A pan-cancer profiling of somatic mutations and tumor microenvironment to reveal mutation dependent immunophenotypic signature differences in KRAS.

Abstract

e14526 Background: The ubiquity of tumor genotyping has identified hundreds of clinically actionable somatic mutations such as KRAS mutations predicting anti-EGFR response in colorectal cancer. Here, we describe an integrative pan-cancer study leveraging the Personalis NeXT Platform across 13 tumor types to reveal a broad portrait of clinically relevant mutations across 36 genes. Given the ascendance of tumor immunotherapy, there is an urgent need to better elucidate associations between clinically relevant gene mutations, patient demographics, and tumor immunobiology. Methods: Paired tumor-normals (n > 450) were sequenced on the Personalis NeXT Platform, a diagnostic platform which simultaneously profiles tumor and immune microenvironments via exome and transcriptome sequencing. Samples were evaluated for the presence of KRAS variants at the G12, G13, and Q61 positions, requiring a minor allele frequency of more than 2%. Additionally, more than 200 clinically relevant amino acid changes were considered across 36 genes. DNA sequencing data was harnessed to profile MSI status, oncovirus status, HLA allele-specific LOH, SNVs, and neoantigens. RNA sequencing data furnished profiles for gene expression, TILs, TCR, BCR, and immune signatures. Statistical tests compared both the presence of clinically relevant mutations, and specific amino acid changes, to each of these DNA and RNA derived features. Results: Immunogenomic analysis with the Personalis NeXT Platform identified KRAS mutations at the G12, G13, and Q61 positions in 6 of the 13 tumor types, including bladder, CRC, liver, NSCLC, pancreatic, and uterine cancers, consistent with known KRAS allelic incidence. 11 different KRAS amino acid substitutions were identified in this cohort, including G12(A/C/D/R/S/V), G13(C/D), and Q61(H/K/L), with 14% of samples positive for KRAS variants across our pan-cancer cohort, including malignancies not associated with KRAS. Immune signatures, including TCRB clones, mutational burden, and TILs signatures demonstrated variability in a KRAS allele-dependent manner. Pancreatic cancers demonstrated a statistically significant increase in macrophage enrichment score (p < 0.001) in KRAS-mutant tumors. Conclusions: Utilizing the Personalis NeXT Platform, our analysis characterized the tumor microenvironment of over 460 samples across 13 tumor types, 36 genes, and over 200 clinically relevant amino acid substitutions. This comprehensive characterization demonstrated significant differences in immune cell signatures in pancreatic cancer, suggestive of an association between the presence of KRAS mutations and immune cell infiltrate composition.