Dissecting the impact of cancer cell plasticity on T-cell mediated anti-tumor immunity and response to immune checkpoint blockade

Abstract

Immune-checkpoint blockade (ICB) has revolutionized cancer treatments by taking the breaks off of T cells capable of killing cancer cells. However, some solid tumor types, including ovarian cancer and breast cancer, have low response rates to ICB [Zou2020, Hamanishi2021]. Additional mechanisms of immune resistance remain to be understood. We asked how tumor cell plasticity, such as epithelial-to-mesenchymal transition (EMT), and tumor-immune interactions in the tumor environment (TME) affect response to immunotherapy. In ovarian cancer, anti-PD1 treated tumors underwent faster EMT progression, and mesenchymal cancer cells upregulated inflammatory pathways. The transcription factor Cebpb was a key driver of the EMT-associated inflammatory program, and genetic inactivation of Cebpb synergized with anti-PD1 therapy. Using CUT&RUN, we found that Cebpb synergized with NF-kB subunit Rela to co-regulate NF-kB and IL6-Stat3 pathways. Cebpb inactivation shifted the tumor cells and macrophages from NF-kB signaling towards interferon signaling, and improved tumor-infiltrating T cell function. EMT also played a role in breast cancer resistance to immunotherapy. Through in vitro and in vivo CRISPR/Cas9 screens, we identified Slc35a2 and Tmem165-mediated altered glycosylation drove mesenchymal-like cancer cell resistance to T cell killing. Inactivation of Slc35a2 or Tmem165 inhibited breast cancer metastasis, and synergized with ICB. Mechanistically, altered N-linked glycosylation, especially hyper-sialylation, formed a negatively-charged glyco-shield on mesenchymal tumor cells to restrain immune synapse formation and reduce anti-tumor T cell killing. In a third project, we found that CDK2 inhibitor tegtociclib, being tested in CCNE1-amplified ovarian and breast cancers, promoted interferon signaling in diverse tumor types. CDK2 inhibition activated BRD4 to upregulate interferon stimulated genes. CDK2 inhibition synergized with ICB by promoting T cell and dendritic cell anti-tumor function, suggesting the potential use of combining CDK2 inhibitor with immunotherapy. In summary, we presented 3 approaches of targeting tumor cell mechanisms of immune evasion, each of which might synergize with ICB in combination.