Abstract P6-11-04: The evaluation of ganitumab/metformin plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 trial

Background: I-SPY 2 is a multicenter, phase 2 trial using response-adaptive randomization within biomarker subtypes to evaluate novel agents when added to standard neoadjuvant therapy for women with high-risk stage II/III breast cancer - investigational agent(I) +paclitaxel(T) qwk, doxorubicin & cyclophosphamide(AC) q2-3 wk x 4 vs. T/AC (control arm). The primary endpoint is pathologic complete response (pCR) at surgery. The goal is to identify/graduate regimens that have ≥85% Bayesian predictive probability of success (statistical significance) in a 300-patient phase 3 neoadjuvant trial defined by hormone-receptor (HR) & HER2 status & MammaPrint (MP). Regimens may also leave the trial for futility (< 10% probability of success) or following accrual of maximum sample size (10%< probability of success <85%). We report the results for experimental arm Ganitumab, a type I insulin-like growth factor receptor (IGF1R) inhibitor. IGF1R inhibitors are known to induce insulin resistance and all patients assigned to Ganitumab received metformin.

Methods: Women with tumors ≥2.5cm were eligible for screening. MP low/HR+ and HER2+ tumors were ineligible for randomization. Hemoglobin A1C≥ 8.0% were ineligible. MRI scans (baseline, 3 cycles after start of therapy, at completion of weekly T and prior to surgery) were used in a longitudinal statistical model to improve the efficiency of adaptive randomization. Ganitumab was given at 12mg/kg q2 weeks and metformin at 850mg PO BID, while receiving ganitumab. Analysis was intention to treat with patients who switched to non-protocol therapy counted as non-pCRs. Ganitumab/metformin was open only to HER2- patients, and eligible for graduation in 3 of 10 pre-defined signatures: HER2-, HR+HER2- and HR-HER2-.

Results: Ganitumab/metformin did not meet the criteria for graduation in the 3 signatures tested. When the maximum sample size was reached, accrual to this arm stopped. Ganitumab/metformin was assigned to 106 patients; there were 128 controls. We report probabilities of superiority for Ganitumab/metformin over control and Bayesian predictive probabilities of success in a neoadjuvant phase 3 trial equally randomized between Ganitumab/metformin and control, for each of the 3 biomarker signatures, using the final pathological response data from all patients. Safety data will be presented.

SignatureEstimated pCR Rate (95% probability interval)Probability Ganitumab/ Metformin Is Superior to ControlPredictive Probability of Success in Phase 3 Ganitumab/ Metformin N = 106Control N = 128  All HER2-22% (13%-31%)16% (10%-23%)89%33%HR+/HER2-14% (4%-24%)12% (4%-19%)66%21%HR-/HER2-32% (17%-46%)21% (11%-32%)91%51%

Conclusion: The I-SPY 2 adaptive randomization study estimates the probability that investigational regimens will be successful in a phase 3 neoadjuvant trial. The value of I-SPY 2 is to give insight about the performance of an investigational agent's likelihood of achieving pCR. For Ganitumab/metformin, no subtype came close to the efficacy threshold of 85% likelihood of success in phase 3, and this regimen does not appear to impact upfront reduction of tumor burden. Our data do not support its continued development for the neoadjuvant treatment of breast cancer.

Citation Format: Yee D, Paoloni M, van't Veer L, Sanil A, Yau C, Forero A, Chien AJ, Wallace AM, Moulder S, Albain KS, Kaplan HG, Elias AD, Haley BB, Boughey JC, Kemmer KA, Korde LA, Isaacs C, Minton S, Nanda R, DeMichele A, Lang JE, Buxton MB, Hylton NM, Symmans WF, Lyandres J, Hogarth M, Perlmutter J, Esserman LJ, Berry DA. The evaluation of ganitumab/metformin plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-11-04.

Abstract P4-06-03: An annotated collection of pre- and post-therapy breast cancer patient-derived xenograft models built from fine needle aspiration samples aligned with ongoing clinical trials documenting response to treatment

BACKGROUND: Patient-derived xenograft (PDX) models of breast cancer replicate the diverse histologic and molecular features of patient tumors and provide a renewable source of human tumor tissue; however collection of tissue by core needle biopsy is problematic due to patient discomfort, bleeding risk and the limited number of passes a patient can tolerate. In addition, FDA guidelines caution that multiple core needle biopsies could lead to an overestimation of the true pCR rate in neoadjuvant trials.

METHODS: To support the neoadjuvant molecular diagnostic and drug development program in TNBC, a pilot study was conducted to determine if fine needle aspiration (FNA) could be used for building PDX models. Prior to engraftment, FNA samples were analysed for cell number and viability.

RESULTS: Six PDX models were successfully generated from eight individual tumor samples. These models retain histologic and molecular features of the original patient tumors as determined by immunohistochemistry, RNA expression profiling, and deep whole-exome and targeted gene sequencing. In addition, the tested PDX models recapitulate the responses to therapies across multiple chemotherapeutic agents.

Based on this success, we have standardized the use of FNAs to generate PDX models both pre- and post-therapy in two ongoing neoadjuvant clinical trials:

1. MDACC 2014-0185 (PI Stacy Moulder, 360 patients), 'Improving outcomes in TNBC using molecular triaging and diagnostic imaging to guide neoadjuvant therapy'

2. MDACC 2014-0045 (PI Jennifer Litton, 20+ patients), 'A pilot study of BMN673 as a neoadjuvant study in patients with a diagnosis of invasive breast cancer and a deleterious BRCA mutation'

 FNA cells (x10^4)Cell viability (%)Total viable cells (x10^4)Study entry biopsy (n=67)144.5050.6544.14Post treatment biopsy (n=16)47.0732.5428.38

To date, treatment-naïve primary tumor samples from 67 patients enrolled onto these neoadjuvant trials, and 16 matched non-responsive post treatment tumor samples have been analysed for cell count and viability (table below) prior to being engrafted into the humanized mammary fat pads of NOD/SCID mice.

CONCLUSION: We have demonstrated success in using FNAs to build PDX models that recapitulate the biology and clinical course of the original tumor. In our pilot study, we successfully generated six PDX models using FNA for TNBC, including some harboring deleterious BRCA1/2 mutations. Because of the high concordance in histologic, genomic, and clinical attributes, we are now using this approach to develop a rich resource of pre- and post-treatment PDX models for the investigation of therapeutic resistance.

Citation Format: Echeverria GV, Chang JT, Cai S, Tu Y, McCoy A, Lau R, Redwood A, Kaffiabasabadi S, Rauch GM, Adrada BE, Jennifer L, Moulder SL, Symmans WF, Piwnica-Worms H. An annotated collection of pre- and post-therapy breast cancer patient-derived xenograft models built from fine needle aspiration samples aligned with ongoing clinical trials documenting response to treatment [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-06-03.

Abstract OT2-01-22: NCT02456857: A phase II trial of liposomal doxorubicin, bevacizumab and everolimus (DAE) in patients (pts) with localized triple-negative breast cancer (TNBC) with tumors predicted insensitive to standard neoadjuvant chemotherapy (NACT)

BACKGROUND: Approximately 50% of TNBC pts treated with standard taxane/anthracycline-based NACT will have chemo-insensitive disease (CID) manifested as extensive residual disease (RCB-II or III) at the time of surgery. 40-80% of these pts will develop recurrence within 3 years of initial diagnosis. Recent advances in molecular profiling have identified subsets of TNBC with distinct, targetable molecular features. We developed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). In the ARTEMIS trial, treatment naïve pts with localized TNBC undergo a pretreatment biopsy and then immediately start their initial phase of anthracycline-based chemotherapy so that the results of the molecular characterization are used in combination with response assessment (clinical exam/diagnostic imaging) to identify CID and inform the second phase of NACT, thus using a 'second hit' strategy in the middle of NACT to overcome drug resistance. The mesenchymal subtypes of TNBC have a high incidence of PI3K pathway activation. Preclinical models demonstrated response to PI3K inhibitors in this subtype. Metaplastic breast cancers make up ∼30% of tumors characterized as 'claudin-low/mesenchymal' by gene signature and are also associated with a high rate of PI3K activating molecular aberrations. A combination regimen of liposomal doxorubicin, bevacizumab and the mTOR inhibitors temsirolimus or everolimus (DAT or DAE) demonstrated response (including durable complete responses) in metastatic metaplastic breast cancer.

PRIMARY OBJECTIVE: Determine the rate of pathologic complete response (pCR/RCB-0) or minimal residual disease (RCB-I) after 4 cycles of DAE for treatment of mesenchymal TNBC deemed to be CID through the ARTEMIS trial

TRIAL DESIGN AND STATISTICAL METHODS: Only pts deemed to have mesenchymal CID on the ARTEMIS trial can enter this non-randomized phase II study. Realizing that pts without response to their initial cycles of chemotherapy have very low chance (5%) of achieving pCR with additional cycles of chemotherapy, it would be clinically meaningful to see pCR in this pt population improved to 20%. Counting pCR (RCB-0) or RCB-I as response, a two-stage Gehan-type design will be employed with 14 pts in the first stage. If at least one pt responds, 23 more pts will be added for a total of 37 pts. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% chance if the true rate is 0.10, 10% if the true rate is 0.15 and 4% if the true rate is 0.20. If accrual continues to the second stage and a total of 37 pts are enrolled, the 95% confidence interval for a 0.20 response rate will extend from 0.10 to 0.35.

BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC enrolled onto ARTEMIS trial, adequate organ, bone marrow and cardiac parameters Exclusion: metastatic disease, pregnant or lactating pts, medical illness that increases chance of moderate to severe toxicity

CORRELATIVE SCIENCE: Correlate vimentin expression by IHC, mesenchymal signatures and PI3K pathway aberrations with response.

Citation Format: Moulder S, Hess K, Rauch M, Astrada B, Litton J, Mittendorf E, Ueno N, Tripathy D, Lim B, Piwnica-Worms H, Thompson A, Symmans WF. NCT02456857: A phase II trial of liposomal doxorubicin, bevacizumab and everolimus (DAE) in patients (pts) with localized triple-negative breast cancer (TNBC) with tumors predicted insensitive to standard neoadjuvant chemotherapy (NACT) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-22.

Abstract P6-11-02: Efficacy of Hsp90 inhibitor ganetespib plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 trial

Background:Pathologic complete response(pCR) after neoadjuvant therapy is an established prognostic biomarker for high-risk breast cancer(BC). Improving pCR rates may identify new therapies that improve survival. I-SPY 2 uses response-adaptive randomization within biomarker subtypes to evaluate novel agents when added to standard neoadjuvant therapy for women with high-risk stage II/III breast cancer; the goal is to identify regimens that have ≥85% Bayesian predictive probability of success (statistical significance) in a 300-patient phase 3 neoadjuvant trial defined by hormone-receptor (HR), HER2 status and MammaPrint (MP). We report the results for Ganetespib, a selective inhibitor of Hsp90 that induces the degradation/deactivation of key drivers of tumor initiation, progression, angiogenesis, and metastasis.Ganetespib + taxanes previously have resulted in a superior therapeutic response compared to monotherapy in multiple solid tumor models including BC.

Methods:Women with tumors ≥2.5cm were eligible for screening and participation. MP low/HR+ tumors were ineligible for randomization. QTcF >470msec and HbA1C >8.0% were ineligible. MRI scans (baseline, +3 cycles, following weekly paclitaxel, T, and pre-surgery) were used in a longitudinal statistical model to improve the efficiency of adaptive randomization. Ganetespib was given with weekly T at 150 mg/m2 IV weekly (3 weeks on, 1 off). Patients were premedicated (dexamethasone 10mg and diphenhydramine HCl 25-50 mg, or therapeutic equivalents). Analysis was intention to treat with patients who switched to non-protocol therapy counted as non-pCRs. The Ganetespib regimen was open only to HER2- patients, and eligible for graduation in 3 of 10 pre-defined signatures: HER2-, HR+/HER2- and HR-/HER2-.

Results:Ganetespib did not meet the criteria for graduation in the 3 signatures tested. When the maximum sample size was reached, accrual stopped. Ganetespib was assigned to 93 patients; there were 140 controls. We report probabilities of superiority for Ganetespib over control and Bayesian predictive probabilities of success in a neoadjuvant phase 3 trial equally randomized between Ganetespib and control, for the 3 biomarker signatures, using the final pCR data from all patients. Safety data will be presented.

SignatureEstimated pCR Rate (95% probability interval)Probability Ganetespib Is Superior to ControlPredictive Probability of Ganetespib Success in a Phase 3 Trial Ganetespib N = 93Control N = 140  All HER2-26% (16%-37%)18% (8%-28%)91%47%HR+/HER2-15% (4%-27%)14% (4%-24%)60%19%HR-/HER2-38% (23%-53%)22% (9%-35%)96%72%

Conclusion:The I-SPY 2 adaptive randomization model efficiently evaluates investigational agents in the setting of neoadjuvant BC. The value of I-SPY 2 is that it provides insight as to the regimen's likelihood of success in a phase 3 neoadjuvant study. Although no signature reached the efficacy threshold of 85% likelihood of success in phase 3, we observed the most impact in HR-/HER2- patients, with a 16% improvement in pCR rate. While our data do not support the continued development of Ganetespib alone for neoadjuvant BC, combinations with Ganetespib, which could potentiate its effect, may be worth pursuing in I-SPY 2 or similar trials.

