CD8+ T cells maintain killing of MHC-I-negative tumor cells through the NKG2D-NKG2DL axis

Pan-Cancer Atlas mRNA expression matrix was downloaded from Cancer Illumina HiSeq data was downloaded from the PanCanAtlas (TCGA) and samples were analyzed for mutations within the B2M gene. Analysis was performed using R (v. 4.2.2). RNA sequencing data from those patients with the B2M mutations (n=132) were compared to RNA sequencing data from 200 patients that were randomly subset from the remaining 10327 patients within the PanCanAtlas dataset. Differential gene expression was evaluated using DeSeq2 (v. 1.38.3).. Differential expression analyses p values were corrected for multiple testing using Benjamini-Hochberg false discovery rate (FDR). Log2(Fold Change) and Benjamini and Hochberg adjusted p values for each gene were plotted using ggplot2 (v. 3.4.2). NKG2D ligands were specifically highlighted to assess expression of ligands in B2M mutant compared to B2M wildtype tumors.