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.

The quality of life index: a pilot study integrating treatment efficacy and quality of life in oncology

The majority of women diagnosed with breast cancer will experience some form of drug-related toxicity and subsequent impairments in Health-related Quality of Life (HRQoL). Despite this, HRQoL is assessed inconsistently and there is no validated method to integrate HRQoL data into the assessment of therapeutic agents. This proof of concept study utilizes data from the neoadjuvant I-SPY 2 clinical trial to describe the development of the Quality of Life Index (QoLI) measure. The QoLI represents a single composite score that incorporates validated longitudinal measures of clinical efficacy and QoL and one that permits a more comprehensive, direct comparison of individual therapeutic agents. Preliminary data suggest the QoLI is able to distinguish between agents based on their efficacy and toxicity; with further validation, the QoLI has the potential to provide more patient-centered evaluations in clinical trials and help guide treatment decision making in breast cancer and other oncologic diseases.

Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types

Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia to evaluate cell lines as models of primary tumors across 22 tumor types. We perform correlation analysis and gene set enrichment analysis to understand the differences between cell lines and primary tumors. Additionally, we classify cell lines into tumor subtypes in 9 tumor types. We present our pancreatic cancer results as a case study and find that the commonly used cell line MIA PaCa-2 is transcriptionally unrepresentative of primary pancreatic adenocarcinomas. Lastly, we propose a new cell line panel, the TCGA-110-CL, for pan-cancer studies. This study provides a resource to help researchers select more representative cell line models.

Cell lines are used ubiquitously in cancer research but how well they represent the tumor type they were derived from is variable. Here, the authors compare transcriptomic profiles of 22 tumor types and cell lines and propose a new comprehensive cell line panel for pan-cancer studies.

Abstract P5-15-01: The use of 18F-FDG PET/CT as an initial staging procedure for stage II-III breast cancer reduces false positives, costs, and time to treatment: A multicenter value analysis in the I-SPY2 trial

Introduction: Diagnostic metastatic staging imaging (SI) for asymptomatic stage I-II patients (pts) is not routinely recommended, but is warranted in stage II-III pts with high risk biological subtypes, where previous trials have shown up to a 15% rate of de novo metastatic disease. NCCN guidelines endorse CT CAP and bone scan (STD) for stage III pts, but not PET/CT, and PET/CT is not covered in most parts of the country. We present data on the performance and value of PET/CT.

Methods: Data were available for 799 high risk clinical stage II-III pts screened for I-SPY2 at UCSF, Uminn, UAB, and Georgetown. Of these, 564 pts ranging in age from 25-81 (median = 48) had complete records that were retrospectively reviewed for SI and potential false positives (FP), defined as incidental findings on SI proven benign by subsequent workup. Economic evaluation was conducted from the payer perspective using the mean national 2018 Medicare Physician Fee Schedule and representative costs from the UCSF billing department. The incremental cost effectiveness ratio (ICER) measured the cost of using PET/CT per percent patient (pt) who avoided a FP.

Results: The rate of de novo metastatic disease was 4.8% (38/799), range 3.6-6.4%. Of the 564 pts with complete records, diagnostic SI varied significantly among the four sites (p &lt; 0.0001). STD was used for most pts at UAB (92.8%, 141/152) and Georgetown (85.7%, 54/63), while PET/CT was used for most pts at UCSF (86.6%, 226/261) and Uminn (63.6%, 56/88). Chest X-ray was used for 29.5% (26/88) at Uminn. There were significantly more pts with FP in the group that received STD (22.1%, 51/231) vs. PET/CT (11.1%, 33/298) (p &lt; 0.05). Mean time between incidental finding on SI to determination of FP was 10.8 days. When controlling for institution, mean time from cancer diagnosis to initiation of neoadjuvant chemotherapy was significantly different between STD (44.3 days) and PET/CT (37.5 days) groups (p &lt; 0.05). When aggregating the four sites using mean costs from the 2018 Medicare Physician Fee Schedule, the mean cost/pt was $1132 for STD vs. $1477 for PET/CT. The mean increase in price from baseline SI costs due to FP workup was $216 (23.6%) for STD vs. $65 (4.6%) for PET/CT. The ICER was $31 per percent pt who avoided a FP. When analyzing UCSF pts alone using representative reimbursements from Medicare, the mean cost/pt was $1236 for STD vs. $1081 for PET/CT; using representative reimbursements from Anthem Blue Cross, the mean cost/pt was $3080 for STD vs. $1662 for PET/CT. The ICERs were -$10 and -$95 per percent pt who avoided a FP, respectively.

Conclusion: As compared to STD metastatic staging workup, PET/CT added value by decreasing FP two-fold. This reduced direct costs of FP workup procedures that took a mean time of 10.8 days to resolve. PET/CT also accelerated treatment start. Reducing the chance of FP workup for metastatic disease is of enormous value to pts. Our data establish the value of PET/CT for staging in our high risk clinical stage II-III trial population and highlight the need for alignment between hospital pricing strategies and payer coverage policies in order to deliver high value care to pts.

Citation Format: Hyland CJ, Varghese F, Yau C, Beckwith H, Khoury K, Varnado W, Hirst G, Chien J, Yee D, Isaacs C, Forero-Torres A, Esserman L, Melisko M, I-SPY2 Consortium. The use of 18F-FDG PET/CT as an initial staging procedure for stage II-III breast cancer reduces false positives, costs, and time to treatment: A multicenter value analysis in the I-SPY2 trial [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 P5-15-01.

Abstract PD4-04: Role of breast MRI in predicting pathologically negative nodes after neoadjuvant chemotherapy in cN0 patients in the I-SPY2 trial

Background

In clinically node-negative (cN0) breast cancer patients with triple negative (TN) and HER2+ disease and breast pathological complete response (breast pCR), low rates of nodal positivity after neoadjuvant chemotherapy (NAC) have been demonstrated. In these patients, the omission of surgical axillary staging has been proposed. However, this information is not routinely known preoperatively. We aimed to validate the correlation between pathologic breast response and pathologic nodal status, and evaluate the relationship between response of the breast tumor on MRI and pathologic nodal status after NAC in cN0 patients in the I-SPY2 trial.

Methods

We identified all patients with cT1-4 cN0 breast cancer prior to NAC from graduated arms of the I-SPY2 trial, a prospective neoadjuvant chemotherapy trial. Absence of residual disease post-NAC was defined as longest diameter (LD) of 0 mm on MRI. Breast pCR was defined as the absence of invasive tumor in the breast at surgery. Associations between ypN0 and patient, MRI, and tumor characteristics were assessed using chi-square tests and univariate regression.

Results

Of 365 cT1-4 cN0 patients included, 128 had HR+/HER2- tumors (35%), 60 HR+/HER2+ tumors (16%), 34 HR-/HER2+ tumors (9%) and 143 TN tumors (39%). Overall, 283 patients (78%) were ypN0 after NAC and 152 patients (42%) had a breast pCR. ypN0 rate was higher in patients with a breast pCR than those with residual disease (93% vs 66%, p&lt;0.001). Patients with HR-/HER2+ and TN tumors were more likely to be ypN0 (97% and 87% respectively) than patients with HR+/HER2- and HR+/HER2+ disease (66% and 71% respectively, p&lt;0.001). Other characteristics associated with ypN0 were tumor grade (grade I 57%, grade II 66%, grade III 84%; p=0.002), MammaPrint Classification (High Risk 1 68% and High Risk 2 87%; p&lt;0.001) and absence of residual tumor in the breast on MRI (87% vs 72% in patients with evidence of tumor on MRI post-NAC/pre-surgery; p=0.003).

In patients with HR-/HER2+, HR+/HER2+, HR-/HER2+ or TN disease and a breast pCR, ypN0 rate was respectively 82%, 96%, 96% and 97% (table 1). In patients with HR+/HER2-, HR+/HER2+, HR-/HER2+ or TN disease and with no evidence of residual disease in the breast on MRI, rate of ypN0 was 71%, 80%, 94% and 96% respectively.

Conclusion

In cT1-4 cN0 breast cancer patients with HR+/HER2+, HR-/HER2+ and TN tumors and a breast pCR, ypN0 rates after NAC are extremely high. In patients with HR-/HER2+ and TN tumors with no residual breast disease on MRI after NAC and pre-surgery, ypN0 rates are high enough to consider omission of axillary surgery. In patients with HR+ tumors, MRI is unsufficiently predictive for pathological response and can therefore not be used to select ypN0 patients. Research on the prediction of ypN0 in cN+ I-SPY2 patients is ongoing.

Nodal status in patients with pCR and absence of residual disease on MRI Number of positive nodesBreast Cancer Subtype0123AllBreast pCR     HR+/HER2-27(82)2(6)4(12)033(100)HR+/HER2+24(96)01(4)025(100)HR-/HER2+24(96)1(4)0025(100)TN67(97)2(3)0069(100)Absence of residual disease on MRI     HR+/HER2-24(71)7(21)3(9)034(100)HR+/HER2+16(80)3(15)01(5)20(100)HR-/HER2+15(94)1(6)0016(100)TN54(96)2(4)0056(100)

Citation Format: van der Noordaa ME, Esserman L, Yau C, Mukhtar R, Price E, Hylton N, 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, van 't Veer L, Hirst G, Lancaster R, Wallace A, Alvaredo M, Symmans F, Asare S, Boughey JC, I-SPY2 Consortium. Role of breast MRI in predicting pathologically negative nodes after neoadjuvant chemotherapy in cN0 patients in the I-SPY2 trial [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 PD4-04.

Abstract P2-14-01: The impact of local therapy on locoregional recurrence in women with high risk breast cancer in the neoadjuvant I-SPY2 TRIAL

Background: In women with breast cancer receiving neoadjuvant chemotherapy, residual cancer burden (RCB) predicts distant recurrence and survival. In those with high risk tumors, locoregional recurrence (LRR) remains a concern, and has been associated with type of local therapy received. We evaluated the impact of local therapy on LRR in the ISPY-2 TRIAL.

Methods: Data were analyzed in Stata 14.2, using Chi2 test, log rank test, and a Cox proportional hazards model. RCB was considered a categorical variable (0/1 versus 2/3), as described in prior publications. Breast surgery categories were lumpectomy +/- radiotherapy, or mastectomy +/- radiotherapy. Axillary surgery was defined as sentinel lymph node (SLN) surgery (≤6 nodes removed) or axillary dissection (&gt;6 nodes).

Results: Follow up data from the I-SPY2 TRIAL were available for 630 patients (median follow up 2.76 yrs, range 0.4-7.2). Type of local therapy was significantly associated with clinical stage at presentation, with stage III patients most frequently undergoing mastectomy + radiation (p&lt;0.001). Women with higher RCB were more likely to undergo mastectomy than those with lower RCB (61.3% vs 48.8% mastectomy rate, p=0.002), and more likely to receive adjuvant radiotherapy (62.0% vs 53.9%, p=0.048). There was no association between clinical stage, type of surgery, or radiotherapy and LRR (Table). Higher RCB was significantly associated with LRR, with 3 year locoregional recurrence free rate of 95.1% in RCB 0/1 versus 89.9% in RCB 2/3 (p=0.003).