Citation Format: Forero A, Yee D, Buxton MB, Symmans WF, Chien AJ, Boughey JC, Elias AD, DeMichele A, Moulder S, Minton S, Kaplan HG, Albain KS, Wallace AM, Haley BB, Isaacs C, Korde LA, Nanda R, Lang JE, Kemmer KA, Hylton NM, Paoloni M, van't Veer L, Lyandres J, Perlmutter J, Hogarth M, Yau C, Sanil A, Berry DA, Esserman LJ. Efficacy of Hsp90 inhibitor ganetespib plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-11-02.

Abstract OT2-01-14: Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489)

BACKGROUND: TNBC has an especially poor prognosis in patients (pts) whose tumor does not respond to anthracycline and taxane-based chemotherapy. Approximately 50% will have chemo-insensitive disease (CID) resulting in extensive residual disease at the time of surgery. 40-80% of these pts will recur < 3 years. Recently developed molecular profiling techniques to identify TNBC subsets detect distinct molecular hallmarks. We designed a clinical trial to identify and characterize CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). Treatment naïve pts with localized TNBC undergo a pretreatment biopsy followed by anthracycline-based chemotherapy (AC). During AC the molecular profile is determined; these results along with the response assessment (clinical exam/diagnostic imaging) will identify CID and guide the second phase of neoadjuvant chemotherapy. Tumor-infiltrating lymphocytes (TIL) have been identified as having prognostic and predictive significance in TNBC pts leading to higher pCR rates post NACT. However, the tumor microenvironment also contains regulatory T cells and myeloid-derived suppressor cells that are immunosuppressive. Programmed death ligand 1 (PD-L1) is expressed in 20% TNBC. Targeting this may lead to a more durable response as compared to chemotherapy alone.

PRIMARY OBJECTIVE: Evaluate the rate of pathologic complete response (pCR)/RCB-0 + residual cancer burden (RCB)-I responses in TNBC pts, determined to have CID after anthracycline-based chemotherapy, then treat with atezolizumab + nab-paclitaxel preoperatively.

TRIAL DESIGN AND STATISITCAL METHODS: Pts deemed to have CID on the ARTEMIS trial can enter this non-randomized phase II study. Pts without response to their initial chemotherapy cycles have a low likelihood (5%) of achieving pCR with additional cycles of chemotherapy. It would be clinically meaningful for pCR to improve to 20%. Counting pCR (RCB-0) or RCB-I as response given similar survival outcomes, a two-stage Gehan-type design will be employed with 14 pts in the first stage. If at least one pt responds, 23 more will be added. This design has a 49% chance of terminating after the first stage if the true response rate is 0.05, 23% chance if the true rate is 0.10, 10% if the true rate is 0.15 and 4% if the true rate is 0.20. If accrual continues to the second stage, the 95% confidence interval for a 0.20 response rate will extend from 0.10 to 0.35.

BRIEF ELIGIBILITY CRITERIA: Inclusion: localized TNBC enrolled onto ARTEMIS and determined to have CID at the time of response assessment after anthracycline chemotherapy, adequate organ, bone marrow and cardiac parameters. Exclusion: prior immunotherapy, IBC, history of autoimmune disease, HIV, Hep-B, Hep-C, active tuberculosis, pregnant.

CORRELATIVE SCIENCE: Evaluate the presence and phenotype of TIL and other immune cell populations in tumor tissue pre/post treatment; determine changes in expression of co-stimulatory and co-inhibitory molecules on tumor cells and immune cells in the microenvironment; evaluate the immune repertoire and cytokine responses in serially collected peripheral blood mononuclear cells and serum respectively.

Citation Format: Litton JK, Moulder S, Helgason T, Clayborn AR, Rauch GM, Gilcrease M, Adrada BE, Huo L, Hess KR, Symmans WF, Thompson A, Tripathy D, Mittendorf EA. Triple-negative first-line study: Neoadjuvant trial of nab-paclitaxel and atezolizumab, a PD-L1 inhibitor, in patients with triple negative breast cancer (TNBC) (NCT02530489) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT2-01-14.

Abstract P4-03-14: Stem cell and macrophage markers are enriched in normal tissue adjacent to inflammatory breast cancer

Introduction: We hypothesized that normal breast tissue in inflammatory breast cancer (IBC) patients contains intrinsic differences, including increased mammary stem cells and macrophage infiltration, which may promote the IBC phenotype.

Materials and Methods: Normal breast tissue at least 5cm away from primary tumors were obtained from mastectomy specimens. This included an initial cohort of 8 IBC patients and 60 non-IBC patients followed by a validation cohort of 19 IBC patients and 25 non-IBC patients. Samples were immunostained for either CD44+CD49f+CD133/2+ stem cell markers or the CD68 macrophage marker and correlated with IBC status. Automated quantitation of positive cells was employed for the validation cohort. We also examined the association between IBC status and previously published tumorigenic stem cell and IBC tumor signatures in the validation cohort samples.

Results: 8 of 8 IBC normal tissue samples expressed CD44+CD49f+CD133/2+ stem cell markers in the initial cohort as opposed to 0/60 non-IBC normal tissue samples (p=0.001). Similarly, the median number of CD44+CD49f+CD133/2+ cells was 25.7 in the IBC validation cohort as opposed to 14.2 in the non-IBC validation cohort (p=0.007). 7 of 8 IBC samples expressed CD68+ macrophages in initial cohort as opposed to 12/48 non-IBC samples (p=0.001). In the validation cohort the median number of CD68+ cells was 3.7 in the IBC cohort vs 1.0 in the non-IBC cohort (p=0.06). Normal tissue of IBC patients was positively associated with a tumorigenic stem cell signature (p=0.02) and with a 79-gene IBC gene signature (p<0.001).

Conclusions: Normal tissue from IBC patients is enriched for both mammary stem cells and macrophages. Further, normal tissue of IBC patients has higher association with both a tumorigenic stem cell signature and IBC-specific tumor signature. Collectively, these data suggest that normal tissue from IBC patients is distinct from non-IBC normal tissue and may support the hypothesis that a primed normal breast contributes to the development of IBC symptoms upon oncogenic insult. Validation of these results in additional normal tissue in cancer-free women would better determine causality.

Citation Format: Reddy JP, Atkinson RL, Larson RA, Burks JK, Smith D, Debeb BG, Ruffell B, Creighton C, Reuben JM, Krishnamurthy S, Symmans WF, Brewster A, Van Laere SJ. Stem cell and macrophage markers are enriched in normal tissue adjacent to inflammatory breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-03-14.

Abstract OT3-02-05: NCI-2016-00367: A phase IIB study of neoadjuvant ZT regimen (enzalutamide therapy in combination with weekly paclitaxel) for androgen receptor (AR)-positive triple-negative breast cancer (TNBC)

BACKGROUND: Approximately 50% of TNBC expresses AR by immunohistochemical (IHC) staining. Luminal androgen receptor (LAR) subtype is heavily enriched in hormonally regulated genes, yet negative for ER by IHC. LAR is associated with low pCR rates and long survival. Preclinical data have shown that taxanes inhibit translocation of AR from the cytoplasm to the nucleus where AR is activated. Combining paclitaxel with enzalutamide may inhibit the AR pathway synergistically thereby increasing pCR rates. We hypothesized that patients with AR-positive TNBC who have chemo-insensitive disease (CID) after initial anthracycline-based chemotherapy treated with ZT would have higher RCB-0 and RCB-I rates than those who receive conventional taxane-based chemotherapy. Our team developed a clinical trial to identify patients with CID (ARTEMIS: A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival). In the ARTEMIS trial, treatment-naïve patients with localized TNBC undergo a pretreatment biopsy and then begin anthracycline-based chemotherapy. Molecular testing results and radiographic response assessment are used to identify CID and will guide the second phase of neoadjuvant chemotherapy (NACT) to overcome CID.

PRIMARY OBJECTIVE: To determine RCB-0 and RCB-I rates of patients with TNBC who have CID to initial anthracycline-based chemotherapy and who received ZT.

TRIAL DESIGN AND STATISTICAL METHODS: Patients with CID from the ARTEMIS trial can enroll in the 12-week ZT (paclitaxel, 80 mg/m2 intravenously per week; enzalutamide, 160 mg orally per day). We will define pCR (RCB-0) or RCB-I as a response, using a Simon optimal 2-stage design with alpha=beta=10% and then setting the threshold for an acceptable pCR or RCB-I rate at 20%. We will enroll 12 patients into the first stage. If no patients experience pCR or RCB-I, we will stop the study after the first stage. If at least 1 patient experiences pCR or RCB-I, we will enroll 25 more patients for a total of 37 patients. We would declare the treatment worthy of further study if at least 4 of the 37 patients experience pCR or RCB-I. This design has a 54% probability of early termination after the first stage if the true pCR or RCB-I probability is 5%. Because patients with CID have a very low chance (5%) of achieving pCR with additional chemotherapy, improving pCR rates to 20% in this patient population would be clinically meaningful.

BRIEF ELIGIBILITY CRITERIA: Inclusion criteria: Primary invasive TNBC patients who have CID under the ARTEMIS trial; AR+ ≥1% nuclear staining by IHC; and adequate physical, organ, bone marrow, and cardiac functions. Exclusion criteria: Pregnant or lactating patients, history of colitis or absorption abnormality, known or suspected brain metastasis or leptomeningeal disease, or history of seizure.

CORRELATIVE SCIENCE: Enumeration of circulating tumor cells (CTCs) and expression of CTC-related gene transcripts will be measured to correlate CTC characteristics and/or gene profiles related to the AR pathway and treatment response to ZT.

Citation Format: Fujii T, Lim B, Helgason T, Hess KR, Gilcrease MZ, Willey JS, Tripathy D, Litton JK, Moulder S, Krishnamurthy S, Yang W, Reuben JM, Symmans WF, Ueno NT. NCI-2016-00367: A phase IIB study of neoadjuvant ZT regimen (enzalutamide therapy in combination with weekly paclitaxel) for androgen receptor (AR)-positive triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-02-05.

Abstract P5-11-18: Trajectory of patient (Pt) reported physical function (PF) during and after neoadjuvant chemotherapy in the I-SPY 2 trial

Background

Patients (pts) receiving chemotherapy for breast cancer experience toxicities impacting short and long-term quality of life (QOL). Within I-SPY 2, a trial adaptively randomizing stage II/III breast cancer pts to neoadjuvant chemotherapy +/- an investigational agent, we are collecting pt reported outcome (PRO) data to understand the impact of investigational agents on QOL. This PRO sub-study provides a unique opportunity to study QOL longitudinally and explore how pt and tumor characteristics, exposure to investigational therapies, and surgical outcome impact QOL.

Methods

Pts enrolled in this trial receive paclitaxel (T) +/- an investigational agent for 12 weeks followed by 4 cycles of doxorubicin and cyclophosphamide (AC). Surveys include the EORTC QLQ-C30 and BR-23, and PROMIS measures for QOL metrics including but not limited to physical function (PF), anxiety, and depression. Surveys are administered pre-chemotherapy to 2 years post-surgery. PF data from the EORTC and PROMIS instruments was analyzed for 238 pts at 5 sites (UCSF, UCSD, U of Pennsylvania, U of Minnesota, and Swedish Cancer Center). 48 pts completed baseline, inter-regimen (between T and AC), pre-operative and post-surgery surveys. Of the 48 pts 32 completed a 6-month follow up (FUP) and 31 completed a 1-year FUP survey. A linear mixed effect model, adjusting for HER2 status and treatment type was used to evaluate changes in PF over time. Sample size is small and statistics are descriptive rather than inferential.

Results

Median age of pts in this analysis was 50 (range 27-72).

Table 1 shows PROMIS & EORTC PF scores in this cohort.Time Point  PROMISEORTC  nMeanSEMeanSEPre-TreatmentAll4852.51.092.02.0 HER2+1553.51.594.12.2 HER2-3352.11.391.12.8Inter-RegimenAll4845.51.282.22.7 HER2+1548.62.384.44.2 HER2-3344.11.381.23.4Pre-SurgeryAll4843.91.179.42.3 HER2+1545.12.275.34.1 HER2-3343.41.381.32.86-Month FUPAll3248.11.487.41.9 HER2+1247.52.285.03.3 HER2-2048.41.888.92.41 Year FUPAll3148.91.488.43.1 HER2+949.12.988.95.4 HER2-2248.81.788.33.8

At baseline, mean PROMIS PF scores were higher than the US average (mean = 50) but declined as expected throughout treatment. HER2+ patients experienced a similar degree of recovery as HER2- pts post-surgery despite adjuvant treatment with Herceptin. Analysis of post-operative PROMIS PF indicated an average score within the U.S. general population (mean =50) but did not return to higher functioning seen at baseline levels (mean 52.5, p-value < 0.05). Analysis of the EORTC PF sub-scale demonstrated a similar trend; however, the baseline and post-operative difference was not significant (p-value=0.15 for both FUP). Finding supports PROMIS PF ability to measure high functioning cancer patients.

Conclusions: Among a subset of pts who completed all surveys in the I-SPY 2 QOL substudy, PF did not return to baseline at 6-12 months post-operatively. Through transition to an electronic platform of data collection we hope to improve compliance with survey completion. We continue to analyze other QOL measures and plan to correlate QOL data with treatment arm, adverse events, comorbidities, and response to neoadjuvant treatment.

