The Mutational Spectrum of Pre- and Post-Neoadjuvant Chemotherapy Triple-Negative Breast Cancers

The response of triple-negative breast cancer (TNBC) patients to pre-operative (neoadjuvant chemotherapy) is a critical factor of their outcome. To determine the effects of chemotherapy on the tumor genome and to identify mutations associated with chemoresistance and sensitivity, we performed whole exome sequencing on pre/post-chemotherapy tumors and matched lymphocytes from 26 patients. We observed great inter-tumoral heterogeneity with no gene mutated recurrently in more than four tumors besides TP53. Although the degree of response to chemotherapy in residual tumors was associated with more subclonal changes during chemotherapy, there was minimal evolution between pre/post-tumors. Indeed, gene sets enriched for mutations in pre- and post-chemotherapy tumors were very similar and reflected genes involved in the biological process of neurogenesis. Somatically mutated genes present in chemosensitive tumors included COL1A2, PRMD15, APOBEC3B, PALB2 and histone protein encoding genes, while BRCA1, ATR, ARID1A, XRCC3 and genes encoding for tubulin-associated proteins were present in the chemoresistant tumors. We also found that the mutational spectrum of post-chemotherapy tumors was more reflective of matching metastatic tumor biopsies than pre-chemotherapy samples. These findings support a portrait of modest ongoing genomic instability with respect to single-nucleotide variants induced by or selected for by chemotherapy in TNBCs.

A micro-flow, high-pH, reversed-phase peptide fractionation and collection system for targeted and in-depth proteomics of low-abundance proteins in limiting samples

We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30-60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and robustness. The method is applicable to targeted mass spectrometry approaches and to in-depth proteomic studies where the amount of sample is limited. Using targeted proteomics with peptide standards, we present the method's analytical parameters, and potential in increasing the detection of low-abundance proteins that are difficult to quantify with direct targeted or global LC-MS analyses. This fractionation system increased peptide signals by up to 18-fold, while maintaining high quantitative precision, with high fractionation reproducibility across varied sample sets. In real applications, it increased the detection of targeted endogenous peptides by two-fold in a 25 cell-cycle-control protein panel, and in-depth MS analyses of nuclear extracts, it allowed the detection of up to 8,896 proteins with 138,417 peptides in 24-concatenated fractions compared to 3,344 proteins with 23,093 peptides without fractionation. In a relevant biological problem of CDK4/6-inhibitors and breast cancer, the method reproduced known information and revealed novel insights, highlighting that it can be successfully applied in studies involving low-abundance proteins and limited samples. •Tested nine high-pH buffer/solvent systems to obtain a robust, effective, and reproducible micro-flow fractionation method which was devoid of commonly encountered LC clogging/pressure issues after months of use.•Peptide enrichment method to improve detection and quantitation of low-abundance proteins in targeted and in-depth proteomic studies.•Can be applied to diverse protein samples where the available amount is limited.

Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens

INTRODUCTION

Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tumor tissue specimens has gained interest in the last 5 years due to technological advances and improved sample collection, as well as biobanking for clinical trials. The real-world implementation of clinical proteomics to these specimens, however, is hampered by tedious sample preparation steps and long instrument acquisition times.

AREAS COVERED

To advance the translation of quantitative proteomics into the clinic, we are comparing the performance of the leading commercial nanoflow liquid chromatography (nLC) system (based on literature reviews), the Easy-nLC 1200 (Thermo Fisher Scientific, Waltham, MA, U.S.A.), to the Evosep One HPLC (Evosep Biosystems, Odense, Denmark). We measured FFPE-tissue digests from 21 biological replicates with a similar gradient on both of the LC systems while keeping the on-column amount (1 µg total protein) and the single-shot data-dependent acquisition-based MS/MS method constant.

EXPERT OPINION

Overall, the Evosep One facilitates robust and sensitive high-throughput sample acquisition, making it suitable for clinical MS. We found the Evosep One to be a useful platform for positioning mass spectrometry-based proteomics in the clinical setting. The clinical application of nLC/MS will inform clinical decision-making in oncology and other diseases.

Abstract P2-11-26: The prognostic role of circulating tumor DNA after neoadjuvant chemotherapy in triple negative breast cancer with residual tumor

Background The presence of residual tumour at surgery (non-pathological complete response or non-pCR) occurs in about half of TNBCs treated with neoadjuvant chemotherapy (NAC) and signals chemoresistance and poor prognosis. Although further adjuvant chemotherapy (Capecitabine/Xeloda) results in improved survival in patients with non-pCR, only about 15% of such patients do benefit. Circulating tumor DNA (ctDNA) is a plasma-based biomarker that can be used to reveal real-time data about the disease and treatment progression. We have previously shown that detection of ctDNA after NAC signals poor prognosis. To validate and extend our previous results using an academic hospital-based tumor bespoke assay, we performed ctDNA measurements in non-pCR TNBC patients at the pre-operative, post-operative, 3 and 6-month time points. Methods Whole exome sequencing (WES) was performed on residual tumors from 34 TNBC patients to identify tumour-specific mutations (5/patient). Digital droplet PCR (ddPCR) assays were developed for these mutations and performed as per our previous work. Patients with at least one detectable mutation were considered ctDNA positive for a given time point. The detection of ctDNA was correlated with relapse-free survival (RFS). Results The overall RFS was 44%, with 56 % of patients received adjuvant Xeloda. Detection of ctDNA at the end of NAC (T1) correlated with poor prognosis of RFS (n = 33, p-value = 0.009, HR = 0.29 (95% CI = 0.12 to 0.74)). Detection of ctDNA after surgery (T2) and while on Xeloda (T3) showed no significant prognostic value for RFS. However, ctDNA detection at the 6-month time point, after Xeloda treatment (T4), showed stronger prognostic value for RFS (n = 17, p-value = 0.004, HR = 0.12 (95% CI = 0.03 to 0.51)). When measuring changes in ctDNA detectability from T1 to T4, 4 patients initially positive became ctDNA negative after the 6-month interval, and only 1 of these 4 had a relapse, compared with 10 of 11 that remained positive at the 6-month time point (p = 0.01, Chi-squared test). 3 of the 4 patients that cleared their ctDNA had received Xeloda. In addition, 2 patients initially negative became ctDNA positive at the 6-month time point (T4) and both relapsed, compared with only 1 of 5 that remained negative at 6 months (p = 0.035, Chi-squared test). For patients who received adjuvant Xeloda ctDNA positivity at T1 was associated with a worse RFS (p-value = 0.028, HR = 3.3884 (95% CI = 1.160 to 13.00)). Conclusion ctDNA testing using ddPCR in an academic hospital-based context at the post-NAC time point as well as at 6 months after surgery identifies an excellent prognostic group in TNBC patients with non-pCR and changes in ctDNA during the adjuvant period have prognostic value. This personalized approach to treatment management is ready for prospective testing in patients who have undergone NAC and require additional chemotherapy.

Citation Format: Talia Roseshter, Anna Klemantovich, Luca Cavallone, Adriana Aguilar-Mahecha, Josiane Lafleur, Oluwadara O. Elebute, Sarah Jenna, Jean-Francois Boileau, Manuela Pelmus, Mark Basik, Cathy Lan. The prognostic role of circulating tumor DNA after neoadjuvant chemotherapy in triple negative breast cancer with residual tumor [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 P2-11-26.

Abstract 4011: Prognostic value of transcriptomic analysis in residual post neo-adjuvant triple negative breast cancer tumors

Background: Triple negative breast cancer is the most aggressive type of breast cancer. Approximately 50% of TNBC patients respond to pre-operative neo-adjuvant chemotherapy (NAC), however those patients with residual disease (non-pathological complete response or non-pCR) have a very poor prognosis. Recently, the use of capecitabine in the adjuvant setting was shown to increase disease-free survival in non-pCR patients. However, there are no biomarkers to identify patients who may benefit from adjuvant capecitabine. Moreover, novel therapeutic targets are needed to treat patients with non-pCR.

Methods: RNA extracted from 32 Formalin Fixed Paraffin Embedded (FFPE) residual post-NAC tumor samples underwent NanoString nCounter gene expression analysis using the BC360 panel as well as RNAseq.

Results: Comparison of tumors from poor (RFS<2 yrs) and good prognosis (RFS>2 yrs) patients showed 65 genes differentially expressed (≥1.5 fold change and p<0.05) by nCounter. 40 of these genes had differential expression also validated by RNAseq (R2= 0.96) and were selected for further pathway analysis. Gene Set Enrichment Analysis (GSEA) showed an enrichment for biological pathways involved in cell cycle, with all genes in this set upregulated in the poor prognosis group. GSEA analysis of 310 upregulated genes identified by RNAseq showed an enrichment for biological pathways associated with cell population proliferation and skin development. Interestingly, one of the upregulated genes identified was TYMS, encoding thymidylate synthase, the target of capecitabine, which showed 2-fold increased expression in the poor prognosis group (p≤0.005).

Conclusion: Our results suggest that residual tumors from TNBC patients who relapse within two years of surgery show transcriptomic evidence of increased proliferation and that expression levels of TYMS may be a potential biomarker to select patients for capecitabine in the adjuvant setting.

