Transcriptional profiling of tumor microenvironment in B2M KO CD40-treated B16 tumors implanted in mice

The immune changes induced by loss of antigen presentation by tumor cells, a common mechanism of acquired resistance to immunotherapy, as well as the mechanisms by which CD40 agonist treatment controls the growth of B2m-null tumors, are unknown. We performed single-cell RNA-seq of total tumor-infiltrating immune cells in control and B2m-null tumors treated with isotype control or CD40 agonist antibodies to identify changes in immune cell states due to tumor cell loss of B2m and agonist CD40 treatment. Overall design: C57BL/6J mice were implanted subcutaneously with 1 x 10^6 B2m-null or control Bro4.1 B16 cells. Mice were treated via intraperitoneal injection with either 100mcg anti-CD40 or rat IgG2a isotype control antibody on days 6, 9, and 12 post tumor implantation. Mice were euthanized on day 14, tumors harvested and immune cells isolated for single-cell RNA-sequencing. Prior to running on the 10x Chromium, cells from individual mice were stained with cell hashtag antibodies and then individual mice from each experimental group were mixed together to run on a single Chromium lane.