Outcome-Related Differences in Gene Expression Profiles of High-Grade Serous Ovarian Cancers Following Neoadjuvant Chemotherapy

Large-scale genomic studies have detailed the molecular landscape of tumors from patients with high-grade serous ovarian cancers (HGSC) who underwent primary debulking surgery and correlated the identified subgroups to survival. In recent years, there is increased use of neoadjuvant chemotherapy (NACT) for patients with HGSC and while abundant data exist for patients who underwent primary debulking, little data are available on the cancer cells remaining after NACT that could lead to recurrences. We aimed to analyze gene expression profiles of NACT-treated HGSC tumor samples, and correlate them to treatment response and outcome. Tumor samples were collected from patients with stage III or IV HGSC (NACT cohort, N = 57) at the time of surgery and diagnosis (biopsy samples N = 8). Tumor content was validated by histologic examination and bioinformatics. Gene expression analysis was performed using a tailored NanoString-based assay, while sequencing was performed using MiSeq. A cross-validated survival classifier revealed patient clusters with either a "Better" or "Worse" prognostic outcome. The association with overall survival remained significant after controlling for clinical variables, and differential gene expression, gene set enrichment analyses, and the appropriate survival models were used to assess the associations between alterations in gene expression in cancer cells remaining after NACT and outcome. Pathway-based analysis of the differentially expressed genes revealed comparatively high levels of cell cycle and DNA repair gene expression in the poor outcome group. IMPLICATIONS: Our work suggests mRNA expression patterns in key genes following NACT may reflect response to treatment and outcome in patient with HGSC.

Abstract P2-02-02: Dynamics of ctDNA changes during neoadjuvant chemotherapy in triple-negative breast cancer patients

Background:

Liquid biopsies to monitor response to treatment are a minimally invasive and highly attractive method for clinical application. Detection of ctDNA in plasma is now highly sensitive thanks to the use of novel highly sensitive and specific techniques such as ddPCR. In the present study we set out to analyze the utility of using ctDNA to monitor response to treatment in patients receiving standard neoadjuvant chemotherapy in triple negative breast cancer.

Methods:

Serial blood was collected from triple negative breast cancer patients participating in the Q-CROC-03 clinical trial (NCT01276899). The trial recruited triple negative breast cancer patients undergoing standard neoadjuvant chemotherapy. Paired biopsies were collected prior and at the end of treatment and serial bloods collected throughout the study. Whole exome sequencing was performed on tissues collected and we identified mutated genes of interest. Cell free DNA (cfDNA) was extracted from 3 ml of plasma and 4-10 variants per patient were analyzed by ddPCR in serial plasma samples collected before and during treatment. Response was measured by evaluating residual cancer burden (RCB), and non-responders were RCBII-III, responders RCB0-I.

Results:

For the present analysis, we identified 60 variants in tumors from 12 patients (9 RCBII-III and 3 RCB0-I). Except for TP53, none of the genes were shared among the tumors. 20% of the variants were not detected in ctDNA at any time point and we did not find any correlation between cfDNA levels and tumor size or response to treatment. The average variant allele frequency (VAF) of all detected variants at baseline was higher in RCBII-III patients than in RCB0-I patients (7.0 vs 0.7 respectively). Interestingly, variants that were detected either only in the pre-chemo tumor or in the post-chemo tumor were frequently detected throughout neoadjuvant therapy, highlighting the ability of ctDNA to capture tumor heterogeneity. In almost all cases, we observed a dramatic decrease in ctDNA VAF after one cycle of chemotherapy, including 30% to non-detectable levels. By the 5th cycle of chemotherapy 97% of detected variants had decreased (average 95% decrease). This decrease in ctDNA VAF was independent of RCB score. In some RCBII-III cases, ctDNA VAF increased prior to surgery, reflecting residual tumor presence.

Conclusion:

ctDNA could be detected in plasma of all early TNBC patients undergoing neoadjuvant chemotherapy with the majority of variants detected in plasma collected at baseline prior to chemotherapy. Once treatment started, the abundance of ctDNA markedly decreased in plasma independently of tumor response. The effect of chemotherapy on levels of ctDNA needs further investigation.

Citation Format: Cavallone L, Adriana A-M, Aldamry M, Lafleur J, Cathy L, Alirezaie N, Bareke E, Majewski J, Ferrario C, Mihalciou C, Roy J-A, Markus E, Robidoux A, Pelmus M, Aleynikova O, Discepola F, Basik M. Dynamics of ctDNA changes during neoadjuvant chemotherapy in triple-negative breast cancer patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-02.

