Genetic determinants of circulating sphingolipid concentrations in European populations

Abstract

Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08x10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases.

Figure 1. Genome-wide association results for sphingolipids.

Manhattan plots show the association signals (−log10 of p-value) on the y-axis versus SNPs according to their position in the genome on the x-axis (build 36). The most interesting candidate genes are highlighted.

Figure 2. Detailed views of the 5 genomic regions demonstrating significant signals.

(A–E) show the 5 regions individually with a representation of all genes near the significant signals and the underlying linkage disequilibrium block structure in the HapMap CEU data (from the UCSC genome browser). Thresholds for significance are indicated by a line.

Figure 3. Major sphingolipid synthesis and trafficking pathways.

Biosynthetic pathways are shown along with the position in these pathways of enzymes encoded by the genes giving statistically significant associations for circulating sphingolipid concentrations.