Abstract NTOC-084: THE PROMISE OF COMBINATIONAL TREATMENT OF HISTONE DEACETYLASE 6 INHIBITOR ACY-1215 AND PROTEASOME INHIBITOR BORTEZOMIB IN SCCOHT

PURPOSE: Small cell carcinoma of the ovary, hypercalcaemic type (SCCOHT) is a rare ovarian cancer that predominantly affects young women with a median age of 24 years. Although half of the tumors are diagnosed at an early stage, the prognosis is dismal due to lack of effective treatment options. In response to drastic increase of protein translation and cellular stress during malignant transformation, cancer cells have evolved to highly depend on protein surveillance pathways to correct or degrade unfolded and misfolded proteins to ensure protein homeostasis. Inhibition of these protein surveillance pathways has been proven to selectively target cancer cells. Particularly, inhibition of proteasome, which degrades more than 80% of cellular proteins, by selective inhibitors leads to accumulation of its substrates and consequently results in activation of apoptotic pathways in highly proliferative cancer cells. However, resistance occurs frequently. As a result several combinational treatments have been investigated in clinical trials with various drugs, such as HDAC6 inhibitor, which shuts down the aggresome-mediated proteolysis. Therefore, we aimed to determine the promise of inhibiting both protein degradation pathways as a novel therapeutic strategy for SCCOHT.

EXPERIMENTAL PROCEDURE: Concentration-effect relationships were determined for both proteasome and HDAC6 inhibitors, alone or in combination, in SCCOHT cell lines and other ovarian carcinoma cell lines using a 3-day cell viability assay measured by crystal violet staining. Cell apoptosis was measured by live cell imaging with activated caspase-3/7. Drug action mechanism was interrogated by Western blotting.

RESULT: SCCOHT cells are hypersensitive to both proteasome inhibitor (Bortezomib) and HDAC6 inhibitor (ACY-1215) with IC50 around low nM and μM, respectively. In addition, both Bortezomib and ACY-1215 inhibited cell proliferation and induced apoptosis in SCCOHT cells. Treatment with ACY-1215 led to inhibition of the aggresome as evidenced by an increased level of acetyl-tubulin, accumulation of polyubiquitinated proteins and upregulation of the unfolded protein response. Combination of Bortezomib and ACY-1215 led to an increased level of poly-ubiquitinated proteins, stronger suppression of cell proliferation and more apoptosis compared to either drug alone in SCCOHT cells, with some dosing having synergistic effect.

CONCLUSION: Our data suggest that ACY-1215 or Bortezomib alone significantly suppressed the growth and induced apoptosis of SCCOHT cells. Combination of ACY-1215 and Bortezomib synergistically increased growth suppression and cell apoptosis and thereby may be a potential rational therapeutic strategy for SCCOHT.

Citation Format: Yuting Shary Chen, Yemin Wang, Anthony Karnezis, Pilar Ramos, Holly Yine, Bernard Weissman, Jeffrey Trent, David Huntsman. THE PROMISE OF COMBINATIONAL TREATMENT OF HISTONE DEACETYLASE 6 INHIBITOR ACY-1215 AND PROTEASOME INHIBITOR BORTEZOMIB IN 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 NTOC-084.

Abstract NTOC-090: TARGETING AND EFFICACY OF THE RECEPTOR TYROSINE KINASE INHIBITOR PONATINIB IN SMALL CELL CARCINOMA OF THE OVARY, HYPERCALCEMIC TYPE, WORKS THROUGH INHIBITION OF PLATELET DERIVED GROWTH FACTOR RECEPTOR (PDGFR)

The work that will be presented strongly suggests the identification of a unique vulnerability of Small Cell Carcinoma of the Ovary-Hypercalcemic Type (SCCOHT) to PDGFR inhibition. SCCOHT is an aggressive subtype of ovarian cancer afflicting young women and children with fewer than 35% of patients surviving two years after diagnosis. Currently, these patients must endure high dose chemotherapy because no effective targeted therapies have been identified. We previously demonstrated that these tumors are driven by inactivating mutations in SMARCA4, one of two ATPases in the SWI/SNF chromatin-remodeling complex. In addition, we have also shown that SCCOHT lacks expression of the alternative SWI/SNF ATPase, SMARCA2. SWI/SNF is a key tumor suppressor complex in diverse cancers and its members are mutationally inactivated in up to 50% of other ovarian cancer subtypes. However, no therapeutic approaches selective for SWI/SNF-dysregulation in cancers are routinely used.