Citation Format: Adriana Aguilar-Mahecha, Yasamin Majedi, Oluwadara Elebute, Josiane Lafleur, Andreas Papadakis, Cathy Lan, Manuela Pelmus, Touhidur Rashid, Sarah Jenna, Mark Basik. Prognostic value of transcriptomic analysis in residual post neo-adjuvant triple negative breast cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4011.

Abstract 1794: The combination of Talazoparib with anti-her2 drugs shows efficacy in drug resistant Her2+ and low Her2 PDX models

Background: Her2+ breast cancer accounts for 15% of breast cancer cases and is primarily treated with a combination of Her2-targeted agents and chemotherapy. While use of targeted agents has substantially improved survival of these patients, clinical drug resistance is prevalent. DNA repair defects are a feature of cancer that has been exploited by targeted agents such as inhibitors of poly-ADP ribose polymerase (PARP). PARP inhibitors have been shown to be effective in patients with germline mutations in other DNA repair factors such as BRCA1/2. There is limited data for the use of PARP inhibitors in HER2+ breast cancers, and in tumors without BRCA1/2 mutations. Using a collection of HER2+ and HER2-low expressing breast cancer patient-derived xenografts (PDXs) that have differential responses to the Her2-targeted agents Trastuzumab, Pertuzumab, and T-DM1, we tested the combination of these agents with Talazoparib (Talzenna™), a clinically approved Parp inhibitor.

Methods: Orthotopically engrafted PDX mouse models resistant to either Trastuzumab or T-DM1 were randomized into treatment arms including Trastuzumab or T-DM1 in combination with Talazoparib, and the single agents alone. Mice are monitored for body weight and change in tumour volume every 2-3 days, then sacrificed at endpoint for survival analysis. We have also generated PDX-derived cells (PDCs) from one model with which to validate in vivo results and perform mechanistic studies. All models are being characterized for copy number changes, somatic mutations, and protein expression by immunohistochemistry.

Results: The combination of Talazoparib and either Trastuzumab or T-DM1 was effective in 3 PDX models, including a Trastuzumab-resistant HER2+ PDX, a T-DM1-resistant HER2+ PDX and a T-DM1-resistant HER2-low expressing PDX. The combinations resulted in significant delays in tumour growth (p<0.05), including a transient tumour regression with the combination T-DM1+Talazoparib in 1 PDX. Median overall survival time was improved with the combination of Trastuzumab +Talazoparib (p<0.05), while the combinations of T-DM1+Talazoparib increased survival time although not significantly. Notably all models have maintained Her2 expression through treatment.

Conclusion: Our results suggest that combining HER-targeted agents with Talazoparib may benefit patients with advanced HER2-therapy resistant HER2+ and low HER2+ breast cancers. Exploratory biomarker analysis and mechanistic studies using PDCs are currently underway in our laboratory.

Citation Format: Kathryn Bozek, Marguerite Buchanan, Cathy Lan, Josiane Lafleur, Cedric Darini, Urszula Krzemien, Adriana Aguilar-Mahecha, Mark Basik. The combination of Talazoparib with anti-her2 drugs shows efficacy in drug resistant Her2+ and low Her2 PDX models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1794.

Abstract 538: Cell-free whole genome sequencing for the detection of cancer in patients with germline BRCA1/2 mutations

Background: Hereditary breast and ovarian cancer syndrome (HBOC) is caused by a germline likely/pathogenic variant in BRCA1 or BRCA2, leading to increased risk of developing breast, ovarian, prostate, and pancreatic cancers. While HBOC patients often undergo regular surveillance including breast imaging, other cancers have no effective screening or biomarkers. One emerging technology is the analysis of circulating tumor DNA (ctDNA), fragments of DNA that are shed from the tumor into the bloodstream. In sporadic cancer, several studies have demonstrated the advantages and sensitivity of cell-free whole genome sequencing (cfWGS) compared to targeted panel sequencing. However, the use of cfWGS for cancer detection in HBOC has not been explored.

Methods: Matched tumor, germline, and plasma were collected from 5 HBOC patients (3 breast, 2 ovarian) as part of the Canada-wide CHARM consortium (https://charmconsortium.ca). Tumor (40x), germline (20x), and plasma (20x) underwent whole genome sequencing (WGS) and subsequent variant calling pipeline using an ensemble of 6 variant callers. Insertions, deletions, and structural variants were not included in downstream analyses. Plasma tumor fraction prediction and copy number alterations were performed using ichorCNA. Detection of tumor associated mutations in plasma was compared to MRDetect software.

Results: Variant calling identified an average of 11,170 tumor (7,649-16,706) and 1,215 (544-3,205) plasma SNVs per patient. Somatic BRCA1/2 mutations were detected in 0/5; whereas deletion of the intact BRCA1/2 allele was identified in 5/5 patients. An average of 24.6% (8.3%-75.9%) of plasma mutations where shared with SNVs identified in matched tumor. Targeted panel deep-sequencing (20,000X) was only able to detect mutations in TP53 in 3/5 cases (0.8% - 8.6%). Plasma derived copy number alterations correlated well with tumor derived copy number alterations in 3/5 cases and ichorCNA predicted tumor fractions ranged from 0.038 to 0.196.

Conclusions: Traditionally, targeted panel sequencing has been used to identify tumor associated mutations in plasma. While this technique is sensitive, major disadvantages include the narrow breadth of the captured regions and the inability to detect deletion events such as those that occur in BRCA1/2. Here we show that plasma WGS is effective for detecting tumor associated mutations in HBOC and is more sensitive than targeted panel sequencing. We are currently expanding our cohort to an additional 20 matched tumor pairs, including patients with pre-diagnosis plasma timepoints.

Citation Format: Derek Wong, Adriana Aguilar-Mahecha, Josiane Lafleur, Clarissa Chan, Kirsten Farncombe, Maia Norman, Leslie Oldfield, Prabhjit Basra, Stephanie Pederson, Johanna Wellum, Stephenie Prokopec, Mark Basik, Raymond H. Kim, Trevor Pugh. Cell-free whole genome sequencing for the detection of cancer in patients with germline BRCA1/2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 538.

HSP90 inhibitors induce GPNMB cell-surface expression by modulating lysosomal positioning and sensitize breast cancer cells to glembatumumab vedotin

Transmembrane glycoprotein NMB (GPNMB) is a prognostic marker of poor outcome in patients with triple-negative breast cancer (TNBC). Glembatumumab Vedotin, an antibody drug conjugate targeting GPNMB, exhibits variable efficacy against GPNMB-positive metastatic TNBC as a single agent. We show that GPNMB levels increase in response to standard-of-care and experimental therapies for multiple breast cancer subtypes. While these therapeutic stressors induce GPNMB expression through differential engagement of the MiTF family of transcription factors, not all are capable of increasing GPNMB cell-surface localization required for Glembatumumab Vedotin inhibition. Using a FACS-based genetic screen, we discovered that suppression of heat shock protein 90 (HSP90) concomitantly increases GPNMB expression and cell-surface localization. Mechanistically, HSP90 inhibition resulted in lysosomal dispersion towards the cell periphery and fusion with the plasma membrane, which delivers GPNMB to the cell surface. Finally, treatment with HSP90 inhibitors sensitizes breast cancers to Glembatumumab Vedotin in vivo, suggesting that combination of HSP90 inhibitors and Glembatumumab Vedotin may be a viable treatment strategy for patients with metastatic TNBC.

Healthcare policy by other means: Cancer clinical research as "oncopolicy"

Social studies of biomedicine often focus on how exogenous policies shape the medical domain. While policy agendas no doubt affect complex biomedical projects, in the present paper we analyze a different dynamic, namely how oncologists enact policy as part of several flagship precision oncology endeavors. Empirically, the article focuses on the U.S. TAPUR trial, the Dutch DRUP trial, and the Canadian CAPTUR trial, which have recently been joined by similar Scandinavian studies. Taken together, these trials represent innovative forms of clinical research that, beyond their varying experimental nature, have been designed to transform the evidential processes to provide access to biomarker-driven treatments. Along with gathering evidence on effectiveness of off-label targeted therapies, their explicit goals include the recentering of a major professional organization around research, and the reframing of healthcare as a learning system seamlessly connecting epistemic, organizational, and economic issues. Accordingly, we analyze the design and implementation of these trials as a form of (onco)policy by other means.

A multiplexed, automated immuno-matrix assisted laser desorption/ionization mass spectrometry assay for simultaneous and precise quantitation of PTEN and p110α in cell lines and tumor tissues

The PI3-kinase/AKT/mTOR pathway plays a central role in cancer signaling. While p110α is the catalytic α-subunit of PI3-kinase and a major drug target, PTEN is the main negative regulator of the PI3-kinase/AKT/mTOR pathway. PTEN is often down-regulated in cancer, and there are conflicting data on PTEN's role as breast cancer biomarker. PTEN and p110α protein expression in tumors is commonly analyzed by immunohistochemistry, which suffers from poor multiplexing capacity, poor standardization, and antibody crossreactivity, and which provides only semi-quantitative data. Here, we present an automated, and standardized immuno-matrix-assisted laser desorption/ionization mass spectrometry (iMALDI) assay that allows precise and multiplexed quantitation of PTEN and p110α concentrations, without the limitations of immunohistochemistry. Our iMALDI assay only requires a low-cost benchtop MALDI-TOF mass spectrometer, which simplifies clinical translation. We validated our assay's precision and accuracy, with simultaneous enrichment of both target proteins not significantly affecting the precision and accuracy of the quantitation when compared to the PTEN- and p110α-singleplex iMALDI assays (<15% difference). The multiplexed assay's linear range is from 0.6-20 fmol with accuracies of 90-112% for both target proteins, and the assay is free of matrix-related interferences. The inter-day reproducibility over 5-days was high, with an overall CV of 9%. PTEN and p110α protein concentrations can be quantified down to 1.4 fmol and 0.6 fmol per 10 μg of total tumor protein, respectively, in various tumor tissue samples, including fresh-frozen breast tumors and colorectal cancer liver metastases, and patient-derived xenograft (PDX) tumors.

