MammaPrint High Research Articles

Elucidating the immune active state of HR+HER2- MammaPrint High 2 early breast cancer.

506 Background: The 70-gene signature, MammaPrint (MP), classifies patients (pts) with early-stage breast cancer (EBC) as having an UltraLow, Low, High 1 (H1), or High 2 (H2) risk of distant recurrence. I-SPY 2 showed that pts with MP H2, HR+HER2- tumors have significantly higher response rates to neoadjuvant chemotherapy + immunotherapy relative to pts with MP H1 tumors. Expression-based immune deconvolution provides more detailed information about immune cell function beyond conventional methods enumerating tumor infiltrating lymphocytes. To elucidate the underlying biology that mediates immune therapy response, we performed in silico analysis of full transcriptome data to characterize immune cell frequencies and antigen presentation in HR+HER2-, MP High Risk EBC from pts enrolled in FLEX. Methods: The prospective, observational FLEX Study (NCT03053193) includes stage I-III pts with EBC who received MP testing and consented to full transcriptome and clinical data collection. Women with HR+HER2-, and MP High Risk invasive ductal EBC were included (n = 2916). Tumors were stratified into MP H1 or MP H2. The R-package Limma was used to preprocess gene expression data. The gene signature-based method xCell was used to determine immune cell abundances for each group based on enrichment score. Expression of genes involved in “antigen processing and presentation KEGG pathway”, and immune regulation, were evaluated between groups. Differences in immune cell frequency and gene expression were determined by a t-test with an adjusted p-value < 0.05. Results: MP classified 79% (n=2292) of HR+HER2- EBC as H1 and 21% (n=624) as H2. Pts with H2 EBC were more likely to be ≤ 50 years (32%) compared to pts with H1 tumors (23%). Although low ER staining (1-10%) tumors were more frequent in H2 vs H1 (15% vs 1%), a majority of H2 tumors (75%) had ER staining > 10%. Nearly 30% of H2 tumors were Grade 1 or 2, whereas 22% of H1 tumors were Grade 3. H2 tumors had significantly higher frequency of antigen presenting cells (APCs) including activated dendritic cells and macrophages, CD4+ memory T cells, CD8+ T cells, memory B cells and plasma cells relative to H1 tumors. The genes expressing PD-1 and PDL-1 and genes involved in antigen processing, including B2Mand TAP1/2, and presentation, i.e., major histocompatibility (MHC) class I ( HLA-A, -B, -F) and class II molecules ( HLA-DM, -DQ), were significantly upregulated in H2 vs H1. Conclusions: H2 tumors exhibited a heighted immune active state compared to H1 tumors among HR+HER2- EBC pts. The presence of APCs and increased antigen presentation, which are critical in eliciting T- and B-cell activation may explain the improved response rates to immunotherapy observed in H2 tumors. Selecting pts based on grade or ER% alone may exclude pts likely to benefit from immune therapy. These data support ongoing trials evaluating the response and benefit of adding immunotherapy to standard of care treatment regimens in MP H2 tumors. Clinical trial information: NCT03053193 .

Abstract PO5-15-04: MammaPrint index predicts neoadjuvant chemosensitivity in patients with HR+HER2- early-stage breast cancer in the real-world evidence FLEX study

Abstract Background: Neoadjuvant chemotherapy (NCT) yields low pathologic complete response (pCR, ypT0/is ypN0) rates in hormone receptor positive (HR+), HER2- early-stage breast cancer (ESBC). Genomic signatures may predict chemosensitivity and treatment benefit better than receptor status based clinical subtyping. The 70-gene expression signature, MammaPrint (MP), classifies patients with ESBC as having a High or Low Risk of distant recurrence. In the NBRST and ISPY2 trials, further stratification of MammaPrint High Risk into High 1 (H1) or High 2 (H2) showed significantly higher pCR rates to NCT or targeted agents in MP H2 cancers compared to MP H1 tumors. We evaluated MammaPrint H1 and H2 status as a biomarker for neoadjuvant chemosensitivity in patients with HR+HER2- ESBC enrolled in the real-world evidence FLEX study. Methods: FLEX (NCT03053193) is an ongoing prospective, observational trial that has currently enrolled 12,328 patients with ESBC who were tested with MammaPrint as standard of care, with or without molecular subtyping signature, BluePrint (BP), and consented to clinically annotated full genome data collection (data locked Feb. 2023). Patients with HR+HER2-, MP High Risk tumors who received NCT (majority received AC-T) and had pCR data available were included in this analysis (n = 214). Patients were stratified into MP H1 (index 0.000 to -0.569) and H2 (index -0.570 to -1.000) groups. BP classified MP High Risk tumors into Luminal B-, HER2-, or Basal-Type. Differences in clinical characteristics and pCR rates between H1 and H2 tumors was assessed by Chi-Squared test and two-sided proportional z-test, respectively. The association between MP H1 and H2, BP subtype, and pCR was assessed using logistic regression and was adjusted for age, race, grade, T stage, N stage, and NCT regimen. Results: MammaPrint classified 142 (66%) cancers as H1 and 72 (34%) as H2 tumors. Age, menopausal status, race, tumor stage, and lymph node status were comparable between both groups. Although most H2 tumors (78%) were Grade 3, only 59% of all Grade 3 tumors were H2. Nearly all (98%) H1 tumors were Luminal B whereas for H2 tumors, 51% were Luminal B and 49% were Basal by BP classification. pCR rate was significantly higher in H2 tumors (29.2%) compared to H1 tumors (6.3%, p < 0.01) (Table). Basal-Type, H2 tumors (n=35) exhibited the highest pCR rate of 37.1%. Among BP Luminal B tumors, those with MP H2 tumors had a significantly higher pCR rate (21.6%) vs. MP H1 tumors (5.8%, p = 0.003). Multivariate analysis revealed MP H2 (OR=4.91, p=0.003) and BP Basal-Type (OR=3.54, p=0.03) were significantly associated with likelihood of pCR, whereas clinical variables were not associated with pCR. Conclusion: These data demonstrate MammaPrint and BluePrint utility to predict the likelihood of achieving pCR after NCT in HR+HER2- ESBC. Although both MP High Risk groups exhibit chemosensitivity, High 2 tumors have higher chemosensitivity than High 1 tumors. MP High 2 status can be utilized to identify ER+ patients who are the most likely to experience pathologic downstaging and pCR after NCT. Also, patients with High 2 tumors treated with PD-L1 or PARP inhibitors in the ISPY2 trial exhibited significantly higher pCR rates than those observed for High 2 tumors treated with NCT alone. These data suggest that for patients with MP High 2 tumors, neoadjuvant use of chemotherapy is appropriate and these patients may further benefit from the addition of targeted agents to standard NCT. Table: Distribution of pCR rates among MammaPrint H1 and H2 and BluePrint molecular subgroups Data presented as # of patients with pCR/(total # patients in subgroup) and as percentage Citation Format: Joyce O'Shaughnessy, Lajos Pusztai, Cathy Graham, Pat Whitworth, Peter Beitsch, Cynthia Osborne, Rakhshanda Rahman, Andrea Menicucci, William Audeh, FLEX Investigators' Group. MammaPrint index predicts neoadjuvant chemosensitivity in patients with HR+HER2- early-stage breast cancer in the real-world evidence FLEX study [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-15-04.

