Figure 1: Tumor-specific CD8+ T cells were expanded by vaccinations and isolated for genome-wide mRNA expression profiling, as described [4]. Briefly, tumor metastases (red) and peripheral blood (blue) samples were obtained from cancer patients with stage III or IV melanoma and an HLA-A*0201 allele. Patients had received monthly subcutaneous (s.c.) vaccinations of peptide Melan-A/MART-1 and adjuvant CpG emulsified in incomplete Freund’s adjuvant (IFA). Number of vaccinations varied by 2 or 5 doses. “Avg” represents the average number of days from final vaccine boost until T cell analyses. Genomewide mRNA expression was determined by microarray (Agilent) of live CD8+ T cells FAC-sorted on HLA-A2: Melan-A/MART-1 tetramer [4]. Differential gene expression between Melan-A/MART-1 specific CD8+ T cells from the tumor (TILN_hypofunctional) and blood (Tumor_PBMC) were systematically compared to previously published gene expression profiles of other CD8+ T cell subsets [5] by gene set enrichment analysis (GSEA) [4,7,8].