Abstract P5-06-02: Ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer

In the developing area of personalized medicine, targeted therapies are mainly based on genomic characterization of each tumor, and is currently proposed as promising strategies for advanced breast cancer (ABC). Despite the promises of advanced genome sequencing, many patients still fail therapy, resulting in disease progression, recurrence, and metastases. Cancer stem cells (CSCs) concept illustrates the non-genetic intrinsic resistance, recapitulates tumor heterogeneity that creates hierarchically organized tumor tissues where a subpopulation of self-renewing cancer stem cells (CSCs) sustains the long- term clonal maintenance of the neoplasm. Evidences indicate that CSCs survive many commonly employed cancer therapeutics. Patient-derived tumor xenograft (PDXs) models recapitulate tumor complexity and heterogeneity at cellular and molecular level.

We aimed to specifically address the therapeutic sensitivity in ABC, by using an ex vivo assay based on PDX prospective collection, fully characterized for genomic alterations.

In this work, we aim at defining for each tumor the best therapy to target breast cancer intratumor heterogeneity, the CSC component. For that, we defined a panel of 44 FDA-approved compounds used for cancer treatment, including breast and other types of cancer, cancer stem cell drugs, chemo or targeted therapies. For each drug, we screened the differential sensitivity of the bulk tumor cells and the CSC components for 12 PDX models using an ex vivo screening approach on short term culture. To assess intra tumor heterogeneity, we set up an original dual strategy: for the bulk cells, an ex vivo assay based on IC50, and for breast CSC component a miniaturized Aldefluor assay. First, we demonstrate that bulk cells and CSCs sensitivity may be dissociated for the same drug in the same PDX models. Then, we observed that whereas bulk cell sensitivity may be correlated to tumor genomic abnormalities, CSC drug sensitivity seems not to follow the rule.CSC are selectively sensitive to specific compounds. We are exploring the pathways that sustain this selective sensitivity in the CSCs components. We are currently identifying targets using mass spectrometry in CSCs and bulk cells.Then, we validated the hits predicted from ex vivo screening assays by in vivo treatment of using PDX models for the selected drugs, and in a patient with ABC.

In that work, we demonstrated that CSCs display different sensitivity profiles than bulk cells to the same agents, irrespective to their genomic background and are identifying the CSC specific targets. Here, we propose a new model of precision medicine based on ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer.

Citation Format: Charafe-Jauffret E, Wicinski J, Cabaud O, Lopez M, Audebert S, Adelaide J, Chaffanet M, Guille A, Goncalves A, Bertucci F, Birnbaum D, Ginestier C. Ex vivo CSC assays for personalized testing of drug susceptibility in advanced breast cancer [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 P5-06-02.

Nectin-4: a new prognostic biomarker for efficient therapeutic targeting of primary and metastatic triple-negative breast cancer

Background

Triple-negative breast cancers (TNBCs) are associated with a poor prognosis. In contrast to other molecular subtypes, they have no identified specific target and chemotherapy remains the only available systemic treatment. The adhesion molecule nectin-4 represents a new potential therapeutic target in different cancer models. Here, we have tested the prognostic value of nectin-4 expression and assessed the therapeutic efficiency of an anti-nectin 4 antibody drug conjugate (ADC) on localised and metastatic TNBC in vitro and in vivo.

Materials and methods

We analysed nectin-4/PVRL4 mRNA expression in 5673 invasive breast cancers and searched for correlations with clinicopathological features including metastasis-free survival (MFS). Immunohistochemistry was carried out in 61 TNBCs and in samples of primary TNBC Patient-Derived Xenografts (PDXs). An anti-nectin-4 antibody eligible for ADC was produced and tested in vitro and in vivo in localised and metastatic TNBC PDXs.

Results

High nectin-4/PVRL4 mRNA expression was associated with poor-prognosis features including the TN and basal subtypes. High PVRL4 mRNA expression showed independent negative prognostic value for MFS in multivariate analysis in TNBCs. Nectin-4 protein expression was not detected in adult healthy tissues including mammary tissue. Membranous protein expression was found in 62% of TNBCs, with strong correlation with mRNA expression. We developed an ADC (N41mab-vcMMAE) comprising a human anti-nectin-4 monoclonal antibody conjugated to monomethyl auristatin-E (MMAE). In vitro, this ADC bound to nectin-4 with high affinity and specificity and induced its internalisation as well as dose-dependent cytotoxicity on nectin-4-expressing breast cancer cell lines. In vivo, this ADC induced rapid, complete and durable responses on nectin-4-positive xenograft TNBC samples including primary tumours, metastatic lesions, and local relapses; efficiency was dependent on both the dose and the nectin-4 tumour expression level.

Conclusion

Nectin-4 is both a new promising prognostic biomarker and specific therapeutic target for ADC in the very limited armamentarium against TNBC.

Abstract P4-13-23: Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH) and patient-derived tumor xenograft (PDX) for precision medicine in advanced breast cancer: A single-center prospective study

Background

Genomic-based approaches in advanced breast cancer (ABC) were recently demonstrated as feasible in the clinical practice, but only a limited number of patients were actually treated with targeted therapies matching genomic alterations, with low antitumor activity. We conducted a pilot study to evaluate whether precision medicine using NGS and aCGH could be implemented prospectively at a single center in ABC patients. In addition, we examined whether PDX could be derived from ABC and thus could help inform therapeutic decision.