Correlation of HER2 low status in I-SPY2 with molecular subtype, response, and survival.

514 Background: HER2low, defined as immunohistochemical (IHC) 1+ or 2+ without HER2 gene amplification, predicted improved progression free and overall survival with trastuzumab deruxtecan (TDXd) compared to chemotherapy in patients (pts) with metastatic breast cancer in Destiny Breast04. Controversy exists regarding the correlation of HER2low with molecular subtypes and outcome. We evaluated these associations in the neoadjuvant ISPY2 trial. Methods: We investigated HER2 IHC class in pts with clinically HER2-negative breast cancer (BC) enrolled in the first 10 arms of ISPY2. To explore the biology of HER2low, we used Fisher’s exact test to assess association of IHC class (0 vs 1+ or 2+) with Response Predictive Subtypes-5 (RPS-5; based on immune, DNA repair damage (DRD), HER2, and luminal markers; PMID: 35623341), SET index [endocrine responsiveness], and Mammaprint high1 (MP1) vs high2 (MP2). Association with pathologic complete response (pCR) was assessed using Fisher’s exact test, and association with distant recurrence free survival (DRFS) was assessed using Cox Proportional Hazards modeling. Results: Of 742 HER2negative pts enrolled in the first 10 arms of ISPY2, local HER2 IHC is available for 585; 299 hormone receptor + (HR+) and 286 triple negative (TN). 63% of pts are HER2low, with HER2low status more frequent in HR+ (71%) compared to TN BC (55%; OR = 1.97; p = 0.00011). There was no clear relationship between HER2low IHC and RPS-5 subtypes or endocrine sensitivity measured by the SET index. There was no significant association of HER2low with pCR overall or within treatment arms (p > 0.05); this was true for TN and HR+ subsets. 562 pts with HER2negative disease have distant recurrence free survival (DRFS) data with a median follow-up of 4.23 yrs. Pts with pCR had excellent outcome (5yr DRFS > 94%), with no impact from HER2low vs 0 status. For pts with nonpCR, after adjusting for HR+ status, the DRFS hazard ratio for HER2low vs 0 status is not significant [0.68(0.46-1.02)]. Within HR+, HER2low is found in > 70% for both SET low and high. HR+/MP1 pts (with generally low pCR rates) are significantly more likely to be HER2low (75%; (172/219)) compared to HR+/MP2 (61%; (49/80)) (OR: 1.79; Fisher p = 0.044). Importantly, 70% of HER2-Immune-/DRD- (78% HR+ and 56% TN), a subtype with low response to all ISPY2-tested agents, are HER2Low. Conclusions: In ISPY2 which enrolls patients with MP high risk BC, HER2low by IHC was frequent and higher in HR+ than TN disease. There was no clear association with molecular markers, pCR or DRFS. The frequency of HER2low in the immune-/DRD- subtype raises the potential for exploring T-DXd in this high risk, low-response setting. Clinical trial information: NCT01042379 .

Abstract P5-05-05: Monitoring for response and recurrence in neoadjuvant-treated hormone receptor-positive HER2-negative breast cancer by personalized circulating tumor DNA testing

Abstract Background: The detection of circulating tumor DNA (ctDNA) may serve as an early predictor of response and recurrence. In this study, we used a tumor-informed ctDNA test to monitor clinical outcomes in patients with high-risk hormone receptor-positive HER2-negative (HR+HER2-) tumors who received neoadjuvant chemotherapy (NAC) on the I-SPY 2 trial (NCT01042379). Methods: We collected blood samples at pretreatment, during (at 3 and 12 weeks after initiation of paclitaxel-based treatment with or without an investigational drug), after NAC prior to surgery, 4 weeks after surgery, and annually until clinical diagnosis of recurrence. Cell-free DNA was isolated from plasma (N=329 samples) and ctDNA was detected using a personalized, tumor-informed multiplex polymerase chain reaction next generation sequencing-based test (SignateraTM). All patients were at high risk for recurrence by MammaPrint. The response endpoints were pathologic complete response (pCR) and residual cancer burden (RCB), and the survival endpoint was event-free survival (EFS). Results: This analysis included 66 patients with HR+HER2- breast cancer who had blood samples collected before, during, after NAC and had at least one blood sample after surgery with sufficient plasma for analysis. 57.1% (32/56) had grade III disease; 72.4% (42/58) were node-positive; 36.2% (21/58) had T3/T4 disease; and 33.3% (22/66) were MammaPrint High 2. The percent ctDNA positivity rates at pretreatment, after NAC prior to surgery, and 4 weeks after surgery were 79.7% (47/59), 6.5% (4/62), and 2% (1/50), respectively. Significantly higher ctDNA positivity rates at pretreatment were observed in patients with larger tumors (95% in T3/T4 vs. 69% in T1/T2, Fisher’s exact p=0.0387), higher grade tumors (94% in Grade III vs. 67% in Grade I/II, p=0.0147) and by MammaPrint score (100% in High 2 vs. 71% in High 1, p=0.0052). In this high-risk HR+/HER2- cohort, 10/66 (15.2%) achieved pCR/RCB 0, who were all ctDNA-negative at surgery. 56/66 (84.8%) had no-PCR, with RCB I (limited residual cancer), II (moderate) and III (extensive) in 7 (10.6%), 31 (47.0%) and 18 (27.3%), respectively. ctDNA-positivity after paclitaxel-based treatment was significantly associated with RCB II/III status (Fisher’s exact p=0.01). All patients in this cohort with persistent ctDNA subsequently had RCB II or III at surgery. 47 patients had paired samples collected after NAC prior to surgery and at 4 weeks after surgery. Of the 47, 91.5% (43/47) were ctDNA-negative at both time points and 8.5% (4/47) were discordant; 1 was ctDNA-negative and later tested ctDNA-positive, while 3 were ctDNA-positive and later tested ctDNA-negative. 61/66 patients had EFS data with a median of 1.6 years of follow up (range: 0.6 to 5.6). 5 tested ctDNA-positive in at least one time point after surgery. Of these, 2 experienced a recurrence (one local relapse and one distant metastasis) and both tested positive at the time of recurrence. For the patient who developed a distant recurrence it was the only blood sample available at a follow-up time point; for the patient who developed a local recurrence, blood from two earlier follow-up time points had tested negative. To date, no recurrences have been observed in those whose test(s) after surgery were negative for ctDNA. Conclusions: The persistence of ctDNA during neoadjuvant therapy is associated with the extent of residual disease in a cohort of patients with HR+HER2- breast cancer in the I-SPY 2 trial and thus may be useful in identifying patients who are not having an optimal response to therapy. I-SPY 2.2 will test whether ctDNA has utility in redirecting therapy to improve surgical outcome and subsequent prognosis. Citation Format: Mark Jesus M. Magbanua, Hope Rugo, Lamorna A. Brown Swigart, Ziad Ahmed, Gillian L. Hirst, Denise M. Wolf, Ruixiao Lu, Ekaterina Kalashnikova, Derrick Renner, Angel Rodriguez, Minetta C. Liu, Christina Yau, Laura J. Esserman, Laura Van ’t Veer, Angela DeMichele. Monitoring for response and recurrence in neoadjuvant-treated hormone receptor-positive HER2-negative breast cancer by personalized circulating tumor DNA testing [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-05-05.

