Altered thymopoiesis in thymoma is associated with defects in negative selection machinery and decreased Treg abundance

Thymomas are rare thymic epithelial tumors harboring a high but variable proportion of lymphocytes without obvious function. Auto-immunity is present in one third of patients at diagnosis. Herein, we performed a phenotypic, scRNAseq, and spatial analysis of both the T cells and tumoral cells. All stages of T cell development -from immature to mature- were present in the tumor suggesting active thymopoiesis in thymoma. However, multiple approaches suggest a maturation blockade at the DN-DP stages. In the mature T cell compartment, the frequency of Tregs was strongly decreased. Notably according to scRNAseq, the transcriptome of tumoral Thymic Epithelial Cells (tTEC) was most similar to that of non-tumoral medullary TEC but the expression of key molecules involved in positive and negative selection was defective. Multiplexed Immunohistochemical Consecutive Staining evidenced a loss of the cortex-medulla zoning in thymoma which may be related to a decrease expression of T cell targeted chemokines by tTEC. Altogether, these results suggest that the thymopoiesis present in thymoma is abnormal and may provide the grounds for the prevalent auto-immunity observed in this disease.