Citation Format: Shah M, Jensen R, Yau C, Straehley I, Berry DA, DeMichele A, Buxton MB, Hylton NM, Perlmutter J, Symmans WF, Tripathy D, Yee D, Wallace A, Kaplan HG, Clark A, Chien AJ, I-SPY 2 Investigators, Esserman LJ, Melisko ME. Trajectory of patient (Pt) reported physical function (PF) during and after neoadjuvant chemotherapy in the I-SPY 2 trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-11-18.

Abstract P6-09-23: SETER/PR - A robust 18-gene predictor of sensitivity to endocrine therapy in metastatic breast cancer

Rationale: A robust index for gene expression related to activity of estrogen (ESR1) and progesterone (PGR) receptors could predict sensitivity to endocrine therapy in metastatic breast cancer.

Methods: Transcripts correlated with ESR1 and PGR expression in 389 hormone receptor-positive breast cancer samples (Affymetrix U133A microarrays) were ranked for reliability according to their pre-analytical (intratumoral heterogeneity, biopsy type) and analytical reproducibility. Eighteen target and ten reference genes were selected and summarized as the SETER/PR index. The SETER/PR index was evaluated in a different set of 140 biopsies from distant metastases of hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer, and in additional pre-analytical and analytical sample cohorts. Thereafter, SETER/PR was translated to a customized format for application to formalin-fixed and paraffin-embedded (FFPE) sections.

Results: Higher SETER/PR in a metastasis was associated with longer progression-free survival (PFS, 9 vs. 2 months) and overall survival (OS, 50 vs. 19 months) following endocrine therapy in the cohort with metastatic breast cancer (MBC) and relapsed disease (n=79), so a cut point was defined in that cohort. SETER/PR was also significantly associated with PFS after adjusting for PR status of the metastasis, presence of visceral metastases, number of previous relapse events, and clinical history of previous sensitivity to endocrine therapy (HR 0.485, 95%CI 0.265 – 0.889, p = 0.019). Technically, SETER/PR was highly reproducible under different pre-analytical and analytical conditions, including host organ contamination. The translated SETER/PR assay used a single 10 µm FFPE tissue section, did not require RNA purification, and represented the microarray results from matched fresh samples with excellent agreement (correlation = 0.980, n = 31).

Conclusion: The SETER/PR index is a new biomarker to predict PFS and OS for patients with HR+/HER2- MBC who receive endocrine therapy. The assay is applicable to FFPE tissue sections from small biopsies of metastases. Additional independent (blinded) validation studies will be necessary to confirm these results.Rationale: A robust index for gene expression related to activity of estrogen (ESR1) and progesterone (PGR) receptors could predict sensitivity to endocrine therapy in metastatic breast cancer.

Methods: Transcripts correlated with ESR1 and PGR expression in 389 hormone receptor-positive breast cancer samples (Affymetrix U133A microarrays) were ranked for reliability according to their pre-analytical (intratumoral heterogeneity, biopsy type) and analytical reproducibility. Eighteen target and ten reference genes were selected and summarized as the SETER/PR index. The SETER/PR index was evaluated in a different set of 140 biopsies from distant metastases of hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer, and in additional pre-analytical and analytical sample cohorts. Thereafter, SETER/PR was translated to a customized format for application to formalin-fixed and paraffin-embedded (FFPE) sections.

Results: Higher SETER/PR in a metastasis was associated with longer progression-free survival (PFS, 9 vs. 2 months) and overall survival (OS, 50 vs. 19 months) following endocrine therapy in the cohort with metastatic breast cancer (MBC) and relapsed disease (n=79), so a cut point was defined in that cohort. SETER/PR was also significantly associated with PFS after adjusting for PR status of the metastasis, presence of visceral metastases, number of previous relapse events, and clinical history of previous sensitivity to endocrine therapy (HR 0.485, 95%CI 0.265 – 0.889, p = 0.019). Technically, SETER/PR was highly reproducible under different pre-analytical and analytical conditions, including host organ contamination. The translated SETER/PR assay used a single 10 µm FFPE tissue section, did not require RNA purification, and represented the microarray results from matched fresh samples with excellent agreement (correlation = 0.980, n = 31).

Conclusion: The SETER/PR index is a new biomarker to predict PFS and OS for patients with HR+/HER2- MBC who receive endocrine therapy. The assay is applicable to FFPE tissue sections from small biopsies of metastases. Additional independent (blinded) validation studies will be necessary to confirm these results.

Citation Format: Sinn BV, Tsai T-H, Lau R, Fu C, Gould R, Murthy R, King TA, Hatzis C, Kwiatkowski DN, Valero V, Symmans WF. SETER/PR - A robust 18-gene predictor of sensitivity to endocrine therapy in metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-23.

Abstract CT076: Women's triple-negative, first-line treatment: Improving outcomes in triple-negative breast cancer using molecular triaging and diagnostic imaging to guide neoadjuvant therapy

BACKGROUND: Triple negative breast cancer (TNBC) is a heterogeneous disease with identified biologically diverse subtypes. There are known differences in response to neoadjuvant chemotherapy (NACT) in TNBC patients with 50% having excellent response to treatment (pCR/Residual cancer burden [RCB]-I) and good survival prognosis, while 50% demonstrate marked residual disease (RCB-II-III) with significantly worse prognosis. Lack of response early into NACT indicates a low chance (5%) of achieving pCR. Thus, it is important to develop diagnostic platforms predictive of pCR, in order to direct patients with responsive disease toward standard NACT and non-responsive disease toward experimental therapies within clinical trials.

METHODS: All patients will undergo biopsy of the primary tumor for molecular analyses, but will then be randomized 2:1 to know these results versus not (control). An algorithm that incorporates pre-defined genomic signatures will determine predicted sensitivity to NACT, which contains anthracyclines and taxanes. All patients will begin standard of care anthracycline based NACT with diagnostic imaging to assess response after 4 cycles. Patients who fit molecular/imaging criteria for non-responsive disease will undergo a second biopsy to confirm tumor cellularity and be offered a clinical trial based upon the initial molecular profiling (if known) or based upon physician/patient choice if randomized to the control arm. Patients who fit criteria for responsive disease in either arm will be recommended to continue with taxane-based NACT. Rates of excellent therapy response (pCR/RCB-I) will be compared between the randomized arms. One additional core and two FNAs will be obtained at the time of each planned biopsy and used to generate cell lines and PDX models for study of therapy resistance.

Inclusion criteria include: Tumor size ?1.5 cm diameter; TNBC by standard assays; ?18 years of age; LVEF ?50%; adequate organ and bone marrow function. Exclusion criteria include: Stage IV disease; history of invasive cancer within 5 years; excisional biopsy of the primary tumor; biopsy site changes that limit response assessment; medically unfit for chemotherapy; prior anthracycline; >grade II neuropathy; Zubrod performance status of >2; history of serious cardiac event.

The study was activated on 11/09/2015. To date, 10 patients have been enrolled.

PRIMARY AIM: Prospectively determine the impact of a molecular diagnostic/imaging platform to guide neoadjuvant therapy in patients with localized invasive TNBC.

SECONDARY AIMS: -Determine the impact of targeted therapy to improve pathological response in chemotherapy resistant disease in patients who are selected for clinical trials based upon molecular features of their tumors. -Generate a translational research platform to facilitate molecular diagnostic development, study mechanisms of acquired resistance, and inform the next generation of clinical trials.

STATISTICAL METHODS: A maximum of 360 patients will be randomized (2:1)using a group sequential design with one-sided O’Brien-Fleming boundaries, with two equally spaced binding interim tests for futility and superiority and one final test, having an overall Type I error .05 and power .80 to detect an improvement in pCR/RCB-I from 50% to 64%.

Citation Format: Zahi Mitri, Naoto T. Ueno, Wei Yang, Vicente Valero, Jennifer K. Litton, Rashmi Murthy, Bora Lim, Nuhad K. Ibrahim, Banu K. Arun, Elizabeth A. Mittendorf, Kelly K. Hunt, Funda Meric-Bernstam, Alastair Thompson, Michael Gilcrease, Helen Piwnica-Worms, Debasish Tripathy, William Fraser Symmans, Stacy Moulder-Thompson. Women's triple-negative, first-line treatment: Improving outcomes in triple-negative breast cancer using molecular triaging and diagnostic imaging to guide neoadjuvant therapy. [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 CT076.

Abstract P3-07-49: Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial

Background: I-SPY2 is a multicenter phase 2 trial in high risk stage II/III breast cancer (BC) using adaptive randomization within biomarker subtypes to evaluate novel agents added to standard neoadjuvant chemotherapy. The first regimen to graduate based on the predicted probability of a higher pCR rate within predefined subsets was veliparib/carboplatin + paclitaxel (VC+T→AC vs T→AC) in triple negative BC (TNBC). In TNBC the residual cancer burden (RCB) is prognostic, whether as a continuous index or grouped into classes, with pCR (RCB-0) and RCB-I classes having identical survival. Therefore, we evaluated the use of RCB to further discriminate between investigational and control arms.

Methods: Site pathologists reported RCB for 99% of subjects in the primary efficacy analysis based on pCR (n=114/115). We compared the distribution of RCB reported as a continuous index in each treatment-subset combination to matched concurrently randomized controls using the Wilcoxon rank sum test for RCB index, and Fisher's Exact test for RCB classes (RCB-0/I vs RCB-II/III). The statistics are descriptive rather than inferential, and given the small sample size have no claim on generalizability. We modified the Bayesian model used to compute the estimated probability of success in a future, randomized, phase 3 trial of 300 subjects, if response were defined by either pCR or RCB-I (RCB0/I), or separately if it were defined by pCR alone.

Results: VC+T→AC led to a significantly lower RCB index than T→AC in TNBC (p=0.0021), with a near-significant trend when those with pCR were excluded (p=0.06). There was no significant difference in RCB distributions in the other breast cancer subtypes treated. In TNBC, the odds ratio (OR) for achieving RCB-0/I in the VC+T→AC arm vs control was 8.2 (95% confidence interval (CI): 2.1–35), whereas the OR for achieving pCR was 4.56 (95% CI: 1.25–19.53). The simulations using response information from I-SPY2 to predict the probability of success for VC+T→AC for TNBC in a future phase 3 trial estimated this probability to be 0.99 if modeled using RCB-0/I as the response endpoint, and 0.90 if modeled using pCR as the response endpoint.

Conclusions: Use of RCB index and classes provided additional insight into the effect of adding VC to T, appearing to magnify the improved treatment response that had been observed with pCR rates in TNBC. It will be important to test in randomized trials whether a decrease in the RCB index relative to controls, and/or increased rates of RCB-0/I class, are predictive of survival benefit in TNBC.

Citation Format: Liu MC, Symmans WF, Yau C, Chen Y-Y, Rugo HS, Olopade OF, Datnow B, Chen B, Feldman M, Kallakury B, Hasteh F, Tickman R, Ritter J, Troxel M, Mhawech-Fauceglia P, Duan X, Berry D, Esserman L, DeMichele A. Residual cancer burden (RCB) with veliparib/carboplatin in the I-SPY2 trial. [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 P3-07-49.

Abstract P5-08-04: Bioscore: A novel staging system for breast cancer patients receiving neoadjuvant chemotherapy

Background: We previously described a novel breast cancer staging system, the CPS+EG score, which incorporates pretreatment clinical stage, post-treatment pathologic stage, estrogen receptor (ER) status and nuclear grade to create an ordinal scale that is predictive of disease-specific survival (DSS) after receipt of neoadjuvant chemotherapy. The prior work predated (1997-2005) routine use of trastuzumab for patients with HER2+ disease. The current study was undertaken to update the staging system with a more contemporary cohort of patients to include patients with HER2+ disease receiving trastuzumab. The impact of using 1% as the cutoff for ER-positivity was also assessed.

Methods: A cohort of 2377 patients treated with neoadjuvant chemotherapy from 2005-2012 was identified. Clinicopathologic characteristics, treatment regimens and patient outcomes were recorded. Patient scores were computed using two versions of the CPS+EG staging system with ER status categorized as positive if >10% or if >1%. Fits of the Cox proportional hazards (PH) model for the two sets of prognostic scores were compared using the Akaike Information Criterion (AIC). HER2 status was then added to the model and the likelihood ratio test was used to determine the improvement in fit.

Results: Median follow-up time was 4.2 years (range, 0.5 to 11.7). Five year DSS was 89% (95% CI: 87%-90%). This cohort validated our previous finding that the CPS+EG score facilitates more refined categorization into prognostic subgroups than initial clinical or final pathologic stage alone (table). The AIC demonstrated that the CPS+EG model fits were nearly identical for ER status categorized using either cutoff, though the fit was slightly better for the >1% cutoff. There were 591 HER2+ patients included; all of them received trastuzumab-based chemotherapy. The improvement in the fit of the model when HER2 status was added was highly significant (p=0.00005) and incorporation of HER2 into the CPS+EG staging system by adding one additional point for HER2-negative status defined the bioscore (table) which again stratified patients with respect to prognosis.

Conclusion: The current study demonstrates a novel bioscore that significantly improves a previously validated prognostic score in patients receiving neoadjuvant chemotherapy and allows the staging system to be applied to patients with HER2+ disease. We recommend that biologic markers and response to treatment be incorporated into the forthcoming revision of the AJCC staging system.