We have now found through multiomic (DNA/RNA), pathway analysis, immunohistochemistry and functional studies 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 (PDGRs). Through integration of high-throughput RNA interference and drug screens in SCCOHT cell lines we have also identified sensitivity to RTK knockdown and inhibitors such as 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. As ponatinib is approved for cancer treatment and showed great potency, we tested this agent in two patient-derived xenograft (PDX) models of SCCOHT. Ponatinib significantly reduced tumor growth in both models. Of the known ponatinib targets, PDGFR and FGFR1 were highly expressed in SCCOHT tumors, suggesting that SCCOHTs are sensitive to ponatinib through the expression of these RTKs. Further, PDGFR-alpha phosphorylation and downstream signaling are strongly inhibited by ponatinib in SCCOHT. In summary we believe this finding may allow a way to be exploited therapeutically through the FDA-approved inhibitor ponatinib.

Citation Format: Jessica D. Lang, William Hendricks, Pilar Ramos, Holly Yin, Chris Sereduk, Jeffrey Kiefer, Yemin Wang, Anthony N. Karnezis, Bernard Weissman, David Huntsman, Jeffrey Trent. TARGETING AND EFFICACY OF THE RECEPTOR TYROSINE KINASE INHIBITOR PONATINIB IN SMALL CELL CARCINOMA OF THE OVARY, HYPERCALCEMIC TYPE, WORKS THROUGH INHIBITION OF PLATELET DERIVED GROWTH FACTOR RECEPTOR (PDGFR) [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 NTOC-090.

A structured latent model for ovarian carcinoma subtyping from histopathology slides

Accurate subtyping of ovarian carcinomas is an increasingly critical and often challenging diagnostic process. This work focuses on the development of an automatic classification model for ovarian carcinoma subtyping. Specifically, we present a novel clinically inspired contextual model for histopathology image subtyping of ovarian carcinomas. A whole slide image is modelled using a collection of tissue patches extracted at multiple magnifications. An efficient and effective feature learning strategy is used for feature representation of a tissue patch. The locations of salient, discriminative tissue regions are treated as latent variables allowing the model to explicitly ignore portions of the large tissue section that are unimportant for classification. These latent variables are considered in a structured formulation to model the contextual information represented from the multi-magnification analysis of tissues. A novel, structured latent support vector machine formulation is defined and used to combine information from multiple magnifications while simultaneously operating within the latent variable framework. The structural and contextual nature of our method addresses the challenges of intra-class variation and pathologists' workload, which are prevalent in histopathology image classification. Extensive experiments on a dataset of 133 patients demonstrate the efficacy and accuracy of the proposed method against state-of-the-art approaches for histopathology image classification. We achieve an average multi-class classification accuracy of 90%, outperforming existing works while obtaining substantial agreement with six clinicians tested on the same dataset.

Clinically-inspired automatic classification of ovarian carcinoma subtypes

CONTEXT

It has been shown that ovarian carcinoma subtypes are distinct pathologic entities with differing prognostic and therapeutic implications. Histotyping by pathologists has good reproducibility, but occasional cases are challenging and require immunohistochemistry and subspecialty consultation. Motivated by the need for more accurate and reproducible diagnoses and to facilitate pathologists' workflow, we propose an automatic framework for ovarian carcinoma classification.

MATERIALS AND METHODS

Our method is inspired by pathologists' workflow. We analyse imaged tissues at two magnification levels and extract clinically-inspired color, texture, and segmentation-based shape descriptors using image-processing methods. We propose a carefully designed machine learning technique composed of four modules: A dissimilarity matrix, dimensionality reduction, feature selection and a support vector machine classifier to separate the five ovarian carcinoma subtypes using the extracted features.

RESULTS

This paper presents the details of our implementation and its validation on a clinically derived dataset of eighty high-resolution histopathology images. The proposed system achieved a multiclass classification accuracy of 95.0% when classifying unseen tissues. Assessment of the classifier's confusion (confusion matrix) between the five different ovarian carcinoma subtypes agrees with clinician's confusion and reflects the difficulty in diagnosing endometrioid and serous carcinomas.

CONCLUSIONS

Our results from this first study highlight the difficulty of ovarian carcinoma diagnosis which originate from the intrinsic class-imbalance observed among subtypes and suggest that the automatic analysis of ovarian carcinoma subtypes could be valuable to clinician's diagnostic procedure by providing a second opinion.