In a Cox model adjusting for clinical stage, tumor subtype, surgical therapy, RCB status, nodal radiation, and age, significant predictors for LRR were tumor subtype and RCB status. Hazard ratio (HR) for LRR in those with RCB 0/1 was 0.39 compared to those with RCB 2/3 (95% CI 0.17-0.87, p=0.021). There was no difference in LRR between breast conservation and mastectomy; within the breast conservation group, those who had lumpectomy alone had higher hazard of LRR compared to those having lumpectomy + radiation (HR 3.1, 95% CI 1.1-9.2, p=0.043).

Conclusions: Extent of surgical therapy was not associated with local tumor control, regardless of advanced tumor stage at presentation. Rather, tumor biology and response to therapy were the best predictors of LRR. These data highlight the opportunity to minimize the morbidity of extensive surgical therapy for patients with excellent response to systemic therapy.

LRR rates by clinical features and treatment status FrequencyLRR RateP valueClinical Stage  0.5I240 (47.5%)5.8% II185 (36.6%)8.7% III80 (15.8%)6.3% Tumor Subtype  0.014ER+PR+Her2-161 (26.4%)3.1% ER+PR-Her2-56 (9.2%)3.6% Her2+176 (28.9%)6.3% Triple negative216 (35.5%)11.1% Local therapy  0.169Lumpectomy85 (13.5%)11.8% Lumpectomy with radiation198 (31.4%)5.6% Mastectomy173 (27.5%)5.2% Mastectomy with radiation174 (27.6%)8.6% Axillary surgery  0.23None5 (0.8%)20% SLN329 (52.2%)5.8% ALND296 (47%)8.5% Axillary radiation  0.535Yes42 (6.7%)9.5% No588 (93.3%)7.0% Axillary management  0.2No surgery or radiation5 (0.8%)20.0% SLN312 (50%)5.3% SLN+Axillary radiation17 (2.7%)8.3% ALND271 (43%)10.3% ALND+Axillary radiation25 (4%)5.4% RCB  0.0020/1293 (50.1%)3.8% 2/3292 (49.9%)10.3% 

Citation Format: Silverstein J, Suleiman L, Yau C, Price ER, Singhrao R, Yee D, DeMichele A, Isaacs C, Albain KS, Chien AJ, Forero-Torres A, Wallace AM, Pusztai L, 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, Leyland-Jones B, Tripathy D, Moulder SL, Rugo HS, Schwab R, Lo S, Helsten T, Beckwith H, I-SPY 2 TRIAL Consortium, Berry DA, Asare SM, Esserman LJ, Boughey JC, Mukhtar RA. The impact of local therapy on locoregional recurrence in women with high risk breast cancer in the neoadjuvant I-SPY2 TRIAL [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 P2-14-01.

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 PD4-03: MRI detection of residual disease following neoadjuvant chemotherapy (NAC) in the I-SPY 2 TRIAL

Background: Detecting residual disease accurately using MRI after NAC to identify both responders and non-responders is essential for de-escalating therapy or redirecting patients to more effective treatment. The purpose of this study is to determine if the combination of longest diameter (LD) and functional tumor volume (FTV) from dynamic contrast enhanced (DCE-) MRI is superior to FTV alone or LD alone for assessing treatment response after neoadjuvant therapy in breast cancer patients.

Methods: Data from patients in the graduated drug arms of the I-SPY 2 trial were included in the analysis. Both LD and FTV were assessed using DCE-MRI after neoadjuvant therapy. LD was measured by the site radiologist as the longest dimension of the enhanced area on early post-contrast images. Functional tumor volume (FTV) was assessed as the sum of voxels with enhancement above specific thresholds within the pre-defined region-of-interest (ROI). A linearized variable was derived to represent the combination of FTV and LD. The area under the receiver operating characteristic curve (AUC) was used to evaluate the assessment of treatment response, pathologic complete response (pCR), defined as no invasive disease in the breast and lymph nodes, and in-breast pCR, defined as no invasive disease in the breast only. The analysis was performed in the full cohort and in breast cancer subtype defined by hormone receptor status and HER2 status.

Results: Among the patient cohort of N=675 with FTV and LD, 247 (37%) did and 428 (41%) did not achieve pCR after neoadjuvant therapy. pCR rates varied among HR/HER2 subtypes (HR+/HER2-: 19%; HR+/HER2+: 38%; HR-/HER2+: 71%; HR-/HER2- (triple negative, TN): 43%). In-breast pathologic complete response rates were slightly higher in each group (full: 41%; HR+/HER2-: 23%; HR+/HER2+: 43%; HR-/HER2+: 72%; HR-/HER2-: 49%). Table 1 shows AUCs for assessing pCR using FTV alone, LD alone, and the variable combining FTV and LD. Higher AUCs were observed in all patient groups using the combined variable. AUC of 0.79 (95% CI: 0.77, 0.81) was observed for the combined variable to assess pCR in the full cohort. AUCs varied from 0.69 to 0.86 among HR/HER2 subgroups (HR+/HER2-: 0.69; HR+/HER2+: 0.74; HR-/HER2+: 0.86; HR-/HER2-: 0.80), with no difference in assessing pCR or in-breast pCR. The performance is best for the HR- subtypes.

Conclusions: Both FTV and LD can be used in the assessment of invasive disease residual after neoadjuvant therapy. The combined variable of FTV and LD achieved highest AUCs, compared to using individual variable alone. Tools to improve performance in the HR+ subsets are underway.

AUCs of MR measurements for identifying pCR  FTV alone (95% CI)LD alone (95% CI)Combined (95% CI)FullWith subtype adj.0.73 (0.71, 0.75)0.77 (0.74, 0.79)0.79 (0.77, 0.81)FullWithout subtype adj0.69 (0.65, 0.73)0.72 (0.68, 0.76)0.75 (0.71, 0.79)HR+/HER2- 0.68 (0.60, 0.77)0.68 (0.59, 0.77)0.69 (0.61, 0.77)HR+/HER2+ 0.65 (0.56, 0.75)0.72 (0.64, 0.80)0.74 (0.66, 0.82)HR-/HER2+ 0.69 (0.55, 0.83)0.82 (0.71, 0.92)0.86 (0.77, 0.95)HR-/HER2- (TN) 0.72 (0.66, 0.79)0.73 (0.67, 0.80)0.80 (0.74, 0.85)

Citation Format: Li W, Newitt D, Yun BL, Kornak J, Joe B, Yau C, Abe H, Wolverton D, Crane E, Ward K, Nelson M, Niell B, Drukteinis J, Oh K, Brandt K, Bang DH, Ojeda H, Eghtedari M, Sheth P, Bernreuter W, Umphrey H, Rosen M, Dogan B, Yang W, Esserman L, Hylton N. MRI detection of residual disease following neoadjuvant chemotherapy (NAC) in the I-SPY 2 TRIAL [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 PD4-03.

Abstract P3-01-02: Detection of circulating tumor cells (CTC) in blood and disseminated tumor cells (DTC) in bone marrow at surgery identifies breast cancer patients (pts) with long-term risk of distant recurrence and breast cancer-specific death

We examined the prognostic impact of CTCs and DTCs detected at the time of definitive surgery in pts diagnosed with early breast cancer (EBC).

Methods: Blood and bone marrow samples from 742 treatment-naïve EBC pts, not eligible for neoadjuvant therapy, were collected immediately prior to surgery. 87% were hormone receptor (HR)-positive, and 71% were node-negative. DTCs (n=584) were enumerated using an EPCAM-based method involving immunomagnetic enrichment and flow cytometry (IE/FC). CTCs were enumerated either by IE/FC (n=288) or CellSearch (n=380). Optimal cutoffs for CTC-/DTC-positivity were selected using Monte-Carlo cross validation. Multivariate Cox regression analysis was performed to determine correlation between levels of CTCs/DTCs vs. distant recurrence-free survival (DRFS) and breast cancer-specific survival (BCSS). The overall median follow-up was 7.1 years for DRFS and and 9.1 years for BCSS, but extended up to 13.3 years in subset analyses (Table 1).

Results: CTC-positivity by CellSearch was associated with HER2-positivity (Fisher p=0.01). Using optimized cutoffs in multivariate analyses, we found that CTC-positive pts by CellSearch had a statistically significant increased risk of distant recurrence (HR 4.93, p=0.0067). Moreover, pts who were CTC-positive by IE/FC had a statistically significant increased risk of breast cancer-specific death (HR=3.54, p=0.0138). DTC status, by itself, was not prognostic; however, when combined with CTC status by IE/FC (n=273), positive detection for both (CTC+DTC+) was significantly associated with increased risk of distant recurrence (HR=3.09, p=0.0270) and breast cancer-specific death (HR=4.55, p=0.0205).

Table 1.Multivariate analysis to determine the prognostic significance of CTCs and DTCs detected at the time of surgery in treatment naive early breast cancer patients. Adjusted for age at diagnosis, tumor size, pathologic stage, HR and HER2 status, node status and grade.  DRFS  BCSS  Variable and Method% positiveHR [95% CI]Wald p-valueMedian f/u [range] Years*HR [95% CI]Wald p-valueMedian f/u [range] Years*CTC+ vs. CTC- by CellSearch94.93[1.56-15.6]0.00676.4 [0.16-13.8]4.50[0.76-26.5]0.09627.5 [0.71-15.0]CTC+ vs. CTC- by IE/FC401.92[0.93-3.95]0.07599.8 [0.09-18.5]3.54[1.29-9.72]0.013813.3 [1.93-18.5]DTC+ vs. DTC- by IE/FC181.46[0.75-2.81]0.26317.5 [0.09-18.5]1.48[0.64-3.42]0.35429.8 [1.55-18.5]CTC+DTC+ vs. CTC-DTC- by IE/FC8**3.09[1.14-8.40]0.02709.8 [0.09-18.5]4.55[1.26-16.39]0.020513.3 [1.93-18.5]*f/u - follow-up; **double positive

Conclusions: We demonstrate the impact of quantitative evaluation of CTCs and DTCs by IE/FC. Our large single institution dataset, in which CTCs and DTCs have been contemporaneously quantitated, has the longest patient follow-up. Simultaneous detection of CTCs and DTCs at the time of definitive surgery in treatment naïve EBC pts is an independent prognostic factor associated with increased long-term risk of distant recurrence and death due to breast cancer. Given the lack of early endpoints for low-risk patients, liquid biopsy may be an important consideration for future studies.

Citation Format: Magbanua MJM, Yau C, Wolf D, Lee JS, Chattopadhyay A, Scott JH, Yoder E, Hwang S, Alvarado M, Ewing CA, Delson AL, van't Veer L, Esserman L, Park JW. Detection of circulating tumor cells (CTC) in blood and disseminated tumor cells (DTC) in bone marrow at surgery identifies breast cancer patients (pts) with long-term risk of distant recurrence and breast cancer-specific death [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 P3-01-02.

