An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer

Treatment with the anti-angiogenic drug bevacizumab in addition to chemotherapy has shown efficacy for breast cancer in some clinical trials, but better biomarkers are needed to optimally select patients for treatment. Here, we present an omics approach where DNA methylation profiles are integrated with gene expression and results from proteomic data in breast cancer patients to predict response to therapy and pinpoint response-related epigenetic events. Fresh-frozen tumor biopsies taken before, during, and after treatment from human epidermal growth factor receptor 2 negative non-metastatic patients receiving neoadjuvant chemotherapy with or without bevacizumab were subjected to molecular profiling. Here, we report that DNA methylation at enhancer CpGs related to cell cycle regulation can predict response to chemotherapy and bevacizumab for the estrogen receptor positive subset of patients (AUC = 0.874), and we validated this observation in an independent patient cohort with a similar treatment regimen (AUC = 0.762). Combining the DNA methylation scores with the scores from a previously published protein signature resulted in a slight increase in the prediction performance (AUC = 0.784). We also show that tumors receiving the combination treatment underwent more extensive epigenetic alterations. Finally, we performed an integrative expression-methylation quantitative trait loci analysis on alterations in DNA methylation and gene expression levels, showing that the epigenetic alterations that occur during treatment are different between responders and non-responders and that these differences may be explained by the proliferation-epithelial-to-mesenchymal transition axis through the activity of grainyhead like transcription factor 2. Using tumor purity computed from copy number data, we developed a method for estimating cancer cell-specific methylation to confirm that the association to response reflects DNA methylation in cancer cells. Taken together, these results support the potential for clinical benefit of the addition of bevacizumab to chemotherapy when administered to the correct patients.

Liver X receptors induce antiproliferative effects in basal-like breast cancer

Liver X receptors (LXRs) are nuclear transcription factors important in the regulation of cholesterol transport, and glucose and fatty acid metabolism. The antiproliferative role of LXRs has been studied in a variety of malignancies and may represent a therapeutic opportunity in cancers lacking targeted therapies, such as triple-negative breast cancer. In this study, we investigated the impact of LXR agonists alone and in combination with carboplatin in preclinical models of breast cancer. In vitro experiments revealed a dose-dependent decrease in tumor cell proliferation in estrogen receptor-positive breast cancer cells, whereas LXR activation in vivo resulted in an increased growth inhibitory effect in a basal-like breast cancer model (in combination with carboplatin). Functional proteomic analysis identified differences in protein expression between responding and nonresponding models related to Akt activity, cell-cycle progression, and DNA repair. Furthermore, pathway analysis suggested that the LXR agonist in combination with carboplatin inhibits the activity of targets of E2F transcription factors and affects cholesterol homeostasis in basal-like breast cancer.

Abstract 5627: Spatial protein profiling by cyclic immunofluorescence to interpret and improve bulk tumor-based predictor of response to chemotherapy with bevacizumab in neoadjuvant breast cancer treatment

Introduction: A limited number of drugs are available for use in breast cancer patients, and several are not in practical use due to the lack of adequate biomarkers. We have recently demonstrated the feasibility of using machine learning on molecular data from bulk tumor analysis to create a nine-protein signature named VEGF-inhibition Response Predictor (ViRP) for selecting BC patients for treatment with chemotherapy and bevacizumab. The ViRP score is currently being validated in the NAPEER+ clinical trial (EudraCT 2021-005850-27). Increasing evidence suggests that spatial organization of cells within the tumor microenvironment influences survival and response to therapy in numerous cancer types. In methods based on bulk tumor analysis all tumor cells are profiled simultaneously with both colocalized and distant stroma and immune cells. We are thus pursuing information on spatial organization of cellular phenotypes expressing selected cancer related proteins including our nine ViRP proteins.

Methods: From the NeoAva (NCT00773695) clinical trial evaluating the effect of bevacizumab in combination with neoadjuvant chemotherapy (n=132 pts), FFPE tissue sections from patients before, during, and after treatment were made. Cyclic immunofluorescence (cyCIF) was used to profile the spatial expression of 32 cancer-signaling and 32 immune-related proteins, comprising our nine ViRP proteins, on FFPE tissue sections from selected patients (n = 20). The Galaxy-ME platform was used for image processing and downstream analysis of spatial protein profiling.

Results: Use of cyCIF for spatial analysis enabled for evaluation of malignant cells in the context of surrounding microenvironmental cells, including immune cells. We found that cell type-specific protein abundance and subcellular localization formed a highly heterogenous pattern in the tissue. This was particularly evident for the nine ViRP proteins, and differences in expression between tumor cell populations will be further elucidated. Among the patients selected for cyCIF analysis, 4 were chosen based on misclassification by the ViRP signature. Ongoing studies focus on revealing spatial expression patterns to optimize the ViRP biomarker and explore why misclassification occurs. Furthermore, the observed molecular biology of the evolving tissues under treatment in responding and non-responding patients may reveal new biomarkers indicative of treatment response or resistance.

Conclusion: We observe that the expression of proteins in tumor tissues is highly heterogeneous, and thus include numerous features not captured by bulk tumor analysis. Future development of new predictive tools and biomarkers that integrate molecular data which is multiparametric and spatial will set the stage for a new class of biomarkers in cancer diagnostics.

Citation Format: Mads Haugland Haugen, David Kilburn, Hongli Ma, Cameron Watson, Allison Creason, Dong Zhang, Maria Aa Dahle, Ole Christian Lingjaerde, Marianne L. Smebye, Oeystein Garred, Mette S. Foersund, Mai T. Nguyen, Gunhild M. Maelandsmo, Gordon Mills, Olav Engebraaten. Spatial protein profiling by cyclic immunofluorescence to interpret and improve bulk tumor-based predictor of response to chemotherapy with bevacizumab in neoadjuvant breast cancer treatment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5627.

Abstract P5-02-21: RAB5 is a generic biomarker for ADC efficacy

Antibody-drug conjugates (ADCs) have demonstrated impressive activity in recent clinical trials in breast cancer. Such targeted therapeutics strongly depends on the presence of target molecules on the tumor cells, and the presence of such target molecules may determine the response of ADCs. However, ADCs are also dependent on cellular uptake, and factors regulating endocytosis as well as intracellular trafficking may strongly influence ADC activity. We have recently demonstrated that the activity of the HER2 targeted ADC trastuzumab emtansine (T-DM1) is dependent on the expression of RAB5A, a protein regulating endocytosis (1). A significant correlation between Rab5A expression and T-DM1 efficacy was found in a panel of HER2 expressing breast- and ovarian cancer cell lines. This result was verified in the I-SPY2 clinical trial where patients with high RAB5A expression were more likely to achieve a pathological complete response following T-DM1 as a neoadjuvant. The result was further validated in patients treated with T-DM1 in the Kamilla study where patients with a high RAB5A had a longer progression free survival. All ADCs should in principle be dependent on endocytosis to exert their activity. This triggered the investigation of proteins regulating endocytosis as predictive biomarkers for ADCs in general. METHODS: HER2-positive breast and ovarian cancer cell lines were evaluated with respect to the sensitivity and efficacy of treatment with T-DM1, trastuzumab deruxtecan, sacituzumab govitecan and the targeted toxin MH3B1/rGel.. The expression levels of proteins involved in endocytosis and endocytic trafficking including RAB4A, RAB5A and RAB11A were investigated in addition to the molecular drug targets (HER2 and TROP2). Cellular drug sensitivity was correlated to the expression levels of the investigated proteins using both RNA and protein as readout. RESULTS: The early endosome marker RAB5A, was found to correlate positively to the activity of trastuzumab deruxtecan, sacituzumab govitecan and MH3B1/rGel in the HER2 positive cell line panel, confirming the importance of RAB5A expression for the activity of these drugs. A significant correlation was found between RAB5A and drug efficacy using both protein and RNA as a readout. CONCLUSION: The present results indicate RAB5A as a generic predictive biomarker for both ADCs and targeted toxins which both depend on cellular uptake for cytotoxic efficacy. The results supports using both protein and RNA as a readout for RAB5A expression and point towards the development of a RAB5A stratification procedure for ADC and targeted toxin treatment. 1. Engebraaten O, Yau C, Berg K, Borgen E, Garred O, Berstad MEB, Fremstedal ASV, DeMichele A, Veer LV, Esserman L, Weyergang A. RAB5A expression is a predictive biomarker for trastuzumab emtansine in breast cancer. Nature communications 2021;12(1):6427 doi 10.1038/s41467-021-26018-z.

Citation Format: Olav Engebraaten, Astrid Medhus, Ane Longva, Anette Weyergang, Kristian Berg. RAB5 is a generic biomarker for ADC efficacy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-21.

High-throughput screen in vitro identifies dasatinib as a candidate for combinatorial treatment with HER2-targeting drugs in breast cancer

Human epidermal growth factor receptor 2-positive (HER2+) breast cancer is an aggressive subtype of this disease. Targeted treatment has improved outcome, but there is still a need for new therapeutic strategies as some patients respond poorly to treatment. Our aim was to identify compounds that substantially affect viability in HER2+ breast cancer cells in response to combinatorial treatment. We performed a high-throughput drug screen of 278 compounds in combination with trastuzumab and lapatinib using two HER2+ breast cancer cell lines (KPL4 and SUM190PT). The most promising drugs were validated in vitro and in vivo, and downstream molecular changes of the treatments were analyzed. The screen revealed multiple drugs that could be used in combination with lapatinib and/or trastuzumab. The Src-inhibitor dasatinib showed the largest combinatorial effect together with lapatinib in the KPL4 cell line compared to treatment with dasatinib alone (p < 0.01). In vivo, only lapatinib significantly reduced tumor growth (p < 0.05), whereas dasatinib alone, or in combination with lapatinib, did not show significant effects. Protein analyses of the treated xenografts showed significant alterations in protein levels compared to untreated controls, suggesting that all drugs reached the tumor and exerted a measurable effect. In silico analyses suggested activation of apoptosis and reduced activity of survival pathways by all treatments, but the opposite pattern was observed for the combinatorial treatment compared to lapatinib alone.

