Validation of rs7132908 as a Causal Variant at the Childhood Obesity chr12q13 Locus Implicates FAIM2

• Published in: Obesity (Silver Spring, Md.) Md.), 2022-11, Vol.30, p.40-41
• Main Authors: Littleton, Sheridan, Volpe, Christina, Maguire, Jean Ann, Bradfield, Jonathan, Pippin, James, Su, Chun, Chesi, Alessandra, Wells, Andrew, Berkowitz, Robert, Pahl, Matthew, Grant, Struan
• Format: Article
• Language: English
• Subjects: Childhood; Gene expression; Obesity; Stem cells
• ISSN: 1930-7381; 1930-739X

Background: Our genome-wide association studies with the Early Growth Genetics Consortium have shown that the FAIM2 locus on chr12q13 is associated with childhood obesity. We hypothesize that rs7132908 is a causal variant at this locus, resides within an enhancer and regulates gene expression to confer obesity risk. Methods: We generated human embryonic stem cell (hESC) lines homozygous for either rs7132908 allele which were validated with karyotyping, de novo CNV analysis and Sanger sequencing at the 10 most likely off-target sites. Each hESC line was then differentiated to a heterogeneous model of the hypothalamic arcuate nucleus and used for snRNA-seq and snATAC-seq. Human primary astrocytes were used for luciferase reporter assays. Results: Chromatin accessibility at rs7132908 was significantly correlated with expression of 26 genes. Three of these were already identified as candidate cis-causal genes by our previous variant-to-gene mapping efforts, namely FAIM2, LIMAI and BCDIN3D. FAIM2 had decreased expression in the differentiated cells with the risk genotype. We also observed decreased chromatin accessibility at both rs7132908 and the FAIM2 promoter in the differentiated cells with the risk genotype. Conversely, LIMAI and BCDIN3D did not yield differential expression or accessibility. We separately validated the allele-specific enhancer activity of rs7132908 for FAIM2. The rs7132908 non-risk allele region increased luciferase expression relative to the FAIM2 promoter alone by a fold change of 1.87, while the risk allele decreased expression by a fold change of 0.68 (P