Abstract 1763: Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway
Authors: Nicola Pantelis A. , Burghel George , Wallace Andrew , Schlecht Helene , Baker Eleanor , Baker Katie , Priest Lynsey , Carter Mathew , Moghadam Sharzad , Rogan Jane , Bristow Robert G. , Newman William , Blackhall Fiona , Lindsay Colin R. 
Published: August 2019

Abstract
Introduction: Lung cancer is the most common cause of cancer-related death. Kirsten rat sarcoma viral oncogene (KRAS) is the most frequently mutated gene in non-small cell lung cancer (NSCLC), occurring in approximately 30% of cases. We characterised the genomic landscape of NSCLCs with an aberrant Ras-Raf-MEK-ERK pathway.
Methods: 121 Greater Manchester patients with resected NSCLC were recruited into the UK 100,000 Genomes Project (Genomics England). Whole genome sequencing (WGS) was performed on tumor specimens and matched blood samples. Data generated was processed by a standard pipeline devised by Genomics England, then mined for mutations in the Ras-Raf-MEK-ERK pathway. NF1 mutation was assessed as a positive control for RAS pathway activation. Tumor mutational burden (TMB), mutational signature profiles and copy number variation (CNV) were also obtained. Clinical characteristics including tumor size, nodal status and stage were documented. Mann-Whitney and Fisher’s exact tests were used for statistical comparisons.
Results: Cancers from 42/121 (34.7%) patients (pts) had a RAS variant, of which 40/42 (95.2%) were KRAS alterations. A single NRAS-mutant adenocarcinoma (Q61L) was identified, as was a HRAS variant, not previously observed in squamous lung cancer (Q61L). Codon 12 was the most frequently mutated KRAS site with four mutant alleles (G12C 17/40 pts, G12V 6/40, G12D 4/40, G12A 2/40). Median TMB was not significantly different between KRAS-mutant cases (8.06, range 1.84-55.2) and KRAS-wildtype samples (7.1, range 0.98-45.32) (p=0.3). Smoking-associated signature 4 was the most common mutational process (37/40 pts, median 50%, range 20-70%), appearing in a mutually exclusive fashion from the intrinsic signature 1 (3/40 pts, median 20% range 10-30%). 47/121 pts (38.8%) showed a KRAS CNV with 34/47 (72.3%) being gains. For NF1, 12/121 (9.9%) variants were identified. 6/12 (50%) were missense variants, each with a different codon affected (5/12 splice site variants, 1/12 frameshift). Median TMB was not significantly higher in NF1-mutants (NF1m: median 11.54, range 4.47-28.27; NF1 WT: median 7.1, 0.98-55.2; p=0.065) and mutational signature 4 was again the most common (11/12, median 40%, range 20-60%). 37/121(30.6%) samples showed NF1 CNV, the majority of which were surprisingly gains (25/37 pts, 67.6%). In terms of clinical outcome, neither KRAS-mutant or NF1-mutant tumors were more likely to occur in later stage III disease (KRASm: 9/30 pts, 30%, p=0.817; NF1m: 5/11 cases, 45.5%; p=0.326).
Conclusions: Approximately one half of this NSCLC cohort recruited from Greater Manchester carried a Ras-Raf-MEK-ERK pathway aberration. These KRAS-mutant tumors were often at an early stage and driven by tobacco as their main aetiological process. The mutual exclusivity of signature 4 and 1 suggests there are further complexities to be established in Ras-driven NSCLC.
Citation Format: Pantelis A. Nicola, George Burghel, Andrew Wallace, Helene Schlecht, Eleanor Baker, Katie Baker, Lynsey Priest, Mathew Carter, Sharzad Moghadam, Jane Rogan, Robert G. Bristow, William Newman, Fiona Blackhall, Colin R. Lindsay. Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1763.