Ray-Coquard, Isabelle L.

Abstract BRCA-associated homologous recombination deficiency (HRD) is present in ~ 50% of high-grade serous carcinomas (HGSC) and predicts sensitivity to platinum-based therapy. However, there is little understanding of why some patients with BRCA-deficient tumors experience unexpectedly poor outcomes. We profiled 154 tumors, enriched for patients with BRCA-deficient tumors that experienced short overall survival (≤ 3 years, n = 42), using whole-genome, transcriptome, and methylation analyses. All but one BRCA-deficient tumor exceeded an accepted HRD genomic scarring threshold. However, patients with BRCA1-deficient HGSC with a more elevated HRD score survived significantly longer. Patients with BRCA2-deficient HGSC and loss of NF1 survived twice as long as those without NF1 loss, whereas PIK3CA or RAD21 amplification defined BRCA2-deficient HGSC with exceptionally short survival. BRCA1-deficient tumors in short survivors had evidence of immunosuppressive c-kit signaling and EMT. In a large HGSC cohort (n = 1,389) including 282 individuals with pathogenic germline BRCA variants (gBRCApv), the location of the mutation within functional domains stratified clinical outcomes. Notably, residual disease after primary surgery had limited prognostic effect in gBRCApv-carriers compared to non-carriers. Our findings indicate that tumor HR proficiency in the context of therapy response and survival is not a binary property, and highlight genomic and immune modifiers of outcomes in BRCA-deficient HGSC.

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.

Abstract Background: Erythropoiesis-stimulating agents (ESAs) reduce anemia in cancer patients; however, there are concerns that ESAs increase mortality in some patients. Within the framework of an international collaboration we thus conducted a patient-level meta-analysis to assess the effects of ESAs on mortality in cancer patients. Methods: We performed a meta-analysis, based on the intention-to-treat principle, of cancer patients enrolled in randomized controlled trials comparing epoetin alfa, epoetin beta or darbepoetin alfa plus red blood cell transfusions as needed versus transfusion alone, for prophylaxis or treatment of anemia while or after receiving anticancer therapy. Patient-level data were obtained and analyzed by independent statisticians at two academic departments. Primary endpoints were on-study mortality and overall survival in patients receiving chemotherapy, defined as all patients from studies in which =/> 70% of study population received chemotherapy, and in all cancer patients regardless of anticancer therapy. On-study mortality was defined as death from any cause between date of randomization and 28 days after end of active study phase. Overall survival was defined as death from any cause between date of randomization and longest follow up available. Hazard ratios (HR) and 95% confidence intervals (CIs) were calculated per study and meta-analyzed with fixed-effects and random-effects models. Stratified multivariable Cox-regression analyses were conducted to assess the impact of baseline imbalances. Tests for interactions were used to identify differences in effect across pre-specified subgroups. All analyses were pre-specified in a peer-reviewed protocol (Bohlius et al. 2008). An independent steering committee consisting of clinicians and methodologists agreed on all analyses and interpretations. Independent investigators and representatives from manufacturers contributing data offered advice, but had no decision-making authority. Results: Data from 13,933 cancer patients enrolled in 53 studies were included in the analysis; 38 trials including 10,441 patients used mainly chemotherapy. Including all cancer patients ESAs increased on-study mortality by 17% (HR 1.17; 95% CI 1.06–1.30), with little evidence for a difference between chemotherapy and other trials (p for interaction=0.42), and worsened overall survival by 6% (HR 1.06; 95% CI 1.00–1.12). In the chemotherapy population on-study mortality was increased by 10% (HR 1.10, 95% CI 0.98–1.24) and overall survival was worsened by 4% (HR 1.04; 95% CI 0.97–1.11). Adjusting for known prognostic factors had little effect on the overall estimates. There was no conclusive evidence for effect modification by patient level characteristics such as age, sex, Hb and Hct at baseline, Hb ceiling, type and stage of tumor or study level characteristics (anticancer treatment, ESA treatment schedules, study design and quality) for the outcomes tested. Conclusion: ESA treatment in cancer patients increased on-study mortality by 17% and worsened overall survival by 6%. For patients undergoing chemotherapy the increase was less pronounced, but could not be excluded. In clinical practice, risks of ESAs must be balanced against benefits of ESAs depending on the clinical circumstances of the individual patient.

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