Pathologic complete response (pCR) rates for HR+/HER2- breast cancer by molecular subtype in the I-SPY2 Trial.

504 Background: Hormone receptor positive (HR+), HER2- breast cancer (BC) is a heterogenous disease. We hypothesized that molecular subtypes capturing luminal, basal, and immune biology could predict response for patients (pts) with HR+/HER2- disease in the I-SPY2 trial. Methods: I-SPY2 trial is a phase II, randomized, adaptive study evaluating multiple investigational agents as neoadjuvant BC therapy; the primary endpoint is estimated pCR rate. Investigational agents are given with control weekly paclitaxel x 12, followed by AC x 4. Regimens graduate when the predicted pCR rate in any signature meets the pre-specified threshold of 85% probability of success in a hypothetical 300 pt randomized, phase 3 trial. We analyzed estimated pCR rates for the 1st 7 investigational agents in the HR+/HER- subset, analyzed by clinical/molecular features: BluePrint (BP) Luminal vs. Basal, Mammaprint High1 [MP1] vs. Mammaprint High2 [MP2], MP2 is < -0.57, Responsive Predictive Subtype-5 (RPS-5) (classification based on HR, HER2, immune, DNA-repair, and basal/luminal markers), histology, and stage/nodal status. Results: 38% (379/987) of pts had HR+/HER2- disease. Only pembrolizumab met the pre-specified graduation criteria for HR+/HER2- BC. pCR rates by treatment arm and molecular subtype are described in the Table. 28% were MP2; 72% were MP1. Overall, pCR rates were higher in pts with MP2 vs MP1 disease (30% vs 11%) including with pembrolizumab (55% vs. 21%). 29% were BP Basal, 71% were BP Luminal; BP Basal was more likely to be MP2 than BP Luminal (77% vs 8%). In all arms except MK2206, HR+/HER2- BP Basal pts were more likely to achieve pCR than BP Luminal pts. For MK2206, BP Luminal pts were more likely to achieve pCR. Immune+ by RPS-5 (39% of HR+/HER2-) predicted pCR to pembrolizumab irrespective of BP Basal or Luminal status (11 pCR/16 pts). Results by histology and stage/nodal status will also be reported. Conclusions: Our data suggest that MP2 and BP Basal signatures identify a subset of HR+/HER2- BC more likely to respond to neoadjuvant therapy; and that an immune signature can identify pts more likely to respond to pembrolizumab. These findings will aid in guiding prioritization of targeted agents with the goal to optimize pCR for all pts. Clinical trial information: NCT01042379. [Table: see text]

Race and response to neoadjuvant chemotherapy according to MammaPrint risk.

578 Background: African-American (AA) women with breast cancer have a less favorable prognosis, likely due to differences in tumor biology. This is not only driven by the higher rate of triple negative/basal tumors in patients with AA ancestry, as worse outcome has also been seen in patients with luminal tumors. The Neoadjuvant BReast Cancer Symphony Trial (NBRST, NCT01479101) was a prospective trial that has shown an association of MammaPrint/BluePrint (MP/BP) with a rate of pathologic Complete Response (pCR) of 2% in Luminal A with 95% Distant Metastasis Free Interval at 3 years. Here, we determine the MP/BP risk distribution, response to therapy, and outcome in African American (AA) and Caucasian (Cau) patients. Methods: NBRST enrolled 1,072 breast cancer patients (pts) in the US (June 2011 and December 2014), median follow-up 34.9 months. The current unplanned analysis compared clinicopathological characteristics, molecular risk assignment and outcome with neoadjuvant chemotherapy (NACT) in AA and Cau pts. Molecular subtyping groups were assessed by MP/BP as follows: Luminal A (MammaPrint Low Risk), Luminal B (MammaPrint High Risk), HER2 and Basal types. Results: Out of 1,072 pts, 157 (15%) were AA, and 780 (73%) were Cau. AA patients were younger at diagnosis (52 vs 54 yrs; p = 0.016), had a higher likelihood of having higher grade (gr 3, 65% vs 53%; p = 0.005), ER-negative (45% vs 33%; p = 0.005) and lymph node positive tumors (71% vs 51; p < 0.001). MP/BP classified more AA patients as Basal type, 45% compared to 33% of Cau patients (p = 0.004). Fewer AA patients were classified as Luminal A (15%) compared to Cau pts (33%; p = 0.004). In multivariate analysis race was a significant factor for higher pCR rates to NACT in AA compared to Cau pts, together with PR, HER2, T-stage and Grade (HR = 1.679, 95% CI = (1.057, 2.67), p = 0.028). The pCR rate to NACT in patients with Basal tumors was 38% and similar in AA and Cau patients. In patients with hormone receptor positive and HER2 negative tumors, patients classified by MP/BP as Luminal A had lower pCR (2%) compared to non-luminal A (13%) (p = 0.0015). MP low risk patients had higher 3 yr DMFS (97%) than MP high risk patients (86%; p = 0.010). DMFS for AA MP Low Risk patients was 100%. Conclusions: In this study, MP was able to identify patients with hormone receptor positive tumors with low sensitivity to chemotherapy and good outcome, irrespective of race, suggesting that this test can be helpful to characterize the tumor’s biology and select patients who will not benefit from chemotherapy independently of their ancestry. Clinical trial information: NCT01479101.

