Low-grade serous ovarian carcinoma (LGSOC) is associated with a poor response to existing chemotherapy, highlighting the need to perform comprehensive genomic analysis and identify new therapeutic vulnerabilities. The data presented here represent the largest genetic study of LGSOCs to date (n = 71), analysing 127 candidate genes derived from whole exome sequencing cohorts to generate mutation and copy-number variation data. Additionally, immunohistochemistry was performed on our LGSOC cohort assessing oestrogen receptor, progesterone receptor, TP53, and CDKN2A status. Targeted sequencing identified 47% of cases with mutations in key RAS/RAF pathway genes (KRAS, BRAF, and NRAS), as well as mutations in putative novel driver genes including USP9X (27%), MACF1 (11%), ARID1A (9%), NF2 (4%), DOT1L (6%), and ASH1L (4%). Immunohistochemistry evaluation revealed frequent oestrogen/progesterone receptor positivity (85%), along with CDKN2A protein loss (10%) and CDKN2A protein overexpression (6%), which were linked to shorter disease outcomes. Indeed, 90% of LGSOC samples harboured at least one potentially actionable alteration, which in 19/71 (27%) cases were predictive of clinical benefit from a standard treatment, either in another cancer's indication or in LGSOC specifically. In addition, we validated ubiquitin-specific protease 9X (USP9X), which is a chromosome X-linked substrate-specific deubiquitinase and tumour suppressor, as a relevant therapeutic target for LGSOC. Our comprehensive genomic study highlighted that there is an addiction to a limited number of unique ‘driver’ aberrations that could be translated into improved therapeutic paths. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Data availability statement
The datasets analysed in the current study are available from the corresponding author, with requests for access subject to review by the COEUR Study Committee.
|path5545-sup-0001-SuppMatMeth.docxWord 2007 document , 54.7 KB||
Supplementary materials and methods
|path5545-sup-0002-SuppFiguresS1-S4.docxWord 2007 document , 12.8 MB||
Figure S1. Combined genomic and clinicopathological analysis
Figure S2. Analysis of loss of heterozygosity and allelic imbalance across chromosome X, including USP9X
Figure S3. Bisulphite sequencing of LGSOC tumours within the USP9X promoter region
Figure S4. Copy-number analysis of USP9X mutant tumours
|path5545-sup-0003-SuppTablesS1-S7.xlsxExcel 2007 spreadsheet , 235.1 KB||
Table S1. Clinical characteristics of the LGSOC cohort
Table S2. Inclusion criteria for genes on the targeted LGSOC SureSelect panel
Table S3. Sequencing metrics
Table S4. Tumour sequencing metrics
Table S5. Variants observed and associated cancer signalling pathways
Table S6. USP9X immunohistochemistry and expression evaluation on the COEUR tissue microarray
Table S7. Significant CN gains and losses across the LGSOC cohort
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
- 1, , , et al. Stage II to IV low-grade serous carcinoma of the ovary is associated with a poor prognosis: a clinicopathologic study of 32 patients from a population-based tumor registry. Int J Gynecol Pathol 2013; 32: 529–535.
- 2, , , et al. Characteristics and outcome of the COEUR Canadian validation cohort for ovarian cancer biomarkers. BMC Cancer 2018; 18: 347.
- 3, , , et al. A survival analysis comparing women with ovarian low-grade serous carcinoma to those with high-grade histology. Onco Targets Ther 2014; 7: 1891–1899.
- 4, , , et al. Neoadjuvant chemotherapy for low-grade serous carcinoma of the ovary or peritoneum. Gynecol Oncol 2008; 108: 510–514.
- 5, , , et al. Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes. Oncotarget 2015; 6: 37663–37677.
- 6, , , et al. Genome-wide analysis of gynecologic cancer: The Cancer Genome Atlas in ovarian and endometrial cancer. Oncol Lett 2017; 13: 1063–1070.
- 7, , , et al. EIF1AX and NRAS mutations co-occur and cooperate in low-grade serous ovarian carcinomas. Cancer Res 2017; 77: 4268–4278.
- 8, , , et al. Low-grade serous carcinomas of the ovary contain very few point mutations. J Pathol 2012; 226: 413–420.
- 9, , , et al. Genomic classification of serous ovarian cancer with adjacent borderline differentiates RAS pathway and TP53-mutant tumors and identifies NRAS as an oncogenic driver. Clin Cancer Res 2014; 20: 6618–6630.
- 10, , , et al. Specimen quality evaluation in Canadian biobanks participating in the COEUR repository. Biopreserv Biobank 2013; 11: 83–93.
- 11, , , et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 2013; 43: 11.10.1–11.10.33.
- 12, , , et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet 2014; 46: 912–918.
- 13, , , et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012; 22: 568–576.
- 14, , , et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 2014; 24: 2022–2032.
- 15, , , et al. Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs. Breast Cancer Res 2018; 20: 3.
- 16, , , et al. Population-based genetic testing of asymptomatic women for breast and ovarian cancer susceptibility. Genet Med 2019; 21: 913–922.
- 17, , , et al. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol 2015; 16: 49.
- 18 Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609–615.
- 19, , , et al. Comparison of expression profiles in ovarian epithelium in vivo and ovarian cancer identifies novel candidate genes involved in disease pathogenesis. PLoS One 2011; 6: e17617.
- 20, , , et al. Impact of age and primary disease site on outcome in women with low-grade serous carcinoma of the ovary or peritoneum: results of a large single-institution registry of a rare tumor. J Clin Oncol 2015; 33: 2675–2682.
