Long-term efficacy and safety of addition of carboplatin with or without veliparib to standard neoadjuvant chemotherapy in triple-negative breast cancer: 4-year follow-up data from BrighTNess, a randomized phase 3 trial

BACKGROUND

Primary analyses of the phase 3 BrighTNess trial showed addition of carboplatin with/without veliparib to neoadjuvant chemotherapy significantly improved pathological complete response (pCR) rates with manageable acute toxicity in patients with triple-negative breast cancer (TNBC). Here, we report 4.5-year follow-up data from the trial.

DESIGN

Women with untreated stage II-III TNBC were randomized (2:1:1) to paclitaxel (weekly for 12 doses) plus either: (a) carboplatin (every 3 weeks for four cycles) plus veliparib (twice daily); (b) carboplatin plus veliparib placebo; or (c) carboplatin placebo plus veliparib placebo. All patients then received doxorubicin and cyclophosphamide (AC) every 2‒3 weeks for four cycles. The primary endpoint was pCR. Secondary endpoints included event-free survival (EFS), overall survival (OS), and safety. Since the co-primary endpoint of increased pCR with carboplatin plus veliparib with paclitaxel versus carboplatin with paclitaxel was not met, secondary analyses are descriptive.

RESULTS

Of 634 patients, 316 were randomized to carboplatin plus veliparib with paclitaxel, 160 to carboplatin with paclitaxel, and 158 to paclitaxel. With median follow-up of 4.5 years, the hazard ratio [HR] for EFS for carboplatin plus veliparib with paclitaxel versus paclitaxel was 0.63 (95% confidence interval [CI] 0.43‒0.92, P=0.02), but 1.12 (95% CI 0.72‒1.72, P=0.62) for carboplatin plus veliparib with paclitaxel versus carboplatin with paclitaxel. In post hoc analysis, HR for EFS was 0.57 (95% CI 0.36‒0.91, P=0.02) for carboplatin with paclitaxel versus paclitaxel. OS did not differ significantly between treatment arms, nor did rates of myelodysplastic syndromes, acute myeloid leukemia, or other secondary malignancies.

CONCLUSION

Improvement in pCR with addition of carboplatin was associated with long-term EFS benefit with a manageable safety profile, and without increasing the risk of second malignancies, while adding veliparib did not impact EFS. These findings support the addition of carboplatin to weekly paclitaxel followed by AC neoadjuvant chemotherapy for early stage TNBC.

Predicted sensitivity to endocrine therapy for stage II-III hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer before chemo-endocrine therapy

BACKGROUND

We proposed that a test for sensitivity to the adjuvant endocrine therapy component of treatment for patients with stage II-III breast cancer (SET2,3) should measure transcription related to estrogen and progesterone receptors (SET_ER/PR index) adjusted for a baseline prognostic index (BPI) combining clinical tumor and nodal stage with molecular subtype by RNA4 (ESR1, PGR, ERBB2, and AURKA).

PATIENTS AND METHODS

Patients with clinically high-risk, hormone receptor-positive (HR+), human epidermal growth factor receptor 2 (HER2)-negative (HR+/HER2-) breast cancer received neoadjuvant taxane-anthracycline chemotherapy, surgery with measurement of residual cancer burden (RCB), and then adjuvant endocrine therapy. SET2,3 was measured from pre-treatment tumor biopsies, evaluated first in an MD Anderson Cancer Center (MDACC) cohort (n = 307, 11 years' follow-up, U133A microarrays), cut point was determined, and then independent, blinded evaluation was carried out in the I-SPY2 trial (n = 268, high-risk MammaPrint result, 3.8 years' follow-up, Agilent-44K microarrays, NCI Clinical Trials ID: NCT01042379). Primary outcome measure was distant relapse-free survival. Multivariate Cox regression models tested prognostic independence of SET2,3 relative to RCB and other molecular prognostic signatures, and whether other prognostic signatures could substitute for SET_ER/PR or RNA4 components of SET2,3.

RESULTS

SET2,3 added independent prognostic information to RCB in the MDACC cohort: SET2,3 [hazard ratio (HR) 0.23, P = 0.004] and RCB (HR 1.77, P < 0.001); and the I-SPY2 trial: SET2,3 (HR 0.27, P = 0.031) and RCB (HR 1.68, P = 0.008). SET2,3 provided similar prognostic information irrespective of whether RCB-II or RCB-III after chemotherapy, and in both luminal subtypes. Conversely, RCB was most strongly prognostic in cancers with low SET2,3 status (MDACC P < 0.001, I-SPY2 P < 0.001). Other molecular signatures were not independently prognostic; they could effectively substitute for RNA4 subtype within the BPI component of SET2,3, but they could not effectively substitute for SET_ER/PR index.

CONCLUSIONS

SET2,3 added independent prognostic information to chemotherapy response (RCB) and baseline prognostic score or subtype. Approximately 40% of patients with clinically high-risk HR+/HER2- disease had high SET2,3 and could be considered for clinical trials of neoadjuvant endocrine-based treatment.

Abstract GS5-05: Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state

Approximately 50% of patients with localized triple negative breast cancer (TNBC) have substantial residual cancer burden following treatment with neoadjuvant chemotherapy (NACT), resulting in distant metastasis and death for most of these patients. While genomic and phenotypic intra-tumor heterogeneity are pervasive features of TNBCs at the time of diagnosis, the functional contributions of heterogeneous tumor cell populations to chemoresistance have not been elucidated.

To investigate tumor evolution accompanying NACT, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC, which retain intra-tumor heterogeneity characteristic of human TNBC. We discovered that some PDX models initially exhibited partial sensitivity to standard front-line NACT (Adriamycin plus Cytoxan, AC). Following AC, residual tumors were resistant to chemotherapy but repopulated tumors with chemo-sensitive cells if left untreated, indicating that tumor cells possessed inherent plasticity. To identify the tumor cell subpopulation(s) conferring chemoresistance, we conducted barcode-mediated clonal tracking in three independent PDX models by introducing a high-complexity pooled lentiviral barcode library into PDX tumor cells which were then orthotopically engrafted into recipient mice. Strikingly, residual tumors maintained the same heterogeneous clonal architecture as naïve tumors. Concordantly, whole-exome sequencing revealed conservation of genomic subclonal architecture throughout treatment. These results were corroborated by genomic sequencing of serial biopsies pre- and post-AC obtained directly from TNBC patients enrolled on an ongoing clinical trial at MD Anderson (ARTEMIS; NCT02276443). Together, these studies revealed that genomically distinct pre-treatment subclones were equally capable of surviving AC to reconstitute tumors after treatment.

