Abstract B012: Characterizing tumor-induced exhaustion in melanoma patients treated with neoadjuvant pembrolizumab

Abstract

Immune checkpoint blockade, including anti-PD-1 therapies, has had unprecedented success in treating various forms of cancer, including melanoma. Yet the majority of patients do not achieve durable clinical remission. The limited understanding of how these therapies work at the cellular and molecular level prevents the optimization required to improve patient outcomes. We performed RNA-seq and ATAC-seq on four sorted T-cell subpopulations (naive CD8 T-cells, non-naive CD8, non-naive CD4 T-cells, T regulatory cells) from patients with metastatic melanoma before and after pembrolizumab treatment. While there were no significant changes before and after treatment in the sorted peripheral blood populations, we identified many alterations in the tumor compared to the blood following treatment. These differences may represent impediments to fully reinvigorating exhausted T-cells and be potential targets for achieving more durable clinical responses. We identified a zinc finger gene, ZC3H12C, as not only one of the most highly upregulated in non-naive CD8 T-cells in the tumor, but it also had the highest number of associated altered open chromatin regions. This gene and its locus are also significantly different in exhausted T-cells compared to effector and memory cells in a mouse model of chronic viral infection using Lymphocytic choriomeningitis (LCMV). This conservation between species suggest an important role in T-cell exhaustion and provided an avenue to test its function in vivo, so we generated ZC3H12C knockout mice using CRISPR-Cas9. Following C13 (chronic) LCMV infection, virus-specific P14 CD8 T-cells lacking ZC3H12C are unable to persist compared to wild type P14 cells. These results suggest ZC3H12C may be critical to the survival of exhausted T-cells in the tumor and their ability to persist after anti-PD1 treatment. Here, we used transcriptomic and epigenetic analysis of a clinical human cancer data set to identify a novel target and used reverse translation in a mouse model to validate its importance in T-cell exhaustion. This gene and more broadly this strategy have the potential to provide immediately useful targets for improving immunotherapies. Citation Format: Josephine R. Giles, Alexander C. Huang, Saskinath Manne, Jorge Henao-Meji, E. John Wherry. Characterizing tumor-induced exhaustion in melanoma patients treated with neoadjuvant pembrolizumab [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B012.