FOXO3 gene variants and human aging: coding variants may not be key players

Abstract

FOXO3 is generally recognized as a "master" gene in aging since its association with longevity has been replicated in multiple organisms and human populations. A group of single nucleotide polymorphisms in linkage disequilibrium with a coding region has been associated with human longevity, but the actual functional variant is unidentified. Therefore, we sequenced the coding region in our long-lived Japanese American population in order to enhance resources for fine mapping this region. We demonstrate that of 38 published variants, 6 are misalignments with homologous nonallelic sequences from FOXO3B (ZNF286B), a pseudogene on a different chromosome; 2 are attributable to ZNF286B only, and the remaining 30 were unconfirmed, indicating that they are very rare and not likely involved in longevity. Furthermore, we identified a novel, unique, nonsynonymous coding variant in exon 3 (Gly566Ala; rs138174682) that is prevalent in multiple ethnic groups but appeared too rare for major longevity effects in our study populations.

Figure 1.

Sequencing strategy. Chromosome 6–specific primers were used to amplify a 1.5-Kb genomic fragment of exon 3. Sequences were generated from 95 individuals of various ethnicities living in Hawaii and screened for nucleotide substitutions. Forward primers are denoted as dark green, whereas reverse primers are light green. The yellow box denotes the protein-coding exon 3, whereas the solid line denotes the noncoding genomic sequence.

Figure 2.

FOXO3 Genomic and FOXO3B mRNA Alignment. Shown is an alignment of the FOXO3 gene (GenBank NM_201559.2), also known as FOXO3A, with the homologous genomic sequences on chromosome 17 (FOXO3B [NR_026718, complement]). Homologies are noted in the top row with green bars. The red arrows refer to the FOXO3 transcript, version 2. The yellow arrows denote the protein-coding exons 2 and 3, and the black boxes denote the noncoding FOXO3B transcript. It is apparent from this alignment that the FOXO3B pseudogene is derived from the FOXO3 processed transcript variant 2, including exons 2–4. The present study assessed single nucleotide polymorphisms from exons 2–3, shown by the yellow arrows. The large intron 2 has been truncated to reduce the size of the figure.