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

Abstract 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<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 P5-16-05: MINT trial yields MammaPrint High1/High2 risk classes associated with significant differences in pCR and receptor subtype

Abstract Background: Previous clinical trials have validated that the 70-gene signature MammaPrintTM provides prognostic and predictive information for early stage breast cancer patients and can identify low risk patients who may safely avoid adjuvant chemotherapy. Additionally, the neo-adjuvant I-SPY 1&2 TRIALs demonstrated that further stratification of patients into MammaPrint High 1 (MP1) and MammaPrint High 2 (MP2) risk groups may help predict chemo-sensitivity. There were significant differences in pathological complete response (pCR) rates for early stage, locally advanced breast cancer patients who were not HR+HER2- MammaPrint Low Risk. Specifically, the PARP inhibitor veliparib in combination with carboplatin recently graduated the I-SPY 2 phase 2 screening trial, having met the 85% predictive probability criterion with a triple-negative breast cancer signature, which was the subset recommended for this regimen's subsequent development. Given these data, we wanted to determine whether the Multi Institutional Neo Adjuvant Therapy MammaPrint Project (MINT) patient population confirmed the MP1/MP2 risk stratification, clarify if there is an associated receptor subtype for MP1/MP2 risk classes, and conclude if the stratification correlates to a significant difference in pCR. Methods: Array data from pre-treatment samples were obtained from 180 patients classified as MammaPrint High Risk, subtyped by IHC and treated with neo-adjuvant chemotherapy according to protocol. Response was measured by centrally assessed residual cancer burden pursuant to guidelines. Patients were then further stratified based on the MammaPrint Index per their classification threshold between MP1/MP2. Fisher's exact test was used to assess significance of association with pCR overall and within hormone receptor (HR) and HER2 subtypes. Results: MP1 vs MP2 risk classes yielded subsets with significant (p=0.007) differences in pCR. 44% (40/92) of MP2 patients achieved a pCR, compared to 24% (21/88) of MP1 patients. Next, we investigated whether the MP1 and MP2 risk classes were associated with receptor subtype. MP1 demonstrated a significant association and MP2 near significance. 32% (21/66) of triple-negative patients were classified as MP2 vs only 3% (2/66) MP1. Similarly, in the overall population, 28% (51/180) HR+HER2- are classified as MP1 vs 4% (8/180) MP2. Results in the pCR population were reflective of these subtype trends. 63% (58/92) of MP2 patients were classified triple-negative, of which nearly one quarter (21/92) had a measured pCR, whereas 58% (51/88) of MP1 patients were HR+HER2- with 3% (3/88) achieving pCR (Table1). Conclusion: This analysis in the MINT patient population supports previously published data and suggests that the MammaPrint High 1/2 risk classification may help predict chemo-sensitivity. Given the statistical significance of these data, we are currently investigating the biological mechanisms distinguishing the MP1/MP2 subgroups that may account for its use as a specific biomarker of response to chemotherapy treatment in future trials. Table 1.MP1MP2HER2+HER2-HER2+HER2-HR+HR-HR+HR-HR+HR-HR+HR-793241322185486456371514518818858Row#1= pCR, #2= RD, #3= Total Citation Format: Blumencranz LE, Shivers SC, Untch S, Treece TD, Yoder E, Blumencranz PW, Cox CE. MINT trial yields MammaPrint High1/High2 risk classes associated with significant differences in pCR and receptor subtype [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 P5-16-05.

Abstract S2-06: DNA repair deficiency biomarkers and MammaPrint high1/(ultra)high2 risk as predictors of veliparib/carboplatin response: Results from the neoadjuvant I-SPY 2 trial for high risk breast cancer

Abstract Background: The PARP inhibitor veliparib in combination with carboplatin (VC) was one of the experimental regimens evaluated in the phase 2 neoadjuvant I-SPY 2 standing trial for high risk breast cancer patients. VC graduated in the triple negative (TN) signature. However, not all TN patients achieved pathologic complete response (pCR) and some HR+HER2- patients responded. The I-SPY 2 biomarker component provides a platform for rigorous evaluation of mechanism-of-action-based markers in the context of established biomarkers (HR, HER2, MammaPrint) within the trial. Here, we report results from 5 investigator-submitted biomarker proposals and the MammaPrint High1/High 2 (MP1/2) classification as specific predictors of VC response. Methods: Data from 116 HER2- patients (VC: 72 and concurrent controls: 44) were available. BRCA1/2 germline mutation was assessed by Myriad Genetics. 3 expression signatures relating to DNA damage repair deficiency (PARPi-7, BRCAness and CIN70) and MP1/2 classification were evaluated on Agilent 44K arrays. PARP1 levels were measured using reverse phase protein arrays. We used logistic modeling to assess biomarker performance. A biomarker is considered a specific predictor of VC response if it associates with response in the V/C arm but not the control arm, and if the biomarker x treatment interaction is significant (likelihood ratio test, p<0.05). In an exploratory analysis, we combined successful biomarkers to refine the 'predicted sensitive' group and used Bayesian modeling to estimate the pCR rates of 'predicted sensitive' TN and HR+HER2- patients in each arm. Results: BRCA1/2 germline mutation status associates with VC response, but its low prevalence in the control arm precludes further evaluation. Of the biomarkers evaluated, three (PARPi-7, BRCAness, and MP1/2) associate with response in the VC arm but not the control arm, and have biomarker x treatment interactions with p < 0.05 that retains significance upon adjusting for HR status. These signatures are only moderately correlated. When we combined the PARPi-7 and MP1/2 classifications using a simple voting scheme, the 40% of TN patients who are PARPi7-high and MP2 have an estimated pCR rate of 79% in the VC arm. In contrast, TN patients negative for at least one of these signatures (PARPi7-low and/or MP1) only have an estimated pCR rate of 35%. Only 9% of HR+/HER2- patients are PARPi7-high and MP2; but these patients also appear more responsive to VC with estimated pCR rates of 49%, compared to 13% in 'biomarker-negative' HR+HER2- patients. Conclusion: If verified in a larger trial, PARPi7, BRCAness and MP1/2 signatures may help refine predictions of VC response, thereby improving patient care. Evaluation of the combined signature for patients treated with platinum-based chemotherapy is ongoing. Citation Format: Wolf DM, Yau C, Sanil A, Glas A, Petricoin C, Wulfkuhle J, Brown-Swigart L, Hirst G, I-SPY 2 TRIAL Investigators, Buxton M, DeMichele A, Hylton N, Symmans F, Yee D, Paoloni M, Esserman L, Berry D, Rugo H, Olapade O, van 't Veer L. DNA repair deficiency biomarkers and MammaPrint high1/(ultra)high2 risk as predictors of veliparib/carboplatin response: Results from the neoadjuvant I-SPY 2 trial for high risk breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-06.