To identify functional addictions of residual tumor cells, we conducted histologic and transcriptomic profiling. Residual tumors following AC-treatment exhibited extensive fibrotic desmoplasia and tumor cell pleomorphism in both PDX models and in serial biopsies obtained from TNBC patients enrolled on the ARTEMIS trial. Strikingly, these AC-induced features were reverted upon regrowth of residual tumors in PDXs and in patients' tumors. Similarly, residual tumors exhibited unique transcriptomic features, many of which are also de-regulated in cohorts of human TNBCs undergoing chemotherapy treatment. These features were nearly completely reverted after tumors regrew, suggesting that the residual tumor state may be a unique and transient therapeutic window. Gene set enrichment analyses revealed that residual tumors had increased activation of oxidative phosphorylation and decreased glycolytic signaling. Pharmacologic targeting of oxidative phosphorylation with a small-molecule inhibitor of mitochondrial electron transport chain complex I (IACS-010759) significantly delayed the regrowth of AC-treated residual tumors in three independent PDX models. Collectively, these studies reveal that a reversible phenotypic state can confer chemoresistance in the absence of genomic selection and that the residual tumor state is a novel therapeutic window for chemo-refractory TNBC.

Citation Format: Echeverria GV, Ge Z, Seth S, Jeter-Jones SL, Zhang X, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Lau R, Shao J, Sun Y, Bristow C, Carugo A, Ma X, Harris A, Wu Y, Moulder S, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS5-05.

Abstract P3-07-01: Towards a therapeutically relevant subtyping scheme for triple-negative breast cancer (TNBC), profiling results from A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival (ARTEMIS)

Triple-negative breast cancer is a highly diverse group of cancers, with poor prognosis, and currently, there are no targeted drugs available in the clinic. In TNBC around 50% percent of the patients respond to chemotherapy, while, the other 50% percent relapse with poor prognosis. There is a need to understand better the targetable mechanisms driving TNBC via integrative analysis of gene-expression, copy-number, and mutational data.

Samples from 220 triple-negative breast cancer (TNBC) pts treated with NACT were prioritized for transcriptomic and genomic profiling. Non-negative matrix factorization was used on array-based profiling to identify six robust (ARTEMIS) subtypes. Comparing ARTEMIS subtypes with Vanderbilt subtypes, revealed significant overlap with 4/6 clusters while identifying two new clusters. Logistic regression on ssGSEA scores vs. subtypes revealed several pathways, selectively enriched specific subtypes. CL1/IM (Immune subtype), was enriched in INFg and INFa, while CL2 (MYC/mTOR), showed enrichment of several proliferation-related pathways. In addition, LAR and M (Mesenchymal) pts formed overlapping clusters, using either method.

Two new subtypes did not associate significantly with any of the previous subtypes. The majority of the tumors from the Vanderbilt BL2 and MSL were reclassified into a CL5 (ANGIO) cluster, which was enriched in angiogenesis geneset, including targetable genes like VEGF and FGFR. Also, an MYO (CL3) subtype was identified, with myogenesis-related genes. Of note, TIL (tumor infiltrating lymphocytes) and LAR quantification using IHC were associated with respective ARTEMIS subtypes. Finally, the IM subtype was significantly associated with higher rates of RCB 0-I and the M (CL4) subtype was associated with higher rates of RCB II-III, irrespective of the neoadjuvant treatment regimen.

ARTEMIS subtypes are a novel classification system for TNBC that is focused on therapeutic translation. Further, we show a possibility to classify previously un-classified (UNS) tumors, which will be validated using additional cohorts (TCGA/METABRIC).

Citation Format: Seth S, Huo L, Rauch G, Lau R, Gilcrease M, Adrada B, Piwnica-Worms H, Symmans WF, Draetta G, Futreal AP, Moulder S, Chang JT. Towards a therapeutically relevant subtyping scheme for triple-negative breast cancer (TNBC), profiling results from A Randomized, TNBC Enrolling trial to confirm Molecular profiling Improves Survival (ARTEMIS) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-07-01.

Abstract P2-07-03: Refining neoadjuvant predictors of three year distant metastasis free survival: Integrating volume change as measured by MRI with residual cancer burden

Background: Patients achieving a pathologic complete response (pCR) following neoadjuvant therapy have significantly improved event-free survival relative to those who do not; and pCR is an FDA-accepted endpoint to support accelerated approval of novel agents/combinations in the neoadjuvant treatment of high risk early stage breast cancer. Previous studies have shown that recurrence risk increased with increasing burden of residual disease (as assessed by the RCB index). As well, these studies suggest that patients with minimum residual disease (RCB-I class) also have favorable outcomes (comparable to those achieving a pCR) within high risk tumor subtypes. In this study, we assess whether integrating RCB with MRI functional tumor volume (FTV), which in itself is prognostic, can improve prediction of distant recurrence free survival (DRFS); and identify a subset of patients with minimal residual disease with comparable DRFS as those who achieved a pCR. Imaging tools can then be used to identify the subset that will do well early and guide the timing of surgical therapy.

Method: We performed a pooled analysis of 596 patients from the I-SPY2 TRIAL with RCB, pre-surgical MRI FTV data and known follow-up (median 2.5 years). We first assessed whether FTV predicts residual disease (pCR or pCR/RCB-I) using ROC analysis. We applied a power transformation to normalize the pre-surgical FTV distribution; and assessed its association with DRFS using a bi-variate Cox proportional hazard model adjusting for HR/HER2 subtype. We also fitted a bivariate Cox model of RCB index adjusting for subtype; and assessed whether adding pre-surgical FTV to this model further improves association with DRFS using a likelihood ratio (LR) test. For the Cox modeling, penalized splines approximation of the transformed FTV and RCB index with 2 degrees of freedom was used to allow for non-linear effects of FTV and RCB on DRFS.

Result: Pre-surgical MRI FTV is significantly associated with DRFS (Wald p&lt;0.00001), and more effective at predicting pCR/RCB-I than predicting pCR alone (AUC: 0.72 vs. 0.65). Larger pre-surgical FTV remains associated with worse DRFS adjusting for subtype (Wald p &lt;0.00001). The RCB index is also significantly associated with DRFS adjusting for subtype (Wald p&lt;0.00001). Adding FTV to a model containing RCB and subtype further improves association with DRFS (LR p=0.0007). RCB-I patients have excellent DRFS (94% at 3 years compared to 95% in the pCR group). Efforts are underway to identify an optimal threshold for dichotomizing pre-surgical FTV and FTV change measures for use in combination with pCR/RCB-I class to generate integrated RCB (iRCB) groups as a composite predictor of DRFS.

Conclusion: Pre-surgical MRI FTV is effective at predicting minimal residual disease (RCB0/I) in the I-SPY 2 TRIAL. Despite the association between FTV and RCB, FTV appears to provide independent added prognostic value (to RCB and subtype), suggesting that integrating MRI volume measures and RCB into a composite predictor may improve DRFS prediction.

