Data from Immunogenetic Metabolomics Reveals Key Enzymes That Modulate CAR T-cell Metabolism and Function

Abstract

<div>Abstract<p>Immune evasion is a critical step of cancer progression that remains a major obstacle for current T cell–based immunotherapies. Hence, we investigated whether it is possible to genetically reprogram T cells to exploit a common tumor-intrinsic evasion mechanism whereby cancer cells suppress T-cell function by generating a metabolically unfavorable tumor microenvironment (TME). In an <i>in silico</i> screen, we identified <i>ADA</i> and <i>PDK1</i> as metabolic regulators. We then showed that overexpression (OE) of these genes enhanced the cytolysis of CD19-specific chimeric antigen receptor (CAR) T cells against cognate leukemia cells, and conversely, <i>ADA</i> or <i>PDK1</i> deficiency dampened this effect. <i>ADA</i>-OE in CAR T cells improved cancer cytolysis under high concentrations of adenosine, the ADA substrate, and an immunosuppressive metabolite in the TME. High-throughput transcriptomics and metabolomics analysis of these CAR T cells revealed alterations of global gene expression and metabolic signatures in both <i>ADA-</i> and <i>PDK1</i>-engineered CAR T cells. Functional and immunologic analyses demonstrated that <i>ADA</i>-OE increased proliferation and decreased exhaustion in CD19-specific and HER2-specific CAR T cells. ADA-OE improved tumor infiltration and clearance by HER2-specific CAR T cells in an <i>in vivo</i> colorectal cancer model. Collectively, these data unveil systematic knowledge of metabolic reprogramming directly in CAR T cells and reveal potential targets for improving CAR T-cell therapy.</p></div>