Abstract 3422: The influence of genetic and clinical factors on the outcome following a diagnosis of small cell carcinoma of the ovary, hypercalcemic type

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is the most common undifferentiated ovarian tumor diagnosed in women below the age of 40. While it is uncommon, with only ∼500 cases reported, it is an extremely aggressive tumor, with long term survival rates of <30% in early stage disease. Recently, we discovered that SCCOHT is a monogenic disease, attributable to germline and somatic deleterious mutations in the chromatin remodeling gene, SMARCA4. Since then, single case reports have been published on women affected with SCCOHT, but no large studies have been conducted on the effect of these mutations, germline or somatic, on the disease. Furthermore, while numerous publications have described the therapies used in single cases or small cohorts of SCCOHT patients, treatment remains varied, with no standardized protocols. In an attempt to clarify which factors have an effect on the course of the disease, we reviewed all published and a cohort of unpublished SCCOHT cases and collected information on the following factors: stage at diagnosis, age at diagnosis, treatment modality used (chemotherapy/radiotherapy/high dose chemotherapy), mutation type (germline/somatic), and length of survival. We were able to acquire information in at least 2 of these parameters in 267 cases and performed multiple analyses. Clinically, we found that the greatest influence on patient outcome was related to stage at diagnosis (p < 0.001) and treatment modality (p = 0.01), while age at diagnosis had no significant effect (p = 0.72). Molecularly, the presence of a germline mutation in the patient did not affect the age of onset (p = 0.86), nor did it have an effect on the length of survival of the patient (p = 0.63). Overall, this is the largest study conducted to date analyzing the influence of clinical factors on the outcome of patients diagnosed with SCCOHT, and is the first large study to analyze the effect of germline mutations on the outcome of these patients.

Citation Format: Leora Witkowski, Catherine Goudie, Pilar Ramos, Anthony N. Karnezis, Talia Boshari, Patricia Pautier, Michel Longy, James A. Knost, Emmanouil Saloustros, W Glenn McCluggage, Martin Hasselblatt, William P. Hendricks, David Huntsman, Douglas A. Levine, Jeffrey Trent, William D. Foulkes. The influence of genetic and clinical factors on the outcome following a diagnosis of small cell carcinoma of the ovary, hypercalcemic type. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3422.

Abstract 1611: Epithelial-mesenchymal-epithelial transition induced by long term exposure to TGFB1 creates cellular heterogeneity

Reversible and dynamic transitions between epithelial and mesenchymal cellular states (EMT/MET) contribute to cancer progression and dissemination. Whereas EMT facilitates initial steps of tumour cell detachment, MET is likely required for colonization at distant sites. Although MET is generally perceived as mirroring EMT, we hypothesize that MET entails its own set of novel and/or differentially active molecular circuitries, generating cells with features distinct from the original epithelial state.

Using an in vitro TGFβ1-induced EMT/MET model, we demonstrated that MET generates co-existing heterogeneous cell populations (Reverted-Epithelial or RE-cells) with novel phenotypic and functional properties, such as increased self-renewal, in vivo increased tumourigenicity and distinct chemoresistance properties.

Overall, our results indicate that MET is a permissive process, driving cellular plasticity towards heterogeneity and with it, creating novel biological signatures of relevance for cancer growth.

Citation Format: Patricia Oliveira, Joana Carvalho, Sara Rocha, Mafalda Azevedo, Andre F. Vieira, Daniel Ferreira, Nuno Mendes, Ines Reis, Joao Vinagre, Alireza Heravi-Moussavi, Joana B. Nunes, Jorge Lima, Valdemar Máximo, Angela Burleigh, Calvin Roskelley, Joana Paredes, Fatima Carneiro, David Huntsman, Carla Oliveira. Epithelial-mesenchymal-epithelial transition induced by long term exposure to TGFB1 creates cellular heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1611.

Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers

Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted “panel” sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care. Between June 2012 and August 2014, 100 adult patients with incurable cancers consented to participate in the Personalized OncoGenomics (POG) study. Fresh tumor and blood samples were obtained and used for whole-genome and RNA sequencing. Computational approaches were used to identify candidate driver mutations, genes, and pathways. Diagnostic and drug information were then sought based on these candidate “drivers.” Reports were generated and discussed weekly in a multidisciplinary team setting. Other multidisciplinary working groups were assembled to establish guidelines on the interpretation, communication, and integration of individual genomic findings into patient care. Of 78 patients for whom WGA was possible, results were considered actionable in 55 cases. In 23 of these 55 cases, the patients received treatments motivated by WGA. Our experience indicates that a multidisciplinary team of clinicians and scientists can implement a paradigm in which WGA is integrated into the care of late stage cancer patients to inform systemic therapy decisions.

