To identify variants that potentially impact human body fat via a role in adipogenesis, we analyzed whole-exome sequence data from a population-based sample of 6809 American Indians with longitudinal measures of BMI. A total of 623,236 exonic variants were detected and those that met the following criteria were prioritized for functional analysis: 1) non-synonymous, stop-gain or frameshift that occurred in ≥5 individuals; 2) a Combined Annotation Dependent Depletion (CADD) score ≥10 (top 10% of deleterious variants); 3) evidence for association with maximum BMI in adulthood (n=6002) or maximum BMI z-score in childhood (n=4882) (P<0.001, adjusted for age, sex, birth year and the first five genetic principal components) and 4) maps to a gene highly expressed in adipose tissue with literature support for a possible role in adipogenesis. The 20 variants which met these criteria had frequency of the BMI-risk allele ranging from 0.0004-0.025 and were characterized in differentiating OP9 cells for a role in lipid accumulation. Variants in PTPRF (P891L), LAMTOR1 (E37K), CCNY (P107R) and ATG5 (I65V) affected triglyceride content, where cells expressing the BMI-risk allele had increased triglycerides as compared to the wild type allele (9.1-20.5%, P=0.05-3x10-4, n=6-10 transfections). Heterozygous carriers for these variants had a higher BMI in adulthood (39.7-54.2 vs. 36.3kg/m2, P=0.05-5x10-4) and/or higher BMI Z-score in childhood (1.2-3.0 vs. 0.3SD, P=0.01-2.1x10-5) as compared to non-carriers. Two of these 4 variants had supportive evidence in other studies; E37K in LAMTOR1 directionally replicated in its association with BMI in GoDarts (P=0.04, n=2902), while I65V in ATG5 associated with waist (P=0.02) or hip circumference (P=0.02) in T2D-GENES (n=12954).
In conclusion, whole-exome sequencing followed by in vitro analysis of lipid accumulation in OP9 cells has identified coding variants that may impact BMI via a role in adipogenesis.
Y.L. Muller: None. S.E. Day: None. C. Koroglu: None. S. Kobes: None. R.L. Hanson: None. W.C. Knowler: None. H. Kim: Employee; Self; Regeneron Pharmaceuticals. C. Van Hout: Employee; Self; Regeneron Genetics Center. N. Gosalia: None. A.R. Shuldiner: Employee; Self; Regeneron Genetics Center. Stock/Shareholder; Self; Regeneron Pharmaceuticals. C. Bogardus: None. L. Baier: None.
National Institute of Diabetes and Digestive and Kidney Diseases