Abstract P1-08-09: High mid-treatment RNA disruption in patients with HER2-negative breast cancer predicts survival benefit after neoadjuvant chemotherapy

BACKGROUND: Ribosomal RNA fragmentation (RNA disruption) measured mid-therapy in breast cancer tumors has been shown to correlate with pCR and improved disease-free survival. Data from the NeoAva clinical trial was used to evaluate RNA disruption index values (RDI) for measurement of therapy efficacy. METHODS: The randomized phase II clinical trial NeoAva investigated the effects of neoadjuvant chemotherapy (FEC) in HER2-negative breast cancer patients with or without bevacizumab. Serial biopsies were taken prior to treatment and after 12 and 25 weeks of treatment. The majority of patients in this study were diagnosed with ER positive tumors (88% of the total 12-week samples). RNA isolation from frozen tumor tissue was carried out using the AllPrep DNA/RNA Mini kit with QIACube (Qiagen), and the quality of the RNA assessed (Agilent 2100 Bioanalyzer). Treatment response was measured using both pathological complete response (pCR) and residual cancer burden (RCB) at the time of surgery, and median follow-up time was 6.8 years. Using the RNA electropherogram data (Agilent Bioanalyzer) generated in this study, RDI values were assessed in pre-therapy samples (n=109), 12-week samples (n=98) and 25-week samples (n=106). RESULTS: RDI values were measured at three timepoints, however only the RDI values assessed from 12 week samples correlated with clinical outcomes. RDI values were higher in patients that achieved a RCB class of either 0 or 1 (n=28) (median RDI=2.6) compared with those patients that had an RCB class of 3 (n=17) (median RDI=1.3) (Mann-Whitney p=0.006). Out of the samples that were analyzed by the RNA disruption assay (RDA), 18 patients achieved a pCR and had a median RDI value of 2.6 compared with a median RDI of 1.8 for those who did not achieve a pCR (n=80); this finding did not reach statistical significance. RDI values measured in samples taken prior to therapy or at 25-weeks did not correlate with either RCB class or subsequent pCR. With 93% and 94% of patients having mid-therapy RDI values greater than 1.1 for RCB class of 0/1 or pCR, respectively, this was chosen as a cut point to generate Kaplan-Meier curves of recurrence free survival. These curves illustrated statistically significant improved survival (HR =2.6; 95% CI 0.8-8.1) for patients with a RDI &gt; 1.1 (p=0.05). Similarly, Kaplan-Meier curves of breast cancer specific survival also demonstrated improved survival (HR = 3.1; 95% CI 0.8-11.7) for patients with a RDI &gt; 1.1 (p=0.03). Kaplan-Meier curves based on pCR/no pCR were generated from the set of patients that had 12-week RDI values assessed and did not demonstrate improved survival in this small, predominantly ER+ group. No survival benefit was found based on RDI values measured prior to therapy or at 25 weeks. Patients that received bevacizumab (n=45) had significantly higher RDI values at 12 weeks (median RDI = 2.5) than patients that did not receive the drug (median RDI = 1.4) (n=53) (Mann-Whitney test p=0.0005). This overall increase in RDI values with bevacizumab resulted in improved survival for patients at a higher RDI cutoff values of 1.6 (p=0.03)(HR = 4.4; 95% CI 0.8-25.1). CONCLUSION: Taken together, our findings suggest that increased RNA disruption measured in tumor biopsies during neoadjuvant chemotherapy correlates with a survival benefit for patients and may be a more useful indicator of therapy efficacy than pCR, particularly for patients with ER positive tumors.

Citation Format: Laura B Pritzker, Mads Haugland Haugen, Hedda von der Lippe Gythfeldt, Twinkle Masilamani, Gabriel Theriault, Renee St-Onge, Lavina D'costa, Ole Christian Lingjaerde, Amadeo Parissenti, Olav Engebraaten. High mid-treatment RNA disruption in patients with HER2-negative breast cancer predicts survival benefit after neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-09.

Detection of phenotype-specific therapeutic vulnerabilities in breast cells using a CRISPR loss-of-function screen

Cellular phenotype plasticity between the epithelial and mesenchymal states has been linked to metastasis and heterogeneous responses to cancer therapy, and remains a challenge for the treatment of triple-negative breast cancer (TNBC). Here, we used isogenic human breast epithelial cell lines, D492 and D492M, representing the epithelial and mesenchymal phenotypes, respectively. We employed a CRISPR-Cas9 loss-of-function screen targeting a 2240-gene 'druggable genome' to identify phenotype-specific vulnerabilities. Cells with the epithelial phenotype were more vulnerable to the loss of genes related to EGFR-RAS-MAPK signaling, while the mesenchymal-like cells had increased sensitivity to knockout of G₂ -M cell cycle regulators. Furthermore, we discovered knockouts that sensitize to the mTOR inhibitor everolimus and the chemotherapeutic drug fluorouracil in a phenotype-specific manner. Specifically, loss of EGFR and fatty acid synthase (FASN) increased the effectiveness of the drugs in the epithelial and mesenchymal phenotypes, respectively. These phenotype-associated genetic vulnerabilities were confirmed using targeted inhibitors of EGFR (gefitinib), G₂ -M transition (STLC), and FASN (Fasnall). In conclusion, a CRISPR-Cas9 loss-of-function screen enables the identification of phenotype-specific genetic vulnerabilities that can pinpoint actionable targets and promising therapeutic combinations.

Baseline microvessel density predicts response to neoadjuvant bevacizumab treatment of locally advanced breast cancer

A subset of breast cancer patients benefits from preoperative bevacizumab and chemotherapy, but validated predictive biomarkers are lacking. Here, we aimed to evaluate tissue-based angiogenesis markers for potential predictive value regarding response to neoadjuvant bevacizumab treatment in breast cancer. In this randomized 1:1 phase II clinical trial, 132 patients with large or locally advanced HER2-negative tumors received chemotherapy ± bevacizumab. Dual Factor VIII/Ki-67 immunohistochemical staining was performed on core needle biopsies at baseline and week 12. Microvessel density (MVD), proliferative microvessel density (pMVD; Factor VIII/Ki-67 co-expression), glomeruloid microvascular proliferation (GMP), and a gene expression angiogenesis signature score, were studied in relation to pathologic complete response (pCR), clinico-pathologic features and intrinsic molecular subtype. We found that high baseline MVD (by median) significantly predicted pCR in the bevacizumab-arm (odds ratio 4.9, P = 0.012). High pMVD, presence of GMP, and the angiogenesis signature score did not predict pCR, but were associated with basal-like (P ≤ 0.009) and triple negative phenotypes (P ≤ 0.041). pMVD and GMP did also associate with high-grade tumors (P ≤ 0.048). To conclude, high baseline MVD significantly predicted response to bevacizumab treatment. In contrast, pMVD, GMP, and the angiogenesis signature score, did not predict response, but associated with aggressive tumor features, including basal-like and triple-negative phenotypes.

Protein Signature Predicts Response to Neoadjuvant Treatment With Chemotherapy and Bevacizumab in HER2-Negative Breast Cancers

PURPOSE

Antiangiogenic therapy using bevacizumab has proven effective for a number of cancers; however, in breast cancer (BC), there is an unmet need to identify patients who benefit from such treatment.

PATIENTS AND METHODS

In the NeoAva phase II clinical trial, patients (N = 132) with large (≥ 25 mm) human epidermal growth factor receptor 2 (HER2)-negative primary tumors were randomly assigned 1:1 to treatment with neoadjuvant chemotherapy (CTx) alone or in combination with bevacizumab (Bev plus CTx). The ratio of the tumor size after relative to before treatment was calculated into a continuous response scale. Tumor biopsies taken prior to neoadjuvant treatment were analyzed by reverse-phase protein arrays (RPPA) for expression levels of 210 BC-relevant (phospho-) proteins. Lasso regression was used to derive a predictor of tumor shrinkage from the expression of selected proteins prior to treatment.

RESULTS

We identified a nine-protein signature score named vascular endothelial growth factor inhibition response predictor (ViRP) for use in the Bev plus CTx treatment arm able to predict with accuracy pathologic complete response (pCR) (area under the curve [AUC] = 0.85; 95% CI, 0.74 to 0.97) and low residual cancer burden (RCB 0/I) (AUC = 0.80; 95% CI, 0.68 to 0.93). The ViRP score was significantly lower in patients with pCR (P < .001) and in patients with low RCB (P < .001). The ViRP score was internally validated on mRNA data and the resultant surrogate mRNA ViRP score significantly separated the pCR patients (P = .016). Similarly, the mRNA ViRP score was validated (P < .001) in an independent phase II clinical trial (PROMIX).

CONCLUSION

Our ViRP score, integrating the expression of nine proteins and validated on mRNA data both internally and in an independent clinical trial, may be used to increase the likelihood of benefit from treatment with bevacizumab combined with chemotherapy in patients with HER2-negative BC.

Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment of ER-positive breast cancer

Antiangiogenic drugs are potentially a useful supplement to neoadjuvant chemotherapy for a subgroup of patients with human epidermal growth factor receptor 2 (HER2) negative breast cancer, but reliable biomarkers for improved response are lacking. Here, we report on a randomized phase II clinical trial to study the added effect of bevacizumab in neoadjuvant chemotherapy with FEC100 (5-fluorouracil, epirubicin and cyclophosphamide) and taxanes (n = 132 patients). Gene expression from the tumors was obtained before neoadjuvant treatment, and treatment response was evaluated by residual cancer burden (RCB) at time of surgery. Bevacizumab increased the proportion of complete responders (RCB class 0) from 5% to 20% among patients with estrogen receptor (ER) positive tumors (P = .02). Treatment with bevacizumab was associated with improved 8-year disease-free survival (P = .03) among the good responders (RCB class 0 or I). Patients treated with paclitaxel (n = 45) responded better than those treated with docetaxel (n = 21; P = .03). Improved treatment response was associated with higher proliferation rate and an immune phenotype characterized by high presence of classically activated M1 macrophages, activated NK cells and memory activated CD4 T cells. Treatment with bevacizumab increased the number of adverse events, including hemorrhage, hypertension, infection and febrile neutropenia, but despite this, the ECOG status was not affected.

