Ovarian Cancer: From Precursor Lesion Identification to Population-Based Prevention Programs

Epithelial ovarian cancer (EOC) is a heterogeneous group of malignancies, including high-grade serous ovarian cancer (HGSC). HGSC is often diagnosed at advanced stages and is linked to TP53 variants. While BRCA variants elevate risk, most HGSC cases occur in individuals without known genetic variants, necessitating prevention strategies for people without known high-risk genetic variants. Effective prevention programs are also needed due to the lack of traditional screening options. An emerging primary prevention strategy is opportunistic salpingectomy, which involves removing fallopian tubes during another planned pelvic surgery. Opportunistic salpingectomy offers a safe and cost-effective preventative option that is gaining global adoption. With the publication of the first cohort study of patients who underwent salpingectomy, specifically for cancer prevention, attention has turned to broadening opportunities for salpingectomy in addition to more targeted approaches. Prevention opportunities are promising with increasing adoption of salpingectomy and the increased understanding of the etiology of the distinct histotypes of ovarian cancer. Yet, further research on targeted risk-reducing salpingectomy with thoughtful consideration of equity is necessary to reduce death and suffering from ovarian cancer.

Generalization optimizing machine learning to improve CT scan radiomics and assess immune checkpoint inhibitors' response in non-small cell lung cancer: a multicenter cohort study

Background

Recent developments in artificial intelligence suggest that radiomics may represent a promising non-invasive biomarker to predict response to immune checkpoint inhibitors (ICIs). Nevertheless, validation of radiomics algorithms in independent cohorts remains a challenge due to variations in image acquisition and reconstruction. Using radiomics, we investigated the importance of scan normalization as part of a broader machine learning framework to enable model external generalizability to predict ICI response in non-small cell lung cancer (NSCLC) patients across different centers.

Methods

Radiomics features were extracted and compared from 642 advanced NSCLC patients on pre-ICI scans using established open-source PyRadiomics and a proprietary DeepRadiomics deep learning technology. The population was separated into two groups: a discovery cohort of 512 NSCLC patients from three academic centers and a validation cohort that included 130 NSCLC patients from a fourth center. We harmonized images to account for variations in reconstruction kernel, slice thicknesses, and device manufacturers. Multivariable models, evaluated using cross-validation, were used to estimate the predictive value of clinical variables, PD-L1 expression, and PyRadiomics or DeepRadiomics for progression-free survival at 6 months (PFS-6).

Results

The best prognostic factor for PFS-6, excluding radiomics features, was obtained with the combination of Clinical + PD-L1 expression (AUC = 0.66 in the discovery and 0.62 in the validation cohort). Without image harmonization, combining Clinical + PyRadiomics or DeepRadiomics delivered an AUC = 0.69 and 0.69, respectively, in the discovery cohort, but dropped to 0.57 and 0.52, in the validation cohort. This lack of generalizability was consistent with observations in principal component analysis clustered by CT scan parameters. Subsequently, image harmonization eliminated these clusters. The combination of Clinical + DeepRadiomics reached an AUC = 0.67 and 0.63 in the discovery and validation cohort, respectively. Conversely, the combination of Clinical + PyRadiomics failed generalizability validations, with AUC = 0.66 and 0.59.

Conclusion

We demonstrated that a risk prediction model combining Clinical + DeepRadiomics was generalizable following CT scan harmonization and machine learning generalization methods. These results had similar performances to routine oncology practice using Clinical + PD-L1. This study supports the strong potential of radiomics as a future non-invasive strategy to predict ICI response in advanced NSCLC.

Household hurricane evacuation during a dual-threat event: Hurricane Laura and COVID-19

This study explores household-level evacuation decision-making in response to Hurricane Laura, in a context where hurricane risk reduction measures contradicted COVID-19 risk reduction measures. Data were collected using a mail-based survey approach from households along the coast of Texas and Louisiana to explore drivers of and barriers to evacuation, including COVID-19 measures such as negative affect, risk perceptions, protective actions, and exposure. Testing for direct and indirect effects among the drivers of and barriers to evacuation, we find that many of our COVID-19 measures did not have a direct effect on evacuation but did have indirect effects through other factors. We also found evidence of both direct and indirect relationships with regards to more conventional drivers of evacuation found in the literature. We close with a discussion of the limitations and implications of this study.

Abstract 2182: The evolution of high grade serous ovarian cancer under the pressure of non-cytotoxic and cytotoxic treatment

Introduction: High-grade serous ovarian cancer (HGSOC) is driven by loss of TP53 and genome instability . Despite the recent success of PARP inhibitors, advanced BRCA mutant and homologous recombination repair deficient (HRD) HGSOC, chemotherapy remains the first line treatment. Little is known about how chemotherapy exposure alters tumor heterogeneity and subsequent response to targeted therapies. Certain mutations may survive the exposure of chemotherapy better than others. The question of whether targeted therapies should be given before or after response to chemotherapy also remains unanswered. We use the principles of natural selection to investigate how HGSOC evolves over time and selection operates on clones in the context of cytotoxic/non-cytotoxic combination therapies, and what changes in genomes/transcriptomes at the single cell level drive tumor progression.

Methods: Cell lines ID8 Trp53 −/−; Brca1 −/− and WT were used to represent defective/proficient homologous recombination were given intraperitoneally to C57B6 mice to develop HGSOC models. Transfected Luciferase expression in the cells used to monitor tumor response to olaparib (Ola)+/- Bevacizumab (BEV-various doses) +/- Atezolizumab (ATz) combinations by bioluminescence imaging (BLI). Ascitic fluid and mouse organs were harvested for the evidence of seeding and identification of biomarkers. In addition, 10 treatment naïve HGSOC PDX were developed in immunodeficient mice and treated with either cisplatin or olaparib. Single-cell whole-genome sequencing (scWGS) was performed using direct library preparation (DLP+). Hierarchical clustering and Sitka are used to identify the clonal structure of each condition following treatment. Phylogenetic tree was computed using copy number data.

Results: In the BRCA WT HRp study group, the greatest response was seen in the triplet Ola+BEV+ATz combinations and interestingly no significant differences were observed using a lower dose of BEV. Furthermore, from scWGS data of PDX passages we captured initial clonal heterogeneity leading to emergent clones. We found evolving copy number changes on chromosome 19, 8, 3 and loss of heterozygosity of TP53.

Conclusion: The triplet combination of low-dose-intensity bevacizumab with other non-cytotoxic drugs was an effective regimen for BRCA WT syngeneic mouse tumors. In HGSOC PDX, we are able to capture diversification between HGSOC PDX passages-specifically after drug exposures.

Citation Format: Farhia Kabeer, Goldman Lam, Naila Adam, Maxwell Douglas, Amal El-Naggar, Forouh Kalantari, Mengke Han, Vinci Au, Michael Van Vliet, Cindy Shen, Sean Beaty, Daniel Lai, Andy Mungall, Richard Moore, Sam Aparicio, Andrew Roth, David Huntsman, Yvette Drew. The evolution of high grade serous ovarian cancer under the pressure of non-cytotoxic and cytotoxic treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2182.

Abstract 4542: Development of a one-step molecular classifier for endometrial carcinoma using an amplicon-based gene panel and next generation sequencing technology

Objectives: Molecular classification of endometrial carcinoma (EC) is now recommended by the WHO, ESGO/ESTRO/ESP and NCCN guidelines. The pragmatic molecular classification tool, ProMisE, identifies four molecular subtypes based on next generation sequencing (NGS) for the detection of somatic pathogenic POLE mutations, and immunohistochemistry for mismatch repair and p53 proteins. ProMisE provides valuable prognostic and predictive information to direct care, however, multiple molecular results are often received from different time periods and/or from different centers which can cause delays. Therefore, we developed a classifier that relies on a single DNA-based NGS test with the goal of recapitulating the prognostic value of ProMisE by producing concordant results.

Methods: Formalin fixed paraffin embedded (FFPE) EC tumor DNA was sequenced using the clinically validated Imagia Canexia Health Find ItTM amplicon-based next generation sequencing gene panel assay. The 38 gene panel assessed single nucleotide variants (SNVs), indels (insertions and deletions), gene amplification and microsatellite instability (MSI) using 21 MSI loci. To compare to the original ProMisE classifier, we identified somatic mutations in POLE, TP53 and MSI-High or MS-Stable for molecular classification. Molecular subtypes assigned by both classifiers were assessed for concordance metrics and Kaplan-Meier survival curves.

Results: The one-step NGS molecular classifier assessed 165 unique patient FFPE EC samples that had previously been assessed by ProMisE. There were 152/165 cases that were concordant between molecular subtype assignment from the original ProMisE and the one-step NGS assay with a kappa statistic of 0.88 and accuracy of 0.92. There were 13 samples that were discordant (original classifications: 3 POLE, 3 MMRd, 2 p53abn, 5 NSMP/p53wt), which will be reviewed in detail. Results were concordant in 14 of 15 cases (93%) when both diagnostic biopsy and hysterectomy specimens were tested. Molecular subtypes maintained their associations with clinical outcomes (progression free survival, disease specific survival, overall survival).

