Contribution of tumour and immune cells to PD-L1 expression as a predictive biomarker in metastatic triple-negative breast cancer: exploratory analysis from KEYNOTE-119

The efficacy of pembrolizumab monotherapy versus chemotherapy increased with increasing programmed death ligand 1 (PD-L1) expression, as quantified by combined positive score (CPS; PD-L1 expression on both tumour cells and immune cells) in patients with previously treated metastatic triple-negative breast cancer (mTNBC) in the phase 3 KEYNOTE-119 study. This exploratory analysis was conducted to determine whether the expression of PD-L1 on tumour cells contributes to the predictive value of PD-L1 CPS in mTNBC. PD-L1 expression in tumour samples was assessed using PD-L1 IHC 22C3 pharmDx and quantified using both CPS and tumour proportion score (TPS; PD-L1 expression on tumour cells alone). Calculated immune cell density (CID) was defined as CPS minus TPS. The ability of each scoring method (CPS, TPS, and CID) to predict clinical outcomes with pembrolizumab was evaluated. With pembrolizumab, the area under the receiver operating characteristic curve was 0.69 (95% CI = 0.58-0.80) for CPS, 0.55 (95% CI = 0.46-0.64) for TPS, and 0.67 (95% CI = 0.56-0.77) for CID. After correction for cutoff prevalence, CPS performed as well as, if not better than, CID with respect to predicting objective response rate, progression-free survival, and overall survival. Data from this exploratory analysis suggest that, although PD-L1 expression on immune cells alone is predictive of response to programmed death 1 blockade in mTNBC, adding tumour PD-L1 expression assessment (i.e. CPS, which combines immune cell and tumour cell PD-L1 expression) may improve prediction. PD-L1 CPS thus remains an effective and broadly applicable uniform scoring system for enriching response to programmed death 1 blockade with pembrolizumab in mTNBC as well as other tumour types.

Evaluation of potential biomarkers for lenvatinib plus pembrolizumab among patients with advanced endometrial cancer: results from Study 111/KEYNOTE-146

BACKGROUND

Lenvatinib plus pembrolizumab demonstrated clinically meaningful benefit in patients with previously treated advanced endometrial carcinoma in Study 111/KEYNOTE-146 (NCT02501096). In these exploratory analyses from this study, we evaluated the associations between clinical outcomes and gene expression signature scores and descriptively summarized response in biomarker subpopulations defined by tumor mutational burden (TMB) and DNA variants for individual genes of interest.

METHODS

Patients with histologically confirmed metastatic endometrial carcinoma received oral lenvatinib 20 mg once daily plus intravenous pembrolizumab 200 mg every 3 weeks for 35 cycles. Archived formalin-fixed paraffin-embedded tissue was obtained from all patients. T-cell-inflamed gene expression profile (TcellinfGEP) and 11 other gene signatures were evaluated by RNA sequencing. TMB, hotspot mutations in PIK3CA (oncogene), and deleterious mutations in PTEN and TP53 (tumor suppressor genes) were evaluated by whole-exome sequencing (WES).

RESULTS

93 and 79 patients were included in the RNA-sequencing-evaluable and WES-evaluable populations, respectively. No statistically significant associations were observed between any of the RNA-sequencing signature scores and objective response rate or progression-free survival. Area under the receiver operating characteristic curve values for response ranged from 0.39 to 0.54; all 95% CIs included 0.50. Responses were seen regardless of TMB (≥175 or <175 mutations/exome) and mutation status. There were no correlations between TcellinfGEP and TMB, TcellinfGEP and microvessel density (MVD), or MVD and TMB.

CONCLUSIONS

This analysis demonstrated efficacy for lenvatinib plus pembrolizumab regardless of biomarker status. Results from this study do not support clinical utility of the evaluated biomarkers. Further investigation of biomarkers for this regimen is warranted.

TRIAL REGISTRATION NUMBER

NCT02501096.

Molecular determinants of clinical outcomes of pembrolizumab in recurrent ovarian cancer: Exploratory analysis of KEYNOTE-100

OBJECTIVE

This prespecified exploratory analysis evaluated the association of gene expression signatures, tumor mutational burden (TMB), and multiplex immunohistochemistry (mIHC) tumor microenvironment-associated cell phenotypes with clinical outcomes of pembrolizumab in advanced recurrent ovarian cancer (ROC) from the phase II KEYNOTE-100 study.

METHODS

Pembrolizumab-treated patients with evaluable RNA-sequencing (n = 317), whole exome sequencing (n = 293), or select mIHC (n = 125) data were evaluated. The association between outcomes (objective response rate [ORR], progression-free survival [PFS], and overall survival [OS]) and gene expression signatures (T-cell-inflamed gene expression profile [TcellinfGEP] and 10 non-TcellinfGEP signatures), TMB, and prespecified mIHC cell phenotype densities as continuous variables was evaluated using logistic (ORR) and Cox proportional hazards regression (PFS; OS). One-sided p-values were calculated at prespecified α = 0.05 for TcellinfGEP, TMB, and mIHC cell phenotypes and at α = 0.10 for non-TcellinfGEP signatures; all but TcellinfGEP and TMB were adjusted for multiplicity.

RESULTS

No evidence of associations between ORR and key axes of gene expression was observed. Negative associations were observed between outcomes and TcellinfGEP-adjusted glycolysis (PFS, adjusted-p = 0.019; OS, adjusted-p = 0.085) and hypoxia (PFS, adjusted-p = 0.064) signatures. TMB as a continuous variable was not associated with outcomes (p > 0.05). Positive associations were observed between densities of myeloid cell phenotypes CD11c+ and CD11c+/MHCII-/CD163-/CD68- in the tumor compartment and ORR (adjusted-p = 0.025 and 0.013, respectively).

CONCLUSIONS

This exploratory analysis in advanced ROC did not find evidence for associations between gene expression signatures and outcomes of pembrolizumab. mIHC analysis suggests CD11c+ and CD11c+/MHCII-/CD163-/CD68- phenotypes representing myeloid cell populations may be associated with improved outcomes with pembrolizumab in advanced ROC.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov, NCT02674061.

Association Between Biomarkers and Clinical Outcomes of Pembrolizumab Monotherapy in Patients With Metastatic Triple-Negative Breast Cancer: KEYNOTE-086 Exploratory Analysis

PURPOSE

In the two-cohort phase II KEYNOTE-086 study (ClinicalTrials.gov identifier: NCT02447003), first-line and second-line or later pembrolizumab monotherapy demonstrated antitumor activity in metastatic triple-negative breast cancer (mTNBC; N = 254). This exploratory analysis evaluates the association between prespecified molecular biomarkers and clinical outcomes.

METHODS

Cohort A enrolled patients with disease progression after one or more systemic therapies for metastatic disease irrespective of PD-L1 status; Cohort B enrolled patients with previously untreated PD-L1-positive (combined positive score [CPS] ≥ 1) metastatic disease. The association between the following biomarkers as continuous variables and clinical outcomes (objective response rate [ORR], progression-free survival [PFS], and overall survival [OS]) was evaluated: PD-L1 CPS (immunohistochemistry), cluster of differentiation 8 (CD8; immunohistochemistry), stromal tumor-infiltrating lymphocyte (sTIL; hematoxylin and eosin staining), tumor mutational burden (TMB; whole-exome sequencing [WES]), homologous recombination deficiency-loss of heterozygosity, mutational signature 3 (WES), mutational signature 2 (apolipoprotein B mRNA editing catalytic polypeptide-like; WES), T-cell-inflamed gene expression profile (Tcell_infGEP; RNA sequencing), and 10 non-Tcell_infGEP signatures (RNA sequencing); Wald test P values were calculated, and significance was prespecified at α = 0.05.

RESULTS

In the combined cohorts (A and B), PD-L1 (P = .040), CD8 (P < .001), sTILs (P = .012), TMB (P = .007), and Tcell_infGEP (P = .011) were significantly associated with ORR; CD8 (P < .001), TMB (P = .034), Signature 3 (P = .009), and Tcell_infGEP (P = .002) with PFS; and CD8 (P < .001), sTILs (P = .004), TMB (P = .025), and Tcell_infGEP (P = .001) with OS. None of the non-Tcell_infGEP signatures were associated with outcomes of pembrolizumab after adjusting for the Tcell_infGEP.

CONCLUSION

In this exploratory biomarker analysis from KEYNOTE-086, baseline tumor PD-L1, CD8, sTILs, TMB, and Tcell_infGEP were associated with improved clinical outcomes of pembrolizumab and may help identify patients with mTNBC who are most likely to respond to pembrolizumab monotherapy.

OUP accepted manuscript

Background

Homologous recombination deficiency (HRD) is a phenotype that is characterized by the inability of a cell to effectively repair DNA double-strand breaks using the homologous recombination repair (HRR) pathway. Loss-of-function genes involved in this pathway can sensitize tumors to poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors and platinum-based chemotherapy, which target the destruction of cancer cells by working in concert with HRD through synthetic lethality. However, to identify patients with these tumors, it is vital to understand how to best measure homologous repair (HR) status and to characterize the level of alignment in these measurements across different diagnostic platforms. A key current challenge is that there is no standardized method to define, measure, and report HR status using diagnostics in the clinical setting.

Methods

Friends of Cancer Research convened a consortium of project partners from key healthcare sectors to address concerns about the lack of consistency in the way HRD is defined and methods for measuring HR status.

Results

This publication provides findings from the group’s discussions that identified opportunities to align the definition of HRD and the parameters that contribute to the determination of HR status. The consortium proposed recommendations and best practices to benefit the broader cancer community.

Conclusion

Overall, this publication provides additional perspectives for scientist, physician, laboratory, and patient communities to contextualize the definition of HRD and various platforms that are used to measure HRD in tumors.

338 Effects of pembrolizumab on the tumor microenvironment (TME) after one presurgery treatment cycle in patients with triple-negative breast cancer (TNBC): phase 1b KEYNOTE-173 study

Background

In the phase 3 KEYNOTE-522 trial, neoadjuvant pembrolizumab+chemotherapy followed by adjuvant pembrolizumab monotherapy resulted in a statistically significant improvement in pathologic complete response (pCR) and event-free survival, compared with neoadjuvant chemotherapy alone, in patients with early-stage TNBC. In the phase 1b KEYNOTE-173 (NCT02622074) trial—another neoadjuvant pembrolizumab+chemotherapy trial—we evaluated TNBC biopsy samples at baseline and collected after one cycle of neoadjuvant pembrolizumab, before the initiation of chemotherapy, to explore the features within the TME at both timepoints that might be potentially predictive of clinical response and the effects of a single cycle of pembrolizumab on cell populations within the TME.