Abstract PD7-06: Molecular subtypes of invasive lobular breast cancer in the I-SPY2 TRIAL

Background: Invasive lobular carcinoma (ILC) of the breast has distinct histological and molecular variations compared to invasive ductal carcinoma (IDC), including absence of the adhesion protein E-cadherin. Recently, molecular subtypes within ILC have been described, with an analysis from The Cancer Genome Atlas (Ciriello et al) identifying three distinct groups within ILC based on gene expression—reactive-like, immune-related, and proliferative. In this study, we applied this 60-gene classifier to a locally advanced cohort of ILC and mixed ILC/IDC cases from patients screening for the I-SPY 2 neoadjuvant chemotherapy trial.

Methods: The I-SPY 2 TRIAL is open to women with more locally advanced, clinically/molecularly (as assessed by MammaPrint) high risk breast cancer. HR+HER2- MammaPrint Low risk patients ineligible for I-SPY 2 randomization are invited to join a MP Low risk registry. 131 ILC and mixed ILC/IDC tumors from these cohorts (I-SPY 2: n=80; low risk registry: n=51) with pre-treatment Agilent microarrays were available for analysis. We used the Classification to Nearest Centroid technique to assign TCGA subtype to our cohort. We assessed association between TCGA subtype, clinical covariates and response to therapy using a chi-square test. We also evaluated the Euclidean distance between each sample and the three subtype centroids. In an exploratory analysis, we used consensus clustering based on the 1000 most varying genes within the HR+HER2- I-SPY ILC cases to generate new unsupervised groupings, and assessed the concordance with the TCGA reactive-like, immune-related and proliferative subtype assignments.

Results: Of the 131 patients included, most (79%) were HR+HER2-, 11% were HR+HER2+, 2% were HR-HER2+ and 8% were HR-HER2- for a total of 10% HR-. 66 were pure ILC, while 65 were mixed ILC/IDC. Upon applying the TCGA 60-gene classifier, the distribution of ILC subtypes was as follows: 33 (25%) were classified as reactive-like, 50 (38%) were immune-related, and 48 (37%) were proliferative. 64% of triple negative cases were reactive-like; while the HR+HER2- and HER2+ cases were more likely to be in the proliferative or immune-related subtype (p=0.037). Among the 80 I-SPY 2 cases, the overall pathologic complete response rate was low (16%) but equivalent to the overall HR+HER2- I-SPY2 population (16%). This did not differ across the groups defined by the TCGA ILC subtypes (p=0.79).

Interestingly, a subset of cases assigned as reactive-like and immune-related were of similar distance to the proliferative subtype centroid as patients assigned to the proliferative subtype. When we used consensus clustering to identify new subsets within our locally advanced ILC cohort, our unsupervised groupings had only 32% concordance with the TCGA ILC subtype assignments.

Conclusion: The low concordance between our consensus cluster groupings and the TCGA subtype groupings may reflect underlying differences within a locally advanced cohort of ILC cases, like I-SPY, that may not be captured in the 60-gene classifier developed from the overall lower stage TCGA cohort. These findings suggest that considerable molecular heterogeneity exists in lobular cancers, which merits further investigation.

Citation Format: Zhu Z, Yau C, Chien AJ, Haddad T, Esserman LJ, van't Veer L, Mukhtar RA, I-SPY2 Consortium. Molecular subtypes of invasive lobular breast cancer in the I-SPY2 TRIAL [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 PD7-06.

Abstract P4-01-12: Low peripheral blood CD4/CD8 ratio at the time of surgery is a negative long-term prognostic factor in women with early stage breast cancer

It is hypothesized that cancer prognosis may be related to the functional status of the immune system. We examined the correlation between peripheral blood CD4/CD8 ratio measured at the time of surgery and clinical outcome in patients diagnosed with early stage breast cancer.

Patient and Methods

Peripheral blood from 57 treatment-naïve early breast cancer patients, not eligible for neoadjuvant chemotherapy, was collected on the day of definitive surgery. CD4+ and CD8+ T cells were enumerated using flow cytometry and the ratio between the two immune cell populations was calculated. Cox regression analyses were performed to determine the relationship between CD4/CD8 ratio vs. distant disease-free survival (DRFS), breast cancer-specific survival (BCSS) and overall survival (OS). The median follow-up times were 10.1 years (range: 0.4-17.5) and 15.0 (range: 1.0-18.5) for DRFS and BCSS/OS, respectively.

Results

The patients' mean age at diagnosis was 54 years old (range: 31-78). 82% were hormone receptor-positive, 21% HER2-positive, and 61% node-negative. The median CD4/CD8 ratio was 2; and a ratio ≤ 2 was considered low. CD4/CD8 ratio was not associated with any of the clinicopathologic variable examined. Multivariate analysis using a survival model that adjusted for potential confounding factors (age, tumor size, grade, stage, hormone receptor, HER2, lymph-node status) revealed that patients with low CD4/CD8 ratio have statistically significant increased risk of distant recurrence (DRFS HR 5.3, Wald p=0.0381) and death (OS HR 3.8 Wald p=0.0271).

Conclusions

Immune dysfunction at the time surgery is correlated with long-term increased risk for metastatic recurrence and death. Larger clinical studies are warranted to confirm the results of this study.

Citation Format: Magbanua MJM, Yau C, Scott JH, van't Veer L, Park JW, Esserman L, Campbell M. Low peripheral blood CD4/CD8 ratio at the time of surgery is a negative long-term prognostic factor in women with early stage 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 P4-01-12.

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 P3-10-14: LIV-1 expression in primary breast cancers in the I-SPY 2 TRIAL

Background: LIV-1 is an estrogen-inducible gene that has been implicated in epidermal-to-mesenchymal transition (EMT) in preclinical models of progression and metastasis. Its expression is associated with node-positivity in breast cancer; and has been detected in a variety of cancer types, including estrogen receptor positive breast cancers. SGN-LIV1A is a novel antibody drug conjugate targeting LIV-1 that is currently being evaluated in the I-SPY 2 TRIAL. In this pilot study, we evaluated LIV-1 levels by IHC within HR/HER2/MammaPrint (MP) defined subtypes among patients screening for the I-SPY 2 TRIAL and its correlation to microarray assessed LIV-1 expression levels.

Method: In a pilot study, LIV-1 IHC staining was performed by Quest Diagnostics on the pre-treatment samples of 38 patients screening for the I-SPY 2 TRIAL. Pre-treatment expression data generated on a custom Agilent 44K platform was also available. We summarized the LIV-1 H-Scores and percent (%)-positivity across the population and within HR/HER2/MP subtypes; and we assessed the Pearson correlation between LIV-1 H-Score and LIV-1 gene expression levels. In addition, we compared the pre-treatment LIV-1 expression levels within HR/HER2/MP subtypes across I-SPY 2 TRIAL patients from completed arms and their relevant controls (n=989) using ANOVA and post-hoc Tukey tests. Our statistics are descriptive rather than inferential; and does not take into account multiplicities of other biomarkers outside of this study.

Results: Of the 38 patients evaluated, 37 have LIV-1 %-positivity &gt; 0; and 18 (47%) have 100% LIV1 positivity. The median LIV-1 H-Score is 200; and 89% of patients (34/38) have moderate/high LIV-1 staining (with H-Score≥100). Of the 34 patients who proceeded onto the trial (and have known HR/HER2/MP status), 9 are triple negative, 19 are HR+HER2-, and 6 are HER2+. Due to our small sample size, we did not further subset the triple negative and HER2+ cases; but within the HR+HER2- patients, 10 are MP1 compared to 9 who are MP2 class. LIV1 H-Score appears highest within the HR+HER2-MP1 cases (median: 290), followed by the HER2+ (median: 216), then the HR+HER2-/MP2 (median: 155), and the TN (median: 120) subtype. LIV1 H-score is significantly correlated with LIV-1 mRNA expression levels (Rp=0.79, p&lt;0.0001). Consistent with these observations, LIV-1 pre-treatment expression levels are significantly higher in the HR+HER2-MP1 group relative to all other HR/HER2/MP defined subtypes (Tukey HSD p &lt; 0.0001) across the I-SPY 2 TRIAL population. The HR+HER2+MP1 group also have high LIV-1 expression levels.

Conclusion: Our result suggest that although LIV-1 expression differs by subtype, it is expressed at a moderate/high level in the majority of patients. The good correlation between IHC and array-based LIV-1 expression levels enables us to leverage the entire existing I-SPY 2 dataset and confirm the high rates of LIV-1 expression across the I-SPY 2 population. Further studies to evaluate LIV-1 expression as a biomarker of response to LIV-1 targeting therapies for the neoadjuvant treatment of breast cancer are warranted and ongoing in I-SPY 2.

Citation Format: Yau C, Brown-Swigart L, Asare S, I-SPY 2 TRIAL Consortium, Esserman L, van' t Veer L, Beckwith H, Forero A, Rugo H. LIV-1 expression in primary breast cancers in the I-SPY 2 TRIAL [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 P3-10-14.

Abstract P3-10-02: Identifying breast cancer molecular phenotypes to predict response in a modern treatment landscape: Lessons from ˜1000 patients across 10 arms of the I-SPY 2 TRIAL

Background: The explosion in new treatment options targeting immune checkpoints, HER signaling, DNA repair deficiency, AKT, and other pathways calls for updated breast cancer subtypes beyond HR and HER2 status to predict which patients will respond to which treatments. Here we leverage the I-SPY 2 TRIAL biomarker program over the past 8 years across 10 treatment arms to elucidate a minimal set of biomarkers that may improve response prediction in a modern treatment context, and to investigate which new patient phenotypes are identified by these response-predictive biomarkers.

Methods: 986 patients were considered in this analysis. Treatments included paclitaxel alone (or with trastuzumab (H) in HER2+) or combined with investigational agents: veliparib/carboplatin (VC); neratinib; MK2206; ganitumab; ganetespib; AMG386; TDM1/pertuzumab (P); H/P; and pembrolizumab (Pembro). 24 prospectively defined, mechanism-of-action and pathway-based expression and phospho-protein signatures/biomarkers assayed from pre-treatment biopsies were previously found to be predictive in a particular agent/arm in pre-specified analysis. Here we evaluate these biomarkers in all patients. We assessed association between each biomarker and response in the population as a whole and within each arm and HR/HER2 subtype using a logistic model. To identify optimal dichotomizing thresholds for select biomarkers, 2-fold cross-validation was repeated 500 times. Our analysis is exploratory and does not adjust for multiplicities.

Results: Our initial set of 24 predictive biomarkers reflects DNA repair deficiency (n=2), immune activation (n=7), ER signaling (n=2), HER2 signaling (n=4), proliferation (n=2), phospho-activation of AKT/mTOR (n=2), and ANG/TIE2 (n=1) pathways, among others. Biomarkers reflecting similar biology are correlated and cluster together. We make use of this correlation structure to reduce the dimensionality of the biomarker set to five predictive signals: proliferation, DNA repair deficiency (DRD), immune-engaged (Immune+), luminal/ER (lum), and HER2-activated. These biomarkers, when dichotomized, identify patient groups with differential predicted sensitivities to I-SPY 2 agents and are present at different proportions within receptor subtypes. For instance, in the HER2- subset, Immune+/DRD+ patients are predicted sensitive to both VC and Pembro, and account for 39% of TN, but only 12% of HR+HER2-. On the other end of the spectrum, only 17% of TN are Immune-/DRD-, compared to the majority (56%) of HR+HER2-. There are also subsets of patients positive for only one marker. For the HER2+ subset, 67% are HER2-activated+, and 25% lum+; of these HER2-activated+ patients are more likely to be Immune+ (44%), vs 23% in lum+. HER2-activated+/Immune+ patients have higher predicted sensitivity to HER2-targeted agents than lum+ or Immune- patients.

