Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes.
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.
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.
Sally M
SM
Hunter
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
Michael S
MS
Anglesio
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.
Georgina L
GL
Ryland
Anatomical Pathology, University of Sydney and University of Western Sydney at Westmead Hospital, Westmead, Australia.
Raghwa
R
Sharma
Department of Gynaecological Oncology, Westmead Hospital, Westmead, Australia.|Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, Westmead Hospital, Westmead, Australia.
Yoke-Eng
YE
Chiew
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.
Simone M
SM
Rowley
Bioinformatics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
Maria A
MA
Doyle
Bioinformatics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
Jason
J
Li
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.|Genetic Pathology Evaluation Centre, Vancouver General Hospital, Vancouver, Canada.
C Blake
CB
Gilks
Anatomical Pathology, Peter MacCallum Cancer Centre, East Melbourne, Australia.|Current address: Saint John Regional Hospital, North Brunswick, Canada.
Phillip
P
Moss
Anatomical Pathology, Peter MacCallum Cancer Centre, East Melbourne, Australia.
Prue E
PE
Allan
Centre for Cancer Research, MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia.|Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia.|Epworth Research Institute, Epworth HealthCare, Richmond, Victoria, Australia.
Andrew N
AN
Stephens
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
David G
DG
Huntsman
Department of Gynaecological Oncology, Westmead Hospital, Westmead, Australia.|Centre for Cancer Research, University of Sydney at Westmead Millennium Institute, Westmead Hospital, Westmead, Australia.
Anna
A
deFazio
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.|The Department of Pathology, University of Melbourne, Parkville, Australia.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.
David D
DD
Bowtell
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.|The Department of Pathology, University of Melbourne, Parkville, Australia.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.
Kylie L
KL
Gorringe
Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Australia.|The Department of Pathology, University of Melbourne, Parkville, Australia.|The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.
Ian G
IG
Campbell
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D018284:Cystadenocarcinoma, Serous / Q000235:genetics* / Q000473:pathology; D059472:Exome / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D014644:Genetic Variation / Q000235:genetics*; D006801:Humans; D008875:Middle Aged; D060787:Neoplasm Grading; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000473:pathology; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D055815:Young Adult
D014408:Biomarkers, Tumor; D012333:RNA, Messenger
borderline; copy number; exome; genomics; serous ovarian tumor