Abstract OT1-13-01: MammaPrint, BluePrint, and full-genome data linked with clinical data to evaluate new gene expression profiles (FLEX)

BACKGROUND: Genomic signatures are revolutionizing the definition, identification, and treatment of breast cancer subtypes. The ability of genomic signatures to enable fine grained stratification of breast cancers to the granular disease level is still generally untested because of the difficulties in aggregating large clinical data sets. In order to stratify breast cancers into actionable subtypes both the full genome data and clinical data must be collected for patients at scale.

DESIGN & METHODS: FLEX is designed as a novel, large-scale, population based, prospective registry. All patients with stage I-III breast cancer who receive MammaPrint (MP) or BluePrint (BP) testing on a primary breast tumor are eligible. FLEX utilizes an adaptive design which enables additional study arms at low incremental effort and cost by allowing targeted substudies to be added. Patients who are enrolled in the initial study will also be eligible for inclusion in any additional study arm where they meet all criteria. Additional study arms and substudies may be investigator-initiated.

SPECIFIC AIMS:

Primary: Create a big-data registry of full genome expression data and clinical data to investigate new gene associations with prognostic and/or predictive value.

Secondary: Generate hypotheses for targeted subset analyses and trials based on full genome data. To date the following substudies have been proposed:

DR. JENNIFER A. CROZIER, BAPTIST MD ANDERSON CANCER CENTER

(1) MP and BP in male breast cancer TYPE: SUBSTUDY; NO ADDITIONAL CONSENT (ICF) REQUIRED. ARMS: ALL (2) MP BP evaluation in breast cancer patients ≥70. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARMS: ALL (3) FG evaluation in ILC. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARMS: ALL (4,5) MP BP relation to PR positivity, Ki67. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARMS: ALL (6) MP BP in metaplastic breast cancer. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARMS: ALL

DR. ADAM M. BRUFSKY, UNIVERSITY OF PITTSBURGH MEDICAL CENTER MAGEE WOMENS HOSPITAL

(1) Response to standard chemotherapy regimens in clinically ER+/PR+/HER2+ (triple positive) patients according to BP molecular subtypes. (2) Expression signatures by response to bisphosphonates in ER+ patients receiving adjuvant therapy, or for osteoporosis after primary treatment. (3) Gene expression in breast cancer patients with obesity. TYPE: SUBSTUDY; DUAL ICF UTILIZED. ARMS: NEOADJUVANT AND ADJUVANT

DR. IAN GRADY, NORTH VALLEY BREAST CLINIC

Impact of genomic risk classification on travel time to receive breast cancer care. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARMS: ALL

DR. THOMAS LOMIS, VALLEY BREAST CARE

Complementary data collection for patients participating in the ODM-201 trial. FLEX provides gene expression for exploratory and signature discovery. TYPE: COMPLEMENTARY; DUAL ICF UTILIZED. ARM: NEOADJUVANT

DR. PAT WHITWORTH, NASHVILLE BREAST CENTER

Genomic reclassification of large tumors eligible to receive NCT therapy. TYPE: SUBSTUDY; NO ADDITIONAL ICF REQUIRED. ARM: NEOADJUVANT

ELIGIBILITY, ACCRUAL

FLEX will enroll a minimum of 10000 patients aged ≥18 with stage I-III breast cancer who sign ICF. Enrollment began April 2017 and 623 patients have been enrolled as of June 2018.

Citation Format: Brufsky AM, Crozier JA, Grady I, Lomis T, Whitworth P, Rehmus E, Srkalovic G, Lee L, Blumencranz P, Baron P, Mavromatis B, Untch S, Blumencranz L, Yoder EB, Audeh W, FLEX Investigators Group. MammaPrint, BluePrint, and full-genome data linked with clinical data to evaluate new gene expression profiles (FLEX) [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 OT1-13-01.

Abstract PD8-04: Neoadjuvant chemotherapy for breast cancer: Nodal downstaging is highly correlated with pathological complete response

Background: Neoadjuvant chemotherapy (NAC) is employed in patients with larger tumors to attempt to downstage locally advanced cancers to allow breast conservation and to assess in vivo tumor response. The Multi-Institutional Neoadjuvant Therapy MammaPrint Project I (MINT) study asked a secondary question of whether complete nodal downstaging could also be achieved with NAC.