Conclusion: The one-step NGS molecular classifier demonstrates high concordance with the original ProMisE classifier including between biopsy and hysterectomy samples. This shows that reliable molecular testing could be obtained from time of first diagnosis. Prognostic value of this new one-step classification tool is maintained. Appropriate interpretation of results is critical, including limiting POLE mutation assignment to a confirmed list of pathogenic mutations and correct order of segregation for ECs with more than one molecular feature. Further validation is needed in a larger cohort to implement into standard of care testing.

Citation Format: Melissa K. McConechy, Amy Jamieson, Amy Lum, Samuel Leung, Adrian Kense, Sonal Brahmbhatt, Ka Mun Nip, Ebru Baran, Dilmi Perera, Kurt Yakimovich, Ruth Miller, C. Blake Gilks, David Huntsman, Jessica N. McAlpine. Development of a one-step molecular classifier for endometrial carcinoma using an amplicon-based gene panel and next generation sequencing technology. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4542.

Abstract 4279: Method for identifying microsatellite instability high DNA abnormality samples

Introduction: Tissue samples with high microsatellite instability (MSI-H) can be indicators of cancerous tumors that are sensitive to certain types of cancer treatments (e.g., immune modulation-checkpoint inhibitor treatment). MSI-H regions can be identified with Polymerase Chain Reaction (PCR) based assays and next-generation sequencing (NGS). However, these MS regions are susceptible to PCR and sequencing errors. We developed a computational method for detecting microsatellite instability high (MSI-H) tumors using next-generation sequencing (NGS) data to accurately identify true MSI-H samples from MS-Stable samples based on an analysis of these MS regions.

Methods: We developed a method for classifying a tissue sample as being microsatellite instability high (MSI-H) without using normal tissue from the same person which doubles the sequencing cost. Furthermore, the algorithm was designed for amplicon targeted assays where it is not always feasible to choose the most predictive MS sites. The machine learning classifier (ML) algorithm is a random forest algorithm with a training set of known MSI-H and MS-Stable samples to learn the relationship between the MSI status and the distribution of repeats in microsatellite regions of genomes using 21 MS loci. A negative control was used to normalize the ML features and therefore reduce the effects of PCR and sequencing errors in noisy MS sites.

Results: The MSI detection algorithm was validated in analytical and clinical samples achieving an accuracy greater than 98%. Analytical samples consist of commercial reference standard samples and well characterized FFPE treated cell-lines. Clinical samples consists of clinical FFPE tumor samples from cancer patients that were orthogonally validated using immunohistochemistry (expression of mismatch repair genes, i.e., MMRnormal vs MMRd) on tumor tissue and/or the Promega MSI PCR using matched tumor/normal. All experiments were performed in the Imagia Canexia Health CAP, CLIA, DAP certified laboratory using the Find It assay standard operating procedures for detecting genomic mutations in solid tumor tissue.

Conclusions: The MSI detection algorithm can accurately identify samples with MSI-H tumors. When used in a clinical setting, these patients can then be directed to treatments such as immune-checkpoint inhibitors.

Citation Format: Dilmi Perera, Sahand Khakabi, Ka Mun Nip, Sonal Brahmbatt, Adrian Kense, Kevin Tam, David Mulder, Melissa McConechy, David Huntsman, Ruth Miller, Rosalía Aguirre-Hernández. Method for identifying microsatellite instability high DNA abnormality samples. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4279.

Molecular Subclasses of Clear Cell Ovarian Carcinoma and Their Impact on Disease Behavior and Outcomes

PURPOSE

To identify molecular subclasses of clear cell ovarian carcinoma (CCOC) and assess their impact on clinical presentation and outcomes.

EXPERIMENTAL DESIGN

We profiled 421 primary CCOCs that passed quality control using a targeted deep sequencing panel of 163 putative CCOC driver genes and whole transcriptome sequencing of 211 of these tumors. Molecularly defined subgroups were identified and tested for association with clinical characteristics and overall survival.

RESULTS

We detected a putative somatic driver mutation in at least one candidate gene in 95% (401/421) of CCOC tumors including ARID1A (in 49% of tumors), PIK3CA (49%), TERT (20%), and TP53 (16%). Clustering of cancer driver mutations and RNA expression converged upon two distinct subclasses of CCOC. The first was dominated by ARID1A-mutated tumors with enriched expression of canonical CCOC genes and markers of platinum resistance; the second was largely comprised of tumors with TP53 mutations and enriched for the expression of genes involved in extracellular matrix organization and mesenchymal differentiation. Compared with the ARID1A-mutated group, women with TP53-mutated tumors were more likely to have advanced-stage disease, no antecedent history of endometriosis, and poorer survival, driven by their advanced stage at presentation. In women with ARID1A-mutated tumors, there was a trend toward a lower rate of response to first-line platinum-based therapy.

CONCLUSIONS

Our study suggests that CCOC consists of two distinct molecular subclasses with distinct clinical presentation and outcomes, with potential relevance to both traditional and experimental therapy responsiveness. See related commentary by Lheureux, p. 4838.

Extracellular vesicle-based biomarker assay for the detection of early-stage ovarian cancer

5542

Background: Detection of cancer with improved discrimination compared to current blood tests could be achieved using an approach that assesses extracellular vesicles (EVs). This approach should have high sensitivity (se) because of EVs abundance in blood and high specificity (sp) by assaying EVs with multiple cancer-related protein and glycosylation epitopes (PGEs) co-localized on their surfaces. We are developing a platform technology that detects multiple cancer-related PGEs co-localized on the same EV using immunoaffinity-capture and proximity-ligation qPCR. In this study, we compare the performance of this technology vs plasma CA125 for correctly categorizing early-stage high-grade serous ovarian cancer (HGSOC) vs healthy/benign ovarian tumors (OT). Methods: We evaluated our EV-based platform technology using 7 PGE combinations to discriminate HGSOC from benign adnexal masses. We first derived a prediction model on a retrospectively collected cohort of 42 HGSOC and 26 benign OT samples from 2 commercial vendors and 24 healthy controls (HC) using a machine-learning algorithm. We validated this model on an independent cohort [89 HGSOC: Stage I (17), II (35), III (37); 192 benign OT] from university-associated biobanks and 124 HC. We also assessed the assay’s performance in plasma from 87 women with off-target cancers and 42 women with inflammatory conditions from commercial vendors. For each sample, we also measured CA125 levels using a commercial ELISA. Results: The prediction model distinguishes HGSOC from benign and HC with an AUC of 0.965 (95% CI 0.93-0.99), with 89.9% (0.82-0.95) se at 98% sp. For stage I/II HGSOC, the model achieves an AUC of 0.942 (0.9-0.99), with 84.6% (0.72-0.93) se at 98% sp. By comparison, CA125 achieves an AUC of 0.875 (0.81-0.94) and 44.2% (0.3-0.59) se at 98% sp. Direct comparison of CA125 and our model shows a significant difference at 98% sp for both all and stage I/II HGSOC (McNemar p-val < 0.001). When comparing HGSOC to HC, there is no significant difference between our model and CA125 (p-val = 1.0). There is a significant difference when comparing patients with all stage and stage I/II HGSOC to patients with benign OT (p-val < 0.001). Our assay had 1 false positive and CA125 had 3 false positives out of 42 inflammatory cases. Conclusions: These preliminary data suggest our platform technology for detecting PGEs co-localized on individual EVs may detect all stages of HGSOC from plasma with high se at a very high sp. Our assay may improve on CA125 by distinguishing stage I/II HGSOC from benign OT and could have clinical utility for both early detection and surgical referral recommendation for benign and malignant OT. While the diverse cohorts in this study may present challenges in interpretation, the reproducibility in an independent cohort is encouraging and supports further investigation using cases and controls from well-defined cohort studies.

Identification of a novel subtype of endometrial cancer with unfavorable outcome using artificial intelligence-based histopathology image analysis

5594

Background: Molecular subtyping of endometrial cancer (EC), unlike histopathological evaluation, offers an objective and reproducible classification system that has strong prognostic value and therapeutic implications. The Proactive Molecular risk classifier for Endometrial cancer (ProMisE) was developed by our team as a pragmatic, cost-effective, and clinically applicable molecular classifier for EC patients. ProMisE has four subtypes: (i) POLE mutant ( POLEmut), (ii) mismatch repair deficient (MMRd), (iii) p53 abnormal (p53abn) by immunohistochemistry, and (iv) NSMP (No Specific Molecular Profile), lacking any of the defining features of the other three subtypes. While ProMisE subtypes are associated with clinical outcomes, within each subtype, there are clinical/prognostic outliers. This is particularly true within the largest ProMisE subtype; NSMP (representing ̃50% of ECs), where a subset of patients experience a very aggressive disease course, comparable to what is observed in patients with p53abn ECs. Methods: We hypothesized that objective assessment of the digitized hematoxylin and eosin (H&E)-stained histopathology slides of the largest and most diverse EC subset, NSMP, could potentially identify clinical outcome outliers. As such, we developed an artificial intelligence (AI)-based image analysis model to identify the NSMP cases that had similar histopathological features to the p53abn subtype, as assessed by H&E stain. We used a discovery cohort of 182 and an external validation cohort of 195 NSMP ECs. Results: Our AI-based image analysis model, based on deep convolutional neural networks, identified 21 (11.5%) out of the 182 NSMP cases with similar histopathological features as p53abn cases. We refer to these cases as ‘p53abn-like’ NSMPs. Compared to the rest of the NSMP cases, these cases had markedly inferior disease-specific survival (DSS) (10-year DSS 58.9% vs. 93.1% ( p<3.44e-8)) and progression-free survival (PFS) (10-year PFS 55.1% vs. 91.4% ( p<3.76e-6)). These findings were confirmed in our validation cohort, with 10.7% of the 195 patients categorized as ‘p53abn-like’ tumors with 10-year DSS of 82% vs. 51.3% ( p<5.28e-5) and PFS of 89.3% vs. 56.6% (p<2.15e-4). Conclusions: Utilizing an AI-based approach for histopathology image analysis, we have discovered ‘p53abn-like’ NSMPs, a novel subtype of NSMP ECs with morphological features similar to p53abn cases. ‘p53abn-like’ NSMPs exhibit similar clinical behavior as p53abn, having noticeably inferior outcome compared to the rest of the NSMP cases in two independent cohorts. These findings warrant further molecular investigation of this novel subtype of EC to identify the biological underpinning and future therapeutic strategies.