Methods

Twenty paired samples (baseline and obtained following one cycle of pembrolizumab before the initiation of chemotherapy) were included. Multiplex immunohistochemistry analyzed deconvoluted cell fractions by spatial localization (tumor compartment, stromal compartment, or total tumor) using three 6-plex panels: T cell (CD3/CD8/FoxP3/Ki67/granzyme B/PD-1), myeloid cell (CD68/CD163/MHCII/arginase/CD33/CD11c), and natural killer cell (CD16/CD56/CD11b/CD20/CD3/CD45). Area under the receiver operating characteristic (AUROC) was used to assess associations between immune subsets and pCR. Analyses were descriptive, with top-ranked findings reported, and were deemed hypothesis generating; no claims of statistical significance are made.

Results

At baseline, 6 of 75 evaluated immune subsets (counting different compartments) showed 95% CIs of AUROC not crossing 0.5 with pCR. These include some myeloid cell populations within the tumor compartment (AUROC, 95% CI), specifically CD11c+ (macrophage and dendritic cell [DC]: 0.85, 0.63–1.00), CD11c+/MHCII+/CD163–/CD68– (DC: 0.76, 0.53–0.99), CD11c+/MHCII–/CD163–/CD68– (nonactivated/immature DC: 0.8, 0.54-1.00), and CD11c+/CD163+ (M2 macrophage: 0.77, 0.55–0.99). Other associations with pCR included baseline CD11c+/MHCII–/CD163–/CD68– (nonactivated/immature DC) within the total tumor (AUROC, 0.76; 95% CI, 0.51–1.00) and the baseline ratio of CD11c/CD3 within the tumor compartment (AUROC, 0.75; 95% CI, 0.52–0.98). Although T-cell associations were relatively weak, specific CD8 subsets, especially CD8+/granzyme B+/Ki67+, showed a trend toward association. Negative correlations between change from baseline and baseline values were observed; therefore, baseline detrending was applied to change from baseline values. One immune subset showed a negative association trend between change from baseline and pCR after baseline detrending: CD163+/MHCII+ (DC3) within the stroma (AUROC, 0.2; 95% CI, 0.0–0.42).

Conclusions

Although the sample size in this exploratory analysis was small (n=20), myeloid cell populations within the tumor compartment at baseline show a promising association trend, as evaluated by AUROC, with pCR after neoadjuvant pembrolizumab+chemotherapy in early-stage TNBC. Changes in immune subsets following one cycle of pembrolizumab were not strongly associated with pCR.

Trial Registration

ClinicalTrials

gov, NCT02622074

Ethics Approval

The study protocol and all amendments were approved by the relevant institutional review board or ethics committee at each study site.

Consent

All patients provided written informed consent to participate in the clinical trial.

Abstract PD14-07: Association between biomarkers and response to pembrolizumab in patients with metastatic triple-negative breast cancer (mTNBC): Exploratory analysis from KEYNOTE-086

Background: In the phase 2 KEYNOTE-086 study (NCT02447003), pembrolizumab monotherapy had durable antitumor activity in a subset of patients with previously treated mTNBC (cohort A; n = 170) and in patients with previously untreated PD-L1-positive mTNBC (cohort B; n = 84). In this exploratory analysis of KEYNOTE-086, we evaluated the association between several biomarkers and response to pembrolizumab. Methods: Cohort A enrolled patients regardless of PD-L1 expression who had documented disease progression following ≥1 systemic therapy for metastatic disease. Cohort B enrolled patients with PD-L1-positive (combined positive score [CPS] ≥1) tumors who had not received prior systemic therapy for metastatic disease. Immunohistochemistry was used to measure PD-L1 CPS and CD8 density; H&E staining for percentage of stromal tumor infiltrating lymphocytes (sTILs); RNA-sequencing for 18-gene T-cell-inflamed gene expression profile (GEP), angiogenesis, and glycolysis signatures; and whole exome sequencing (paired tumor and germline) for TMB (TMB-H defined as ≥175 mut/exome), HRD-LOH (DNA damage), Signature 3, and APOBEC. Biomarkers were analyzed as continuous variables in cohorts A and B combined and individually. Area under the receiver operating characteristic curve was estimated between each biomarker and overall response rate (ORR). Wald test P-values were calculated using logistic regression adjusted for cohort and Eastern Cooperative Oncology Group performance status. Germline and somatic BRCA1/2 mutations were pooled; one-sided P-value was calculated using Fisher’s exact test. Spearman’s correlation was used for correlations. Results: Biomarker data were available in the following number of patients: 253 (99.6%; PD-L1), 204 (80.3%; CD8), 187 (73.6%; GEP), 171 (67.3%; TMB/HRD), 228 (89.8%; sTILs), 163 (64.2%; Signature 3/APOBEC), and 132 (52.0%; angiogenesis/glycolysis). When data from cohorts A and B were combined, PD-L1 CPS (median 2; IQR 0-10), CD8 (median 159; IQR 62-319), GEP (median -0.34; IQR -0.57 to -0.11), TMB (median 82 mut/exome; IQR 50-139), and sTILs (median 5; IQR 2-20) were significantly associated with ORR (Table). There were moderate correlations between PD-L1 and GEP (r = 0.532), PD-L1 and sTILs (r = 0.451), and GEP and sTILs (r = 0.490). No correlation was observed between TMB and PD-L1 (r = 0.038), GEP (r = -0.035), and sTILs (r = -0.031). When cohorts were combined, TMB was significantly associated with ORR, PFS, and OS after adjustment for PD-L1, GEP, CD8, or sTILs. HRD-LOH score, Signature 3, and APOBEC were not significantly associated with ORR (Table); P for BRCA1/2 was 0.2385. The angiogenesis signature was associated with lack of response while the glycolysis signature was associated with response to pembrolizumab (Table). Conclusions: In this exploratory biomarker analysis from KEYNOTE-086, higher levels of PD-L1, GEP, TMB, CD8 IHC, sTILs, and the glycolysis signature were associated with increased response to pembrolizumab monotherapy. These findings may help identify patients with mTNBC who are most likely to respond to pembrolizumab.

Table. Association of Biomarkers as Continuous Variables With Pembrolizumab Objective ResponseBiomarkerCombined Cohorts AUCCombined Cohorts P*Combined Cohorts Multitest corrected PCohort A AUCCohort B AUCPD-L10.6740.040-0.5440.654GEP0.7480.003-0.8370.561TMB0.6270.007-0.5480.710CD8 IHC0.760.000020.000120.850.68sTILs0.6710.012-0.6320.641HRD0.3940.874-0.5220.316Signature 30.6830.072-0.6970.736APOBEC0.5280.537-0.6740.623Angiogenesis0.6770.0090.0450.6610.731Glycolysis0.6120.0090.0360.8590.459AUC, area under the curve.*One-sided P-values are shown for all biomarkers except for Signature 3 and APOBEC, for which 2-sided P-values are shown.

Citation Format: Sherene Loi, Peter Schmid, Javier Cortes, David W. Cescon, Eric P. Winer, Deborah L. Toppmeyer, Hope S. Rugo, Michelino De Laurentiis, Rita Nanda, Hiroji Iwata, Ahmad Awada, Antoinette R. Tan, Roberto Salgado, Vassiliki Karantza, Petar Jelinic, Anran Wang, Lingkang Huang, Razvan Cristescu, Lakshman Annamalai, Jennifer Yearley, Jennifer Yearley, Sylvia Adams. Association between biomarkers and response to pembrolizumab in patients with metastatic triple-negative breast cancer (mTNBC): Exploratory analysis from KEYNOTE-086 [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD14-07.

Abstract PD14-04: Contribution of tumor and immune cells to PD-L1 as a predictive biomarker in triple-negative breast cancer (TNBC): Analysis from KEYNOTE-119

Background: Pembrolizumab monotherapy did not significantly improve overall survival (OS) as second- or third-line treatment for metastatic TNBC vs chemotherapy in the randomized, open-label, phase 3 KEYNOTE-119 study (NCT02555657; N = 622). However, the benefit of pembrolizumab compared with chemotherapy appeared to be greater with increasing PD-L1 expression as quantified by combined positive score (CPS; defined as the number of PD-L1–staining cells [tumor cells, lymphocytes, macrophages] divided by the total number of viable tumor cells, multiplied by 100). In the current exploratory analysis, we aimed to determine whether expression of PD-L1 on tumor cells contributes to the value of PD-L1 as a predictive biomarker in metastatic TNBC.Methods: Patients with centrally confirmed TNBC and 1 or 2 prior systemic treatments for metastatic disease were enrolled in KEYNOTE-119. Patients were randomly assigned 1:1 to pembrolizumab 200 mg Q3W or investigator’s choice of single-agent chemotherapy (capecitabine, eribulin, gemcitabine, or vinorelbine). PD-L1 expression in tumor samples was assessed using PD-L1 IHC 22C3 pharmDx and quantified per tumor proportion score (TPS; defined as the percentage of PD-L1–expressing tumor cells [partial or complete membrane staining] relative to total number of tumor cells) and CPS. Quantitative immune cell density (QID) was defined as CPS minus TPS. QID isolates immune cells but may be truncated when TPS is high. The ability of each scoring method (TPS, CPS, and QID) to predict objective response rate (ORR) with pembrolizumab, including receiver operating characteristics (ROC) analysis, and OS hazard ratios (HRs; pembrolizumab vs chemotherapy) was evaluated.Results: Tumor samples were available for 601 patients (pembrolizumab, 309; chemotherapy, 292) in KEYNOTE-119. ORR was 9.7% (30/309) with pembrolizumab and 11.3% (33/292) with chemotherapy when PD-L1 expression status was not considered. In the pembrolizumab arm, the area under the ROC curve (AUROC; 95% CI) was 0.69 (0.58-0.80) for tumor samples scored for CPS, 0.66 (0.55-0.77) for QID, and 0.55 (0.46-0.64) for TPS. ROC analysis is shown in the Table. At each cutoff, QID had lower estimated sensitivity (ie, missed responders) and a lower Youden Index compared with CPS. The number of missed responders (of 30 total in the pembrolizumab arm) for QID relative to CPS were 2, 5, 5, 6, 2, and 2 at cutoffs of 1, 10, 20, 30, 40, and 50, respectively. Across all practical cutoffs, the OS HR tended to be slightly smaller for CPS than QID. At cutoffs corresponding to the upper percentiles of 10, 20, 40, and 60, OS HRs were 0.497, 0.658, 0.758, and 0.850, respectively, for CPS vs 0.572, 0.712, 0.814, and 0.863, respectively, for QID. QID appeared to be orthogonal to TPS (r = -0.03 for all 601 observations; r = -0.04 after eliminating 7 potentially truncated values).Conclusions: Trends estimated using KN119 suggest that tumor cell expression is an important component of PD-L1 as a predictive biomarker of pembrolizumab efficacy in metastatic TNBC. In this exploratory analysis, when immune cells alone were used to measure PD-L1 expression, a meaningful number of responders was missed and OS benefit trended toward higher HR estimates. Tumor and immune cell PD-L1 expression may represent distinct (presumably negative modulatory) mechanisms.

