We identified two variants that associate with apoB concentrations in Mexicans. Our genetic analysis showed association, significant after adjusting for multiple testing, with rs1424032 located on 16q21 and rs1349411 on 12p13.31 in a total of 1,998 individuals from Mexican dyslipidemic families and a case/control study sample. The 16q21 locus is a highly conserved non-coding region, and the 12p13.31 locus includes the APOBEC1 gene, which is an excellent candidate gene for serum apoB levels, as it is involved in the editing of APOB mRNA in the small intestine.
As our sample size was not sufficiently powered for genome-wide association we focused our association analyses on regions of the genome that were supported by linkage analysis using highly prevalent tagSNPs, for which we have greatest statistical power. We are also encouraged by the number of coincident location of the linkage signals in the Mexican FCHL families with previous positive signals in Caucasian FCHL families (supplementary table 2
).6, 8, 20
Importantly, both SNPs rs1424032 and rs1349411 are located in regions that provided genome-wide evidence of linkage (lod > 3.3) in previous studies of FCHL.6, 20
Mexicans are an admixed population, descended from a recent mix of Amerindian and European ancestry with a small proportion of African ancestry.21
To screen for true association signals we used family-based association method that is robust to population stratification and admixture.13
We also examined whether apoB levels and/or the associations of rs1424032 and rs1349411 were influenced by global ancestry in the unrelated case/control sample using European/Amerindian informative markers. To reduce sources of heterogeneity both the dyslipidemic families and case/control study sample were recruited by the same dyslipidemia clinic. We recognize that differences in ascertainment criteria may potentially cause heterogeneity. However, we feel that additional significance and conformation were obtained for the SNPs rs1424032 and rs1349411 by utilizing a variety of resources that includes families with multiple affected individuals and population based case/control individuals.
We studied apoB as our primary phenotype in individuals at increased risk to develop CAD. The results from several prospective epidemiological studies have demonstrated that apoB levels are superior to LDL-C and TC levels in predicting the risk of CAD.22
This is because apoB is present in all atherogenic lipoprotein particles with each particle containing exactly one molecule of apoB. Thus, the measurement of apoB represents the total number of atherogenic particles,22
yet apoB levels are not routinely measured and investigated in genetic studies for lipids and/or CAD.
ApoB exists in two forms: apoB-100 and apoB-48. ApoB-100 is synthesized in the liver and is present in VLDL, IDL and LDL particles. ApoB-48 is produced in the small intestine from apoB-100 by RNA editing and is necessary for the assembly of chylomicrons for the absorption of dietary fats.23
The SNP rs1349411 is an excellent candidate for apoB levels and lipoprotein metabolism as it resides near the APOBEC1
gene that is necessary for the production of apoB-48 from apoB-100.23
In previous reports, mice homozygous for targeted deletion of the Apobec1
gene were viable and fertile with no phenotype other than unfavorable changes in lipoprotein metabolism, such as elevated LDL fraction and low HDL-C levels.24
However, mice express Apobec1
in both liver and small intestine, while in humans, APOBEC1
is expressed exclusively in the small intestine.23
As apoB-48 concentrations increase after a fat-rich meal relative to that of apo B-100,23
we intend to compare the postprandial amount of apoB-48 relative to apoB-100 between rs1349411genotype groups in future studies. Although extensive resequencing is warranted to identify all putative regional causal variants, such a diet study could provide a direct conformation for the molecular mechanism of this locus.
The SNP rs1424032 resulted in a P-value of 6 × 10−6
in the FCHL families. This SNP is located in a region that has been consistently replicated in numerous linkage studies for FCHL and HDL-C.6, 8
Although there are no known genes, RNAs or spliced expressed sequence tags near rs1424032, the LD interval of rs1424032 contains many conserved sequences predicted to function as regulatory elements. Recent findings suggest that functional effects may be mediated by remote regulatory elements.25,26
Hence, the susceptibility gene could lie beyond the interval of the association. As rs1424032 is located in the most replicated region for FCHL, it is tempting to speculate that it may potentially influence underling susceptibility gene(s) in this region. The next-by flanking genes, cadherin 8 and 11 which are 1 and 2 Mb away, have not been implicated in lipid metabolism previously. This potential long-range regulatory effect warrants investigation in future studies.
To conclude, it is important to identify genes contributing to the increased susceptibility to hyperlipidemia and CAD in Mexicans, as this population is underinvestigated for the genetic factors conferring the high susceptibility. We identified two loci that are significantly associated with a clinically important atherosclerotic lipid phenotype in the Mexican population.