Citation Format: Hylton NM, Symmans WF, Yau C, Li W, Hatzis C, Isaacs C, Albain KS, Chen Y-Y, Krings G, Wei S, Harada S, Datnow B, Fadare O, Klein M, Pambuccian S, Chen B, Adamson K, Sams S, Mhawech-Fauceglia P, Magliocco A, Feldman M, Rendi M, Sattar H, Zeck J, Ocal I, Tawfik O, Grasso LeBeau L, Sahoo S, Vinh T, Yang S, Adams A, Chien AJ, Ferero-Torres A, Stringer-Reasor E, Wallace A, Boughey JC, Ellis ED, Elias AD, Lang JE, Lu J, Han HS, Clark AS, Korde L, Nanda R, Northfelt DW, Khan QJ, Viscusi RK, Euhus DM, Edmiston KK, Chui SY, Kemmer K, Wood WC, Park JW, Liu MC, Olopade O, Tripathy D, Moulder SL, Rugo HS, Schwab R, Lo S, Helsten T, Beckwith H, Haugen PK, van't Veer LJ, Perlmutter J, Melisko ME, Wilson A, Peterson G, Asare AL, Buxton MB, Paoloni M, Clennell JL, Hirst GL, Singhrao R, Steeg K, Matthews JB, Sanil A, Berry SM, Abe H, Wolverton D, Crane EP, Ward KA, Nelson M, Niell BL, Oh K, Brandt KR, Bang DH, Ojeda-Fournier H, Eghtedari M, Sheth PA, Bernreuter WK, Umphrey H, Rosen MA, Dogan B, Yang W, Joe B, I-SPY 2 TRIAL Consortium, Yee D, Pusztai L, DeMichele A, Asare SM, Berry DA, Esserman LJ. Refining neoadjuvant predictors of three year distant metastasis free survival: Integrating volume change as measured by MRI with residual cancer burden [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-03.

Abstract P1-15-02: Withdrawn

This abstract was withdrawn by the authors.

Citation Format: Schwab R, Clark A, Yau C, Wolf D, Chien AJ, Majure M, Ewing C, Wallace A, Roesch E, Helsten T, Forero A, Stringer-Reasor E, Vaklavas C, Nanda R, Jaskowiak N, Boughey J, Haddad T, Han H, Lee C, Albain K, Isaacs C, Elias A, Ellis E, Shah P, Lang J, Lu J, Tripathy D, Kemmer K, Yee D, Haley B, Korde L, Edmiston K, Northfelt D, Viscusi R, Khan Q, I-SPY 2 Consortium, Symmans WF, Perlmutter J, Hylton N, Rugo H, Melisko M, Wilson A, Singhrao R, Asare S, van't Veer L, DeMichele A, Berry D, Esserman L. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-02.

Abstract P4-08-20: Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancer

Background: The clinical management of patients with metastatic HR-positive breast cancer is often uncertain due to decreased sensitivity to anti-estrogen therapy over time. Recently, we developed a targeted RNAseq based 18-transcript SET ER/PR assay of endocrine sensitivity from biopsies of metastatic cancer. In this work we assess the effect of pre-analytical factors, specifically RNA extraction methods for FFPE tissue samples, on the reliability of the targeted RNAseq assay.

Methods: FFPE blocks and matched fresh frozen (FF) sections from 12 tumors were collected at MD Anderson Cancer Center. RNA from FFPE slides was extracted in duplicate using three kits (Norgen, Qiagen, Roche), and RNAseq libraries from all samples were prepared using Kapa Total RNAseq kit. Targeted RNA libraries were prepared using droplet-based PCR (RainDance), and also by transcriptome-wide RNAseq for comparison. Reads were mapped to genomic sequence using STAR and expression was quantified using RSEM. Expression data were normalized based on expression of 10 reference genes. The effect of FFPE RNA extraction kit on the reliability of the SET index was assessed using linear mixed effects model (LME) analysis, and agreement with FF was assessed using the concordance correlation coefficient (CCC).

Results: Analysis of the whole transcriptome RNAseq data confirmed minimal 3'-end transcript bias from FFPE samples, irrespective of transcript size or FFPE kit. All 18 genes included in the SET index had high overall concordance between FFPE and FF (median CCC percentile=98.8, range 57.2-99.9 for Norgen; similar for the other two kits) and relatively consistent bias across genes, as estimated by the random effects of the LME model. Furthermore, compared to random 18-gene indices, concordance in the SET index values between FF and FFPE was higher than 99.8% of the random samples, verifying the analytical reliability of the selected genes. For the targeted RNAseq assay, RNA from FFPE extracted with the Norgen kit showed the highest concordance compared to FF (CCC=0.956, 95%CI 0.871-0.985). In general, the analytical variation of SET from FFPE samples was greater than that from FF (1.71-2.71 fold greater), with the lowest variation associated with the Norgen kit. The SET index values from targeted RNAseq for both FF and FFPE samples were consistently lower compared to transcriptome-wide RNAseq but were highly correlated, with the Norgen kit having the highest correlation between targeted and transcriptome-wide RNAseq (rho=0.915).

Conclusions: All three FFPE RNA extraction kits have excellent analytical performance compared to FF samples. The Norgen kit may be marginally better yielding higher concordance with FF and lower analytical variation between replicates. All genes in the SET ER/PR showed very good analytical performance in comparison to random indices and individual genes. Targeted gene RNA sequencing appears very promising as a platform for clinical deployment of quantitative assays, showing only a small (fixable) bias compared to RNAseq.

Citation Format: Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Symmans WF, Hatzis C. Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-20.

Prognostic implications of residual disease tumor-infiltrating lymphocytes and residual cancer burden in triple-negative breast cancer patients after neoadjuvant chemotherapy

BACKGROUND

For primary triple-negative breast cancer (TNBC) treated with neoadjuvant chemotherapy (NAC), higher pretreatment tumor-infiltrating lymphocytes (TILs) correlates with increased pathologic complete response (pCR) rates, and improved survival. We evaluated the added prognostic value of residual disease (RD) TILs to residual cancer burden (RCB) in predicting survival post-NAC.

PATIENTS AND METHODS

We combined four TNBC NAC patient cohorts who did not achieve pCR. RD TILs were investigated for associations with recurrence-free survival (RFS), and overall survival (OS) using Cox models with stromal TILs as a continuous variable (per 10% increment). The likelihood ratio test was used to evaluate added prognostic value of RD TILs.

RESULTS

A total of 375 RD TNBC samples were evaluable for TILs and RCB. The median age was 50 years, with 62% receiving anthracycline/taxane chemotherapy. The RCB class after NAC was 11%, 50%, and 39% for I, II, and III, respectively. The median RD TIL level was 20% (IQR 10-40). There was a positive correlation between RD TIL levels and CD8+ T-cell density (ρ = 0.41). TIL levels were significantly lower with increasing post-NAC tumor (P = 0.005), nodal stage (P = 0.032), but did not differ by RCB class (P = 0.84). Higher RD TILs were significantly associated with improved RFS (HR: 0.86; 95% CI 0.79-0.92; P < 0.001), and improved OS (HR: 0.87; 95% CI 0.80-0.94; P < 0.001), and remained significant predictors in multivariate analysis (RFS P = 0.032; OS P = 0.038 for OS). RD TILs added significant prognostic value to multivariate models including RCB class (P < 0.001 for RFS; P = 0.021 for OS). The positive prognostic effect of RD TILs significantly differed by RCB class for RFS (PInt=0.003) and OS (PInt=0.008) with a greater magnitude of positive effect observed for RCB class II than class III.

