Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer (single cell RNA-seq)

We utilized 10X single cell RNA sequencing to investigate in murine liver how Atg16l1 deletion in AKPS colorectal cancer organoids impacted phenotypic programming of organoid cells and myeloid cells in the tumor microenvironment. Atg16l1 KO and Wt cells were inoculated into the liver of NSG mice via HTV injection. Tumors were harvested following ~3 weeks of growth and live Calcein blue+ 7ADD– cells were sorted into tumor (eGFP+CD45–) and immune (eGFP–CD45+) cells. Overall design: Two mice each were inoculated with Atg16l1 wildtype and knockout organoids. Cells from each mouse were sorted into tumor and immune cells. Cells from two mice were then pooled to generate 4 samples (one each) for Atg16l1 wildtype tumor cells, Atg16l1 knockout tumor cells, immune cells from Atg16l1 wildtype tumor microenvironment, and immune cells from Atg16l1 knockout tumor microenvironment.