Immune stimulatory effect of anti-EpCAM immunotoxin - improved overall survival of metastatic colorectal cancer patients

Introduction: In a recent phase I trial in a heterogeneous group of carcinoma patients with advanced disease, we did not observe objective responses by CT at 8 weeks in patients treated with either the anti-EpCAM immunotoxin MOC31PE alone or administered in combination with the immunosuppressor cyclosporin (CsA). We have now assessed overall survival (OS) data for the two groups to reveal potential differences, and to elucidate putative underlying mechanisms.Material and methods: The OS time of MOC31PE monotherapy (34 patients) and MOC31PE in combination with CsA (23 patients), was assessed. Pre- and post-treatment patient sera were analyzed in a multiplex immunoassay, and the immunogenic effects of MOC31PE were studied in vitro and in a dendritic cell maturation assay.Results: When the data were analyzed for all treated patients regardless of cancer type, the MOC31PE alone group had a median OS of 12.7 months (95% CI = 5.6-19.8 months) compared to 6.2 months (95% CI = 5.6-6.8 months) (p=.066) for the patients treated with MOC31PE + CsA group. For the subgroup of patients with colorectal cancer, the median OS survival was 16.3 months (95% CI = 5.6-27.0) for the MOC31PE only cohort (n = 15), compared to 6.0 months (CI = 5.8-6.2) (p < .001) for the combination group. The cytokine profile in patient sera and the in vitro immunological studies indicate that MOC31PE induced an immunogenic response leading to T-cell activation; a response that was suppressed in patients treated with MOC31PE + CsA.Conclusions: The results reveal a promising clinical benefit of anti-EpCAM immunotoxin treatment in patients with advanced disease, an effect apparently explained by a previously unknown immunogenic effect of MOC31PE.

Serum levels of inflammation-related markers and metabolites predict response to neoadjuvant chemotherapy with and without bevacizumab in breast cancers

Angiogenesis is necessary for tumor growth and has been targeted in breast cancer; however, it is unclear which patients will respond and benefit from antiangiogenic therapy. We report noninvasive monitoring of patient response to neoadjuvant chemotherapy given alone or in combination with anti-vascular endothelial growth factor (bevacizumab) in a randomized clinical trial. At four time points during neoadjuvant chemotherapy ± bevacizumab of receptor tyrosine-protein kinase erbB-2-negative breast cancers, we measured metabolites and inflammation-related markers in patient's serum. We report significant changes in the levels of several molecules induced by bevacizumab, the most prominent being an increase in pentraxin 3 (PTX3) and von Willebrand factor (VWF). Serum levels of AXL, VWF and pulmonary and activation-regulated cytokine (PARC/CCL18) reflected response to chemotherapy alone or in combination with bevacizumab. We further analyzed serum cytokines in relation to tumor characteristics such as gene expression, tumor metabolites and tumor infiltrating leukocytes. We found that VWF and growth-differentiation factor 15 tumor mRNA levels correlated with their respective serum protein levels suggesting that these cytokines may be produced by tumors and outflow to the bloodstream while influencing the tumor microenvironment locally. Finally, we used binomial logistic regression which allowed to predict patient's response using only 10 noninvasive biomarkers. Our study highlights the potential of monitoring circulating levels of cytokines and metabolites during breast cancer therapy.

miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer

One of the hallmarks of cancer is sustained angiogenesis. Favorable results have been reported in some breast cancer (BC) patients receiving antiangiogenic therapy with bevacizumab (Bev) in combination with chemotherapy, and further knowledge on how Bev can be optimally combined with conventional treatment to increase efficacy is strongly needed. In this randomized, neoadjuvant phase II clinical trial, 132 patients with HER2-negative, nonmetastatic BC were treated with Bev in combination with sequential chemotherapy. Biopsies were sampled before treatment, after 12 weeks with anthracycline and after taxane therapy at week 25. MicroRNA (miRNA) expression profiling was performed on biopsies from each time point. Altogether, 241 biopsies were analyzed with the aim of identifying miRNA-based biomarkers of response to therapy. Results from the miRNA analyses were reported for the ER-positive cohort, which were previously demonstrated to benefit from antiangiogenic therapy in this study. For both treatment arms of this cohort, significantly different expression was observed for 217 miRNAs between objective responding and nonresponding patients before treatment initiation. These miRNAs have been linked to regulation of epithelial-mesenchymal transition, metastasis, and tumor growth, among other processes. Bev in combination with chemotherapy resulted in similar miRNA changes to chemotherapy alone. However, the deregulation of miRNA expression occurred earlier in the Bev arm. In both arms, tumor suppressor miRNAs were found upregulated after treatment, while oncogenic miRNAs were downregulated in the Bev arm. Patients responding to Bev showed a strong correlation between deregulated miRNAs and decreased proliferation score during the course of treatment, with downregulation of miR-4465 as the strongest indicator of reduced proliferation. Integrative analyses at miRNA-, gene-, and protein expression further indicated a longitudinal decrease in proliferation. Altogether, the results indicate that proliferation might represent a predictive factor for increased Bev sensitivity, which may aid in the identification of patients who could potentially benefit from Bev.

Circulating Tumor Cells in Breast Cancer Patients Treated by Neoadjuvant Chemotherapy: A Meta-analysis

Background

We conducted a meta-analysis in nonmetastatic breast cancer patients treated by neoadjuvant chemotherapy (NCT) to assess the clinical validity of circulating tumor cell (CTC) detection as a prognostic marker.

Methods

We collected individual patient data from 21 studies in which CTC detection by CellSearch was performed in early breast cancer patients treated with NCT. The primary end point was overall survival, analyzed according to CTC detection, using Cox regression models stratified by study. Secondary end points included distant disease-free survival, locoregional relapse-free interval, and pathological complete response. All statistical tests were two-sided.

Results

Data from patients were collected before NCT (n = 1574) and before surgery (n = 1200). CTC detection revealed one or more CTCs in 25.2% of patients before NCT; this was associated with tumor size (P < .001). The number of CTCs detected had a detrimental and decremental impact on overall survival (P < .001), distant disease-free survival (P < .001), and locoregional relapse-free interval (P < .001), but not on pathological complete response. Patients with one, two, three to four, and five or more CTCs before NCT displayed hazard ratios of death of 1.09 (95% confidence interval [CI] = 0.65 to 1.69), 2.63 (95% CI = 1.42 to 4.54), 3.83 (95% CI = 2.08 to 6.66), and 6.25 (95% CI = 4.34 to 9.09), respectively. In 861 patients with full data available, adding CTC detection before NCT increased the prognostic ability of multivariable prognostic models for overall survival (P < .001), distant disease-free survival (P < .001), and locoregional relapse-free interval (P = .008).

Conclusions

CTC count is an independent and quantitative prognostic factor in early breast cancer patients treated by NCT. It complements current prognostic models based on tumor characteristics and response to therapy.

Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data

The usefulness of mechanistic models to disentangle complex multiscale cancer processes, such as treatment response, has been widely acknowledged. However, a major barrier for multiscale models to predict treatment outcomes in individual patients lies in their initialization and parametrization, which needs to reflect individual cancer characteristics accurately. In this study, we use multitype measurements acquired routinely on a single breast tumor, including histopathology, MRI, and molecular profiling, to personalize parts of a complex multiscale model of breast cancer treated with chemotherapeutic and antiangiogenic agents. The model accounts for drug pharmacokinetics and pharmacodynamics. We developed an open-source computer program that simulates cross-sections of tumors under 12-week therapy regimens and used it to individually reproduce and elucidate treatment outcomes of 4 patients. Two of the tumors did not respond to therapy, and model simulations were used to suggest alternative regimens with improved outcomes dependent on the tumor's individual characteristics. It was determined that more frequent and lower doses of chemotherapy reduce tumor burden in a low proliferative tumor while lower doses of antiangiogenic agents improve drug penetration in a poorly perfused tumor. Furthermore, using this model, we were able to correctly predict the outcome in another patient after 12 weeks of treatment. In summary, our model bridges multitype clinical data to shed light on individual treatment outcomes. SIGNIFICANCE: Mathematical modeling is used to validate possible mechanisms of tumor growth, resistance, and treatment outcome.

Cabazitaxel-loaded Poly(2-ethylbutyl cyanoacrylate) nanoparticles improve treatment efficacy in a patient derived breast cancer xenograft

The effect of poly(2-ethyl-butyl cyanoacrylate) nanoparticles containing the cytotoxic drug cabazitaxel was studied in three breast cancer cell lines and one basal-like patient-derived xenograft model grown in the mammary fat pad of immunodeficient mice. Nanoparticle-encapsulated cabazitaxel had a much better efficacy than similar concentrations of free drug in the basal-like patient-derived xenograft and resulted in complete remission of 6 out of 8 tumors, whereas free drug gave complete remission only with 2 out of 9 tumors. To investigate the different efficacies obtained with nanoparticle-encapsulated versus free cabazitaxel, mass spectrometry quantification of cabazitaxel was performed in mice plasma and selected tissue samples. Nanoparticle-encapsulated drug had a longer circulation time in blood. There was approximately a three times higher drug concentration in tumor tissue 24 h after injection, and two times higher 96 h after injection of nanoparticles with drug compared to the free drug. The tissue biodistribution obtained after 24 h using mass spectrometry analyses correlates well with biodistribution data obtained using IVIS® Spectrum in vivo imaging of nanoparticles labeled with the fluorescent substance NR668, indicating that these data also are representative for the nanoparticle distribution. Furthermore, immunohistochemistry was used to estimate infiltration of macrophages into the tumor tissue following injection of nanoparticle-encapsulated and free cabazitaxel. The higher infiltration of anti-tumorigenic versus pro-tumorigenic macrophages in tumors treated with the nanoparticles might also contribute to the improved effect obtained with the nanoparticle-encapsulated drug. Tumor infiltration of pro-tumorigenic macrophages was four times lower when using nanoparticles containing cabazitaxel than when using particles without drug, and we speculate that the very good therapeutic efficacy obtained with our cabazitaxel-containing particles may be due to their ability to reduce the level of pro-tumorigenic macrophages in the tumor. In summary, encapsulation of cabazitaxel in poly(2-ethyl-butyl cyanoacrylate) nanoparticles seems promising for treatment of breast cancer.

Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

Background

Chemotherapeutic agents such as anthracyclines and taxanes are commonly used in the neoadjuvant setting. Bevacizumab is an antibody which binds to vascular endothelial growth factor A (VEGFA) and inhibits its receptor interaction, thus obstructing the formation of new blood vessels.

Methods

A phase II randomized clinical trial of 123 patients with Her2-negative breast cancer was conducted, with patients treated with neoadjuvant chemotherapy (fluorouracil (5FU)/epirubicin/cyclophosphamide (FEC) and taxane), with or without bevacizumab. Serial biopsies were obtained at time of diagnosis, after 12 weeks of treatment with FEC ± bevacizumab, and after 25 weeks of treatment with taxane ± bevacizumab. A time course study was designed to investigate the genomic landscape at the three time points when tumor DNA alterations, tumor percentage, genomic instability, and tumor clonality were assessed. Substantial differences were observed with some tumors changing mainly between diagnosis and at 12 weeks, others between 12 and 25 weeks, and still others changing in both time periods.