CONCLUSIONS

TIL levels in TNBC RD are significantly associated with improved RFS and OS and add further prognostic information to RCB class, particularly in RCB class II.

Abstract P1-07-01: HLA class I expression is associated with tumor-infiltrating lymphocytes and response and survival after neoadjuvant chemotherapy in hormone receptor-positive, HER2-negative breast cancer

Background: Interactions between cancer cells and the host immune system influence tumor biology, response to therapy and patient survival and their modulation offers promising new approaches for cancer therapy. The downregulation or loss of HLA class I expression in breast cancer cells might be an effective mechanism to evade the recognition by the immune system facilitating malignant behavior.

Aim: To evaluate the association of tumor-infiltrating lymphocytes (TILs) with HLA class I expression and its theranostic value for therapy response and survival after neoadjuvant chemotherapy.

Methods: HLA class I expression was evaluated by immunohistochemistry in a cohort of 732 pre-therapeutic core biopsies from breast cancer patients treated within the neoadjuvant GeparTrio trial. Patients received anthracycline- and taxane-based neoadjuvant therapy and adjuvant endocrine treatment if hormone receptor-positive (HR+). A publicly available microarray dataset of pre-therapeutic core biopsies from 508 breast cancer patients that received neoadjuvant chemotherapy and endocrine treatment if HR+ was used for validation of the results. The association of HLA class I expression with predefined genomic signatures for immune cell populations was evaluated in publicly available data from the cancer genome atlas.

Results: HLA class I expression was associated with TILs (p &lt; 0.001) and was predictive of better response to neoadjuvant chemotherapy in the subgroup of patients with HR+/HER2- breast cancer (14 % in tumors with high HLA vs. 7 % in tumors with low HLA, p = 0.029). Interestingly, high HLA was also predictive for shorter progression-free survival in univariate analysis (HR 1.590, 95 % CI 1.062—2.380; p = 0.024) and after adjustment to clinical and pathological parameters (HR 1.701, 95 % CI 1.105—2.618; p = 0.016). The results could be validated in the independent microarray-based dataset (HR 1.521, 95% CI 1.088 – 2.129; p = 0.0142). HLA class I was not associated with therapy response or survival in hormone receptor-negative breast cancer. HLA class I was associated with a predefined signature for T-cells and cytotoxic T- cells in the cancer genome atlas dataset (rho = 0.546).

Conclusion: HLA class I expression is associated with better response but shorter progression-free survival in HR+/HER2- breast cancer following neoadjuvant chemotherapy. The underlying mechanisms warrant further investigation.

Citation Format: Sinn BV, Weber K, Denkert C, Fasching PA, Schmitt WD, Thomas K, Ingold-Heppner B, van Mackelenbergh M, Symmans WF, Marmé F, Taube E, Müller V, Kunze CA, Schem C, Pfitzner BM, Stickeler E, von Minckwitz G, Loibl S. HLA class I expression is associated with tumor-infiltrating lymphocytes and response and survival after neoadjuvant chemotherapy in hormone receptor-positive, HER2-negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-07-01.

Abstract P6-03-05: Risk of needle-track seeding with serial ultrasound guided biopsies in triple negative breast cancer

Background: Image-guided percutaneous needle biopsy of the breast is a common procedure. In breast cancer patients (pts) undergoing core biopsies and surgical resection on the same day, the rate of tumor cell displacement along the needle track has been reported to be up to 50%. However, the clinical significance of this finding in triple negative breast cancer (TNBC) patients (pts) undergoing serial biopsies while receiving neoadjuvant chemotherapy (NACT) is unknown. Here we report the incidence of needle-track seeding (NTS) in a cohort of TNBC pts enrolled on a molecular triaging protocol involving serial biopsies of the index breast lesion.

Methods: We reviewed the clinical records of 144 consecutive TNBC pts enrolled on a molecular triaging protocol at MD Anderson Cancer Center. Per protocol, all pts underwent a pre-treatment research biopsy and were initiated on anthracycline based NACT (AC). Pts with inadequate response to front-line NACT were encouraged to undergo additional biopsies of the index breast lesion prior to switching therapies. Serial breast ultrasound (US) was performed to monitor therapeutic response and incidental evidence of needle-track seeding noted on US was documented.

Results: Clinicopathological characteristics of the pts are summarized in Table 1. 89% (128/144) of pts had a diagnostic breast biopsy done at another center prior to presenting at MDACC. To date, we have performed 209 US guided biopsies of index breast lesions in 144 pts. 92% (193/209) of these biopsies were done mainly for research purposes. 1.4% (2/144) of pts were found to have evidence of NTS on follow up US. The first pt had a T1N0 (1.9cm), grade 3, invasive ductal carcinoma (IDC) at diagnosis. She underwent a diagnostic biopsy followed by a research biopsy before initiating AC. She was found to have NTS as well as progression of disease (PD) on follow up US after 2 cycles of AC. The second pt had a T2N0 (3cm), grade 3 IDC at diagnosis. She underwent a diagnostic biopsy at another center, followed by a research biopsy before initiating AC. Like the first pt, she was found to have NTS and PD on follow up US after 2 cycles of AC. Both pts are currently on neoadjuvant clinical trials of novel agents.

Conclusion: The rate of NTS detected on US in TNBC pts undergoing serial biopsies of index breast lesions while receiving NACT is low and further studies are needed to determine the impact of serial biopsies on long term outcomes in TNBC.

Table 1: Patient CharacteristicsCharacteristicN=144Age - Median (years, interquartile range)55 (46-62)Tumor Size Mean (cm, standard deviation)3.4 (2.2)T1 – n(%)35 (24)T2 – n(%)89 (62)T3 – n(%)19 (13)T4 – n(%)1 (1)Clinical Nodal Status Negative – n(%)74 (51)Positive – n(%)70 (49)Grade 1 – n(%)1 (1)2 – n(%)17 (12)3 – n(%)124 (86)Unknown – n(%)2 (1)Histologic Subtype Invasive ductal carcinoma – n(%)121 (84)Invasive lobular carcinoma – n(%)2 (1)Mixed ductal and lobular carcinoma – n(%)3 (2)Metaplastic carcinoma – n(%)13 (9)Not specified – n(%)5 (3)Laterality Right – n(%)72 (50)Left – n(%)72 (50)

Citation Format: Yam C, Santiago L, Candelaria RP, Adrada BE, Rauch GM, Hess KR, Litton JK, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Huo L, Thompson AM, Gilcrease MZ, Symmans WF, Moulder SL, Yang W. Risk of needle-track seeding with serial ultrasound guided biopsies in triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-03-05.

