Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses [bulk RNA-seq]

Therapeutic targeting of immune checkpoint pathways, that are exploited by tumors to evade the immune system, can result in increased overall survival for some patients with specific types of cancers. The endogenous antitumor response is limited in part by the absence of tumor-reactive T cells, an inevitable consequence of thymic central tolerance mechanisms ensuring their deletion to protect against autoimmunity. In this study, we show that compared to wild-type mice, tumor rejection induced by immune checkpoint blockade is significantly enhanced in Aire-deficient mice, the epitome of central tolerance breakdown. The observed synergy in tumor rejection extended to different tumor models and was accompanied by increased numbers of activated T cells expressing high levels of genes such as Gzma, Gzmb, Perforin, Cxcr3, and tumors contained high levels of the chemokines Cxcl9 and Cxcl10 compared to wild-type mice. Furthermore, there was an enrichment of T cells expressing markers associated with the potent anti-tumor tissue-resident memory T cells expressing Cd103. Consistent with Aire’s central role in T cells repertoire selection, single cell TCR sequencing unveiled the expansion of several clones with high tumor reactivity. Together, these results show that a break in central tolerance in combination with immune checkpoint blockade can potently enhance anti-tumor immunity and serve as a model system to unmask novel anti-tumor therapies. Tumor (B16F10) bearing Aire+/+ and Aire-/- mice were treated with anti-CTLA4 or control antibodies and harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4592014-GSM4592033). Tumor (MC38) bearing Aire+/+ and Aire-/- mice were treated with anti-PD1 or control antibodies and tumors, spleens and lymph nodes were harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4591941-GSM4592013).