Abstract 859: Gene and pathway differences between MammaPrint High1/High2 risk classes: results from the I-SPY 2 TRIAL in breast cancer

Abstract BACKGROUND: Further stratification of the 70-gene MammaPrint(TM) prognostic signature into ‘high’ and ‘ultra-high’ risk groups may help predict chemo-sensitivity. In I-SPY 2, patients were classified as MammaPrint High1 (MP1) or MammaPrint (ultra) High2 (MP2), using a threshold predefined by the median cut-point of I-SPY 1 participants who fit the eligibility criteria for I-SPY 2. MP1/2 classification was added to HR and HER2 to define the subtypes used in the I-SPY 2 adaptive randomization engine. The first two experimental agents/combinations to graduate from I-SPY 2 were veliparib/carboplatin (V/C) in the TN subset, and neratinib (N) in the HR-HER2+ subset. MP2 was found to be a sensitivity marker for V/C but not N, whereas MP1 class appears associated with resistance to N within the HER2- subset. Despite these associations with response, it remains unclear whether MP1/MP2 classification represents differences in tumor biology. Here, we present exploratory analysis to elucidate the pathway differences between the MP classes. METHODS: 263 patients (V/C: 71, N: 115, and controls: 77) with pre-treatment Agilent 44K microarrays and MP1/2 class assessments were considered in this analysis. To identify signature genes associated with MP1 vs. MP2 class, we (1) apply a Wilcoxon rank sum test and (2) fit a logistic model. P-values are corrected for multiple comparisons using the Benjamini-Hochberg (BH) method, with a significance threshold of BH p<0.05 from both tests. We then perform pathway enrichment analysis using DAVID. In addition, we perform multivariate analysis adjusting for receptor subtype. Our study is exploratory and does not adjust for multiplicities of other biomarkers in the trial but outside this study. RESULTS: 63% (165/263) of patients are MP1 class and 37% (98/263) MP2. MP1/2 class is associated with receptor subtype (Fisher's exact test: p<2E-16), where 71% of TN patients are MP2 and 96% of HR+HER2+ patients are MP1. Of the 70 signature genes, 86% (60/70) differ in expression between MP1 and MP2, with 70% (42/60) expressed at a higher level in MP2, including CDCA7, MELK and CENPA. In a whole transcriptome analysis, 10,500 genes (of ∼30,000) appear differentially expressed. Following adjustment for HR and HER2 status, 4368 genes are significantly differentially expressed between MP1 and MP2. By DAVID enrichment analysis, the biggest pathway-level differences are found in cell cycle, proliferation, and DNA repair, with the MP2 set showing higher expression. CONCLUSION: MP2 class appears associated with higher expression of cell cycle & DNA repair genes. Association between MP2 class and response to V/C suggests that higher cell cycle activity may contribute to V/C sensitivity. Citation Format: Denise M. Wolf, Christina Yau, Lamorna Brown-Swigart, Gillian Hirst, Meredith Buxton, Melissa Paoloni, I-SPY 2 TRIAL Investigators, Olufunmilayo Olopade, Angela De Michele, Fraser Symmans, Hope Rugo, Don Berry, Laura Esserman, Laura van ‘t Veer. Gene and pathway differences between MammaPrint High1/High2 risk classes: results from the I-SPY 2 TRIAL in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 859.

Abstract P1-14-03: The evaluation of trebananib plus standard neoadjuvant therapy in high-risk breast cancer: Results from the I-SPY 2 TRIAL

Abstract 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 (< 10% probability of success) or following accrual of maximum sample size (10%< probability of success <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 P3-06-29: MammaPrint High1/High2 risk class as a biomarker of response to neratinib plus standard neoadjuvant therapy for breast cancer in the I-SPY 2 TRIAL

Abstract Background: Further stratification of the 70-gene MammaPrintTM signature into ‘high’ and ‘ultra-high’ risk groups may help predict chemo-sensitivity. In I-SPY 2, patients were classified as MammaPrint High1 (MP1) or MammaPrint (ultra) High2 (MP2), with MP2 defined as MP_score <-0.154. MP1/MP2 classification was added to HR and HER2 to define the cancer subtypes used in the I-SPY 2 adaptive randomization engine. Neratinib (N), one of the experimental agents evaluated in I-SPY 2, graduated in the HR-HER2+ signature. All patients received at least standard chemotherapy (paclitaxel followed by doxorubicin/cyclophosphamide; T->AC). HER2- patients were randomized to receive N+T- >AC vs. T->AC. For HER2+ patients, neratinib was administered in place of trastuzumab (N+T->AC vs. H+T->AC). Here, we assess the performance of MP1/MP2 class as a specific biomarker of neratinib response. Methods: 115 patients in the neratinib arm and 76 concurrently randomized controls had Agilent 44K microarrays and pCR data available for analysis. We assess association between MP1/MP2 and response in the neratinib and control arms alone using Fisher’s exact test, and relative performance between arms (biomarker x treatment interaction, likelihood ratio p < 0.05) using a logistic model. This analysis is also performed adjusting for HR status as a covariate, and in receptor subsets. Our study is exploratory with no claims for generalizability of the data. Statistical calculations are descriptive (e.g. p-values are measures of distance with no inferential content). Our analyses do not adjust for multiplicities of other biomarkers in the trial but outside this study. Results: There are 133 MP1 patients (neratinib: 74, Control: 59) and 58 MP2 patients (neratinib: 41, Control: 17), 84% (49) of which are Her2-. The distribution of pCR rates among MP1/MP2 dichotomized groups are summarized in Table 1. Neratinib (n=115)Control (n=76)MP1 (n=74)MP2 (n=41)MP1 (n=59)MP2 (n=17)HER2- (n=105)0 / 1715 / 337 / 395 / 16HER2+ (n=86)22 / 574 / 85 / 200 / 1 MP2, one of the 10 eligible signatures, did not meet the graduation threshold; and MP1/MP2 did not show a significant biomarker x treatment interaction (OR in neratinib relative to control arm = 1.25). The MP1/MP2 x treatment interaction remains non-significant after adjustment for HR and HER2 status (p=0.54). In HER2- patients receiving neratinib, 45% (15/33) of MP2 patients achieved a pCR, compared to 0% (0/17) of MP1 patients. In the HER2- controls, there is a 31% pCR rate in MP2 (5/16) vs. 18% in MP1 (7/39) patients (OR=2.14). This difference in performance between treatment arms appears significant (p=0.041). 90% of HER2+ patients are MP1, thus MP1/MP2 status x treatment interaction within the HER2+ subtype cannot be evaluated. Conclusion: Within the I-SPY 2 population as a whole, MP1/MP2 stratification does not appear to be a specific biomarker of response to neratinib relative to the control arm. The number of HER2- patients is small and precludes any definitive conclusion, but these data motivate further investigation of the biological mechanisms distinguishing MP1 from MP2 to better understand chemotherapy and/or neratanib responsiveness. Citation Format: Christina Yau, Denise M Wolf, Ashish Sanil, Jo Chien, Anne Wallace, Judy Boughey, Doug Yee, Debu Tripathy, Angela DeMichele, Rita Nanda, Steven Chiu, Claudine Isaacs, Kathy Albain, Hank Kaplan, Stacey Moulder, Rebecca Viscusi, Donald Northfelt, Kirsten Edmiston, Anthony Elias, Toncred Styblo, Barbara Haley, Lamorna Brown-Swigart, Susan Flynn, Gillian L Hirst, Meredith Buxton, Nola Hylton, Melissa Paoloni, W Fraser Symmans, Laura Esserman, Don Berry, Minetta C Liu, John W Park, Laura van 't Veer. MammaPrint High1/High2 risk class as a biomarker of response to neratinib plus standard neoadjuvant therapy for breast cancer in the I-SPY 2 TRIAL [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-29.