Abstract POSTER-TECH-1119: Phylogenetic portraits of high grade serous ovarian cancer

High Grade Serous Ovarian Cancer (HGSOvCa) is characterized by genomic instability resulting from deficient DNA repair processes primarily due to TP53 mutation and BRCA abnormalities. Genomic instability has been shown to result in significant intratumoral heterogeneity, with temporally and spatially separated tumours exhibiting unique mutational profiles. A key unanswered question is whether genomic instability produces functionally relevant driver mutations, or whether the tumours complement of driver mutations predates the emergence of instability.

We sought to reconstruct the evolutionary histories of the tumours of 8 HGSOvCa patients using spatial and temporal profiling of somatic mutations. For each patient, we collected multiple tumour biopsies resected from primary and metastatic sites at the time of surgery. We then used whole genome shotgun sequencing to identify somatic point mutation, rearrangement and copy number changes present at each site. We used novel computational techniques to unmix the signal produced by sequencing of a mixture of tumour cells, and infer the genomic architecture of clonal populations in each tumour sample. Additionally, we used phylogenetic inference techniques to reconstruct the ancestral relationships between the genomically distinct clones identified in each patient. We classified mutations as occurring ancestrally (before clonal divergence) or occurring on a descendent lineage.

We identified multiple well known driver mutations occurring in descendent lineages of the tumour phylogeny, including mutations in CDKN2A, BCL6 and ERBB2. Aberrant site specific expression patterns were concomitant with genomic changes. Furthermore, we identified instances of convergent evolution, including independent deletion of wild type RAD51B in a patient with a germline RAD51B mutation. Reconstruction of clonal phylogenies enabled inference of metastatic spread. In one patient, a minor subclone of a right ovary tumour acquired an ERBB2 amplification, then subsequently populated all other metastatic sites sampled by the experiment. Finally, from our analyses we concluded that in many HGSOvCa, genomic instability and associated copy number changes result in the deletion of a significant number of point mutations, with implications for phylogenetic reconstruction using traditional techniques.

Citation Format: Andrew McPherson, Andrew Roth, David Huntsman, Jessica McAlpine, Sohrab Shah. Phylogenetic portraits of high grade serous ovarian cancer [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-TECH-1119.

Hereditary diffuse gastric cancer: updated clinical guidelines with an emphasis on germline CDH1 mutation carriers

Germline CDH1 mutations confer a high lifetime risk of developing diffuse gastric (DGC) and lobular breast cancer (LBC). A multidisciplinary workshop was organised to discuss genetic testing, surgery, surveillance strategies, pathology reporting and the patient's perspective on multiple aspects, including diet post gastrectomy. The updated guidelines include revised CDH1 testing criteria (taking into account first-degree and second-degree relatives): (1) families with two or more patients with gastric cancer at any age, one confirmed DGC; (2) individuals with DGC before the age of 40 and (3) families with diagnoses of both DGC and LBC (one diagnosis before the age of 50). Additionally, CDH1 testing could be considered in patients with bilateral or familial LBC before the age of 50, patients with DGC and cleft lip/palate, and those with precursor lesions for signet ring cell carcinoma. Given the high mortality associated with invasive disease, prophylactic total gastrectomy at a centre of expertise is advised for individuals with pathogenic CDH1 mutations. Breast cancer surveillance with annual breast MRI starting at age 30 for women with a CDH1 mutation is recommended. Standardised endoscopic surveillance in experienced centres is recommended for those opting not to have gastrectomy at the current time, those with CDH1 variants of uncertain significance and those that fulfil hereditary DGC criteria without germline CDH1 mutations. Expert histopathological confirmation of (early) signet ring cell carcinoma is recommended. The impact of gastrectomy and mastectomy should not be underestimated; these can have severe consequences on a psychological, physiological and metabolic level. Nutritional problems should be carefully monitored.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

Human cancers, including breast cancers, comprise clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution, underpinning important emergent features such as drug resistance and metastasis. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours. However, the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours have not been systematically examined at single-cell resolution. Here we show, using deep-genome and single-cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single-cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies using patient-derived breast cancer xenoengraftment.

Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas

Background

Ovarian low-grade serous carcinoma (LGSC) has fewer mutations than ovarian high-grade serous carcinoma (HGSC) and a less aggressive clinical course. However, an overwhelming majority of LGSC patients do not respond to conventional chemotherapy resulting in a poor long-term prognosis comparable to women diagnosed with HGSC. KRAS and BRAF mutations are common in LGSC, leading to clinical trials targeting the MAPK pathway. We assessed the stability of targetable somatic mutations over space and/or time in LGSC, with a view to inform stratified treatment strategies and clinical trial design.

