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

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.