Methods: This analysis included 147 eligible invasive breast cancer patients with high tumor burdens, classified as cT2-4N0-3M0 (T2 greater than 3.5cm if N0). Patients who had a positive core biopsy and/or fine needle aspiration (FNA) on an axillary node prior to starting NAC were included in this analysis. Those who had a surgical sentinel lymph node biopsy were not included. Nodal involvement was established following neoadjuvant treatment by axillary lymph node dissection (ALND).

Results: This population was 54% postmenopausal, average age 53 yrs (range 25 to 80 yrs). Tumor characteristics were 91% invasive ductal carcinoma; 65% T2, 29% T3, 6% T4; 87% LN1, 13% LN2-3; 3% low grade, 38% intermediate grade, 59% high grade; 65% ER-positive, 49% PR-positive, and 28% HER2-positive by immunohistochemistry; 84% High Risk (HR) and 16% Low Risk (LR) by MammaPrint (MP). After NAC, 45% (66/147) of these LN-positive patients were down-staged to ypN0 and also achieved a complete pathological response in the primary tumor. The potential for down-staging was inversely-related to tumor burden, where 47% (60/128) of N1, 35% (6/17) of N2, and 0% (0/2) of N3 patients were down-staged to ypN0. There were 3 patients who were down-staged (2 N2 to N1, and 1 N3 to N2), but not to ypN0. At surgery, 34% (44/128) of patients had no change, and 19% (24/129) progressed in LN staging.

Pre vs Post NAC Nodal StagePre NAC Nodal StageypN0ypN1ypN2ypN3TotalcN16044222128cN2626317cN3  112Total6646296147

Conclusions: We confirmed that upon achieving a complete response of the primary tumor that there was also a pathologic complete response in the LN. About 53% of patients had no change or progression of LN involvement following NAC.

Citation Format: Blumencranz P, Habibi M, Treece T, Blumencranz L, Yoder E, Audeh W, Carter E, McNaughton L, Roussos J, Shivers S, Acs G, Cox C, MINT Investigators Group. Neoadjuvant chemotherapy for breast cancer: Nodal downstaging is highly correlated with pathological complete response [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 PD8-04.

Abstract P4-08-10: MammaPrint identifies 46% of patients, age ≤50 years with oncotype RS 18-30, as low risk and safe to forgo chemotherapy

Background: The PROMIS trial (NCT01617954) previously showed that an OncotypeDx (ODx) Intermediate Recurrence Score (RS 18-30) led to uncertainty in prescribing chemotherapy (CT), especially in the middle of the intermediate range from RS 21-26 where an equal number of patients were recommended to receive and forego CT (Tsai, JAMA Oncology 2018). Forty-seven percent (3183/6711) of randomized TAILORx patients were classified as RS 18-25 and are well represented in PROMIS. These patients with RS 18-25 may still lack definitive CT recommendation following TAILORx, reflexing to age and menopausal status to make a decision. Here, we re-evaluate PROMIS using the subgroup analyses adopted by TAILORx. Methods: MammaPrint (MP) risk of recurrence was determined for ODx intermediate patients by standard diagnostic testing (Agendia, Irvine, CA). Clinical risk was assessed using the MINDACT, modified Adjuvant Online! algorithm (Cardoso, NEJM 2016). The MP high and low risk classification, and patient and tumor characteristics were re-evaluated and subdivided by RS 18-25 vs. RS 26-30. Results: The 840 eligible patients in PROMIS were classified as 61.3% (515/840) clinically low risk and 37.0% (311/840) clinically high risk (including 84 lymph node positive patients). Half (342/684) of all patients with an RS 18-25 and 20.5% (32/156) patients with RS 26-30 were MP low risk. There was no significant difference in the distribution of MP risk in women age ≤50 yrs vs. >50 years (Yates chi-square P=0.62); MP classified 46.4% (84/181) patients age ≤50 yrs and 44.0% (290/659) patients age >50 yrs as low risk. In the clinically-low risk subset of 515 patients, there was also no significant difference in the distribution of MP risk by age (Yates chi-square P=0.89); MP classified 48.3% (56/116) patients age ≤50 yrs and 49.6% (198/399) patients age >50 yrs as low risk. Conclusions: In light of TAILORx and uncertain CT benefit in women ≤50 yrs, MammaPrint provides a definitive high or low risk answer and identifies 46% of these women who may safely forego CT based on MINDACT data. An analysis of young patients in the MINDACT trial showed that MP low risk patients age <45 yrs and 45-55 yrs had very good 5-yr DMFS of 95-98%, in both clinically low and high risk groups (Alders, SABCS 2017).

