Identification and characterization of two functional variants in the human longevity gene FOXO3

Friederike Flachsbart,Céline Derbois,Robert Häsler,Hélène Blanché,Guillermo G Torres,André Franke ,Anne Luzius,Amke Caliebe,Susanne Sebens,Kathrin Pallauf,Ben Krause‐Kyora ,Dmitriy Drichel,Sandra May,Kaare Christensen,Gerald Rimbach,Janina Dose,Andreas Till,Abdou Elsharawy,Marianne Nygaard,Alexander Arlt,Pilar Galán ,Michael Förster ,Marlene Jentzsch,Claudia Geismann,Wolfgang Lieb,Philip Rosenstiel,Lene Christiansen,Michael Nothnagel,Liljana Gentschew,Nandini Badarinarayan,Carolin Knecht,Stefan Schreiber,Jean‐François Deleuze ,Almut Nebel

doi:10.1038/s41467-017-02183-y

Abstract

FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown. Here, we perform resequencing of the FOXO3 locus and single-nucleotide variant (SNV) genotyping in three European populations. We find two FOXO3 SNVs, rs12206094 and rs4946935, to be most significantly associated with longevity and further characterize them functionally. We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs. Specifically, in luciferase reporter assays, the longevity alleles of both variants show considerable enhancer activities that are reversed by IGF-1 treatment. An eQTL database search reveals that the alleles are also associated with higher FOXO3 mRNA expression in various human tissues, which is in line with observations in long-lived model organisms. In summary, we present experimental evidence for a functional link between common intronic variants in FOXO3 and human longevity.

Highlights

Danish Aging Research Center, and the Danish Twin Registry, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, J
forkhead box O3 (FOXO3) is consistently annotated as a human longevity gene, the functional variants and the underlying mechanisms have not been identified yet
We report on the characterization of the two associated single-nucleotide variants (SNVs) rs12206094 and rs4946935 that were detected after resequencing of the FOXO3 gene and association testing in German, French, and Danish longevity samples

Summary

Introduction

6 Institute of Human Nutrition and Food Science, Kiel University, Hermann-Rodewald-Straße 6, 24118 Kiel, Germany. 8 Centre National de Recherche en Génomique Humaine CNRGH-CEA, 91000 Evry, France. The identification of the involved genes and variants still remains a challenge even though the first ever genetic association of the apolipoprotein E allele ε4 with longevity was already reported in 19942. Since this finding has been replicated in numerous studies[3,4]. FOXO3 is consistently annotated as a human longevity gene, the functional variants and the underlying mechanisms have not been identified yet. Our data provide evidence for a functional link between common intronic variants in FOXO3 and the longevity phenotype in humans

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