Results

In both treatment arms, good responders (GR) and non-responders (NR) displayed significant difference in genomic instability index (GII) at time of diagnosis. In the combination arm, copy number alterations at 25 loci at the time of diagnosis were significantly different between the GR and NR. An inverse aberration pattern was also observed between the two extreme response groups at 6p22-p12 for patients in the combination arm. Signs of subclonal reduction were observed, with some aberrations disappearing and others being retained during treatment. Increase in subclonal amplification was observed at 6p21.1, a locus which contains the VEGFA gene for the protein which are targeted by the study drug bevacizumab. Of the 13 pre-treatment samples that had a gain at VEGFA, 12 were responders. Significant decrease of frequency of subclones carrying gains at 17q21.32-q22 was observed at 12 weeks, with the peak occurring at TMEM100, an ALK1 receptor signaling-dependent gene essential for vasculogenesis. This implies that cells bearing amplifications of VEGFA and TMEM100 are particularly sensitive to this treatment regime.

Conclusions

Taken together, these results suggest that heterogeneity and subclonal architecture influence the response to targeted treatment in combination with chemotherapy, with possible implications for clinical decision-making and monitoring of treatment efficacy.

Trial registration

NCT00773695. Registered 15 October 2008

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0601-y) contains supplementary material, which is available to authorized users.

Noninvasive profiling of serum cytokines in breast cancer patients and clinicopathological characteristics

Cancers elicit an immune response by modifying the microenvironment. The immune system plays a pivotal role in cancer recognition and eradication. While the potential clinical value of infiltrating lymphocytes at the tumor site has been assessed in breast cancer, circulating cytokines – the molecules coordinating and fine-tuning immune response – are still poorly characterized.

Using two breast cancer cohorts (MicMa, n = 131, DCTB, n = 28) and the multiplex Luminex platform, we measured the levels of 27 cytokines in the serum of breast cancer patients prior to treatment. We investigated the cytokine levels in relation to clinicopathological characteristics and in perspective of the tumor infiltrating immune cells predicted from the bulk mRNA expression data.

Unsupervised clustering analysis of the serum cytokine levels in the MicMa cohort identified a cluster of pro-inflammatory, pro-angiogenic, and Th2-related cytokines which was associated with poor prognosis. Notably high levels of platelet derived growth factor BB (PDGF) reflected a more aggressive tumor phenotype and larger tumor size. A significant positive correlation between serum levels of interferon gamma-induced protein 10 (IP10) and its mRNA expression at the tumor site suggested that tumor-IP10-production may outflow to the bloodstream. High IP10 serum levels were associated with a worse prognosis. Finally, we found serum levels of both PDGF and IP10 associated with enrichment scores of specific tumor infiltrating immune cells.

Our study suggests that monitoring cytokine circulating levels in breast cancer could be used to characterize breast cancers and the immune composition of their microenvironment through readily available biological material.

Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab

A high concentration of circulating vascular endothelial growth factor (VEGF) in cancer patients is associated with an aggressive tumor phenotype. Here, serum levels of 27 cytokines and blood cell counts were assessed in breast cancer patients receiving neoadjuvant chemotherapy with or without bevacizumab (Bev) in a randomized cohort of 132 patients with non-metastatic HER2-negative tumors. Cytokine levels were determined prior to treatment and at various time-points. The cytotoxic chemotherapy regimen of fluorouracil, epirubicin, and cyclophosphamide (FEC) had a profound impact on both circulating white blood cells and circulating cytokine levels. At the end of FEC treatment, the global decrease in cytokine levels correlated with the drop in white blood cell counts and was significantly greater in the patients of the Bev arm for cytokines, such as VEGF-A, IL-12, IP-10 and IL-10. Among patients who received Bev, those with pathological complete response (pCR) exhibited significantly lower levels of VEGF-A, IFN-γ, TNF-α and IL-4 than patients without pCR. This effect was not observed in the chemotherapy-only arm. Certain circulating cytokine profiles were found to correlate with different immune cell types at the tumor site. For the Bev arm patients, the serum cytokine levels correlated with higher levels of cytotoxic T cells at the end of the therapy regimen, which was indicative of treatment response. The higher response rate for Bev-treated patients and stronger correlations between serum cytokine levels and infiltrating CD8T cells merits further investigation.

Ceramide-containing liposomes with doxorubicin: time and cell-dependent effect of C6 and C12 ceramide

Doxorubicin, a widely used chemotherapeutic drug, has several potential high-risk side effects including cardiomyopathy. Furthermore, cellular resistance to this drug develops with time. By using liposomes as carrier vesicles both the side effects and drug resistance might be avoided. In this study we have investigated the cytotoxic effect of doxorubicin encapsulated in liposomes with and without ceramides containing 6 or 12 carbon atoms in the N-amidated fatty acyl chains. The short-chain ceramide species were included in the liposomal compositions due to their pro-apoptotic properties, which might cause a synergistic anticancer effect. We demonstrate that the ceramide species enhance the liposomal doxorubicin toxicity in a cell-specific manner. The C6-ceramide effect is most pronounced in cervical cancer cells (HeLa) and colon cancer cells (HCT116), whereas the C12-ceramide effect is strongest in breast cancer cells (MDA-MB-231). Moreover, the study reveals the importance of investigating cell toxicity at several time points and in different cell-lines, to assess drug-and formulation-induced cytotoxic effects in vitro. Furthermore, our data show that the cytotoxicity obtained with the nanocarriers in vitro, does not necessarily reflect their ability to inhibit tumor growth in vivo. We speculate that the larger effect of Caelyx® than our liposomes in vivo is due to a greater in vivo stability of Caelyx®.

Serum N-glycome alterations in breast cancer during multimodal treatment and follow-up

Using our recently developed high-throughput automated platform, N-glycans from all serum glycoproteins from patients with breast cancer were analysed at diagnosis, after neoadjuvant chemotherapy, surgery, radiotherapy and up to 3 years after surgery. Surprisingly, alterations in the serum N-glycome after chemotherapy were pro-inflammatory with an increase in glycan structures associated with cancer. Surgery, on the other hand, induced anti-inflammatory changes in the serum N-glycome, towards a noncancerous phenotype. At the time of first follow-up, glycosylation in patients with affected lymph nodes changed towards a malignant phenotype. C-reactive protein showed a different pattern, increasing after first line of neoadjuvant chemotherapy, then decreasing throughout treatment until 1 year after surgery. This may reflect a switch from acute to chronic inflammation, where chronic inflammation is reflected in the serum after the acute phase response subsides. In conclusion, we here present the first time-course serum N-glycome profiling of patients with breast cancer during and after treatment. We identify significant glycosylation changes with chemotherapy, surgery and follow-up, reflecting the host response to therapy and tumour removal.

Abstract 4329: Targetable nodes in fibroblast-supported melanoma cells that show resistance to BRAF inhibitors

Metastatic melanoma is notorious for the ability to change its phenotype in response to signals from the microenvironment, which might influence how melanoma responds to therapy. We have disclosed an association between fibroblast-induced phenotypic alterations in melanoma and resistance to the mutated BRAF inhibitor vemurafenib (BRAFi). This signifies the need to find other targets than BRAF to eliminate stroma-influenced melanoma cells. To approach this challenge, we performed proteomic analysis and cancer drug sensitivity screening, comparing fibroblast-supported versus non-supported melanoma cells. We showed that the effect of fibroblasts was critically dependent on cell-cell proximity, where melanoma cells get trapped in a fibronectin network, produced by adjacent fibroblasts. In such environment, melanoma cells down-regulate melanocytic programs (MITF-driven), gain mesenchymal features (AXL, PDGFR, fibronectin) and activate stress/inflammatory-response signaling pathways (JNK and STAT3). Altogether, this indicates fibroblast-induced melanoma transition to a de-differentiated, mesenchymal-like, pro-inflammatory phenotype. Melanoma cells with such phenotype were less responsive to BRAF/MAPK inhibitors and a number of other targeted drugs. However, they showed enhanced sensitivity to PI3K/mTOR inhibitors and, particularly, an inhibitor of GSK3b, stimulating Wnt/b-catenin signaling. Further, we employed flow cytometry to measure the levels of Ki67 and pS6 in single melanoma cells upon different conditions/treatments. Such analysis allowed discrimination of cell subpopulations representing a proliferative and a quiescent cellular state, and nicely reflected the influence of the tested drugs in the presence or absence of fibroblasts. We observed a subpopulation of proliferative pS6high/Ki67high melanoma cells, which remained after treatment with BRAFi if fibroblasts were present. This, fibroblast-protected BRAFi-resistant cell subpopulation, could be reduced/eliminated by PI3K or GSK3b inhibitors, verifying PI3K/GSK3 as potential targets in fibroblast-rich tumors. Currently, we are using mass cytometry (CyTOF) to further characterize cell subpopulations with respect to multiple markers related to cell signaling and immune interactions. Preliminary results indicate that not only signaling protein levels, but also levels of immunoregulatory proteins are altered in melanoma cells that get support from the fibroblasts. In conclusion, we demonstrate fibroblast-induced melanoma switching to a mesenchymal-like pro-inflammatory phenotype, which favors melanoma resistance to BRAF inhibitors, but sensitizes to inhibitors of PI3K/mTOR-associated signaling. CyTOF-analysis of complex tumor-stroma cell systems is used to search for additional strategies to target stroma-supported melanoma cells, either at the level of signaling, or immune interactions.

Citation Format: Kotryna Seip, Marco V. Haselager, Kjetil Jørgensen, Marco Albrecht, Mads H. Haugen, Eivind Valen Egeland, Philippe Lucarelli, Thomas Sauter, Olav Engebraaten, Gunhild M. Mælandsmo, Lina Prasmickaite. Targetable nodes in fibroblast-supported melanoma cells that show resistance to BRAF inhibitors [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 4329. doi:10.1158/1538-7445.AM2017-4329

Abstract 1813: Bevacizumab potentiates the proteomic response to neoadjuvant chemotherapy in breast cancer patients: Rppa exploration of consecutive tumor samples in the NeoAva randomized phase II trial

Antiangiogenic therapy using bevacizumab has proven effective for a number of cancers; however, in breast cancer there is an unmet need to identify patients that benefit from such treatment. Sampling of tumor biopsies before and during treatment, as well as at the time of surgery enables the assessment of response at multiple molecular levels. At the proteomic level reverse phase protein analysis (RPPA) support expression of numerous cancer associated proteins simultaneously, which can further be used to unravel molecular mechanisms associated with clinical response to bevacizumab treatment.