Synchronous metastatic skull base chordoma to the breast: case report and literature review

CLINICAL SCENARIO

During routine staging work-up for a left breast mass, a 68-year-old woman complained of dysphagia and dysphonia. During further investigations, a left-sided lesion at the foramen magnum was observed on brain imaging. Both lesions were biopsied and showed a classical chordoma.

MANAGEMENT

The skull-base lesion and the breast lesion were surgically resected, and adjuvant radiotherapy was given.

SUMMARY

Chordoma is a rare primary central nervous system tumour that seldom metastasizes. The lung is the most common site of metastasis. Synchronous breast metastasis from a skull-base chordoma is very rare, and a safe management option includes a maximum resection followed by adjuvant radiotherapy.

Abstract P6-03-03: The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy

The prognosis of triple negative breast cancer that shows resistance and/or incomplete response to cytotoxic chemotherapy is poor. In order to understand the mechanisms of resistance to chemotherapy and the genomic evolution of TNBCs treated with chemotherapy, an international multi-center biopsy-driven clinical trial was created for the collection and study of drug-resistant primary and metastatic freshly frozen tumors (Q-CROC-03: NCT01276899). We consented 60 patients with operable TNBC undergoing neoadjuvant Anthracycline/Taxane-based chemotherapy for pre and post-treatment biopsies as well as collection of residual tumor at the time of surgery and serial blood sampling. In 12-15 patients, adequate residual tumor material was available for genomic studies, which included whole exome sequencing, array CGH, gene expression microarray profiling and RNAseq of paired tumors. Whole exome sequencing revealed clonal shifts as well as the relatively infrequent appearance of novel mutations in individual tumors, without any recurrently detected variants. Array CGH revealed a remarkable stability in the number of DNA copy number alterations with a few functional alterations enriched for in the residual tumor, including an amplicon involving the NFIB gene. Finally, gene expression profiling showed shifts towards the immune-modulatory and basal TNBC subtypes after chemotherapy as well as an increase in the expression of several targetable genes, including DUSP1, a dual specificity phosphatase. In the 4 cases of primary and matching metastatic tumors, the post-NAC residual tumor had acquired changes many of which persisted in the metastatic sites, indicating that the analysis of the residual tumors can provide a partial picture of genomic changes present in metastases but not in the primary tumor. In summary, the genomic characterization of residual post-NAC tumor tissue provides important information for the development of novel therapeutic strategies for drug-resistant TNBCs as well as a portrait of genomic evolution of TNBCs subjected to chemotherapy.

Citation Format: Basik M, Aguilar-Mahecha A, Lafleur J, Bareke E, Przybytkowski E, Alirezaie N, Discepola F, Légaré S, Kovacina B, Lan C, Mihalcioiu CL, Robidoux A, Marcus E, Roy J-A, Pelmus M, Aleynikova O, Nabavi S, Tonellato P, Majewski J. The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-03.

Comparing indocyanine green, technetium, and blue dye for sentinel lymph node mapping in endometrial cancer

BACKGROUND AND AIMS

With the debate over extent of lymphadenectomy in endometrial cancer, sentinel lymph node (SLN) mapping may provide a focused approach to evaluate the most relevant lymph nodes (LN) while minimizing the complications. We evaluated SLN mapping using filtered technetium(99), indocyanine green (ICG), and blue dye.

METHODS

Prospective evaluation of 100 patients who underwent SLN mapping by using submucosal and deep stromal cervical injections of technetium(99), ICG, and blue dye as part of the staging for endometrial cancer.

RESULTS

286 SLNs were mapped (2.9 per patient) in 92% of patients. The bilateral detection rate was 76%. ICG had a significantly higher SLN detection rate than blue dye in both overall (87% vs 71%, respectively; p=0.005) and bilateral (65% vs 43%, respectively; p=0.002) detection, but similar SLN detection rates compared to technetium(99) in both overall (87% vs 88%, respectively; p=0.83) and bilateral (65% vs 71%, respectively; p=0.36) detection. In eight cases, the SLN was in the para-aortic area and in 14 cases in the pre-sacral, hypogastric vein, or parametrial area. In nine cases, the SLN was positive for metastasis, and in seven cases the SLN was the only positive node. One SLN was falsely negative. No complications or anaphylactic reactions occurred.

CONCLUSION

Intra-operative SLN mapping using cervical injection is feasible in patients with endometrial cancer and yields adequate detection rates. It allows mapping of SLNs in areas (pre-sacral, hypogastric vein, parametrial) not routinely sampled. Given the poorer performance of blue dye, surgeons may omit its use if a combination of ICG and technetium(99) is used.