In all, these molecular phenotypes predict sensitivity to one or more I-SPY 2 investigational agents for 75% of the ˜ 1000 patients.

Conclusion: Molecular phenotypes reflecting proliferation, immune engagement, HER2-activation, luminal/ER-signaling, and DNA repair deficiency may provide a roadmap to guide treatment prioritization for emerging therapeutics.

Citation Format: Wolf DM, Yau C, Wulfkuhle J, Petricoin E, Campbell M, Brown-Swigart L, Hirst G, Asare S, Zhu Z, Lee EP, Delson A, Pohlmann P, I-SPY 2 TRIAL Consortium, Hylton N, Liu MC, Symmans F, DeMichele A, Yee D, Berry D, Esserman L, van 't Veer L. Identifying breast cancer molecular phenotypes to predict response in a modern treatment landscape: Lessons from ˜1000 patients across 10 arms of the I-SPY 2 TRIAL [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 P3-10-02.

Abstract PD6-08: Analysis of immune infiltrates (assessed via multiplex fluorescence immunohistochemistry) and immune gene expression signatures as predictors of response to the checkpoint inhibitor pembrolizumab in the neoadjuvant I-SPY 2 trial

Background: Pembrolizumab (Pembro), an anti-PD-1 immune checkpoint inhibitor, has been approved for the treatment of a variety of cancers including melanoma, non-small cell lung cancer, head and neck squamous cell carcinoma, and urothelial carcinoma. Pembro was recently evaluated in HER2- breast cancer patients in the neoadjuvant I-SPY 2 TRIAL and graduated in the triple negative (TN), HR+HER2-, and HER2- signatures. HER2- patients were randomized to receive Pembro+paclitaxel followed by doxorubicin/cyclophosphamide (P+T -&gt; AC) vs. T -&gt; AC. We and others have shown that TN breast cancers tend to have high numbers of immune infiltrates, including T cells and tumor associated macrophages (TAMs). We evaluated expression signatures representing 14 immune cell types (TILs, T cells, CD8 T cells, exhausted T cells, Th1, Tregs, cytotoxic cells, NK, NK CD56dim, dendritic cells, mast cells, B cells, macrophages, and neutrophils) as specific predictors of response to Pembro.

Methods: Data from 248 patients (Pembro: 69; controls: 179) were available. Pre-treatment biopsies were assayed using Agilent gene expression arrays. Signature scores are calculated by averaging cell type specific genes. All I-SPY 2 qualifying biomarker analyses follow a pre-specified analysis plan. We used logistic modeling to assess biomarker performance. A biomarker is considered a specific predictor of Pembro response if it associates with response in the Pembro arm but not the control arm, and if the biomarker x treatment interaction is significant (likelihood ratio test, p&lt;0.05). This analysis is also performed adjusting for HR status as covariates, and within receptor subsets. For successful biomarkers, we use Bayesian modeling to estimate the pCR rates of 'predicted sensitive' patients in each arm. Our statistics are descriptive rather than inferential and do not adjust for multiplicities of other biomarkers outside this study.

Results: 10 out of the 14 cell-type signatures tested are associated with response in the Pembro arm. Higher expression levels of 9 of these cell-type signatures are associated with higher pCR rates (T cells, exhausted T cells, Th1, cytotoxic cells, NK, NK CD56dim, dendritic cells, B cells, and macrophages), whereas higher mast cell signature expression is associated with non-pCR. Interestingly, many of these same signatures also associate or trend towards association with response in the control arm; and in a model adjusting for HR status, only 3 of these signatures (Th1, B cells and dendritic cells) show significant interaction with treatment. Within the whole population and the TN subtype, the dendritic cell signature is the strongest predictor of specific response to Pembro (OR/1SD: 4.04 and 4.4, LR p &lt; 0.001 overall and in TN). Although other immune signatures (T cells, exhausted T cells, NK, and macrophages) also associate with response in the Pembro arm in the TN subtype, only the dendritic cell and Th1 signatures have a significant interaction with treatment. In contrast, in the HR+HER2- subtype, only 3 signatures (Th1, B cells, and mast cells) associate with response to Pembro; but none of these signatures have significant interaction with treatment. Of note, in both the Pembro and control arms, HR+HER2- patients with higher average mast cell marker expression have lower pCR rates (OR/1SD: 0.33 and 0.51, LRp: 0.006 and 0.04 in Pembro and control arm).

Conclusion: As expected, multiple immune cell expression signatures are predictive of response in the Pembro arm; but only dendritic cells and Th1 cells are specific to Pembro in both the population as a whole and the TN subtype. Interestingly, the presence of mast cells may impede response, especially in HR+HER2- patients. Correlation of these signatures with multiplex-IF immune markers is pending.

Citation Format: Campbell M, Yau C, Borowsky A, Vandenberg S, Wolf D, Rimm D, Nanda R, Liu M, Brown-Swigart L, Hirst G, Asare S, van't Veer L, Yee D, DeMichele A, Berry D, Esserman L. Analysis of immune infiltrates (assessed via multiplex fluorescence immunohistochemistry) and immune gene expression signatures as predictors of response to the checkpoint inhibitor pembrolizumab in the neoadjuvant I-SPY 2 trial [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 PD6-08.

Abstract PD2-14: Participation in a personalized breast cancer screening trial does not increase anxiety at baseline

Introduction: The purpose of this study is to examine whether participation in a personalized screening trial is associated with anxiety or breast cancer worry. The Patient Centered Outcomes Research Institute recently funded WISDOM (Women Informed to Screen Depending On Measures of risk), which is a randomized trial that tests the safety and efficacy of basing starting age, stopping age, frequency and modality of breast cancer screening on individual risk (Clinical Trials Identifier NCT02620852).

Methods: In WISDOM, participants can be randomized to annual screening or personalized screening arm, or self-select an arm an observational cohort. This interim analysis examined the first 1817 participants to determine if the personalized risk arm is acceptable and to explore whether baseline anxiety was associated with study arm. For acceptability our target was to have &gt;60% of participants agree to randomization. Participants completed questions about their Risk Perception, the PROMIS Anxiety short form 8a (total scores 8-40 with higher scores indicating more anxiety), and Breast Cancer Risk Worry (BCRW) survey (total scores 5-20) with higher scores indicating more worry) at baseline and before they were given information on their personal risk or study assignment. For the purposes of these analyses, we defined high anxiety to be the percentage of participants scoring =&gt;22 on the PROMIS and &gt;8 on the BCRW.

Results: The participants were recruited from three sites (UCSD, UCSF, Sanford Health). Of the 1817 initial participants, 1643 completed the baseline questionnaire. Participants has a mean age of 57 years (SD 9). 15.8% felt their chances of developing breast cancer was high, 19.5% felt their chance of developing breast cancer was greater than the average women, and 56.6% felt their lifetime risk of developing breast cancer was &gt;25. Risk perception was not significantly different between women who opted to be randomized versus the observational arm.

The majority of participants were willing to be randomly assigned to an arm (1071/1643, 65.1%). Of those who joined the observational cohort, the majority selected personalized risk arm (474/572, 82.9%). Overall, PROMIS anxiety scores were low at baseline (14.0 MEAN (SD 4.6)) as were the Breast Cancer Risk Worry scores (5.7 MEAN (SD 1.05)). Less than 8% of participants had PROMIS scores &gt;22 and that did not vary across the randomized or observational groups (P=0.2)). About 2% of participants had a BCRW scores &gt;8. Women who worried with breast cancer were more likely to select to be in the observational (3.5%) than randomized (1.7%) arm of the study (P=0.02).

Conclusions: For the women approached to participate in Wisdom, personalized screening was acceptable alternative to annual mammography. Participants in general overestimated their lifetime risk of breast cancer, had very low anxiety and low breast cancer worry. Those who were worried about breast cancer opted more often for the observational arm of the study to allow them to choose between the personalized versus annual arm. Future analyses will follow participants prospectively to determine adherence to assigned or selected arm, and whether anxiety changes after receipt of their personalized risk information.

Citation Format: Naeim A, Sepucha K, Wenger N, Eklund M, Annette S, Madlensky L, van't Veer L, Parker B, Yau C, Cink T, Anton-Culver H, Borowsky A, Petruse A, Sarrafan S, Stover-Fiscalini A, LaCroix A, Adduci K, Wisdom Advocate Partners, Laura E. Participation in a personalized breast cancer screening trial does not increase anxiety at baseline [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 PD2-14.

Abstract PD6-14: Analysis of DNA repair deficiency biomarkers as predictors of response to the PD1 inhibitor pembrolizumab: Results from the neoadjuvant I-SPY 2 trial for stage II-III high-risk breast cancer

Background: Pembrolizumab (P), an anti-PD-1 immune checkpoint inhibitor, has been approved for treatment of microsatellite instability-high and mismatch repair deficient cancers. In I-SPY 2, patients were randomized to receive standard chemotherapy alone or in combination with an experimental agent. P was one of the experimental agents evaluated in HER2- patients in I-SPY 2 and graduated in the TN, HR+HER2-, and HER2- signatures. We hypothesize that a combination of two signatures predicting response to veliparib/carboplatin therapy in I-SPY 2 [MammaPrint High2 (MP2)/PARPi7-high] and reflecting DNA damage repair deficiency, may also predict response to P. In addition, we also tested 9 gene expression signatures reflecting different aspects of DNA damage and repair: FA, MMR, BER, HR, TLS, NER, NHEJ, DR, and DNA damage sensing (DDS) pathways.

Methods: Data from 249 patients (P: 69 and controls: 180) were available. Pre-treatment biopsies were assayed using Agilent gene expression arrays. All I-SPY 2 qualifying biomarker analyses follow a pre-specified analysis plan. We used logistic modeling to assess biomarker performance. A biomarker is considered a specific predictor of P response if it associates with response in the P arm but not the control arm, and if the biomarker x treatment interaction is significant (likelihood ratio test, p&lt;0.05). This analysis is also performed adjusting for HR status as a covariate, and within receptor subsets, sample size permitting. For successful biomarkers, we use Bayesian modeling to estimate the pCR rates of 'predicted sensitive' patients in each arm. Our statistics are descriptive rather than inferential and do not adjust for multiplicities of other biomarkers outside this study.

