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. 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).