- 21, , , et al. KRAS/BRAF analysis in ovarian low-grade serous carcinoma having synchronous all pathological precursor regions. Int J Mol Sci 2016; 17: 625.
- 22, , , et al. Association of p16 expression with prognosis varies across ovarian carcinoma histotypes: an Ovarian Tumor Tissue Analysis consortium study. J Pathol Clin Res 2018; 4: 250–261.
- 23, . ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Mol Biosyst 2016; 12: 477–479.
- 24, . Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet 2011; 88: 440–449.
- 25, , . Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet 2013; Chapter 7: Unit7.20.
- 26, , . Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009; 4: 1073–1081.
- 27, , , et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014; 46: 310–315.
- 28, , , et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet 2016; 99: 877–885.
- 29, , , et al. Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary. J Pathol 2010; 221: 49–56.
- 30, , , et al. OncoKB: A Precis Oncology Knowledge Base. JCO Precis Oncol 2017; 1: PO.17.00011.
- 31, , , et al. Selumetinib in women with recurrent low-grade serous carcinoma of the ovary or peritoneum: an open-label, single-arm, phase 2 study. Lancet Oncol 2013; 14: 134–140.
- 32, , , et al. BRAF mutations in low-grade serous ovarian cancer and response to BRAF inhibition. JCO Precis Oncol 2018; 2: 1–14.
- 33, , , et al. Microtubule actin cross-linking factor 1, a novel target in glioblastoma. Int J Oncol 2017; 50: 310–316.
- 34, , , et al. Overcoming resistance to single-agent therapy for oncogenic BRAF gene fusions via combinatorial targeting of MAPK and PI3K/mTOR signaling pathways. Oncotarget 2017; 8: 84697–84713.
- 35, , , et al. The cBio Cancer Genomics Portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012; 2: 401–404.
- 36, , , et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013; 6: pl1.
- 37, , , et al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol Cell Biol 2008; 28: 2825–2839.
- 38, , , et al. ARID1A mutation sensitizes most ovarian clear cell carcinomas to BET inhibitors. Oncogene 2018; 37: 4611–4625.
- 39, , , et al. Clinical benefit in response to palbociclib treatment in refractory uterine leiomyosarcomas with a common CDKN2A alteration. Oncologist 2017; 22: 416–421.
- 40, , , et al. Exceptional response to palbociclib in metastatic collecting duct carcinoma bearing a CDKN2A homozygous deletion. JCO Precis Oncol 2017; 1: 1–5.
- 41, , , et al. Palbociclib for treatment of metastatic melanoma with copy number variations of CDK4 pathway: case report. Chin Clin Oncol 2018; 7: 62.
- 42, , . A novel suicide gene therapy for the treatment of p16Ink4a-overexpressing tumors. Oncotarget 2018; 9: 7274–7281.
- 43, , , et al. Markers of MEK inhibitor resistance in low-grade serous ovarian cancer: EGFR is a potential therapeutic target. Cancer Cell Int 2019; 19: 10.
- 44, , , et al. La FAM fatale: USP9X in development and disease. Cell Mol Life Sci 2015; 72: 2075–2089.
- 45, , , et al. Escape from X inactivation varies in mouse tissues. PLoS Genet 2015; 11: e1005079.
- 46 ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57–74.
- 47, , , et al. Exome sequencing landscape analysis in ovarian clear cell carcinoma shed light on key chromosomal regions and mutation gene networks. Am J Pathol 2017; 187: 2246–2258.
- 48, , , et al. The molecular origin and taxonomy of mucinous ovarian carcinoma. Nat Commun 2019; 10: 3935.
- 49, , , et al. PARP inhibitors in platinum-sensitive high-grade serous ovarian cancer. Cancer Chemother Pharmacol 2018; 81: 647–658.
- 50, , , et al. Hormonal maintenance therapy for women with low-grade serous cancer of the ovary or peritoneum. J Clin Oncol 2017; 35: 1103–1111.
- 51, , , et al. PARAGON: a Phase II study of anastrozole in patients with estrogen receptor-positive recurrent/metastatic low-grade ovarian cancers and serous borderline ovarian tumors. Gynecol Oncol 2019; 154: 531–538.
- 52, , , et al. Exploiting MEK inhibitor-mediated activation of ERα for therapeutic intervention in ER-positive ovarian carcinoma. PLoS One 2013; 8: e54103.
- 53, , , et al. Molecular comparison of interval and screen-detected breast cancers. J Pathol 2019; 248: 243–252.
- 54, , , et al. An immunohistochemical algorithm for ovarian carcinoma typing. Int J Gynecol Pathol 2016; 35: 430–441.
- 55, , , et al. The LAST guidelines in clinical practice: implementing recommendations for p16 use. Am J Clin Pathol 2015; 144: 844–849.
- 56, , , et al. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res 2015; 3: 9.
- 57, , , et al. Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents. Cancer Discov 2012; 2: 366–375.
- 58, , , et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res 2012; 72: 5454–5462.
- 59, , , et al. Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br J Cancer 2012; 107: 1776–1782.
- 60, , , et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 2013; 494: 492–496.
- 61, , , et al. PureCN: copy number calling and SNV classification using targeted short read sequencing. Source Code Biol Med 2016; 11: 13.
- 62, , , et al. Panel testing for familial breast cancer: calibrating the tension between research and clinical care. J Clin Oncol 2016; 34: 1455–1459.
- 63, , , et al. The human genome browser at UCSC. Genome Res 2002; 12: 996–1006.
References 53–63 are cited only in the supplementary material.