In this phase II clinical trial, patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or not. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment. Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor biopsies were removed before start of treatment, at week 12 at the start of taxane-based tharapy and at the time of surgery. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific.

The addition of bevacizumab to the chemotherapy do not alter proteomic response from week 0 to 25 to such extent that this patient group cluster naturally together. While the proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins, the combination treatment (FEC100 + bevacizumab) induced substantially more effect on the regulation of each protein. This suggests that bevacizumab treatment have the capability to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, possibly due to a de-vascularized and less accessible tumor. An exception to this observation was a few phospho-proteins that do seem to have sustained stronger regulation over the whole treatment period. We are in the process of analyzing in more detail the impact of phosphorylation and thus protein activation states on treatment response.

Deciphering molecular response and activity regulation at the proteomic level is a promising approach and may reveal novel knowledge with potential important clinical relevance.

Citation Format: Mads H. Haugen, Ole Christian Lingjaerde, Marit Krohn, Wei Zhao, Evita M. Lindholm, Laxmi Silwal-Pandit, Elin Borgen, Øystein Garred, Anne Fangberget, Marit M. Holmen, Ellen Schlichting, Helle K. Skjerven, Steinar Lundgren, Erik Wist, Bjørn Naume, Gunhild M. Maelandsmo, Yiling Lu, Anne-Lise Boerresen-Dale, Gordon B. Mills, Olav Engebraaten. Bevacizumab potentiates the proteomic response to neoadjuvant chemotherapy in breast cancer patients: Rppa exploration of consecutive tumor samples in the NeoAva randomized phase II trial [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 1813. doi:10.1158/1538-7445.AM2017-1813

The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer

Purpose: Chemotherapy-induced alterations to gene expression are due to transcriptional reprogramming of tumor cells or subclonal adaptations to treatment. The effect on whole-transcriptome mRNA expression was investigated in a randomized phase II clinical trial to assess the effect of neoadjuvant chemotherapy with the addition of bevacizumab.Experimental Design: Tumor biopsies and whole-transcriptome mRNA profiles were obtained at three fixed time points with 66 patients in each arm. Altogether, 358 specimens from 132 patients were available, representing the transcriptional state before treatment start, at 12 weeks and after treatment (25 weeks). Pathologic complete response (pCR) in breast and axillary nodes was the primary endpoint.Results: pCR was observed in 15 patients (23%) receiving bevacizumab and chemotherapy and 8 patients (12%) receiving only chemotherapy. In the estrogen receptor-positive patients, 11 of 54 (20%) treated with bevacizumab and chemotherapy achieved pCR, while only 3 of 57 (5%) treated with chemotherapy reached pCR. In patients with estrogen receptor-positive tumors treated with combination therapy, an elevated immune activity was associated with good response. Proliferation was reduced after treatment in both treatment arms and most pronounced in the combination therapy arm, where the reduction in proliferation accelerated during treatment. Transcriptional alterations during therapy were subtype specific, and the effect of adding bevacizumab was most evident for luminal-B tumors.Conclusions: Clinical response and gene expression response differed between patients receiving combination therapy and chemotherapy alone. The results may guide identification of patients likely to benefit from antiangiogenic therapy. Clin Cancer Res; 23(16); 4662-70. ©2017 AACR.

Fatigue During and After Breast Cancer Therapy-A Prospective Study

CONTEXT

Chronic fatigue (CF) in breast cancer (BC) survivors is multifactorial and may be caused by immune activation triggered by BC or its treatment. In the Neoadjuvant Avastin in Breast Cancer study, BC patients received neoadjuvant chemotherapy (FEC100→taxane) ± bevacizumab, a monoclonal antibody with fatigue as a potential side effect.

OBJECTIVES

To examine fatigue levels and prevalence of CF before and during chemotherapy and at follow-up, and their associations with C-reactive protein (CRP) and clinical variables.

METHODS

Eighty-four HER2-negative patients with cT2-4N0-3M0 BC responded to questionnaires and had CRP measured before treatment (T0), after FEC100 (T1), after taxanes before surgery (T2), and at two-year follow-up (T3).

RESULTS

The prevalence of CF increased from 8% at T0 to 36% at T3, P < 0.0001. Fatigue levels peaked during chemotherapy from 12.0 at T0 to 20.0 at T2, and declined to 16.7 at T3, P < 0.001. Women with CF at T3 had higher fatigue levels at T0, T2, and T3 than those without CF (P ≤ 0.01). Psychological distress (P = 0.03) and pain (P = 0.04) at T3 were associated with CF at T3. Only psychological distress remained a significant predictor in multivariate analysis. CRP increased from T0 to T1 (P < 0.01) and declined to baseline values at T3, but changes were not associated with bevacizumab treatment. No association was found between bevacizumab or CRP, and fatigue levels or CF.

CONCLUSION

Neither bevacizumab treatment nor low-grade systemic inflammation as measured by CRP was associated with the increased fatigue levels and raised prevalence of CF, observed during and after BC therapy. Increased fatigue levels at baseline and psychological distress at T3 were associated with CF at T3.

Abstract 3268: Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - a randomized phase II study

BACKGROUND: In this phase II clinical trial, patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or no bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

HYPOTHESIS: RPPA proteomic analyses support identification of molecular mechanisms associated with clinical response to bevacizumab treatment.

METHODS: Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific. Data from protein analyses was compared to previously generated mRNA expression data.

RESULTS: Several proteins were found for which expression prior to treatment (week 0) reflected a better response on tumor shrinkage in the combination treatment arm (chemotherapy+bevacizumab): E.g. good responders had lower PDGFR-beta expression, and this was also observed at the mRNA level, while this result was not identified in the mono treatment arm (chemotherapy alone) on either level. The proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins; however, the combination treatment (FEC100 + bevacizumab) induced substantially more effect on regulation of each protein. This might reflect the capability of bevacizumab treatment to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, and reveals a possible need for further studies investigating changes in protein expression and correlation to response of a given treatment. Of particular interest were proteins that switched direction of regulation between the FEC and taxane-based regimes, however, these effects were not confined to the combination treatment and thus probably not due to the added bevacizumab. We are in the process of analyzing the impact of phosphorylation and thus protein activation states on treatment response. The above mentioned results have potentially important clinical relevance and will be further investigated with respect to subtypes and the biological pathways affected by antiangiogenic therapy.

Citation Format: Mads H. Haugen, Ole Christian Lingjaerde, Marit Krohn, Evita M. Lindholm, Laxmi Silwal-Pandit, Elin Borgen, Øystein Garred, Anne Fangberget, Marit M. Holmen, Ellen Schlichting, Helle Skjerven, Steinar Lundgren, Erik Wist, Bjoern Naume, Gunhild M. Maelandsmo, Yiling Lu, Anne-Lise Boerresen-Dale, Gordon B. Mills, Olav Engebraaten. Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - a randomized phase II study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3268.

Abstract A36: Protein expression analysis of intratumor heterogeneity in a luminal-like breast cancer xenograft

Estrogen receptor is a key driver in breast cancer and is expressed in about 75% of breast tumors. ER positive tumors are susceptible to endocrine therapies; however, the major obstacle for curative treatment is recurrence due to resistance to anti-estrogens. Endocrine therapies may induce a selective pressure promoting growth of estrogen independent cell subclones. Our aim was to reveal molecular changes occurring in tumors in response to anti-estrogen treatment, and to identify subpopulations of cells able to withstand anti-estrogen treatment.

A luminal-like estrogen-dependent orthotopically growing xenograft model was treated with fulvestrant, or exposed to estrogen deprivation. The effect of ER-signaling inhibition was analyzed using quantitative mass spectrometry (MS) -based proteomic analysis and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS). Cell surface marker expression (CD24 and SSEA-4) was monitored by flow cytometry, allowing detailed comparison of protein expression between intratumor cell subpopulations.

We found that both modes of anti-estrogen therapy restrained tumor growth and induced expression of enzymes involved in TCA cycle, oxidative phosphorylation and fatty acid beta-oxidation. This was accompanied by changes in levels of specific metabolites indicative of a possible reprogramming of cell metabolism and utilization of oxidative phosphorylation in preference to aerobic glycolysis (decrease in Warburg effect). Furthermore, anti-estrogen treatment seemed to have selective effects on intratumor cell subpopulations, specified by expression of the markers CD24 and SSEA-4. More specifically, highly tumorigenic CD24low/SSEA-4low (dbl. low) cells were eliminated and the seemingly more benign CD24high/SSEA-4high (dbl. high) cells were enriched in the residual tumor. When comparing the proteome in dbl. low verus dbl. high cells sorted from untreated tumors, metabolism was one of the most differentially enriched processes. Enzymes involved in glycolysis, TCA cycle, respiratory electron transport chain and fatty acid were more abundant in the dbl. high subpopulation.

These results suggest that cancer cells may reprogram their metabolism in response to anti-estrogen therapy to support a less estrogen-dependent phenotype. Moreover, subpopulations of cells with different metabolism may exist within the growing tumor, and these may respond differently to anti-estrogen treatment.

Citation Format: Nirma Skrbo, Ufuk Kirik, Alexandr Kristian, Paolo Cifani, Linn Antberg, Siver A. Moestue, Olav Engebraaten, Gunhild M. Mælandsmo, Kristin Andersen, Peter James, Therese Sørlie. Protein expression analysis of intratumor heterogeneity in a luminal-like breast cancer xenograft. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A36.

Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells

In this study, Pfister et al. identified a new mutant p53 target gene, VEGFR2, and demonstrated that mutant p53 stimulates expression of VEGFR2 by cooperating with the SWI/SNF chromatin remodeling complex to superactivate the VEGFR2 gene. They also show that >50% of all mutant p53-regulated gene expression is mediated by SWI/SNF, providing insight into the observation that mutant p53 alters the expression of many genes.