Precise Quantitation of PTEN by Immuno-MRM: A Tool To Resolve the Breast Cancer Biomarker Controversy

The tumor suppressor PTEN is the main negative regulator of PI3K/AKT/mTOR signaling and is commonly found downregulated in breast cancer (BC). Conflicting data from conventional immunoassays such as immunohistochemistry (IHC) has sparked controversy about PTEN's role as a prognostic and predictive biomarker in BC, which can be largely attributed to the lack of specificity, sensitivity, and interlaboratory standardization. Here, we present a fully standardized, highly sensitive, robust microflow immuno-MRM (iMRM) assay that enables precise quantitation of PTEN concentrations in cells and fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissues, down to 0.1 fmol/10 μg of extracted protein, with high interday and intraday precision (CV 6.3%). PTEN protein levels in BC PDX samples that were determined by iMRM correlate well with semiquantitative IHC and WB data. iMRM, however, allowed the precise quantitation of PTEN-even in samples that were deemed to be PTEN negative by IHC or western blot (WB)-while requiring substantially less tumor tissue than WB. This is particularly relevant because the extent of PTEN downregulation in tumors has been shown to correlate with severity. Our standardized and robust workflow includes an 11 min microflow LC-MRM analysis on a triple-quadrupole MS and thus provides a much needed tool for the study of PTEN as a potential biomarker for BC.

Abstract PS4-48: Development of a multiplexed protein panel using a targeted proteomics approach for the study of CDK4/6 inhibitors resistance in hormone receptor positive breast cancer

Background Breast cancer is the most common malignancy in woman and hormone receptor positive breast cancer represents approximately 70% of all cases. These patients are treated with endocrine therapies aimed at disrupting hormone receptor signaling and estrogen production which improves survival and allows a cure in early stages. However, recurrent disease, metastatic dissemination and drug resistance limit the survival of patients. The limitations regarding endocrine therapy have prompted the search for new therapeutic targets, such as CDK4/6 Inhibitors. Despite the improved disease control that CDK4/6 Inhibitors offer to patients, not all patients respond to these drugs and some patients whose tumors respond to CDK4/6 Inhibitors eventually develop acquired resistance. No proven biomarkers of CDK4/6 Inhibitors efficacy exist to date, and there is a need for diagnostic tools that could stratify patients to save costs and the burden of unnecessary therapy. Our aim is to perform a quantitative evaluation of marker proteins with a developed multiplexed panel using targeted mass spectrometry (MS)-based proteomics for 25 proteins from the CDK/RB/E2F-pathway which have been shown in the literature to be central to CDK4/6I resistance. Material and Methods We developed Multiple Reaction Monitoring (MRM) MS methods for the 25 target proteins from the CDK/RB/E2F-pathway using synthetic heavy-isotope-labeled standards with the aim of creating MRM assays to enable specific, sensitive and precise quantitation of these proteins in small amounts of cell line and tissue samples. Moreover, we developed a high resolution peptide fractionation system using high-pH micro-flow liquid chromatography (LC) which is required to overcome the problem of small samples amounts while improving analytical assay sensitivity in the analysis of complex biological matrices such as breast cancer biopsies. The MCF-7 human breast cancer cell line was used as model during method development. Proteins from cell lysates were isolated, reduced, alkylated and digested with trypsin. The resulting tryptic peptides were micro-flow fractionated into 70 fractions and the developed nano-LC-MS MRM assays were used for peptide detection and quantification. Data were analyzed using Skyline. Results Our developed micro-flow fractionation method allowed us to work on limited amounts of samples (60ug), and increased the possibility to detecting low abundance proteins such as cell cycle components. Using the MCF-7 cell model, we are able to identify and quantify 17 proteins out of the 25 from our panel: CDK1, CDK2, CDK4, Cyclin B1, Cyclin D1, Cyclin D3, Cyclin E1, RB1, E2F-3, E2F-4, E2F-5, ESR1, TOP2A, TYMS, EZH2, MKI67, BIRC5. Conclusion We have developed a highly specific MS-based multiplexed assay with peptide standards targeting 25 proteins relevant to CDK4/6 Inhibitors breast cancer treatment. Our micro-flow fractionation method increased assay sensitivity and allows for the analysis of small sample amounts. In the future we will apply this workflow to samples such as Patient Derived Xenografts models, breast cancer tissues and FFPE samples in order to identify the predictive value of these potential biomarkers for responsiveness to CDK4/6 Inhibitors.

Citation Format: Marta Zurawska, Adriana Aguilar-Mahecha, Mark Basik, Michal Dadlez, Dominik Domanski. Development of a multiplexed protein panel using a targeted proteomics approach for the study of CDK4/6 inhibitors resistance in hormone receptor positive breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-48.

Abstract B21: Protein quantitation assays for Akt, PI3K p110α, and PTEN to assess PI3K pathway activity in tumor tissue

Introduction: Many clinical trials for inhibitors targeting the PI3K pathway now include genetic screening of tumors to try to select probable treatment responders. Genetic testing identifies some relevant mutations, but this approach does not address many mechanisms of PI3K pathway regulation. Epigenetic changes and post-translational modifications may increase pathway activity without any detectable DNA mutation. Where mutations are detected, mutated proteins may not be expressed or may be quickly degraded. Direct measurement of oncogenic proteins may therefore offer more useful molecular profiles for characterizing cancer-driving alterations and matching patients with appropriate treatments.

Purpose: The purpose of this study was to develop and implement protein quantitation assays to accurately assess PI3K pathway activity in tumors, as a means of matching patients with targeted cancer treatments.

Methods: Protein extracted from tumor tissue lysate is subjected to proteolytic digestion to generate proteotypic peptides used for protein quantitation. Synthetic stable isotope-labeled peptides are added to the digest as an internal standard, after which the target peptides are immuno-enriched with antibodies coupled to magnetic beads. MS analysis is then performed by either eluting peptides for measurement with liquid chromatography multiple reaction monitoring tandem MS (LC-MRM-MS/MS) or by spotting beads onto a plate for matrix-assisted laser desorption MS (MALDI-MS). External calibration curves are used for accurate quantitation.

Results: We developed and implemented MS-based methods to determine the concentration of PI3K pathway proteins in tumor samples. The developed methods enable precise and reproducible quantitation of Akt1, Akt2, PI3K P110α, and PTEN. We were able to distinguish and quantify specific isoforms, including phospho-Akt1 (Ser473), phospho-Akt2 (Ser474), and mutant-Akt (E17K). Endogenous protein levels were quantified in cell lines, fresh-frozen tumor samples, and formalin-fixed, paraffin embedded tumor tissue. 10 μg of protein extract per analyte was sufficient for quantitation. Subsets of assays could be multiplexed through simultaneous or sequential enrichment without compromising assay performance.

Novel Aspect: The multiplexing of immuno-MALDI assays through sequential enrichment and the immuno-MRM-MS assays for PTEN and mutant Akt represent new developments. Recent adoption of monoclonal antibodies for Akt1 will facilitate this assay's translation to a clinical setting.

Conclusions: This panel of quantitative proteomics assays enables comprehensive PI3K pathway assessment in tumor tissues. Previously collected genetically screened tumor samples were obtained with patient consent (as approved by the Jewish General Hospital Research Ethics Committee). Samples will be analyzed to assess PI3K pathway activity and determine its correlation to clinical features and response to PI3K-targeted treatments.

Note: This abstract was not presented at the conference.

Citation Format: Constance A. Sobsey, Robert Popp, Sahar Ibrahim, Bjoern C Froehlich, Adriana Aguilar-Mahecha, Mark Basik, Gerald Batist, Christoph Borchers. Protein quantitation assays for Akt, PI3K p110α, and PTEN to assess PI3K pathway activity in tumor tissue [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B21.

