Konecny, Gottfried E.

Abstract Purpose: Gene expression–based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features. Experimental Design: Adopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting. Results: Gene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations. Conclusions: We validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications. See related commentary by McMullen et al., p. 5271

5515 Background: IGF signaling has been implicated in the pathogenesis and progression of ovarian cancer (OC). Single agent activity and safety of ganitumab (AMG 479), a fully human monoclonal antibody against IGF-1R that blocks binding of IGF1 and IGF2, were evaluated in asymptomatic patients with platinum-sensitive recurrent OC. Differential expression of IGF-1R pathway genes in OC underscores the potential of developing predictive biomarkers for patient selection. Methods: Pts with CA125 progression (GCIG criteria) and/or measurable disease per RECIST failing primary platinum-based therapy received 18 mg/kg of ganitumab q3w. Objective response rate per RECIST or CA125 criteria was the primary end point (complete response, CR; partial response, PR). Secondary end points included, progression-free survival (PFS) and safety. Tumor tissue was collected for gene expression profiling (Nanostring) and sequencing. Results: From 02/2009 to 05/2010, 61 pts were accrued from 20 centers. Pt characteristics were: Serous (77%), median platinum-free interval (11 months), measurable disease (74%), and ECOG performance status 0 (67%). According to CA125 criteria median PFS was 6.8 months (95%CI, 2.8-10.8); 2 CR (3.4%) 2 PR (3.4%), and 38 stable disease (SD, 64%) were observed. When using RECIST criteria, median PFS was 2.1 months (95%CI, 2.0-2.8), 2 PR (3.4%) and 22 SD (38%) were observed. Toxicity has been mild; grade 2 hyperglycemia was seen in 5 pts (8.2%). Grade 3 related events included hearing loss (1), nausea (1), asthenia (2), fatigue (1), and hypersensitivity (5). There were no grade 4 or 5 treatment-related events. Efficacy is being correlated with gene expression profiles and mutational data. Conclusions: IGF-1R inhibition with ganitumab was well tolerated and demonstrated modest single-agent activity in unselected patients with platinum-sensitive recurrent OC. However, encouraging activity was seen in a subset of patients. Ongoing predictive biomarker analyses may facilitate patient selection. Clinical trial information: NCT00719212.

5510 Background: Transcriptional profiling of ovarian cancers has proven to be complex. As such it has been difficult to validate existing signatures across studies. Cancer Genome Atlas (TCGA) researchers have identified four molecular subtypes of high-grade serous ovarian cancer (HGSOC). However, survival duration did not differ significantly for the TCGA subtypes. Potential limitations of the TCGA data include short clinical follow-up (45% were alive at the time of last follow-up) and the need to unify gene expression measures from multiple platforms. Methods: Clinically annotated stage-II–IV HGSOC samples (n = 175) with >70% tumor cell content were profiled using the Agilent Whole Human Genome 4 x 44K chip. To identify subtypes non-negative matrix factorization (NMF) of mRNA expression was performed using ~2000 genes with the highest variability across patients. In parallel differentially expressed genes were identified using the Rosetta Similarity Search Tool as well as analysis of variance based on genes known to be involved in epithelial to mesenchymal transition. Results: Median follow-up time was 35 months (range, 0–202 months, 12% were alive at the time of last follow-up). NMF clustering confirmed four HGSOC subtypes (immunoreactive, differentiated, proliferative, and mesenchymal) on the basis of gene content in the clusters. Pathway signatures with therapeutic potential were identified for individual or multiple subtypes. Survival differed significantly between the four molecular subgroups in univariate (Hazard Ratio [HR] 2.4, 95% CI 1.5-4.1, p = 0.007) and multivariate (HR 2.3, 95% CI 1.3-4.0, p = 0.003) analyses when accounting for age, stage, grade, and postoperative residual tumor. Using the supervised clustering approach two distinct molecular subtypes of HGSOC based on epithelial and mesenchymal gene expression signatures were identified with significantly different survival outcomes. Conclusions: Here we independently validate and expand upon the molecular TCGA classification of HGSOC. The potential of these two prognostic classifiers may lie in their ability to recognize categories of patients that are more likely to respond to particular therapies.