Methods

Eleven LGSC cases with primary and recurrent paired samples were identified (stage IIB-IV). Tumor DNA was isolated from 1–4 formalin-fixed paraffin-embedded tumor blocks from both the primary and recurrence (n = 37 tumor and n = 7 normal samples). Mutational analysis was performed using the Ion Torrent AmpliSeq^TM Cancer Panel, with targeted validation using Fluidigm-MiSeq, Sanger sequencing and/or Raindance Raindrop digital PCR.

Results

KRAS (3/11), BRAF (2/11) and/or NRAS (1/11) mutations were identified in five unique cases. A novel, non-synonymous mutation in SMAD4 was observed in one case. No somatic mutations were detected in the remaining six cases. In two cases with a single matched primary and recurrent sample, two KRAS hotspot mutations (G12V, G12R) were both stable over time. In three cases with multiple samplings from both the primary and recurrent surgery some mutations (NRAS Q61R, BRAF V600E, SMAD4 R361G) were stable across all samples, while others (KRAS G12V, BRAF G469V) were unstable.

Conclusions

Overall, the majority of cases with detectable somatic mutations showed mutational stability over space and time while one of five cases showed both temporal and spatial mutational instability in presumed drivers of disease. Investigation of additional cases is required to confirm whether mutational heterogeneity in a minority of LGSC is a general phenomenon that should be factored into the design of clinical trials and stratified treatment for this patient population.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2407-14-982) contains supplementary material, which is available to authorized users.

Germline mutations in MAP3K6 are associated with familial gastric cancer

Gastric cancer is among the leading causes of cancer-related deaths worldwide. While heritable forms of gastric cancer are relatively rare, identifying the genes responsible for such cases can inform diagnosis and treatment for both hereditary and sporadic cases of gastric cancer. Mutations in the E-cadherin gene, CDH1, account for 40% of the most common form of familial gastric cancer (FGC), hereditary diffuse gastric cancer (HDGC). The genes responsible for the remaining forms of FGC are currently unknown. Here we examined a large family from Maritime Canada with FGC without CDH1 mutations, and identified a germline coding variant (p.P946L) in mitogen-activated protein kinase kinase kinase 6 (MAP3K6). Based on conservation, predicted pathogenicity and a known role of the gene in cancer predisposition, MAP3K6 was considered a strong candidate and was investigated further. Screening of an additional 115 unrelated individuals with non-CDH1 FGC identified the p.P946L MAP3K6 variant, as well as four additional coding variants in MAP3K6 (p.F849Sfs*142, p.P958T, p.D200Y and p.V207G). A somatic second-hit variant (p.H506Y) was present in DNA obtained from one of the tumor specimens, and evidence of DNA hypermethylation within the MAP3K6 gene was observed in DNA from the tumor of another affected individual. These findings, together with previous evidence from mouse models that MAP3K6 acts as a tumor suppressor, and studies showing the presence of somatic mutations in MAP3K6 in non-hereditary gastric cancers and gastric cancer cell lines, point towards MAP3K6 variants as a predisposing factor for FGC.

The underlying genetic mutations involved in 60% of inherited gastric cancer cases remain unknown. Here we present a large, extended pedigree with familial gastric cancer and an association in part of the family with a mutation in MAP3K6. The conservation, predicted pathogenicity of the variant, tissue distribution, and known function of MAP3K6 made this a strong candidate that warranted further investigation. Examination of an additional 115 unrelated probands identified additional mutations in MAP3K6, including a truncating mutation.

Abstract 1282: Genetic basis of hereditary gastric cancer: Beyond the CDH1 locus

Importance. Hereditary gastric cancer (HGC) is a rare, autosomal dominant susceptibility syndrome characterized either by early onset diffuse gastric cancer and lobular breast cancer or aggregates of intestinal gastric cancer. The genetic etiology of &lt;50% of families classified as hereditary diffuse gastric cancer (HDGC) can be attributed to pathogenic germline mutations in the gene CDH1 (which encodes a crucial cellular adhesion molecule, E-cadherin). Unfortunately, the genetic basis of CDH1-negative HDGC families and all familial intestinal gastric cancers is unknown.

Objectives. 1) Determine whether pathogenic germline mutations in genes related to upper gastrointestinal disorders (UGI) are causative in HGC and 2) show that a targeted multiplexed next generation sequencing approach is effective and efficient for detecting such mutations.