Targeted Molecular Sequencing of Recurrent and Multifocal Non-HPV-associated Squamous Cell Carcinoma of the Vulva

Recurrent vulvar squamous cell carcinomas (SCCs) are a poorly understood and aggressive group of treatment-resistant neoplasms. Currently, it remains unclear whether these are in fact recurrences of the same primary tumor, or the development of entirely new tumors. Here, to address this question, we examined the mutational profile of a series of patients with recurrent or multifocal non-human papilloma virus (HPV)-associated vulvar SCC. We performed a targeted 33-gene next-generation sequencing panel on a series of 14 patients with recurrent or multifocal non-HPV-associated vulvar SCC and precursor neoplasms. This amounted to 54 cases (33 SCC, 1 verrucous carcinoma, 13 differentiated vulvar intraepithelial neoplasia, and 7 differentiated exophytic vulvar intraepithelial lesion), with 79 mutations detected altogether. TP53 [51/79 (65%)] was the most frequently mutated gene. Mutations in PIK3CA [16/79 (20%)), HRAS [6/79 (8%)], PTEN [4/79 (5%)], EGFR [1/79 (1%)], and GNAS [1/79 (1%)] were occasionally seen. Most patients with SCC [5/9 (56%)] recurrent, 4/5 (80%) multifocal] demonstrated a clonal relationship, and harbored the same mutations in the same genes in metachronous or synchronous tumors. A subset of the recurrent tumors [2/5 (40%)] recurred with additional mutations. These clonal relationships were shared between SCC and differentiated vulvar intraepithelial neoplasia in each case. By contrast, a small number of recurrent tumors [3/9 (33%)] demonstrated novel mutations, entirely different from the primary tumor. Thus, our findings suggest that recurrent non-HPV-associated vulvar SCC can arise from 2 mechanisms.

Sphingosine-kinase-1 expression is associated with improved overall survival in high-grade serous ovarian cancer

Purpose

Sphingosine-kinase-1 (SPHK1) is a key enzyme of sphingolipid metabolism which is involved in ovarian cancer pathogenesis, progression and mechanisms of drug resistance. It is overexpressed in a variety of cancer subtypes. We investigated SPHK1 expression as a prognostic factor in epithelial ovarian cancer patients.

Methods

Expression analysis of SPHK1 was performed on formalin-fixed paraffin-embedded tissue from 1005 ovarian cancer patients with different histological subtypes using immunohistochemistry. Staining intensity of positive tumor cells was assessed semi-quantitatively, and results were correlated with clinicopathological characteristics and survival.

Results

In our ovarian cancer collective, high levels of SPHK1 expression correlated significantly with complete surgical tumor resection (p = 0.002) and lower FIGO stage (p = 0.04). Progression-free and overall survival were further significantly longer in patients with high-grade serous ovarian cancer and overexpression of SPHK1 (p = 0.002 and p = 0.006, respectively).

Conclusion

Our data identify high levels of SPHK1 expression as a potential favorable prognostic marker in ovarian cancer patients.

Supplementary Information

The online version of this article (10.1007/s00432-021-03558-x) contains supplementary material, which is available to authorized users.

p53 Immunohistochemical patterns in HPV-related neoplasms of the female lower genital tract can be mistaken for TP53 null or missense mutational patterns

We have recently encountered p53 immunohistochemical (IHC) patterns in human papillomavirus (HPV)-associated carcinomas of the gynecologic tract, which were confused with absent (null) or overexpression TP53 mutational staining. We therefore evaluated p53 and p16 IHC in 25 squamous cell carcinomas (SCC) (16 vulva, 4 Bartholin's gland, and 5 cervix), 20 endocervical adenocarcinomas (EDAC), 14 high-grade squamous intraepithelial lesions (HSIL), 2 adenocarcinoma in situ (AIS), all of which exhibited morphologic features of HPV. Only cases showing diffuse/strong block-like p16 staining were included for further study. All EDACs underwent TP53 sequencing and HPV in situ hybridization (ISH) was performed in selected cases. p53 IHC staining fell into two main patterns. The most common was designated as "markedly reduced (null-like)" (absence or significantly attenuated staining in >70% of cells), which could be confused with true null mutational pattern. This was present in 14/25 (56%) SCCs, 7/14 (50%) HSILs, and 18/20 (90%) EDACs. The second notable pattern was "mid-epithelial (basal sparing)" (distinct absence of staining in basal cells juxtaposed with strong staining in parabasal cells), seen in 10/25 (40%) SCC, 7/14 (50%) HSIL, and none of the EDACs. There was scattered weak to moderate p53 staining (conventional wild type) in 1/25 (4%) SCC and 2/20 (10%) EDAC. No cases showed strong/diffuse overexpression. One EDAC had a TP53 missense mutation and exhibited "markedly reduced (null-like)" staining. HPV ISH revealed an inverse relationship with p53, cells positive for HPV mRNA were negative for p53. Knowledge of these patterns can help pathologists avoid misinterpreting p53 status in the setting of HPVA cancers.

Evaluation of human papillomavirus (HPV) prediction using the International Endocervical Adenocarcinoma Criteria and Classification system, compared to p16 immunohistochemistry and HPV RNA in-situ hybridization

Background

The International Endocervical Adenocarcinoma Criteria and Classification (IECC) separated endocervical adenocarcinomas into human papillomavirus (HPV) associated (HPVA) and non–HPV-associated (NHPVA) categories by morphology alone. Our primary objective was to assess the accuracy of HPV prediction by the IECC system compared to p16 immunohistochemistry and HPV RNA in-situ hybridization (RISH). Our secondary goal was to directly compare p16 and HPV RISH concordance.

Methods

Cases were classified by IECC and stained for p16 and HPV RISH on tissue microarray, with discordant p16/HPV RISH cases re-stained on whole tissue sections. Remaining discordant cases (p16/HPV, IECC/p16, IECC/HPV discordances) were re-reviewed by the original pathologists (n = 3) and external expert pathologists (n = 2) blinded to the p16 and HPV RISH results. Final IECC diagnosis was assigned upon independent agreement between all reviewers.

Results

One hundred and eleven endocervical adenocarcinomas were classified originally into 94 HPVA and 17 NHPVA cases. p16 and HPV RISH was concordant in 108/111 cases (97%) independent of the IECC. HPV RISH and p16 was concordant with IECC in 103/111 (93%) and 106/111 (95%), respectively. After expert review, concordance improved to 107/111 (96%) for HPV RISH. After review of the eight discordant cases, one remained as HPVA, four were reclassified to NHPVA from HPVA, two were unclassifiable, and one possibly represented a mixed usual and gastric-type adenocarcinoma.

Conclusions

p16 and HPV RISH have excellent concordance in endocervical adenocarcinomas, and IECC can predict HPV status in most cases. Focal apical mitoses and apoptotic debris on original review led to the misclassification of several NHPVA as HPVA.

Abstract LB-038: Novel functional insights revealed by distinct protein-protein interactions of the residual SWI/SNF complex in SMARCA4-deficient small cell carcinoma of the ovary, hypercalcemic type

Chromatin remodeling plays a critical role in tumor suppression as demonstrated by 20% of human cancers bearing inactivating mutations in SWI/SNF chromatin remodeling complex members. Mutations in different SWI/SNF subunits drive a variety of adult and pediatric tumor types, including non-small cell lung cancers, rhabdoid tumors, medulloblastomas, and ovarian cancers. Small cell carcinoma of the ovary hypercalcemic type (SCCOHT) is an aggressive subtype of ovarian cancer occurring in young women. Nearly all (&gt;98%) SCCOHTs have inactivating mutations in SMARCA4, which encodes 1 of 2 mutually exclusive catalytic subunits of the SWI/SNF complex. Less than half of SCCOHT patients survive 5 years despite aggressive surgery and multimodal chemotherapy. Empirical support for effective SCCOHT treatments is scarce, in part because of the poor understanding of SCCOHT tumorigenesis. To gain insight into the functional consequences of SWI/SNF subunit loss, we defined SWI/SNF composition and its protein-protein interactions (PPIs) by immunoprecipitation and mass spectrometry (IP-MS) of SWI/SNF subunits in 3 SCCOHT cell lines. Comparing these results to a cell line containing a wild-type SWI/SNF complex, the interaction of most canonical core SWI/SNF subunits was observed in all SCCOHT cell lines at a lower abundance. The SCCOHT SWI/SNF also lacked ATPase module subunits and showed a drastic reduction in PBAF-specific subunit interactions. The wild-type and SCCOHT SWI/SNF subunits immunoprecipitated a shared set of 26 proteins, including core SWI/SNF subunits and RNA processing proteins. We observed 131 proteins exclusively interacting with the wild-type SWI/SNF complex including isoform-specific SWI/SNF subunits, members of the NuRD complex, and members of the MLL3/4 complex. We observed 60 PPIs exclusive to the SCCOHT residual SWI/SNF shared in at least 2 of the 3 SCCOHT cell lines, including many proteins involved in RNA processing. Differential interactions with the residual SWI/SNF complex in SCCOHT may further elucidate altered functional consequences of SMARCA4 mutations in these tumors as well as identify synthetic lethal targets that translate to other SWI/SNF-deficient tumors.

