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

We utilized bulk RNA sequencing to assess intrinsic differences between wildtype and autophagy-defective (Atg16l1 deleted) AKPS colorectal cancer organoids in both untreated and IFN gamma treated conditions. AKPS mutations consist of loss-of-function in tumor suppressors Apc, Trp53, Smad4, and gain-of-function in oncogenic Kras(G12D). Overall design: Examination of 2 clones from Atg16l1-wildtype and Atg16l1-deleted AKPS colorectal cancer organoids, with or without IFN gamma treatment. There are two technical replicates from each clone for each one of the four conditions (WT untreated, WT treated, KO untreated, KO treated)