Abstract P5-17-08: A phase Ib/II study of leronlimab combined with carboplatin in patients with CCR5+ metastatic triple-negative breast cancer (mTNBC)

Background C-C Chemokine Ligand type-5 (CCR5) is overexpressed in >95% of TNBC and has been correlated with disease progression. Moreover, enhancement of DNA repair signaling by CCR5 activation may contribute to chemotherapy resistance. Therefore, blocking CCR5 may result in increased immune response against tumor cells and synergize with chemotherapy. Leronlimab (PRO 140) is a humanized monoclonal antibody to CCR5. Preclinical data showed leronlimab binds human CCR5, blocks CCR5-mediated signaling, and CCL5-induced breast cancer cell invasion. The therapeutic antibody leronlimab has been administered to over 800 healthy and HIV-1 infected individuals with good tolerance and without obvious dose-related toxicity, making it an ideal partner for chemotherapy combinations in TNBC. Methods In this ongoing phase 1B/2 study, patients with CCR5+ mTNBC with ≤2 line of therapy in the metastatic setting (no prior carboplatin) are treated with weekly subcutaneous leronlimab (3 dose levels, 3+3 dose escalation) and a fixed dose of carboplatin AUC 5 on day 1 with a 21-day dose-limiting toxicity (DLT) window, followed by expansion in 30 patients with CCR5+ mTNBC who are naïve to chemotherapy in the metastatic setting or who have failed first-line combination of chemotherapy (excluding carboplatin) and a checkpoint inhibitor in the metastatic setting. CCR5 positivity is centrally assessed by IHC and defined as >10% CCR5 staining in primary or metastatic tumor cells and/or high predominance of CCR5+ tumor-infiltrating leukocytes (TIL). Primary objectives are safety, tolerability, determination of maximum tolerated dose, and determination of the recommended phase 2 dose (RP2D). Results Fifteen patients had archived tumor tissue assessed for CCR5 expression, with 12 being CCR5 positive (median expression 20%, range 0 - 100%, and 7 out of 12 high CCR5+ TILs) . A total of ten patients (median age 51 years; median 2 prior therapies) have been enrolled at 3 dose levels (350, 525, and 700 mg). In the second cohort, 1 additional patient was inadvertently enrolled. All patients completed the DLT assessment period and no DLTs have been observed. Patients received between 3 and 27 doses of leronlimab with the number of cycles ranging from 1 to 9. Five patients remain on treatment. The most common treatment-emergent adverse events (TEAEs) by any grade were: fatigue (6/10), headache (4/10), constipation (3/10), and nausea (3/10). The following grade ≥3 TEAEs were reported: neutropenia, anemia, thrombocytopenia, hyponatremia, hypertension, diarrhea and headache. Serious Adverse Events were reported in 2 patients (grade 2 sepsis and grade 3 headache). The following leronlimab treatment related adverse events (TRAEs) occurred (all grade 1): injection site reaction in cohort 1, fatigue (n=2) and headache in cohort 2. Three carboplatin TRAEs ≥3 were reported in one patient in cohort 1: thrombocytopenia, anemia and leukopenia. Two out of seven patients eligible for response achieved a confirmed partial response, and 4 patients stable disease. Conclusions Leronlimab, in combination with carboplatin, has been well-tolerated in all 3 dose levels with early signs of anti-tumor activity in patients with CCR5+ mTNBC. The study is currently enrolling patients at the RP2D dose of leronlimab 700mg in combination with carboplatin AUC 5 in the phase 2 part of the trial. Clinical trial information: NCT03838367

Citation Format: Massimo Cristofanilli, Namita Chittoria, Sima Ehsani, Hallgeir Rui, Milana Dolezal, Lisette Stork-Sloots, Femke de Snoo, Christopher Recknor, Vandana Abramson. A phase Ib/II study of leronlimab combined with carboplatin in patients with CCR5+ metastatic triple-negative breast cancer (mTNBC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-17-08.