Clinical Stage5-yr DSS (95%CI)Pathologic Stage5-yr DSS (95%CI)CPS+EG Score (1% cutoff for ER+)5-yr DSS (95%CI)Bioscore5-yr DSS (95%CI)0 097% (95-98%)098% (92-100%)097% (78-10)%)IA96% (75-99%)IA95% (92-97%)198% (96-99%)199% (95-100%)IIA96% (94-97%)IB90% (76-98%)294% (91-95%)297% (95-98%)IIB90% (87-92%)IIA91% (87-94%)387% (84-90%)393% (90-95%)IIIA85% (80-89%)IIB86% (81-90%)475% (69-80%)486% (82-89%)IIIB78% (70-85%)IIIA80% (75-84%)552% (40-63%)571% (64-77%)IIIC76% (70-81%)IIIB64% (42-80%)60648% (35-60%) IIIC64% (55-72%)   70

Citation Format: Mittendorf EA, Vila J, Tucker SL, Chavez-MacGregor M, Smith BD, Symmans WF, Sahin AA, Hortobagyi GN, Hunt KK. Bioscore: A novel staging system for breast cancer patients receiving 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 P5-08-04.

Recommendations for standardized pathological characterization of residual disease for neoadjuvant clinical trials of breast cancer by the BIG-NABCG collaboration

Neoadjuvant systemic therapy (NAST) provides the unique opportunity to assess response to treatment after months rather than years of follow-up. However, significant variability exists in methods of pathologic assessment of response to NAST, and thus its interpretation for subsequent clinical decisions. Our international multidisciplinary working group was convened by the Breast International Group-North American Breast Cancer Group (BIG-NABCG) collaboration and tasked to recommend practical methods for standardized evaluation of the post-NAST surgical breast cancer specimen for clinical trials that promote accurate and reliable designation of pathologic complete response (pCR) and meaningful characterization of residual disease. Recommendations include multidisciplinary communication; clinical marking of the tumor site (clips); and radiologic, photographic, or pictorial imaging of the sliced specimen, to map the tissue sections and reconcile macroscopic and microscopic findings. The information required to define pCR (ypT0/is ypN0 or ypT0 yp N0), residual ypT and ypN stage using the current AJCC/UICC system, and the Residual Cancer Burden system were recommended for quantification of residual disease in clinical trials.

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

BACKGROUND

The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC.

DESIGN

A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches.

CONCLUSIONS

The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.

Residual proliferative cancer burden to predict long-term outcome following neoadjuvant chemotherapy

BACKGROUND

The purpose of this study was (i) to test the hypothesis that combining Ki67 with residual cancer burden (RCB) following neoadjuvant chemotherapy, as the residual proliferative cancer burden (RPCB), provides significantly more prognostic information than either alone; (ii) to determine whether also integrating information on ER and grade improves prognostic power.

PATIENTS AND METHODS

A total of 220 patients treated with neoadjuvant chemotherapy for primary breast cancer were included in the study. Analyses employed a Cox proportional hazard model. Prognostic indices (PIs) were created adding in Ki67, grade and ER to RCB. Leave-one-out cross-validation was used to reduce bias. The overall change in χ(2) of the best model for each index was used to compare the prognostic ability of the different indices.

RESULTS

All PIs provided significant prognostic information for patients with residual disease following neoadjuvant chemotherapy. RPCB (χ(2) = 61.4) was significantly more prognostic than either RCB (χ(2) = 38.1) or Ki67 (χ(2) = 53.8) alone P < 0.001. A PI incorporating RCB, Ki67 grade and ER provided the most prognostic information overall and gave χ(2) = 73.8.

CONCLUSIONS

This study provides proof of principle that the addition of post-treatment Ki67 to RCB improves the prediction of long-term outcome. Prediction may be further improved by addition of post-treatment grade and ER and warrants further investigation for estimating post-neoadjuvant risk of recurrence. These indices may have utility in stratifying patients for novel therapeutic interventions after neoadjuvant chemotherapy.

Abstract 1186: Patient-derived breast cancer xenografts demonstrate molecular evolution in the phosphatidylinositol 3-kinase pathway upon engraftment

Introduction: Patients with breast cancer who do not respond to standard systemic therapy have a poor prognosis. There is a pressing need to develop in vivo models of breast cancer to test novel therapeutics. Directly implanting tumors into immunodeficient mice may more accurately recapitulate human tumor characteristics compared to cell line xenografts. We tested the feasibility of generating breast cancer xenografts (BCXs) and the effect of serial passage on tumor characteristics.

Methods: Tumors from 48 patients with breast cancer were implanted. Patient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, and a series of BCXs were characterized with next generation sequencing, molecular inversion probe arrays and reverse phase protein arrays. Results: BCXs were established in 15 (31%) of 48 patients and 13 have been serially passaged. BCX engraftment was higher in patients with triple negative compared to ER or PR+ breast cancer (11 of 18, 61% vs. 4 of 30, 13%, p=0.001), and in patients who received neoadjuvant chemotherapy (13 of 25, 52% vs. 2 of 23, 9%, p=0.002). 7 patients developed metastases after surgery; in 5, BCXs developed before distant relapse. Compared to patient tumors, BCXs demonstrated genomic instability. Although mutation status, copy numbers and proteomic profiles were often maintained, an activating PIK3CA mutation was acquired in one BCX lineage and loss of PTEN in another. Proteomics demonstrated activation in PI3K/mTOR signaling in BCXs compared with patient tumors. Notably, 2 of 48 models demonstrated a transformation to induce mouse tumors.

Conclusions: BCXs can be established prior to relapse from breast cancer, especially in patients with poor response to neoadjuvant chemotherapy. Although molecular profiles of BCX are mostly similar to the patient tumor that was implanted, differences such as aberrations in PI3K signaling can occur. Future studies will determine whether molecular evolution in BCXs reflect that seen upon progression/relapse and the potential of in vivo models for individualization of treatment.

Citation Format: Priscilla F. McAuliffe, Argun Akcakanat, Kurt Evans, Agda Karina Eterovic, Hao Zhao, Ken Chen, Takafumi Sangai, Huiqin Chen, Kim-Anh Do, Ashley M. Holder, Chandeshwar Sharma, William Fraser Symmans, Mihai Gagea, Katherine A. Naff, Aysegul Sahin, Asha S. Multani, Gordon B. Mills, Ana Maria Gonzalez-Angulo, Funda Meric-Bernstam. Patient-derived breast cancer xenografts demonstrate molecular evolution in the phosphatidylinositol 3-kinase pathway upon engraftment. [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 1186. doi:10.1158/1538-7445.AM2014-1186

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

BACKGROUND

The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC.

DESIGN

A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches.

CONCLUSIONS

The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.

Open-label randomized clinical trial of standard neoadjuvant chemotherapy with paclitaxel followed by FEC versus the combination of paclitaxel and everolimus followed by FEC in women with triple receptor-negative breast cancer†

BACKGROUND

Everolimus synergistically enhances taxane-induced cytotoxicity in breast cancer cells in vitro and in vivo in addition to demonstrating a direct antiproliferative activity. We aim to determine pharmacodynamics changes and response of adding everolimus to standard neoadjuvant chemotherapy in triple-negative breast cancer (TNBC).

PATIENTS AND METHODS

Phase II study in patients with primary TNBC randomized to T-FEC (paclitaxel 80 mg/m(2) i.v. weekly for 12 weeks, followed by 5-fluorouracil 500 mg/m(2), epirubicin 100 mg/m(2), and cyclophosphamide 500 mg/m(2) every 3 weeks for four cycles) versus TR-FEC (paclitaxel 80 mg/m(2) i.v. and everolimus 30 mg PO weekly for 12 weeks, followed by FEC). Tumor samples were collected to assess molecular changes in the PI3K/AKT/mTOR pathway, at baseline, 48 h, 12 weeks, and at surgery by reverse phase protein arrays (RPPA). Clinical end points included 12-week clinical response rate (12-week RR), pathological complete response (pCR), and toxicity.

RESULTS

Sixty-two patients were registered, and 50 were randomized, 27 received T-FEC, and 23 received TR-FEC. Median age was 48 (range 31-75). There was downregulation of the mTOR pathway at 48 h in the TR-FEC arm. Twelve-week RR by ultrasound were 29.6% versus 47.8%, (P = 0.075), and pCR were 25.9% versus 30.4% (P = 0.76) for T-FEC and TR-FEC, respectively. mTOR downregulation at 48 h did not correlate with 12-week RR in the TR-FEC group (P = 0.58). Main NCI grade 3/4 toxicities included anemia, neutropenia, rash/desquamation, and vomiting in both arms. There was one case of grade 3 pneumonitis in the TR-FEC arm. No grade 3/4 stomatitis occurred.

CONCLUSION

The addition of everolimus to paclitaxel was well tolerated. Everolimus downregulated mTOR signaling but downregulation of mTOR at 48 h did not correlate with 12-week RR in the TR-FEC group.

CLINICAL TRIAL NUMBER

NCT00499603.

Which threshold for ER positivity? a retrospective study based on 9639 patients

BACKGROUND

Guidelines for the use of chemotherapy and endocrine therapy recently recommended that estrogen receptor (ER) status be considered positive if ≥1% of tumor cells demonstrate positive nuclear staining by immunohistochemistry. In clinical practice, a range of thresholds are used; a common one is 10% positivity. Data addressing the optimal threshold with regard to the efficacy of endocrine therapy are lacking. In this study, we compared patient, tumor, treatment and survival differences among breast cancer patients using ER-positivity thresholds of 1% and 10%.

METHODS

The study population consisted of patients with primary breast carcinoma treated at our center from January 1990 to December 2011 and whose records included complete data on ER status. Patients were separated into three groups: ≥10% positive staining for ER (ER-positive ≥10%), 1%-9% positive staining for ER (ER-positive 1%-9%) and <1% positive staining (ER-negative).

RESULTS

Of 9639 patients included, 80.5% had tumors that were ER-positive ≥10%, 2.6% had tumors that were ER-positive 1%-9% and 16.9% had tumors that were ER-negative. Patients with ER-positive 1%-9% tumors were younger with more advanced disease compared with patients with ER-positive ≥10% tumors. At a median follow-up of 5.1 years, patients with ER-positive 1%-9% tumors had worse survival rates than did patients with ER-positive ≥10% tumors, with and without adjustment for clinical stage and grade. Survival rates did not differ significantly between patients with ER-positive 1%-9% and ER-negative tumors.

CONCLUSIONS

Patients with tumors that are ER-positive 1%-9% have clinical and pathologic characteristics different from those with tumors that are ER-positive ≥10%. Similar to patients with ER-negative tumors, those with ER-positive 1%-9% disease do not appear to benefit from endocrine therapy; further study of its clinical benefit in this group is warranted. Also, there is a need to better define which patients of this group belong to basal or luminal subtypes.

Abstract P3-01-04: Obesity induces functional transcriptomic changes enhancing the cancer hallmarks of estrogen receptor-positive breast cancer

Obesity increases the risk of cancer death among postmenopausal women with estrogen receptor-positive (ER+) breast cancer, but the direct evidence for the mechanisms is lacking. The purpose of this study is to demonstrate direct evidence for the mechanisms mediating this epidemiologic phenomenon. Transcriptomic profiles of pretreatment biopsies from a prospective cohort of 137 ER+ breast cancer patients were analyzed. A transgenic and an orthotopic/syngeneic obese mouse models were created to phenocopy obese patients and evaluate the effect of obesity on breast carcinogenesis and tumor progression, and to explore further direct mechanisms. Functional transcriptomic analysis of untreated human ER+ breast cancer revealed that obesity was associated with increased insulin signaling among others. Many of the functional changes in obese patients were linked to cancer hallmarks. Obese mouse models recapitulated the functional transcriptomic landscape of obesity-associated changes seen in human ER+ breast cancer and demonstrated the role of the Akt/mTOR pathway in obesity-induced breast carcinogenesis and tumor progression. Functional transcriptomic analysis identified 85 biological functions common to humans and mice. An in vitro co-culture model revealed that adipocyte-secreted adipokines (e.g., TIMP-1) regulate adipocyte-induced breast cancer cell proliferation and invasion. The human transcriptomic data provided direct evidence for the roles of hyperinsulinemia, estrogen signaling, adipokine secretion, and inflammation in the link between obesity and ER+ breast cancer. Our animal experiments provide strong evidence for the causal relationship between obesity and accelerated carcinogenesis and cancer progression and for potential therapeutic interventions by blocking these signaling pathways.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-01-04.

Abstract P4-05-09: Estrogen receptor (ER) mRNA expression and molecular subtype distribution in breast cancers that are ER-negative but progesterone receptor-positive by immunohistochemistory

Purpose: We examined Estrogen receptor (ER) mRNA expression and molecular subtypes in breast cancers that are Progesterone receptor (PR) positive but ER negative by immunohistochemistry (IHC) to assess if these cancers molecularly resemble true ER positive cancers.