Mutant p53 impacts the expression of numerous genes at the level of transcription to mediate oncogenesis. We identified vascular endothelial growth factor receptor 2 (VEGFR2), the primary functional VEGF receptor that mediates endothelial cell vascularization, as a mutant p53 transcriptional target in multiple breast cancer cell lines. Up-regulation of VEGFR2 mediates the role of mutant p53 in increasing cellular growth in two-dimensional (2D) and three-dimensional (3D) culture conditions. Mutant p53 binds near the VEGFR2 promoter transcriptional start site and plays a role in maintaining an open conformation at that location. Relatedly, mutant p53 interacts with the SWI/SNF complex, which is required for remodeling the VEGFR2 promoter. By both querying individual genes regulated by mutant p53 and performing RNA sequencing, the results indicate that >40% of all mutant p53-regulated gene expression is mediated by SWI/SNF. We surmise that mutant p53 impacts transcription of VEGFR2 as well as myriad other genes by promoter remodeling through interaction with and likely regulation of the SWI/SNF chromatin remodeling complex. Therefore, not only might mutant p53-expressing tumors be susceptible to anti VEGF therapies, impacting SWI/SNF tumor suppressor function in mutant p53 tumors may also have therapeutic potential.

Abstract P4-11-14: Molecular response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study

The NeoAva study is a phase II clinical trial of patients with HER2 negative primary tumors of ≥25 mm treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or no bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

Tumor response were evaluable in 131 patients; of which 66 received bevacizumab in addition to chemotherapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. mRNA expression profiling was performed on Agilent 8x60K platform and the tumors were classified into LuminalA, LuminalB, Her2-enriched, Basal and Normal-like subtypes using the PAM50 classifier. Ratio of the tumor size at final pathology assessment, and at inclusion (by radiology assessment) was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Genomic Grade Index (GGI scores) based on expression profiles of 97 genes (including cell-cycle and proliferation genes) were calculated.

There were no significant differences in the tumor size, lymph node, hormone receptor status or PAM50 subtypes between the treatment arms. pCR in breast and axilla were obtained in 14 (21.1%) patients in the chemo+bev arm, and in 7 (10.6%) patients in the chemo-only arm. Tumors that obtained pCR were in higher number ER negative and TP53 mutated and exhibited Basal-like phenotype. The overall pCR rates were higher in the ER negative tumors compared to ER positive tumors {39.1% (9 of 23) vs 11.1% (12 of 108)}. However, addition of bevacizumab seemed to improve pCR in the ER positive patient group (9 vs 3) and not in ER negative patient group (5 vs 4).

On evaluating the continuous response variable, ER status, TP53 mutation status and PAM50 subtypes were significantly associated to response (p &lt; 0.001). GGI scores were highly correlated to response (p&lt; 0.001), i. e tumors with higher GGI scores showed better response. Importantly, when the chemo+bev and the chemo-only arms were evaluated separately, although similar trend of associations was observed in both arms, the associations were found to be enhanced in the chemo+bev arm.

Next, we evaluated a shift in PAM50 subtypes across the timepoints. A shift towards a better prognosis group, i.e Luminal A or Normal-like profile was observed in response to therapy. Distribution of Luminal A and Normal-like tumors at week 25, (and not at screening or week 12) was significantly different in the chemo+bev vs chemo-only group (p = 0.026, Fisher’s exact test).

GGI scores regressed across timepoints reflecting the loss of aggressive and proliferating component of the tumors in response to therapy. GGI scores in the chemo+bev group became significantly lower (p &lt; 0.01) already at week 12. This suggests that the removal of the proliferating component of the tumors by chemotherapy is accelerated and improved by addition of bevacizumab.

These results, with potentially important clinical relevance will be further investigated with respect to subtypes and the molecular changes induced by antiangiogenic therapy.

Citation Format: Olav Engebraaten, Laxmi Silwal-Pandit, Marit Krohn, Elen K Møller, Silje Nord, Thomas Fleischer, Hedda von der Lippe Gythfelt, Elin Borgen, Øystein Garred, Anne Fangberget, Marit Muri Holmen, Ellen Schlichting, Helle Skjerven, Steinar Lundgren, Vessela N Kristensen, Ole Christian Lingjaerde, Erik Wist, Bjørn Naume, Anne-Lise Børresen-Dale. Molecular response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-11-14.

Photochemically mediated delivery of AdhCMV-TRAIL augments the TRAIL-induced apoptosis in colorectal cancer cell lines

Tumor targeting is an important issue in cancer gene therapy. We have developed a light-specific transduction method, named photochemical internalization (PCI), to enhance gene expression from adenoviral vectors selectively in illuminated areas. Tumor necrosis factor related apoptosis inducing ligand (TRAIL) has been shown to induce apoptosis in cancer cells, and the aim of this study was to investigate the potential of PCI to enhance transgene expression from AdhCMV-TRAIL and evaluate its impact on apoptotic induction in the two human colorectal cancer cell lines HCT116 and WiDr. PCI-mediated delivery of AdhCMV-TRAIL enabled an increased expression of TRAIL, induced a synergistic reduction in cell viability compared to the individual action of AdhCMV-TRAIL and photochemical treatment, and enhanced the induction of apoptosis demonstrated by an increase in cytoplasmic histone-associated DNA fragments, caspase-8 and caspase-3 activation, PARP cleavage and a decrease in the mitochondrial membrane potential. The synergistic effect could be related to the enhanced TRAIL expression in PCI-treated samples and a modest sensitization of the cancer cells to TRAIL induced apoptosis due to the photochemical treatment. Furthermore, an increased cleavage of Bid and a cell line dependent reduction in the expression levels of anti-apoptotic Bcl-2 family members were observed and could possibly contribute to the enhanced apoptotic level in samples exposed to the combined treatment. The presented results indicate that photochemically mediated delivery of AdhCMV-TRAIL allows a selective enhancement in cell killing, and suggest that PCI may be relevant and advantageous for therapeutic gene delivery in vivo.

Abstract 2053: Dynamic 18F-FDG PET parameters variation in patient-derived breast cancer xenograft and correlation with outcome following treatment with cytotoxic agents

Using pharmacokinetic modeling for dynamic 18FDG PET (D-PET) the temporal and spatial uptake pattern of 18FDG may be separated into components reflecting perfusion and metabolism. Patient-derived breast cancer xenografts (bcPDX) reflect morphology, gene and protein expression profiles of those in patients. The outcome for conventional treatment with cytotoxic agents may be dependent on the perfusion and tumor aggressiveness among others. The purpose of this study was to utilize D-PET for assessment of perfusion and glucose metabolism of 6 bcPDX and correlate these parameters with treatment outcome.

Each of the 6 bcPDX, 3 basal-like (HBCx12a, HBCx28, HBCx39) and 3 luminal-like (HBCx3, HBCx34, MAS98.06), were inoculated bilateral in mammary fat pad of 6 athymic nude mice (ANM). D-PET (1hour scan) was performed with injections of 10 MBq 18FDG. A well-established three-compartment FDG distribution model was fitted to the uptake curves voxel-by-voxel. The rate constants k1 and k3, and vascular fraction vp were calculated. Each of 6 bcPDX was inoculated in 20 ANM. When tumors measured 500mm3, mice received either vehicle or paclitaxel 15mg/kg twice a week, doxorubicin 8mg/kg once every three week or carboplatin 10mg/kg once a week for 6 weeks. Tumor double time was calculated and correlated to k1, k3 and vp using a Spearman rank test.

The median k1, k3, vp and tumor double time (TDT) (see table) were significantly different for the majority all bcPDX(p&lt;0.05). TDT was not significantly correlated to k1, k3 and vp except for paclitaxel treatment, where TDT was increased for models with low k1, k3 and vp can be explained by higher treatment resistance of well vascularized and perfused tumor with high glucose metabolism. We showed that different bcPDX have different perfusion and glucose metabolism as measured by D-PET with low intermodal variations except HBCx28. D-PET appeared to be a robust technique and potentially can be used for monitoring of these parameters.

Pharmacokinetic Modeling and treatment results and correlation between it.Median tumor double time (TDT)Median rate constants and vascular fractionsTreatment agentVehiclePaclitaxelDoxorubicinCarboplatinMedian perfusion rate constant, k1 (1/min)Median metabolic rate constant, k3 (1/min)Vascular fraction, Vp (%)Model CodeHBCx3Luminal-like, ER+2047731350.11980.02040.9540HBCx28Basal-like, tripple negative614182750.24840.05882.1815HBCx34Luminal Like, ER+11831536220.05080.00840.5200HBCx39Basal-like, tripple negative840216220.06510.00940.7125HBCx12ABasal-like, tripple negative1451631170.08810.03750.3.3470MAS98.06,Limunal-like, ER+1814931390.07650.10671.3190Spearman correlation coeficientk1 and TDT0.029-0.657-0.086-0.029p-value0.9570.156^0.8720.957k3 and TDT0.143-0.771-0.143-0.029p-value0.7870.072*0.7870.957Vp and TDT0.787-0.8860.2000.086p-value0.9570.019**0.7040.872

Citation Format: Alexandr Kristian, Mona-Elizabeth Revheim, Hong Qu, Gunhild Mælandsmo, Olav Engebraaten, Eirik Malinen. Dynamic 18F-FDG PET parameters variation in patient-derived breast cancer xenograft and correlation with outcome following treatment with cytotoxic agents. [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 2053. doi:10.1158/1538-7445.AM2014-2053

Positron emission tomography and pharmacokinetics of 2-[18F]-fluoroethyl choline for metabolic studies in breast cancer xenografts

BACKGROUND

Breast carcinomas (BC) can have abnormal choline (Cho) metabolism. Earlier studies indicated that Cho uptake can differ between different subtypes of BC. The purpose of this study was to investigate uptake of 2-[(18)F]-fluoroethyl-choline ([(18)F]FECh) in three different patient-derived breast cancer xenografts (BCXs) using dynamic positron emission tomography (dPET).

MATERIAL AND METHODS

Nine athymic nude mice bearing bilateral MAS98.12 (basal-like), HBCx34 or MAS98.06 (both luminal B) BCXs were subjected to a 90-minute dPET scan following a bolus injection of 10 MBq of [(18)F]FECh. A Patlak Plot analysis and a well-established two-tissue compartment model were fitted to the uptake curves of the whole tumors, providing estimates of transfer rates between the vascular, non-metabolized and metabolized compartments. Patlak slope KP and intercept V, the rate constants k₁, k₂, k₃, the intravascular fraction vb and MR[(18)F]FECh were estimated. Additionally, analyses of terminal blood samples and tumor cell suspension incubated with [(18)F]FECh were performed.

