Gene Set Enrichment Analysis (GSEA) was performed comparing Grade 3 vs. Grade 1+2 tumors, using the Hallmark gene sets (36 (link)) with the software provided by the Broad Institute (https://software.broadinstitute.org/gsea/index.jsp ), as described before (23 (link)–25 (link), 29 (link)).
Measurements of immune activities, such as relative fractions of different types of immune cells in TME or T cell receptor (TCR) diversity, were estimated from tumor gene expression with CIBERSORT, a bioinformatic algorithm using the TCGA-BRCA cohort (37 (link)). The counts of neoantigen load were represented as Insertion and deletion (Indel) mutation, which was collated from the Pan-Cancer Atlas study of Thorsson et al (37 (link)). Cytolytic activity score (CYT) was defined as the geometric mean of grandzyme A (GZMA) and Perforin 1 (PRF1) expression values in transcripts per million (TPM), as described previously (38 (link), 39 (link)). Additionally, given METABRIC and GSE25066 transcriptomes were derived from the microarray, we used the geometric mean of GZMA and PRF1 expression values to estimate cytolytic activity in these two cohorts.
Measurements of immune activities, such as relative fractions of different types of immune cells in TME or T cell receptor (TCR) diversity, were estimated from tumor gene expression with CIBERSORT, a bioinformatic algorithm using the TCGA-BRCA cohort (37 (link)). The counts of neoantigen load were represented as Insertion and deletion (Indel) mutation, which was collated from the Pan-Cancer Atlas study of Thorsson et al (37 (link)). Cytolytic activity score (CYT) was defined as the geometric mean of grandzyme A (GZMA) and Perforin 1 (PRF1) expression values in transcripts per million (TPM), as described previously (38 (link), 39 (link)). Additionally, given METABRIC and GSE25066 transcriptomes were derived from the microarray, we used the geometric mean of GZMA and PRF1 expression values to estimate cytolytic activity in these two cohorts.