Citation Format: Elizabeth Raupach, Krystine Garcia-Mansfield, Ritin Sharma, Apurva Hegde, Victoria David-Dirgo, Yemin Wang, Chae Young Shin, Lan Tao, Salvatore Facista, Rayvon Moore, Jessica Lang, Victoria Zismann, Krystal Orlando, Monique Spillman, Anthony Karnezis, Lynda Bennett, David Huntsman, Jeffrey Trent, William Hendricks, Bernard Weissman, Patrick Pirrotte. Novel functional insights revealed by distinct protein-protein interactions of the residual SWI/SNF complex in SMARCA4-deficient small cell carcinoma of the ovary, hypercalcemic type [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-038.

The coming 15 years in gynaecological pathology: digitisation, artificial intelligence, and new technologies

Surgical pathology forms the cornerstone of modern oncological medicine, owing to the wealth of clinically relevant information that can be obtained from tissue morphology. Although several ancillary testing modalities have been added to surgical pathology, the way in which we view and interpret tissue morphology has remained largely unchanged since the inception of our profession. In this review, we discuss new technological advances that promise to transform the way in which we access tissue morphology and how we use it to guide patient care.

Abstract B17: Modeling ovarian cancer in mice using in vivo electroporation and CRISPR-mediated genome editing

Ovarian cancer is the fifth largest cause of cancer-related deaths in women. The vast majority of ovarian cancers are epithelial ovarian cancers, and high-grade serous carcinoma (HGSC) is the most common and most lethal epithelial ovarian cancer. In the last 10 years, it has been recognized that the cell of origin of most HGSCs is within the fallopian tube epithelium, instead of the ovarian surface epithelium. However, the early events in disease progression still remain poorly defined, because HGSC is usually diagnosed at advanced stages and there is a lack of proper animal models recapitulating human disease progression. My group has recently developed a unique strategy for generating mouse ovarian cancer models, which is a combination of in vivo fallopian tube electroporation, Cre-mediated lineage tracing and CRISPR-mediated gene modifications. As proof of principle, we generated a highly metastatic HGSC model by targeting four tumor suppressor genes. The female mice targeted these four genes generated ovarian tumors within 5 months after electroporation and peritoneal metastasis within 6 months. After 6 months, ascites formation was observed in two third of those females. Interestingly, similar to human ovarian cancer patients, we observed two metastatic patterns, miliary and nonmiliary. Our unique strategy has several advantages over the current mouse cancer models: 1) high flexibility permitting many gene combinations/modifications and host genetic backgrounds to be tested; 2) control over the size and area of targeted cells (the low-frequency mosaic transfection pattern better recapitulates the sporadic nature of human tumorigenesis); 3) the ability to track genetically modified cells by fluorescent reporters, permitting analysis of tumor initiation and early metastasis; and 4) highly metastatic mouse models with immune competency.

Citation Format: Keerthana Harwalkar, Katie Teng, Jocelyn Arceneau, Yifan Zhao, Dave Farnell, Matt Ford, Tuyet Nhung Tun Nu, David Huntsman, Yojiro Yamanaka. Modeling ovarian cancer in mice using in vivo electroporation and CRISPR-mediated genome editing [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B17.

Abstract B30: The effect of OCP use on the incidence of precancerous p53 lesions in fallopian tube fimbria

Background: High-grade serous ovarian carcinoma (HGSOC) accounts for &gt;70% of ovarian cancer-related deaths and is the most common ovarian cancer histotype, most originating from precancerous p53 lesions in the fallopian tube (FT) fimbria. Use of oral contraceptive pills (OCPs) for 5 years or more is associated with a &gt;40% reduction in risk of HGSOC, but the mechanism is unknown. We hypothesize that OCP use reduces the incidence of p53 lesions. Our preliminary data show higher incidence of p53 lesions in post- compared to premenopausal women; therefore we aim to quantify p53 lesions in postmenopausal women who previously did or did not use OCPs. This will provide insight into the protective effects of OCPs against HGSOC.

Preliminary Results: We determined the presence of p53 lesions by immunohistochemistry (IHC) in FT of women up to 40 years old (n=27) and &gt;60 years old (n=24) who underwent salpingectomies for noncancer reasons. p53 lesions were identified in 3/27 cases of the younger cohort (11%) and in 10/24 of the older cohort (42%). Thus, we conclude an increased incidence of p53 lesions in older compared to younger women.

Proposed Design: IHC for p53 will be performed on FT fimbria of women &gt;55 years old who received salpingectomy for noncancer reasons. Based on an assumed reduction in p53 lesions of 35% in women who used OCPs for 5 years or more compared to nonusers (25 vs. 42%), analysis of 190 cases from each group will provide &gt;80% power (p&lt;0.05). Cases will be identified through Population Data BC and blind analysis by p53 IHC will be performed at the Vancouver General Hospital. Data will be flowed back to Pop Data BC to compare to OCP data.

Conclusion: Our preliminary study found that 42% of postmenopausal women had p53 lesions, informing this study design. The study registered through this abstract will be the first to examine the impact of OCPs on the earliest known precursors of HGSOC.

Citation Format: Kendall Greening, Anthony Karnezis, Dawn Cochrane, David Farnell, Lien Hoang, Gillian Hanley, David Huntsman. The effect of OCP use on the incidence of precancerous p53 lesions in fallopian tube fimbria [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B30.

Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy

Whether mutations in cancer driver genes directly affect cancer immune phenotype and T cell immunity remains a standing question. ARID1A is a core member of the polymorphic BRG/BRM-associated factor chromatin remodeling complex. ARID1A mutations occur in human cancers and drive cancer development. Here, we studied the molecular, cellular, and clinical impact of ARID1A aberrations on cancer immunity. We demonstrated that ARID1A aberrations resulted in limited chromatin accessibility to IFN-responsive genes, impaired IFN gene expression, anemic T cell tumor infiltration, poor tumor immunity, and shortened host survival in many human cancer histologies and in murine cancer models. Impaired IFN signaling was associated with poor immunotherapy response. Mechanistically, ARID1A interacted with EZH2 via its carboxyl terminal and antagonized EZH2-mediated IFN responsiveness. Thus, the interaction between ARID1A and EZH2 defines cancer IFN responsiveness and immune evasion. Our work indicates that cancer epigenetic driver mutations can shape cancer immune phenotype and immunotherapy.

Redefinition of familial intestinal gastric cancer: clinical and genetic perspectives

BACKGROUND

Familial intestinal gastric cancer (FIGC) remains genetically unexplained and without testing/clinical criteria. Herein, we characterised the age of onset and disease spectrum of 50 FIGC families and searched for genetic causes potentially underlying a monogenic or an oligogenic/polygenic inheritance pattern.

METHODS

Normal and tumour DNA from 50 FIGC probands were sequenced using Illumina custom panels on MiSeq, and their respective germline and somatic landscapes were compared with corresponding landscapes from sporadic intestinal gastric cancer (SIGC) and hereditary diffuse gastric cancer cohorts.

RESULTS

The most prevalent phenotype in FIGC families was gastric cancer, detected in 138 of 208 patients (50 intestinal gastric cancer probands and 88 unknown gastric cancer histology relatives), followed by colorectal and breast cancers. After excluding benign and intronic variants lacking impact in splicing, 12 rare high-quality variants were found exclusively in 11 FIGC probands. Only two probands carried potentially deleterious variants, but lacked somatic second-hits, weakly supporting the monogenic hypothesis for FIGC. However, FIGC probands developed gastric cancer at least 10 years earlier and carried more TP53 germline common variants than SIGC (p=4.5E-03); FIGC and SIGC could be distinguished by specific germline and somatic variant profiles; there was an excess of FIGC tumours presenting microsatellite instability (38%); and FIGC tumours displayed significantly more somatic common variants than SIGC tumours (p=4.2E-06).

