Single-nucleus transcriptional and chromatin accessibility profiling of mouse hypothalamic LepRb neurons reveals cell type-specific cis-regulatory elements linked to human obesity

Leptin receptor-expressing hypothalamic neurons (LepRHypo) are key regulators of energy balance, yet a comprehensive, cell type-resolved, chromatin accessibility map of these neurons is lacking. We profiled [~]20,000 LepRHypo nuclei using single-nucleus multiome (snRNA-seq/snATAC-seq), identifying 39 transcriptionally and epigenetically distinct clusters, including AgRP (two subtypes), Pomc (two subtypes), Foxb1, Irx5/3 (three subtypes), Nts, PNOC (two subtypes), Kiss1/Pdyn (KNDy, two subtypes), Ghrh, Tcf7l2, and Sf1/Nr5a1 (three subtypes) populations. We also identified three Glp1r-expressing clusters with the highest Lepr enrichment, each marked by distinct molecular signatures. Cluster-specific open chromatin regions (OCRs) delineated putative cis-regulatory elements unique to each LepRHypo subtype. Mouse cell-type specific OCRs conserved in the human genome were identified; a subset were proximal to genes with high Human Genetic Evidence (HuGE) scores for obesity-related traits, overlapped obesity-associated GWAS loci, and/or coincided with eQTLs, including variants with the potential to influence human energy balance. Together, these data provide cell type-specific cis-regulatory atlas of LepRHypo neuronal subtypes, including Glp1r/Lepr-enriched populations, and highlight evolutionarily conserved, subtype-specific regulatory elements, associated candidate genes, and putative functional variants that may modulate LepRHypo subtype function and influence energy homeostasis and obesity susceptibility in humans.