Methods

ABC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials.gov, NCT01521676). Tumor tissue from locally recurrent or metastatic disease was immediately frozen after dedicated biopsy. Genomic profiling included high-resolution 4x180K aCGH (Agilent Technologies, Massy, France) and DNA sequencing, using a library of 365 cancer candidate genes (HaloPlex target enrichment kit, Agilent technologies, Santa Clara, CA, USA) and MiSeq analyzer (Illumina, San Diego, CA, USA) with 2x150-bp, paired-end at about 300x coverage. In a subset of patients, fresh tumor was implanted orthotopically in humanized cleared fat pads of NSG mice for establishing xenotransplants.

Results

A total of 34 ABC patients were included, with the following characteristics: median age 54 years (35-77); molecular subtypes: 11 triple-negative (32%), 12 luminal non-HER2 (35%), 4 luminal HER2 (12%), 3 HER2 non-luminal (9%), and 4 unknown (12%); 33 with previous chemotherapy (97%); 22 with previous endocrine treatment (35%); 7 with previous anti-HER2 (21%). Tumor biopsies were obtained from liver (15), skin (6), peritoneum (4), breast (3), node (3), lung (1), pleura (1), and ascitis (1), with a median tumor cellularity of 70% (range 10-90%). aCGH and NGS were available from 34 and 33 patients, respectively. An actionable target was found in 28 patients (82%), corresponding to 66 targets, including 37 mutations (8 in PIK3CA, 7 TP53, 4 ESR1, 2 AKT1, 2 BRCA2, 2 HER2), 22 amplifications (7 for CCND1, 2 CCNE1, 2 FGFR1, 2 IGF1R) and 7 homozygous deletions (3 for PTEN, 2 CDKN2A/B,1 BRCA2, 1 STK11). A targeted therapeutic proposal was possible, either in a clinical trial (N=18, 52%) or using already registered drugs (N=17, 50%). Ten patients actually received a targeted treatment, 1 of them experienced objective response and 1 showed stable disease for more than 6 months. Of 26 patients subjected to mouse implantation, 10 had successful xenografting (6 triple-negative, 2 HER2, 1 luminal non-HER2, 1 subtype non-attributed), with a median time to reach 10 mm of 148 days. These PDX will be used as models to understand the patient's therapeutic response.

Conclusion

Precision medicine using high-throughput DNA sequencing and aCGH can be implemented at a single center in the context of clinical practice and may allow direct therapeutic proposal in 1/3 of patients, but antitumor activity was minimal. PDX may be obtained in a significant fraction of patients, especially in triple-negative and HER2 subtypes, and could phenotypically complement genomic data.

Citation Format: Gonçalves A, Bertucci F, Chaffanet M, Guille A, Garnier S, Adelaide J, Carbuccia N, Brunelle S, Piana G, Cabaud O, Thomassin-Piana J, Paciencia-Gros M, Chereau-Ewald E, Lambaudie E, Sabatier R, Tarpin C, Provansal M, Jalaguier-Coudray A, Extra J-M, Sarran A, Pakradouni J, Viens P, Lopez M, Ginestier C, Charafe-Jauffret E, Birnbaum D. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH) and patient-derived tumor xenograft (PDX) for precision medicine in advanced breast cancer: A single-center prospective study. [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 P4-13-23.

Abstract P5-03-01: Cancer stem cells predict engraftment and poor prognosis of primary breast tumors

Breast cancer is a major health problem and heterogeneity of the disease has been considered as a strong limitation to find the best therapies to cure cancer, overcome recurrences and metastases. The establishment of models that reflect tumor biology and metastatic progression is critical to develop successful new therapeutic strategies. In the breast, orthotopic xenografts currently appear as the best models to study tumor growth, metastasis and develop tools for prognosis prediction. Furthermore, mouse transplant assays have been used to assess cancer stem cell (CSC) activity and demonstrate that leukemia and many solid tumors are organized along a hierarchical model.

Despite the promise of the CSC model sustained by mouse transplantation assays, the clinical relevance of xenografts studies to identify determinants of stemness able to influence clinical outcome remains challenging. In breast cancer, transcriptional programs from functionally validated CSC populations remain to be deciphered.

Here, we report the establishment of a bank of primary breast tumor-derived xenografts (xenobank). We showed that the xenografts retain the main features of primary tumors, that engraftment is correlated with the presence of CSC in tumors, and that engraftment in the mouse is able to predict prognosis in patients. This suggests that CSCs may govern breast cancer prognosis. We established the gene expression profiles of functionally validated ALDEFLUOR-positive CSC populations (breast CSC-GES) and demonstrated their clinical relevance. Among 2609 patients with breast cancers, we validated that he expression of the breast CSC-GES is correlated with poor outcome and metastasis in uni-and multivariate analysis (5-year MFS was 70% CI95 [67–74] in the breast CSC-positive class and 80% (CI95 [77–83]) in the breast CSC-negative class (p = 5.5E−04 with log-rank test). Furthermore, we identified a core of 19 genes commonly expressed in breast CSC, murine embryonic, neural and hematopoietic stem cells programs and demonstrated for each gene its ability to modulate breast CSC population, being implicated in self-renewing or differentiation programs. We found that the core of genes in common between four stem cell gene expression studies (CE-BCSC-3SC) displayed an adverse prognostic impact for patients with breast cancer. The core contained genes implicated in oxidative phosphorylation, detoxification, lipid metabolism, and genomic stability, and these shared determinants of stemness influenced clinical outcome.

Thus, we show ed that CSCs from orthotopically engrafted primary breast tumors have clinical and biological relevance. This functionally validated CSC population is highly correlated with survival and express genes governing main stem cell functions, substantiating a major prediction of the CSC model and opening further promises for new CSC therapies using valid preclinical models.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-01.