Patients and Methods: Patients were those with newly diagnosed ERBB2-negative breast cancer treated with neoadjuvant chemotherapy containing sequential taxane and antheracycline-based regimens (then endocrine therapy if ER-positive by IHC). ER and PR status was determined by IHC in 501 primary breast cancers in routine pathology laboratory. Gene expression profiling was done with the Affymetrix U133A gene chip (Gene Expression Omnibus number: GSE25066). We compared expressions of ESR1, MKI67 mRNA and molecular subtypes determined by the PAM 50 classifier between IHC-ER-positive/PR-positive (n = 223), ER-positive/PR-negative (n = 73), ER-negative/PR-positive (n = 20), and ER-negative/PR-negative (n = 185) cancers. We also plotted survival curves by ER and PR status based on IHC.

Results: ER or PR positivity by IHC was defined ≥ 1% staining. ER positivity by ESR1 mRNA expression was defined as &gt; 10.18 previously published. Among the IHC-ER-negative/PR-positive, ER-positive/PR-negative, and both ER/PR-positive, and ER/PR-negative patients, 25%, 79%, 96% and 12% were positive by ESR1 mRNA expression, respectively. The average ESR1 expression was significantly higher in the ER/PR-positive and ER-positive/PR-negative cohorts compared with the ER-negative/PR-positive or ER/PR-negative cohorts. The average MKI67 mRNA expression was significantly higher in the ER-negative/PR-positive and ER/PR-negative cohorts. Among the ER-negative/PR-positive patients, 15% were luminal A, 5% were Luminal B, and 65% were basal like; among the ER-positive/PR-negative patients, 59% were luminal type. The relapse free survival rate of ER-negative/PR-positive patients was equivalent to ER/PR-positive or ER-positive/PR-negative, and significantly better than that of the ER-negative/PR-negative cohort.

Conclusion: Only 20-25% of the ER-negative/PR-positive tumors show molecular features of ER-positive cancers (i.e high ER mRNA expression and luminal molecular class). These cancers also have higher proliferation rate than ER-positive cancer. However, the survival of these cancers with only chemotherapy is similar to ER-positive cancers with chemotherapy and endocrine therapy, and is better than ER-negative cancers. The contribution of endocrine therapy to this good outcome is to be invested in the future.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-09.

Gene expression profiles of inflammatory breast cancer: correlation with response to neoadjuvant chemotherapy and metastasis-free survival

BACKGROUND

Inflammatory breast cancer (IBC) is an aggressive disease. To date, no molecular feature reliably predicts either the response to chemotherapy (CT) or the survival. Using DNA microarrays, we searched for multigene predictors.

PATIENTS AND METHODS

The World IBC Consortium generated whole-genome expression profiles of 137 IBC and 252 non-IBC (nIBC) samples. We searched for transcriptional profiles associated with pathological complete response (pCR) to neoadjuvant anthracycline-based CT and distant metastasis-free survival (DMFS) in respective subsets of 87 and 106 informative IBC samples. Correlations were investigated with predictive and prognostic gene expression signatures published in nIBC (nIBC-GES). Supervised analyses tested genes and activation signatures of 19 biological pathways and 234 transcription factors.

RESULTS

Three of five tested prognostic nIBC-GES and the two tested predictive nIBC-GES discriminated between IBC with and without pCR, as well as two interferon activation signatures. We identified a 107-gene signature enriched for immunity-related genes that distinguished between responders and nonresponders in IBC. Its robustness was demonstrated by external validation in three independent sets including two IBC sets and one nIBC set, with independent significant predictive value in IBC and nIBC validation sets in multivariate analysis. We found no robust signature associated with DMFS in patients with IBC, and neither of the tested prognostic GES, nor the molecular subtypes were informative, whereas they were in our nIBC series (220 stage I-III informative samples).

CONCLUSION

Despite the relatively small sample size, we show that response to neoadjuvant CT in IBC is, as in nIBC, associated with immunity-related processes, suggesting that similar mechanisms responsible for pCR exist. Analysis of a larger IBC series is warranted regarding the correlation of gene expression profiles and DMFS.

Differential pathologic complete response rates after neoadjuvant chemotherapy among molecular subtypes of triple-negative breast cancer

1005

Background: By gene profiling, Lehmann et al. (J Clin Invest 121:2750-2767, 2011) reported that triple-negative breast cancer (TNBC) can be classified into 6 clusters—basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal stem-like (MSL), and luminal androgen receptor (LAR)—plus an unstable (UNS) cluster. While it is clear that patients with TNBC differently respond to chemotherapy, the clinical relevance of these molecular TNBC subtypes is unknown. Methods: We qualitatively reproduced the Lehmann et al. experiments using Affymetrix CEL files from the public datasets. We identified 130 TNBC gene expression microarrays obtained from 03/00 to 03/10. All patients had received neoadjuvant chemotherapy containing sequential taxane and anthracycline-based regimens and had evaluable pathological tumor response data. Median follow-up was 68.1 months. (5.1-147.5). We classified TNBC samples using Lehmann’s gene signatures, then performed Fisher's exact test to correlate TNBC subtype and pCR status. To assess the independent utility of TNBC subtype for predicting pCR status, we fit a logistic regression model to our data and used age, clinical stage, treatment regimens, and nuclear grade as potential explanatory factors. We also performed comparison of the subtypes with the PAM50 intrinsic subtypes and RCB index. Results: The BL1 subtype had the highest pCR rate (52%); BL2 and LAR the lowest (0% and 10%, respectively). TNBC subtype and pCR status were significantly associated (p = 0.044). TNBC subtype was an independent predictor of pCR status (p = 0.022) by a likelihood ratio test.The Lehmann’s subtype classification better predicted pCR status than did the PAM50 intrinsic subtypes (basal-like vs. non basal-like). Conclusions: Dividing TNBC into 7 subtypes predicts high vs. low pCR rate. The 7-subtype classification may lead to innovative personalized medicine strategies for patients with TNBC. There is a need for prospective validation of the hypothesis that pCR rates associated with the seven TNBC subtypes will predict long-term patient outcome.

Correlation of intratumor gene expression heterogeneity with chemotherapy sensitivity in breast cancer

1013

Background: The goal of this study was to develop a method to quantify intratumor heterogeneity of cancers using gene expression data. We compared gene expression heterogeneity between different molecular subtypes of breast cancer and between basal like cancers with or without pathologic complete response (pCR) to neoadjuvant chemotherapy. Methods: Affymetrix U133A gene expression data of 335 stage I-III breast cancers were analyzed. Molecular class was assigned using the PAM50 predictor. All patients received neoadjuvant chemotherapy. We measured tumor heterogeneity by the Gini index (GI) calculated individually for each case over the expression of all probe sets and random subsets. The GI was used as a metric of inequality of gene expression distributions between cases. The higher the GI, the greater the inequality of the expression distribution. Results: Basal like cancers (n=138) had greater heterogeneity than luminal cancers (n=197) (mean GI values 24.51 vs 23.05, p<0.001) and luminal B (n=71) cancers had greater heterogeneity compared to Luminal A (n=126) cancers (24.49 vs 22.25, p<0.001). Among the basal-like cancers, those with pCR (n=44) had significantly higher heterogeneity compared to cancers with residual disease (RD, n=94) (26.10 vs 23.77, p<0.001). Significant differences in GI between cancer subtypes remained for as low 2500 randomly selected probe sets. Conclusions: Breast cancer subtypes differ in intratumor gene expression heterogeneity. Greater degree of heterogeneity correlate with greater chemotherapy sensitivity. Importantly, among basal-like cancers only the heterogeneity metric differed significantly between cases with pCR or RD but not individual genes expression values or gene signatures.

Integration of Ki67 with residual cancer burden (RCB) compared to Ki67 or RCB alone to predict long-term term outcome following neoadjuvant chemotherapy

535

Background: RCB and Ki67 after neoadjuvant chemotherapy have each been shown to predict long-term outcome. Their combined use might provide greater prognostic information. RCB requires collection of data beyond that in routine pathological work-up of residual disease, which may not be required when Ki67 is added. Aims: (i) To test the hypothesis that combining Ki67 and RCB as the residual proliferative cancer burden (R-P-CB) provides significantly more prognostic information than either alone. (ii) To determine if a simplified algorithm integrating Ki67 and standard characteristics of residual disease can provide as much information. Methods: Cases at the Royal Marsden Hospital between 2002-2010 were identified and residual disease assessed. The primary endpoint of the study was time to recurrence. The primary analysis compared the prognostic information from Ki67, RCB and R-P-CB. Analyses employed a Cox proportional hazards model. Prognostic indices (PIs) were also created adding Ki67, grade and ER to the RCB and AJCC staging. Leave-one-out cross validation was used to reduce bias. The overall change in chi-square (ΔX2) of the best model for each index was used to compare the prognostic ability of the different indices a ΔX2 of more than 3.84 indicates statistical significance. Results: A total of 222 evaluable patients were included in the study, median age was 50 with a median follow up of 60 months. The addition of Ki67 improved the prognostic power of all indices. The R-P-CB (ΔX2=69.5) was significantly more prognostic than the RCB alone (ΔX2=35) and Ki67 alone (ΔX2=41.4). A novel proliferative residual cancer index (PRECI) using post-treatment values of T size, number of involved lymph nodes, grade, ER status (±) and Ki67 gave ΔX2=81.1 and performed similarly to a model including the RCB, Ki67, ER and grade (ΔX2=80.2). Conclusions: Addition of Ki67 to RCB improved prediction of long-term outcome. In this study, a novel index the PRECI provided as much prognostic information as a more complex assessment involving RCB and warrants further investigation for estimating post-neoadjuvant risk of recurrence.

Breast cancer evaluation and targeted investigational therapy (BEAT-IT): A pilot prospective tissue testing to guide clinical trial selection

532

Background: An increasing number of molecularly targeted drugs are now available in Phase I and II clinical trials. Many of these drugs target specific molecular abnormalities such as mutated, amplified or rearranged genes. Our hypothesis is that cancers that carry a molecular abnormality that corresponds to the mechanism of action of a given investigational drug are more sensitive to that particular drug than other cancers. The objective of this study is to perform molecular analysis of metastatic breast cancer biopsies (bx) using methods already established within CLIA approved laboratories, and to use the results to triage pts to various therapeutic clinical trials or standard of care therapy. Methods: Four core needle biopsies (CNB) and 4 fine needle aspirations (FNA), or 8 FNA are obtained from the most safely accessible metastatic site in a single bx session. Pathological confirmation of successful aspiration is performed. Two core bx (or 4 FNA passes) are formaldehyde fixed and paraffin embedded for Immunohistochemistry (IHC), FISH and mutation analysis (CMS11 or CMS46) and 4 FNA are placed in RNA-later and snap-frozen for transcriptional profiles and storage. Samples are transferred to the Molecular Diagnostic, IHC, and Cytogenetics Laboratories. All reports are included in the electronic medical record. Results: FromFeb 2012 to Jan 2013, 142 pts referred, 128 pts registered, 101 bx completed and 78 (77%) bx with available results. Bx sites included: liver (37), lymph node (26), soft tissue (16), bone (13), lung (5), other (4). Successful results were obtained for IHC: PTEN (73%), AR (78%), MET (73%), FISH: EML4-ALK (78%) and MET (74%), and mutation analysis (76%). To date, there have been no reported hospitalizations, ER visits, bleeding, pain, infection or organ dysfunction at the bx sites. 16 pts have been treated on trials with investigational agents hypothesized to result in response based upon the molecular profile of the tumor. Conclusions: Prospective tissue collection to determine the molecular targets and to evaluate pts for clinical trial selection is feasible and safe.

10-year outcomes of breast cancer patients with histologically confirmed axillary lymph node metastases and pathologic complete response after primary systemic chemotherapy

1017

Background: Pathologic complete response (pCR) of tumors in the breast and axillary lymph nodes (ALN) after primary systemic chemotherapy (PST) is associated with an excellent outcome. A previous analysis showed superior 5-year overall survival (OS) and relapse-free survival (RFS) for patients who achieved an ALN pCR after PST compared to those without a pCR in 5 prospective clinical trials. This study is an expanded analysis of all patients treated with PST at our institution examining the impact of ALN pCR on 10-year OS and RFS. Methods: Patients with clinical stage II/III and pathologically confirmed ALN metastases who underwent PST were categorized into 1 of 2 groups: ALN pCR and ALN residual disease. Additional data were collected, including breast cancer subtype, clinical tumor size, and lymph node staging, pathologic tumor (T) stage, and class of PST. RFS and OS were estimated by the Kaplan-Meier product limit method. Subset analyses were performed on patients with HER2-positive cancer. Results: 1,600 women diagnosed between 1989 and 2007 were identified. Median follow-up was 79 months (5-277); 454 (28.4%) achieved an ALN pCR. ALN pCR was associated with triple-negative and higher grade cancers, lower clinical stage, and lower pathologic breast T stage. 5-year OS and RFS estimates were similar to prior analysis. The 10-year OS was 85% and 58% and the 10-year RFS 83% and 55% (p < 0.001), for patients who achieved an ALN pCR and those with residual ALN disease. For HER2-positive breast cancers, 67.3% of patients who received HER2-targeted therapy achieved an ALN pCR vs. 32.3% without HER2-targeted therapy (p < 0.001). For patients receiving HER2-targeted therapy for HER2-positive breast cancer (n = 153), the 10-year OS was 92% and 52% (p = 0.006), and the 10-year RFS was 89% and 59% (p < 0.001) for those with and without an ALN pCR. Conclusions: ALN pCR is an excellent early surrogate marker for long-term outcome, 10-year RFS and OS. In HER2-positive breast cancers, HER2-targeted therapy is associated with high rates of pCR. Despite the aggressive nature of their disease, patients who achieve ALN pCR with PST have an excellent 10-year prognosis.