CONCLUSION

This study proposed the first data-driven testing criteria for FIGC families, and supported FIGC as a genetically determined, likely polygenic, gastric cancer-predisposing disease, with earlier onset and distinct from patients with SIGC at the germline and somatic levels.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Low-grade serous ovarian cancer: State of the science

In January 2019, a group of basic, translational, and clinical investigators and patient advocates assembled in Miami, Florida, to discuss the current state of the science of low-grade serous carcinoma of the ovary or peritoneum-a rare ovarian cancer subtype that may arise de novo or following a diagnosis of serous borderline tumor. The purpose of the conference was to review current knowledge, discuss ongoing research by established researchers, and frame critical questions or issues for future directions. Following presentations and discussions, the primary objective was to initiate future collaborations, uniform database platforms, laboratory studies, and clinical trials to better understand this disease and to advance clinical care outside the boundaries of single academic institutions. This review summarizes the state of the science in five principal categories: epidemiology and patient outcomes, pathology, translational research, patient care and clinical trials, and patients' perspective.

Developing a Highly Specific Biomarker for Germ Cell Malignancies: Plasma miR371 Expression Across the Germ Cell Malignancy Spectrum

PURPOSE

Our objective was to evaluate operating characteristics, particularly specificity and positive predictive value (PPV), by mapping plasma miR371 expression to actual clinical events in patients with a history of germ cell tumor.

PATIENTS AND METHODS

One hundred eleven male patients with a history of or newly diagnosed germ cell tumors were evaluable. Biospecimens obtained before confirmed clinical events were analyzed for miR371 expression with blinding of providers and laboratory personnel to analytic results or clinical status, respectively. Cases (patients with clinically confirmed active germ cell malignancy [aGCM]) and controls (patients with no clinically confirmed aGCM) were assigned over the course of the management. Patients were assigned risk status (high, low, or moderate) based on the composite clinical picture at time points in management.

RESULTS

Considering all cases and controls and results of prospectively obtained biosamples analyzed for miR371 expression, 46 (35%) of 132 samples had clinically confirmed aGCM over the course of management; 44 (96%) of these 46 patients had plasma miR371 expression (true positives) with no false positives. Two (4%) of 46 patients had no miRNA expression despite pathologic confirmation of aGCM (false negatives). Plasma miR371 expression in confirmed aGCM had a specificity, sensitivity, positive predictive value, and negative predictive value of 100%, 96%, 100%, and 98%, respectively. Interpretation of sensitivity and negative predictive value is limited by modest follow-up. Specificity and sensitivity were 100% and 98%, 100% and 92%, and 100% and 97% in the low-, moderate-, and high-risk groups, respectively, with a median follow-up time of 15 months.

CONCLUSION

Plasma miR371 expression predicts aGCM with high specificity and positive predictive value. Although other operating characteristics of miR371 await longer follow-up for more complete definition, the findings of a highly specific liquid biopsy strongly support moving forward with large-scale, real-world clinical trials to further define full operating characteristics and to identify clinical utility and areas of patient benefit.

Abstract DP-006: THE EFFECT OF AGE AND OCP USE ON THE INCIDENCE OF PRE-CANCEROUS P53 LESIONS AND THE DEVELOPMENT OF HIGH GRADE SEROUS OVARIAN CARCINOMA

BACKGROUND: High grade serous ovarian cancer (HGSOC) accounts for &gt;70% of ovarian cancer related deaths and is the most common ovarian cancer histotype, most originating from pre-cancerous p53 lesions in the fallopian tube (FT) fimbria. Use of oral contraceptive pills (OCPs) for 5 years or more is associated with &gt;40% reduction in risk of HGSOC, but the mechanism is unknown. We hypothesize that OCP use reduces the incidence of p53 lesions. Our preliminary data show higher incidence of p53 lesions in post- compared to pre-menopausal women, therefore we aim quantify p53 lesions in post-menopausal women who previously did or did not use OCPs. This will provide insight into the protective effects of OCPs against HGSOC.

PRELIMINARY RESULTS: We determined the presence of p53 lesions by immunohistochemistry (IHC) in FT of women up to 40 years old (n=27) and &gt;60 years old (n=24) who underwent salpingectomies for non-cancer reasons. p53 lesions were identified in 3/27 cases of the younger cohort (11%) and in 10/24 of the older cohort (42%). Thus, we conclude an increased incidence of p53 lesions in older compared to younger women.

PROPOSED DESIGN: IHC for p53 will be performed on FT fimbria of women &gt;55 years old who received salpingectomy/hysterectomy for non-cancer reasons. Based on an assumed reduction in p53 lesions of 35% in women who used OCPs for 5 years or more compared to non-users (25 vs. 42%), analysis of 190 cases from each group will provide &gt;80% power (p&lt;0.05). Cases will be identified through Population Data BC and blind analysis by tp53 IHC will be performed at the Vancouver General Hospital. Post-menopausal status will be confirmed by endometrium histology and data flowed back to Pop Data BC to compare to OCP data.

CONCLUSION: Our preliminary study found that 42% of post menopausal women had p53 lesions, informing this study design. The study registered through this abstract will be the first to examine the impact of OCPs on the earliest known precursors of HGSOC.

Citation Format: Kendall Greening, Anthony Karnezis, Dawn Cochrane, Gillian Hanley, David Huntsman. THE EFFECT OF AGE AND OCP USE ON THE INCIDENCE OF PRE-CANCEROUS P53 LESIONS AND THE DEVELOPMENT OF HIGH GRADE SEROUS OVARIAN CARCINOMA [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr DP-006.

A comprehensive gene-environment interaction analysis in Ovarian Cancer using genome-wide significant common variants

As a follow-up to genome-wide association analysis of common variants associated with ovarian carcinoma (cancer), our study considers seven well-known ovarian cancer risk factors and their interactions with 28 genome-wide significant common genetic variants. The interaction analyses were based on data from 9971 ovarian cancer cases and 15,566 controls from 17 case-control studies. Likelihood ratio and Wald tests for multiplicative interaction and for relative excess risk due to additive interaction were used. The top multiplicative interaction was noted between oral contraceptive pill (OCP) use (ever vs. never) and rs13255292 (p value = 3.48 × 10-4 ). Among women with the TT genotype for this variant, the odds ratio for OCP use was 0.53 (95% CI = 0.46-0.60) compared to 0.71 (95%CI = 0.66-0.77) for women with the CC genotype. When stratified by duration of OCP use, women with 1-5 years of OCP use exhibited differential protective benefit across genotypes. However, no interaction on either the multiplicative or additive scale was found to be statistically significant after multiple testing correction. The results suggest that OCP use may offer increased benefit for women who are carriers of the T allele in rs13255292. On the other hand, for women carrying the C allele in this variant, longer (5+ years) use of OCP may reduce the impact of carrying the risk allele of this SNP. Replication of this finding is needed. The study presents a comprehensive analytic framework for conducting gene-environment analysis in ovarian cancer.

Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis

We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).

Validation of plasma miR-371a-3p expression in patients with metastatic and early stage germ cell tumor

526

Background: Identification of relapsing/residual viable germ cell malignancy (GCM) is often challenging in patients with CSI on surveillance or with residual post-chemotherapy disease. The presence of a biomarker for GCM would overcome the uncertainty of the current methods and improve the quality of care of those patients. Methods: A 2-cohorts pilot study involving patients with clearcut evidence of GCM (clinical stage IS, metastatic and GCM prior orchiectomy) for the development cohort and patients with CSI with or without signs of tumor relapse and patients with metastatic GCM post-chemotherapy for the validation cohort. Blood samples collected in Streck tubes were obtained prior to chemotherapy for the development cohort and post-orchiectomy, at the time of suspicious relapse or post-chemotherapy in the validation cohort. Plasma miR-371a-3p (miR371) was analyzed by RT-PCR. Positive predictive value (PPV), sensitivity, specificity, negative predictive values (NPV) and AUC of the ROC for miR371 and standard diagnostic tools (CT scan, AFP, BHCG and LDH) were calculated correlating qualitative miR371 expression to the presence of viable GCM. Results: 132 patients were enrolled into the development (33 pts) and validation (99 pts) cohorts. Within the development cohort 31/33 pts were miR371 positive, 2/33 pts were negative. 31 true positives were found among the 31 miR371 positive patients for a PPV of 100% (31/31). Two true negatives were found among the 2 patients who had no miR371 expression identified (teratoma, lymphoma). The validation cohort was chosen to evaluate the methodology among patients with predicted lower volumes or no clinically apparent disease. 13/99 patients within the validation cohort were miR371 positive and all 13 had subsequent confirmation of viable GCM. For the overall study of 132 pts, PPV was 100% (46/46), NPV 98%, sensitivity 96% and specificity 100%, the AUC of the ROC was 0.96. Conclusions: Detectable circulating miR-371a-3p levels predict viable GCM and may represent a strategy for biological rather than radiographic assessment for surveillance of early stage and for post-treatment patients. Larger studies to validate these and like results have been planned.

Selected medical interventions in women with a deleterious BRCA mutation: a population-based study in British Columbia

Background

We examined the uptake of risk-reducing interventions, including bilateral mastectomy, risk-reducing salpingo-oophorectomy, oral contraceptive pills, tamoxifen, and raloxifene, for the entire population of women with a deleterious BRCA1 or BRCA2 mutation in the Canadian province of British Columbia.

Methods

This retrospective population-based study used data available in British Columbia for all women who, between 1996 and 2014, were tested and found to have a BRCA mutation. Rates of risk-reducing interventions stratified according to the type of BRCA mutation and prior history of breast or gynecologic cancer (ovary, fallopian tube, peritoneal) are presented. Cancers diagnosed in women with a BRCA mutation after disclosure of their mutation status are also presented.