RESULTS

[(18)F]FECh uptake in all BCXs was similar to surrounding normal tissue, thus creating no image contrast. The average liver uptake was 10 times higher than the tumor uptake. The uptake in MAS98.12 was higher than in the other two BCXs during the whole course of the acquisition, and was significantly higher than in HBCx34 at 10-30 minutes after injection. No significant differences were found for k1, MR[(18)F]FECh and intravascular fraction vb. Patlak slope KP, k₂ and k₃ were significantly lower for the MAS98.12 xenograft, in line with in vitro results. KP was correlated with both MR[(18)F]FECh and k₃.

CONCLUSIONS

dPET demonstrated that different subtypes of breast cancer have different uptake of [(18)F]FECh. Differences in rate constants and KP were in line with in vitro uptake in cell suspensions and earlier spectroscopy and gene expression analysis.

Associations between tumor vascularization assessed by in vivo DCE-MRI and the presence of disseminated tumor cells in bone marrow in breast cancer patients at the time of diagnosis

PURPOSE

To explore possible associations between in vivo pharmacokinetic dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) parameters and the presence of disseminated tumor cells (DTCs) in bone marrow in breast cancer patients at the time of diagnosis.

MATERIALS AND METHODS

Thirty-seven women with breast cancer (stage T2-4N0-1M0) were included. Patients were classified as DTC+ if one or more DTCs were detected by immunocytochemistry. DCE-MRI was acquired with a radial 3D T1 -weighted spoiled gradient echo sequence with k-space weighted image contrast. K(trans), kep, and ve were calculated using the extended Tofts model and a population-derived arterial input function. The nonparametric Mann-Whitney U-test was used to compare the histogram distributions of the pharmacokinetic parameters for the DTC+ and the DTC- patients.

RESULTS

DTCs were detected in 7 of the 37 patients (19%). In DTC+ patients, the distribution of tumor K(trans) and kep were significantly (P < 0.01) more shifted towards lower values than in DTC- patients.

CONCLUSION

An association between vascular dependent pharmacokinetic DCE-MRI parameters and the presence of DTCs were found. Compared to DTC- patients, DTC+ patients had poorer perfusion and permeability, indicative of hypoxia. Thus, pharmacokinetic parameters might be surrogate biomarkers of metastatic potential and future relapse.

Interplay of choline metabolites and genes in patient-derived breast cancer xenografts

Introduction

Dysregulated choline metabolism is a well-known feature of breast cancer, but the underlying mechanisms are not fully understood. In this study, the metabolomic and transcriptomic characteristics of a large panel of human breast cancer xenograft models were mapped, with focus on choline metabolism.

Methods

Tumor specimens from 34 patient-derived xenograft models were collected and divided in two. One part was examined using high-resolution magic angle spinning (HR-MAS) MR spectroscopy while another part was analyzed using gene expression microarrays. Expression data of genes encoding proteins in the choline metabolism pathway were analyzed and correlated to the levels of choline (Cho), phosphocholine (PCho) and glycerophosphocholine (GPC) using Pearson’s correlation analysis. For comparison purposes, metabolic and gene expression data were collected from human breast tumors belonging to corresponding molecular subgroups.

Results

Most of the xenograft models were classified as basal-like (N = 19) or luminal B (N = 7). These two subgroups showed significantly different choline metabolic and gene expression profiles. The luminal B xenografts were characterized by a high PCho/GPC ratio while the basal-like xenografts were characterized by highly variable PCho/GPC ratio. Also, Cho, PCho and GPC levels were correlated to expression of several genes encoding proteins in the choline metabolism pathway, including choline kinase alpha (CHKA) and glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). These characteristics were similar to those found in human tumor samples.

Conclusion

The higher PCho/GPC ratio found in luminal B compared with most basal-like breast cancer xenograft models and human tissue samples do not correspond to results observed from in vitro studies. It is likely that microenvironmental factors play a role in the in vivo regulation of choline metabolism. Cho, PCho and GPC were correlated to different choline pathway-encoding genes in luminal B compared with basal-like xenografts, suggesting that regulation of choline metabolism may vary between different breast cancer subgroups. The concordance between the metabolic and gene expression profiles from xenograft models with breast cancer tissue samples from patients indicates that these xenografts are representative models of human breast cancer and represent relevant models to study tumor metabolism in vivo.

Abstract P4-14-01: A time course study of genomic instability in breast cancer patients receiving neoadjuvant therapy with or without bevacizumab

Tumor heterogeneity is an area of intense research, revealing tumors with high complexity consisting of different subclones and infiltrating cells. Identification of subclones that are resistant to therapy may be critical to improve treatment outcome.

The NeoAva study is a randomized phase II, clinical trial of Her2 negative breast cancer patients treated in a neoadjuvant setting with chemotherapy (FEC and taxane) +/- bevacizumab. Core needle biopsies were obtained at screening and after 12 weeks, and the tumor was surgically removed after 25 weeks. DNA copy number changes in the tumors were analyzed using Affymetrix SNP Array 6.0. Allele specific copy number changes were assessed using the Allele-Specific Copy number Analysis of Tumors (ASCAT) algorithm (Van Loo, Norgard et al., PNAS 2010) and allele-specific Piecewise Constant Fitting (asPCF) algorithms (Nilsen, Liestol et al., BMC Genomics 2012). Measures of genomic instability were obtained through the complex arm-wise aberration index (CAAI) that captures local rearrangements (‘firestorms’) (Russnes, Vollan et al., Sci Transl Med 2010).

Changes in copy number aberrations between the three different time points were observed in almost all tumors. Some tumors showed a decrease in tumor percentage and aberrations after just 12 weeks of treatment, where others showed loss of aberrations only at the time of surgery (25 weeks). Most of the tumors that did retain aberrations at all time points during treatment, did not demonstrate any decrease in tumor size. Other profiles indicated subclonal reduction, where some aberrations are kept throughout treatment and others disappear. Many of the tumors shrinking in size showed fewer whole arm aberrations than before treatment, but retained their focal amplicons. Some of the tumor aberrations seem to disappear after 12 weeks, but to reappear after 25 weeks, but with the addition of novel aberration.

Complex rearrangements were identified in 67% of tumors before treatment. The most frequent ‘firestorms’ were found on 20p, 11q and 8p. Some events were persistent through therapy, but the majority changed. An association between complex tumor genomes and patients having progressive disease/non-responders were observed.

These results show the complex structure of a tumor and suggest that heterogeneity will influence the response to treatment. The subclonal patterns of tumors may be of great importance for clinical decision-making, as well as for monitoring treatment efficacy.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-14-01.

Abstract P4-14-02: Molecular response in breast cancer tumors treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - A randomized phase II study

Patients treated with bevacizumab in addition to regular neoadjuvant chemotherapy achieve an increased rate of pathological complete response (pCR). The molecular characteristics of responding and non-responding tumors, including how treatment combinations influence the gene expression profiles and the signaling pathways, may be useful predictors of antiangiogenic response.

The NeoAva study included patients with HER2 negative primary tumors of ≥25 mm that were randomized (1:1) to receive neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) with or without bevacizumab. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to final pathology assessment.

In the first part of the study 74 patients were evaluable for tumor response. The tumor size at time of inclusion was T2, T3 and T4 in 24.3%, 67.6% and 8.1% of the patients, respectively. Lymph node metastases were detected in 56.7% of the patients at inclusion and 82.4% were hormone receptor positive. There were no significant differences in the tumor size, lymph node or hormone receptor status between the treatment arms.

The patients were randomized with bevacizumab + chemotherapy (n = 37) and treatment with chemotherapy alone (n = 37). Of the nine patients who achieved pCR in breast and axilla (12.2%), seven patients received bevacizumab (7/37), while two were treated with chemotherapy alone (2/37). Four of the patients with pCR were hormone receptor negative, of which three received bevacizumab. Of the remaining five hormone receptor positive tumors that achieved complete response, four received bevacizumab.

In the second part of the study we evaluated gene expression signatures by RNA microarray and the time-response of pathways to treatment, using pathway analysis that integrates copy number and gene expression (Paradigm). Biopsies for molecular analyses were collected before therapy, after 12 weeks, and at surgery. Treatment associated gene expression changes to chemotherapy were subtracted, and bevacizumab associated differential expression was observed for 1069 genes. Furthermore, molecular profiling of the tumor tissue was performed at DNA level by copy number analysis (Affymetrix, SNP6.0) and mRNA level by gene expression arrays(Agilent 60K). At the screening time point, we found high proliferation through the activity of cyclin E and B and the transcription factors E2F1 and FOXM1. At 12 weeks, there was a strong increase in predicted p53 signaling, due to increased activity of downstream target genes. The 12 week timepoint was also characterized by an increase of Calmodulin 1, MAPK3, as well as Peroxisome proliferator-activated receptor alpha (PPAR-alpha), and both trends continued to the 25 week time point. At 25 weeks, there were broad increases in ERK1/2, JUN, and FOS signaling. The 25 week timepoint also showed a T-cell response signature that from increased activity of GATA3, IL6/IL6R, IL4, and NFATC1 and NFATC2. These results suggest that there are measurable and strongly significant aberrations in molecular activity during treatment, which may be useful to monitor treatment response.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-14-02.

Proteomic characterization of breast cancer xenografts identifies early and late bevacizumab-induced responses and predicts effective drug combinations

PURPOSE

Neoangiogenesis is an important feature in tumor growth and progression, and combining chemotherapy and antiangiogenic drugs have shown clinical efficacy. However, as treatment-induced resistance often develops, our goal was to identify pathways indicating response and/or evolving resistance to treatment and inhibit these pathways to optimize the treatment strategies.

EXPERIMENTAL DESIGN

To identify markers of response and/or resistance, reverse-phase protein array (RPPA) was used to characterize treatment-induced changes in a bevacizumab-responsive and a nonresponsive human breast cancer xenograft. Results were combined with bioinformatic modeling to predict druggable targets for optimization of the treatment.

RESULTS

RPPA analysis showed that both tumor models responded to bevacizumab with an early (day 3) upregulation of growth factor receptors and downstream signaling pathways, with persistent mTOR signaling until the end of the in vivo experiment. Adding doxorubicin to bevacizumab showed significant and superior growth inhibition of basal-like tumors, whereas no additive effect was seen in the luminal-like model. The combination treatment corresponded to a continuous late attenuation of mTOR signaling in the basal-like model, whereas the inhibition was temporary in the luminal-like model. Integrating the bevacizumab-induced dynamic changes in protein levels with bioinformatic modeling predicted inhibition of phosphoinositide 3-kinase (PI3K) pathway to increase the efficacy of bevacizumab monotherapy. In vivo experiments combining bevacizumab and the PI3K/mTOR inhibitor BEZ235 confirmed their significant and additive growth-inhibitory effect in the basal-like model.