Utility of prognostic genomic tests in breast cancer practice: The IMPAKT 2012 Working Group Consensus Statement

BACKGROUND

We critically evaluated the available evidence on genomic tests in breast cancer to define their prognostic ability and likelihood to determine treatment benefit.

DESIGN

Independent evaluation of six genomic tests [Oncotype Dx™, MammaPrint(®), Genomic Grade Index, PAM50 (ROR-S), Breast Cancer Index, and EndoPredict] was carried out by a panel of experts in three parameters: analytical validity, clinical validity, and clinical utility based on the principles of the EGAPP criteria. PANEL STATEMENTS: The majority of the working group members found the available evidence on the analytical and clinical validity of Oncotype Dx™ and MammaPrint(®) to be convincing. None of the genomic tests demonstrated robust evidence of clinical utility: it was not clear from the current evidence that modifying treatment decisions based on the results of a given genomic test could result in improving clinical outcome.

CONCLUSIONS

The IMPAKT 2012 Working Group proposed the following recommendations: (i) a need to develop models that integrate clinicopathologic factors along with genomic tests; (ii) demonstration of clinical utility should be made in the context of a prospective randomized trial; and (iii) the creation of registries for patients who are subjected to genomic testing in the daily practice.

Abstract P1-07-06: Effect of biospecimen variables on proteomic biomarker assessment in breast cancer

Background: PI3K/Akt/mTOR signaling is being actively pursued as a therapeutic target. We sought to determine how tumor heterogeneity and biospecimen variables affect assessment of PI3K/Akt/mTOR pathway activation.

Methods: Intraoperative image-guided core-needle biopsies (CNB) of primary breast tumors were prospectively collected in 53 patients with invasive breast cancer. After surgery, specimens were collected from the center and periphery of the excised tumor. CNB, central and peripheral surgical specimens were assessed with reverse phase proteomic arrays (RPPA), H&E and immunohistochemistry (IHC).

Results: The expression of standard of care markers ER, PR, and HER2 by RPPA correlated well between biospecimen types. Overall, there was a significant correlation between the expression of 132 (86%) of 154 different markers in the center and periphery; the correlation was significantly higher for smaller tumors, and with shorter cold ischemia time. Expression of many investigational prognostic markers and druggable targets on CNB correlated with expression in the surgical specimen (average of center and periphery), while others, such as EGFR and c-MET, had a weak correlation. Of 154 RPPA markers, 132 (86%) were not statistically different between the center and periphery, and 97 (67%) were not different between the CNB and the surgical specimen. On analysis of the PI3K/AKT/mTOR pathway, pAkt S473 and PTEN had a significant correlation between central and peripheral specimens, and between CNB and surgical specimens. However, pAkt S473, pS6 S235/236 and pS6 240/244 levels were higher in CNB than the central specimens both by RPPA and by IHC. When patients were classified by RPPA PI3K pathway activation score, there was a moderate agreement between classification on the CNB and central specimens (Cohen's Kappa 0.539). However 9 of 20 tumors classified as having PI3K activation on CNB were classified as not having pathway activation on central specimens.

Conclusions: There is remarkable homogeneity in expression of biomarkers within a tumor. However, proteomic markers are differentially expressed by biospecimen type and other preanalytic variables. PI3K pathway activation is greater in CNB compared to surgical samples.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-07-06.

Abstract P3-06-14: Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer

Purpose: Triple-negative breast cancer (TNBC) is a highly heterogeneous disease. TNBC patients with pathologic complete response (pCR) have excellent survival, but those with residual disease after neoadjuvant chemotherapy have significantly worse outcome. However, some patients having extensive residual cancer burden after neoadjuvant chemotherapy do not relapse, and we hypothesize that there may be subgroups with diverse prognosis among these chemoresistant TNBC patients.

Methods: Forty-nine cases with residual cancer from 111 TNBC patients treated with neoadjuvant chemotherapy (in M.D. Anderson Cancer Center, 2000–2006) constituted the discovery cohort. Twenty-five chemoresistant samples from 47 neoadjuvant chemotherapy-treated TNBC (in Baylor College of Medicine and Methodist Hospital, 2002–2006) were chosen for validation. Extended validation was performed in 269 operable TNBC predicted to be chemoresistant (using a JAMA-published genomic predictor) from public databases.

Results: By comparing the gene expression data from cases in relapse with those from un-relapsed cases, we established a 7-gene prognostic signature (including AR, ESR2, GATA3, GBX2, KRT16, MMP28, and WNT11) using dChip and gene enrichment analyses. In the discovery cohort, the signature showed positive predictive value (PPV; i.e., cumulative relapse rate of patients predicted to relapse in 3 years) of 95.4% and negative predictive values (NPV; i.e., relapse-free survival of patients predicted not to relapse in 3 years) of 100%. In the validation cohort, the classifier predicted correctly with PPV of 75.0% and NPV of 76.9% at 3 years. Compared with patients predicted not to relapse, those predicted to relapse had a hazard ratio of 3.37 (95% CI, 1.15–9.85) for disease recurrence or death in 3 years. In an extended validation cohort of 269 patients, our signature discriminated chemoresistant TNBC in overall cohort (PPV, 52.4%; NPV, 77.7%; log rank P &lt; 0.0001), or each subset (e.g., log rank p = 0.001 for Rotterdam set; p = 0.013 for Frankfurt set), with adjusted overall hazard ratio of 2.07 (95% CI, 1.26–3.39). This signature was the only marker that could effectively predict the relapse in patients with chemoresistant TNBC. Of note, the subgroup predicted not to relapse was characterized by high expression of luminal-like genes (AR, GATA3), while the subgroup predicted to have high possibility of relapse was characterized by high expression of cancer stem cell and epithelial-to-mesenchymal transition associated genes (WNT11, MMP28). The former corresponded to the luminal AR subtype and the latter to the mesenchymal stem-like subtype, according to Pietenpol's TNBC subtype classification.

Conclusion: We developed a clinically useful prognostic signature for chemoresistant TNBC. For these chemoresistant TNBC patients, new therapeutic strategies targeting AR-activation or cancer stem cells need to be developed.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-14.

Abstract P2-10-10: Clinical implications of molecular heterogeneity in highly proliferative, ER-positive, HER2-negative breast cancer

Objectives: Different clinical behaviors are observed in tamoxifen-treated and untreated ER-positive, HER2-negative highly-proliferative breast cancer (BC) that demonstrate either high (highERS) or low (lowERS) expression of estrogen-related genes (Bianchini SABCS 2011). LowERS tumors are intrinsically endocrine resistant and at significant risk of relapse in the first 5 yrs after diagnosis. We studied lowERS and highERS BC in pts treated with neoadjuvant chemotherapy (NAC) and examined prognostic and predictive markers in the highest risk group of lowERS BC.

Methods: We examined affymetrix gene expression data from 193 ER+/HER2−, high proliferation BC from pts treated with taxane-anthracycline-based NAC followed by endrocrine therapy. Previously defined cut-offs for markers of proliferation (MKS), and estrogen-related genes were applied (Bianchini SABCS 2011). Within the lowERS group, we examined pts treated with no systemic adjuvant therapy (n = 137; 50 events); adjuvant tamoxifen-only (n = 141; 36 events); and NAC (n = 127, 27 RCB0/I). We performed gene enrichment analysis for 2617 gene sets with known biological function (by 5000 random permutations). Primary endpoints were distant event free survival (DEFS) with follow-up censored at 5-yrs and pathological response (pathR) using the residual cancer burden (RCB) (Symmans JCO 2007).

Results: The median follow-up of the NAC series was 3.1yrs. The DEFS at 4yrs was 0.94 [0.87–1.00] and 0.70 [0.60–0.81] in the high and low ERS groups, respectively (p = 0.004) (despite the higher rate of pathR (RCB0/I) to NAC in the low ERS group (9.5% and 21.9%; p = 0.04)). The pathR was prognostic in the lowERS group [HR 9.1 (CI 1.23–67.4); p = 0.009] but not in highERS (p = 0.485). In contrast, a different outcome was observed in BC with RCBII-III, were the 4-yrs DEFS was 0.93 [0.86–1.00] and 0.61 [0.49–0.76] in high and low ERS group, respectively (p = 0.0007). In the lowERS group there was substantial overlap in biological functions associated with prognosis in both tamoxifen-treated and untreated pts. At a conservative threshold of p &lt; 0.0005, 38 gene sets were significant (31 good-prognosis involved in adaptive immune function, inflammation and chemotaxis and 7 poor prognosis gene sets involved in regulation of nuclear division and cell polarity). Only proliferation-related gene sets were predictive of RCB0/I. MKS as a continuous variable was predictive of pathR beyond clinical variables [OR 5.43 (2.04–16.1); p = 0.001].

Conclusions: Among ER+/HER2−, high proliferation BC the highERS group showed a low pathR rate with excellent prognosis even if there was residual disease. The lowERS group showed a higher rate of pathR which was significantly prognostic for good outcome. Lack of pathR in this group predicted for very poor prognosis despite subsequent adjuvant endocrine treatment. The clinical behaviour and aggressiveness of this subgroup is similar to triple negative tumors. The prognostic relevance of immune function provides a rationale for testing immunotherapeutic strategies in this subgroup.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-10-10.

Abstract P1-07-09: Estrogen receptor positivity: 10% or 1%?

Background. Guidelines by the American Society of Clinical Oncology and the College of American Pathologists recently recommended that estrogen receptor (ER) status should be considered positive if 1% of tumor cells demonstrate positive nuclear staining by immunohistochemistry. Historically, 10% nuclear staining defined ER-positive status and impacted decision-making regarding endocrine therapy. Currently, no optimal threshold exists for ER either by clinically validating patient outcomes in prospective clinical trials or independently validated from systematically collected archived specimens from randomized clinical trials. In this study, we examined patient, tumor and treatment differences among patients by ER status: ER-positive ≥10%, ER-positive 1–10% and ER negative (&lt;1%). We compared recurrence-free survival (RFS), disease-specific survival (DSS) and overall survival (OS) among patients with different ER staining categories and adjusted by clinical stage, adjuvant chemo and endocrine therapy.

Method. Patients with primary breast carcinoma treated at our center who had complete ER status from January 1990 to December 2011 were included in this study. Patients were excluded if they presented with recurrent or metastatic disease. For statistical analyses, patients who underwent surgery for breast cancer were separated into three groups: ER-positive ≥10%, ER-positive 1–10% and ER negative. Analyses comparing various clinical and pathologic characteristics among patients with different ER status were performed. Survival rates were calculated by the Kaplan-Meier method.

Result. Patients whose tumors were ER-positive 1–10% (2.7%) were younger (median age 53 Vs. 56 years, P &lt; 0.0001), more likely to have invasive ductal carcinoma histology with more advanced disease (clinical stage II/III 50.4% Vs. 37.3%, p &lt; 0.0001), and were more likely to receive neoadjuvant chemotherapy (40.9% vs. 25.6%, P &lt; 0.0001), adjuvant chemotherapy (45.5% vs. 31.2%, P &lt; 0.0001), and less likely to receive adjuvant endocrine therapy (19.5% vs. 78.6%, P &lt; 0.0001) compared to patients with ER-positive tumors ≥ 10%. They were also more likely to have HER-2-positive (29.1% vs. 13.4%, P &lt; 0.0001) and grade III disease (82.1% vs. 29.6%, P &lt; 0.0001). Compared to patients with ER negative, patients with ER-positive 1–10% had earlier stage disease (clinical stage II/III 50.4% Vs. 59.3%, p = 0.01), were less likely to receive neoadjuvant chemotherapy (40.9% vs. 48.2%, p = 0.02), and more likely to receive adjuvant endocrine therapy (19.5% vs. 12.6%, p = 0.002). At a median follow-up of 5.1 years, patients with ER-positive 1–10% had worse RFS, DFS and OS rates compared to patients with ER-positive tumors ≥ 10%. The RFS, DFS and OS rates between patients with ER-positive 1–10% and ER negative did not differ significantly. Patients with ER-positive 1–10% and negative still had worse RFS, DSS and OS rates compared to patients with ER-positive tumors ≥ 10% after adjusted by clinical stage, adjuvant chemo and endocrine therapy.

Conclusion. Patients whose tumors are ER-positive at 1–10% have clinical and pathologic characteristics different from those whose tumors are ER-positive ≥10%. Similar to patients whose tumors are ER negative, those with ER-positive disease at 1–10% do not appear to benefit from endocrine therapy.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-07-09.

Cell line derived multi-gene predictor of pathologic response to neoadjuvant chemotherapy in breast cancer: a validation study on US Oncology 02-103 clinical trial

Background

The purpose of this study is to assess the predictive accuracy of a multi-gene predictor of response to docetaxel, 5-fluorouracil, epirubicin and cyclophosphamide combination chemotherapy on gene expression data from patients who received these drugs as neoadjuvant treatment.

