Molecular Characterization of KRAS Wild-type Tumors in Patients with Pancreatic Adenocarcinoma

Abstract

Purpose: KRAS mutation (MT) is a major oncogenic driver in pancreatic ductal adenocarcinoma (PDAC). A small subset of PDACs harbor KRAS wild-type (WT). We aim to characterize the molecular profiles of KRAS WT PDAC to uncover new pathogenic drivers and offer targeted treatments.

Experimental design: Tumor tissue obtained from surgical or biopsy material was subjected to next-generation DNA/RNA sequencing, microsatellite instability (MSI) and mismatch repair status determination.

Results: Of the 2,483 patients (male 53.7%, median age 66 years) studied, 266 tumors (10.7%) were KRAS WT. The most frequently mutated gene in KRAS WT PDAC was TP53 (44.5%), followed by BRAF (13.0%). Multiple mutations within the DNA-damage repair (BRCA2, ATM, BAP1, RAD50, FANCE, PALB2), chromatin remodeling (ARID1A, PBRM1, ARID2, KMT2D, KMT2C, SMARCA4, SETD2), and cell-cycle control pathways (CDKN2A, CCND1, CCNE1) were detected frequently. There was no statistically significant difference in PD-L1 expression between KRAS WT (15.8%) and MT (17%) tumors. However, KRAS WT PDAC were more likely to be MSI-high (4.7% vs. 0.7%; P < 0.05), tumor mutational burden-high (4.5% vs. 1%; P < 0.05), and exhibit increased infiltration of CD8+ T cells, natural killer cells, and myeloid dendritic cells. KRAS WT PDACs exhibited gene fusions of BRAF (6.6%), FGFR2 (5.2%), ALK (2.6%), RET (1.3%), and NRG1 (1.3%), as well as amplification of FGF3 (3%), ERBB2 (2.2%), FGFR3 (1.8%), NTRK (1.8%), and MET (1.3%). Real-world evidence reveals a survival advantage of KRAS WT patients in overall cohorts as well as in patients treated with gemcitabine/nab-paclitaxel or 5-FU/oxaliplatin.

Conclusions: KRAS WT PDAC represents 10.7% of PDAC and is enriched with targetable alterations, including immuno-oncologic markers. Identification of KRAS WT patients in clinical practice may expand therapeutic options in a clinically meaningful manner.

Figure 1:

Molecular alterations seen in KRAS-WT tumors. 1A: Mutation rates detected by NGS. 1B: Alteration rates detected by immunohistochemistry, copy number amplification rates detected by NGS and fusion rates detected by RNA sequencing. Bars are color coded according to the oncogenic pathways of each biomarker. 1C: BRAF mutations seen in the cohort categorized into class 1, 2 and 3 based on mechanism of action.

Figure 2:

Comparison of immune checkpoint inhibitor-associated biomarkers in KRAS WT and MT tumors. An asterisk indicates a significant difference.

Figure 3:

Volcano plot comparing molecular alterations of KRAS MT vs. WT tumors. NGS: Next-Gen Sequencing detected mutations. Only molecular alterations significantly different (adjusted p<0.05) are labeled. Full results can be found in Supplemental table 4.

Figure 4:

An oncoprint displaying the molecular alteration patten of the 233 PDAC tumors. Each row represents a biomarker of either fusion, mutation or copy number amplification, as well as genomic signatures such as TMB or MSI/MMR. Red, blue and green represents TMB-H, MSI-high/MMR-deficient or mutations detected using DNA-sequencing; green represents copy number amplification detected by DNA sequencing, while navy blue represents fusions detected by RNA Sequencing. Grey represents no alteration detected while blanks represent unavailable data (indeterminate results due to low coverage or noisy signals). Bars on the right represents the prevalence of molecular alterations of each row.

Figure 5:

Comparison of Tumor Microenvironment (TME) characteristics in KRAS MT vs. WT tumors. 5A: Lymphocyte cell fractions estimated by RNA sequencing using Quantiseq.5B: Stromal cell populations estimated by RNA sequencing using MCP counter.**: significantly different after correcting for multiple comparison; * trending differences.

Figure 6:

rwOS in KRAS MT and KRAS WT tumors. 6A: overall survival (calculated from tissue collection to last day of contact) of KRAS WT compared to KRAS MT patients; 6B: overall survival of KRAS MT compared to KRAS MT patients with metastatic tumors; 6C: comparison of survival of KRAS WT patients treated with 5FU and oxaliplatin (calculated from start of treatment to last day of contact) with KRAS MT; 6D: comparison of survival of KRAS WT patients treated with gemcitabine and abraxane with KRAS MT; 6E: overall survival (from tissue collection to last day of contact) of KRAS WT patients with or without TP53 mutation.

Figure 7:

Genomic profiling of advanced pancreatic adenocarcinoma to determine targetable molecular abnormalities. Drugs with an * indicate FDA-approved agents for treatment in pancreatic adenocarcinoma. KRAS WT tumors are enriched with several targetable mutations when compared to KRAS MT tumors. Currently, olaparib approval by the FDA is limited to treating patients with germline BRCA1/2 mutations only. WT: wild type. MT: mutant. PDAC: pancreatic ductal adenocarcinoma. SOC: standard of care.