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

Abstract

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. Herein, we performed a phenotypic, single-cell RNA sequencing (scRNAseq), 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 scRNAseq analysis showed that 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 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 tTEC. 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.