Methods

Tumor samples were obtained from patients with stage II-III breast cancer before starting neoadjuvant chemotherapy with four cycles of 5-fluorouracil/epirubicin/cyclophosphamide (FEC) followed by four cycles of docetaxel/capecitabine (TX) on US Oncology clinical trial 02-103. Most patients with HER-2-positive cancer also received trastuzumab (H). The chemotherapy predictor (TFEC-MGP) was developed from publicly available gene expression data of 42 breast cancer cell-lines with corresponding in vitro chemotherapy sensitivity results for the four chemotherapy drugs. No predictor was developed for treatment with trastuzumab. The predictive performance of TFEC-MGP in distinguishing cases with pathologic complete response from those with residual disease was evaluated for the FEC/TX and FEC/TX plus H group separately. The area under the receiver-operating characteristic curve (AU-ROC) was used as the metric of predictive performance. Genomic predictions were performed blinded to clinical outcome.

Results

The AU-ROC was 0.70 (95% CI: 0.57-0.82) for the FEC/TX group (n=66) and 0.43 (95% CI: 0.20-0.66) for the FEC/TX plus H group (n=25). Among the patients treated with FEC/TX, the AU-ROC was 0.69 (95% CI: 0.52-0.86) for estrogen receptor (ER)-negative (n=28) and it was 0.59 (95% CI: 0.36-0.82) for ER-positive cancers (n=37). ER status was not reported for one patient.

Conclusions

Our results indicate that the cell line derived 291-probeset genomic predictor of response to FEC/TX combination chemotherapy shows good performance in a blinded validation study, particularly in ER-negative patients.

DNA repair metagene signature as a prognostic and predictive factor in molecular breast cancer subtypes

1012

Background: We aimed to assess the prognostic and predictive role of DNA repair genes in breast cancer (bc) molecular subtypes. Methods: We evaluated Affymetrix gene expression profiling from untreated N- patients (N = 684), neoadjuvant treated tumors with taxanes- (N = 320), anthracyclines- (N = 211), and cisplatin- (N = 22) containing regimens. We assessed within 3 BC molecular subgroups (ER+/HER2-, HER2+, and ER-/HER2-) bimodality distribution, prognosis by association with distant relapse (N = 454, N = 105, and N = 125) and predictive value for likelihood of pathological complete response (pCR) (N = 208, N = 105, and N = 240). Moreover, we explored the function of relevant genes in BC cell lines. Results: Three genes (ERCC2, XRCC3, and RECQL4) showed bimodality in each bc subtype. Eight genes were associated with poor prognosis (including RECQL4) and 1 gene with good prognosis (ATM) [P < .0001] only in ER+/HER2- tumors. Our results suggest a subtype and treatment specific association with pCR although they did not satisfy stringent criteria for false discovery correction. In ER-/HER2- mismatch repair (MR) (MSH2 and MSH6) and MTMR15 genes were associated with response and resistance to taxane-containing regimens, respectively. TOP2A was the only gene associated with response to anthracycline but not taxanes in HER2+ tumors. RECQL4 had a positive trend with higher pCR in both ER+ and ER-/HER2- tumors. In in vitro studies we found that RECQL4 interacts with PARP1 and that the expression of these genes was correlated with sensitivity to chemotherapy and PARP inhibitors. Conclusions: We identified MR genes as potential predictive markers of response to taxanes-based regimens in ER-/HER2-. A novel gene RECQL4 showed bimodal distribution, prognostic value, and a trend for predictive association with response to taxanes-based chemotherapy, which was also confirmed by in vitro analysis. ATM deserves further evaluation as prognostic marker in ER+/HER2-.

A dendritic metagene that predicts prognosis and endocrine resistance in breast cancer

545

Background: High expression of dendritic-associated genes in estrogen receptor-positive (ER+), highly proliferative breast cancer is associated with good prognosis in untreated patients (pts) and poor response to neoadjuvant endocrine therapy (Dunbier SABCS 2010). We examined the prognostic and predictive value of a dendritic metagene (DM) signature in subgroups defined by proliferation and estrogen-related genes (Bianchini SABCS 2011). Methods: We evaluated Affymetrix HGU133A-based gene expression profiles from ER+ untreated (n=511) and adjuvant tamoxifen (TAM)-treated pts (n=606). Three previously defined scores were assessed: MKS for proliferation (Bianchini, Cancer Res 2010); estrogen-related score (ERS) adopted from Oncotype DX; and DM (Bianchini JCO 2010). Median cut-off points were used. Outcome was assessed according to distant relapse. Results: DM was significantly predictive for early (within 5 years) relapse. In TAM-treated pts with low-MKS tumors, DM was not significantly prognostic. The table shows hazard ratios (HRs) for low vs. high-DM by ERS in untreated and TAM-treated pts with high-MKS. In low-DM, the 5-yrs distant-event free survival was 92.3% and 60.6% (HR 6.58 (2.55-17.0); p<0.001) and in high-DM it was 80.7% and 79.8% (HR 1.06 (0.48-2.32); p=0.88), respectively in high and low-ERS respectively. The interaction between DM and ERS was significant only in TAM-treated tumors (p=0.003). In high-MKS/low-ERS tumors, DM retained significance over the 10-year period in multivariate analysis adjusting for clinical variables (HR= 2.27 (1.13-4.58); p=0.02). Conclusions: For high-MKS, untreated and TAM-treated tumors with low-ESR, high-DM is associated with a low risk of relapse, and for untreated tumors with high-ERS. These data suggest that high infiltration of tumor by dendritic cells may be a novel mechanism of endocrine resistance. DM could refine risk in poor prognosis ER+ tumors and rationalize immuno-modulating strategies. [Table: see text]

Use of next-generation sequencing (NGS) to detect high frequency of targetable alterations in primary and metastatic breast cancer (MBC)

10559

Background: The aim of this study was to assess the frequency of genomic alterations in breast cancer potentially treatable with approved targeted agents or investigational drugs in clinical trials. NGS was performed in a CLIA setting (Foundation Medicine). Methods: DNA was extracted from needle biopsies of 33 pre-therapy primary and 17 MBCs (mean age 52 yrs; 58% ER+, 20% HER2+, 30% triple negative) obtained prospectively for biomarker discovery and preserved in RNAlater. Patients with MBC received an average of 7 drugs (range 5-17) including adjuvant therapy before biopsy for this research; 13 biopsies were from soft tissues, 3 from liver and 1 from bone. Sequencing was targeted to 3230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer. Average median depth was >1200x. Results: All biopsies yielded sufficient DNA. NGS revealed a total of 117 known driver mutations across 36 genes (per-tumor average=2.5, range 1-6), including 37 base substitutions (32%), 28 indels (24%), 42 amplifications (36%) and 10 homozygous deletions (9%). NGS identified HER2 gene amplification in 6/7 cases scored HER2+ by FISH. The average number of functionally important alterations was surprisingly similar, 2.3 in primaries vs 2.8 in heavily treated MBCs (p=0.32). Remarkably, 25/33 (76%) of primary and 14/17 (82%) of MBCs had at least 1 genomic alteration targetable with an FDA approved drug or novel agent in clinical trials. These included: ERBB2 alterations (n=9), PIK3CA mutations (n=8), NF1 mutations (n=4, candidate for PI3K/MEK inhibitors), AKT1-3 mutations (n=5, PI3K inhibitors), BRCA1/2, (n=6, PARP inhibitors), and CCND2 (n=3)/CDKN2A (n=3) mutations (CDK inhibitors). Numerous other alterations with less apparent therapeutic implications were also observed. Conclusions: Comprehensive NGS profiling in breast cancer needle biopsies showed high frequency of genomic alterations linked to a clinical treatment option or clinical trials of targeted therapies. These results demonstrate it is feasible to use NGS to guide targeted therapy. Prospective testing of the diagnostic/predictive value of this patient selection approach is currently under way.

Progression of genomic signatures in local and metastatic estrogen receptor-positive (ER+) breast cancer: Relevance to palliative treatment

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Background: Biological progression of ER+ breast cancer accelerates clinical progression and resistance to treatments. Methods: One laboratory used Affymetrix U133A gene expression microarrays to profile 588 biopsy samples from patients with ER+ breast cancer: 74 AJCC Stage I, 155 Stage IIA, 105 Stage IIB, 127 Stage III, 127 Stage IV (27 at presentation, 100 relapsed). We evaluated stage dependence of ER [ESR1, PGR, sensitivity to endocrine therapy (SET) index], proliferation [MKI67, AURKA, genomic grade index (GGI)], invasion [PLAU (uPA)], PI3-kinase (PIK3CA-GS), VEGF, genomic subtype [PAM50, 3-gene classifier (ESR1, ERBB2, AURKA)], and housekeeper control genes. Significance was evaluated through ordinal median regression (P < 0.002, for multiple testing) after adjusting for staging method (clinical or pathologic). Exploratory Cox regression analyses of progression-free survival (PFS) and overall survival (OS) were performed when treatment was hormonal therapy (HT, N=58) or chemotherapy (CT, N=27) after biopsy of metastatic ER+ breast cancer (MBC). Results: Stage progression was associated with reduced SET index and increased proliferation (GGI, MKI67, AURKA) and metabolism (GAPDH). These changes occurred between Stages IIB and III, and Stages III and IV. Luminal B and proliferation subtypes were more prevalent in Stage IV and less in Stage I. Interestingly, invasion (PLAU) genes were lower in MBC. Only SET index demonstrated a significant interaction with treatment (HT or CT) for MBC (PFS: p=0.018). SET was predictive of PFS and OS following HT, as a continuous score (PFS: HR=0.69, 95%CI 0.49 to 0.97, p=0.035; OS: HR=0.61, 95%CI 0.40 to 0.94, p=0.025) or dichotomized at median value (PFS: HR=0.43, 95%CI 0.24 to 0.76, p=0.003; OS: HR=0.37, 95%CI 0.18 to 0.77, p=0.006). Genomic subtype was prognostic for PFS irrespective of treatment type. High PIK3CA-GS expression predicted OS in the HT subset. Conclusions: Stage progression was associated with decreased ER-related transcription (SET) and increased proliferation, grade, higher risk subtype, and metabolism. In MBC samples, only SET index was predictive of PFS and OS with palliative hormonal therapy.

P1-07-09: Estrogen Receptor (ER) mRNA and ER-Related Gene Expression in Breast Cancers That Are 1%-10% ER-Positive by Immunohistochemistry

Purpose: Our goal was to examine whether borderline estrogen receptor (ER)-positive cancers, defined as 1–10% positivity by immunohistochemistry (IHC), show the same global gene expression pattern and high ESR1 mRNA expression as ER-positive cancers or are more similar to ER-negative cancers.

Patients and methods: ER status was determined by IHC in 465 primary breast cancers and with Affymetrix U133A gene chip (ESR1 mRNA gene expression: Probe set = 205225_at). We compared expressions of ESR1 mRNA and a 106-probe set ER-associated gene signature score between ER-negative (n=183), 1–9% (n=25), exactly 10% (n=6), and &gt; 10% ER-positive (n=251) cancers. We also assessed the molecular class of the borderline ER-positive cases using the PAM-50 classifier.

Results: Among the 1–9%, 10% and &gt; 10% IHC positive cases, 24%, 67% and 92% were also ER-positive by ESR1 mRNA expression. The average ESR1 expression was significantly higher in the &gt; 10% IHC-positive cohorts compared to the 1–9% or completely negative cases but in these latter two cohorts ER expression was similarly low. The average ER gene signature scores were similar for the ER-negative and 1–9% IHC-positive cases, but significantly lower than in &gt; 10% ER-positive cases. None of the 1–9% ER-positive cases were classified as Luminal A, 2 were Luminal B and 12 were Basal-like. Among the 10% ER-positive cases, 2 were Luminal A and 1 was Luminal B. Conclusion: Overall, 24% of the 1–9% and 67% of the 10% ER-positive cancers show ESR1 mRNA levels and gene signatures that are consistent with ER-positive, potentially endocrine sensitive tumors.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-09.

Gene pathways associated with prognosis and chemotherapy sensitivity in molecular subtypes of breast cancer

BACKGROUND

We hypothesized that distinct biological processes might be associated with prognosis and chemotherapy sensitivity in the different types of breast cancers.

METHODS

We performed gene set analyses with BRB-ArrayTools statistical software including 2331 functionally annotated gene sets (ie, lists of genes that correspond to a particular biological pathway or biochemical function) assembled from Ingenuity Pathway Analysis and Gene Ontology databases corresponding to almost all known biological processes. Gene set analysis was performed on gene expression data from three cohorts of 234, 170, and 175 patients with HER2-normal lymph node-negative breast cancer who received no systemic adjuvant therapy to identify gene sets associated prognosis and three additional cohorts of 198, 85, and 62 patients with HER2-normal stage I-III breast cancer who received preoperative chemotherapy to identify gene sets associated with pathological complete response to therapy. These analyses were performed separately for estrogen receptor (ER)-positive and ER-negative breast cancers. Interaction between gene sets and survival and treatment response by breast cancer subtype was assessed in individual datasets and also in pooled datasets. Statistical significance was estimated with permutation test. All statistical tests were two-sided.