Prognostic and predictive value of circulating tumor DNA during neoadjuvant chemotherapy for triple negative breast cancer

Response to neoadjuvant chemotherapy (NAC) in triple negative breast cancer (TNBC) is highly prognostic and determines whether adjuvant chemotherapy is needed if residual tumor is found at surgery. To evaluate the predictive and prognostic values of circulating tumor DNA (ctDNA) in this setting, we analyzed tumor and serial bloods from 26 TNBC patients collected prior, during, and after NAC. Individual digital droplet PCR assays were developed for 121 variants (average 5/patient) identified from tumor sequencing, enabling ctDNA detection in 96% of patients at baseline. Mutant allele frequency at baseline was associated with clinical characteristics. Levels drastically fell after one cycle of NAC, especially in patients whose tumors would go on to have a pathological complete response (pCR), but then rose significantly before surgery in patients with significant residual tumor at surgery (p = 0.0001). The detection of ctDNA early during treatment and also late at the end of NAC before surgery was strongly predictive of residual tumor at surgery, but its absence was less predictive of pCR, especially when only TP53 variants are considered. ctDNA detection at the end of neoadjuvant chemotherapy indicated significantly worse relapse-free survival (HR = 0.29 (95% CI 0.08–0.98), p = 0.046), and overall survival (HR = 0.27 95% CI 0.075–0.96), p = 0.043). Hence, individualized multi-variant ctDNA testing during and after NAC prior to surgery has prognostic and predictive value in early TNBC patients.

Breast cancer mammospheres secrete Adrenomedullin to induce lipolysis and browning of adjacent adipocytes

Background

Cancer cells cooperate with cells that compose their environment to promote tumor growth and invasion. Among them, adipocytes provide lipids used as a source of energy by cancer cells and adipokines that contribute to tumor expansion. Mechanisms supporting the dynamic interactions between cancer cells and stromal adipocytes, however, remain unclear.

Methods

We set-up a co-culture model with breast cancer cells grown in 3D as mammospheres and human adipocytes to accurately recapitulate intrinsic features of tumors, such as hypoxia and cancer cell–adipocytes interactions.

Results

Herein, we observed that the lipid droplets’ size was reduced in adipocytes adjacent to the mammospheres, mimicking adipocyte morphology on histological sections. We showed that the uncoupling protein UCP1 was expressed in adipocytes close to tumor cells on breast cancer histological sections as well as in adipocytes in contact with the mammospheres.

Mammospheres produced adrenomedullin (ADM), a multifactorial hypoxia-inducible peptide while ADM receptors were detected in adipocytes. Stimulation of adipocytes with ADM promoted UCP1 expression and increased HSL phosphorylation, which activated lipolysis. Invalidation of ADM in breast cancer cells dramatically reduced UCP1 expression in adipocytes.

Conclusions

Breast tumor cells secreted ADM that modified cancer–associated adipocytes through paracrine signaling, leading to metabolic changes and delipidation. Hence, ADM appears to be crucial in controlling the interactions between cancer cells and adipocytes and represents an excellent target to hinder them.

Abstract 4108: The use of conditionally reprogrammed cells for high throughput screening for novel drug combinations to treat drug resistant triple negative breast cancers

Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer, with prognosis tightly dependent on its responsiveness to cytotoxic chemotherapy. Indeed, overcoming chemoresistance is a major unmet need in this disease. Patient derived xenografts (PDXs) are now widely used in research since they faithfully represent the patient's tumor. However, testing novel drug combinations is a challenge in these models since it is time consuming and quite expensive to test each novel combination. The development of conditionally reprogrammed cells (CRCs) offers the opportunity to perform high throughput screens on clinically relevant models in a more timely and less expensive manner. To this end, we developed a 7 CRCs from PDXs of drug-resistant TNBC tumors. We characterized these CRCs at the molecular level and validated drug resistance to confirm they matched treatment response in both clinical and PDX tumors from which they were derived. These CRCs underwent high-throughput screens of both compound and shRNA libraries of genes targeted by FDA-approved drugs to identify novel drug combinations as well as genetic vulnerabilities that could re-sensitize these cells to carboplatin or paclitaxel chemotherapy. We found that drugs such as mitomycin C and oxfendazole were putative chemo-sensitizers while genes such as ATR and CDK2 were identified as novel genetic vulnerabilities. Treatment of these drug-resistant cells with combinations of carboplatin with mitomycin C or with an ATR inhibitor resulted in synergistic growth inhibition in proliferation and colony formation assays. We are further validating these combinations in organoid models derived from PDXs. These results have the potential to lead to novel therapeutic strategies against chemoresistant TNBCs.

Citation Format: Adriana Aguilar-Mahecha, Catherine Chabot, Nancy Santos-Martinez, Cedric Darini, Midhet Hajira, Tim Kong, Genevieve Morin, Sidong Huang, Morag Park, Mark Basik. The use of conditionally reprogrammed cells for high throughput screening for novel drug combinations to treat drug resistant triple negative breast cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4108.

Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors

Subsets of breast tumors present major clinical challenges, including triple-negative, metastatic/recurrent disease and rare histologies. Here, we developed 37 patient-derived xenografts (PDX) from these difficult-to-treat cancers to interrogate their molecular composition and functional biology. Whole-genome and transcriptome sequencing and reverse-phase protein arrays revealed that PDXs conserve the molecular landscape of their corresponding patient tumors. Metastatic potential varied between PDXs, where low-penetrance lung micrometastases were most common, though a subset of models displayed high rates of dissemination in organotropic or diffuse patterns consistent with what was observed clinically. Chemosensitivity profiling was performed in vivo with standard-of-care agents, where multi-drug chemoresistance was retained upon xenotransplantation. Consolidating chemogenomic data identified actionable features in the majority of PDXs, and marked regressions were observed in a subset that was evaluated in vivo. Together, this clinically-annotated PDX library with comprehensive molecular and phenotypic profiling serves as a resource for preclinical studies on difficult-to-treat breast tumors.

A Unique Morphological Phenotype in Chemoresistant Triple-Negative Breast Cancer Reveals Metabolic Reprogramming and PLIN4 Expression as a Molecular Vulnerability

The major obstacle in successfully treating triple-negative breast cancer (TNBC) is resistance to cytotoxic chemotherapy, the mainstay of treatment in this disease. Previous preclinical models of chemoresistance in TNBC have suffered from a lack of clinical relevance. Using a single high dose chemotherapy treatment, we developed a novel MDA-MB-436 cell-based model of chemoresistance characterized by a unique and complex morphologic phenotype, which consists of polyploid giant cancer cells giving rise to neuron-like mononuclear daughter cells filled with smaller but functional mitochondria and numerous lipid droplets. This resistant phenotype is associated with metabolic reprogramming with a shift to a greater dependence on fatty acids and oxidative phosphorylation. We validated both the molecular and histologic features of this model in a clinical cohort of primary chemoresistant TNBCs and identified several metabolic vulnerabilities including a dependence on PLIN4, a perilipin coating the observed lipid droplets, expressed both in the TNBC-resistant cells and clinical chemoresistant tumors treated with neoadjuvant doxorubicin-based chemotherapy. These findings thus reveal a novel mechanism of chemotherapy resistance that has therapeutic implications in the treatment of drug-resistant cancer. IMPLICATIONS: These findings underlie the importance of a novel morphologic-metabolic phenotype associated with chemotherapy resistance in TNBC, and bring to light novel therapeutic targets resulting from vulnerabilities in this phenotype, including the expression of PLIN4 essential for stabilizing lipid droplets in resistant cells.

Precision Medicine Tools to Guide Therapy and Monitor Response to Treatment in a HER-2+ Gastric Cancer Patient: Case Report

Trastuzumab, has played a major role in improving treatment outcomes in HER-2 positive gastric cancer. However, once there is disease progression there is a paucity of evidence for second line therapy. Patient-derived xenografts (PDXs) in combination with liquid biopsies can help guide individual therapeutic decisions and have now started to be studied. In the present case we established a PDX model from a metastatic HER-2+ gastric cancer patient and after the first engraftment passage we performed a mouse clinical trial to test T-DM1 as an alternative therapy for the patient. The PDX tumor response served as a guide to administer T-DM1 therapy to the patient who responded to treatment before relapsing 6 months later. Throughout out the clinical follow up of the patient, ctDNA levels of HER-2 copy number and a PIK3CA mutation were monitored and we found their correlation with drug response and disease progression to outperform that of CEA levels. This study highlights the utility of applying precision medicine tools combining PDX models to guide therapy with circulating tumor DNA (ctDNA) to monitor treatment response and disease progression.

Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells

Prostate cancer (PCa) is the most common cancer amongst men. A novel androgen receptor (AR) antagonist, enzalutamide (ENZA) has recently been demonstrated to enhance the effect of radiation (XRT) by impairing the DNA damage repair process. This study aimed to identify a radiosensitive gene signature induced by ENZA in the PCa cells and to elucidate the biological pathways which influence this radiosensitivity. We treated LNCaP (AR-positive, hormone-sensitive PCa cells) and C4-2 (AR-positive, hormone-resistant PCa cells) cells with ENZA alone and in combination with androgen deprivation therapy (ADT) and XRT. Using one-way ANOVA on the gene expression profiling, we observed significantly differentially expressed (DE) genes in inflammation-and metabolism-related genes in hormone-sensitive and hormone-resistant PCa cell lines respectively. Survival analysis in both the TCGA PRAD and GSE25136 datasets suggested an association between the expression of these genes and time to recurrence. These results indicated that ENZA alone or in combination with ADT enhanced the effect of XRT through immune and inflammation-related pathways in LNCaP cells and metabolic-related pathways in C4-2 cells. Kaplan–Meier analysis and Cox proportional hazard models showed that low expression of all the candidate genes except for PTPRN2 were associated with tumor progression and recurrence in a PCa cohort.

