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. Autoimmunity is present in one third of patients at diagnosis. In this study, we performed a phenotypic, single-cell RNA sequencing and spatial analysis of both the T cells and tumoral cells. T cells at all stages of T-cell development-from immature to mature-were present in the tumor, suggesting active thymopoiesis in thymoma. However, data generated through multiple approaches suggested a maturation blockade at the double-negative to double-positive stage of T-cell development. In the mature T-cell compartment, the frequency of regulatory T cells was strongly decreased. The single-cell RNA sequencing analysis showed that the transcriptome of tumoral thymic epithelial cells (TEC) was most similar to that of nontumoral medullary TEC, but the expression of key molecules involved in positive and negative selection was defective. Multiplexed IHC consecutive staining revealed a loss of the cortex-medulla zoning in thymoma, which may be related to a decrease in the expression of T cell-targeted chemokines by tumoral TEC. Altogether, these results suggest that the thymopoiesis present in thymoma is abnormal and may be the cause of the prevalent autoimmunity observed in this disease.