Lung, and Blood Institute and the National Cancer Institute (Bethesda, MD), the Donald W. Reynolds Foundation (Las Vegas, NV), the Doris Duke Charitable Foundation, and the Foundation Leducq (Paris, FR), with collaborative scientific and genotypic support provided by Amgen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: DS is an employee of Celera. A member of the immunoglobulin superfamily of adhesion receptors, ICAM-1 is expressed on endothelial cells where it serves as a receptor for the leukocyte integrins LFA-1 and Mac-1 [1]. A soluble form of ICAM-1 (sICAM-1) is present in plasma and is thought to arise from proteolytic cleavage of the extra-cellular domains of ICAM-1. Although the physiologic function of soluble ICAM-1 remains to be fully defined, plasma concentration of sICAM-1 have a predictive value for the risk of myocardial infarction, ischemic stroke, peripheral arterial disease and noninsulin-dependent diabetes mellitus in epidemiological studies [24]. We recently described a genome-wide association study of sICAM-1 in 6,578 apparently healthy women from the Womens Genome Health Study (WGHS), which confirmed a known association at the ICAM1 locus and identified a novel association at the ABO locus [5]. These results were subsequently replicated in large-scale genomics studies from Barbalic [6] et al. and Qi [7] et al. Nevertheless, the total variance explained by these associations remained low (8.4%) as compared to the relatively high heritability estimates (from 0.34 to 0.59) [8,9] for sICAM-1. We therefore hypothesized that other, weaker, common genetic determinants of sICAM-1 remained to be discovered. To explore this issue, we performed a larger genome-wide association study (GWAS), evaluating 334,295 SNPs in 22,435 apparently healthy women of European ancestry from the WGHS. We found that 67 SNPs passed our pre-specified threshold of genome-wide significance of P,561028 for association with sICAM-1 (Table S1 and Figure 1A). These SNPs clustered within 5 loci in the vicinity of ABO (9q34.2), RELA (11q13.1), SH2B3 (12q24.12), ICAM1 (19p13.2) and PNPLA3 (22q13.31). The ICAM1 [10,11] and ABO [5] loci have previously been identified Soluble Intercellular Adhesion Molecule 1 (sICAM-1) is an inflammatory marker that has been associated with several common diseases such as diabetes, heart disease, stroke, and malaria. While it is known that blood concentrations of sICAM-1 are at least partially genetically determined, our current knowledge of which genes mediate this effect is limited. Taking advantage of technologies allowing us to interrogate genetic variation on a whole-genome basis, we found that variation in the NFKBIK, PNPLA3, RELA, and SH2B3 genes are important determinant of sICAM-1 blood concentrations. The NFKBIB and RELA genes are involved in regulation of inflammation. These observations are significant because this is the first report of genetic association within these extensively studied inflammation genes. The PNPLA3 gene has previously been associated with liver disease, and the SH2B3 gene has been associated with a multitude of traits including cardiovascular disease. Extension of these associations to sICAM-1 adds to the intriguing diversity of effects of these genes. as contributing to sICAM-1 levels, but the SH2B3, RELA and PNPLA3 loci were not previously shown to be associated with sICAM-1. The genomic context of these three latter loci is illustrated in Figure 2A, 2B and 2C. In order to determine whether more than one non-redundant association signal could be detected at each of these five loci, we applied a model selection algorithm. The SNP with the lowest Pvalue for association was the only one retained at every locus with the exception of the ICAM1 locus, where 5 SNPs were selected by the model (Table 1). Interestingly, model selected SNPs at the ICAM1 locus showed lower P-value when they were all included in a single multivariate model than when considered separately. Three of the model selected SNPs at the ICAM1 locus (rs281437, rs1801714 and rs11575074) were not significant at a genome-wide level of significance in a univariate analysis. We performed two analyses to determine if the multiple SNPs selected at the ICAM1 locus were the result of an underlying association with a known but untyped variant. First, we tested all imputed SNPs (using MACH) within 1.5 Mb of rs1799969 (the lead SNP at that locus) for association with adjusted sICAM-1 levels. No imputed SNP was more significant than the directly genotyped rs1799969. Second, we tested the same set of imputed SNPs after additional adjustment of sICAM-1 levels for the effect of model selected SNPs. No additional SNP was associated at genome-wide significance. The 5 SNPs at the ICAM1 locus selected by our algorithm were also used in haplotype analysis using WHAP [12], as implemented in PLINK [13] (Table 2). The estimate of the proportion of variance attributable to haplotypes, as well as their regression coefficients, is consistent with the linear model of these same SNPs, reinforcing the adequacy of an additive model to explain the association. Next we tested whether any additional SNPs are associated with sICAM-1 levels after adjustment for the model sele (...truncated)