Results

The final study cohort consisted of 885 patients with a deleterious BRCA1 (n = 474) or BRCA2 (n = 411) mutation. Of the women with no prior breast cancer, 30.8% carrying a BRCA1 mutation and 28.3% carrying a BRCA2 mutation underwent bilateral mastectomy. Of women with no prior gynecologic cancer, 64.7% carrying a BRCA1 mutation and 62.2% carrying a BRCA2 mutation underwent risk-reducing bilateral salpingo-oophorectomy. Rates of chemoprevention with oral contraceptive pills and tamoxifen or raloxifene were low in all groups. In this cohort, 23 gynecologic and 70 breast cancers were diagnosed after disclosure of BRCA mutation status.

Conclusions

Our results suggest reasonable uptake of risk-reducing interventions in high-risk women. To minimize the occurrence of breast and ovarian cancer in women with a BRCA1 or BRCA2 mutation, more attention could be paid to ensuring that affected women receive proper counselling and follow-up.

DNA hypermethylation within TERT promoter upregulates TERT expression in cancer

Replicative immortality is a hallmark of cancer cells governed by telomere maintenance. Approximately 90% of human cancers maintain their telomeres by activating telomerase, driven by the transcriptional upregulation of telomerase reverse transcriptase (TERT). Although TERT promoter mutations (TPMs) are a major cancer-associated genetic mechanism of TERT upregulation, many cancers exhibit TERT upregulation without TPMs. In this study, we describe the TERT hypermethylated oncological region (THOR), a 433-bp genomic region encompassing 52 CpG sites located immediately upstream of the TERT core promoter, as a cancer-associated epigenetic mechanism of TERT upregulation. Unmethylated THOR repressed TERT promoter activity regardless of TPM status, and hypermethylation of THOR counteracted this repressive function. THOR methylation analysis in 1,352 human tumors revealed frequent (>45%) cancer-associated DNA hypermethylation in 9 of 11 (82%) tumor types screened. Additionally, THOR hypermethylation, either independently or along with TPMs, accounted for how approximately 90% of human cancers can aberrantly activate telomerase. Thus, we propose that THOR hypermethylation is a prevalent telomerase-activating mechanism in cancer that can act independently of or in conjunction with TPMs, further supporting the utility of THOR hypermethylation as a prognostic biomarker.

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants

The variant curation guidelines published in 2015 by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) provided the genetics community with a framework to assess variant pathogenicity; however, these rules are not gene specific. Germline pathogenic variants in the CDH1 gene cause hereditary diffuse gastric cancer and lobular breast cancer, a clinically challenging cancer predisposition syndrome that often requires a multidisciplinary team of experts to be properly managed. Given this challenge, the Clinical Genome Resource (ClinGen) Hereditary Cancer Domain prioritized the development of the CDH1 variant curation expert panel (VCEP) to develop and implement rules for CDH1 variant classifications. Here, we describe the CDH1 specifications of the ACMG/AMP guidelines, which were developed and validated after a systematic evaluation of variants obtained from a cohort of clinical laboratory data encompassing ∼827,000 CDH1 sequenced alleles. Comparing previously reported germline variants that were classified using the 2015 ACMG/AMP guidelines to the CDH1 VCEP recommendations resulted in reduced variants of uncertain significance and facilitated resolution of variants with conflicted assertions in ClinVar. The ClinGen CDH1 VCEP recommends the use of these CDH1-specific guidelines for the assessment and classification of variants identified in this clinically actionable gene.

Abstract IA19: Granulosa cell and other rare ovarian cancers: Genomic-derived diagnostics and emergent management strategies

Granulosa cell tumors, Sertoli-Leydig tumors, and small cell hypercalcemic ovarian cancers are clinically and biologically distinct. In the past few years the key mutations underpinning these mutations have been discovered. This has led to improved diagnostics for granulosa cell tumors and small cell hypercalcemic ovarian cancer. The discovery of pathognomonic mutations has led to the development of model systems and a better understanding of all three cancer types and for small cell ovarian cancer new treatment strategies.

Citation Format: David Huntsman. Granulosa cell and other rare ovarian cancers: Genomic-derived diagnostics and emergent management strategies. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA19.

Abstract B22: Capturing L1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers as a way to track tumor development

Endometrioid ovarian cancer (ENOC) and clear cell ovarian cancer (CCOC) share a common precursor lesion, endometriosis (ectopic growth of uterine lining), hence the designation endometriosis-associated ovarian cancer (EAOC). Women with endometriosis have up to three-fold increased risk of developing ENOC and CCOC. Efforts have been made to look for biomarkers that can help identifying women at risk of developing cancer; however, there are currently no biomarkers that stratify risk of cancer development. We performed whole-genome sequencing (WGS) on 29 ENOC and 35 CCOC cases and observed a frequent transduction event originating from an active LINE-1 (L1) retrotransposable element in the TTC28 gene. Such event occurred in 34% (10/29) of ENOC, and 31% (11/35) of CCOC cases. L1 retrotransposons are repetitive, mobile genetic elements capable of taking downstream DNA fragments and inserting them into random genomic locations via a process called 3’ transduction. Approximately 70-100 different potentially active L1s are epigenetically silenced in normal tissues, but tend to be reactivated in cancers. We subsequently used PCR to validate these TTC28-L1 transductions, and compared their presence to single nucleotide variations (SNVs) and frameshift mutations in formalin-fixed, paraffin-embedded (FFPE) tumor tissues from different tumor sites for 4 ENOC and 3 CCOC cases. We found that these transduction events along with classical driver mutations were almost ubiquitous across the tumor sites, suggesting these L1 events likely occurred early in the malignant transformation of EAOCs.

We developed a low-input, probe-based capture assay to test the presence of TTC28-L1 transductions as an alternative method to performing WGS. Oligonucleotide probes tiling 1 kb downstream of active L1s are used to capture DNA fragments containing the transduced DNA, and the fragments are sequenced on the MiSeq next-generation sequencing platform. Analyses are performed using the Geneious software and the published bioinformatics tool Socrates, specific for detecting DNA fragments with split reads (fragments with ends aligning to different parts of the genome). We successfully validated the assay on 9 cases with WGS data: 7 EAOC cases with TTC28-L1 transductions and 2 EAOC cases without TTC28-L1 transductions. DNA extracted from frozen tumor and buffy coat (normal control) were used for each case, and FFPE tissues were used for selected cases. All reads containing the transduction events aligned to genomic coordinates corresponding to the WGS data.

While L1-mediated DNA transductions are often passenger events during tumorigenesis, our data suggest that they likely occur early in ovarian cancer tumorigenesis. Our data show that this probe-based capture assay provides an alternative method to WGS, and may be useful in detecting active 3’ transductions in novel cases to track the development of ovarian tumors.

Citation Format: Zhouchunyang Xia, Dawn Cochrane, Michael Anglesio, Winnie Yang, Miguel Alcaide, Tayyebeh Nazeran, Janine Senz, Amy Lum, Ali Bashashati, Yikan Wang, Ryan Morin, Sohrab Shah, David Huntsman. Capturing L1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers as a way to track tumor development. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B22.

Abstract B39: The origins of endometriosis-associated cancers

Both clear cell ovarian carcinoma (CCOC) and endometrioid ovarian carcinoma (ENOC) are associated with ovarian endometriotic cysts, which is believed to be the precursor lesion of these cancers. Women with endometriotic cysts have up to a 3-fold increased risk of developing CCOC and ENOC. It is perplexing that these two clinically distinct histotypes of ovarian cancer arise from the same precursor lesion. We have performed whole-genome sequencing of ovarian cancer histotypes and found that while some genomic features are more common to one histotype than the other, there is not a single feature that is unique to either histotype. Lacking genomic evidence that could explain the differences between these histotypes, we hypothesized that these cancers arise from distinct cells of origin within endometrial tissue, and the cellular context accounts for their differences. We performed global proteomic analysis of ovarian cancer histotypes and identified CTH as a marker for CCOC. Upon examination of normal Müllerian tissues, we found that CTH is highly expressed in the ciliated cells of endometrium (both ectopic endometrium and endometriosis) and of the fallopian tube, with very little expression in the secretory cells of these tissues. We also find that other ciliated cell markers are expressed in CCOC, whereas endometrial secretory cell markers are expressed in ENOC. We propose a new model of CCOC and ENOC histogenesis wherein ENOC is derived from cells of secretory cell lineage whereas CCOC is derived from, or shares similarities to, cells of ciliated cell lineage. There remain, however, many unanswered questions. For example, while CCOC and ENOC occur at roughly equal prevalence, ciliated cells of the endometrium are rare compared to secretory cells. Cells in the endometriotic cyst are exposed to factors such as inflammation and reactive oxygen species, which could influence differentiation of endometrial progenitor cells into the secretory or ciliated cell lineage. To test factors that promote ciliated cell differentiation in normal endometrium, we treated organoid cultures of normal endometrium with IL-6 and Notch pathway modulators. We propose that ovarian cancer histotypes arise from different cells of origin and that the biology of the normal cells will be partly responsible for determining the phenotype of the cancers.