Table. ROC AnalysisCutoffCPS SensCPS SpecCPS YICPS PrevQID SensQID SpecQID YIQID PrevTPS SensTPS SpecTPS YITPS Prev010011001100110.8330.3660.1990.6540.7670.4160.1820.6020.3000.7890.0890.220100.5670.7170.2840.3110.4000.8140.2140.2070.2000.8920.0920.117200.5000.8490.3490.1840.3330.9250.2580.1000.1670.9320.0990.078300.3670.8920.2590.1330.1670.9570.1240.0550.1000.9430.0430.061400.2000.9350.1350.0780.1330.9860.1190.0260.0670.9530.0200.049500.2000.9570.1570.0580.1330.9930.1260.0190.0670.9680.0340.036

Citation Format: Eric P. Winer, Oleg Lipatov, Seock-Ah Im, Anthony Goncalves, Eva Muñoz-Couselo, Keun Seok Lee, Zbigniew Nowecki, Peter Schmid, Kenji Tamura, Laura Testa, Isabell Witzel, Shoichiro Ohtani, Stephanie Hund, Karina Kulangara, Vassiliki Karantza, Jaime A. Mejia, Junshui Ma, Petar Jelinic, Lingkang Huang, Kenneth Emancipator, Javier Cortes. Contribution of tumor and immune cells to PD-L1 as a predictive biomarker in triple-negative breast cancer (TNBC): Analysis from KEYNOTE-119 [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD14-04.

Abstract A31: The two most potent PARP inhibitors increase expression levels of innate immune response genes in BRCA wild-type HGSC tumors

Background: Poly (ADP-ribose) polymerase (PARP) inhibitors have transformed treatment of ovarian cancer in the past decade. Most of the currently active PARP inhibitors have similar ability to inhibit PARP’s enzymatic activity. However, it has been previously reported that velipairb, rucaparib, olaparib, niraparib, and talazoparib vary in their PARP trapping potency levels. Veliparib was also characterized to be mainly a catalytic inhibitor while the other four drugs were determined to be both PARP trappers and catalytic inhibitors, with talazoparib being the most potent PARP trapper. Responses in many patients with HGSC tumors are limited, particularly those women without known mutations in BRCA1 or BRCA2. Recently, PARP inhibitors have been reported to influence innate immune responses. For these reasons, there are ongoing clinical trials testing the safety and efficacy of PARP inhibitors in combination with various immune checkpoint inhibitors. The objective of this study is to compare the effect of the five most clinically active PARP inhibitors on type 1 interferon regulated genes and the PD-L1 gene.

Methods: Two high-grade serous ovarian cancer cell lines were used in this study: CAOV3 (TP53 mutant) and OVCAR3 (TP53 mutant, CCNE1-amplified, and EMSY-amplified). The cell lines were treated for 48 hours with the PARP inhibitors listed above as well as a vehicle control (DMSO). Gene expression was measured using TaqMan assays. CXCL10 (IP-10) protein expression levels were determined via an ELISA assay.

Summary of the Data: Talazoparib upregulated CXCL10 gene expression in both OVCAR3 and CAOV3 cell lines. These results were translated to the protein level, as we observed an increase in IP-10 protein expression levels after talazoparib treatment in the OVCAR3 cell line. IP-10 protein levels were also significantly increased when treated with the second most potent PARP inhibitor, niraparib. A statistically significant effect was not observed after treatment with the three other PARPis. Futhermore, CD274 (PD-L1) gene expression levels were significantly increased after talazoparib and not veliparib treatment in the CAOV3 cell line.

Conclusions: Our data suggest that there are distinct effects exhibited among PARP inhibitors on innate immune pathways. The two most potent PARP inhibitors, niraparib and talazoparib, had the greatest effect on these pathways, specifically in BRCA wild-type HGSCs, compared to the three other drugs. These finding support the idea that we need to define the best PARP inhibitor to use in future clinical trials when combining this group of anticancer agents with immune checkpoint inhibitors.

Citation Format: Monica Wielgos-Bonvallet, Danhui Weng, Petar Jelinic, Douglas A. Levine. The two most potent PARP inhibitors increase expression levels of innate immune response genes in BRCA wild-type HGSC tumors [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 A31.

Association of tumor mutational burden (TMB) and clinical outcomes with pembrolizumab (pembro) versus chemotherapy (chemo) in patients with metastatic triple-negative breast cancer (mTNBC) from KEYNOTE-119

1013

Background: In the randomized, open-label, phase 3 KEYNOTE-119 study (NCT02555657) , OS was not significantly different with pembro monotherapy versus chemo in second- or third-line settings for mTNBC; however, the pembro treatment effect increased with increasing PD-L1 enrichment. We evaluated the association of TMB with efficacy of pembro monotherapy versus chemo in patients with previously treated mTNBC. Methods: Patients with centrally confirmed TNBC and 1 or 2 prior systemic treatments for metastatic disease were enrolled. Patients were randomly assigned 1:1 to pembro 200 mg Q3W or single-agent chemo per investigator’s choice of capecitabine, eribulin, gemcitabine, or vinorelbine. Association of TMB, as measured by FoundationOne CDx (Foundation Medicine), with response was an exploratory objective evaluated using receiver operator characteristic (ROC) analysis, logistic regression (ORR), and Cox regression (OS; PFS) within treatment arms; estimates of efficacy based on TMB cutpoint used a prespecified cutpoint of 10 mut/Mb. Results: TMB data were available for 253/601 (42.1%) treated patients (pembro, n = 132; chemo, n = 121); baseline characteristics were similar to that of the overall study population. One-sided P values for the association of TMB and clinical outcomes in pembro-treated patients were 0.154 for ORR, 0.014 for PFS, and 0.018 for OS; the area under the ROC curve ([AUROC] 95% CI) for predicting ORR was 0.58 (0.43-0.73). Two-sided P values for the association of TMB and clinical outcomes in chemo-treated patients were 0.114 for ORR, 0.478 for PFS, and 0.906 for OS; AUROC (95% CI) was 0.43 (0.27-0.59). Twenty-six patients had TMB ≥10 mut/Mb. Thus, the prevalence of TMB ≥10 mut/Mb was ~10%. Outcomes based on TMB cutpoint are reported in the Table. Conclusions: Data from this exploratory analysis from KEYNOTE-119 suggest a potential positive association between TMB and clinical benefit with pembro but not chemo in patients with mTNBC. Although precision is limited by sample size and the number of patients with TMB ≥10 mut/Mb, ORR and HRs for OS suggested a trend towards increased benefit with pembro versus chemo in patients with TMB ≥10 mut/Mb. Clinical trial information: NCT02555657 . [Table: see text]

Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

Chromatin accessibility data can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. We develop a computational strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine chromatin accessibility data with large tumor expression data and model the effect of enhancers on transcriptional programs in multiple cancers. We generate a new ATAC-seq data profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and apply PSIONIC to 723 patient and 96 cell line RNA-seq profiles from ovarian, uterine, and basal breast cancers. Our computational framework enables us to share information across tumors to learn patient-specific TF activities, revealing regulatory differences between and within tumor types. PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome. To validate PSIONIC-derived prognostic TFs, we perform immunohistochemical analyses in 31 uterine serous tumors for ETV6 and 45 basal breast tumors for MITF and confirm that the corresponding protein expression patterns are also significantly associated with prognosis.

Abstract 3370: Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers

Epigenomic data on transcription factor occupancy and chromatin accessibility can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. We develop a computational strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine cell line chromatin accessibility data with large tumor expression data sets and model the effect of enhancers on transcriptional programs in multiple cancers. We generated a new ATAC-seq data set profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and applied PSIONIC to 723 patient and 96 cell line RNA-seq profiles from ovarian, uterine, and basal breast cancers. Our computational framework enables us to share information across tumors to learn patient-specific TF activities, revealing regulatory differences between and within tumor types. Many of theidentified TFs were significantly associated with survival outcome in basal breast, uterine serous and endometrioid carcinomas. To validate one PSIONIC-derived prognostic TF, we performed immunohistochemical analyses in 31 uterine serous tumors for ETV6 and confirmed that the corresponding protein expression pattern was also significantly associated with prognosis. Moreover, PSIONIC-predicted activity for MTF1 in cell line models correlated with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy.

Citation Format: Hatice Ulku Osmanbeyoglu, Fumiko Shimizu, Angela Rynne-Vidal, Tsz-Lun Yeung, Petar Jelinic, Samuel C. Mok, Gabriela Chiosis, Douglas A. Levine, Christina Leslie. Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers [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 3370.

Abstract 531: The cGAS-STING pathway as a driver of the immune-reactive microenvironment in small cell carcinoma of the ovary, hypercalcemic type

Introduction: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive malignancy affecting young women. The disease is characterized by a monogenic mutation of SMARCA4, a key member of the SWI/SNF complex. The treatment options are limited, and survival rates are poor. We have previously reported clinical responses in patients undergoing treatment with anti-PD1 immunotherapy, despite a low mutational burden. The responses were attributed to elevated PD-L1 expression and T-cell infiltration in SCCOHT. To better understand the mechanisms of the immune reactive microenvironment we sought to determine the role of the innate immune response driven by the STING pathway after radiotherapy.

