Single cell ATAC-sequencing analysis of human SUV39H1-knockout CAR T compared to control CAR T cells (mock) in a xenograft model of lung adenocarcinoma

We have observed that the inactivation of SUV39H1 enhances 41BBz-CAR T cell long-term persistence, providing protection against tumor relapses and rechallenges in a xenograft mouse model of lung adenocarcinoma. The purpuse of this study was to profile chromatin accessibility of SUV39H1-deficient compared to mock 41BBz-CAR T cells by single-cell assay for transposase accessible chromatin (scATAC-seq) on FACS-sorted T cells eight days after CAR T cell infusion into the mice. Overall design: NSG mice that received intravenous injections of tumor cells (A549) ectopically expressing CD19 that develop tumors in the lungs, were treated 21 days later with 0,9 million of 41BBz-CAR T cells (i.v.) that were SUV39H1-knockout (CRISPR/Cas9 technology) or controls CAR T cells (same CRISPR/Cas9 protocol with a sgRNA that does not have any complimentary sequence in the genome). CAR T cells were isolated from lungs at day 8 after infusion, T-cells were FACS sorted and subjected to Chromium Single Cell ATAC protocol (for each condition there were three biological replicates from pooled mice).