Citation Format: Dawn Cochrane, Basile Tessier-Cloutier, Katherine Lawrence, Tayyebeh Nazeran, Anthony Karnezis, Clara Salamanca, Timothy Lee, Angela Cheng, Jessica McAlpine, Lien Hoang, Blake Gilks, David Huntsman. The origins of endometriosis-associated cancers. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B39.

Abstract 3673: Targeting the epigenome of small cell hypercalcemic carcinoma of the ovary, hypercalcemic type (SCCOHT)

Small cell carcinoma of the ovary hypercalcemic type (SCCOHT) is a rare and poorly differentiated cancer that impacts young women with an average 2-year survival of less than 35%. We and others have discovered the inactivating mutations of SMARCA4 as the only consistent genetic alternation in SCCOHT genomes. SMARCA4 is the ATPase of the SWI/SNF chromatin-remodeling complex, which modulates chromatin accessibility to regulate transcription and plays critical roles in many biologic processes such as cell cycle control, apoptosis, and differentiation. SCCOHT also lacks the expression of SMARCA2, the alternative ATPase in the complex, contrasting the requirement of SMARCA2 for survival of most SMARCA4-deficient cancer cells. This suggest that the complete loss of chromatin-remodeling activity may rewire the epigenome and create opportunities for synthetic lethal targeting. A rational epigenetic drug screen identified EZH2 inhibitors and HDAC inhibitors as promising therapeutic agents in SCCOHT cells. We confirm that catalytic inhibition of EZH2 selectively suppressed the growth of SCCOHT cells in vitro and in xenograft models through activation of apoptosis and differentiation. Pan-HDAC inhibitors also displayed a more robust anticancer effect in SCCOHT cells than other in other ovarian cancer cell lines. Furthermore, combined treatment of EZH2 inhibitors and pan-HDAC inhibitors increased the global acetylation level at histone H3K27 site and synergistically suppressed the growth of SCCOHT cell lines and xenografts through robust induction of apoptosis. Although EZH2 or HDAC inhibitor treatment led to re-expression of SMARCA2, depletion of SMARCA2 had only minimal effect on drug response. Proteomic analysis identified key signaling pathways underlying the efficacy of epigenetic therapy that are under investigation. Therefore, inactivation of SWI/SNF chromatin remodeling complex may drive SCCOHT development through PRC2-dependent rewiring of the epigenome. Targeting these oncogenic events can be the feasible strategies for treatment of SCCOHT that warrant clinical investigation.

Citation Format: Yemin Wang, Shary Yu-ting Chen, Shane Colborne, Krystal Orlando, Jessica Lang, Anthony Karnezis, William Hendricks, Gregg Morin, Bernard Weissman, Jeffrey Trent, David Huntsman. Targeting the epigenome of small cell hypercalcemic carcinoma of the ovary, hypercalcemic type (SCCOHT) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3673.

A population-based analysis of germline BRCA1 and BRCA2 testing among ovarian cancer patients in an era of histotype-specific approaches to ovarian cancer prevention

Background

Identifying female carriers of BRCA1 and BRCA2 mutations is imperative for prevention of ovarian cancer and breast cancer. There are five major histologic subtypes of ovarian cancer and high grade serous cancer (the most common) is reported in 75–100% of BRCA1 and BRCA2 mutation carriers. We examined histology-based referral to the Hereditary Cancer Program following an educational prevention campaign recommending BRCA1 and BRCA2 mutation screening for all high-grade serous cancer patients.

Methods

We conducted a population-based retrospective study in the province of British Columbia, Canada that included all patients visiting the Hereditary Cancer Program for genetic counselling for BRCA1 and BRCA2 mutation between 2001 and 2014. We examined the difference in rates of BRCA1 and BRCA2 testing between serous cancer patients and endometrioid and clear cell cancer patients using a differences in differences analysis. We also calculated the mean number of family members tested for every BRCA1 and BRCA2 identified ovarian cancer patient before and after the educational campaign.

Results

There were 5712 women tested for a BRCA1 and BRCA2 mutation at the HCP between 2001 and 2014, 887 of which had previously received a diagnosis of ovarian cancer. By 2013, 43% of serous cancer patients were being tested for BRCA1 and BRCA2 mutations compared with 20% of endometrioid and clear cell patients (p < 0.001). The mean number of family members tested for each BRCA1 and BRCA2 positive ovarian cancer patient increased after the educational campaign from 2.54 to 3.27 (p = 0.071), and the number of family members identified as BRCA positive also increased significantly.

Conclusions

Recommendations for histology-based referral significantly increased the likelihood of serous cancer patients being tested for BRCA mutations. There was also an increase in the number of carrier tests performed for each BRCA1 and BRCA2 index ovarian cancer patient.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4153-8) contains supplementary material, which is available to authorized users.

The driver landscape of sporadic chordoma

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma.

Abstract B04: RAD51 expression as a biomarker of homologous recombination deficiency in ovarian cancer

RAD51 is a critical component of the homologous recombination pathway, forming a nucleoprotein filament that enables strand exchange and templated error-free DNA repair. The tumor suppressors BRCA1 and BRCA2 interact with RAD51 to control its activity on DNA. Defects in homologous recombination in tumors are clinically relevant, with evidence of synthetic lethality of such cancers to poly ADP ribose polymerase (PARP) inhibitors.

Mutations in RAD51 are uncommon in cancer, but aberrant over-expression of RAD51 has been reported as a mechanism to overcome a recombination defect in in-vitro models. However there are no large scale studies on RAD51 expression in clinically annotated data sets. Here we report a series of experiments to study RAD51 protein expression in ovarian cancer, a tumor type where recombination defects are prominent and being evaluated in several clinical trials of PARP inhibition. Analysis of DNA repair protein expression in formalin fixed clinical tissue is challenging, and our experiments highlight recent advances in quantitative microscopy that are generalizable to other clinical scenarios as well.

We first evaluated several commercially available monoclonal antibodies to RAD51 using siRNA depleted cell blocks, to identify an appropriate reagent and staining conditions for formalin fixed paraffin embedded (FFPE) material. We then analyzed RAD51 expression in a collection of 600 ovarian cancer samples obtained through the British Columbia Cancer Agency (BCCA) OvCare consortium, using a combination of multiplexed immunofluorescence staining and automated spectral microscopy to quantify staining on a per-cell basis. We find that RAD51 expression displays a Gaussian distribution in this cohort of high grade epithelial cancers, with no obvious correlation to BRCA mutation status. RAD51 sub-nuclear foci, which are a commonly used measure of homologous recombination in-vitro, did not prove to be accurately quantifiable in FFPE material.

We then stained for RAD51 in a collection of approximately 250 ovarian cancer samples obtained from the SCOTROC4 trial. This clinical trial enrolled women with ovarian cancer into two treatment arms with fixed dose and escalated doses of carboplatin. Platinum sensitivity has been shown to correlate with sensitivity to PARP inhibitors, due to the requirement of homologous recombination for repair of platinum adducts. Therefore this trial offers a unique opportunity to study the predictive significance of biomarkers of homologous recombination in-vivo. In our analysis of this data set, we find that samples in the lowest quartile of RAD51 expression displayed a significantly improved survival after platinum chemotherapy, consistent with decreased HR in these cases. These are the first data on RAD51 in a clinical trial dataset of platinum sensitivity.

Our study highlights methods and technical challenges for the quantitative analysis of DNA repair proteins in human clinical trial specimen, and describes a potential biomarker for synthetic lethal approaches targeting homologous recombination deficiency.

Citation Format: Michal M. Hoppe, David SP Tan, Diana GZ Lim, Anthony Karnezis, David Huntsman, Jennifer Steel, Xinxue Liu, James Paul, Liz-Anne Lewsley, Nadeem Siddiqui, Robert Brown, Anand D. Jeyasekharan. RAD51 expression as a biomarker of homologous recombination deficiency in ovarian cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B04.

Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci

We previously identified associations with ovarian cancer outcome at five genetic loci. To identify putatively causal genetic variants and target genes, we prioritized two ovarian outcome loci (1q22 and 19p12) for further study. Bioinformatic and functional genetic analyses indicated that MEF2D and ZNF100 are targets of candidate outcome variants at 1q22 and 19p12, respectively. At 19p12, the chromatin interaction of a putative regulatory element with the ZNF100 promoter region correlated with candidate outcome variants. At 1q22, putative regulatory elements enhanced MEF2D promoter activity and haplotypes containing candidate outcome variants modulated these effects. In a public dataset, MEF2D and ZNF100 expression were both associated with ovarian cancer progression-free or overall survival time. In an extended set of 6,162 epithelial ovarian cancer patients, we found that functional candidates at the 1q22 and 19p12 loci, as well as other regional variants, were nominally associated with patient outcome; however, no associations reached our threshold for statistical significance (p<1×10-5). Larger patient numbers will be needed to convincingly identify any true associations at these loci.