CONCLUSIONS

Treatment with bevacizumab caused compensatory upregulation of several signaling pathways. Targeting such pathways increased the efficacy of antiangiogenic therapy.

Triple-negative breast cancer and the need for new therapeutic targets

Triple-negative breast cancers (TNBCs) are a diverse and heterogeneous group of tumors that by definition lack estrogen and progesterone receptors and amplification of the HER2 gene. The majority of the tumors classified as TNBCs are highly malignant, and only a subgroup responds to conventional chemotherapy with a favorable prognosis. Results from decades of research have identified important molecular characteristics that can subdivide this group of breast cancers further. High-throughput molecular analyses including sequencing, pathway analyses, and integrated analyses of alterations at the genomic and transcriptomic levels have improved our understanding of the molecular alterations involved in tumor development and progression. How this knowledge should be used for rational selection of therapy is a challenging task and the subject of numerous ongoing research programs. This review summarizes the current knowledge on the clinical characteristics and molecular alterations of TNBCs. Currently used conventional therapeutic strategies and targeted therapy studies are discussed, with references to recently published results on the molecular characterization of TNBCs.

Low-molecular contrast agent dynamic contrast-enhanced (DCE)-MRI and diffusion-weighted (DW)-MRI in early assessment of bevacizumab treatment in breast cancer xenografts

PURPOSE

To investigate the effect of bevacizumab treatment on vascular architecture and function in two xenograft models with different angiogenic properties using diffusion-weighted magnetic resonance imaging (DW-MRI) and dynamic contrast-enhanced MRI (DCE-MRI).

MATERIALS AND METHODS

Mice carrying basal-like (MAS98.12) or luminal-like (MAS98.06) orthotopic breast cancer xenografts were treated with bevacizumab (5 mg/kg), doxorubicin (8 mg/kg), or both drugs in combination. DW-MRI and DCE-MRI were performed before and 3 days after treatment using a Bruker 7T preclinical scanner. Mean microvessel density (MVD) and proliferating microvessel density (pMVD) in the tumors were determined for evaluation of vascular response to bevacizumab treatment.

RESULTS

No changes in DCE-MRI or DW-MRI parameters were observed in untreated controls during the experiment period. DW-MRI showed increased apparent diffusion coefficient (ADC) values in all treatment groups in both basal-like and luminal-like xenografts. DCE-MRI showed increased contrast agent uptake, particularly in central regions of the tumors, after bevacizumab/combination treatment in both xenograft models. This was accompanied by decreased MVD and pMVD in basal-like xenografts. Doxorubicin treatment had no effect on DCE-MRI parameters in any of the xenograft models.

CONCLUSION

Both DW-MRI and DCE-MRI demonstrated an early response to bevacizumab treatment in the xenograft tumors. Increased contrast agent uptake and reduced MVD/pMVD is consistent with a normalization of vascular function.

Abstract P5-17-02: Molecular response in breast cancer tumors treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - a randomized phase II study

Withdrawn by Author

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-17-02.

Subtype-specific response to bevacizumab is reflected in the metabolome and transcriptome of breast cancer xenografts

Antiangiogenic therapy with bevacizumab has shown varying results in breast cancer clinical trials. Identifying robust biomarkers for selecting patients who may benefit from such treatment and for monitoring response is important for the future use of bevacizumab. Two established xenograft models representing basal-like and luminal-like breast cancer were used to study bevacizumab treatment response on the metabolic and gene expression levels. Tumor samples were obtained from mice treated with bevacizumab, doxorubicin or a combination of the two drugs, and high resolution magic angle spinning magnetic resonance spectroscopy and gene expression microarray analysis was performed. Combination treatment with bevacizumab showed the strongest growth inhibiting effect in basal-like tumors, and this was reflected by a significant change in the metabolomic and transcriptomic profiles. In the luminal-like xenografts, addition of bevacizumab did not improve the effect of doxorubicin. On the global transcriptomic level, the largest gene expression changes were observed for the most efficient treatment in both models. Glycerophosphocholine showed opposite response in the treated xenografts compared with untreated controls; lower in basal-like and higher in luminal-like tumors. Comparing combination therapy with doxorubicin monotherapy in basal-like xenografts, 14 genes showed significant differential expression, including very low density lipoprotein receptor (VLDLR) and hemoglobin, theta 1 (HBQ1). Bevacizumab-treated tumors were associated with a more hypoxic phenotype, while no evidence was found for associations between bevacizumab treatment and vascular invasion or tumor grade. This study underlines the importance of characterizing biological differences between subtypes of breast cancer to identify personalized biomarkers for improved patient stratification and evaluation of response to therapy.

Gefitinib in Combination with Weekly Docetaxel in Patients with Metastatic Breast Cancer Caused Unexpected Toxicity: Results from a Randomized Phase II Clinical Trial

In patients with metastatic breast cancer, taxane treatment demonstrates activity but is not curative. Targeted treatment modalities are therefore necessary in order to improve outcomes in this group. A randomized placebo-controlled phase II trial was initiated to evaluate effect and toxicity of gefitinib (250 mg QD) and docetaxel 35 mg/m² (six of seven weeks) (NCT 00319618). The inclusion of 66 patients was planned. The study was closed due to treatment-related toxicity. Of the 18 included patients, seven (of which three received gefitinib) were withdrawn from the study due to toxicity. Of the nine patients receiving gefitinib and chemotherapy, one achieved a partial response and four stable disease. In the chemotherapy of nine patients, four had a partial response and four stable disease. The breast cancer patients in this study were genotyped using a panel of 14 single-nucleotide polymorphisms (SNPs), previously found associated with docetaxel clearance in a cohort of lung cancer patients. We were unable to identify genes related to toxicity in this study. Nevertheless, toxicity was aggravated by the addition of the tyrosine kinase inhibitor. In conclusion, despite adequately tolerated as monotherapy, combination regimens should be carefully considered for overlapping adverse events in order to avoid increased treatment-related toxicity.

Effect of antiangiogenic therapy on tumor growth, vasculature and kinase activity in basal- and luminal-like breast cancer xenografts

Several clinical trials have investigated the efficacy of bevacizumab in breast cancer, and even if growth inhibiting effects have been registered when antiangiogenic treatment is given in combination with chemotherapy no gain in overall survival has been observed. One reason for the lack of overall survival benefit might be that appropriate criteria for selection of patients likely to respond to antiangiogenic therapy in combination with chemotherapy, are not available. To determine factors of importance for antiangiogenic treatment response and/or resistance, two representative human basal- and luminal-like breast cancer xenografts were treated with bevacizumab and doxorubicin alone or in combination. In vivo growth inhibition, microvessel density (MVD) and proliferating tumor vessels (pMVD = proliferative microvessel density) were analysed, while kinase activity was determined using the PamChip Tyrosine kinase microarray system. Results showed that both doxorubicin and bevacizumab inhibited basal-like tumor growth significantly, but with a superior effect when given in combination. In contrast, doxorubicin inhibited luminal-like tumor growth most effectively, and with no additional benefit of adding antiangiogenic therapy. In agreement with the growth inhibition data, vascular characterization verified a more pronounced effect of the antiangiogenic treatment in the basal-like compared to the luminal-like tumors, demonstrating total inhibition of pMVD and a significant reduction in MVD at early time points (three days after treatment) and sustained inhibitory effects until the end of the experiment (day 18). In contrast, luminal-like tumors only showed significant effect on the vasculature at day 10 in the tumors having received both doxorubicin and bevacizumab. Kinase activity profiling in both tumor models demonstrated that the most effective treatment in vivo was accompanied with increased phosphorylation of kinase substrates of growth control and angiogenesis, like EGFR, VEGFR2 and PLCγ1. This may be a result of regulatory feedback mechanisms contributing to treatment resistance, and may suggest response markers of value for the prediction of antiangiogenic treatment efficacy.

13C high-resolution-magic angle spinning MRS reveals differences in glucose metabolism between two breast cancer xenograft models with different gene expression patterns

Tumor cells have increased glycolytic activity, and glucose is mainly used to form lactate and alanine, even when high concentrations of oxygen are present (Warburg effect). The purpose of the present study was to investigate glucose metabolism in two xenograft models representing basal-like and luminal-like breast cancer using (13) C high-resolution-magic angle spinning (HR-MAS) MRS and gene expression analysis. Tumor tissue was collected from two groups for each model: untreated mice (n=19) and a group of mice (n=16) that received an injection of [1-(13) C]-glucose 10 or 15 min before harvesting the tissue. (13) C HR-MAS MRS was performed on the tumor samples and differences in the glucose/alanine (Glc/Ala), glucose/lactate (Glc/Lac) and alanine/lactate (Ala/Lac) ratios between the models were studied. The expression of glycolytic genes was studied using tumor tissue from the same models. In the natural abundance MR spectra, a significantly lower Glc/Ala and Glc/Lac ratio (p<0.001) was observed in the luminal-like model compared with the basal-like model. In the labeled samples, the predominant glucose metabolites were lactate and alanine. Significantly lower Glc/Ala and Glc/Lac ratios were observed in the luminal-like model (p<0.05). Most genes contributing to glycolysis were expressed at higher levels in the luminal-like model (fdr<0.001). The lower Glc/Ala and Glc/Lac ratios and higher glycolytic gene expression observed in the luminal-like model indicates that the transformation of glucose to lactate and alanine occurred faster in this model than in the basal-like model, which has a growth rate several times faster than that of the luminal-like model. The results from the present study suggest that the tumor growth rate is not necessarily a determinant of glycolytic activity.

Metabolic effects of signal transduction inhibition in cancer assessed by magnetic resonance spectroscopy

Despite huge efforts in development of drugs targeting oncogenic signalling, the number of such drugs entering clinical practice to date remains limited. Rational use of biomarkers for drug candidate selection and early monitoring of response to therapy may accelerate this process. Magnetic resonance spectroscopy (MRS) can be used to assess metabolic effects of drug treatment both in vivo and in vitro, and technological advances are continuously increasing the utility of this non-invasive method. In this review, we summarise the use of MRS for monitoring the effect of targeted anticancer drugs, and discuss the potential role of MRS in the context of personalised cancer treatment.