An integrated stress response via PKR suppresses HER2+ cancers and improves trastuzumab therapy

Trastuzumab is integral to HER2+ cancer treatment, but its therapeutic index is narrowed by the development of resistance. Phosphorylation of the translation initiation factor eIF2α (eIF2α-P) is the nodal point of the integrated stress response, which promotes survival or death in a context-dependent manner. Here, we show an anti-tumor function of the protein kinase PKR and its substrate eIF2α in a mouse HER2+ breast cancer model. The anti-tumor function depends on the transcription factor ATF4, which upregulates the CDK inhibitor P21^CIP1 and activates JNK1/2. The PKR/eIF2α-P arm is induced by Trastuzumab in sensitive but not resistant HER2+ breast tumors. Also, eIF2α-P stimulation by the phosphatase inhibitor SAL003 substantially increases Trastuzumab potency in resistant HER2+ breast and gastric tumors. Increased eIF2α-P prognosticates a better response of HER2+ metastatic breast cancer patients to Trastuzumab therapy. Hence, the PKR/eIF2α-P arm antagonizes HER2 tumorigenesis whereas its pharmacological stimulation improves the efficacy of Trastuzumab therapy.

The HER2 monoclonal antibody, Trastuzumab, is the current standard treatment for HER2+ cancers but resistance to therapy occurs. Here, the authors show that activation of the PKR/eIF2α-P pathway exhibits anti-tumor effects in HER2+ cancer and is required for the response to Trastuzumab.

Abstract LB-177: Quantification of cell signaling proteins by immuno-MALDI

Introduction. To improve cancer patient stratification and overcome the drawbacks of currently used approaches to assess signaling pathway proteins, we set out to develop immuno-matrix assisted laser ionization/desorption (iMALDI) assays combined with a phosphatase-based phosphopeptide quantitation (PPQ) approach to measure PI3K/AKT/mTOR pathway activity. Specifically, we targeted the C-terminal tryptic peptides of AKT1 and AKT2 due to their involvement in full kinase activation.

Methods. Following trypsin digestion of cell lysate, stable isotope-labeled standard (SIS) peptides are added. After splitting the solution, one aliquot is treated with phosphatase. Bead-coupled antibodies enrich the non-phosphorylated target peptides, which are washed and spotted onto a MALDI plate, and acidic MALDI matrix elutes the peptides. The resulting light/heavy ratios of both aliquots allow the calculation of protein expression levels and peptide phosphorylation stoichiometry.

Results. The iMALDI assays were validated for linear range and accuracy, as well as interference screening, requiring only ~50 µg of total cell or tissue lysate protein to quantify both AKT1 and AKT2 expression levels and phosphorylation stoichiometry. CVs of technical replicates were found to consistently be below 10%. We were able to quantify AKT1 and AKT2 from various cell lines and fresh frozen tumor samples, including SW480 and HCT116 colon cancer cell lines, MDA-MB-231 breast cancer cells, and colon cancer and breast cancer tumor lysates. Further, a direct comparison of matched fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues showed that the expression levels and phosphorylation stoichiometry quantified differ depending on the tissue preservation method, and that phosphorylation stoichiometries above 30% occur in only a small subset of samples. A direct comparison of four pairs of normal and adjacent tumor tissues showed elevated AKT1 phosphorylation stoichiometry of ~40% in a colorectal cancer liver metastasis, and significantly elevated AKT1 (3.6-fold) and AKT2 (2.2-fold) expression levels in a surgical breast tumor sample.

Future directions. In a next step, patient-derived mouse xenograft tissue samples, collected after specific drug treatment, will be analyzed, and the AKT results will be correlated to genomic data to answer the hypothesis whether the AKT expression levels and phosphorylation stoichiometries correlate with response to treatment.

Citation Format: Robert Popp, René P. Zahedi, André LeBlanc, Yassene Mohammed, Adriana Aguilar-Mahecha, Oliver Pötz, Mark Basik, Gerald Batist, Christoph H. Borchers. Quantification of cell signaling proteins by immuno-MALDI [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-177.

Abstract 2149: Use of PDXs and patient-derived cell lines to uncover unconventional drug therapies and combinations for the treatment of drug-resistant cancers

The use of patient derived models for pre-clinical drug testing provides a unique opportunity for testing non-conventional therapies and novel drug combinations to overcome drug resistance in cancer. We have established 22 models from breast cancer, 20 PDXs were engrafted in house and two were generated from live tissue obtained from PDXs established in a partner lab. The overall engraftment rate in house was of 24%. Engraftment varied according to BC subtype: 38% (3/8) for ER-HER2+ and 33% (17/51) for TNBC. No PDXs could be generated from ER+PR+Her2- tumors (0/13) or ER+HER2+ breast cancers (0/11). Post-chemotherapy drug resistant tumors engrafted with better success (18/55) compared to non-treated tumors (2/28). In 3 patients, we established PDX models with tissues collected at different anatomical sites, enabling the study of tumor heterogeneity. For one patient, 2 PDX models were established from serial samples after different lines of chemotherapy. Molecular profiling at the copy number and mutation level has confirmed the molecular stability of our models over engraftment passages. Drug studies were performed to validate clinical drug response and models were also treated with unconventional drugs and drug combinations to overcome drug resistance. Drugs that resulted in significant tumor regression in drug resistant TNBC models included irinotecan as well as olaparib in combination with an angiogenesis inhibitor. We successfully established one PDX model from a recurrent Her2+ gastric tumor resistant to trastuzumab. In this model, treatment with T-DM1 alone as well as with pertuzumab/trastuzumab resulted in complete tumor regression, while everolimus significantly inhibited tumor growth. This PDX study provided an alternative clinical management for the patient who subsequently received T-DM1 and showed clinical response, validating the results obtained in the PDX model. To develop a more agile model, we also established conditionally reprogrammed cell lines directly from patient tumors or from PDX models. Drug resistant conditionally reprogrammed cells from Her2+ breast cancers harboring a FGFR1 amplification were found to be sensitive to FGFR inhibitors, chloroquine, and a CDK4/6 inhibitor. Correlation of drug responses between conditionally reprogrammed cells and matched PDX models will be presented. These live tumor models enable timely and clinically pertinent drug testing, which has the potential to expand the known therapeutic arsenal as well as provide truly personalized therapy to cancer patients.

Citation Format: Marguerite Buchanan, Catherine Chabot, Josiane Lafleur, Urszula Krzemien, Cathy Lan, Olga Savichtcheva, Jean-François Boileau, Cristiano Ferrario, Paul Savage, Morag Park, Gerald Batist, Adriana Aguilar-Mahecha, Mark Basik. Use of PDXs and patient-derived cell lines to uncover unconventional drug therapies and combinations for the treatment of drug-resistant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2149.

Abstract 5894: Stromal fibroblasts from metastatic breast cancer promote proliferation and migration of breast cancer cell and regulate its stemness

Breast cancer is one of the most common causes of cancer-related death in women in the world. Although most research is focused on the tumor cells, it is important to elucidate the molecular nature of the tumor-stromal relationship to truly understand the biology of breast tumor growth. Cancer-associated fibroblasts (CAFs) are the major cellular constituents in the tumor microenvironment. CAFs are in direct contact with the adjacent cancer cells and crosstalk with them through soluble cytokines, growth factors and exosomes during carcinogenesis in human breast cancer. To determine for the first time the function of CAFs in metastatic sites of breast cancer, we collected CAFs from human patients of metastatic sites (m-CAFs) and compared them with CAFs from primary tumor (p-CAFs) and normal fibroblasts (NFs). We found that m-CAFs expressed higher levels of α-smooth muscle actin (SMA) compared with p-CAFs and NFs. The proliferation of MDA-MB-436 breast cancer cells was significantly increased by treatment with conditioned medium (CM) from m-CAFs compared with p-CAFs in vitro. Also, CM by m-CAFs induced paclitaxel resistance in MDA-MB-436 cells, suggesting that soluble factors produced by m-CAFs promote chemo-resistance, to a greater extent than CM from p-CAFs. The migration and invasion ability of MDA-MB-436 cells co-cultured with m-CAFs CM was significantly greater than that of the p-CAFs CM. m-CAFs outperformed the p-CAFs and NFs in terms of their ability to promote sphere-forming activity in a 3D in vitro culture model. Furthermore, m-CAFs protected MDA-MB-436 cells from the cytotoxic effects of doxorubicin more than p-CAFs in this spheroid 3-D culture. When MDA-MB-436 cells were sorted from these spheroids and grew in the respective CMs, they showed higher expression of the stemness markers of CD44+CD24- compared with cells obtained from p-CAFs/MDA-MB-436 spheroids. Also these cells from the co-culture with m-CAFs experienced with the cadherin switch. Nanog has been demonstrated to promote chemoresistant and epithelial-mesenchymal transition (EMT). The results displayed that MDA-MB-436 cells incubated with the CM from the m-CAFs had a higher expression of Nanog compared with that of p-CAFs. RNA-seq results showed that IGF2 is one of the most different genes between m-CAFs and p-CAFs, its expression was more significant in m-CAFs co-cultured with MDA-MB-436 cells than p-CAFs. The signaling pathway in MDA-MB-436 cells were comparable between co-cultured with m-CAFs CM and the IGF2 stimulation at 2 hours. All these data illustrates that fibroblasts isolated from metastatic site differed in terms of their ability to promote breast cancer cells progression compared to p-CAFs. Our data suggests that m-CAFs are more potent than p-CAFs in inducing the proliferation, migration, drug resistance and cancer stemness of breast cancer cells in an in vitro model.