Results: MP2 status associates with pCR in P (OR=7.7; p=0.00021), but also to a lesser extent in the control arm (OR=2.4:p=0.045), with an OR ratio of 3.3 which trends toward significance, even after adjusting for HR status (LR p=0.083). A majority of TN patients are MP2; and TN/MP2 patients have an estimated pCR rate of 67% in P (vs. 23% in control). Although only ~30% of HR+HER2- patients were MP2, their estimated pCR rate in P is 61%, compared to 29% in unselected HR+/HER2- patients. PARPi7 predicted response in the P arm only in the HR+HER2- group (LR p= 0.025), but not in the population as a whole or the TN subtype. Combining MP2 and PARPi7 into MP2/PARPi7-high did not improve performance over MP2 as a single biomarker. Of the 9 DDR pathway signatures tested, both BER and DDS associate with pCR in P, but only DDS (which includes ATM, ATR, CHEK1-2) associates with pCR in the P arm (LR p=0.00029), and not the control arm (LR p=0.53), with a significant interaction with treatment (LR p=0.0064) that retains significance in a model adjusting for HR status. When dichotomized to optimize the biomarker x treatment interaction, the estimated pCR rate is 75% in P vs 18% in control, in the DDS+ subset.

Conclusion: In this small study, MP2 status and a DNA damage sensing pathway but not the PARPi7 or other repair pathways show promise as predictive biomarkers for immune checkpoint inhibition therapy in breast cancer.

Citation Format: Yau C, Wolf D, Brown-Swigart L, Hirst G, Sanil A, Singhrao R, I-SPY 2 TRIAL Investigators, Asare S, DeMichele A, Berry D, Esserman L, van 't Veer L, Nanda R, Liu M, Yee D. Analysis of DNA repair deficiency biomarkers as predictors of response to the PD1 inhibitor pembrolizumab: Results from the neoadjuvant I-SPY 2 trial for stage II-III high-risk 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 PD6-14.

Abstract LB-158: Germline mutations in PALB2, BRCA1 and RAD51C observed in gastric cancer cases

Gastric cancer (GC) is the third common cause of cancer related deaths worldwide and its risk is partially mediated by inherited factors. However, the majority of GC heritability remains to be discovered. The goal of this study was to identify novel GC genes. To identify novel GC genes, we undertook a multi-staged approach of whole exome sequencing (WES), followed by targeted sequencing and genotyping in germline DNA samples from hereditary diffuse GC (HDGC) and isolated GC cases recruited in Europe and Latin America. We also performed WES in 4 available tumor samples to analyze loss of heterozygosity and somatic mutation signature. Our study identified eleven cases with mutations in homologous recombination repair (HR) genes, including seven with PALB2 mutations, three with BRCA1 mutations and one with a RAD51C mutation. Out of 361 total unrelated GC cases analyzed, 6.45% of the HDGC cases (2 out of 31) and 2.7% (9 out of 330) of isolated/non-HDGC cases had mutations in PALB2, BRCA1 or RAD51C. Most of these mutations are known as pathogenic in other cancer types and three were shared by multiple Hispanic and European cases. None of these mutations were present in 1,170 population-matched controls (P=5.75x10-7). Tumor samples from four mutation carriers exhibited mutational signature indicative of defects in HR pathway. Our results suggest that mutations in HR genes are likely involved in GC susceptibility. Our findings have potential clinical implications as these cases and their families could benefit from risk reducing surveillance and possibly benefit from platinum or PARP inhibitor based therapies.

Citation Format: Ruta Sahasrabudhe, Paul Lott, Mabel Bohorquez, Ted Toal, Ana Estrada, John Suarez, Alejandro Brea-Fernández, Jose Cameselle-Teijeiro, Carla Pinto, Irma Ramos, Alejandra Mantilla, Rodrigo Prieto, Alejandro Corvalan, Enrique Norero, Carolina Alvarez, Teresa Tapia, Pilar Carvallo, Luz Gonzalez, Alicia Cock-Rada, Angela Solano, Florencia Neffa, Adriana Della Valle, Chris Yau, Gabriela Soares, Alexander Borowsky, Xiao-You Han, Li-JI He, Phillip Taylor, Alisa Goldstein, Nan Hu, Javier Torres, Magdalena Echeverry, Clara Ruiz-Ponte, Manuel Teixeira, Luis G. Carvajal-Carmona. Germline mutations in PALB2, BRCA1 and RAD51C observed in gastric cancer cases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-158. doi:10.1158/1538-7445.AM2017-LB-158

Germline Mutations in PALB2, BRCA1, and RAD51C, Which Regulate DNA Recombination Repair, in Patients With Gastric Cancer

Up to 10% of cases of gastric cancer are familial, but so far, only mutations in CDH1 have been associated with gastric cancer risk. To identify genetic variants that affect risk for gastric cancer, we collected blood samples from 28 patients with hereditary diffuse gastric cancer (HDGC) not associated with mutations in CDH1 and performed whole-exome sequence analysis. We then analyzed sequences of candidate genes in 333 independent HDGC and non-HDGC cases. We identified 11 cases with mutations in PALB2, BRCA1, or RAD51C genes, which regulate homologous DNA recombination. We found these mutations in 2 of 31 patients with HDGC (6.5%) and 9 of 331 patients with sporadic gastric cancer (2.8%). Most of these mutations had been previously associated with other types of tumors and partially co-segregated with gastric cancer in our study. Tumors that developed in patients with these mutations had a mutation signature associated with somatic homologous recombination deficiency. Our findings indicate that defects in homologous recombination increase risk for gastric cancer.

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 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 PD7-02: Identification of breast cancers with an indolent disease course: 70 gene indolent threshold validation in a Swedish randomized trial of tamoxifen vs. not, with 20 year outcomes

Importance: The frequency of cancers with indolent behavior has increased with screening. We asked whether an ultralow risk threshold on a multigene classifier would identify women whose cancers had an indolent course over 2 decades of follow-up, and which features were most predictive of outcome.

Methods: An ultralow risk threshold of the FDA-cleared MammaPrint 70-gene expression score was set to predict long-term absence of breast cancer-specific mortality in the absence of systemic therapy. The Stockholm Tamoxifen (STO) trial conducted between 1976 and 1990, where postmenopausal women with clinically detected node-negative breast cancers &lt;3cm were randomized to receive tamoxifen versus not, was used for validation. Immunohistochemistry markers (n=727) and Agilent microarrays for MammaPrint risk scoring (n=652) were performed from formalin-fixed paraffin-embedded primary tumor blocks. Recursive partitioning was performed using the rpart package in R to select variables and construct a regression tree that best predicts 20-year breast cancer specific survival. Input variables include: age, period of diagnosis, grade, hormone receptor status, HER2 and Ki69 status, 70-gene risk categories (high, low but not ultra, or ultralow), treatment arm and tumor size; and cross-validation was used to select the final regression tree model.

Results: In this trial conducted in the era before mammographic screening, 58% and 42% were MammaPrint low and high risk, respectively, while 15% were above the ultralow threshold. In the tamoxifen treated arm, women with tumors above the ultralow threshold had no deaths at 15 years and their 20-year disease-specific survival rates of 97%; whereas if untreated, their survival rates were 94%. Recursive partitioning identified the ultralow threshold classification as the first primary split in the model. Once the indolent tumors were partitioned out, among women with tumors below the ultralow threshold, the next most prognostic feature was size, where patients with tumors &gt;20mm have worse breast cancer specific survival. The last split in the model divides the patients with tumors ≤20mm into 70-gene high risk vs low but not ultralow risk groups.

Conclusions and Relevance: A threshold of the 70-gene MammaPrint assay can identify patients with indolent disease whose long-term risk of death from breast cancer after surgery alone is exceedingly low. This threshold emerged as the most prognostic variable, followed by tumor size, and mammaprint high vs. low but not ultralow in our recursive partitioning analysis. This suggests that finding indolent tumors early at a small size may not have much impact on patient outcome. Determining the presence of an ultralow risk breast cancer may prevent overtreatment. Conversely, once the indolent tumors are taken out of consideration, both biology and size impact outcome, and finding these tumors at a small size is likely still important and supports screening in this postmenopausal node negative population.

Citation Format: Esserman LJ, Yau C, Thompson CK, van't Veer LJ, Borowsky AD, Hoadley KA, Tobin NP, Nordenskjöld B, Fornander T, Stål O, Benz CC, Lindström LS. Identification of breast cancers with an indolent disease course: 70 gene indolent threshold validation in a Swedish randomized trial of tamoxifen vs. not, with 20 year outcomes [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 PD7-02.

Abstract P2-05-03: Intra-tumor heterogeneity of the estrogen receptor predicts less benefit from tamoxifen therapy and poor long-term breast cancer patient survival – Retrospective analyses of the STO-3 randomized trial

Background

We and others have shown that the clinically used breast cancer markers alter their expression throughout tumor progression, influencing patient survival (Lindström et al, JCO 2012). What are the likely explanations to our findings? Here, we aimed to determine whether breast cancer intra-tumor heterogeneity of the estrogen receptor (ER) is a marker of tumor aggressiveness and benefit of tamoxifen therapy in a large randomized trial.

Material and methods

The Stockholm Tamoxifen (STO-3) trial enrolled postmenopausal lymph node negative breast cancer patients with a tumor size of less than 30 mm, between 1976 and 1990, to be randomized to receive adjuvant tamoxifen versus not. From the original randomized trial cohort approximately half of the patients (778 patients) had primary tumor formalin-fixed paraffin-embedded blocks available and were included in our study. No significant differences in age and period of diagnosis, type of surgery received, receptor status, tumor grade and size were observed between the treatment arms.

All tumor slides were immunostained in a central laboratory using the SP1 antibody. ER slides were scored by two independent breast cancer pathologists assessing the fraction of cancer cells for each ER intensity level (0, +1, +2 or +3) compared to established standards. The resulting distribution of ER stained tumor cells defines intra-tumor heterogeneity of ER (Rao's quadratic entropy (QE),Potts et al, Lab Invest 2012). Intra-tumor heterogeneity was categorized using the third tertile as cut-off for high heterogeneity (726 patients).

Analyses of long-term breast cancer specific survival (25 years) by intra-tumor heterogeneity of ER were performed using univariate Kaplan-Meier and multivariate Cox proportional hazard modeling adjusting for treatment arm, age and period of diagnoses, ER, progesterone receptor (PR), HER2, Ki-67, tumor grade, and tumor size. Further, a test of correlation was performed to investigate whether intra-tumor heterogeneity of ER was correlated to the percentage of ER positive cells, the H-Score or the Luminal A and B subtype (PAM50).

Results

In the univariate Kaplan-Meier analyses, a statistically significant difference in long-term survival by intra-tumor heterogeneity of ER was seen for all patients (log rank, P=0.018), tamoxifen treated arm (log rank, P=0.0033), but not untreated arm (log rank, P=0.19). However in the multivariate analysis, patients with high intra-tumor heterogeneity of ER in the treated arm as well as in the untreated arm had an almost two-fold increased long-term risk of fatal breast cancer disease as compared to patients with low or intermediate heterogeneity (Treated arm: HR, 2.06; 95% CI, 1.04-4.07 and Untreated arm: HR, 1.71; 95% CI, 1.01-2.87).

No significant correlation of intra-tumor heterogeneity to the tested variables was seen.

Conclusions

Patients with high intra-tumor heterogeneity of ER had less benefit from tamoxifen therapy and an increased long-term risk of fatal breast cancer disease. Our findings should be clinically relevant since therapy benefit was evaluated in a randomized trial with long-term follow-up.

