The Baboon Genotype-Tissue Expression (GTEx) Project

PROJECT SUMMARY The baboon (Papio hamadryas) has emerged as a valuable primate model, offering profound insights into human health, behavior, and evolution. Despite their genetic and physiological resemblance to humans, the availability of baboon genetic resources, and the complex social dynamics within baboon colonies, population-based functional genomic studies in baboons and other non-human primates remain limited. To address this gap, we propose to capitalize on a unique and extensive resource—a large-scale collection of baboon tissue samples, amassed over a 13-year period at the Southwest National Primate Research Center (SNPRC). This collection encompasses 51 diverse tissue types, each sampled from at least 60 genetically characterized baboons. Such a comprehensive baboon tissue collection is unmatched in any other non-human primate species and offers an unparalleled opportunity for studying gene regulation across multiple tissues. The goal of this project is to conduct a large-scale, multi-tissue functional genomic study of gene regulation in baboons. Inspired by the Genotype-Tissue Expression (GTEx) Project in humans, our study aims to generate a comprehensive catalog of gene expression data derived from dozens of baboon tissues in a large sample of genotyped individuals. By leveraging bulk and single-cell RNA sequencing technologies, we will acquire transcriptomic data from 60 baboons across 51 tissues, encompassing vital organs such as the brain, heart, lung, liver, and adipose tissues, among others. Building upon the comprehensive baboon tissue collection and utilizing advanced genomic techniques, we will map expression quantitative trait loci (eQTLs) in baboon tissues. Drawing inspiration from the GTEx Project, we will determine the spatial distribution of eQTLs across genes and regulatory regions, explore patterns of eQTL sharing and tissue specificity, and disentangle the effects of cell type composition on gene expression by leveraging single-cell RNA-seq data. We will also investigate potential sex-specific effects on gene expression and cell type composition, enhancing our understanding of sexually dimorphic gene regulation in baboons. To maximize the impact and accessibility of our findings, we will develop the Baboon GTEx Portal—an open-access portal for baboon genomic data. Inspired by the successful human GTEx portal, this interactive website will provide unrestricted access to baboon data, eQTL information, and other research outcomes. To enable seamless comparisons with human GTEx data, the portal will incorporate a module for identifying orthologous genes and syntenic regions between baboons and humans, facilitating comprehensive comparative genomic studies in primates.