Abstract P3-06-25: MammaPrint High1/High2 risk class as a biomarker of response to veliparib/carboplatin plus standard neoadjuvant therapy for breast cancer in the I-SPY 2 TRIAL

Abstract Background: Further stratification of the 70-gene MammaPrintTM signature into ‘high’ and ‘ultra-high’ risk groups may help predict chemo-sensitivity. In I-SPY 2, patients were classified as MammaPrint High1 (MP1) or MammaPrint (ultra) High2 (MP2), with MP2 defined as MP_score <-0.154. MP1/MP2 classification was added to HR and Her2 to define the cancer subtypes used in the I-SPY 2 adaptive randomization engine. HER2- patients were randomized to receive standard chemotherapy or the oral PARP inhibitor veliparib in combination with carboplatin (V/C) and chemotherapy. V/C graduated in the triple-negative (TN) signature, where MP2 was not an eligible signature for graduation. Here, we assess the performance of MP1/MP2 class as a specific biomarker of response to V/C. Methods:115 HER2- patients (V/C: 71 and concurrent controls: 44) were considered in this analysis. We assess association between MP1/MP2 and response in the V/C and control arms alone using Fisher’s exact test, and relative performance between arms (biomarker x treatment interaction, likelihood ratio p < 0.05) using a logistic model. This analysis is also performed adjusting for HR status as a covariate. To assess MP1/MP2 in the context of the graduating signature, we added the MP2 patients to the graduating TN subset and evaluated the treatment effect in this ‘biomarker-positive’ group. Our study is exploratory with no claims for generalizability of the data. Statistical calculations are descriptive (e.g. p-values are measures of distance with no inferential content). This analysis does not adjust for multiplicities of other biomarkers in the trial but outside this study. Results: In the V/C arm vs. concurrent controls, there were 66 MP1 (V/C: 32, Control: 34) and 49 MP2 patients (V/C: 39, Control: 10), 78% of which are TN. The distribution of pCR rates among MP1/MP2 dichotomized groups are summarized in Table 1. V/C (n=71)Control (n=44)MP1 (n=32)MP2 (n=39)MP1 (n=34)MP2 (n=10)TN (n=59)3 / 819 / 303 / 132 / 8HR+HER2- (n=56)1 / 244 / 94 / 210 / 2 The OR between MP1/MP2 risk groups for predicting pCR is 9.71 in the V/C arm (p=6.63E-05), in comparison to an OR of 0.97 in the control arm (p=1). There is a significant biomarker x treatment interaction (p=0.023), which remains upon adjusting for HR status (p= 0.028). Based on the I-SPY 2 Bayesian model, a Phase III trial with 300 MP2 patients has a 95% predictive probability of success. When the MP2 patients are added to the graduating TN subset, the OR associated with V/C is 4.36, which is comparable to that of the TN signature (OR: 4.29), while increasing the prevalence of biomarker-positive patients by ∼10%. Conclusion: In our exploratory analysis, MP2 suggests higher sensitivity to V/C combination therapy relative to controls. This observation has prompted an investigation into the biological mechanisms distinguishing the MP1/MP2 subtype that may account for this specificity. Citation Format: Denise M Wolf, Christina Yau, Ashish Sanil, Jo Chien, Anne Wallace, Angela DeMichele, Hank Kaplan, Doug Yee, Claudine Isaacs, Kathy Albain, Rebecca Viscuzi, Judy Boughey, Stacey Moulder, Steven Chui, Qamar Khan, Toncred Styblo, Kirsten Edmiston, Donald Northfelt, Anthony Elias, Barbara Haley, Debu Tripathy, Lamorna Brown-Swigart, Susan Flynn, Gillian Hirst, Meredith Buxton, Nola Hylton, Melissa Paoloni, Fraser Symmans, Laura Esserman, Don Berry, Hope Rugo, Olufunmilayo I. Olopade, Laura van 't Veer. MammaPrint High1/High2 risk class as a biomarker of response to veliparib/carboplatin plus standard neoadjuvant therapy for breast cancer in the I-SPY 2 TRIAL [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-25.

Abstract P1-08-01: MammaPrint ultra-high risk score is associated with response to neoadjuvant chemotherapy in the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)

Abstract Background: Increasingly, gene expression tests are being used with standard clinicopathological markers to assess risk of recurrence in breast cancer and to guide treatment. The 70-gene signature (MammaPrint™) was recently validated in a prospective study as an effective tool for identifying low risk patients who may avoid chemotherapy without compromising outcome. MammaPrint scores have been shown to differentiate likelihood of neoadjuvant chemotherapy response. Here we hypothesize that a further stratification of the 70-gene signature into ‘high-risk’ and ‘ultra-high risk’ groups might yield improved predictors of chemo-sensitivity and patient outcome. Methods: Agilent 44K array data from pre-treatment biopsies were obtained from 149 I-SPY 1 TRIAL patients treated with neoadjuvant anthracycline-based chemotherapy. These data were used to compute each patient's MammaPrint score and risk category (good vs. poor threshold 0.4). Of these patients, 138 were either in the ‘poor’ outcome group (136) or in the ‘good’ outcome group but Her2+ (2). The median score cut-point based on these 138 patients equals -0.154, and was used to further stratify patients into MammaPrint High1 (MP1) or MammaPrint (ultra) High2 (MP2) groups, with MP1 defined as ≤ -0.154 and MP2 defined as >-0.154 (69 MP1, 69 MP2). Outcome parameters included pathologic complete response (pCR) after therapy and recurrence free survival (RFS). Fisher's exact test was used to assess association with pCR overall and within hormone receptor (HR) and Her2 subtypes, and Cox proportional hazards modeling to assess association with RFS. 29 patients who received Herceptin and 4 without pCR data were excluded from analysis, yielding 105 evaluable patients. Results: Though all receptor subtypes were represented in MP1 and MP2 subgroups, the majority of MP1 patients were HR+/Her2- (54%), whereas MP2 patients were more evenly distributed among triple negative (TN; 38%), HR+/Her2- (22%), HR-/Her2+ (22%) and HR+/Her2+ (18%) subtypes. 25/105 patients achieved pCR: 8 (15%) in the MP1 group and 17 (33%) in the MP2 group. Applying Fisher's exact test, we found that a significantly higher percentage of pCR was observed for MP2 patients in the overall population (p = 0.038), but not within receptor subtypes; though there was a trend towards a higher pCR rate in MP2 patients within the HR+/Her2- subset (p = 0.071). The greater sensitivity of MP2 to chemotherapy may in part be driven by differences in receptor subtype distribution, as well as a relationship between MP2 status and proliferation; we found that MP1/2 classification was highly associated with Ki67 (low/intermediate: <25% positive; high:>25% positive) (p = 3.3E-5), with MP2 patients having more Ki67 positive cells. No significant differences in RFS were observed between MP1 and MP2 subsets, likely because MP2 patients, who respond best, are also at the highest risk of relapse. Conclusion: These analyses suggest that additional MammaPrint score stratification within the ‘poor’ biology group might be a useful for developing companion diagnostics to neoadjuvant therapies, a hypothesis currently being tested in the adaptive randomization engine of the I-SPY 2 clinical trial. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-01.