Methods: The cGAS-STING expression of cell lines with SMARCA4 loss (H1299), SMARCA4 knockdown (293T SMARCA4) and SMARCA4 wild type (CAOV3, OVCAR4) were analyzed following 10 Gy of irradiation. We evaluated the expression of the cGAS-STING cytosolic DNA sensing pathway by measuring time-dependent expression of cGAS dependent interferon stimulated genes CCL5 and CXCL10. Finally, we analyzed the number of micronuclei formed in SCCOHT model cell lines BIN67 and SCCOHT-1 following irradiation using multi-parametric immunofluorescence.

Results: In H1299 (SMARCA4 loss), there was an 1847-fold increase (p=0.02) in CCL5 and 3954-fold increase in CXCL10 (p=0.09) at 6 days post-irradiation in comparison to non-irradiated controls. In 293T cells with stable knockdown of SMARCA4, there was a 2.8-fold increase in expression of CCL5 (p &lt; 0.01) and a 1.6-fold increase CXCL10 (p=0.26), 6 days after irradiation compared to irradiated wild type cells. In the SMARCA4 wild type cell lines CAOV3 and OVCAR4, there was no statistically significant upregulation of CCL5 and CXCL10. There were more micronucleated cells per high power field after irradiation in BIN67 (21.2% vs 9.30%, p=0.1) and SCCOHT-1 (9.4% vs 0.0%, p=0.03) compared to non-irradiated controls.

Conclusion: SCCOHT is a low mutational burden cancer with demonstrated response to immune checkpoint blockade. Our research shows that following irradiation, the innate immune response triggered by cGAS-STING may be driving the immune reactive microenvironment of SCCOHT. The loss of SMARCA4 may play a role in activating the innate immune response. Better characterization of the association between the SWI/SNF complex and immune reactivity should lead to a broader use for immune checkpoint inhibitors.

Citation Format: Elke Van Oudenhove, Jay R. Patibandla, Selim Misirlioglu, Ernesto Arostegui Fernandez, Petar Jelinic, Douglas A. Levine. The cGAS-STING pathway as a driver of the immune-reactive microenvironment in small cell carcinoma of the ovary, hypercalcemic type [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 531.

Abstract 3970: PARP inhibitors increase expression of Type I interferon regulated genes mainly through trapping

Background: Currently, there are multiple ongoing clinical trials testing the efficacy of various poly (ADP-ribose) polymerase (PARP) inhibitors in combination with immune checkpoint blockade across many cancer types. However, there is no rationale as to which PARP inhibitor is best to use in these studies. Two PARPis (rucaparib and talazoparib) have been reported to activate IFN signaling genes through the stimulator of interferon genes (STING) pathway. The objective of this study is to characterize the effect of all clinically active PARPis on Type I interferon (IFN) regulated genes. We also aim to identify whether this effect is dependent on CHK1, which we have previously reported to be activated by PARP trappers (rucaparib, olaparib, niraparib, and talazoparib) and not by the mainly catalytic inhibitor (veliparib).

Methods: CCL5 and CXCL10 gene expression levels were measured using qRT-PCR in 293T after two days of treatment with the PARP inhibitors (velipairb, rucaparib, olaparib, niraparib, and talazoparib). CXCL10 mRNA levels were also measured in HGSOC BRCA wild-type cell lines (OVCAR3 and CAOV3) after two days of treatment with veliparib and talazoparib. We also measured CCL5 and CXCL10 expression after veliparib and niraparib treatment in 293T cells with stable CHK1 overexpression.

Results: The four PARP trappers consistently increased CCL5 and CXCL10 expression in 293T cells. Although, veliparib had little to no effect on the expression of these two genes as compared to the other four PARPis. CXCL10 mRNA levels were significantly upregulated after talazoparib treatment (p&lt;0.01) but not affected after veliparib treatment in CAOV3 cells. Similarly, an increase in CXCL10 gene expression was observed in OVCAR3 cells (p&lt;0.05). Although, veliparib also had a modest but not significant effect on CXCL10 levels. CCL5 and CXCL10 gene expression consistently increased when treated with niraparib in 293T cells with stable CHK1 overexpression. This same effect was not observed after veliparib treatment in 293T cells that stably overexpressed CHK1.

Conclusions: Our results suggest that all PARP trappers promote expression of IFN Type I regulated genes which may be dependent on CHK1 expression. These findings may better define the most ideal PARP and immune checkpoint inhibitor combination.

Citation Format: Monica E. Wielgos, Petar Jelinic, Douglas A. Levine. PARP inhibitors increase expression of Type I interferon regulated genes mainly through trapping [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 3970.

CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary

Inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. SCCOHT patient tumors are deficient in cyclin D1 yet retain the retinoblastoma-proficient/p16INK4a-deficient profile associated with positive responses to CDK4/6 inhibitors. Thus, our findings indicate that CDK4/6 inhibitors, approved for a breast cancer subtype addicted to CDK4/6 activation, could be repurposed to treat SCCOHT. Moreover, our study suggests a novel paradigm whereby critically low oncogene levels, caused by loss of a driver tumor suppressor, may also be exploited therapeutically.

Abstract PR02: Exploring the effects of PARP inhibition on CHK1 activation as a potential determinant of synergy with CHK1 inhibition

PARP inhibitors (PARPi) have improved the outcomes of patients with high-grade serous ovarian carcinomas (HGSOC) whose tumors harbor mutations in homologous recombination genes such BRCA1 and BRCA2. However, only 20% of cases with this aggressive subtype of ovarian cancer benefit from PARPi, thus highlighting the essential need to identify novel therapeutic strategies for the remainder of these patients. We have recently reported that off-target effects vary among two PARP inhibitors with different trapping potencies. The FDA-approved PARPi, Olaparib, activated the checkpoint kinase 1 (CHK1) protein at serine 345 and arrested cells in the G2/M phase; however, these effects were not observed after treatment with Veliparib, the least potent PARPi measured by the PARP trapping ability.

In this study, we treated HGSOC cell lines with the five most clinically advanced PARP inhibitors and investigated the effect of varying PARP trapping potencies on the expression levels of major proteins that are involved in cell cycle pathways via Western blot and cell cycle analysis. The synergy between the most potent (Talazoparib) or least potent PARP trappers and a CHK1 inhibitor was also explored in HGSOC patient-derived xenograft (PDX) models. We hypothesize that PARP inhibitors that do not have an effect on the cell cycle will have greater synergy with CHK1 inhibitors. Our results reveal that the four most potent PARP trappers—olaparib, rucaparib, niraparib, and talazoparib--activate CHK1 protein and decrease total protein levels of CHK1’s downstream substrate CDC25C. However, we did not observe any significant changes in expression levels in these two proteins after treatment with veliparib. We also observed an arrest in the S/G2 phase of the cell cycle after treatment with the four most potent PARP inhibitors. Finally, the growth of our PDX model was significantly inhibited by combined treatment with veliparib and the CHK1 inhibitor MK-8776 compared to either single-agent therapy or talazoparib combined with MK-8776. These results suggest that there is a distinct off-target effect that differs among the least and most potent PARP inhibitors, with veliparib being more synergistic with CHK1 inhibition. This study will help to expand the use of PARP inhibitors in combination with CHK1 inhibitors and emphasizes the importance of single-agent off-target effects to develop optimal combination therapies.

This abstract is also being presented as Poster A11.

Citation Format: Monicka Wielgos-Bonvallet, Paulina Cybulska, Elke Van Oudenhove, Petar Jelinic, Douglas A. Levine. Exploring the effects of PARP inhibition on CHK1 activation as a potential determinant of synergy with CHK1 inhibition. [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 PR02.

Abstract B26: Immune-active microenvironment in SCCOHT: Rationale for therapy with immune checkpoint blockade

Introduction: Small cell carcinoma of the ovaries, hypercalcemic type (SCCOHT) is a rare and very aggressive malignancy with limited treatment options. SCCOHT is described as an epigenetically altered SMARCA4-mutated monogenic disease, but the exact mechanism of SCCOHT tumorigenesis is not clear. Immune checkpoint-targeting antibodies have not been considered as a suitable treatment option for SCCOHT, because this cancer is characterized by a small number of mutations. Anecdotal reports of patients with SCCOHT responding to PD-1 blockade have challenged this view. We aimed to characterize the immune microenvironment of SCCOHT in order to evaluate a rationale for therapy with PD-1/PD-L1 targeting antibodies.

Methods: To test whether SCCOHT tumors were identified by the immune system, we examined PD-L1 expression and T cell populations within tumor samples. The immune landscape was profiled using quantitative immunofluorescence and gene expression profiling.

Results: Most tumors showed PD-L1 expression and prominent T cell infiltration, with PD-L1 being primarily limited to tumor-infiltrating immune cells. Gene expression analyses revealed upregulation of genes related to T-cell infiltration and cytolytic function in the PD-L1-high tumors. We hypothesize that PD-L1 upregulation in SCCOHT is an adaptive immune response to T-cell infiltration, as has been previously reported for several other cancer types.

Conclusions: Our findings provide an impetus for further investigation of PD-1/PD-L1 as a potential therapy for patients with SCCOHT. More generally, these results challenge the prevailing view that tumor immunogenicity is primarily driven by mutational burden, calling for identification of additional immune pathways involved in tumor recognition.

Citation Format: Elke Van Oudenhove, Petar Jelinic, Jacob Ricca, Narciso Olvera, Taha Merghoub, Douglas A. Levine, Zamarin Dmitriy. Immune-active microenvironment in SCCOHT: Rationale for therapy with immune checkpoint blockade. [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 B26.

Abstract 335: Variable off-target effects of clinically advanced PARP inhibitors

High-grade serous ovarian carcinoma (HGSOC) is the most common subtype of ovarian cancer with low 5-year survival rates. Inhibitors of poly (ADP-ribose) polymerase (PARP) are promising novel agents that uniquely target HGSOCs with DNA repair deficiencies. The majority of patients with DNA repair proficient HGSOCs do not respond to PARP inhibitor monotherapy, highlighting the need for novel treatment approaches for these women. The goal of this study was to expand the patient population that could benefit from PARP inhibition by identifying the off-target effects that are favorable in combination with CHK1 inhibitors among the five most clinically advanced PARP inhibitors.