Abstract Background: Most patients with advanced OC relapse after initial standard platinum-based chemotherapy, and eventually the disease becomes platinum-resistant. Niraparib (ZEJULA®) was the first selective poly(ADP-ribose) polymerase inhibitor (PARPi) approved in the United States and Europe for maintenance treatment in patients with recurrent OC regardless of BRCA mutation status. Preclinical evidence suggests that niraparib activates the stimulator of interferon genes pathway to increase immune cell infiltration and synergizes with anti-PD-1 therapy. Additionally, hypoxia induces contextual synthetic lethality by impairing homologous recombination, and therefore induction of hypoxia by inhibition of angiogenesis could lead to synergy with PARPi. In the TOPACIO/KEYNOTE-162 trial, niraparib in combination with pembrolizumab has shown efficacy in recurrent, platinum-resistant OC. Niraparib in combination with the anti-angiogenic agent bevacizumab is under study for the treatment of recurrent platinum-sensitive OC (AVANOVA trial) and advanced OC following response on frontline platinum-based chemotherapy (OVARIO trial). TSR-042 is an anti-PD-1 humanized monoclonal antibody that has shown clinical activity as monotherapy in early phase trials. Cohort A of the OPAL trial will evaluate the novel triple combination of the PARPi niraparib, angiogenesis inhibitor bevacizumab, and PD-1 inhibitor TSR-042 in patients with platinum-resistant OC who are naïve to PARPi therapy. Methods: Eligible patients will have high-grade recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer of the ovary and progressed ≤6 months from completion of ≥4 cycles of platinum-based chemotherapy. Additional key eligibility criteria include 1-2 prior lines of anticancer therapy for OC, no prior therapy with an anti-PD-1 or anti-PD-L1 antibody, and no prior therapy for OC with a PARPi. Patients will receive a combination regimen of 500 mg TSR-042 on day 1 of each 3-week cycle for 4 cycles, then 1000 mg on day 1 of every other cycle beginning on cycle 5 until progression or toxicity, 15 mg/kg bevacizumab on day 1 of each 3-week cycle for up to 15 months, and niraparib 300 mg or 200 mg (for patients <77 kg or platelet count <150,000/µL at screening) daily until disease progression or toxicity. The primary endpoint is to evaluate treatment efficacy by confirmed objective response rate per investigator-assessed RECIST v1.1 criteria. Secondary objectives are evaluation of progression-free survival, overall survival, duration of response, and disease control rate. Exploratory objectives are to identify potential biomarkers of tumor response, including BRCA status and homologous recombination repair gene status and to evaluate the evolution of the molecular profile of the tumor and tumor microenvironment in response to treatment. Clinical trial identification: NCT03574779 Citation Format: Joyce Liu, Camille Gunderson, Andrea Wahner Hendrickson, Elena Ratner, Elisabeth Diver, John Moroney, Rebecca C. Arend, Melinda Louie-Gao, Sarah Wang, Katarina Luptakova, Gottfried E. Konecny. An open-label Phase II study of combination of TSR-042, bevacizumab, and niraparib in patients with platinum-resistant ovarian cancer (OC): Cohort A of the OPAL trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT157.

Abstract A key resistance mechanism to platinum-based chemotherapies and PARP inhibitors in BRCA-mutant cancers is the acquisition of BRCA reversion mutations that restore protein function. To estimate the prevalence of BRCA reversion mutations in high-grade ovarian carcinoma (HGOC), we performed targeted next-generation sequencing of circulating cell-free DNA (cfDNA) extracted from pretreatment and postprogression plasma in patients with deleterious germline or somatic BRCA mutations treated with the PARP inhibitor rucaparib. BRCA reversion mutations were identified in pretreatment cfDNA from 18% (2/11) of platinum-refractory and 13% (5/38) of platinum-resistant cancers, compared with 2% (1/48) of platinum-sensitive cancers (P = 0.049). Patients without BRCA reversion mutations detected in pretreatment cfDNA had significantly longer rucaparib progression-free survival than those with reversion mutations (median, 9.0 vs. 1.8 months; HR, 0.12; P < 0.0001). To study acquired resistance, we sequenced 78 postprogression cfDNA, identifying eight additional patients with BRCA reversion mutations not found in pretreatment cfDNA. Significance: BRCA reversion mutations are detected in cfDNA from platinum-resistant or platinum-refractory HGOC and are associated with decreased clinical benefit from rucaparib treatment. Sequencing of cfDNA can detect multiple BRCA reversion mutations, highlighting the ability to capture multiclonal heterogeneity. This article is highlighted in the In This Issue feature, p. 151