Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis [bulkRNA-seq]

Suppressive myeloid cells can contribute to immunotherapy resistance, but their role in response to checkpoint inhibition (CPI) in anti-PD-1 refractory cancers, such as biliary tract cancer (BTC), is largely unknown. We use multiplexed single-cell transcriptomic and epitope sequencing to profile greater than 200,000 peripheral blood mononuclear cells from advanced BTC patients (n=9) and matched healthy donors (n=8). Following anti-PD-1 treatment, CD14+ monocytes expressing high levels of immunosuppressive cytokines and chemotactic molecules (CD14CTX) increase in the circulation of patients with BTC tumors that are CPI-resistant. CD14CTX can directly suppress CD4+ T cells and induce SOCS3 expression in CD4+ T cells rendering them functionally unresponsive. The CD14CTX gene signature associates with worse survival in patients with BTC as well as in other anti-PD-1 refractory cancers. These results demonstrate that monocytes arising after anti-PD-1 treatment can induce T cell paralysis as a distinct mode of tumor-mediated immunosuppression leading to CPI resistance. We performed bulkRNAseq on peripheral blood samples for use in demultiplexing single cell RNAseq data used in our publication. RNA was extracted from minimum 2.5 x 105 cells per PBMC sample and each sample was sequenced at a depth of at least 2 x 107 reads per cell on the Illumina Novaseq S4.