A Comprehensive Framework for Systems Immune Monitoring in Patients with Cancer

Abstract

The immune system is a complex network of cells spread throughout the body, spanning dozens of tissue types and locations. A complete understanding of a systemic immune response, like those required for the regression of malignant tumors, requires the ability to monitor not only individual cellular populations with various phenotypes and functional states, but also the immune network as a whole. Traditional approaches that focus on one cell type or one protein of interest over look cells of unusual or unexpected phenotype. In order to better understand the systemic immune response in human patients, mass cytometry tools were developed and applied to samples from cancer patients. This single-cell biology results in the measurement of >40 protein features on millions of immune cells within clinical samples. The analysis required to interpret the resulting data is susceptible to bias, time-consuming, and challenging to compare across studies. Here, an ensemble of unsupervised tools was developed to evaluate four essential types of immune cell information, incorporate change over time, and address diverse immune monitoring challenges. The four complementary properties characterized were: 1) systemic plasticity, 2) change in population abundance, 3) change in signature population features, and 4) novelty of cellular phenotype. Three systems immune monitoring studies were selected to challenge this ensemble approach. In serial biopsies of melanoma tumors undergoing targeted therapy, the ensemble approach revealed enrichment of double-negative (DN) T cells. Melanoma tumor resident DN T cells were abnormal and phenotypically distinct from those found in non-malignant lymphoid tissues, but similar to those found in glioblastoma and renal cell carcinoma. Overall, ensemble systems immune monitoring provided a robust, quantitative view of change in both the system and cell subsets, allowed transparent review by human experts, and revealed abnormal immune cells present across multiple human tumor types.