Abstract GS6-06: Identifying metastatic drivers in patient-derived xenograft models of triple negative breast cancer

Metastases are responsible for the vast majority of deaths due to breast cancer. Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high rates of metastasis and poor prognosis. We are employing patient derived xenograft (PDX) models of TNBC to identify drivers of metastasis. Tumor samples are obtained from the breast tumors of patients with TNBC and engrafted immediately into the humanized mammary fat pads of immune compromised mice. Lentiviral transduction was employed to express bioluminescent and fluorescent markers in two independent PDX models of TNBC. Using these models, we demonstrated that human breast tumors are capable of completing all stages of the metastatic cascade in mice, and metastatic lesions are observed in organs normally found in patients with metastatic breast cancer including lung, liver, bone, brain, and lymph nodes. Dynamic and reversible epithelial to mesenchymal transition (EMT) was observed as tumors metastasized to lung and were re-passaged to recipient mouse mammary glands. Lung metastases were isolated using bioluminescence imaging and lung metastasis gene expression signatures were generated. Metastasis signatures from two independent PDX models were compared to identify genes that were commonly de-regulated in lung metastases relative to corresponding mammary tumors. Comprehensive gain-of-function screens were then conducted in vivo to identify functional drivers of TNBC metastasis. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a metastatic driver in this screen. CEACAM5 mRNA and protein levels were elevated in lung metastases relative to corresponding mammary gland tumors in mice. In addition, we demonstrated that CEACAM5 expression was upregulated in the lung metastases of breast cancer patients, and its expression inversely correlated with patient survival. Our data indicate that the metastatic function of CEACAM5 is to promote growth of breast tumors in the lung by inducing MET (mesenchymal to epithelial transition).

Citation Format: Powell E, Shao J, Picon HM, Ge Z, Echeverria GV, Peoples M, Bristow C, Cai S, Tu Y, McCoy AM, Piwnica-Worms D, Draetta G, Edwards JR, Moulder SL, Symmans WF, Heffernan TP, Liang H, Piwnica-Worms H. Identifying metastatic drivers in patient-derived xenograft models of triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS6-06.

Abstract P1-07-22: Androgen receptor positivity is associated with nodal disease in triple negative breast cancer

Background: Gene expression profiling (GEP) has identified several molecularly distinct subtypes of triple negative breast cancer (TNBC). Currently, GEP-based molecular diagnostics are not routinely used in clinical decision making due to the lack of proven benefit, costs involved and long turnaround time. However, two molecularly distinct subtypes of TNBC, the luminal androgen receptor (AR) and mesenchymal subtypes, have surrogate CLIA-certified immunohistochemical (IHC) markers, AR and vimentin (VM), respectively, which have the potential for application in the clinic. Here we report the rates of AR and VM positivity and their association with clinicopathological characteristics in a cohort of TNBC pts receiving NACT.

Methods: As part of an ongoing molecular triaging protocol, 144 pts with stage I-III TNBC underwent a pretreatment biopsy for molecular characterization (MC) prior to initiating neoadjuvant chemotherapy (NACT). IHC for AR and VM were performed using commercially available antibodies. AR+ and VM+ were defined as ≥10% and ≥50% staining, respectively. Pts were randomized 2:1 to know (intervention arm, n=93) and not know (control arm, n=51) the MC results. The charts of pts randomized to the intervention arm were reviewed. Categorical variables were analyzed using Fisher's exact test. Ordinal and continuous variables were analyzed using the Wilcoxon rank-sum test and Student's t test as appropriate.

Results: 31% (29/93) and 16% (15/93) of pts were AR+ and VM+, respectively. Only 4% (4/93) of pts were both AR+ and VM+. Clinicopathological characteristics are summarized in Table 1. AR+ pts were more likely to have clinically node positive disease as compared to AR- pts (66% vs 34%, p=0.007). There were no significant differences in clinical tumor size or grade between AR+ and AR- pts. VM+ and VM- pts had similar clinicopathological characteristics.

Conclusion: Pts with AR+ TNBC were more likely to have node positive disease. The impact of AR+ on long term outcomes should be investigated in prospective studies.

Table 1: Association between patient characteristics and AR/VM status AR  VM   AR+ (n=29)AR- (n=64)p-valueVM+ (n=15)VM- (n=78)p-valueAge - Median (years, interquartile range)58 (48-65)52 (46-61)0.05855 (48-64)56 (47-62)0.88Clinical Tumor Size      Mean (cm, standard deviation)3.5 (1.8)3.0 (1.8)0.2872.7 (1.7)3.3 (1.9)0.31T1 – n(%)5 (17)21 (33)0.2307 (47)19 (24)0.098T2 – n(%)21 (72)36 (56) 7 (47)50 (64) T3 – n(%)3 (10)7 (11) 1 (7)9 (12) Clinical Nodal Status      Negative – n(%)10 (34)42 (66)0.0078 (53)44 (56)1.00Positive – n(%)19 (66)22 (34) 7 (47)34 (44) Grade      2 – n(%)6 (21)5 (8)0.0763 (20)8 (10)0.293 – n(%)23 (79)59 (92) 12 (80)70 (90) 

Citation Format: Yam C, Huo L, Hess KR, Litton JK, Yang W, Piwnica-Worms H, Mittendorf EA, Ueno NT, Lim B, Murthy RK, Damodaran S, Helgason T, Thompson AM, Santiago L, Candelaria RP, Rauch GM, Adrada BE, Symmans WF, Gilcrease MZ, Moulder SL. Androgen receptor positivity is associated with nodal disease in triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-07-22.

Molecular Profiling Using Breast Cancer Subtype to Plan for Breast Reconstruction

BACKGROUND

Molecular profiling using breast cancer subtype has an increasing role in the multidisciplinary care of the breast cancer patient. The authors sought to determine the role of breast cancer subtyping in breast reconstruction and specifically whether breast cancer subtyping can determine the need for postmastectomy radiation therapy and predict recurrence-free survival to plan for the timing and technique of breast reconstruction.

METHODS

The authors reviewed prospectively collected data from 1931 reconstructed breasts in breast cancer patients who underwent mastectomy between November of 1999 and December of 2012. Reconstructed breasts were grouped by breast cancer subtype and examined for covariates predictive of recurrence-free survival and need for postmastectomy radiation therapy.

