Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with <i>BRCA1</i> and <i>BRCA2</i> Mutations

George, Joshy; Alsop, Kathryn; Etemadmoghadam, Dariush; Hondow, Heather; Mikeska, Thomas; Dobrovic, Alexander; deFazio, Anna; Smyth, Gordon K.; Levine, Douglas A.; Mitchell, Gillian; Bowtell, David D.L.

doi:10.1158/1078-0432.ccr-13-0066

Cited by 86 publications

(72 citation statements)

References 48 publications

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“…S2A). Although BRCA1 impairment has been correlated with the expression of TIL-related genes in HGSC (30,31), the PC and B-cell gene signatures showed no association with BRCA1 impairment (including germline mutations, somatic mutations, and DNA methylation; c 2 P ¼ 0.7415; Fig. 6I) nor BRCA2 mutation (c 2 P ¼ 0.9142).…”

Section: Identification Of a Minimal Plasma Cell Gene Expression Signmentioning

confidence: 94%

Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

Kroeger

Milne

Nelson

2016

Clinical Cancer Research

469

335

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Purpose: CD8+ tumor-infiltrating lymphocytes (TIL) are key mediators of antitumor immunity and are strongly associated with survival in virtually all solid tumors. However, the prognostic effect of CD8+ TIL is markedly higher in the presence of CD20+ B cells, suggesting that cooperative interactions between these lymphocyte subsets lead to more potent antitumor immunity. Experimental Design: We assessed the colocalization patterns, phenotypes, and gene expression profiles of tumor-associated T- and B-lineage cells in high-grade serous ovarian cancer (HGSC) by multicolor IHC, flow cytometry, and bioinformatic analysis of gene expression data from The Cancer Genome Atlas. Results: T cells and B cells colocalized in four types of lymphoid aggregate, ranging from small, diffuse clusters to large, well-organized tertiary lymphoid structures (TLS) resembling activated lymph nodes. TLS were frequently surrounded by dense infiltrates of plasma cells (PC), which comprised up to 90% of tumor stroma. PCs expressed mature, oligoclonal IgG transcripts, indicative of antigen-specific responses. PCs were associated with the highest levels of CD8+, CD4+, and CD20+ TIL, as well as numerous cytotoxicity-related gene products. CD8+ TIL carried prognostic benefit only in the presence of PCs and these other TIL subsets. PCs were independent of mutation load, BRCA1/2 status, and differentiation antigens but positively associated with cancer–testis antigens. Conclusions: PCs are associated with the most robust, prognostically favorable CD8+ TIL responses in HGSC. We propose that TLS facilitate coordinated antitumor responses involving the combined actions of cytolytic T cells and antibody-producing PCs. Clin Cancer Res; 22(12); 3005–15. ©2016 AACR.

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Section: Identification Of a Minimal Plasma Cell Gene Expression Signmentioning

confidence: 94%

Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

Kroeger

Milne

Nelson

2016

Clinical Cancer Research

469

335

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“…We, therefore, stratified tumors from the Australian Ovarian Cancer Study (n = 194) by BRCA1/2 germ-line mutation (13), somatic mutation, or methylation status (14) and accurately measured CCNE1 copy number by quantitative PCR (qPCR) (Fig. 1B).…”

Section: Ccne1mentioning

confidence: 99%

Synthetic lethality betweenCCNE1amplification and loss ofBRCA1

Etemadmoghadam

Weir

Au-Yeung

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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198