Citation Format: Yirui Gui, Adriana Aguilar-Mahecha, Marguerite Buchanan, Mark Basik. Stromal fibroblasts from metastatic breast cancer promote proliferation and migration of breast cancer cell and regulate its stemness [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 5894. doi:10.1158/1538-7445.AM2017-5894

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

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

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

Abstract 709: Resistance to paclitaxel in triple negative breast cancer cells is associated with ABCB1 gene rearrangement

Breast cancer represents a heterogeneous group of tumors that exhibit a wide spectrum of clinical, pathologic, and molecular features. Of these tumors, triple-negative breast cancer (TNBCs), shows one of the most aggressive clinical behaviors with distinctive metastatic patterns and very poor prognosis. Due to the “triple negative” status of receptor expression, TNBC patients do not benefit from hormonal therapies or treatments targeted against HER2. Therefore, chemotherapy and, in particular, taxane-based therapy (e.g. paclitaxel) remains the treatment of choice for patients with TNBC. Paclitaxel (PTX) is among the most effective anti-cancer agents developed in the past decades, which is widely used in the treatment of patients with locally advanced and metastatic breast cancer. TNBCs are initially highly responsive to PTX however; the majorities of TNBC patients acquire resistance and develop progressive disease. Therefore, development of resistance to chemotherapeutic agents is the major obstacle to the successful treatment of TNBC patients. In vitro studies on cell lines with acquired resistance provide models for characterization of the biological mechanisms of resistance. We have developed five resistant TNBC cell lines by exposure of cells to increasing concentrations of PTX. We used an integrative analysis of array CGH and gene expression data to gain insights into the interplay of functional changes of the genome in TNBC resistant cell lines. Integrative analysis of aCGH and gene expression revealed deregulated genes whose expression was correlated with their copy number alterations. The most highly up-regulated gene in all 5 resistant cell lines was ABCB1. This up-regulation was accompanied by gene amplification in three resistant cell lines: BT20R, SUM149R and MDA-468 but not in 2 other lines, MDA-MB-231 and MDA-MB-436. The overexpression of ABCB1 at protein level was confirmed only in the three resistant cell lines with the gene amplification, suggesting that changes in ABCB1 copy number may result in gene activation and acquisition of PTX resistance. Array CGH analysis of 7q21.12 in BT20R, SUM149R and MDA-468R revealed similar, but not identical, breakpoints in ABCB1. Using 5′RACE, we identified novel inter-chromosomal translocations of ABCB1 in 2 drug resistance cell lines containing ABCB1 breakpoints. These genomic rearrangements occurred in the 5′ un-translated region (UTR) of ABCB1. The deletion of the 5′UTR of ABCB1 in these resistant cell lines may serve to overcome a translation initiation block, which would then favor the expression of ABCB1. Thus the detection of ABCB1 genomic rearrangements may be a candidate biomarker to predict resistance to paclitaxel in triple negative breast cancers. To our knowledge, we are the first to report ABCB1 amplification and ABCB1 gene fusions as a potential mechanism of drug resistance in TNBC cell lines.

Citation Format: Elaheh Ahmadzadeh, Ewa Przybytkowski, Regina Kiu, Adriana Aguilar-Mahecha, Mark Basik. Resistance to paclitaxel in triple negative breast cancer cells is associated with ABCB1 gene rearrangement. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 709. doi:10.1158/1538-7445.AM2015-709

Abstract 4320: Genomic change in residual triple-negative breast cancers after neoadjuvant chemotherapy

Background: Triple negative breast cancer (TNBC) is characterized by its aggressive phenotype and its genomic instability. TNBC patients who do not respond to neoadjuvant chemotherapy have a very poor prognosis. Currently, little is known about the mechanisms of drug resistance and how to overcome it in TNBC. Our study aims at identifying molecular factors enriched for in residual TNBC tumors after standard neoadjuvant chemotherapy.

Methods: We obtained specimens from 60 TNBC patients participating in a clinical trial (Q-CROC-03). Biopsies were collected prior to and after standard neoadjuvant chemotherapy and residual cancer was collected at the time of surgery. Matched tumor specimens (pre and post) from 9 patients were analyzed by array comparative genomic hybridization (CGH), gene expression microarrays and whole exome sequencing. All samples contained &gt;50% tumor cellularity.

Results: Gene expression data was used to identify the different TNBC subtypes (TNBCtype). Six of the 7 subtypes were represented in at least one sample from our cohort. In the post-chemo samples, we observed a change in TNBC subtype compared to the pre-chemo samples in 6 pairs. The most common switch was to the Immuno Modulatory subtype (IM). aCGH analysis showed relatively few differences in copy number variants (CNV) following chemotherapy in 3 out of 8 patients. Whole exome sequencing revealed increased allele frequency or appearance of de novo mutations in TP53 gene in the residual cancers of 2 of the 3 patients presenting differences in CNVs post treatment. Interestingly, pathway analyses revealed that genes involved in DNA binding, chromosomal organization and nucleosome organization were differentially expressed (&gt;2fold) in 2 of the patients with CNV changes. Our results suggest that increased levels of TP53 mutations and altered transcriptional expression of genes involved in chromosomal functions could be associated with the presence of CNV changes in drug resistant tumors.

Conclusion: In summary, the genome of TNBCs does not undergo major changes during neoadjuvant chemotherapy; however, enrichment for or de novo TP53 mutations is associated with the appearance of novel CNVs in drug resistant residual tumors.

Citation Format: Adriana Aguilar-Mahecha, Ewa Przybytkowski, Josiane Lafleur, Cathy Lan, Stephanie Légaré, Najmeh Alirezaie, Carole Séguin, Federico Discepola, Bojan Kovacina, Catalin Mihalcioiu, André Robidoux, Elizabeth Marcus, Josée Anne Roy, Manuela Pelmus, Olga Aleynikova, Sheida Nabavi, Jacek Majewski, Mark Basik. Genomic change in residual triple-negative breast cancers after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4320. doi:10.1158/1538-7445.AM2015-4320

Glycoproteomic comparison of clinical triple-negative and luminal breast tumors

Triple-negative (TN) breast cancer accounts for ∼ 15% of breast cancers and is characterized by a high likelihood of relapse and a lack of targeted therapies. In contrast, luminal-type tumors that express the estrogen and progesterone receptors (ER+/PR+) and lack expression of human epidermal growth factor receptor 2 (Her2-) are treated with targeted hormonal therapy and carry a better prognosis. To identify potential targets for the development of future therapeutics aimed specifically at TN breast cancers, we have used a hydrazide-based glycoproteomic workflow to compare protein expression in clinical tumors from nine TN (Her2-/ER-/PR-) and nine luminal (Her2-/ER+/PR+) patients. Using a label-free LC-MS based approach, we identified and quantified 2264 proteins. Of these, 90 proteins were more highly expressed and 86 proteins were underexpressed in the TN tumors relative to the luminal tumors. The expression level of four of these potential targets was verified in the original set of tumors by Western blot and correlated well with our mass-spectrometry-based quantification. Furthermore, 30% of the proteins differentially expressed between luminal and TN tumors were validated in a larger cohort of 406 TN and 469 luminal tumors through corresponding differences in their mRNA expression in publically available microarray data. A group of 29 of these differentially expressed proteins was shown to correctly classify 88% of TN and luminal tumors using microarray data of their associated mRNA levels. Interestingly, even within a group of TN breast cancer patients, the expression levels of these same mRNAs were able to significantly predict patient survival, suggesting that these proteins play a role in the aggressiveness seen in TN tumors. This study provides a comprehensive list of potential targets for the development of diagnostic and therapeutic agents specifically aimed at treating TN breast cancer and demonstrates the utility of using publicly available microarray data to further prioritize potential targets.

Testing devices or experimental systems? Cancer clinical trials take the genomic turn

Clinical trials are often described as machine-like systems for generating specific information concerning drug safety and efficacy, and are understood as a component of the industrial drug development processes. This paper argues that contemporary clinical trials in oncology are not reducible to mere drug testing. Drawing on ethnographic fieldwork and interviews with researchers in the field of oncology from 2010 to 2013, we introduce a conceptual contrast between trials as testing machines and trials as clinical experimental systems to draw attention to the ways trials are increasingly being used to ask open-ended scientific questions. When viewed as testing machines, clinical trials are seen as a means to produce answers to straightforward questions and deviations from the protocol are seen as bugs in the system; but practitioners can also treat trials as clinical experimental systems to investigate as yet undefined problems and where heterogeneity becomes a means to produce novel biological or clinical insights. The rise of "biomarker-driven" clinical trials in oncology, which link measurable biological characteristics such as genetic mutations to clinical features such as a patient's response to a particular drug, exemplifies a trend towards more experimental styles of clinical work. These transformations are congruent with changes in the institutional structure of clinical research in oncology, including a movement towards more flexible, networked research arrangements, and towards using individual patients as model systems for asking biological questions.