Molecular subtyping to predict better clinical and pathologic tumor response in operable early-stage breast cancer treated with docetaxel-capecitabine with or without trastuzumab.

11090 Background: Classification into molecular subtypes is important for the selection of therapy for patients with early breast cancer. Here we determine rates of pathological complete response (pCR) in early stage breast cancer to neoadjuvant capecitabine plus docetaxel, +/- trastuzumab, and investigate MammaPrint together with the molecular subtyping profile BluePrint as markers of pathological response in comparison to other biomarkers. Methods: This analysis was carried out on data from 122 patients enrolled in a multicenter study (XeNA) of neoadjuvant therapy for four 21-day cycles with capecitabine 825 mg/m2 plus docetaxel 75 mg/m2if HER2-, and a standard trastuzumab dose if HER2+ (Glück , BCRT 2011). Clinical and pathological features, TP53 mutation analysis and PAM50 results were collected through GEO at NCBI (GSE22358). MammaPrint and BluePrint outcomes were determined from the available gene expression data and resulted in 4 distinct molecular groups: Luminal A (MammaPrint Low Risk/Luminal-type), Luminal B (MammaPrint High Risk/ Luminal-type), Basal-type and HER2-type. Results: In patients who completed 4 cycles of chemotherapy and surgery the overall pCR rate was 16%. Stratified by BluePrint pCR was observed in 1/15 (7%) of the Luminal A and 2/44 (5%) of Luminal B, in 10/22 (45%) of the HER2-type and in 7/41 (17%) of the Basal-type. The response rate among TP53 mutated patients was 6/61 (26%), which was significantly higher than TP53 wild-type patients (3/54 4%; p=0.012). Concordance of BluePrint/MammaPrint with PAM50 molecular subtyping was 61%. Conclusions: Molecular Subtyping with BluePrint and MammaPrint can identify better outcomes of patients in the neo-adjuvant setting. Patients with Luminal A breast cancer have a good baseline prognosis with excellent survival and may not benefit from chemotherapy (Glück, SABCS 2013). MammaPrint and BluePrint provide predictive information for patients treated with treated with docetaxel-capecitabine +/- trastuzumab.

Abstract P3-05-01: Molecular subtyping improves stratification of patients into diagnostically more meaningful risk groups

Abstract Background: Microarray-based gene expression profiling demonstrated that breast cancer is a heterogeneous group of different diseases characterized by distinct molecular aberrations, rather than one disease. Improved understanding of the molecular phenotypes of the disease has already shown prognostic and predictive value and, when prospectively applied, could have dramatic implications in establishing a more personalized approach to the management of early-stage breast cancer. Combined use of MammaPrint and a molecular subtyping profile (BluePrint) identifies disease subgroups with marked differences in long-term outcome and response to neo-adjuvant therapy [Glück et al. ASCO 2012]. The aim of this study was to evaluate the implication of accurate molecular subtyping using MammaPrint and BluePrint in women with early-stage breast cancer treated at US Institutions following National Comprehensive Cancer Network (NCCN) standard guidelines. Methods: 208 frozen tumor samples from consecutive BC patients (TI-III, N0-Ib) were obtained from 2 US centers. Median age at diagnosis was 56 years (range 28–89 years). Between 1992 and 2010 patients were treated either with breast-conserving therapy or mastectomy with axillary lymph node dissection followed by systemic adjuvant therapy when indicated. Sixty-three percent of patients received adjuvant endocrine therapy (ET), 58% received adjuvant chemotherapy (CT) and 32% received both. Hormone Receptor (HR) and HER2 status were assessed by immunohistochemistry (IHC) and fluorescent in-situ hybridization (FISH), following standard guidelines. Median follow-up was 11.3 years. Survival was assessed for patient groups according to local pathological assessment and compared with molecular classification of patients (centrally assessed full genome expression at Agendia laboratory). Results: Standard HR and HER2 status assessment revealed that 57% of all tumors examined were luminal-like (ER/PR positive, HER2 negative), 20% HER2 positive and 24% triple negative. Molecular classification demonstrated discordance in the following clinical groups: 16 out of 41 patients previously identified as HER2 positive were reclassified as Luminal-type, with 97% 5-year distant metastases-free survival (DMFS) for Luminal A (MammaPrint Low Risk/Luminal-type) and 98% for Luminal B (MammaPrint High Risk/Luminal-type). Ten patients identified with clinical triple-negative tumors were reclassified with molecular subtyping as HER2 positive (n = 6) and Luminal-type (n = 4). Of the patients classified with BluePrint Basal-type tumors, 58 (28%) had a 5-year DMFS of 82% (81% received adjuvant CT). Of those with HER2-type tumors, 25 (12%) had a 5-year DMFS of 76% (88% received adjuvant CT without trastuzumab). Discordant cases are being centrally re-assessed for ER, PR and HER2. Conclusions: This retrospective study showed that Molecular Subtyping with BluePrint and MammaPrint leads to clinically significant prognostic and molecular stratification. The use of MammaPrint and BluePrint in the management of patients with primary breast cancer should be considered for a more accurate selection of adjuvant therapies in this era of personalized medicine. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-05-01.