163

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High-grade serous ovarian cancers (HGSCs) are characterized by a high frequency of TP53 mutations, BRCA1/2 inactivation, homologous recombination dysfunction, and widespread copy number changes. Cyclin E1 (CCNE1) gene amplification has been reported to occur independently of BRCA1/2 mutation, and it is associated with primary treatment failure and reduced patient survival. Insensitivity of CCNE1-amplified tumors to platinum cross-linking agents may be partly because of an intact BRCA1/2 pathway. Both BRCA1/2 dysfunction and CCNE1 amplification are known to promote genomic instability and tumor progression. These events may be mutually exclusive, because either change provides a path to tumor development, with no selective advantage to having both mutations. Using data from a genome-wide shRNA synthetic lethal screen, we show that BRCA1 and members of the ubiquitin pathway are selectively required in cancers that harbor CCNE1 amplification. Furthermore, we show specific sensitivity of CCNE1-amplified tumor cells to the proteasome inhibitor bortezomib. These findings provide an explanation for the observed mutual exclusivity of CCNE1 amplification and BRCA1/2 loss in HGSC and suggest a unique therapeutic approach for treatment-resistant CCNE1-amplified tumors.RNAi | pan-cancer | CDK2 | cell cycle | DNA repair E pithelial ovarian cancer is complex and histologically diverse but still largely treated as a single disease with limited stratification based on histological or molecular characteristics. High-grade serous ovarian cancer (HGSC) accounts for the majority of epithelial ovarian cancer-related deaths (>60%), and almost no improvement in survival has been observed in the last 20 y (1). Widespread copy number changes are a hallmark of HGSC, including focal amplification of Cyclin E1 (encoded by CCNE1), which is associated with primary treatment failure (2) and reduced survival (3). Amplification of CCNE1 is one of very few well-defined molecular targets in HGSC.Cyclin E1 forms a complex with cyclin-dependent kinase 2 (CDK2) to regulate G1/S transition as well as having kinase-independent functions, including in DNA replication (4). Ovarian cell lines with CCNE1 amplification show a specific dependency for maintenance of CCNE1 expression (5, 6). We have validated CDK2 as a therapeutic target by showing selective sensitivity to suppression either by gene knockdown or using small molecule inhibitors (7), consistent with findings in breast cancer (8).Recent genomic studies have revealed a high frequency of BRCA1/2 (Breast cancer 1/2, early onset) inactivation and homologous recombination (HR) dysfunction in HGSC (9). Alterations of genes in the HR pathway include germ-line and somatic mutations of BRCA1 or BRCA2 (∼20% of patients) and epigenetic silencing of BRCA1 by hypermethylation (∼10%). Other genes inactivated by deletion, mutation, or hypermethylation include ATM, ATR, RAD51C, and PTEN (∼10%), key Fanconi anemia members (∼5%), and amplification or mutation of EMSY (∼8%). Collectively, at least 50% of HGSCs are...

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“…Complete copy number and gene expression microarray data are available from the Gene Expression Omnibus (Accession ID GSE48921). Methods for the analysis of copy number data obtained from The Cancer Genome Atlas (TCGA) are described elsewhere (16).…”

Section: Snp and Gene Expression Microarraysmentioning

confidence: 99%

“…S9A). To determine whether the association with WGD was specific to CCNE1 amplification and not a generalized increase in copy number events, we assessed the proportion of genome-amplified segments in each tumor subset (16). Interestingly, tumors with more than 1 WGD events had fewer regions of copy number amplification, suggesting a specific association with CCNE1 (Fig.…”

Section: Primary Tumors With Ccne1 Gene Amplification Are Associated mentioning

confidence: 99%

Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells inCCNE1-Amplified Ovarian Cancer

Etemadmoghadam

Au-Yeung

Wall

et al. 2013

Clinical Cancer Research

Self Cite

100

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Purpose: Amplification of cyclin E1 (CCNE1) is associated with poor outcome in breast, lung, and other solid cancers, and is the most prominent structural variant associated with primary treatment failure in highgrade serous ovarian cancer (HGSC). We have previously shown that CCNE1-amplified tumors show amplicon-dependent sensitivity to CCNE1 suppression. Here, we explore targeting CDK2 as a novel therapeutic strategy in CCNE1-amplified cancers and mechanisms of resistance.Experimental Design: We examined the effect of CDK2 suppression using RNA interference and smallmolecule inhibitors in SK-OV-3, OVCAR-4, and OVCAR-3 ovarian cancer cell lines. To identify mechanisms of resistance, we derived multiple, independent resistant sublines of OVCAR-3 to CDK2 inhibitors. Resistant cells were extensively characterized by gene expression and copy number analysis, fluorescence-activated cell sorting profiling and conventional karyotyping. In addition, we explored the relationship between CCNE1 amplification and polyploidy using data from primary tumors.Results: We validate CDK2 as a therapeutic target in CCNE1-amplified cells by showing selective sensitivity to suppression, either by gene knockdown or using small-molecule inhibitors. In addition, we identified two resistance mechanisms, one involving upregulation of CDK2 and another novel mechanism involving selection of polyploid cells from the pretreatment tumor population. Our analysis of genomic data shows that polyploidy is a feature of cancer genomes with CCNE1 amplification.Conclusions: These findings suggest that cyclinE1/CDK2 is an important therapeutic target in HGSC, but that resistance to CDK2 inhibitors may emerge due to upregulation of CDK2 target protein and through preexisting cellular polyploidy.

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Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations

Cited by 86 publications

References 48 publications

Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

Synthetic lethality betweenCCNE1amplification and loss ofBRCA1

Resistance to CDK2 Inhibitors Is Associated with Selection of Polyploid Cells inCCNE1-Amplified Ovarian Cancer

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