Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes

Abstract

Low grade serous ovarian tumours are a rare and under-characterised histological subtype of epithelial ovarian tumours, with little known of the molecular drivers and facilitators of tumorigenesis beyond classic oncogenic RAS/RAF mutations. With a move towards targeted therapies due to the chemoresistant nature of this subtype, it is pertinent to more fully characterise the genetic events driving this tumour type, some of which may influence response to therapy and/or development of drug resistance. We performed genome-wide high-resolution genomic copy number analysis (Affymetrix SNP6.0) and mutation hotspot screening (KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53) to compare a large cohort of ovarian serous borderline tumours (SBTs, n = 57) with low grade serous carcinomas (LGSCs, n = 19). Whole exome sequencing was performed for 13 SBTs, nine LGSCs and one mixed low/high grade carcinoma. Copy number aberrations were detected in 61% (35/57) of SBTs, compared to 100% (19/19) of LGSCs. Oncogenic RAS/RAF/ERBB2 mutations were detected in 82.5% (47/57) of SBTs compared to 63% (12/19) of LGSCs, with NRAS mutations detected only in LGSC. Some copy number aberrations appeared to be enriched in LGSC, most significantly loss of 9p and homozygous deletions of the CDKN2A/2B locus. Exome sequencing identified BRAF, KRAS, NRAS, USP9X and EIF1AX as the most frequently mutated genes. We have identified markers of progression from borderline to LGSC and novel drivers of LGSC. USP9X and EIF1AX have both been linked to regulation of mTOR, suggesting that mTOR inhibitors may be a key companion treatment for targeted therapy trials of MEK and RAF inhibitors.

Keywords: borderline; copy number; exome; genomics; serous ovarian tumor.

Figure 1. Genomic aberration levels in serous ovarian tumours

A. Cumulative copy number aberrations of LGSC cohort (n = 19, top panel) and SBT (n = 57, middle panel); and copy number difference plot (lower panel). Blue indicates copy number gains while red indicates copy number losses. The solid pink bars underneath indicate regions of genomic aberration that are enriched in LGSC compared to SBT (p < 0.01, FET), while solid red bars indicate highly significant enrichment (p < 0.001, FET). B. Fraction of the genome altered and C. Intrachromosomal breakpoint counts. Data points represent individual tumours, with mean and standard deviation of each cohort plotted. For the HGSC cohorts, light grey indicates typical TP53 mutant tumour, orange indicates TP53 wildtype tumour, blue indicates RAS/RAF mutations co-occuring with TP53 mutations, black indicates RAS/RAF mutant-TP53 wildtype tumour.

Figure 2. Exome sequencing summary

A. Exome variant counts, by consequence type. B. Tumour-level SNV counts demonstrating an enrichment of the common C > T change, which is consistent with age-acquired cytosine deamination. C. Aggregate mutation signature. Peaks at NpCpG > NpTpG, with the exception of TpCpG > TpTpG.

Figure 3. Mutation patterns in low grade serous ovarian tumours

Genes recurrently mutated and cancer genes mutated in low grade serous ovarian tumours. Cancer association is based on literature; COSMIC Cancer Gene Census (accessed January 2015); IntOGen driver genes are classified as HCD, high confidence drivers or CD, candidate drivers.

Figure 4. Molecular drivers of low grade serous ovarian tumours

Proteins circled in red indicate mutated genes identified in this study. Along with the central components of the ERBB2/RAS/RAF/MAPK pathway, a number of tumours also carried concurrent mutations in regulators of the pathway.