Abstract P3-06-11: Response and long-term outcomes after neo-adjuvant chemotherapy: Pooled dataset of patients stratified by molecular subtyping using MammaPrint and BluePrint

Abstract Background: Classification into molecular subtypes may increasingly be important for the selection of therapy for patients with early-stage breast cancer. Previous analyses had shown that breast cancer subtypes have distinct clinical outcome [Sorlie et al. PNAS 2001; Esserman et al. BCRT 2011]. In our study, we analyzed the response to neo-adjuvant chemotherapy and long-term outcomes using the 70-gene profile (MammaPrint) together with an 80-gene molecular subtyping profile (BluePrint). Methods: This analysis was performed on data from 421 patients: 141 patients from the I-SPY I trial; 230 patients from the biomarker discovery program at MD Anderson (131 and 99 respectively; Hess et al. JCO 2006; Iwamoto et al. BCRT 2011]; and 50 patients from the City of Hope [Somlo et al. ASCO 2010]. All patients were treated in the neo-adjuvant setting with chemotherapy. MammaPrint and BluePrint outcomes were determined from either 44K Agilent arrays run at Agendia or available through the I-SPY I data portal, or from Affymetrix U133A arrays. The combination of MammaPrint and BluePrint resulted in four distinct molecular groups: Luminal A (MammaPrint Low Risk/Luminal-type), Luminal B (MammaPrint High Risk/ Luminal-type), Basal-type and HER2-type. Results: The overall pCR of this patient cohort was 22% but differed substantially among the defined BluePrint molecular subgroups. pCR was observed in 3% of the Luminal A and 12% of Luminal B, in 38% of the HER2-type and in 42% of the Basal-type samples. 42% of patients with clinical HER2-positive phenotype are classified as Luminal-type by BluePrint: eight patients as Luminal A and 34 patients as Luminal B. 5-year distant metastases-free survival (DMFS) of patients with HER2-type by BluePrint who achieve pCR is 87%, compared with 78% for clinical HER2+ patients with pCR. These data are in line with a recent retrospective analysis of a large cohort of patients, which showed that pCR rate is not a suitable surrogate for clinical HER2+/Hormone Receptor-positive patients and is not associated with outcome [von Minckwitz et al. JCO 2012]. BluePrint classifies more patients as Basal-type (n = 120) with higher pCR rate (42%), compared with clinical subtyping (triple negative, n=93) with a pCR rate of 31%. Despite including eight clinical HER2+ and 11 triple-negative patients, those with BluePrint Luminal A subtype (n = 88) have excellent 5-year DMFS of 94% and appear to have no benefit from chemotherapy (low pCR rate). Conclusions: Molecular subtyping using BluePrint with MammaPrint can help to improve outcomes of patients in the neo-adjuvant setting over clinical subtyping. We observed differences in pCR and DMFS following neo-adjuvant treatment in groups stratified by MammaPrint and BluePrint; for example, patients with Luminal A breast cancer (assessed with MammaPrint and BluePrint) have a good baseline prognosis with excellent survival and may not benefit from chemotherapy. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-11.

Molecular subtyping using MammaPrint and BluePrint as an outcome predictor in U.S. breast cancer (BC) patients.

9 Background: Combined use of MammaPrint and a molecular subtyping profile (BluePrint) identifies disease subgroups with marked differences in long-term outcome and response to neo-adjuvant therapy (Glück SABCS2011). The aim of this study was to evaluate the prognostic value of Molecular Subtyping using MammaPrint and BluePrint in women with early stage BC treated at U.S. institutions following National Comprehensive Cancer Network (NCCN) standard guidelines. Methods: Frozen tumor samples from 180 BC patients (TI-III, N0-Ib) median age 57 years at diagnosis (range 28-89) were suitable for hybridization on full genome array. MammaPrint and BluePrint Molecular Subtypes were determined and survival for Luminal A (MammaPrint Low Risk), Luminal B (MammaPrint High Risk), HER2-type and Basal-type patients was assessed. Patients were treated either with breast conserving therapy or mastectomy with axillary lymph node dissection between 1992 and 2005. The median follow-up is 12.7 years. 71% was ER positive and 20% Her2 positive by IHC/FISH. 58% received adjuvant endocrine therapy (ET) (excluding 13 patients unknown treatment), 64% received adjuvant chemotherapy (CT) (excluding 12 patients unknown treatment) and 33% received both. Results: 61 (34%) Patients with MammaPrint Low Risk/Luminal-type (Luminal A) showed 5-year DFS of 97% (34% received CT and 69% ET) and 50 (28%) patients with MammaPrint High Risk/Luminal-type (Luminal B) had a 5-year DFS of 98% (60% received CT and 68% ET). Patients with BluePrint Basal-type tumors (46 (26%)) had a 5-year DFS of 80% (78% received CT); HER2-type (23 (13%)) had a 5-year DFS of 78% (87% received CT without HER2 targeted therapy). Conclusions: In this retrospective study evaluating 180 US patients with early BC treated according to standard guidelines we showed how combining BluePrint with MammaPrint can detect molecularly defined subgroups of patients who are at high risk of recurrence (HER2 and Basal-type). Furthermore, we confirmed that molecularly defined Luminal type disease is associated with excellent disease-free survival. MammaPrint and BluePrint molecular and prognostic stratification should be prospectively evaluated for therapeutic selection.

Molecular subtyping using MammaPrint and BluePrint as an outcome predictor in 180 U.S. breast cancer (BC) patients.

577 Background: Combined use of MammaPrint and a molecular subtyping profile (BluePrint) identifies disease subgroups with marked differences in long-term outcome and response to neo-adjuvant therapy (Glück SABCS2011). The aim of this study was to evaluate the prognostic value of Molecular Subtyping using MammaPrint and BluePrint in women with early stage BC treated at US Institutions following National Comprehensive Cancer Network (NCCN) standard guidelines. Methods: Frozen tumor samples from 180 BC patients (TI-III, N0-Ib) median age 57 years at diagnosis (range 28-89) were suitable for hybridization on full genome array. MammaPrint and BluePrint Molecular Subtypes were determined and survival for Luminal A (MammaPrint Low Risk), Luminal B (MammaPrint High Risk), HER2-type and Basal-type patients was assessed. Patients were treated either with breast conserving therapy or mastectomy with axillary lymph node dissection between 1992 and 2005. The median follow-up is 12.7 years. 71% was ER positive and 20% Her2 positive by IHC/FISH. 58% received adjuvant endocrine therapy (ET) (excluding 13 patients unknown treatment), 64% received adjuvant chemotherapy (CT) (excluding 12 patients unknown treatment) and 33% received both. Results: 61 (34%) Patients with MammaPrint Low Risk/Luminal-type (Luminal A) showed 5-year DFS of 97% (34% received CT and 69% ET) and 50 (28%) patients with MammaPrint High Risk/Luminal-type (Luminal B) had a 5-year DFS of 98% (60% received CT and 68% ET). Patients with BluePrint Basal-type tumors (46 (26%)) had a 5-year DFS of 80% (78% received CT); HER2-type (23 (13%)) had a 5-year DFS of 78% (87% received CT without HER-2 targeted therapy). Conclusions: In this retrospective study evaluating 180 US patients with early BC treated according to standard guidelines we showed how combining BluePrint with MammaPrint can detect molecularly defined subgroups of patients who are at high risk of recurrence (HER2 and Basal-type). Furthermore, we confirmed that molecularly defined Luminal type disease is associated with excellent disease-free survival. MammaPrint and BluePrint molecular and prognostic stratification should be prospectively evaluated for therapeutic selection.