Abstract 1238: Targeting the platelet derived growth factor receptor (PDGFR) with the receptor tyrosine kinase inhibitor ponatinib in small cell carcinoma of the ovary, hypercalcemic type

Subunits of the SWI/SNF chromatin-remodeling complex are tumor suppressors that are inactivated in ~20% of all cancers, yet few targeted treatments have shown selective activity in SWI/SNF-mutant cancers. Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, aggressive ovarian cancer in young women that is universally driven by SWI/SNF dysregulation. Given that two-year survival following standard high-dose chemotherapy and radiation in SCCOHT is less than 35%, a great need exists for effective targeted therapies to improve outcomes for these women. We previously demonstrated that SCCOHT tumors are driven by inactivating mutations in SMARCA4, one of two mutually exclusive SWI/SNF ATPases. In addition, we have shown that SCCOHT lacks expression of the alternative SWI/SNF ATPase, SMARCA2. We have now found through integrated genomic and functional analyses in SCCOHT tumors and cell lines that SMARCA4 loss correlates with increased expression of receptor tyrosine kinases (RTKs) including the platelet derived growth factor receptors (PDGFRs). Through integration of high-throughput RNA interference and drug screens in SCCOHT cells we have identified sensitivity to RTK knockdown and RTK inhibitors including the FDA-approved oncology drug, ponatinib. These data corroborate prior studies showing RTK dependence in rhabdoid tumors, rare cancers that are also driven by mutations in the SWI/SNF complex. Of the known ponatinib targets, PDGFR-alpha and FGFR1 were highly expressed in SCCOHT tumors, as confirmed in RNA-Seq data (four tumors) and a SCCOHT tissue microarray (TMA; ten tumors). Furthermore, PDGFR-alpha and -beta phosphorylation and downstream signaling are inhibited by ponatinib in SCCOHT cells, suggesting that these tumors are sensitive to ponatinib due to dependence on signaling through these RTKs. Finally, given ponatinib’s potency in vitro and the proposed mechanism of action, we tested this agent in xenograft models of SCCOHT. In addition to confirming efficacy in a SCCOHT cell line xenograft model, superior efficacy was demonstrated in two patient-derived xenograft (PDX) models of SCCOHT with ponatinib. Thus, ponatinib effectively targets SWI/SNF-mutant SCCOHT tumors through inhibition of PDGFR signaling and may have clinical utility for the treatment of these cancers.

Citation Format: Jessica Diane Lang, William Hendricks, Pilar Ramos, Holly Yin, Chris Sereduk, Jeffrey Kiefer, Yemin Wang, Anthony N. Karnezis, Bernard Weissman, David Huntsman, Jeffrey Trent. Targeting the platelet derived growth factor receptor (PDGFR) with the receptor tyrosine kinase inhibitor ponatinib in small cell carcinoma of the ovary, hypercalcemic type [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1238. doi:10.1158/1538-7445.AM2017-1238

Abstract AP32: THE METHYLTRANSFERASE EZH2 IS A VULNERABLE TARGET IN SMALL CELL CARCINOMA OF THE OVARY, HYPERCALCEMIC TYPE (SCCOHT)

PURPOSE: SCCOHT is a rare, poorly differentiated and very deadly ovarian tumor that mainly affects young women with the median age in twenties. Recently, we and others have discovered that the genome of SCCOHT was minimally disturbed compared to common malignancies with the inactivation mutations of SMARCA4 being the only recurrent genetic alternation in SCCOHT genome. SMARCA4 is the ATPase of the SWI/SNF chromatin-remodeling complex, which is the master regulator of gene transcription through controlling the accessibility of chromatin and therefore plays critical roles in many biological processes such as cell cycle control, apoptosis, and differentiation. Recently, a genetic antagonism has been observed between some SWI/SNF complex components and the histone methyltransferase EZH2 of the polycomb repressive complex 2 (PRC2), suggesting that EZH2 may be a vulnerable target in certain SWI/SNF-deficient tumor. Therefore, we aimed to determine the promise of defeating SCCOHT through targeting EZH2 in the present study.

METHODS: The EZH2 protein expression was determined by immunohistochemistry on the SCCOHT tissue microarray. Cell viability, cell cycle and apoptosis were measured by crystal violet staining, FACS analysis and live cell imaging with activated caspase-3/7 staining, respectively. The proteomic profiles of SCCOHT cells were determined by Mass Spectrometry using the TMT-labeled peptide fractions. Two SCCOHT xenograft mouse models were established from BIN67 and SCCOHT1 cells, respectively, in immune-deficient mice were used for the evaluation of EPZ-6438 efficacy in vivo.

RESULT: All (24/24) SCCOHT expressed abundant EZH2 protein. In comparison to other ovarian cell lines, SCCOHT cells displayed hypersensitivity to two EZH2 inhibitors (GSK126 and EPZ-6438) and EZH2 shRNA. Furthermore, EPZ-6438 induced cell cycle arrest, apoptosis and cell differentiation in SCCOHT cells, accompanying by the induction of genes involved in cell proliferation, apoptosis and differentiation. Treatment of EPZ-6438 in SCCOHT xenograft-bearing mice delayed tumor progression, improved the survival of mice. Further, re-expression of SMARCA4 suppressed the expression of EZH2 and the global level of histone H3K27 trimethylation, induced the expression of PRC2 targets that are induced by EZH2 inhibitors and triggered differentiation of SCCOHT cells. In addition, we also discovered that SCCOHT cells are hypersensitive to multiple inhibitors of histone deacetylase (HDAC), which is known to cooperate with EZH2 to silence certain target genes. Combined treatment of EPZ-6438 and Quisinostat (an HDAC inhibitor) synergistically suppressed the proliferation of SCCOHT cells.

CONCLUSION: Our data suggest that EZH2 is a promising therapeutic target for fighting SCCOHT. Combined pharmacological targeting of both EZH2 and HDAC may provide a novel treatment option for SCCOHT patients.

Citation Format: Yemin Wang, Shary Chen, Anthony Karnezis, Nancy Dos Santos, Pilar Ramos, Sarah Maines-Bandiera, Christine Chow, Bernard Weissman, Jeffrey Trent, David Huntsman. THE METHYLTRANSFERASE EZH2 IS A VULNERABLE TARGET IN SMALL CELL CARCINOMA OF THE OVARY, HYPERCALCEMIC TYPE (SCCOHT) [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr AP32.

Abstract DPOC-014: BEYOND CODING MUTATIONS: USING RETROTRANSPOSONS TO PREDICT OVARIAN CANCER DEVELOPMENT

PURPOSE: Women with endometriosis, a painful condition caused by displaced endometrial tissue, have a 3-fold increased risk of developing endometrioid ovarian cancer (ENOC) and clear cell ovarian cancer (CCOC). How two distinct cancers arise from the same precursor lesion is unknown. Sensitive biomarkers are needed to identify women with endometriosis at risk of developing cancer. We performed whole genome sequencing on 29 ENOC and 36 CCOC cases and observed a highly frequent insertion event originating from an active LINE-1 (L1) retrotransposon in the TTC28 gene. L1 retrotransposons are mobile genetic elements that can take downstream DNA pieces and insert them into random genomic locations in a process called 3' transduction. L1s are epigenetically silenced in normal tissues, but are known to become activated in a variety of cancers. A recent study showed a stepwise loss of methylation across various L1 loci between normal endometrium, contiguous endometriosis (endometriosis adjacent to tumor), and ENOC/CCOC tissues. We hypothesize that TTC28 L1 retrotransposon is an early event in the transformation of endometriosis into ENOC and CCOC and such events could be used as biomarkers for endometriosis with high cancer risk.

METHODS: We compared the presence of TTC28 L1 3' transductions to six SNVs and frame shifts mutations in normal, endometriosis, and tumor tissues from different anatomical sites in four ENOC and four CCOC cases. PCR followed by Sanger sequencing was used to detect TTC28 L1 insertions, and micro-fluidic PCR assay followed by MiSeq sequencing used to detect SNV/frameshift mutations. To broaden the analysis we will use a target capture sequencing method to track novel TTC28 and other L1 transductions. In these experiments probes tiling 1kbp downstream of L1s will be used to capture DNA fragments containing L1 transductions; the captured fragments will be sequenced on the MiSeq. We will assess the difference in TTC28 L1 methylation status between normal, endometriosis, and tumor tissues via the sequencing of bi-sulfite treated DNA.

RESULTS: TTC28 L1 retrotransposition insertion is present at all 5 tumor sites in 75% (6/8) of cases, and is present in 3/5 or 4/5 tumor sites in the remaining cases. Analysis shows that TTC28 L1 insertion preceded some SNV and/or frameshift mutations. Preliminary results show that TTC28 L1 promoters are unmethylated in tumors with L1 insertions. Future experiments involving additional cases with endometriosis tissues will be performed. We expect to see L1 promoter hypomethylation and L1 transductions in endometriosis tissues.

CONCLUSION: TTC28 L1 promoter hypomethylation and TTC28 L1 transductions may be early events in the transformation of endometriosis to cancer that can be explored as a method to predict tumor development. The development of a target capture assay to detect novel L1 transductions will be crucial for investigating cases without whole genome sequencing data. Ultimately, we hope to detect L1 insertions in plasma samples, and use L1 insertions as a biomarker to identify high-risk endometriosis cases.

Citation Format: Zhouchunyang Xia, Dawn Cochrane, Michael S Anglesio, Tayyebeh M Nazeran, Janine Senz, Amy Lum, Ali Bashashati, Yi Kan Wang, Sohrab P Shah, David Huntsman. BEYOND CODING MUTATIONS: USING RETROTRANSPOSONS TO PREDICT OVARIAN CANCER DEVELOPMENT [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr DPOC-014.