Multimodal single-cell profiling identifies nclTECs and links chromatin remodeling to TEC differentiation and self-antigen expression modes.

The thymic epithelium consists of a diverse set of cells that generate tissue-restricted antigens (TRAs) for presentation to developing thymocytes, ensuring selection of functional and self-tolerant T cell receptors. Combining single-cell multimodal profiling and immunofluorescence microscopy, we characterize the cellular heterogeneity and chromatin accessibility landscape of human pediatric thymic epithelial cells (TECs) and infer regulatory programs underlying their differentiation and TRA expression. We describe a NEURL2+ cTEC-like population (nclTECs), which we suggest facilitates thymocyte maturation and comprises both progenitors and thymic nurse cells. We also report two mTEC(III) populations, exhibiting different localization and morphological features. Further, we reveal substantial changes in chromatin accessibility along predicted TEC differentiation trajectories and propose a model in which distinct chromatin landscapes reflect regulatory mechanisms controlling TRA expression. Our results contribute to a framework for understanding TEC differentiation and function in immune disease and cancer and may guide thymus-based therapeutic strategies.