In our original application for R01 HD056465 we hypothesized and proved that distillation of the genetic component contributing to obesity is easier to determine in children, where environmental exposure has had less of an impact due to a relatively short period of lifetime. During our first renewal, we successfully expanded this programmatic line of research by identifying additional variants. During the last funding cycles, we carried out a series of non-hypothesis-driven studies that were directed at uncovering loci that predispose to childhood obesity by conducting various genome-wide based approaches. For instance, employing a powered two-stage study design in a consortium setting, where cases were defined as being in the ?95th percentile of BMI, we identified novel association signals which we subsequently replicated. This first NICHD funded study was ultimately published in Nature Genetics, with the subsequent larger trans-ethnic study being more recently reported. Intense genome-wide association studies (GWAS) efforts by the community have yielded key variants robustly associated with measures of adiposity, both in children and adults. Interestingly, while macro-level gene sets analysis of overall GWAS findings for adult waist-to-hip ratio (WHR) have implicated adipogenesis, comparable analyses of adult BMI GWAS datasets implicate central nervous system (CNS) processes. Despite these macro-level analyses, an important caveat of GWAS is that they only report genomic association signals and not necessarily the precise localization of culprit genes. As such, GWAS have not strictly represented an era of gene target discovery, rather it was simply a decade of signal discovery. One clear example of this is with progress in understanding the obesity GWAS signal that resides within an intronic region of FTO. Specifically, the signal is now known to influence the expression of nearby genes, IRX3, IRX5 and RFGRIP1L, rather than the `host' gene itself. These discoveries suggest that the FTO variant is actually an enhancer embedded in one gene that influences the expression of other causal genes. Since we already have dedicated infrastructure, namely the Center for Spatial and Functional Genomics at the Children's Hospital of Philadelphia (CHOP), to conduct such `variant to gene mapping' efforts, our team is poised to determine at scale how our reported childhood obesity loci affect the expression of specific genes in neuronal relevant cells, namely neural precursors, microglia, astrocytes and hypothalamic neurons. This involves the integration of high resolution `3D Genomics', `Assay for Transposase Accessible Chromatin sequencing' (ATAC-seq), RNA-seq and CRISPR. This final step will enable us to fully infer effector genes. Thus, the premise of this renewal is to uncover the correct functional context of the childhood obesity variants identified by our GWAS in order to translate these discoveries into meaningful benefits for pediatric care.
Our genome wide association studies (GWAS) of childhood obesity have revealed key loci influencing risk for the trait, with the data increasingly pointing to central nervous system processes. However, at the individual locus level, GWAS only reports genomic signals associated with a given trait and not necessarily the precise localization of culprit effector genes. Given the need for `variant to gene mapping', we will utilize `3D Genomic' and CRISPR based screens in iPSC-derived neuronal cell types to pinpoint the causal gene(s) at each key childhood obesity GWAS-implicated locus.
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