Molecular heterogeneity and differential metabolic signatures in thymic adipocytes

Adipocyte depots throughout the body are physiologically and molecularly distinct. With age, adipocytes increase in and around aged thymi. Yet thymic adipocytes lack molecular characterization. We developed methods to isolate adipocyte nuclei from mouse thymi. Single-nucleus multi-omic analysis of male and female mice aged 4-9 months reveals that thymic adipocytes are heterogeneous, with two distinct populations. One subpopulation harbors a transcription and chromatin signature consistent with beige fat. Another subpopulation resembles classic white adipose tissue and expresses genes associated with epithelial-to-mesenchymal transition (EMT). Analysis of differentially open chromatin identifies binding sites for Foxn1 and HIF-1α/Arnt in the white adipose population, consistent with a thymic epithelial and/or hypoxic origin for these cells. Immunofluorescence confirmed the expression of UCP1 protein in cells in subcapsular cortical regions of the thymic parenchyma. This resource reveals a complex milieu of thymic adipocytes and identifies multiple avenues for probing their ontogeny, dynamics, and functional significance.