RNA sequencing of primary acute lymphoblastic leukemia xenograft brains with and without treatment with chimeric antigen receptor T (CAR-T) cell therapy

NSG mice were IP injected with 30mg/kg busulfan. The following day, mice received 1,000,000-3,000,000 primary blasts derived from the peripheral blood of patients with ALL. Mice were monitored for engraftment for ~10-13 weeks via tail vein bleeding for engraftment. Some mice received high dose CAR-T cell therapy and an isotype control antibody treatment. RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA). RNA-seq analyses of brain sections harvested from mice treated with CAR-T cells showed significant upregulation of genes regulating the T cell receptor, cytokine receptors, T cell immune activation, T cell trafficking, and T cell and myeloid cell differentiation. Xenografts treated with CAR-T cell therapy developed neurotoxicity. Overall design: RNA sequencing was performed on brain tissue of NSG primary acute lymphoblastic leukemia (ALL) xenografts with and without CAR-T cell treatment using three biological replicates for each condition