Citation Format: Lindström LS, Yau C, Czene K, Thompson CK, van't Veer LJ, Nordenskjöld B, Stål O, Fornander T, Benz CC, Borowsky AD, Esserman LJ. Intra-tumor heterogeneity of the estrogen receptor predicts less benefit from tamoxifen therapy and poor long-term breast cancer patient survival – Retrospective analyses of the STO-3 randomized 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 P2-05-03.

Abstract P3-05-02: Quantitative ERα measurements in TNBC from the I-SPY 2 TRIAL correlate with HER2-EGFR co-activation and heterodimerization

Background: We have previously described that TNBC patients whose tumors have both HER2 Y1248 phosphorylation (pHER2) “high” and phospho-EGFR Y1173 (pEGFR) “high” have increased response (pCR) to neratinib in the I-SPY2 TRIAL. We hypothesize that the paradoxical finding of a response prediction signature comprised of HER2 activation in a HER2 IHC/FISH-negative population means there must be a ligand-driven biochemical event responsible for the HER2 phosphorylation because HER2 mutations were also not found to be significant. Exploratory analysis of additional cellular signaling events and protein expression levels in pre-treatment, LCM-purified tumor epithelium by reverse phase protein microarray (RPPA) included semi-quantitative measurement of total levels of estrogen receptor alpha (ERα), which has been previously shown to be able to act as a membrane non-genomic signaling molecule through direct interaction with various tyrosine kinases including EGFR and HER2. Since ERα has been previously shown to act as a ligand and co-stimulate (activate) HER2 and EGFR when present at low levels, we investigated whether or not RPPA-measured ERα levels in the TNBC cohort analyzed to date were higher in tumors with both pHER2 “high” and pEGFR “high” levels and thus provide evidence explaining how HER2-EGFR activation is occurring in TNBC.

Methods: Using RPPA analysis, we measured 118 analytes in lysates of LCM tumor epithelium obtained from the pre-treatment biopsy samples of 86 TNBC (Allred=0) patients in the I-SPY2 TRIAL analyzed to date. Cutpoints for pEGFR and pHER2 were determined previously by ROC analysis for pCR correlation in the neratinib treated TNBC population, and used here to dichotomize the pHER2 and pEGFR data in the larger TNBC population. Wilcoxon Rank Sum testing was performed using the continuous variable total ERα data and compared the TNBC that were both pHER2 and pEGFR “high” (N=39) to the rest of the TNBC population (N=47). Total ERα values were then divided into “high” and “low” groups based on the TNBC population median value in order to determine frequency/percentages within each class. Our study is exploratory with no claims for generalizability of the data, and calculations are descriptive (e.g. p-values are measures of distance with no inferential content).

Results: Total ERα values were obtained in 84/86 TNBC tumors analyzed. Total levels of ERα were higher (p&lt; 0.006) in TNBC tumors with pHER2 and pEGFR “high” levels. 68% (26/38) of tumors in the pHER2 and pEGFR “high” group had ERα levels above the population median compared to 35% (16/46) in the rest of the TNBC population.

Conclusion: Our exploratory analysis reveals that ERα levels are significantly higher in TNBC with pHER2 and pEGFR activation and may be behaving as a direct signaling ligand in TNBC and driving HER2-EGFR signaling. This ERα-pHER2/pEGFR association was missed by current ER and HER2 clinical laboratory testing techniques, and if validated in larger independent study sets could suggest that utilization of new protein-based techniques defining ER more quantitatively could be helpful to understand tumor biology and therapeutic response prediction, especially in the context of TNBC that are ostensibly ER negative.

Citation Format: Gallagher RI, Yau C, Wolf DM, Dong T, Hirst G, Brown-Swigart L, ISPY-2 TRIAL Investigators, Buxton M, DeMichele A, van't Veer L, Yee D, Paoloni M, Esserman L, Berry D, Park J, Petricoin EF, Wulfkuhle JD. Quantitative ERα measurements in TNBC from the I-SPY 2 TRIAL correlate with HER2-EGFR co-activation and heterodimerization [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 P3-05-02.

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.

The administration of intermittent parathyroid hormone affects functional recovery from trochanteric fractured neck of femur: a randomised prospective mixed method pilot study

Aims

We wished to assess the feasibility of a future randomised controlled trial of parathyroid hormone (PTH) supplements to aid healing of trochanteric fractures of the hip, by an open label prospective feasibility and pilot study with a nested qualitative sub study. This aimed to inform the design of a future powered study comparing the functional recovery after trochanteric hip fracture in patients undergoing standard care, versus those who undergo administration of subcutaneous injection of PTH for six weeks.

Patients and Methods

We undertook a pilot study comparing the functional recovery after trochanteric hip fracture in patients 60 years or older, admitted with a trochanteric hip fracture, and potentially eligible to be randomised to either standard care or the administration of subcutaneous PTH for six weeks. Our desired outcomes were functional testing and measures to assess the feasibility and acceptability of the study.

Results

A total of 724 patients were screened, of whom 143 (20%) were eligible for recruitment. Of these, 123 were approached and 29 (4%) elected to take part. However, seven patients did not complete the study. Compliance with the injections was 11 out of 15 (73%) showing the intervention to be acceptable and feasible in this patient population.

Take home message: Only 4% of patients who met the inclusion criteria were both eligible and willing to consent to a study involving injections of PTH, so delivering this study on a large scale would carry challenges in recruitment and retention. Methodological and sample size planning would have to take this into account. PTH administration to patients to enhance fracture healing should still be considered experimental.

Cite this article: Bone Joint J 2016;98-B:840–5.

A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies

One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.

Abstract P5-08-12: Co-expression modules identified from published immune signatures reveals five distinct immune subtypes in breast cancer

Introduction

Immune modulating therapies offer an attractive novel approach in the treatment of breast cancer. There is a growing body of literature demonstrating that immune-related expression signatures predict breast cancer prognosis and chemo- and/or targeted therapy responsiveness. However, it is unclear how these signatures relate to one another. Here we evaluated 58 immune signatures in breast cancer and generated co-expression modules to classify patients into immune subtypes.

Methods

We evaluated 58 published expression signatures related to immune function in 5 breast cancer gene expression datasets (TCGA (n=817), METABRIC (n=1992), EMC344 (n=344), pooled triple negative: GSE31519 (n=579), pooled neoadjuvant chemotherapy treated: GSE25066 (n=508)). For each dataset, consensus clustering was used to subset the signatures based on their co-expression pattern. Signatures in the same consensus cluster across all 5 datasets were used to define immune modules. Module scores were computed as the average across their constituent signatures. Patients were classified into immune subtypes based on their module scores using consensus clustering. Overall survival (OS) differences between immune subtypes were assessed using Cox proportional hazard modeling in basal breast cancers from the METABRIC dataset (n=329).

Results

Consensus clustering of the 58 expression signatures consistently yields four distinct co-expression modules across the five datasets. These modules appear to represent distinct immune components and signals, with constituent signatures relating to: 1) T-cells and/or B-cells (T/B-cell), 2) interferon (IFN), 3) transforming growth factor beta (TGFB), 4) core serum response, dendritic cells and/or macrophages (CSR). Of note, the T/B-cell module contains 20 of the 58 signatures evaluated; and the CSR module is highly correlated to proliferation (r=0.81). Subtyping of patients based on these co-expression modules consistently yields subsets that fall into five major immune subtypes. The expression pattern of the four modules within each immune subtype is summarized below:

 T/B-cellIFNTGFBCSRT/B-cell/IFN HighHighHighIntermediateIntermediateIFN/CSR HighLowHighLowHighImmune LowLowLowLowLowCSR HighLowLowLowHighTGFB HighLowLowHighLowImmune Co-expression Modules (columns); Immune Subtypes (rows)

These immune subtypes are associated with differences in overall survival in the METABRIC basal breast cancer cases, where the CSR High subtype has the worst outcome (10-year OS: 23%). In comparison, the subsets corresponding to the T/B-cell/IFN High subtype have better outcomes (Hazard ratio: 0.43, p = 0.018). In contrast, no significant outcome differences were observed between the poor outcome CSR-High subtype and the remaining three immune subtypes (p&gt;0.05).

Conclusion

Our exploratory study identified four distinct immune co-expression modules (T/B-cell, IFN, TGFB, or CSR) from a collection of published immune signatures. Using these modules, we identified 5 immune subtypes with prognostic significance in basal breast cancers. We propose to test representative signatures from the 4 modules and the combined immune subtypes as predictive biomarkers of response to immunotherapies.

Citation Format: Amara D, Wolf D, van 't Veer L, Esserman LJ, Campbell MJ, Yau C. Co-expression modules identified from published immune signatures reveals five distinct immune subtypes in breast cancer. [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 P5-08-12.

Abstract P1-14-03: The evaluation of trebananib 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 a series of novel agents when added to standard neoadjuvant therapy for women with high-risk stage II/III breast cancer. The primary endpoint is pathologic complete response (pCR). The goal is to identify/graduate regimens with ≥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 trebananib, an angiopoietin-1/2-neutralizing peptibody that inhibits interaction with the Tie2 receptor.

Methods: Women with tumors ≥2.5cm were eligible for screening. MP low/HR+/HER2- tumors were ineligible for randomization. Serial MRI scans (baseline, 2 during treatment and pre-surgery) were used in a longitudinal model to improve the efficiency of adaptive randomization. Participants are categorized into 8 subtypes based on: HR status, HER2 status and MP High 1 (MP1) or High 2 (MP2). MP1 and MP2 are determined by a predefined median cut-point of I-SPY 1 participants who fit the eligibility criteria for I-SPY 2. Trebananib was initially assigned to HER2- patients only; once safety data with trastuzumab (H) were obtained, it was also assigned to HER2+ patients. Analysis was intent to treat -- patients who switched to non-protocol therapy were designated non-pCRs.

Results: Trebananib +/-H did not meet the criteria for graduation in any of the 10 signatures tested. When the maximum sample size was reached, accrual ceased. We report probabilities of trebananib +/-H being superior to control and Bayesian predictive probabilities of success in a 1:1 randomized neoadjuvant phase 3 trial for the 10 biomarker signatures, using the final pCR data from all patients.

SignatureEstimated pCR Rate (95% probability interval)Probability Trebananib Is Superior to ControlPredictive Probability of Success in Phase 3Trebananib (n=134)Control (n=133)ALL0.259(0.16 -0.36)0.158(0.09-0.23)0.9860.564HR+0.157(0.05-0.26)0.115(0.03- 0.20)0.8050.281HR-0.378(0.22-0.53)0.207(0.11- 0.31)0.9910.784HER2+0.279(0.07-0.49)0.17(0.04-0.30)0.8790.553HER2-0.254(0.15-0.36)0.155(0.08-0.23)0.9810.555MP20.342 (0.19-0.49)0.177(0.07-0.28)0.9910.786HR-/HER2-0.368 (0.21-0.53)0.201(0.10-0.30)0.9880.771HR-/HER2+0.444(0.15-0.74)0.244(0.07-0.42)0.9260.739HR+/HER2+0.201(0.01-0.39)0.135(0.01-0.26)0.7750.41HR+/HER2-0.143(0.04-0.24)0.11(0.03-0.19)0.7580.248

Citation Format: Albain KS, Leyland-Jones B, Symmans F, Paoloni M, van 't Veer L, DeMichele A, Buxton M, Hylton N, Yee D, Lyandres Clennell J, Yau C, Sanil A, I-SPY 2 Trial Investigators, Berry D, Esserman L. The evaluation of trebananib plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 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 P1-14-03.

