Single-cell profiling of natural killer and innate lymphoid cells in thymic epithelial tumors

Thymic epithelial tumors (TETs) are rare and heterogeneous tumors arising from thymic epithelial cells. According to the World Health Organization, TETs are classified as thymomas, further divided into A, AB, B1, B2 and B3 histotypes, and thymic carcinomas (TCs), with a worsening of the prognosis as the lesion progresses from A thymomas to TC. Notably, thymomas show a strong association with autoimmune disorders and immunotherapy-related adverse reactions, posing significant challenges to the effective use of this treatment. Using flow cytometry and single-cell RNA sequencing, we profiled intratumoral and circulating immune cells of 64 TET patients compared with 14 healthy controls. TETs characterized by active intratumoral thymopoiesis, namely type AB, B1 and B2 thymomas, showed negligible NK cell infiltration. In contrast, type A and B3 thymomas, along with TCs, showed higher amounts of infiltrating NK cells. In A and B3 thymomas, CD56bright NK cells and innate lymphoid cells predominated, whereas TCs were mostly enriched in CD56dim NK cells. Compared with A and B3 thymomas, NK cells in TCs showed a more cytotoxic and effector profile, which was however tempered by an increased expression of immune checkpoints. Overall, these findings highlight a potential role of NK cells in shaping the anti-tumoral immune response in TETs, suggesting that NK cells may contribute to the worse prognosis of TCs and represent promising target of immunotherapeutic approaches.