NEW YORK (GenomeWeb) – Researchers from the Albert Einstein College of Medicine have sequenced the APOE genes of 450 centenarians and 500 controls to look for genetic differences that lead to longevity, confirming previous studies that the APOE2 allele is associated with longevity and identifying two known regulatory variants that were depleted in the healthy older population.
The study, which was published in Mechanisms of Ageing and Development this week, builds on genome-wide association studies that have pointed to the genomic region containing the APOE gene as being associated with longevity.
Previous studies have also identified the APOE4 allele as being associated with Alzheimer's disease, and in this study the researchers found that the individuals in their older cohort were significantly less likely to have the APOE4 allele.
To further understand the specific variants involved, the researchers used a targeted next-generation sequencing strategy to sequence the APOE gene in 450 individuals of Ashkenazi Jewish descent who were all older than 95 years of age and 500 controls who had a mean age of 73 and no family history of longevity.
The researchers used NimbleGen's SeqCap capture method to target the exons and a 2 kb promoter of APOE and then indexed and pooled samples in groups of 25 for sequencing on the Illumina HiSeq 2000.
They then used a bioinformatics method, called Pool-seq, which was designed to identify rare and common SNPs by looking at the distribution counts across multiple pools. The method employs statistics to determine whether a variant is a real call or due to sequencing error.
The team noted that their sequencing protocol did not perform well in one particular exon of APOE due to having a high percentage of G and C bases. That exon was known to have two previously validated variants, so the researchers used Taqman SNP genotyping to screen for those variants.
They found that the APOE2 allele were enriched in the 95-year-plus population — present at 9.8 percent frequency, compared to 6 percent frequency in the control population. The APOE4 allele was found less frequently in the older population compared to the control — at 9.6 percent versus 15.7 percent. In addition, the APOE2/3 genotype was significantly enriched in the older population compared to the controls, while the APOE3/4 genotype was depleted, consistent with previous studies.
In addition, they found two variants in the promoter region that were significantly depleted in the older population compared to the control group. The two regulatory variants have recently been identified in other studies of Alzheimer's disease and longevity, and the researchers found that they were both predicted to be functional based on the RegulomeDB tool, "implicating the potential role of regulatory variants in a longevity association," the authors wrote.
The team also identified 17 novel variants in the APOE gene, although none of them were significantly associated with longevity.
Next, the team looked at the health consequences of carrying the various APOE alleles, which are involved in lipid metabolisms. They found that the individuals with the APOE2 allele had significantly lower levels of low-density lipoprotein. Carriers of the APOE3 and APOE4 alleles tended to have higher lipid levels, although the trend was not statistically significant.
The researchers noted that the study is suggestive of "a functional effect of the APOE allele and genotype that may lead to longevity." They added, "It would be interesting to further understand a protective role of longevity-associated, predicted functional variants in [the] APOE gene" in future studies.