Cell cycle and western blot analysis revealed that the four most potent PARP trappers (rucaparib, olaparib, niraparib, and talazoparib) have a strong effect on the cell cycle. The PARP trappers in particular activated CHK1 through phosphorylation at the serine 345 residue, decreased total protein levels of CDC25C, and arrested cells in the S/G2 phase of the cell cycle. These results were not observed after treatment with veliparib, the least potent PARP trapper. We created phospo-CHK1 mutants to confirm CHK1 activation at serine 345 and to further investigate whether potent PARP trappers activate CHK1 on serine 317, another residue that is also phosphorylated in response to replication stress. The data suggest that PARP trappers activate CHK1 at both the serine 317 and 345 phosphorylation sites.

Next, we examined whether PARP inhibition-induced activation of CHK1 is a determinant of synergy between PARP and CHK1 inhibitors. We exposed one of our established BRCA wild-type, TP53 mutant HGSOC patient-derived xenograft models to a PARP1 inhibitor (veliparib or talazoparib) or to the CHK1 inhibitor (MK-8776) or a combination of PARP and CHK1 inhibitors. CHK1 inhibition slightly increased sensitivity to talazoparib compared to single agent therapy. However, the tumor volume was significantly reduced by the combination of CHK1 inhibition and veliparib treatment compared to either single agent alone. This study suggests that there are off-target cell cycle effects that vary among the five most clinically-advanced PARP inhibitors that likely influence the response to combinatorial treatment. We propose the use of PARP and CHK1 inhibition as a strategy for HGSOC patients who would otherwise have minimal benefit to PARP inhibitor monotherapy.

Citation Format: Monica E. Wielgos, Jay Patibandla, Michelle Firlit, Elke Van Oudenhove, Paulina Cybulska, Petar Jelinic, Douglas A. Levine. Variable off-target effects of clinically advanced PARP inhibitors [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 335.

Abstract 282: Inferring transcriptional regulatory programs in gynecological cancers

Cancer cells acquire genetic and epigenetic alterations that often lead to dysregulation of oncogenic signal transduction pathways, which in turn alter downstream transcriptional programs. Transcription factors (TFs) are the main link between signaling pathways and the transcriptional regulatory programs. The Cancer Genome Atlas (TCGA) has studied several of the most common and aggressive gynecologic tumors including high-grade serous ovarian carcinomas (HGSOC), uterine carcinosarcoma (UCS), and the serous-like subset of endometrial cancer (UCEC), together with basal breast cancer, which shares many genomic features with serous ovarian tumors. TFs impacts on gene regulation have not been well characterized in gynecological and basal breast cancers. The majority of these tumors lack accurate predictors of response and resistance and share an unmet need for adequate treatment of recurrent disease. We developed a multitask learning framework for integrating regulatory sequence from ATAC-mapped promoters and enhancers from cell line models with RNA-seq data from patient tumors in order to infer transcription factor (TF) regulatory activities and explore similarities and differences between uterine, ovarian, and basal breast tumors. We showed that our multitask learning framework enables us to selectively share the information across tumors and strongly improves the accuracy of gene expression prediction models for gynecological and basal breast tumors. Our analysis identified histologic type specific and common TF regulators of gene expression as well as predicted distinct dysregulated transcriptional regulators downstream of somatic alterations in these different cancers. Moreover, many of the identified TF regulators were significantly associated with survival outcome within the histological subtype. Computationally dissecting the role of TFs in these cancers may ultimately lead to new therapeutics tailored to groups of subtypes or individuals.

Citation Format: Hatice U. Osmanbeyoglu, Petar Jelinic, Douglas Douglas, Christina Leslie. Inferring transcriptional regulatory programs in gynecological cancers [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 282.

Immune-Active Microenvironment in Small Cell Carcinoma of the Ovary, Hypercalcemic Type: Rationale for Immune Checkpoint Blockade

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), is a highly aggressive monogenic cancer driven by SMARCA4 mutations. Here, we report responses to anti-PD1 immunotherapy in four patients and characterize the immune landscape of SCCOHT tumors using quantitative immunofluorescence and gene expression profiling. Unexpectedly for a low mutation burden cancer, the majority of the tumors (eight of 11 cases) demonstrated PD-L1 expression with strong associated T-cell infiltration (R2 = 0.60-0.95). PD-L1 expression was detected in both tumor and stromal cells, with macrophages being the most abundant PD-L1-positive cells in some tumors (three of 11 cases). Transcriptional profiling revealed increased expression of genes related to Th1 and cytotoxic cell function in PD-L1-high tumors, suggesting that PD-L1 acts as a pathway of adaptive immune resistance in SCCOHT. These findings suggest that although SCCOHT are low-mutational burden tumors, their immunogenic microenvironment resembles the landscape of tumors that respond well to treatment with PD-1/PD-L1 blockade.

Small cell cancers of the female genital tract: Molecular and clinical aspects

OBJECTIVE

Extra-pulmonary small cell carcinomas of the gynecologic tract (EPSCC-GTs) are a rare group of aggressive malignancies associated with poor prognoses and limited treatment options. Here, we review the clinical and molecular aspects of EPSCC-GTs and discuss how understanding their molecular features can assist in their diagnosis and the identification of novel effective treatments.

METHODS

We searched PubMed and Scopus for articles using the following keywords: "small cell carcinoma" in combination with "neuroendocrine", "ovary", "vagina", "fallopian tube", "vulva", "endometrium", "uterus", "cervix", or "gynecologic". Articles were limited to those published in English from January 1984 to October 2017.

RESULTS

EPSCC-GTs account for 2% of all gynecologic malignancies. The molecular features of EPSCC-GTs are largely understudied and unknown, with the exception of small cell carcinoma (SCC) of the ovary, hypercalcemic type (SCCOHT) and SCC of the cervix (SCCC). In nearly all cases, SCCOHT displays mutation in a single gene, SMARCA4, a member of the SWI/SNF chromatin remodeling complex. The loss of expression of the SWI/SNF protein SMARCA2 is another feature of SCCOHT. Dual negative staining for SMARCA2 and SMARCA4 is specific for SCCOHT and is generally used by gynecologic pathologists for the accurate diagnosis of this malignancy. Mutational analysis of SCCC has shown alterations in PIK3CA, KRAS and TP53, of which the last is the most common, although other actionable mutations have been identified. The molecular features of other EPSCC-GTs are largely unknown.

CONCLUSIONS

Due to their rarity, the majority of EPSCC-GTs are understudied and poorly understood. As demonstrated in the case of SCCOHT, unraveling the mutational profiles of these tumors can lead to improved diagnosis and the identification of novel therapeutic targets.

Abstract LB-A04: Transcriptional regulatory programs in gynecological cancers

Cancer cells acquire genetic and epigenetic alterations that often lead to dysregulation of oncogenic signal transduction pathways, which in turn alter downstream transcriptional programs. The Cancer Genome Atlas (TCGA) has studied several of the most common and aggressive gynecologic tumors including high-grade serous ovarian carcinomas (HGSOC), uterine carcinosarcoma (UCS), and the serous-like subset of endometrial cancer (UCEC), together with basal breast cancer, which shares many genomic features with serous ovarian tumors. These tumors all lack accurate predictors of response and resistance and share an unmet need for adequate treatment of recurrent disease. We developed a multitask learning framework for integrating regulatory sequence from ATAC-mapped promoters and enhancers with RNA-seq data from patient tumors in order to infer transcription factor (TF) regulatory activities and explore similarities and differences between endometrial, ovarian, and basal breast tumors. We showed that our multitask learning framework enables us to selectively share the information across tumors and strongly improves the accuracy of gene expression prediction models for gynecological and basal breast tumors. Our analysis identified histologic type specific and common TF regulators of gene expression as well as predicted distinct dysregulated transcriptional regulators downstream of somatic alterations in these different cancers. Moreover, many of the identified TF regulators were significantly associated with survival outcome within the histological subtype. Computationally dissecting the role of TFs in these cancers may ultimately lead to new therapeutics tailored to subtype or individual.

Citation Format: Hatice U. Osmanbeyoglu, Petar Jelinic, Douglas Levine, Christina S. Leslie. Transcriptional regulatory programs in gynecological cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A04.

The EMSY threonine 207 phospho-site is required for EMSYdriven suppression of DNA damage repair

BRCA1 and BRCA2 are essential for the repair of double-strand DNA breaks, and alterations in these genes are a hallmark of breast and ovarian carcinomas. Other functionally related genes may also play important roles in carcinogenesis. Amplification of EMSY, a putative BRCAness gene, has been suggested to impair DNA damage repair by suppressing BRCA2 function. We employed direct repeat GFP (DR-GFP) and RAD51 foci formation assays to show that EMSY overexpression impairs the repair of damaged DNA, suggesting that EMSY belongs to the family of BRCAness proteins. We also identified a novel phospho-site at threonine 207 (T207) and demonstrated its role in EMSY-driven suppression of DNA damage repair. In vitro kinase assays established that protein kinase A (PKA) directly phosphorylates the T207 phospho-site. Immunoprecipitation experiments suggest that EMSY-driven suppression of DNA damage repair is a BRCA2-independent process. The data also suggest that EMSY amplification is a BRCAness feature, and may help to expand the population of patients who could benefit from targeted therapies that are also effective in BRCA1/2-mutant cancers.

Abstract 3422: miR-200c-driven mesenchymal-to-epithelial transition as a therapeutic target in uterine carcinosarcomas

Introduction and purpose of study: Uterine carcinosarcoma (UCS) is an aggressive and rare malignancy with poor prognosis and limited treatment options. These biphasic tumors, consisting of epithelial and mesenchymal components, are hypothesized to evolve from less aggressive endometrial adenocarcinomas (EACs) through epithelial-mesenchymal transition (EMT). EMT is a reversible process, and mesenchymal-epithelial transition (MET) has been shown to decrease tumor aggressiveness. Inducing MET has been suggested for treatment of cancers with a mesenchymal phenotype. In our studies, we investigated the importance of EMT in the evolution of UCS by depleting miR-200, a family of microRNAs critical for EMT, in EAC cell lines. We also explored the role of miR-200 overexpression as a driving force for MET in UCS with a focus on finding novel therapeutic approaches to the treatment of this aggressive disease.