RESULTS

Of the reconstructed breasts, 753 (39 percent) were luminal A, 538 (27.9 percent) were luminal B, 224 (11.6 percent) were luminal HER2, 143 (7.4 percent) were HER2-enriched, and 267 (13.8 percent) were triple-negative breast cancer. Postmastectomy radiation therapy was delivered in 69 HER2-enriched patients (48.3 percent), 94 luminal HER2 patients (42 percent), 200 luminal B patients (37.2 percent), 99 triple-negative breast cancer patients (37.1 percent), and 222 luminal A patients (29.5 percent) (p < 0.0001). Luminal A cases had better recurrence-free survival than HER2-enriched cases, and triple-negative breast cancer cases had worse recurrence-free survival than HER2-enriched cases. Luminal B and luminal HER2 cases had recurrence-free survival similar to that for HER2-enriched cases. Luminal A subtype was associated with the best recurrence-free survival. Subtyping may have improved the breast surgery planning for 33.1 percent of delayed reconstructions that did not require postmastectomy radiation therapy and 37 percent of immediate reconstructions that did require postmastectomy radiation therapy.

CONCLUSION

This study is the first publication in the literature to evaluate breast cancer subtype to stratify risk for decision making in breast reconstruction.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Risk, III.

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 (&lt; 10% probability of success) or following accrual of maximum sample size (10%&lt; probability of success &lt;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 &gt;470msec and HbA1C &gt;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 &lt; 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&lt;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 &lt; 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 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 P3-06-04: Investigating clonal dynamics in triple negative breast cancer chemoresistance

Approximately 50% of triple-negative breast cancer (TNBC) patients have extensive residual disease following neoadjuvant chemotherapy (NAC). These patients have a four-fold increase in mortality risk and an increased risk of distant metastases within three years (1). Understanding the molecular basis of resistance to NAC is expected to provide opportunities to better treat patients in the primary setting. Extensive intratumoral subclonal heterogeneity has been well documented in primary, treatment-naïve TNBC (2). Subclonal populations harboring distinct molecular profiles may confound targeted therapy strategies, yet the functional impact of subclonal heterogeneity in TNBC resistance to therapy is unknown. We are implementing DNA barcoding to quantitatively track changes in subclonal architecture pre- and post-treatment in patient-derived xenograft (PDX) models of TNBC in order to design novel combination therapies. Such barcoding strategies have been used to monitor clonal dynamics in breast cancer PDXs with great sensitivity (3).

We have established an orthotopic PDX from a treatment-naïve TNBC patient (PIM1, procured from a patient later found to have chemoresistant disease). In order to model chemoresistance, we treated PIM1 with Adriamycin and cyclophosphamide (AC), standard of care NAC for TNBC patients, which resulted in partial response but left residual disease. To characterize subclonal dynamics in response to NAC, we transduced freshly isolated PIM1 cells with a lentiviral library expressing 25 million unique DNA barcodes (Cellecta) using conditions to ensure each transduced cell contained a single unique barcode. Transduced cells were selected with puromycin, then orthotopically implanted into immuno-compromised mice. High-throughput barcode sequencing revealed reproducible maintenance of greater than 60,000 unique barcodes in PDX tumors. Comparison of barcode distribution in tumors treated with vehicle or NAC will reveal whether NAC selects for a subpopulation of cells during the development of resistance. Future directions will include whole-exome and RNA sequencing to characterize genomic changes associated with alterations in barcode distribution in response to NAC treatment. Our ultimate goal is to identify novel combination therapies to eliminate subclones that contribute to chemoresistance in primary TNBC.

References

1. Cortazar P, et al. (Pathological complete response and long-term clinical benefit in breast cancer: the CTNeoBC pooled analysis. The Lancet 384(9938):164-172.

2. Shah SP, et al. (2012) The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486(7403):395-399.

3. Nguyen LV, et al. (2014) DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts. Nat Commun 5.

Citation Format: Echeverria GV, Seth S, Moulder S, Symmans W, Chang J, Cai S, Heffernan T, Piwnica-Worms H. Investigating clonal dynamics in triple negative breast cancer chemoresistance. [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 P3-06-04.

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 &gt;10% or if &gt;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 &gt;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.

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.

Comparison of molecular subtype distribution in triple-negative inflammatory and non-inflammatory breast cancers

Introduction

Because of its high rate of metastasis, inflammatory breast cancer (IBC) has a poor prognosis compared with non-inflammatory types of breast cancer (non-IBC). In a recent study, Lehmann and colleagues identified seven subtypes of triple-negative breast cancer (TNBC). We hypothesized that the distribution of TNBC subtypes differs between TN-IBC and TN-non-IBC. We determined the subtypes and compared clinical outcomes by subtype in TN-IBC and TN-non-IBC patients.

Methods

We determined TNBC subtypes in a TNBC cohort from the World IBC Consortium for which IBC status was known (39 cases of TN-IBC; 49 cases of TN-non-IBC). We then determined the associations between TNBC subtypes and IBC status and compared clinical outcomes between TNBC subtypes.

Results

We found the seven subtypes exist in both TN-IBC and TN-non-IBC. We found no association between TNBC subtype and IBC status (P = 0.47). TNBC subtype did not predict recurrence-free survival. IBC status was not a significant predictor of recurrence-free or overall survival in the TNBC cohort.

Conclusions

Our data show that, like TN-non-IBC, TN-IBC is a heterogeneous disease. Although clinical characteristics differ significantly between IBC and non-IBC, no unique IBC-specific TNBC subtypes were identified by mRNA gene-expression profiles of the tumor. Studies are needed to identify the subtle molecular or microenvironmental differences that contribute to the differing clinical behaviors between TN-IBC and TN-non-IBC.

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.

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.

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.

Different Biological Processes Are Associated with Prognosis and Chemotherapy Sensitivity in the Different Molecular Subtypes of Breast Cancer

Background: Breast cancer includes multiple different molecular subtypes. We hypothesized that different biological processes and molecular markers may be associated with prognosis and chemotherapy sensitivity in the different subtypes.Methods: We performed gene set analysis in ER-positive/HER-2-normal (ER+) and ER-negative/HER-2-normal (ER-) cancers separately to identify gene sets that are associated with prognosis and chemotherapy sensitivity. We tested 5295 different, functionally annotated gene sets (GS) that collectively represent almost all known biological and metabolic pathways in human cells. Significance was estimated with permutation test. Three separate cohorts on untreated HER2-normal patients (n=234, n=175, n=170) and 3 cohorts of patients with neoadjuvant therapy (n=198, n=85, n=61) were included in this analysis. We performed analysis of each data set separately and also as pooled data.Results: When data sets were analyzed individually, 753 to 938 GS were associated with prognosis (P≤0.05) in ER+ cancers including 186 common to all, and 408 to 579 GS were associated with prognosis in ER- cancers including 1 common to all and 141 common to at least two data sets. Within each data set, the number of overlapping GS between the ER+ and ER- prognostic lists ranged from 33 to 112. In the neoadjuvant data sets, 555 to 674 GS were associated with response in ER+ cancers (195 common to at least two, 4 common to all) and 543 to 730 in ER- cancers (268 common to two, 22 common to all). When the predictive GS for ER+ cancers were compared to those for ER- cancers, there were only 10 GS in common. A meta analyses of the combined prognostic data sets yielded 384 GS with p≤0.0001 in ER+ cancers and 47 in ER- cancers, respectively, with 12 GS common to both. A meta analyses of the combined neoadjuvant data sets yielded 92 GS associated with pCR in ER+ cancers and 110 GS in the ER- cancers. Only 2 GS were common to both. Functional analysis indicated that DNA replication, mitotic spindle checkpoint and plasma cell function were the most common prognostic pathways in ER+ cancer. T cell differentiation, glycolipid metabolism and immune functions were the most commonly prognostic pathways in ER- cancer with a notable absence of proliferation related gene sets. DNA replication, spindle and microtubule activity and cell cycle regulation were associated with chemotherapy response in ER+ cancers; oxidative stress, blood vessel formation in ER- cancers.Conclusion: These data indicate that prognosis and chemotherapy response are associated with different gene sets in ER+ and ER- cancers.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6124.