Abstract A041: Targeting EGFR reverses paclitaxel resistance associated with ABCB1 overexpression in triple-negative breast cancer

Background: Breast cancer represents a heterogeneous group of tumors that exhibit a wide spectrum of clinical, pathologic, and molecular features. Of these tumors, triple-negative breast cancer (TNBCs), shows one of the most aggressive clinical behaviors with distinctive metastatic patterns and very poor prognosis. TNBC is characterized by the absence of expression of estrogen receptor, progesterone receptor, and low levels of human epidermal growth factor (HER2). Paclitaxel (PTX) is among the most effective anti-cancer agents developed in the past decades, which is widely used in the treatment of patients with locally advanced and metastatic breast cancer. TNBCs are initially highly responsive to PTX however; the majorities of TNBC patients acquire resistance and develop progressive disease. Therefore, acquired resistance to paclitaxel has become one of the major obstacles in the successful treatment of patients with TNBC. Several mechanisms of resistance to paclitaxel has been identified, however there is little data about mechanisms of resistance to chemotherapy in TNBCs.

Methods: In order to investigate the molecular mechanisms of acquired resistance to PTX in TNBCs, we developed four resistant TNBC cell lines (BT20, SUM149, MA-MB-231 and MDA-MB-436) by exposure of cells to increasing concentrations of PTX. We used an integrative analysis of array CGH and gene expression data to gain insights into the interplay of functional changes of the genome in TNBC resistant cell lines.

Results: We found a novel amplification of the ABCB1 gene in BT20 and SUM149 resistant cell lines only. Gene expression analysis revealed significant up-regulation of expression of ABCB1 and EGFR ligands in SUM149 and BT20 resistant cells compared to parental cell lines. The functional activity of ABC transporters assessed using Rhodamine 123 efflux assay demonstrated a marked increase in the efflux of rhodamine in SUM149-R and BT20-R, which was reversed by verapamil. We treated resistant cells with two anti-EGFR drugs, lapatinib and neratinib, which are also known ABC transporter inhibitors, and found that both drugs inhibited rhodamine 123 efflux and restored sensitivity to PTX in these PTX-resistant TNBC cells.

Conclusion: This is the first report of ABCB1 gene amplification in paclitaxel resistant triple negative breast cancer cells. Our results suggest that ABCB1 gene amplification and EGFR ligand over-expression plays a critical role in the development of PTX resistance in TNBC cells, and that this resistance can be targeted by therapy with anti-EGFR agents. Thus, ABCB1 gene amplification and EGFR ligand expression may be novel predictive biomarkers for both chemotherapy and anti-EGFR therapy in TNBCs.

Citation Format: Elaheh Ahmadzadeh, Ewa Przybytkowski, Adriana Aguilar-Mahecha, Mark Basik. Targeting EGFR reverses paclitaxel resistance associated with ABCB1 overexpression in triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A041.

Abstract LB-225: Resistance to paclitaxel in triple negative breast cancer cells is associated with ABCB1 overexpression and gene amplification, and can be reversed by anti-EGFR targeting

Background: Due to the absence of expression of estrogen, progesterone and HER2 receptors, triple negative breast cancer (TNBC) patients do not benefit from targeted therapies. Therefore, chemotherapy remains the only treatment of choice for patients with TNBC. Despite initial clinical responses to chemotherapy, the majority of TNBC patients acquire resistance and develop progressive disease. There is little data about mechanisms of resistance to chemotherapy in TNBCs.

Methods: We investigated the molecular mechanisms of acquired resistance to paclitaxel (PTX) in TNBCs. Four TNBC cell lines (BT20, SUM149, MA-MB-231 and MDA-MB-436) were cultured in the presence of increasing concentrations of paclitaxel until they acquired resistance. Gene expression and aCGH analysis were performed on all parental and resistant pairs.

Results: We found a novel amplification of the ABCB1 gene in BT20 and SUM149 resistant cell lines only. Gene expression analysis revealed significant up-regulation of expression of ABCB1 and EGFR ligands in SUM149 and BT20 resistant cells compared to parental cell lines. The functional activity of ABC transporters assessed using rhodamine 123 efflux assay demonstrated a marked increase in the efflux of rhodamine in SUM149-R and BT20-R which was reversed by verapamil. We treated resistant cells with two anti-EGFR drugs, lapatinib and neratinib, which are also known ABC transporter inhibitors, and found that both drugs inhibited rhodamine 123 efflux and restored sensitivity to PTX in these PTX-resistant TNBC cells.

Conclusion: This is the first report of ABCB1 gene amplification in paclitaxel resistant triple negative breast cancer cells. Our results suggest that ABCB1 gene amplification and EGFR ligand over-expression plays a critical role in the development of PTX resistance in TNBC cells, and that this resistance can be targeted by therapy with anti-EGFR agents. Thus, ABCB1 gene amplification and EGFR ligand expression may be novel predictive biomarkers for both chemotherapy and anti-EGFR therapy in TNBCs.

Citation Format: Elaheh Ahmadzadeh, Ewa Przybytkowski, Adriana Aguilar-Mahecha, Mark Basik. Resistance to paclitaxel in triple negative breast cancer cells is associated with ABCB1 overexpression and gene amplification, and can be reversed by anti-EGFR targeting. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-225. doi:10.1158/1538-7445.AM2013-LB-225

Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome

The characterization of molecular alterations specific to cancer facilitates the discovery of predictive and prognostic biomarkers important to targeted therapeutics. Alterations critical to cancer therapeutics include copy number alterations (CNAs) such as gene amplifications and deletions as well as genomic rearrangements resulting in gene fusions. There are two genome-wide technologies used to detect CNAs: next generation sequencing (NGS) and dense microarray based comparative genomic hybridization, termed array CGH (aCGH). aCGH is a mature robust technology of lower cost and more accessible than NGS. This chapter describes the protocol steps and analysis required to obtain reliable aCGH results from clinical samples. Technical options and various necessary compromises related to the nature of clinical material are considered and the consequences of these choices for data analysis and interpretation are discussed. The chapter includes brief description of the data analysis, even though analysis is often performed by bioinformaticians. Today's cancer research requires collaboration of clinicians, molecular biologists, and mathematicians. Acquaintance with the basic principles related to the extraction of the data from arrays, its normalization and the algorithms available for analysis provides a baseline for mutual understanding and communication.

Biopsy-driven study to identify biomarkers of drug resistance in patients with triple-negative breast cancer

87

Background: Resistance to chemotherapy is the underlying cause of death in most patients dying of breast cancer. Patients with early stages of breast cancer whose tumor is or becomes resistant to chemotherapy have a poor prognosis, while women with advanced breast cancer live as long as their tumors respond to chemotherapy. Because of the great difficulty of obtaining clinical samples from drug resistant tumors in patients, there is scant information about molecular factors from actual drug resistant tumors. This project aims to systematically profile resistant triple negative breast cancers (TNBCs) in order to discover molecular “resistance” genes/proteins as a first step to develop strategies to overcome drug resistance. Methods: Paired biopsies are collected from TNBC patients (NCT01276899). Four needle core biopsies are collected before the initiation of treatment and 2 weeks before surgery or at the time of progression in the neoadjuvant and metastatic settings respectively. Paired biopsies will undergo Next Gen Sequencing, flow sorted aCGH analysis, gene expression and miRNA profiling as well as phosphoproteomic profiling using reverse phase protein arrays. Results: We have currently enrolled 28 patients in the neoadjuvant setting and 3 metastatic patients. We have standardized the methods of collection and processing of tissue and blood specimens to ensure their molecular integrity and compatibility with different genomic and proteomic molecular platforms. Analysis of tumor cellularity has been incorporated into our quality control and we have optimized the extraction of nucleic acids to obtain high yields and optimal quality. In parallel, we have generated acquired resistance to paclitaxel in a panel of TNBC cell lines. These cell lines will also undergo genomic profiling and exome sequencing to identify molecular markers of resistance that will be correlated with the markers found in patient samples. Conclusions: This project will allow us to identify the molecular factors responsible for drug resistance in TNBCs and enable the elaboration of strategies to overcome resistance.

The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines

Blood sample processing and handling can have a significant impact on the stability and levels of proteins measured in biomarker studies. Such pre-analytical variability needs to be well understood in the context of the different proteomics platforms available for biomarker discovery and validation. In the present study we evaluated different types of blood collection tubes including the BD P100 tube containing protease inhibitors as well as CTAD tubes, which prevent platelet activation. We studied the effect of different processing protocols as well as delays in tube processing on the levels of 55 mid and high abundance plasma proteins using novel multiple-reaction monitoring-mass spectrometry (MRM-MS) assays as well as 27 low abundance cytokines using a commercially available multiplexed bead-based immunoassay. The use of P100 tubes containing protease inhibitors only conferred proteolytic protection for 4 cytokines and only one MRM-MS-measured peptide. Mid and high abundance proteins measured by MRM are highly stable in plasma left unprocessed for up to six hours although platelet activation can also impact the levels of these proteins. The levels of cytokines were elevated when tubes were centrifuged at cold temperature, while low levels were detected when samples were collected in CTAD tubes. Delays in centrifugation also had an impact on the levels of cytokines measured depending on the type of collection tube used. Our findings can help in the development of guidelines for blood collection and processing for proteomic biomarker studies.

