Factors contributing to Chimeric Antigen Receptor T-cell Therapy efficacy in pediatric oncology patients

Immune cell populations are composed of multiple cell types and their functions are tightly connected through their interactions. Cancer immunotherapy enhances the immune system's ability to recognize and fight cancer and diminish cancer's ability to evade the immune system. In Chimeric Antigen Receptor T-cell (CAR-T) therapy, T-cells are engineered to eliminate cancer cells by targeting cell surface markers. Problems with CAR-T therapy include relapse due to loss of persistence of CAR-T cells and loss of CD19 expression on leukemia cells. The mechanisms of CAR-T failure need to be elucidated and exploring these mechanisms will identify potential treatment options and improve outcomes. Utilizing single-cell RNA seq (scRNA-seq), we investigated the interactions between CAR-T cells and the immune cells in pediatric ALL patients who've received CAR-T therapy. We analyzed the lymphocyte composition and gene expression profile at different time-points of ALL patients through CAR-T cell therapy. We have compared this data in responders with relapse patients after CAR-T infusion. Focusing on significantly altered immune cell populations and their gene markers, we employ in vitro and in vivo models to validate their function. Overall design: PBMC or BMMC from the patients' blood or bone marrow were isloated by EasySep™ Direct Human PBMC Isolation Kit following the manufacturer's instructions. Then they were used for single-cell RNA-Seq library generation by 10X Genomics Chromium Single Cell 3' Reagent kit (V2/V3). The library were sequenced by HiSeq 4000/Novaseq at the IGM Genomics core, UCSD.