Methods & Participants. 115 probands from families who met clinical criteria for HDGC (n=108) or FIGC (n=7) were included. HDGC participants have all previously tested negative for CDH1 variants. A custom panel of 55 genes previously associated with heritable UGI disorders was designed through literature research and collaborative efforts. The germline DNA of probands from each family was sequenced for all targeted regions using the MiSeq platform. Candidate variants were selected based on likelihood of pathogenicity (protein truncating, rare/novel pathogenic missense variants) then validated via Sanger sequencing. Tumour materials from mutation-carriers were analyzed for loss of heterozygosity via immunohistochemistry and/or second hit analysis. When available, germline DNA of additional family members was collected for segregation analysis.

Results. We have identified clearly pathogenic mutations in unrelated HGC families, including two protein truncating mutations each in CTNNA1 and BRCA2 genes and two rare, pathogenic missense mutations each in SDHB and STK11 genes. Additional protein truncating mutations were identified in moderately penetrant genes ATM (4 families), MSR1 (2 families), and PALB2 (1 family). Overall, 13% of families included in this study were found to have pathogenic (8) or likely pathogenic (7) mutations in genes included on our custom panel. Tumour material was available from probands with truncating CTNNA1 variants, revealing distinct loss of protein expression using immunohistochmistry. This further supports the likelihood of pathogenicity.

Conclusion & Relevance. Using a targeted next generation sequencing approach that significantly reduced sequencing cost while simultaneously improving turn-around time, we show that HGC families can carry pathogenic mutations outside the CDH1-locus, including genes commonly associated with other UGI syndromes. The genetic basis of the remaining families likely lies in yet to be discovered susceptibility genes or, in the case of HDGC, additional abnormalities at the CDH1-locus.

Citation Format: Samantha Hansford, Hector LiChang, Pardeep Kaurah, Michelle Woo, Karey Shumansky, David F. Schaeffer, Giovanni Corso, George Zogopoulos, Steven Gallinger, Hugo Pinheiro, Franco Roviello, Carla Oliveira, David Huntsman. Genetic basis of hereditary gastric cancer: Beyond the CDH1 locus. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1282. doi:10.1158/1538-7445.AM2014-1282

Abstract 4283: Whole genome sequencing is superior to cancer panels to aid in decision-making in patients with advanced malignancies

Background: It is increasingly common to use targeted cancer panels to assess for informative or actionable targets to guide cancer treatment. We compared the utility of information obtained from such a panel compared to whole genome and transcriptome sequencing.

Methods: Eligible subjects with incurable cancers for whom there were limited or no standard chemotherapy options, have several samples analyzed: a fresh tumour biopsy; a blood sample for normal comparison; and archival tumours when available. Samples underwent both the Ion Torrent AmpliSeq cancer panel analysis and comprehensive DNA (80X) and RNA sequencing followed by in-depth bioinformatic analysis to identify somatic mutations, copy number alterations, structural rearrangements, and corresponding gene expression changes that may be cancer “drivers” or provide informative (diagnostic) or actionable/druggable targets. Aberrant pathways were matched to drug databases and manual literature reviews undertaken to identify drugs that may be useful or potentially contraindicated; a report is generated and discussed in a multidisciplinary team.

Results: Between July 2012 - November 2013, 51 subjects have consented and 45 have been sequenced: 12 breast, 7 lung; 4 colorectal, 3 squamous, 3 adrenal; 2 pancreas; 2 sarcomas, and 1 of each of nasopharynx, primary unknown, CLL-peripheral mantle cell, parotid, anal, appendix, peripheral T-cell, prostate, ovary, endometrial, glioma, and mesothelioma. The median number of lines of chemo prior to sequencing was 3.

Of the first 40 cases, the panel did not yield informative or actionable results in 60% of cases: 36% of the cases the panel did not detect any somatic variants and in a further 24% TP53 mutations were the only variants identified. In the other 40% of cases, the panel might have identified an informative abnormality but when put into context of the pathways that can be drawn with the whole genome and transcriptome data the detected panel abnormalities were not comprehensive enough to guide treatment decisions. Examples include: in two colon cancer patients the panel detected a KRAS mutation in one and a RET mutation in the other, however both were actually inactivating mutations and therefore unlikely to be good targets. In contrast, the full genomic data was informative in 70% of cases and treatments were delivered based on the results in 60%, in this heavily pretreated population.