MammaPrint Risk by RS and AgeMammaPrint RiskRS 18-25  RS 26-30  GrandClassification≤50 yrs>50 yrsAll Ages≤50 yrs>50 yrsAll AgesTotalHigh Risk7426834223101124466Low Risk8026234242832374All15453068427129156840

Citation Format: Soliman H, Lo S, Qamar R, Budway R, Levine E, Whitworth P, Mavromatis B, Zon R, Untch S, Treece T, Blumencranz L, Audeh W, Tsai M, PROMIS Investigators Group. MammaPrint identifies 46% of patients, age ≤50 years with oncotype RS 18-30, as low risk and safe to forgo chemotherapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-10.

Abstract P2-09-19: Genomic biomarker for resistance to palbociclib in the NeoPalAna trial

Background: Cyclin-dependent kinase (CDK) 4/6 inhibitors are being evaluated in the adjuvant setting for patients with resected early stage hormone receptor positive (HR+) and HER2 negative (HER2-) breast cancer (BC). However, biomarkers that predict benefit from this class of agents are unknown. We have recently reported results from the phase II neoadjuvant NeoPalAna trial which demonstrated that palbociclib (Pal) enhanced the anti-proliferative activity when added upon anastrozole (Ana) monotherapy in estrogen receptor (ER) positive and HER2 negative breast cancers. Interestingly, a small group of patients was resistant to Pal, exhibiting persistent tumor cell proliferation (Ki67 >2.7%) on the combination of Ana and Pal. In this study, we evaluated the utility of a research algorithm for the 70-gene signature (70-GS) in identifying Pal resistant versus sensitive patients. Methods: Serial biopsies were collected from patients at four treatment timepoints: baseline (BL), cycle 1 day 1 (C1D1) following 28 days of Ana monotherapy, cycle 1 day 15 (C1D15) at 2 weeks post the addition of Pal, and at surgery (Surg). RNA was extracted from frozen tumor biopsies at each timepoint and run on Agilent full genome microarrays (GSE93204) at Washington University. As an exploratory analysis, genes from the GPL8253 array that match the 70-GS were used to calculate a research approximation of the 70-GS index (r-GS). The distribution of the r-GS across Ki67 response groups was evaluated. Results: Ki67 had previously been measured at each timepoint, and used to classify patients as being either Ana-sensitive (C1D1 Ki67 ≤2.7%), Pal-sensitive (C1D1 Ki67 >2.7%, C1D15 Ki67 ≤2.7%), or Pal-resistant (C1D15 Ki67 >2.7%). The r-GS was differentially regulated between sensitive (AI or Pal) and Pal-resistant groups at BL (p=0.012), C1D1 (p=0.039), and C1D15 (p=0.022). The r-GS values varied widely across patients at BL, and generally became more positive (more low risk) with treatment. There was no correlation between Ki67 levels and r-GS. Furthermore, gene expression analysis was performed to elucidate the difference between Pal-sensitive vs. Pal-resistant patients, and Ana-sensitive vs. Pal-sensitive patients. Conclusions: While on-treatment Ki67 indicated drug responsiveness, baseline r-GS significantly stratified patients into sensitive (Ana or Pal) versus Pal-resistant groups in the neoadjuvant setting. This preliminary finding suggests that the 70-GS may have clinical utility in identifying patients resistant to Pal for future studies. Additionally, results of the gene expression analysis may help to further develop genomic biomarkers for Pal and Ana sensitivity and resistance.

Citation Format: Hoog JW, Treece T, Blumencranz L, Audeh W, Sanati S, Ellis MJ, Ma CX. Genomic biomarker for resistance to palbociclib in the NeoPalAna 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 P2-09-19.