Integrated Single-Nucleus and Epigenomic Profiling Reveals Coordinated Neuro-Glial and Chromatin Remodeling in the Type 2 Diabetic Hypothalamus

Abstract

Highlights What are the main findings? • Integrated single-nucleus transcriptomic and tissue-level chromatin accessibility profiling identifies coordinated neuronal, oligodendrocyte-lineage, and regulatory remodeling in the hypothalamus of an HFD/STZ-induced T2D mouse model.• Multi-omic evidence highlights activation of the Npy regulatory axis and identifies an increased Cntnap2-positive oligodendrocyte-lineage transcriptional state associated with altered predicted neuron–glia communication. What are the implications of the main findings? • The study extends the cellular landscape of diabetes-associated hypothalamic remodeling beyond neuronal populations by implicating oligodendrocyte-lineage states and neuro–glial signaling networks.• The Npy-associated transcriptional and chromatin changes and the Cntnap2-positive oligodendrocyte-lineage state provide testable molecular and cellular features for future studies of hypothalamic metabolic regulation and neuron–glia interactions in diabetes. Abstract The hypothalamus is a central regulator of systemic energy balance and glucose homeostasis, yet how type 2 diabetes (T2D) alters its cellular and regulatory landscape remains incompletely understood. Here, we integrated single-nucleus RNA sequencing (snRNA-seq) with bulk ATAC-seq to characterize hypothalamic remodeling in an HFD/STZ-induced T2D mouse model. High-resolution snRNA-seq revealed pronounced cell type-specific alterations involving several neuronal subpopulations, including Gal.Nts.Npy, Nxph4.Adcyap1, and Lmx1a.Gpr149.Tcf4 neurons, together with substantial changes in oligodendrocyte-lineage cells. Increased Npy expression was accompanied by greater tissue-level chromatin accessibility at the Npy locus, providing convergent evidence for activation of the hypothalamic Npy regulatory axis. Pseudotime analysis further showed increased representation of a transcriptionally distinct Cntnap2-positive oligodendrocyte-lineage state, together with reduced representation of canonical myelination-associated states. Ligand–receptor analysis predicted reduced signaling across selected neuron–oligodendrocyte interactions and altered communication among glial populations. Collectively, these findings reveal coordinated neuronal, oligodendrocyte-lineage, intercellular signaling, and chromatin-accessibility alterations in the diabetic hypothalamus, and identify the Npy regulatory axis and Cntnap2-positive oligodendrocyte-lineage state as candidate features for further mechanistic investigation.