Conclusions: The future of cancer medicine lies in genomic profiling to assist therapeutic decision-making. The cancer panel has advantages in terms of speed and cost; however it has not been as informative for identifying candidate druggable driver events and it has missed critical genomic abnormalities that have changed diagnoses. Given the complexity of the cancer genome it is our observation that the panels do not provide the depth and context required to make treatment decisions for the majority of patients with cancer.

Citation Format: Janessa J. Laskin, Yaoqing Shen, Howard Lim, Karen A. Gelmon, Daniel Renouf, Stephen Yip, David Huntsman, Anna Tinker, Cheryl Ho, Stephen Chia, Yvonne Li, Katayoon Kasaian, Peter Eirew, Sreeja Leelakumari, Richard Moore, Samuel Aparicio, Yusanne Ma, Steven Jones, Marco Marra. Whole genome sequencing is superior to cancer panels to aid in decision-making in patients with advanced malignancies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4283. doi:10.1158/1538-7445.AM2014-4283

Abstract LB-202: The rare, highly malignant small cell carcinoma of the ovary displays common inactivating germline and somatic mutations in the tumor suppressor SMARCA4

Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) is a rare and highly aggressive malignancy that affects children and young women at a mean age of 24 (range 14 months - 58 years). SCCOHT is refractory to standard of care therapy for ovarian cancer, with ∼75% mortality within 18 months of diagnosis. The early age of onset of SCCOHT and reports of familial occurrence in some cases, strongly suggest an underlying hereditary etiology. To understand the molecular pathogenesis of SCCOHT, we performed next-generation genomic sequencing on a series of tumor and germline samples from SCCOHT patients. This analysis revealed germline and somatic inactivating mutations in SMARCA4, a subunit of the SWI/SNF chromatin-remodeling complex, in 75% (9/12) of SCCOHT patients. Moreover, immunohistochemical (IHC) analysis of 15 tumors revealed that 87% (13/15) of tumors lacked SMARCA4 protein. The high prevalence of SMARCA4 mutations in SCCOHT has not been previously reported in other, more common ovarian carcinomas. We therefore examined the expression of SMARCA4 protein in 300 ovarian carcinomas of different histologies by IHC and found SMARCA4 protein loss in only 6 tumors. In addition, the BIN-67 SCCOHT cell line, which harbors 2 splice site mutations in SMARCA4, showed complete absence of SMARCA4 protein by Western blot while representative cell lines from 4 other ovarian carcinoma subtypes as well as immortalized granulosa cells (SVOG) and adult granulosa tumor cells (KGN) all maintained SMARCA4 expression. The prevalence of germline and sporadic SMARCA4 mutations as well as frequent SMARCA4 protein loss in SCCOHTs implicates this gene as a tumor suppressor in this cancer and more broadly suggests a role for the SWI/SNF complex in its pathogenesis. In addition to providing evidence to the pathogenesis of SCCOHT, this finding provides the opportunity to develop treatment approaches for SCCOHT based on targeting vulnerabilities of SMARCA4-deficient cells.

Citation Format: Pilar Ramos, Anthony Karnezis, David Craig, Aleksandar Sekulic, Megan Russell, William Hendricks, Michael Barrett, Karey Shumansky, Yidong Yang, Sohrab Shah, Leah Prentice, Marco Marra, Jeffrey Kiefer, Victoria Zismann, Troy McEachron, Bodour Salhia, Joseph Pressey, John Farley, Stephen Anthony, Richard Roden, Heather Cunliffe, David Huntsman, Jeffrey Trent. The rare, highly malignant small cell carcinoma of the ovary displays common inactivating germline and somatic mutations in the tumor suppressor SMARCA4. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-202. doi:10.1158/1538-7445.AM2014-LB-202

Abstract LB-312: The somatic mutational landscape of ovarian clear cell carcinoma and its precursor lesions

Clear Cell ovarian carcinomas (CCC) represent ∼10% of ovarian carcinomas, with outcomes for high-stage cases significantly worse than the more common high-grade serous form. Response to standard chemotherapies are poor and efforts to improve treatment strategies are confounded by studies grouping ovarian histologies together, as well as a general lack of molecular background data on CCC. CCC frequently occurs in a background of endometriosis. The complete mutational landscape, the molecular basis of the transformation of endometriosis and patterns of clonal evolution in CCC are not understood.