Experimental procedures: To test whether UCSs evolve from EACs, we depleted miR-200b/c in EAC cell lines, Ishikawa and MFE-280. For the MET studies, we stably overexpressed miR-200c in UCS cell lines, SNU685 and JHUCS1. Gene expression was measured using TaqMan and whole transcriptome sequencing (RNA-seq) assays. Immunoblotting was performed on the EMT-relevant proteins. Cell adhesion and in vitro cell proliferation were measured using commercially available assays. In vivo tumor growth of JHUCS1 miR-200c-overexpressed cells was measured in xenografted mice.

Summary of the data: Compared to EAC cells, UCS cells had undetectable miR-200c expression. Depletion of miR-200b/c in EAC cells resulted in expected increased ZEB1 and decreased E-cadherin expression. The lack of increased N-cadherin, vimentin and morphologic changes, even in the presence of exogenous TGF-β suggests partial EMT induction. Overexpression of miR-200c in UCS cells resulted in full MET, with a decrease in ZEB1, ZEB2, N-cadherin and vimentin and an increase in E-cadherin. Increased cellular adhesion was observed along with typical MET morphologic changes. miR-200c overexpression led to inhibited UCS cell proliferation and metabolic activity. Overexpression of miR-200c in vivo resulted in substantially smaller tumors compared to mice bearing control UCS cells.

Conclusions: Our data suggest that mechanisms additional to, or other than EMT, are necessary for the evolution of UCS from EAC. UCS cell lines, however, readily undergo robust MET in the setting of increased miR-200c expression rendering them less aggressive. These findings suggest that miR200 overexpression through advanced microRNA therapeutics may lead to new options for the treatment of uterine carcinosarcomas.

Citation Format: Jill H. Tseng, Maria Bisogna, Lien N. Hoang, Narciso Olvera, Douglas A. Levine, Petar Jelinic. miR-200c-driven mesenchymal-to-epithelial transition as a therapeutic target in uterine carcinosarcomas [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 3422. doi:10.1158/1538-7445.AM2017-3422

Abstract 3415: RNF43 somatic mutations in endometrioid ovarian cancers occur in the setting of synchronous endometrioid endometrial cancers

Introduction: Somatic frameshift mutations in RNF43 have previously been filtered out in cancer genome sequencing projects given that they occur in homopolymer tracts and resemble polymerase slippage errors. Two RNF43 hotspot mutations have been identified and validated in endometrioid endometrial cancer (EEC) and appear to negatively regulate Wnt signaling. These frameshift mutations occur at codons R117 and G659. Due to shared clinical and morphologic features of EEC and endometrioid ovarian cancer (EmOC), we determined the frequency of RNF43 somatic mutations in EmOC.

Methods: We reviewed the clinical and pathologic features of EmOC samples diagnosed from 2006 to 2015, retrieved from laboratory databases and institutional archives. DNA was extracted from formalin-fixed, paraffin-embedded tumor samples using standard protocols. Sanger and next-generation sequencing (NGS) were used to screen for hotspot mutations at codons R117 and G659 with custom designed primers. NGS at each hotspot was covered with a minimum sequencing depth of 400X.

Results: Forty-seven EmOC patients with available tumor specimens were identified and included in the analysis. The median age at diagnosis was 55 years old (range 34-84). The majority of patients had FIGO stage I or stage II disease (n=38, 81%). Thirteen (28%) patients had synchronous endometrial endometrioid or mixed histology tumors. Two (4.3%) RNF43 somatic mutations at codon G659 were identified in both Sanger and NGS from the EmOC tumor specimens. No mutations at codon R117 were identified. The allele fractions of the G659 mutations were 4.3% and 2.8% seen in 33 and 18 reads with a coverage of 775X and 646X, respectively. A review of pathology reports indicated that both mutated samples had synchronous EECs. These two mutated samples represent 15.4% of cases diagnosed with synchronous EmOC and EEC in this cohort.

Conclusions: RNF43 somatic mutations are uncommon in EmOCs and associated with synchronous EECs. Recent massively parallel sequencing data suggests that EmOCs in the setting of synchronous EECs are clonally related and disseminated cells are related to nearby anatomic structures. Our data supports that RNF43 somatic mutations in EmOC are clonally expanded from EECs likely through trans-tubal migration.

Citation Format: Defne L. Levine, Fanny Dao, Narciso Olvera, Katherine LaVigne, David B. Solit, Petar Jelinic. RNF43 somatic mutations in endometrioid ovarian cancers occur in the setting of synchronous endometrioid endometrial cancers [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 3415. doi:10.1158/1538-7445.AM2017-3415

Abstract MIP-062: THE EMSY THREONINE 207 PHOSPHO–SITE IS REQUIRED FOR EMSY–DRIVEN SUPPRESSION OF DNA DAMAGE REPAIR

PURPOSE OF STUDY: EMSY, a putative DNA damage repair gene, is amplified in over 10% of high-grade serous ovarian carcinoma (HGSOC) cases. EMSY overexpression has been hypothesized to antagonize BRCA2 via direct interaction and compromise the homology-directed repair (HDR) of DNA double strand breaks. EMSY's role as a transcription factor has been described in a protein kinase AKT1 phosphorylation-dependent manner. The purpose of this study was to decipher EMSY's role in HDR and to assess the importance of its phosphorylation in this context.

EXPERIMENTAL PROCEDURES: We measured HDR activity in several cell lines (U2OS osteosarcoma, H1299 non-small cell lung carcinoma and OVCAR8 HGSOC) using the DR-GFP reporter assay and RAD51 foci assessment. Endogenous immunoprecipitations (IPs) were performed with low stringency lysis buffer and protein A/G-plus agarose. V5-tagged EMSY constructs were made using the Invitrogen's Gateway TOPO cloning system. These constructs were further used to create EMSY phospho-mutants. Cells were transfected by either electroporation or FuGene reagent. For the in vitro kinase assays, EMSY constructs were sub-cloned and expressed in BL21 STAR bacteria and purified using Invitrogen's Champion pET102 Expression kit. Recombinant protein kinases were obtained from Active Motif and CellSignaling. Forskolin and H-89 were obtained from Santa Cruz Biotechnology.

SUMMARY OF THE DATA: EMSY overexpression resulted in decreased HDR activity in all three DR-GFP cell lines, thus supporting the hypothesis that EMSY overexpression impairs HDR. V5-tagged EMSY overexpressing and endogenous immunoprecipitation experiments demonstrated no interaction between EMSY and BRCA2, suggesting EMSY's role in HDR to be BRCA2-independent. We confirmed that EMSY is phosphorylated by AKT1 at serine 209 phospho-site and identified a previously unknown phospho-site at threonine 207. We identified protein kinase A (PKA) as a kinase targeting EMSY T207. Furthermore, by performing both DR-GFP assay and RAD51 foci assessment in OVCAR8 cells that overexpress WT EMSY or either phospho-mutant, we demonstrated that mutant EMSY-S209A affects HDR activity similar to the WT EMSY while EMSY-T207A does not. This suggests the importance of PKA and the T207 phospho site for the EMSY-driven HDR suppression.

CONCLUSIONS: EMSY-overexpressing cells show decreased HDR activity, demonstrating EMSY's relevance to the HDR pathway. Our data support the notion that EMSY-driven HDR impairment is BRCA2-interaction-independent and challenges the currently held impression that EMSY overexpression mimics the BRCA2-depleted phenotype via direct interaction. We found a new phospho-site at EMSY T207 and identified PKA as a targeting kinase. Phosphorylation of EMSY at T207, but not S209 phospho-site is necessary for EMSY-driven suppression of HDR. We suggest that an increase in EMSY's T207 phosphorylation in patients bearing EMSY-amplified tumors could enhance BRCAness and render these patients more sensitive to drugs effective in HDR-impaired setting, such as PARP inhibitors.

Citation Format: Petar Jelinic, Laura A. Eccles, Jill Tseng, Paulina Cybulska, Simon N. Powell, Douglas A. Levine. THE EMSY THREONINE 207 PHOSPHO–SITE IS REQUIRED FOR EMSY–DRIVEN SUPPRESSION OF DNA DAMAGE REPAIR [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 MIP-062.

Abstract A03: The EMSY threonine 207 phospho-site is required for EMSY-driven suppression of DNA damage repair

Introduction: EMSY, a putative DNA damage repair gene, is amplified in over 10% of high-grade serous ovarian carcinoma (HGSOC) cases. EMSY overexpression has been hypothesized to antagonize BRCA2 via direct interaction and compromise the homology-directed repair (HDR) of DNA double strand breaks. Its role as a transcription factor has been described in a protein kinase AKT1 phosphorylation-dependent manner. The purpose of this study was to decipher EMSY's role in HDR and to assess the importance of its phosphorylation in this context.

Experimental procedures: We measured HDR activity in several cell lines (U2OS osteosarcoma, H1299 non-small cell lung carcinoma and OVCAR8 HGSOC) using the DR-GFP reporter assay and RAD51 foci assessment. Endogenous immunoprecipitations (IPs) were performed with low stringency lysis buffer and protein A/G-plus agarose. V5-tagged EMSY constructs were made using the Invitrogen's Gateway TOPO cloning system. These constructs were further used to create EMSY phospho-mutants. Cells were transfected by either electroporation or FuGene reagent. For the in vitro kinase assays, EMSY constructs were sub-cloned and expressed in BL21 STAR bacteria and purified using Invitrogen's Champion pET102 Expression kit. Recombinant protein kinases were obtained from Active Motif and CellSignaling. Forskolin and H-89 were obtained from Santa Cruz Biotechnology.

Summary of the data: EMSY overexpression resulted in decreased HDR activity in all three DR-GFP cell lines, thus supporting the hypothesis that EMSY overexpression impairs HDR. V5-tagged EMSY overexpressing and endogenous immunoprecipitation experiments demonstrated no interaction between EMSY and BRCA2, suggesting EMSY's role in HDR to be BRCA2-independent. We confirmed that EMSY is phosphorylated by AKT1 at serine 209 phospho-site and identified a previously unknown phospho-site at threonine 207. We identified protein kinase A (PKA) as a kinase targeting EMSY T207. Furthermore, by performing both DR-GFP assay and RAD51 foci assessment in OVCAR8 cells that overexpress WT EMSY or either phospho-mutant, we demonstrated that mutant EMSY-S209A affects HDR activity similar to the WT EMSY while EMSY-T207A does not. This suggests the importance of PKA and the T207 phospho site for the EMSY-driven HDR suppression.

