1. Somatic promoters correlate with immunoediting signatures.
Somatic promoters correlate with immunoediting signatures. A, Schematic outlining alternative promoter usage [H3K4me3 box, overlapping gastric cancer (GC) in red and normal gastric tissue in blue] leading to alternative transcript usage (transcript box) and N-terminally truncated protein isoforms (protein box). B, Bar plot showing the average percentage of peptides with predicted high-affinity binding to MHC class I (HLA-A, B, and C, IC50 ≤ 50 nmol/L). N-terminal peptides associated with recurrent somatic promoters (alternative promoters) show significantly enriched predicted MHC I binding compared with canonical gastric cancer peptides (P < 0.01, Fisher test), random peptides from the human proteome (P < 0.001), and C-terminal peptides (P < 0.01) derived from the same genes exhibiting the N-terminal alterations. Canonical peptides refer to peptides derived from protein-coding genes overexpressed in gastric cancer through nonalternative promoters. C, Percentage (%) of high-affinity peptides predicted to bind different patient-specific HLA alleles categorized by somatic gain or loss. Most alleles have a greater number of N-terminal lost peptides predicted to have high binding affinity. The percentage of patients bearing specific HLA alleles is denoted inside the brackets. D, Quantification of somatic promoter expression using NanoString profiling. Top, distinct NanoString probes were designed to measure the expression of alternate and canonical promoter–driven transcripts. Two probes were designed for each gene, a canonical probe at the 5′ transcript marked by unaltered H3K4me3, and an alternate probe at the 5′ transcript of the somatic promoter. Bottom, heat map of alternative promoter expression from 95 gastric cancer and matched normal samples. Gastric cancer samples have been ordered left to right by their levels of somatic promoter usage. E, Association between somatic promoters and T-cell immune correlates. NS, not significant. Samples with high somatic promoter usage are in red, whereas those with low usage are in blue. Top left, expression of T-cell markers CD8A (P = ) and the T-cell cytolytic markers GZMA (P = ) and PRF1 (P = ) in gastric cancer samples with either high or low somatic promoter usage (SG cohort). Samples with high alternative promoter usage show lower expression of immune markers. All P values are from Wilcoxon one-sided test. Top right, Kaplan–Meier analysis comparing overall survival curves between validation samples with high somatic promoter usage (top 25%) and low somatic promoter usage (bottom 25%; HR = 2.56, P = 0.02). Bottom left, expression of T-cell markers CD8A (P = 0.02), GZMA (P = 0.01), and PRF1 (P = 0.03) in TCGA STAD with either high or low somatic promoter usage. T-cell markers were evaluated by RNA-seq [transcripts per million (TPM)]. Bottom right, expression of T-cell markers CD8A (P = 0.035), GZMA (P = 0.001), and PRF1 (P = 0.025) in Asian Cancer Research Group (ACRG) gastric cancer samples with either high or low somatic promoter usage. All P values are from Wilcoxon one-sided test. F, EPIMAX heat map of total cytokine responses (fold change relative to actin) for 15 peptide pools against 9 donors. G, Individual cytokine responses against 15 peptides for two individual donors (donor 2 and donor 3) showing complex cytokine responses (FC ≥ 2). *, P < 0.05; **, P < 0.01; ***, P <
Aditi Qamra et al. Cancer Discov 2017;7:
©2017 by American Association for Cancer Research