The Molecular Anatomy of Breast Cancer Stroma; Independent Prognostic Role in ER-Positive and ER-Negative Cancers

BackgroundIn this paper we examine the various molecular components of a breast cancer stromal gene signature and correlate these with clinical phenotype and outcome including prognosis and response to preoperative chemotherapy.MethodsWe compared Affymetrix HGU133A-based gene expression profiles of 37 matching core needle biopsies (CNB) and fine-needle aspirations (FNA) from the same cancers. Genes over-expressed in CNB relative to the FNA were defined as the “stromal signature”. Gene expression data from 56 breast cancer cell lines, two separate neoadjuvant data sets (n=233, n=103), 3 independent cohorts of node negative, untreated patients (n=286, n=198, n=200) and 259 estrogen receptor-positive (ER+) tamoxifen-treated patients were used to assess the prognostic and predictive values of these genes in ER+ and ER- cancers separately. Univariate and multivariate Cox analyses were performed. Metagenes were defined as average expression of co-clustered genes.Results293 probe sets (206 genes) were significantly over-expressed in the CNBs (false discovery rate ≤ 0.001, fold-change ≥ 3). These genes overlapped with previously reported stromal signatures and fell into several co-expression clusters including a B-cell/Plasma Cell (B-cell), Dendritic cell, extracellular matrix (ECM), and TGFb-receptor metagenes. Interestingly, ER+ and ER- cancers showed a significantly different stroma-gene expression pattern, and many stromal genes were also differentially expressed between ER+ and ER- breast cancer cell lines. The ECM and TGFb metagenes had modest and variable prognostic value across different datasets in both ER groups. The Dendritic and B cell metagenes were highly co-expressed, but the B-cell metagene had more robust and consistent prognostic value. The B-cell metagene was statistically significant prognostic in univariate and multivariate analysis in ER+/High proliferative and ER- tumors, but it was not prognostic in ER+/Low proliferative tumors. In the 3 different node negative, untreated patient cohorts, the ER+/High proliferative cancers in the lowest B-cell metagene tertile had 10-year distant metastasis free survival (DMFS) of 0.18 (0.07-0.46), 0.22 (0.06-0.75), and 0.44 (0.21-0.92) compared to 0.71 (0.54-0.94), 0.89 (0.71-1.00) and 0.89 (0.71-1.00) in the highest tertile. Among the ER- cancers, the lowest B cell metagene group had 10-year DMFS of 0.57 (0.44-0.75), 0.63 (0.48-0.83), and 0.44 (0.25-0.76) compared to 0.93 (0.81-1.00), 0.83 (0.64-1.00) and 0.83 (0.58-1.00) in the highest B-cell metagene group in each prognostic dataset, respectively. The B-cell metagene was also prognostic in univariate (HR 0.83 (0.71-0.98) p=0.03) and multivariate (HR 0.80 (0.68-0.94) p=0.007) analysis in the Tamoxifen-treated cohort. None of the above stromal metagenes showed reproducible association with response to chemotherapy.ConclusionsThe B-cell/Plasma cell metagene component of the “stroma-related genes” is a robust and reproducible prognostic marker in ER+/High proliferative and also in ER- cancers. Other stromal genes are variably expressed in ER+ and ER- tumors and many are also expressed by neoplastic cells in culture and by primary tumors and carry less reproducible prognostic value.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 105.

Secreted Frizzled Receptor Protein 1 (sFRP-1) as Both a Potential Novel Biomarker of Triple Negative Breast Cancer (TNBC), and Its Sensitivity Against Taxane/Anthracycline Containing Neoadjuvant Chemotherapy

Background: Patients with triple negative breast cancer (TNBC) carry an unfavorable prognosis despite an increased response to chemotherapy compared to other breast cancer subtypes. While tumor grade/proliferation is one major determinant of chemosensitivity in TNBC, we have recently suggested additional (molecular) features to have a significant impact as well.Material and Methods: Differential gene expression analysis was performed between TNBC (n=27) versus non-TNBC (n=106) using gene expression profiles (Affymetrix U133A) from breast cancers of patients treated with neoadjuvant taxane/anthracycline chemotherapy at MDACC (Hess et al. 2006). Differentially expressed genes were validated using profiles of 286 patients with breast cancer who did not receive systemic therapy (Wang et al. 2006). Genes were tested for (a) an association with relapse free survival, (b) an association with response to neoadjuvant chemotherapy and (c) correlation with Ki67 expression. siRNA knockdown experiments using triple negative and non-triple negative cell lines were carried out using both (a) a proliferation assay and (b) a chemosensitivity assay.Results: The secreted frizzled receptor protein 1 (sFRP-1), a member of the wnt-pathway, was identified as the top differentially overexpressed gene in TNBC (i.e. false discovery rate [FDR] &lt; 0,0001) and successfully validated in the independent dataset. In TNBC, sFRP-1 expression showed no association with relapse-free survival, but significantly correlated with an increased sensitivity to neoadjuvant chemotherapy. Importantly, it did not correlate with expression of Ki67 in TNBC. siRNA-mediated knockdown of sFRP-1 expression intriple negative MDA-MB 468 breast cancer cell lines was associated with increased proliferation and most importantly decreased sensitivity to paclitaxel in vitro.Conclusion: We suggest sFRP-1 as a novel marker of (a) the triple negative breast cancer phenotype in general and (b) its chemosensitivity to taxane-containing chemotherapy independent of Ki67 expression. Preliminary siRNA-based cell culture experiments suggest sFRP-1 to play a causal role with regard to chemosensitivity of TNBC rather than solely constituting a novel marker thereof.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4047.