RESULTS

For ER-positive cancers, from 370 to 434 gene sets were associated with prognosis (P ≤ .05) and from 209 to 267 gene sets were associated with chemotherapy response in analysis by individual dataset. For ER-positive cancers, 131 gene sets were associated with prognosis and 69 were associated with pathological complete response (P ≤.001) in pooled analysis. Increased expression of cell cycle-related gene sets was associated with poor prognosis, and B-cell immunity-related gene sets were associated with good prognosis. For ER-negative cancers, from 175 to 288 gene sets were associated with prognosis and from 212 to 285 gene sets were associated with chemotherapy response. In pooled analyses of ER-negative cancers, 14 gene sets were associated with prognosis and 23 were associated with response. Gene sets involved in sphingolipid and glycolipid metabolism were associated with better prognosis and those involved in base excision repair, cell aging, and spindle microtubule regulation were associated with chemotherapy response.

CONCLUSION

Different biological processes were associated with prognosis and chemotherapy response in ER-positive and ER-negative breast cancers.

Abstract P2-09-39: Multi-Gene Predictors Developed from Breast Cancer Cell Lines To Predict Response to Chemotherapy: A Validation Study on US Oncology Study 02-103

PURPOSE: Multi-gene predictors (MGPs) of response to multidrug chemotherapy regimens were developed using an in vitro chemoresponse assay in which cell lines were exposed to chemotherapy. The goal of this study was to assess the predictive value of these MGPs using clinical breast cancer patient gene expression data from a clinical trial. METHOD: US Oncology 02-103 was a phase II trial in which women with stage II/III breast cancer were treated with neoadjuvant chemotherapy consisting of four cycles of fluorouracil/epirubicin/cyclophosphamide (FEC) followed by four cycles of docetaxel/capecitabine (TX). Most HER-2 positive patients also received trastuzumab. MGPs of FEC, TX and TFEC (docetaxel/fluorouracil/epirubicin/cyclophosphamide) sensitivity were developed using in vitro assay results from breast cancer cell lines exposed to these drug combinations and publicly-available gene expression data for the same cell lines. MGPs were not developed for trastuzumab treatment. Area under the receiver-operator curve (AUC) was used to evaluate the performance of the three MGPs’ to predict patient pathologic complete response (pCR). Patients who did or did not receive trastuzumab were evaluated separately. Validation was performed blindly and the predictors were applied without knowledge of patient clinical outcome. RESULTS: Eighty-six patients had genomic data available and were included in this analysis. The predictive performance of the FEC, TX and TFEC MGPs were AUCs of 0.72, 0.69, and 0.73, respectively, in the patients who received FEC-TX chemotherapy without trastuzumab (n=61). Within this group, higher AUCs were observed in ER-negative patients compared to ER-positive patients (0.69, 0.72, 0.74 vs. 0.64, 0.54, 0.62, respectively). The prediction accuracies were low (AUCs = 0.43, 0.56 and 0.43) for patients who received trastuzumab together with chemotherapy (n=25) as expected, indicating that the MGPs may have the potential to be regimen-specific.

CONCLUSION: Cell line-derived MGPs of multidrug chemotherapy regimens showed promising performance in this blinded validation study, particularly among patients with ER-negative breast cancers. Further clinical data are needed to confirm this finding.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-09-39.

Abstract PD07-03: A Genomic Predictor of Survival Following Taxane-Anthracycline Chemotherapy for Breast Cancer

Background: There is currently no predictive assay for patients with clinical Stage II-III breast cancer from which predicted sensitivity to treatment is associated with high probability of survival following chemotherapy.

Patients & Methods: We performed Affymetrix gene expression microarrays of prospectively collected tumor biopsies from 508 patients with newly diagnosed HER2-normal invasive breast cancer prior to neoadjuvant taxane-anthracycline chemotherapy followed by adjuvant endocrine therapy (if hormone receptor-positive). The predictor was developed from 310 samples (from MDACC & I-SPY) by combining: 1) a signature to predict sensitivity to endocrine therapy (SET); 2) estrogen receptor (ER)-stratified predictive signatures of resistance to chemotherapy, defined as extensive residual cancer burden (RCB-III) or relapse within 3 years; and 3) ER-stratified predictive signatures of response to chemotherapy, defined as pathologic complete response (pCR) or minimal RCB (RCB-I). The predictor classified tumors as treatment sensitive if high or intermediate SET, or if predicted to be responsive (and not resistant) to chemotherapy. Otherwise, tumors were classified as treatment insensitive. The predictor was then tested on an independent cohort (N= 198, 98% with clinical Stage II-III) who received neoadjuvant (N= 180) or adjuvant (N= 18) taxane-anthracycline chemotherapy (from MDACC, USO, GEICAM, Peru, LBJ). Distant relapse-free survival (DRFS) was evaluated at a 3-year median follow up using negative predictive value (NPV, absence of event if predicted to be sensitive), and absolute risk reduction (ARR) for those predicted to be sensitive (versus insensitive), with 95% confidence interval (CI). The independent predictive value was assessed in multivariate Cox regression analysis based on the likelihood ratio test (P≥0.05). Results: Patients in the independent validation cohort who were predicted to be treatment sensitive (28%) had excellent DRFS, with NPV 92% (CI 85-100) and significant absolute risk reduction (ARR 18%, CI 6-28) at 3 years, compared to those predicted to be insensitive. This was similar to the DRFS observed in patients who achieved pCR after they completed neoadjuvant chemotherapy (NPV 93%, CI 85-100). Predictions were accurate in each phenotypic subset: ER+/HER2- (30% predicted sensitive, NPV 97%, CI 91-100; ARR 11%, CI 0.1-21) and ER-/HER2- (26% predicted sensitive, NPV 83%, CI 68-100; ARR 26%, CI 4-28). Predicted treatment sensitivity (HR 0.20, CI 0.07-0.57), ER+ status (HR 0.32, CI 0.17-0.63), clinical tumor stage T3-4 (HR 2.04, CI 1.07-3.88) and age &gt;50 (HR 0.50, CI 0.25-0.98) were significant in a multivariate model that also included clinical nodal status, grade, and type of taxane used.

Conclusion: We report validation results for the first molecular predictor of sensitivity to neoadjuvant/adjuvant systemic therapy for clinical Stage II-III breast cancer that is independently associated with excellent DRFS in those predicted to be sensitive. Predictions were accurate for both ER+/HER2- and ER-/HER2- invasive breast cancer.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD07-03.

Biologic and immunologic effects of preoperative trastuzumab for ductal carcinoma in situ of the breast

BACKGROUND

Through this study, the authors sought to investigate the biologic and immunologic effects of preoperative trastuzumab in patients with ductal carcinoma in situ (DCIS) of the breast.

METHODS

Patients with DCIS were enrolled in this open-label phase 2 trial and tested for HER2. Trastuzumab was given by intravenous infusion (8 mg/kg). The patients then had surgery 14 to 28 days after treatment. Tissue and peripheral blood samples were obtained before therapy and at the time of surgery to examine residual disease and immunologic response.

RESULTS

Median age of the 69 enrolled patients was 53 years, mean mammographic size of the DCIS lesions was 5.2 ± 1.2 cm, and 24 patients (35%) were found to have HER2 overexpression/amplification (12 received trastuzumab and 12 untreated patients provided tissue for blinded, controlled biomarker analyses). No overt histologic evidence of response was noted. No significant change in mean pretherapy staining for Ki-67 (44.3 ± 3.4%) and cleaved caspase-3 (2.6 ± 0.8%) was noted when surgical specimens from drug-treated patient samples were compared with those not treated. Trastuzumab significantly augmented antibody-dependent cell mediated cytotoxicity (ADCC) in 100% of patients; this was demonstrated to be mediated through CD56+ degranulating natural killer cells (P < .01). One patient developed a significant anti-HER2 humoral CD4 T-cell response.

CONCLUSIONS

Single-dose monotherapy with trastuzumab for patients with HER2-positive DCIS does not result in significant, clinically overt, histologic, antiproliferative, or apoptotic changes, but does result in the ability to mount ADCC mediated through natural killer cells and may also induce T-cell dependent humoral immunity. Further studies of trastuzumab for DCIS appear warranted. Cancer 2011. © 2010 American Cancer Society.

Prognostic impact of discordance between triple-receptor measurements in primary and recurrent breast cancer

BACKGROUND

We evaluated discordance in expression measurements for estrogen receptor (ER), progesterone receptor (PR), and HER2 between primary and recurrent tumors in patients with recurrent breast cancer and its effect on prognosis.

METHODS

A total of 789 patients with recurrent breast cancer were studied. ER, PR, and HER2 status were determined by immunohistochemistry (IHC) and/or FISH. Repeat markers for ER, PR, and HER2 were available in 28.9%, 27.6%, and 70.0%, respectively. Primary and recurrent tumors were classified as triple receptor-negative breast cancer (TNBC) or receptor-positive breast cancer (RPBC, i.e. expressing at least one receptor). Discordance was correlated with clinical/pathological parameters.

RESULTS

Discordance for ER, PR, and HER2 was 18.4%, 40.3%, and 13.6%, respectively. Patients with concordant RPBC had significantly better post-recurrence survival (PRS) than discordant cases; patients with discordant receptor status had similarly unfavorable survival as patients with concordant TNBC. IHC scores for ER and PR showed weak concordance between primary and recurrent tumors. Concordance of HER2-FISH scores was higher.

CONCLUSIONS

Concordance of quantitative hormone receptor measurements between primary and recurrent tumors is modest consistent with suboptimal reproducibility of measurement methods, particularly for IHC. Discordant cases have poor survival probably due to inappropriate use of targeted therapies. However, biological change in clinical phenotype cannot be completely excluded.

Genomic grade index is associated with response to chemotherapy in patients with breast cancer

PURPOSE The genomic grade index (GGI) is a 97-gene measure of histological tumor grade. High GGI is associated with decreased relapse-free survival in patients receiving either endocrine or no systemic adjuvant therapy. Herein we examined whether GGI predicts pathologic response to neoadjuvant chemotherapy in patients with HER-2-normal breast cancer. METHODS Gene expression data (gene chips) was generated from fine-needle aspiration biopsies (n = 229) prospectively collected before neoadjuvant paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide chemotherapy. Pathologic response was quantified using the residual cancer burden (RCB) method. The association between the GGI and pathologic response was assessed in univariate and multivariate analyses. The performance of a response predictor combining clinical variables and GGI was evaluated under cross-validation. Results Eighty-five percent of grade 1 tumors had low GGI, 89% of grade 3 tumors had high GGI, and 63% of grade 2 tumors had low GGI. Among both estrogen receptor (ER)-positive and -negative cancers, high GGI score was associated with pathologic complete response (RCB-0) or minimal residual disease (RCB-1). A multivariate model combining GGI and clinical parameters had an overall accuracy of 71%, compared with 58% for the GGI alone, for prediction of pathologic response. However, high GGI score was also associated with significantly worse distant relapse-free survival in patients with ER-positive cancer (P = .005), and was not associated with survival in patients with ER-negative cancer. CONCLUSION High GGI is associated with increased sensitivity to neoadjuvant paclitaxel plus fluorouracil, adriamycin, and cyclophosphamide chemotherapy in both ER-negative and ER-positive patients, but it remains a predictor of worse survival in ER-positive patients.

Targeting of breast cancer with non-oncology drugs – possible novel therapeutic option for triple-negative breast cancer

Abstract #2119

Introduction: Triple-negative breast cancer (TNBC) is defined by lack of ER, and PR expression and normal HER2 expression. It is characterized by aggressive biological presentation and unfavorable outcome. It is associated with frequent lack of response to current chemotherapy agents. Recently, 392 drugged genes that serve as targets for 1557 both oncologic and non-oncologic drugs were identified from the pharmacologic database DrugBank (Lauss et al. Pharmacogenomics 2007). In this study, we compared expression levels of these known drug targets between TNBC and receptor-positive cancers. Methods: Gene expression profiles were obtained from fine needle biopsies of newly diagnosed early stage breast cancer before any therapy (n=133, MDACC dataset). Differential expression of these genes was validated in a second independent data set (n=286, Rotterdam dataset) and in a panel of cell lines (n=19). In order to assess the functional relevance of known drug targets overexpressed in TNBC we performed in vitro experiments. Cell lines were treated with various concentrations of selected drugs alone or in combination with paclitaxel. Results: We mapped 675 U133A probe sets representing 347 unique drug targets to the Affymetrix U133A Genechip. 44 drug targets were overexpressed in TNBC compared to non-TNBC in the MDACC dataset. Thirty-three of these (75%) were also overexpressed among TNBC compared to non-TNBC in the Rotterdam dataset. Glutathione-S-transferase pi (GSTpi, target of clomipramine) was the most highly and consistently overexpressed target in human TNBC and in estrogen- and HER2-receptor-negative breast cancer cell lines. The GSTpi overexpressing (and triple negative) human mammary cell line HBL-100 showed dose-dependent inhibition of growth after 144 hrs of incubation with clomipramine, whereas growth of the GSTpi-low expressing (non-triple negative) breast cancer cell lines MCF-7 and SKBR3 was not inhibited by this drug. Treatment with clomipramine did not alter sensitivity to paclitaxel in either cell line in vitro. Conclusion: Gene expression analysis indicates that targets for several known drugs are over expressed in TNBC relative to other types of breast cancers. We hypothesize that some of these drugs may influence the behavior of TNBC and may represent future therapeutic options. Further experiments are needed to fully explore the functional implications of these findings; however, our preliminary results suggest that inhibition of GSTpi with clomipramine leads to inhibition of cell growth of TNBC cell lines in vitro.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2119.