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 P6-08-03: Functional detection and inhibition of the targetable oncogenic kinome of chemotherapy-treated triple-negative breast cancer cells

Background: Triple-negative breast cancer (TNBC) accounts for 10-15% of all breast cancer cases. A major area of innovation in TNBC is identifying potential treatment targets, especially in TNBC cells which survive chemotherapy. Our previous study showed that TNBC cells displayed deregulated kinase-dependent signaling cascades, and uniquely divergent phospho-circuits could be distinguished between TNBC vs non-TNBC cell lines [2014 SABCS abstract 1672, poster P2-05-09]. We further hypothesized that specific dysfunctional phospho-signaling network played a key role in the early adaptive changes in DNA damage response of TNBC cells exposed to DNA damaging chemotherapeutic agents.

Methods: TNBC cell lines MDA-MB-231 and MDA-MB-436 were treated with 5-fluorouracil (5-Fu), carboplatin and doxorubicin at their respective half maximal inhibitory concentrations (ic50s). MiSeq gene sequencing of the untreated vs treated TNBC cells was performed to investigate whether exposure to chemotherapy agents for 3-day's duration would induce additional adaptive genetic mutation. Apoptosis and cell-cycle distribution of the untreated and treated TNBC cells were analyzed with flow cytometry. The functional phospho-signature of each TNBC cell sample was analyzed using a high throughput experimental platform that monitors the level of activity of myriad kinases at once. This technique used over 450 phospho-sensing probes, including over 150 controls in an aqueous-based assay to simultaneously and directly measure the phospho-catalytic activity of phosphorylating enzymes in cell lysates. The kinome activities of the untreated vs treated TNBC cell lines were compared respectively, and the most significantly deranged and functionally altered phospho-signaling cascades and their related kinases were identified as the early adaptive changes of the survived TNBC cells after the 3-day exposure to DNA damage chemotherapies.

Results: Using the two TNBC cell lines treated with the three chemotherapies, we made 8 cell line samples, including 6 treated and 2 untreated as the control. MiSeq gene sequencing showed no significant additional adaptive genetic mutations in the treated TNBC cells after the 3-day short-term exposure to 5-Fu, carboplatin and doxorubicin. 36 phospho-signatures were generated and validated for repeatability and robustness. The kinase activity signature of each TNBC sample was analyzed and compared to each other using unsupervised hierarchical clustering. The phospho-sensing assay revealed that phospho-signaling cascades related to CHK1/2 and IKK kinases were differentially altered in the untreated vs treated TNBC cell lines, which, when respectively inhibited by AZD7762 and IKK16, successfully increased growth inhibition and cell death of TNBCs.

Conclusions: We identified specific phospho-fingerprints of the early adaption of TNBC cell lines and combinatorial targeted therapies that improve treatment outcome. Our next goal is to identify specific phosphorylation cascades in a broader range of cell lines and tumor tissues, to explore the actionable, kinase-dependent mechanisms critical to the DNA damage-induced adaptive reprogramming of TNBCs and early changes driving drug-resistance.

Citation Format: Pan B, Olow A, Sun Q, Mori M, Lee PRE, Hartog M, Wang C, Wolf D, Yau C, van 't Veer L, Coppé J-P. Functional detection and inhibition of the targetable oncogenic kinome of chemotherapy-treated triple-negative breast cancer cells. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-03.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden

Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 amplification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal diversity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater diversity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.

Abstract P6-04-01: Protein pathway activation mapping of LCM tumor epithelium from I-SPY 1 TRIAL surgical specimens reveals activation of receptor tyrosine kinase drug target signaling networks in the non-responding patient cohort

Background: Identification of alternative therapeutic strategies is critically needed for patients who do not achieve complete clinical response in the neoadjuvant setting, and in particular, from that cohort with the most aggressive disease (shortest relapse-free survival (RFS)). The I-SPY 1 TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane-based chemotherapy that provides longitudinal biopsy specimens and extensive molecular and clinical/pathological characterization of non-responding patients. Methods: Tumor epithelium was procured by Laser Capture Microdissection (LCM) from frozen surgical specimens of 27 patients who did not achieve complete pathological response in the I-SPY1 TRIAL. Reverse Phase Protein Microarray (RPPA) technology was used to measure the levels of 120 key signaling proteins including drug targets for Phase I-III and FDA-approved therapeutics. Cox proportional hazard univariate and multivariate analyses were used to evaluate RFS correlates. Significance threshold was p = &lt;0.05. Results: Univariate analysis of pathway activation revealed a number of actionable/druggable targets, particularly receptor tyrosine kinase (RTK) activation, where increased phosphorylation of ALK (Y1586), EGFR (Y1173), ERBB3 (Y1289), cABL (T735), and FAK (Y576/Y577) was significantly associated with aggressive disease (shorter RFS). Higher levels of SRC (Y527) inhibitory phosphorylation were also significantly associated with early recurrence. Coordinate activation of downstream targets of these RTKs, such as RAS-GRF S916, SHC (Y317), MEK (S217/221) and the Aurora kinases were also associated with early relapse in this study set. In multivariate analyses controlling for receptor subtype (HR+/HER2-, triple-negative (TN), HER2+), the associations between shorter RFS and RTK pathway activation including EGFR, ERBB3, cABL and FAK activation and SRC inhibition, as well as RAS-GRF and SHC phosphorylation remained significant. Conclusions: This unique functional protein pathway/proteomic analysis of LCM-isolated tumor epithelium by RPPA in surgical specimens taken from patients who did not achieve complete pathological response provides evidence for a significant number of druggable RTK pathway targets in patients with residual disease who are most at risk to die from breast cancer. Activation of ALK, EGFR, ERBB3, ABL, FAK, along with downstream RAS-ERK and Aurora kinase signaling activation in this cohort provide new insights into tumor progression along with distinct, actionable information on new therapeutic modalities to test in patients with progressing disease. Identification of new therapeutic strategies for patients who progress or recur early after neoadjuvant therapy is critical and, if validated in larger independent cohorts, could lead to rationalized personalized therapy-based trials. This strategy is being utilized in the I SPY 2 TRIAL as we introduce pathway-directed therapeutics in the neoadjuvant setting and are employing the RPPA platform to determine whether these agents are impacting their intended pathway. This work was partially supported by NIH grants CA31946 and CA33601.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-04-01.

Abstract P6-06-21: A 5-gene predictor of triple negative breast cancer outcome that also correlates with immune checkpoint receptor expression

Background: It is becoming increasingly clear that immune responses play an important role in determining triple negative (Tneg) breast cancer prognosis. Thus, emerging immunotherapeutic strategies, such as targeting immune checkpoint co-receptors (e.g. CTLA4 or PD-1), offer an attractive novel approach. However, to date, there are no established predictive biomarkers to identify Tneg patients most likely to benefit from these immunotherapies. We recently identified a 5-gene prognostic signature (TNFRSF17, CLIC5, HLA-F, CXCL13, XCL2), referred to as the Integrated Cytokine Score (ICS). Interestingly, the ICS showed functional linkage through both type 1 (interferon-γ (IFNG)) and type 2 (IL-10) immune response pathways. Here, we hypothesized that the ICS would be associated with the expression of IFNG as well as immune checkpoint genes and may therefore serve as a surrogate biomarker for targeted immunotherapies.

Method: Transcriptome data from a set of 94 node negative chemotherapy naïve Tneg tumors were pooled from three independent microarray datasets (GSE2034, GSE5327 and GSE7930). The ICS was computed as the scaled sign-corrected average of the 5 signature genes, such that a high ICS is indicative of low immune function, which in turn translates to a higher recurrence risk. We explored the correlation between the ICS and the expression of IFNG, IL-10 and 3 different immune checkpoint co-receptor genes: CTLA4 (cytotoxic T-lymphocyte antigen 4), PD-1/PDCD1 (programmed cell death protein-1) and LAG3 (lymphocyte activation gene 3). In addition, Cox proportional hazard modeling was used to evaluate the association with distant metastasis free survival (DMFS).

Results: The ICS is significantly prognostic (hazard ratio associated with 1 standard deviation increase = 1.48 (1.04 - 2.10), p = 0.03). ICS strongly anti-correlated (p&lt;0.05) with IFNG (r = -0.66), CTLA4 (r = -0.38), PD-1/PDCD1 (r = -0.25) and LAG3 (r = -0.60) expression. Interestingly, despite this strong correlation and the prognostic significance of the ICS, none of these four immune genes were significantly associated with Tneg DMFS (p = 0.31 - 0.86). IL-10 expression was not correlated with ICS (r = -0.04) or DMFS (p = 0.43).

Conclusion: Our current findings suggest that Tneg tumors with a low ICS have elicited a type-1 (IFNG pathway) antitumor immune response. However, since the tumor is essentially “self”, this results in the activation of negative immunoregulatory networks that prevent autoimmunity (checkpoint co-receptors). Thus, the prognostic 5-gene ICS may also be a useful biomarker for immune checkpoint blockade, which could become an alternative therapeutic strategy to traditional chemotherapy for low-ICS Tneg patients who are at reduced risk of metastatic recurrence. In contrast, we propose that high-ICS Tneg tumors do not elicit type-1 antitumor immune responses or subsequent immunoregulatory network activation. For these high-ICS patients at increased risk of metastatic recurrence, additional immunotherapeutic approaches capable of enhancing both recruitment and activation of immune effector cells, as well as checkpoint blockade, may be necessary.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-06-21.

Abstract P1-02-06: Assigning luminal A versus luminal B subtype using the Ki67 index in patients with hormone receptor positive (HR+) breast cancer enrolled in the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)

Background: Prognostically distinct subtypes of BC defined by gene expression include luminal A, luminal B, HER2-enriched, basal-like and normal breast-like tumors. Luminal subtypes express estrogen receptor (ER)-related genes; patients with luminal B tumors have a poorer prognosis and higher proliferation compared to those with luminal A tumors. For HR+ disease, accessible and affordable surrogates for identification of luminal subtypes may aid in selecting appropriate systemic therapy and assessing eligibility to novel agent clinical trials targeted toward specific biology. Recent studies support use of Ki67 positivity by immunohistochemistry (IHC) with a cut point of 15%, along with standard receptors, as an appropriate surrogate for luminal B.

Methods: 116 I-SPY 1 TRIAL patients with intrinsic subtype assignments had Ki-67 IHC-stained pre-treatment whole tissue sections available for digital image quantification. The percentage of Ki67-positive nuclei was quantified using the Aperio Nuclear V9 (cell quantification) algorithm. Intrinsic subtype was previously determined by standard methods applied to Agilent 44K gene expression data. We selected the 49 patients with HR+/HER2- tumors for this analysis. Ki67 positivity was categorized into two groups: low (&lt;15%) and high (≥15%). Association between intrinsic subtype and Ki67 was determined using Fisher's exact method.