Conclusions: EMSY-overexpressing cells show decreased HDR activity, demonstrating EMSY's relevance to the HDR pathway. Our data support the notion that EMSY-driven HDR impairment is BRCA2-interaction-independent and challenges the currently held impression that EMSY overexpression mimics the BRCA2-depleted phenotype via direct interaction. We found a new phospho-site at EMSY T207 and identified PKA as a targeting kinase. Phosphorylation of EMSY at T207, but not S209 phospho-site is necessary for EMSY-driven suppression of HDR. We suggest that an increase in EMSY's T207 phosphorylation in patients bearing EMSY¬-amplified tumors could enhance BRCAness and render these patients more sensitive to drugs effective in HDR-impaired setting, such as PARP inhibitors.

Citation Format: Petar Jelinic, Laura Eccles, Jill Tseng, Paulina Cybulska, Simon N. Powell, Douglas Levine. The EMSY threonine 207 phospho-site is required for EMSY-driven suppression of DNA damage repair [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr A03.

Abstract PR01: EMSY impairs DNA damage repair in a phosphorylation-dependent manner

Background: EMSY, a putative DNA damage repair gene, is amplified in over 10% of high-grade serous ovarian carcinoma (HGSOC) cases. EMSY was initially identified as a BRCA2-interacting protein. Its overexpression has been hypothesized to antagonize BRCA2 and therefore compromise the homology-directed repair (HDR) of DNA double strand breaks; however, this has not been proven. Although EMSY's role in HDR has yet to be elucidated, it is known to be phosphorylated by the protein kinase AKT1. The purpose of this study was to decipher EMSY's role in HDR and to assess the importance of its phosphorylation in this context. In addition, we sought to test whether EMSY overexpressing cells are sensitive to HDR-targeted therapies such as PARP inhibitors.

Methods: We measured HDR activity in several cell lines (U2OS osteosarcoma, H1299 non-small cell lung carcinoma and OVCAR8 HGSOC) using the DR-GFP reporter assay and RAD51 foci assessment according to standard protocols. Endogenous immunoprecipitations (IPs) were performed in 293T, HeLa and OVCAR8 cells with low stringency lysis buffer and protein A/G-plus agarose. V5-tagged EMSY constructs were made using the Invitrogen's Gateway TOPO cloning system. These constructs were further used to create EMSY phospho-mutants. Cells were transfected by either electroporation or FuGene reagent. For the in vitro kinase assays, EMSY constructs were sub-cloned and expressed in BL21 STAR bacteria and purified using Invitrogen's Champion pET102 Expression kit. Recombinant active protein kinase A (PKA) and AKT1 were obtained from Active Motif and CellSignaling, respectively. Colony formation assay was used to assess the sensitivity of EMSY-overexpressing cells to PARP inhibitors (SelleckChem).

Results: V5-IP experiments in V5-tagged EMSY overexpressing 293T cells demonstrated no interaction between EMSY and BRCA2. This was further confirmed by endogenous immunoprecipitation in three cell lines: 293T, HeLa and OVCAR8. EMSY overexpression resulted in decreased HDR activity in all three DR-GFP cell lines (U2OS, H1299 and OVCAR8), thus supporting the hypothesis that EMSY-overexpression impairs HDR. We confirmed that EMSY is phosphorylated by AKT1 at serine 209 phospho-site and identified a previously unknown phospho-site at threonine 207. By using kinase prediction bioinformatic tools, we identified protein kinase A (PKA) as a potential kinase targeting EMSY T207. This was confirmed by in vitro kinase assay. Furthermore, by performing both DR-GFP assay and RAD51 foci assessment in OVCAR8 cells that overexpress WT EMSY or either phospho-mutant, we demonstrated that mutant EMSY-S209A affects HDR activity similar to the WT EMSY while EMSY-T207A does not. This suggests the importance of the T207 phospho site for the EMSY-driven HDR suppression. Finally, EMSY-overexpressing cells were more sensitive to the PARP inhibitors olaparib and veliparib when compared to mock cells.

Conclusions: Our data demonstrates that BRCA2 and EMSY do not interact. This supports the notion that EMSY-driven HDR impairment is BRCA2-interaction-independent and challenges the currently held impression that EMSY overexpression mimics the BRCA2-depleted phenotype via direct interaction. EMSY-overexpressing cells show decreased HDR activity, demonstrating EMSY's relevance to the HDR pathway. We found a new phospho-site at EMSY's T207 and identified PKA as a targeting kinase. Moreover, phosphorylation of EMSY at T207, but not S209 phospho-site is necessary for EMSY-driven suppression of HDR. Finally, EMSY-overexpressing cells are sensitive to PARP inhibition suggesting that the patients bearing EMSY-amplified ovarian cancer may benefit from HDR-targeted therapies.

Citation Format: Petar Jelinic, Laura Eccles, Simon N. Powell, Douglas A. Levine. EMSY impairs DNA damage repair in a phosphorylation-dependent manner. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr PR01.

Abstract LB-91: SMARCA4 mutations in small cell carcinoma of the ovary

Background: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, highly aggressive form of ovarian cancer primarily diagnosed in young women. The molecular basis of this disease is unknown, and there are limited therapeutic options. The tissue of origin remains speculative, and SCCOHT is still categorized as a miscellaneous tumor by the World Health Organization.

Methods: We performed target capture and massively parallel DNA sequencing to a mean depth 442x across 279 key cancer-associated genes in 12 SCCOHT samples. All mutations were validated using orthogonal techniques and their somatic nature was determined by sequencing matched germline DNA. Mutation expression and the consequence of splice site variants were determined through RNA sequencing. Protein expression was determined through immunoblotting and immunohistochemistry. Functional significance was determined through in vitro manipulation using over-expression and knockdown constructs.

Results: All 12 patients (median age 26.5 yrs; range 18-42 yrs) had inactivating bi-allelic variants in the chromatin regulator SMARCA4, including splice site, nonsense, and frameshift mutations or exon deletions. One patient had a germline mutation with somatic loss of the wild-type allele. All mutations were detected in RNA transcripts, and splice site variants resulted in transcribed introns. Immunoblotting and immunohistochemistry confirmed loss of SMARCA4 protein expression in 7 of 9 cases with mutations and available tissue. SMARCA4 somatic mutations were more common in SCCOHT than other solid tumors found in The Cancer Genome Atlas (p &lt; 2.22 x 10-16). Ectopic re-introduction of SMARCA4 resulted in a dose-dependent suppression of cell growth and an expected increase in p21. Stable depletion of SMARCA4 using lentiviral expressed short hairpin RNA led to an increase in cell growth as measured by an XTT proliferation assay.

Conclusions: SMARCA4 SWI/SNF chromatin-remodeling complex mutations were uniformly identified in all SCCOHT examined. The SCCOHT tumors had few other mutations in the panel of sequenced genes. The inactivating mutations are infrequently mutated in other solid tumors and are consistent with the characteristics of a tumor suppressor. Most of the identified mutations reside within the known helicase catalytic domains of SMARCA4, suggesting a role in tumorigenesis. One case contained a germline mutation, which is consistent with prior reports suggesting a hereditary component to this disease. These data suggest that canonical mutations in SMARCA4 are an important therapeutic target for further investigation.

Citation Format: Petar Jelinic, Jennifer Mueller, Narciso Olvera, Fanny Dao, Sasinya N. Scott, Ronak Shah, JianJiong Gao, Nikolaus Schultz, Mithat Gonen, Robert A. Soslow, Michael F. Berger, Douglas A. Levine. SMARCA4 mutations in small cell carcinoma of the ovary. [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-91. doi:10.1158/1538-7445.AM2014-LB-91

New insights into PARP inhibitors' effect on cell cycle and homology-directed DNA damage repair

In preclinical and clinical studies, olaparib and veliparib are the most represented PARP inhibitors (PARPi), which mainly target homologous DNA damage repair pathway-deficient cancer cells. Their off-target effects are not fully understood, especially with regard to cell cycle and homology-directed DNA damage repair. Our objective was to comparatively evaluate olaparib and veliparib in this context and correlate our findings with their therapeutic potential. We used a well-established direct repeat GFP (DR-GFP) reporter assay in U2OS(DR-GFP) and H1299(DR-GFP) cells and measured DNA damage repair activity upon drug treatment. Olaparib-treated U2OS(DR-GFP) cells showed a dramatic decrease in DNA damage repair versus veliparib irrespective of inhibitory potency. We demonstrate that this effect was a result of olaparib's strong effect on the cell cycle. Unlike in veliparib-treated U2OS(DR-GFP) cells, in olaparib-treated cells S-phase decreased and G(2)-phase increased sharply, indicating a G(2)-phase arrest-like state and replicative stress. This was further confirmed by upregulation of p53 and p21 and accumulation of cyclin A. Lack of the same effect in p53-null H1299(DR-GFP) cells suggested that olaparib's effect is p53 related, which was confirmed in p53-depleted U2OS(DR-GFP) and p53-null HCT116 cells. Importantly, we also demonstrate that olaparib, but not veliparib, induced a robust phosphorylation of Chk1, a crucial component of the replicative stress response pathway. Our data show olaparib and veliparib differ in their off-target effects; olaparib, unlike veliparib, mitigates DNA damage repair activity via G(2) cell-cycle arrest-like effect in a p53-dependent manner. These off-target effects may add to PARPis' anticancer properties.

Abstract B26: Non-catalytic effects of PARP inhibitors in the context of cell cycle and homology-directed DNA damage repair

Background: Poly (ADP)-ribose polymerase inhibitors (PARPis) target PARPs, the stress sensing proteins that respond to DNA single-strand breaks. PARP inhibition has been extensively explored in pre-clinical and clinical studies with successes demonstrated in homology-directed DNA damage repair (HDR) pathway-deficient ovarian cancer patients. The inhibitory potential of PARPis is well established; however non-catalytic effects that may add to their therapeutic properties are not fully understood. Our objective was to comparatively evaluate non-catalytic inhibitory properties, particularly in the context of cell cycle and HDR, of the most widely tested PARPis in pre-clinical and clinical studies, olaparib and veliparib.