We performed whole genome sequencing and gene expression profiling on 19 CCC to uncover candidate somatic alterations (mutations and, copy number aberrations) and measure their effect on transcriptional networks as candidates for driver mutations. We then performed targeted deep sequencing on the primary tumor samples, metastases and, from a subset of cases, adjacent or distant typical and atypical endometriosis. We used statistical modeling approaches to validate mutations, quantify the degree of clonal diversity and trace patterns of selection through oncogenic transformation.

Mutations in ARID1A and PIK3CA were by far the most frequent aberrations seen in the cohort (ARID1A: 10/19 cases; PIK3CA: 8/19 cases). The majority of ARID1A mutant cases exhibited bi-allelic loss of function. Two non-ARID1A mutant cases showed alterations in other SWI/SNF complex components. Amongst the 24 most significant candidate drivers impacting expression, five genes (PIK3CA, CTNNB1, TP53, PPP2R1A and KRAS) were known drivers. No association between PIK3CA or ARID1A status with disease stage, genomic instability, or mutation load was observed. Analysis of deep sequencing data suggested the presence of multiple clones in every case. For each case with matching precursor lesions, we observed multiple mutations in at least one such lesion. Cases with ARID1A and PIK3CA mutations always showed evidence of these mutations in their precursor lesions. The proportion of mutations from the primary tumor that were also present in precursor lesions varied widely across the cohort from approximately 10% to nearly 100%.

Our data support both ARID1A and PIK3CA mutations as early events in CCC. The pattern of endometriosis transformation could be associated with somatic mutations in all cases. This suggests that candidate tumor-initiating mutations and global- or individually- targetable features should be a focus to improve management of this disease. Finally, we suggest that patterns of mutational conservation across the series of precursor lesions presents an opportunity for early screening of endometriosis tissues as an indicator of transformation potential.

Citation Format: Ali Bashashati, Michael Anglesio, Yikan Wang, Gavin Ha, Janine Senz, Winnie Yang, Steve Kalloger, Leah Prentice, Satoshi Yanagida, Clara Salamanca, Galina Soukhatcheva, Anthony Karnezis, Hector Chang, Martin Hirst, Anne-Marie Mes-Mason, Aikou Okamoto, Marco Marra, Blake Gilks, Sohrab Shah, David Huntsman. The somatic mutational landscape of ovarian clear cell carcinoma and its precursor lesions. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-312. doi:10.1158/1538-7445.AM2014-LB-312

Abstract 544: Recurrent DICER1 hotspot mutations in endometrial cancer and their impact on microRNA biogenesis

Alternation in genes associated with microRNA (miRNA) biogenesis pathway may lead to miRNA dysregulation, and is implicated in a variety of human malignancies. Previously our group identified recurrent somatic “hotspot” mutations (E1705, D1709, D1810, E1813) in a critical miRNA-processing gene, DICER1, in rare sex cord-stromal tumors. During miRNA biogenesis, the two RNase III domains of DICER1 form an intramolecular dimer, which leads to the cleavage of the precursor miRNA (pre-miRNA) hairpin and generate mature 5p and 3p miRNAs from 5’ and 3’ arms of the precursor hairpin respectively. Studies have shown that the hotspot mutations in the RNase IIIb metal binding domain could impair DICER1's ability to generate mature 5p miRNAs, leading to global loss of 5p miRNAs.

Recently, in collaboration with The Cancer Genome Atlas (TCGA), we identified DICER1 hotspot mutations in a small subset of endometrial cancer from TCGA cohort (6/248) as well as our own tumor bank (6/307), suggesting disruption of DICER1 is implicated in a common malignancy. We also found an additional recurrent mutation G1809R and demonstrated that it has similar detrimental effects on miRNA biogenesis as hotspot mutations through deep sequencing and realtime PCR. Using Illumina Miseq targeted resequencing and Sanger sequencing, we observed biallelic DICER1 mutations in RNase IIIb domain in some but not all cases. miRNA deep sequencing confirmed that 5p miRNAs are decreased in both cell line models and endometrial tumors with hotspot mutations. Bioinformatic analysis of RNA sequencing profiles from TCGA dataset predicted hotspot DICER1 mutations to have greater functional impact than non-hotspot DICER1 mutations on gene expression. The oncogenic properties of DICER1 hotspot mutations are currently under investigation.

Citation Format: Jiamin Chen, Yemin Wang, Melissa McConechy, Michael Anglesio, Janine Senz, Winnie Yang, Jamie Rosner, Andy Chu, Grace Cheng, Gregg Morin, David Huntsman. Recurrent DICER1 hotspot mutations in endometrial cancer and their impact on microRNA biogenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 544. doi:10.1158/1538-7445.AM2014-544