Q-CROC-03: A prospective biopsy driven clinical trial to study the mechanisms of resistance to chemotherapy in triple-negative breast cancer patients

TPS1139

Background: Resistance to chemotherapy or targeted agents is the cause of death in most patients dying of breast cancer and one of the major challenges presently faced by oncologists. In triple negative breast cancers (TNBCs), drug resistance emerges quicker than in other breast cancer subtypes and contributes to the poor prognosis seen in these patients. The lack of targeted therapies to treat TNBC highlights the important need to better understand the molecular mechanisms contributing to chemotherapy resistance in order to develop new therapeutic strategies. However, the difficulty in obtaining tissue samples from drug resistant tumors has been one of the limiting factors in this field of study. Methods: We have designed a prospective phase II clinical trial where paired biopsies are collected from chemotherapy resistant TNBCs (NCT01276899). Four needle core biopsies are collected before the initiation of treatment and 2 weeks before surgery or at the time of progression in the neoadjuvant and metastatic settings respectively. Metastatic sites eligible for biopsy include liver, lung, skin and lymph nodes. This study is presently recruiting at 5 major health centers in Quebec and will soon open in the USA. We have currently enrolled 13 patients in the neoadjuvant setting and 2 metastatic patients. Major challenges in patient enrolment will be discussed. We have standardized the methods of collection and processing of tissue and blood specimens to ensure their molecular integrity and compatibility with different genomic and proteomic molecular platforms. Analysis of tumor cellularity has been incorporated into our quality control and we have optimized the extraction of nucleic acids to obtain high yields and optimal quality. Paired biopsies will undergo Next Gen Sequencing, flow sorted aCGH analysis, gene expression and miRNA profiling as well as phosphoproteomic profiling using reverse phase protein arrays. Collection of clinical data will allow molecular profiling data to be linked to clinical response data so as to determine DNA, RNA and protein factors correlated with tumor resistance to chemotherapy.

Abstract B24: De novo and acquired resistance to first-line standard therapy in colorectal cancer: from cell lines to metastatic tumors

Introduction: Personalized medicine (PM) is a concept that has raised high expectations amongst scientists, clinicians, and patients. An emerging approach is to examine tumor biopsy material for genomic changes that are known targets of currently available therapeutic agents, with the assumption that a clinical benefit will be observed if the target is inhibited. While striking anecdotal reports are predictable from this approach, the clinical impact of these agents is limited by the inevitable development of therapeutic resistance. Our focus is on the design of parallel research programs using both in vitro and in vivo strategies, in an effort to delay or inhibit resistance. We present here preliminary data for a signature of resistance to standard first-line treatment - fluorouracil, folinic acid, oxaliplatin and bevacizumab (FOLFOX/B) using cell line models of resistance to this regimen. In parallel, we are conducting a prospective study to identify biomarkers of clinical resistance to first-line therapy in patients with metastatic colorectal cancer (CRC) (NCT00984048).

Methods: Ten established CRC cell lines were treated with FOLFOX/B and categorized as resistant or sensitive based on IC50 values. In parallel, patients who consented to an initial biopsy and one at disease progression following an initial response were identified as intrinsically resistant or as having acquired resistance during treatment. CRC cell lines that were initially sensitive were rendered resistant to mimic the acquired resistance in patients, by serial passages with gradual increases in concentration of the combination regimen. We compared microarray data from three sensitive and three resistant cell lines.

Results: We found a different expression pattern from microarray data comparing sensitive and resistant cell lines, thereby indicating a potential signature of resistance to FOLFOX/B. Interestingly, we found that the Src family kinase Lyn was overexpressed in resistant cells lines. Treating cells with non-cytotoxic concentration of dasatinib, a dual Src family kinase and Abl inhibitor, sensitized both the parental sensitive cells and the cells with acquired resistance to FOLFOX/B, thereby suggesting that combination treatment with dasatinib may be effective in delaying or inhibiting resistance. We have thus far collected needle core biopsies from liver metastases from forty patients who agreed to partake in this multi-center trial. Eligible patients have confirmed metastatic CRC, measurable disease, and consent to three needle-core biopsies (NCBs) of a non-resectable liver metastasis before treatment and at resistance, as well as serial blood collection throughout the study. Using standard operating procedures developed for this trial, we were able to both preserve morphology and obtain high-quality genomic material from biopsy tissue. We will determine if the resistance signature and overexpression of Lyn observed in the resistant CRC cell lines are similarly demonstrated in patients that were intrinsically resistant to FOLFOX/B.

Conclusions: We have designed parallel in vitro and in vivo experiments to study resistance to standard first-line treatment for mCRC. These studies provide insight on metastatic signatures of resistance and suggest combination therapies to delay or inhibit therapeutic resistance in patients.

Abstract 5534: Building the organization framework for biopsy-driven translational research: The Quebec Clinical Research Organization in Cancer (Q-CROC) experience

Introduction: The success of personalized medicine in oncology relies on translational research efforts to identify biomarkers that will influence clinical management. The discovery and validation of biomarkers is a concerted effort requiring an organizational framework that is often underestimated. The Quebec Clinical Research Organization in Cancer (Q-CROC) consortium is a multi-disciplinary and multi-institutional group of scientists and clinicians devoted to integrating and enhancing translational and clinical research capacity in Quebec. We describe here the organizational framework driving a multicenter, prospective study to identify biomarkers of clinical resistance to first-line therapy in metastatic colorectal cancer (NCT00984048, Q-CROC-01). Results: The Q-CROC consortium has put in place an organizational infrastructure to support the activities and operations of its translational projects. We identified and addressed several critical issues during the course of the Q-CROC-01 translational project that were also common to our subsequent biomarker-driven trial in lymphoma (Q-CROC-02, NCT01238692) and breast cancer (Q-CROC-03, NCT01276899). Examples of these issues include: (i) feasibility and burden of tissue collection at participating sites, (ii) limiting pre-analytical variability in blood and tissue specimens for functional downstream applications, (iii) verification of tumor content on biopsy specimens, (iv) tracking sample flow, (v) integration of clinical data with discovery platforms, and (vi) engaging participation throughout all steps of the project. In part to address the above issues, we established five operational Cores: clinical, biobank, biospecimen processing, bioanalytical and bioinformatic. A further challenge was the integration between these Cores, who for the most part operated in silos. We observed that a critical element to unify all components of the consortium was a scientific project management team, consisting of dedicated individuals regularly interacting with each Core to ensure that objectives were aligned and deliverables were met. This academic framework for translational research may be comparable to that of multicenter clinical trials undertaken by industry, but some challenges, including financial and time constraints, data sharing and IP agreements, and engagement of its members, may be more palpable in the academic setting. Conclusion: Infrastructure science is underestimated and under-reported in translational cancer research and is crucial to the success of any large-scale biomarker discovery effort. Our experience with three multi-institutional biomarker-driven trials is that progress hinges upon the availability of an infrastructure that is not only the sum of its parts but that provides a concrete link between each component.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5534. doi:1538-7445.AM2012-5534

Abstract 770: Overcoming Trastuzumab resistance with the novel pan-erbb inhibitor AZD8931

Approximately 15-20% of all invasive breast carcinomas overexpress the HER-2 receptor, a membrane surface-bound receptor tyrosine kinase upstream of critical proliferation and cell survival pathways. Trastuzumab, a humanized monoclonal antibody to the extracellular domain of HER-2, has proven to be a beneficial treatment for patients diagnosed as HER-2+, but does have its limitations. A majority of advanced HER-2 positive breast cancer patients will develop resistance to the therapy within the first year while many others do not respond to the drug when used alone. The purpose of this study was to determine whether AZD8931, a reversible pan-ERBB inhibitor that equipotently inhibits the tyrosine kinase-activity of EGFR, HER-2, and HER-3, could reverse this resistance in established trastuzumab-resistant BT474 and SKBR3 cell lines. To account for tumor heterogeneity in HER-2+ tumors, response to AZD8931 was examined in both ER-positive (BT474) and ER-negative (SKBR3) cell lines. Proliferation assays were used to assess the efficacy of AZD8931 alone and in combination with trastuzumab. Results showed significantly diminished cell growth in all tested cell lines, including those resistant to trastuzumab, at clinically relevant concentrations of AZD8931 (&lt;2µM). Furthermore, when AZD8931 was tested in conjunction with trastuzumab, the resistance to trastuzumab was reversed using clinically relevant doses of trastuzumab. Using combination indices, it was found that AZD8931 synergizes well with trastuzumab and could be used as a combination therapy for both trastuzumab-sensitive and trastuzumab-resistant breast cancer patients. Western blot analyses confirmed the results of cell proliferation assays as p-EGFR, p-HER-2, p-HER-3, p-Akt, and p-MAPK, were all reduced after treatment with AZD8931. Thus, AZD8931 alone or in combination with trastuzumab may be an effective therapy in HER2+ breast cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 770. doi:1538-7445.AM2012-770