A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation

Abstract

Background: Metabolic syndrome (MetS) is an aberration associated with increased risk for cancer and inflammation. Adiponectin, an adipocyte-produced abundant protein hormone, has countering effect on the diabetogenic and atherogenic components of MetS. Plasma levels of adiponectin are negatively correlated with onset of cancer and cancer patient mortality. We previously performed microsatellite linkage analyses using adiponectin as a surrogate marker and revealed two QTLs on chr5 (5p14) and chr14 (14q13).

Methods: Using individuals from 85 extended families that contributed to the linkage and who were measured for 42 clinical and biologic MetS phenotypes, we tested QTL-based SNP associations, peripheral white blood cell (PWBC) gene expression, and the effects of cis-acting SNPs on gene expression to discover genomic elements that could affect the pathophysiology and complications of MetS.

Results: Adiponectin levels were found to be highly intercorrelated phenotypically with the majority of MetS traits. QTL-specific haplotype-tagging SNPs associated with MetS phenotypes were annotated to 14 genes whose function could influence MetS biology as well as oncogenesis or inflammation. These were mechanistically categorized into four groups: cell-cell adhesion and mobility, signal transduction, transcription and protein sorting. Four genes were highly prioritized: cadherin 18 (CDH18), myosin X (MYO10), anchor protein 6 of AMPK (AKAP6), and neuronal PAS domain protein 3 (NPAS3). PWBC expression was detectable only for the following genes with multi-organ or with multi-function properties: NPAS3, MARCH6, MYO10 and FBXL7. Strong evidence of cis-effects on the expression of MYO10 in PWBC was found with SNPs clustered near the gene's transcription start site. MYO10 expression in PWBC was marginally correlated with body composition (p = 0.065) and adipokine levels in the periphery (p = 0.064). Variants of genes AKAP6, NPAS3, MARCH6 and FBXL7 have been previously reported to be associated with insulin resistance, inflammatory markers or adiposity studies using genome-wide approaches whereas associations of CDH18 and MYO10 with MetS traits have not been reported before.

Conclusions: Adiponectin QTLs-based SNP association and mRNA expression identified genes that could mediate the association between MetS and cancer or inflammation.

Figure 1

Manhattan plots of SNP associations with MetS phenotypes within adiponectin QTL at 5p14. Dark blue dots depict levels of association of identifier phenotypes with all SNPs in the region determined from 1 LOD reduction from the peak [chr5: 9,792,000-23,021,100 (NCBI36/hg18)]. Vertical axis represents minus logarithm of the p-values and horizontal represents the chromosomal position (Mb). Levels of QTL-wide significance thresholds are shown by the dash lines. Red lines indicate the significant level (p_α=0.05= 2.11×10^-5) and blue lines indicate suggestive level p_α=0.1= 4.11×10^-5). A) Association patterns of all the SNPs of the region with weight phenotype. Transcripts defined by UCSC genome browser (31, 32) are shown below the Manhattan plot, by blue bars. SNPs that show highest association with weight are located in gene CDH18 (framed in orange). B) SNP associations with BMI. C) SNP associations with plasma levels of adiponectin. SNPs with strongest associations are mapped to MYO10, shown framed in the lower panel and the blown-up picture. The second locus of peak signals (pointed by an arrow) is mapped to be 400kb upstream of CDH18, framed in green.

Figure 2

Manhattan plots of SNP associations with MetS phenotypes within adiponectin QTL at 14q13. Dark Blue dots depict levels of association of identifier phenotypes with all SNPs in the region determined from 1 LOD reduction from the peak [chr14: 23,131,000-36,761,868 (NCBI36/hg18)]. Vertical axis represents minus logarithm of the p-values and horizontal represents the chromosomal position (Mb). Levels of QTL-wide significance thresholds are shown by the dash lines. Red lines indicate the significant level (p_α=0.05= p_α=0.05=1.86×10^-5) and blue lines indicate suggestive level p_α=0.1= 3.72×10^-5). A) Association patterns of all the SNPs of the region with RQ phenotype. Transcripts defined by UCSC genome browser (31, 32) are shown below the Manhattan plot, by blue bars. SNPs that show highest association with weight are located in gene AKAP6 (framed in red). B) SNP associations with triglycerides. SNPs that show highest associations with triglycerides are mapped to the transcription factor gene NPAS3.

Figure 3

Cis-effects of tagging SNPs located at chr5p14 on PWBC expression of MYO10 gene. Association significance level (shown by –log₁₀p-value) with MYO10 gene expression of each tagging-SNP of the 1 LOD-score drop of adiponectin QTL at chr5: 9,792,000-23,021,100bp (NCBI36/hg18) is plotted against its respective genomic position using LocusZoom [35]. The position of each typed SNPs is also depicted in black bars above the plot. Red horizontal line shows the significance cutoff after Bonferoni-correction (p_α=0.05=1.4×10^-5). The color of the dot that represents each SNP on the plot shows the degree of correlation with rs2434960, the variant with the highest significance levels of cis-effect on MYO10 expression. Correlation (r²) scale is depicted on the right. Genes mapped to this region are shown below the plot, with their directionality on the chromosome strand depicted. MYO10 gene is framed in orange. In the blow-up figure on the right, functional genomics data from ENCODE consortium [33,34] of the region with the strongest cis-effect evidence in our analysis is shown in the UCSC Genome Browser view [31,32]. The four SNPs with the highest significance levels of cis-effects are labeled as red dots on MYO10 gene track. ENCODE functional genomics tracks shown include evidence of enhancer- and promoter-associated histone modifications (H3K4Me1, H3K4Me3 and H3K27Ac), DNase hypersensitivity clusters and transcription factor binding assays.