Results: The 49 pts with HR+/HER2- disease were classified by gene expression into intrinsic subtypes as follows: 26 (53%) luminal A, 15 (31%) luminal B, 2 (4%) HER2-enriched, 6 (12%) basal, and 0 normal. The fraction of Ki67 positive cells ranged from 0.28% to 86.8%, with a mean of 20.5%. The mean Ki67 positive fraction was 13% and 24% in LumA and LumB subgroups, respectively. Using the 15% cutoff, Ki67 was low in 25 (51%) and high in 24 (49%) cases. The majority of luminal A tumors have low Ki67 (17/26, 65%) and luminal A subtype was associated with Ki67 (p = 0.047). However, nearly a third of tumors with low Ki67 are not luminal A (8/25, 32%). High Ki67 tumors were distributed among luminal A (18%), luminal B (18%), basal (10.2%), and HER2-enriched (2%) subtypes; luminal B subtype was not associated with high Ki67 (p = 0.36) in this cohort.

Conclusion: In this high-risk population, 16% of HR+/HER2- tumors were either basal or HER2-enriched by intrinsic subtyping. Low Ki67 (&lt;15%) was associated with luminal A; this did not exclude other subtypes. In this well characterized group, high Ki67 (≥15%) in combination with ER status did not serve as a surrogate for luminal B subtype. These results suggest that intrinsic subtype classifications reflect information beyond that captured by hormone receptor status combined with Ki67 positivity.

This research was partially supported by NIH CA31946 and CA33601.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-06.

Abstract P3-04-01: Protein pathway activation mapping of the I-SPY 1 biopsy specimens identifies new network focused drug targets for patients with triple negative tumors

Background: Identification of new therapies and predictive biomarkers is needed for patients with triple negative (TN) breast cancer. Elucidating pathway activation in cancer is critical as these proteins represent targets for many of the new molecular therapeutics and companion diagnostic markers. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane-based chemotherapy that provides longitudinal biopsy specimens and molecular and clinical/pathological characterization.

Methods: Tumor epithelium was procured by Laser Capture Microdissection from 149 pretreatment frozen biopsy specimens (T1) and 102 frozen biopsy specimens collected 1–4 days after first chemotherapy treatment (T2). Reverse Phase Protein Microarray was used to measure the activation of 39 and 100 signaling proteins in the T1 and T2 biopsies, respectively, including drug targets for Phase I-III and FDA cleared therapeutics. Associations between pathway activation and response to chemotherapy (RCB 0/1 vs. 2/3) and relapse-free survival (RFS) were evaluated for the triple-negative (TN) patient population at each time point and for changes between T1 and T2. Significance thresholds for response and RFS were as follows: Wilcoxon rank sum test p &lt; 0.05; Cox proportional hazard model, likelihood ratio p &lt; 0.05.

Results: We focused our analysis on protein changes in patients who had poor clinical outcomes (Table 1)

Abstract P4-09-02: A robust signature of long-term clinical outcome in breast cancer

Background: Multigene prognostic signatures derived from high-dimensional mRNA expression data have been proposed to forecast patient outcome and predict chemotherapy benefit more accurately than standard clinical parameters. However, many prognostic signatures fail to predict late recurrences occurring 10 or more years following initial diagnosis. Furthermore, breast cancer subtypes canonically associated with favorable biology, particularly estrogen-receptor positive disease, are characterized by a higher frequency of late recurrences. Patients identified as being at a higher risk of late recurrence might benefit from more prolonged systemic (hormonal) therapy; as such, the goal of this research has been to develop a prognostic signature that can faithfully stratify patient risk up to and beyond 10 years of follow-up.

Methods: A novel multiplexed Cox modeling approach was applied to microarray data obtained from an untreated, node-negative patient cohort with long-term follow-up (n = 141) to train the signature. The long-term prognostic signature was subsequently validated in an additional group of patients (n = 154) that were mostly node-positive (94%) and administered adjuvant chemotherapy (71%). The performance of the signature was compared to existing clinicopathological parameters and genomic signatures using Cox proportional hazards analysis. Logistic regression modeling was employed to evaluate the added benefit to discriminatory accuracy obtained by incorporating the long-term prognostic signature alongside current biomarkers to predict 10-year overall survival.

Results: The long-term signature was able to stratify patient risk with unprecedented accuracy compared to standard clinicopathological and genomic features in both the training and the validation cohorts; none of the patients predicted to have good biology (n = 47 and 38) died within 10 years in either cohort, whereas only 34% and 44% of patients predicted to have poor biology (n = 47 and 46) survived 10 years in the training and validation cohorts, respectively. Within the validation series, the signature was able to identify patients at risk of metastasis with the highest hazard ratio in comparison to other prognostic signatures (univariate hazard ratio of 14.0 [95% CI 3.2–58; p = 0.00083], adjusted hazard ratio of 5.2 [95% CI 1.2–22; p = 0.0257] when corrected for standard clinicopathological markers). Adding the long-term prognostic signature to existing prognostic biomarkers led to significantly improved classification of patients into appropriate 10-year overall survival risk categories (Net Reclassification Improvement of 25.1% in validation series at &gt;5% risk threshold, p = 0.0123).

Conclusions: We were able to identify a 200-gene long-term signature able to stratify patient risk with superior accuracy over a relatively long follow-up period. We are currently using this algorithm to develop prognostic signatures for other cancer types, and are using similar multiplexed algorithms to develop gene signatures able to predict response to neoadjuvant therapy.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-09-02.

Abstract P3-04-02: Protein pathway activation mapping of I-SPY 1 biopsy specimens identifies new network focused drug targets for patients with HR+/HER2− tumors

Background: Profiling protein signaling activation in cancer is critical as these proteins represent targets for new molecular therapeutics. The I-SPY TRIAL (CALGB 150007/150012, ACRIN 6657) is a trial of neoadjuvant anthracycline- and taxane- based chemotherapy that longitudinally collected biopsy specimens and molecular and clinical/pathological characterization.

Methods: Tumor epithelium was procured by Laser Capture Microdissection from 149 pretreatment frozen biopsy specimens (T1) and 102 frozen biopsy specimens (T2, 1–4 days post-chemotherapy). Reverse Phase Protein Microarray technology was used to quantitatively measure the activation of 39 and 100 key signaling proteins in the T1 and T2 biopsies, respectively, including numerous drug targets for Phase I-III and FDA-cleared therapeutics. Associations between protein activation and response to chemotherapy (RCB 0/1 vs 2/3) and relapse-free survival (RFS) were evaluated for the HR+/HER2− patient population at each time point and for changes between T1 and T2. Significance thresholds for response and RFS were as follows: Wilcoxon rank sum test p &lt; 0.05; Cox proportional hazard model, likelihood ratio p &lt; 0.05.

Results: We focused our analysis on protein changes in patients who had poor clinical outcomes (Table 1)

Abstract P2-05-01: Gene expression changes associated with response to neoadjuvant chemotherapy are observed early in treatment: results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)

Background: Prior gene expression profiling studies have identified markers that are predictive of chemotherapy response using pre-treatment biopsies. However, this approach does not account for chemotherapy-induced perturbation in signaling within tumors early in treatment that may predict response to therapy with superior sensitivity to baseline signatures. We hypothesized that measuring early changes in gene expression induced by neoadjuvant chemotherapy might yield improved markers of treatment efficacy and patient outcome.

Methods: Transcriptome data from 34K probe cDNA microarrays were assembled using serial biopsies obtained from 36 I-SPY 1 TRIAL patients before treatment (T1), and 24-72 hours after beginning neoadjuvant anthracycline-based chemotherapy (T2). Outcome parameters included residual cancer burden (RCB) after therapy and recurrence free survival (RFS). Gene expression changes occurring between T1 and T2 (T2-T1) were compared between known responders (RCB 0/1) and non-responders (RCB 2/3) using a permutation test based on the t-statistic; Cox proportional hazards modeling was used to identify early response genes associated with RFS. Due to the small sample sizes, we adopted a relaxed significance threshold for outcome associations (p-value&lt;0.005 without multiple testing correction). Pathway analyses were performed with Ingenuity IPA software.

Results: 97 genes were found to be differentially altered upon comparing early gene expression changes (T2-T1) between responders (RCB 0/1) and non-responders (RCB 2/3). Ingenuity IPA software identified cell cycle as the top enriched pathway (p = 0.0008) among these differentially altered genes, with responders showing relative up-regulation of translation regulator EIF4EBP1 and cell cycle regulators CDKN2B and SMARCB1 after treatment. Survival analysis identified changes (T2-T1) in 293 genes as significantly associated with RFS; these genes were enriched in pathways including lipid antigen presentation by CD1, cell death and drug metabolism, and notch signaling. Surprisingly, only 4 genes were associated with both RCB and RFS, likely reflecting a prognostic signal from the many non-responding patients with favorable outcomes. Intrinsic subtype assignments were 75% concordant between time points T1 and T2, with basal classifications remaining stable (13/13) and some inter-conversion among LumA, LumB, Her2, and Normal (9/23). Interestingly, a larger number of genes were associated with chemotherapy response when one considered the change in expression (T2-T1), rather than absolute expression levels at T1 (17 genes) or at T2 (87 genes). Moreover, there was negligible overlap between these three response associated gene sets (T1, T2, and T2-T1 change), indicating that early expression changes may provide information beyond signatures obtained at static time points.

Conclusion: These analyses suggest that pre-treatment, early treatment and early changes provide non-redundant information on chemotherapy responsiveness and outcome. Early expression changes might be combined with data from pre-treatment biopsies to construct early predictors of non-response, an essential component within an adaptive treatment framework.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-05-01.

Absence of interferon-gamma release assay conversion following tuberculin skin testing

BACKGROUND

The tuberculin skin test (TST) has been the established screening method for tuberculosis (TB) for over a century. Interferon-gamma release assays (IGRAs) using Mycobacterium tuberculosis-specific antigens are increasingly used as diagnostic tests for TB. Tuberculin comprises multiple antigens, including the antigens used in the QuantiFERON-TB Gold In-Tube (QFT-GIT) assay. Exposure to these antigens by means of a TST may prime an immune response that leads to a false-positive result in a subsequent IGRA, limiting the validity of IGRAs in patients in whom these tests are performed sequentially. The current data on the influence of prior TST on IGRAs show inconsistent results.

METHODS

Sixteen non-bacille Calmette-Guérin immunised medical students with no history of TB exposure and minimal risk of exposure to TB during the study period were tested simultaneously with a TST and QFT-GIT. The QFT-GIT assay was repeated 6 and 10 weeks later.

RESULTS

At baseline, all TST and QFT-GIT results were negative and remained negative 6 and 10 weeks after the TST.

CONCLUSION

These data show that negative QFT-GIT results are reproducible and suggest that a TST does not result in conversion of subsequent QFT-GIT assays in the absence of concomitant TB exposure. Therefore, a positive QFT-GIT should not be attributed to boosting induced by a previous TST.