Methods: To measure DNA damage repair activity upon PARPi treatment, we used a well-established DR-GFP reporter assay in two model cell lines, U2OSDR-GFP and H1299DR-GFP. Cell cycle progression was assessed by staining with propidium iodide and monitored by flow cytometry. Depletion of p53 in U2OSDR-GFP cells was performed by standard siRNA knock-down technique using electroporation for transfection. Immunoblotting was used to confirm cell cycle results and demonstrate replicative stress on the protein expression levels.

Results: We found a dramatic decrease in DNA damage repair activity in olaparib versus veliparib-treated U2OSDR-GFP cells, regardless of their inhibitory potency. This decrease in HDR activity was a result of olaparib triggering a cell cycle arrest-like state as a response to strong replicative stress. Lack of the same effect in p53-null H1299DR-GFP cells suggests that olaparib's effect is p53-dependent, which was confirmed in U2OSDR-GFP cells depleted of p53. Our data also suggest that cells treated with veliparib are more ambivalent towards p53 status, a difference in comparison to olaparib-treated cells.

Conclusion: These data demonstrate that olaparib and veliparib differ in their non-catalytic inhibitory effects, with olaparib but not veliparib mitigating DNA damage repair activity via cell cycle arrest-like effects in a p53-WT background. This new insight into olaparib's and veliparib's mechanism of action should be considered when developing inclusion criteria for treatment of ovarian cancer patients with these PARP inhibitors or others.

Citation Format: Petar Jelinic, Douglas A. Levine. Non-catalytic effects of PARP inhibitors in the context of cell cycle and homology-directed DNA damage repair. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B26.

Abstract 3158: Transcription factor SOX11 decreases viability in ovarian carcinoma cells

Objective: The Cancer Genome Atlas (TCGA) evaluated nearly 500 advanced serous ovarian carcinomas and identified four gene expression subclasses. The transcription factor SOX11 was markedly overexpressed in the proliferative subtype and associated with phosphorylation of other cell cycle related proteins including CHEK2, WWTR1, and EIF4EBP1. We tested the hypothesis that over-expression of SOX11 will decrease proliferation of ovarian cancer cells through transcriptional repression.

Methods: SOX11 was overexpressed via lipofectamine transfection in the TP53 wild-type ovarian cancer cell line SKOV3 and the TP53 mutated ovarian cancer cell line OVCAR3. Cell proliferation was assessed 48 hours after transfection using the VisionBlue fluorescence-based viability assay. Cell cycle analysis was performed utilizing a propidium iodide (PI) assay followed by fluorescence-activated cell sorting (FACS). Finally migration of SOX11-transfected cells was analyzed in comparison to mock-transfected controls via monolayer scratch assay.

Results: Successful overexpression of the SOX11 protein was confirmed using GFP fluoroscopy and western blot 24 and 48 hours following transfection. Cell viability was reduced by 14-63% at 48 hours in SOX11-transfected SKOV3 cells compared to mock controls (P = 0.01) in a dose dependent fashion. Cell cycle was unaffected by SOX11 overexpression. Finally, the monolayer scratch assay demonstrated that cells overexpressing SOX11 migrated more slowly than mock controls (median velocity 3.92 vs. 6.19 um/hr, P = 0.001). Data from OVCAR3 cells are currently being analyzed and will be presented.

Conclusions: Overexpression of SOX11 resulted in decreased cell viability without affecting cell cycle. Further studies will assess the mechanism of this decreased viability which may involve diversion toward an apoptotic pathway when SOX11 is overexpressed or regulation by transcription repressors such as WWTR1. SOX11 suppression has been shown in lymphoma to be associated with more aggressive tumors through mechanisms associated with lysophosphatidic acid growth regulation, offering mechanistic associations with ovarian cancer. Ongoing work will determine the relationship between SOX11 and TP53 mutation frequently found in high-grade serous carcinoma. These studies will help to explain the differential outcomes seen across high-grade serous ovarian carcinoma.

Citation Format: Caryn M. St. Clair, Stephanie L. Wethington, Maria Bisogna, Fanny Dao, Petar Jelinic, Douglas A. Levine. Transcription factor SOX11 decreases viability in ovarian carcinoma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3158. doi:10.1158/1538-7445.AM2013-3158

Validated gene targets associated with curatively treated advanced serous ovarian carcinoma

OBJECTIVES

High-grade serous ovarian cancer (HGSOC) mostly presents at an advanced stage and has a low overall survival rate. However, a subgroup of patients are seemingly cured after standard initial therapy. We hypothesize that the molecular profiles of these patients vary from long-term survivors who recur.

METHODS

Patients with advanced HGSOC who underwent primary cytoreductive surgery and platinum-based chemotherapy were identified from The Cancer Genome Atlas (TCGA) and institutional (MSKCC) samples. A curative-intent group was defined by recurrence-free survival of >5years. A long-term recurrent group was composed of patients who recurred but survived >5years. RNA was hybridized to Affymetrix U133A transcription microarrays. The NanoString nCounter gene expression system was used for validation in an independent patient population.

RESULTS

In 30 curative and 84 recurrent patients, class comparison identified twice as many differentially expressed probes between the groups than expected by chance alone. TCGA and MSKCC data sets had 19 overlapping genes. Pathway analyses identified over-represented networks that included nuclear factor kappa B (NFkB) transcription and extracellular signal-regulated kinase (ERK) signaling. External validation was performed in an independent population of 28 curative and 38 recurrent patients. Three genes (CYP4B1, CEPT1, CHMP4A) in common between our original data sets remained differentially expressed in the external validation data.

CONCLUSIONS

There are distinct transcriptional elements in HGSOC from patients likely to be cured by standard primary therapy. Three genes have withstood rigorous validation and are plausible targets for further study, which may provide insight into molecular features associated with long-term survival and chemotherapy resistance mechanisms.

Sin3B expression is required for cellular senescence and is up-regulated upon oncogenic stress

Serial passage of primary mammalian cells or strong mitogenic signals induce a permanent exit from the cell cycle called senescence. A characteristic of senescent cells is the heterochromatinization of loci encoding pro-proliferative genes, leading to their transcriptional silencing. Senescence is thought to represent a defense mechanism against uncontrolled proliferation and cancer. Consequently, genetic alterations that allow senescence bypass are associated with susceptibility to oncogenic transformation. We show that fibroblasts genetically inactivated for the chromatin-associated Sin3B protein are refractory to replicative and oncogene-induced senescence. Conversely, overexpression of Sin3B triggers senescence and the formation of senescence-associated heterochromatic foci. Although Sin3B is strongly up-regulated upon oncogenic stress, decrease in expression of Sin3B is associated with tumor progression in vivo, suggesting that expression of Sin3B may represent a barrier against transformation. Together, these results underscore the contribution of senescence in tumor suppression and suggest that expression of chromatin modifiers is modulated at specific stages of cellular transformation. Consequently, these findings suggest that modulation of Sin3B-associated activities may represent new therapeutic opportunities for treatment of cancers.

Loss of imprinting and cancer

Imprinting is defined as the parental allele-specific expression of a very limited set of genes (about 50-80). This regulation depends upon an epigenetic marking of parental alleles during gametogenesis. Monoallelic expression ensures that the levels of the proteins encoded by imprinted genes, important factors of embryonic growth, placental growth or adult metabolism, are assured. Without precise control of their expression, developmental abnormalities result, as is shown by a number of hereditary over-growth syndromes, including Beckwith-Wiedemann syndrome. The regulation of imprinted genes is largely dependent on methylation marks, which are laid down during embryological development of germ cells. Once in place, the methylation status of precise chromosomal regions, Imprinting Control Regions (ICRs), is read by either of two mechanisms, chromatin barrier formation or untranslated RNAs, thereby ensuring that only the maternal or paternal allele is expressed. Each imprinted gene is classified as maternal or paternal according to the expressed allele. The stability of the marked regions in somatic cells is maintained through each cellular replication by a methylation enzyme complex containing Dnmt1. Although the major reading mechanisms of imprinted status are known, chromatin boundary formation by CTCF and untranslated RNAs, the molecules elaborating the initial ICR methylation, are just being uncovered. Mis-regulation of imprinted gene expression (loss of imprinting [LOI]) is seen frequently and precociously in a large variety of human tumours, making LOI a potentially valuable tool for both diagnosis and treatment. In fact, LOI is presently considered the most abundant and most precocious alteration in cancer. The present review proposes a mechanism responsible for LOI, as well as its eventual value in tumour diagnosis and prognosis.

The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation

Expression of imprinted genes is restricted to a single parental allele as a result of epigenetic regulation—DNA methylation and histone modifications. Igf2/H19 is a reciprocally imprinted locus exhibiting paternal Igf2 and maternal H19 expression. Their expression is regulated by a paternally methylated imprinting control region (ICR) located between the two genes. Although the de novo DNA methyltransferases have been shown to be necessary for the establishment of ICR methylation, the mechanism by which they are targeted to the region remains unknown. We demonstrate that CTCFL/BORIS, a paralog of CTCF, is an ICR-binding protein expressed during embryonic male germ cell development, coinciding with the timing of ICR methylation. PRMT7, a protein arginine methyltransferase with which CTCFL interacts, is also expressed during embryonic testis development. Symmetrical dimethyl arginine 3 of histone H4, a modification catalyzed by PRMT7, accumulates in germ cells during this developmental period. This modified histone is also found enriched in both H19 ICR and Gtl2 differentially methylated region (DMR) chromatin of testis by chromatin immunoprecipitation (ChIP) analysis. In vitro studies demonstrate that CTCFL stimulates the histone-methyltransferase activity of PRMT7 via interactions with both histones and PRMT7. Finally, H19 ICR methylation is demonstrated by nuclear co-injection of expression vectors encoding CTCFL, PRMT7, and the de novo DNA methyltransferases, Dnmt3a, -b and -L, in Xenopus oocytes. These results suggest that CTCFL and PRMT7 may play a role in male germline imprinted gene methylation.

The testes-specific factor CTCFL (also called BORIS) can cooperate with the arginine histone methyltransferase (PRMT7) to induce de novo DNA methylation at an imprinting control region.