Consistent Principal Components from Triple Negative Breast Cancer Expression Profiles Yields Agent Specific Predictors of Chemotherapy Response

Genome scale expression profiling is likely to yield improved methods for optimizing therapy for individual breast cancer patients. Microarray based predictors of response to chemotherapy have been described for ER-positive tumors, but supervised methods haven't yielded highly accurate predictors of response in triple-negative breast cancer (TNBC). The problem of deriving predictive or prognostic classifiers is not trivial, and care must be taken to avoid pitfalls such as data set-specific noise and overfitting.To overcome these problems, we developed a two-stage unsupervised method to derive consistent metagenes from multiple data sets. In the first stage, we used principal component analysis to identify aspects of gene expression profiles that are consistently observed in multiple starting data sets. We then identified a subset of genes that best captured the information derived from these components. In the second stage, we factorized this subset of genes and derived metagenes applicable to any external data set. With this method, overfitting is eliminated by virtue of the unsupervised approach, and data set-specific noise is reduced by selecting only components presented in multiple data sets.We first applied our method to four TNBC data sets not obtained in a neoadjuvant setting and derived four metagenes. We then applied these metagenes to another four independent data sets annotated with response to various neoadjuvant therapies in order to assess their predictive performances. Two of the metagenes were associated with response: one predicted pathological complete response (pCR) in the two TFAC cohorts but not in the other two cohorts (Fig. a); the other was associated with pCR to TFAC, residual disease (RD) to epirubicin single agent, but not with response to FEC (Fig. b). Notably, these metagenes derived in an unsupervised manner were more strongly predictive than were classifiers derived using conventional supervised methods.As conclusion, we report and validate an unsupervised strategy as a robust and powerful alternative to supervised methods for deriving predictors for response to chemotherapy from microarray data. If confirmed in additional independent cohorts, these metagenes may lead to clinical tests to optimize therapy for individual TNBC patients.Figure 1. ROC curves indicate the association between two metagenes and agent-specific pathological complete response to neoadjuvant therapy.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3163.

Evaluation of the Predictive Performance and Regimen Specificity of a 30-Gene Predictor of Pathologic Complete Response in a Prospective Randomized Neoadjuvant Clinical Trial for Stage I-III Breast Cancer

Purpose: To prospectively evaluate in a randomized trial if a previously reported multigene predictor of pathologic complete response (pCR) to preoperative weekly paclitaxel and fluorouracil-doxorubicin-cyclophosphamide (T/FAC) chemotherapy can accurately predict pCR to neoadjuvant T/FAC chemotherapy, and if it also predicts pCR to FAC only chemotherapy. Furthermore, it is unknown if the T/FAC regimen is superior to 6 courses of FAC; therefore we compare the pCR rates for patients who receive T/FAC versus FACx6 preoperative chemotherapy.Materials and Methods: Patients with stage I-III breast cancer (n=273) were randomly assigned to receive either 12 courses of weekly paclitaxel followed by 4 courses of FAC (T/FAC, n=138), or 6 courses of FAC (FACx6, n=135) neoadjuvant chemotherapy. All patients underwent a pretreatment FNA biopsy of the tumor for gene expression profiling on oligonucleotide microarrays, and treatment response prediction (pCR versus residual disease, RD) was performed using the multigene predictor. Predicted and observed pathologic responses were compared independently in the two treatment arms.Results: The pCR rate was 19% with T/FAC and 9% with FACx6 (p&lt;0.05). In the T/FAC arm, the positive predictive value (PPV) of the genomic predictor was 38% (95%CI:21-56%), the negative predictive value (NPV) 88% (CI:77-95%), sensitivity 63% (CI:38-84%), specificity 72% (CI:60-82%), and the AUC 0.711. In the FAC only treatment arm, the PPV was 9% (CI:1-29%), the NPV 92% (CI:83-97%), sensitivity 29% (CI:4-71%), specificity 75% (CI:64-84%), and the AUC 0.584. This suggests that the genomic predictor is regimen-specific. In a multivariate analysis including age, tumor size, nodal status, histologic grade, HER2 and estrogen receptor (ER) status and the genomic predictor, only ER status was a significant predictor of pCR.Discussion: Pathologic complete response rate was significantly higher in the T/FAC arm compared to the FACx6 arm indicating a higher efficacy of the paclitaxel containing arm. Patients who were predicted to achieve pCR to T/FAC had a significantly higher pCR rate (38%) than unselected patients (19%) or patients predicted to have RD (12%) when treated with this regimen. These results confirm that the multigene predictor can identify patients with greater than average sensitivity to T/FAC chemotherapy.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 101.

Clinical Subtype-Derived p53 Gene Signature Is Predictive of Prognosis and Response to Chemotherapy in ER-Positive but Not in ER-Negative Breast Cancers

BackgroundBreast cancer is a collection of molecularly distinct neoplastic diseases and therefore, we hypothesized that p53 gene mutations may lead to different transcriptional changes in the different molecular subtypes and these may translate into subtype-dependent prognostic and predictive values.MethodsWe developed gene expression-based predictors of p53 status separately for estrogen receptor-positive (ER+) and -negative (ER-) breast cancers from a publicly available data set with known p53 mutation status (n=251). We validated the two signatures on an independent cohort of cancers (n=103) with known p53 functional status and tested their prognostic and predictive values on two other cohorts of breast cancers that received no systemic adjuvant therapy (n=255; n=198), and on one cohort of ER+ patients treated with adjuvant tamoxifen (n=277). We also examined if the p53 signatures were associated with chemotherapy sensitivity in ER+ and ER- cancers, respectively in two separate neoadjuvant data sets (n=233; n=103).ResultsWe developed a 39-gene p53 signature derived from 213 ER+ and a 30-gene p53 signature derived from 38 ER- breast cancers with no overlapping genes. External validation showed a sensitivity and specificity of 89% and 54%, respectively for the 39-gene signature in ER+ breast cancers; and 82% and 61%, respectively for the 30-gene signature in ER- cancers. The 39-gene signature was predictive of worse distant metastasis free survival (DMFS) in ER+ cancers with p53 dysfunction in both prognostic data sets (Hazard ratio (HR): 2.3 (95% confidence interval (CI):1.25-4.23, p=0.005 and HR:2.17 (95%CI:0.85-5.56, p=0.09). It remained predictive of worse DMFS even after tamoxifen adjuvant therapy (HR=2.43, 95%CI: 1.35-4.38, p&lt;0.0001). In contrast it was associated with higher chemotherapy sensitivity in ER+ cancers. Its predictive accuracy for pathologic complete response was of 68% (95%CI: 64-70%), sensitivity 89% (95%CI: 58-98%), specificity 67% (95%CI: 65-68%), positive predictive value 15% (95%CI: 10-17%), and negative predictive value 99% (95%CI: 96-100%) in ER+ cancers. The prognostic and predictive values remained significant in multivariate analysis. The same 39-gene signature was not prognostic or predictive in ER- cancers. The 30-gene signature derived from ER- tumors had no chemotherapy response predictive value in either ER- or ER+ cancers. The p53 dysfunctional cases showed better survival in the absence of any adjuvant therapy among ER- cancers. It had no prognostic value in ER+ cancers.ConclusionThese observations support the hypothesis that predictive or prognostic biomarkers may be best developed separately for different clinical and molecular subsets of breast cancer. P53 dysfunction is clinically most relevant in ER+ breast cancers.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6122.