Endometrioid ovarian cancer and endometriotic cells exhibit the same alteration in the expression of interleukin-1 receptor II: to a link between endometriosis and endometrioid ovarian cancer

AIM

Endometrioid carcinoma of the ovary is the third most common type of epithelial ovarian cancer. Endometrioid tumors as well as endometriotic implants are characterized by the presence of epithelial cells, stromal cells, or a combination of booth, that resemble the endometrial cells, suggesting a possible endometrial origin of these tumors. Th1 cytokines including interleukin (IL)-1 have been reported to be involved in both endometriosis and ovarian carcinogenesis. We assessed the expression of receptors of IL-1 (IL-1RI and IL-1RII, the signal transducer and the specific inhibitor of IL-1, respectively) in cells of the most common subtypes of ovarian cancer compared to endometrial cells.

MATERIAL & METHODS

IL1-Rs expression was analyzed at the levels of the protein and mRNA using immunofluorescent and real-time polymerase chain reaction methods, respectively.

RESULTS

We showed that endometrioid cells exhibit a specific decrease of IL-1RII expression, whereas IL-1RI was constantly expressed in all studied cell subtypes.

CONCLUSION

As already reported in endometriotic cells, endometrioid ovarian cancer cells exhibit the same alteration in the expression of IL-1RII, a key protector against tumorigenic effects of IL-1. Our findings highlight a common signature between endometrioid ovarian cancer and implants of endometriosis, which needs to be fully explored.

Expression of interleukin-1 (IL-1) ligands system in the most common endometriosis-associated ovarian cancer subtypes

OBJECTIVES

Endometrioid carcinoma of the ovary is one of the most types of epithelial ovarian cancer associated to endometrioisis. Endometrioid tumors as well as endometriotic implants are characterized by the presence of epithelial cells, stromal cells, or a combination of booth, that resemble the endometrial cells, suggesting a possible endometrial origin of these tumors. Pro-inflammatory cytokines, including interleukin-1 (IL-1) have been reported to be involved in both endometriosis and ovarian carcinogenesis. The major objective of this study was to determine the level expression of IL-1 ligands system (IL-1alpha, IL-1beta and IL-1RA) in the most common subtypes of ovarian cancer cells compared to endometrial cells.

METHODS

We used primary endometrial cells, endometrial cell line RL-952 and different subtypes of epithelial ovarian cancer cell lines including TOV-112D (endometrioid), TOV-21G (clear cell) and OV-90 (serous). Immunofluorescence and real-time PCR analysis were used respectively for detecting IL-1 ligands at the levels of cell-associated protein and mRNA. Soluble IL-1 ligands were analyzed by ELISA.

RESULTS

We demonstrated that IL-1 ligands were expressed by all endometriosis-associated ovarian cancer subtypes and endometrial cells. In contrast to other cancer ovarian cells, endometrioid cells exhibit a specific decrease of cell-associated IL-1RA expression and its soluble secretion.

CONCLUSION

Endometrioid ovarian cancer exhibits an alteration in the expression of IL-1RA, a key protector against tumorogenic effects of IL-1. This alteration evokes the same alteration observed in endometriotic cells in previous studies. This suggests a possible link between the endometrium, the tissue ectopic endometriosis and endometrioid ovarian cancer.

Evaluation ofMDM2 andCDK4 amplification by real-time PCR on paraffin wax-embedded material: a potential tool for the diagnosis of atypical lipomatous tumours/well-differentiated liposarcomas

Atypical lipomatous tumours/well-differentiated liposarcomas and dedifferentiated liposarcomas are characterized by 12q13-15 region amplification. In contrast, this molecular event has not been reported in benign lipomas. Within the 12q13-15 chromosomal region, the MDM2, SAS, HMGA2, and CDK4 genes are the most frequent targets of amplification. A series of lipomas (36 cases) and liposarcomas (48 cases) was analysed for MDM2 and CDK4 gene amplification by real-time PCR. MDM2 and CDK4 gene amplification was detected in 2.8% and 5.6% of lipomas and 98.2% and 82.4% of liposarcomas, respectively. Moreover, co-amplification of the two genes as well as a higher-level amplification was observed more frequently in dedifferentiated liposarcomas than in atypical lipomatous tumours/well-differentiated liposarcomas. Real-time PCR proved to be a fast and reliable method to characterize lipomas and liposarcomas by quantification of MDM2 and CDK4 gene amplification. It is applicable to paraffin wax-embedded tissues and could be useful when histological diagnosis is difficult.