Prospective study to measure the impact of MMprofiler on treatment intention in newly diagnosed multiple myeloma patients (PROMMIS)

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Background: Multiple Myeloma (MM) is recognized as a heterogeneous group of patients with varying response and outcome of their disease, associated with various risk factors including genetic aberrations. Risk adapted treatment strategies are beginning to emerge (e.g. mSMART), which include gene expression signatures. SKY92, a 92-gene prognostic signature, classifies MM patients as “high” or “standard” risk. It has been reported to be a robust predictor for Overall and Progression Free Survival (Kuiper 2012, 2015). Here we report the preliminary impact of SKY92 on risk classification and treatment intention decisions in newly diagnosed MM patients enrolled in the PRospective Observational Multiple Myeloma Impact Study (PROMMIS). Methods: Patients with MM had their BM aspirate analyzed using the MMprofiler with SKY92. The physician completed questionnaires with his/her treatment intention, before and after knowing SKY92 results. Results: 39 MM patients were enrolled from 5 US centers. The SKY92 signature classified 15 patients (38%) as high risk. Prior to knowing SKY92 results, physicians regarded 20 (51%) patients as clinically high risk, for whom SKY92 indicated 12 patients to be standard risk. Upon revealing SKY92, 8 patients were then considered standard risk by the physician. For 2 patients with concordant high risk classification results, the confirmation of the risk classification was considered helpful. The impact of treatment intention decisions in clinical high risk patients was 40% (8 out of 20). In the 19 patients (49%) that were regarded clinically standard risk prior to knowing SKY92, SKY92 indicated 7 patients to be high risk. Physicians agreed to this classification. For 4 patients with concordant risk classification, the confirmation was found helpful. The impact of treatment intention decisions in clinical standard risk patients was 37% (7 out of 19). Conclusions: Preliminary results from the PROMMIS trial indicate that SKY92 impacts the physician’s treatment intention for 38% of patients with newly diagnosed MM. Moreover, the physicians found the SKY92 result useful for 54% of the patients. This underlines the relevance and need for assessment of SKY92 in MM patients, and associated risk stratified treatment paradigm. Clinical trial information: NCT02911571.

Race and response to neoadjuvant chemotherapy according to MammaPrint risk

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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.

Pertuzumab/Trastuzumab/CT Versus Trastuzumab/CT Therapy for HER2+ Breast Cancer: Results from the Prospective Neoadjuvant Breast Registry Symphony Trial (NBRST)

BACKGROUND

Pertuzumab became a standard part of neoadjuvant therapy for human epidermal growth factor receptor 2-positive (HER2+) breast cancers approximately halfway through Neoadjuvant Breast Registry Symphony Trial (NBRST) enrollment, providing a unique opportunity to determine biologically which clinical HER2+ patients benefit most from dual targeting. As a neoadjuvant phase 4 study, NBRST classifies patients by both conventional and molecular subtyping.

METHODS

Of 308 clinical HER2+ patients enrolled in NBRST between 2011 and 2014 from 62 U.S. institutions, 297 received neoadjuvant chemotherapy (NCT) with HER2-targeted therapy and underwent surgery. This study compared the pathologic complete response (pCR) rate of BluePrint versus clinical subtypes with treatment, specifically differences between trastuzumab (T) treatment and trastuzumab and pertuzumab (T/P) treatment.

RESULTS

In this study, 60% of the patients received NCT-T, and 40% received NCT-T/P. The overall pCR rate (ypT0/isN0) was 47%. BluePrint classified 161 tumors (54%) as HER2 type, with a pCR rate of 65%. This was significantly higher than the pCR rate for the 91 HER2+ tumors (31%) classified as luminal (18%) (p = 0.00001) and the 45 tumors (15%) classified as basal (44%) (p = 0.0166). The patients treated with T/P had higher pCR rates than those treated with trastuzumab alone. The difference was most pronounced in the BluePrint luminal patients (8 vs. 31%). The highest pCR was reached by the BluePrint HER2-type patients treated with T/P (76%).

CONCLUSIONS

The addition of pertuzumab leads to increased pCR rates for all HER2+ patient groups except for the BluePrint basal-type patients. This better response was most pronounced for the BluePrint luminal-type patients.

Chemosensitivity and Endocrine Sensitivity in Clinical Luminal Breast Cancer Patients in the Prospective Neoadjuvant Breast Registry Symphony Trial (NBRST) Predicted by Molecular Subtyping

PURPOSE

Hormone receptor-positive (HR+) tumors have heterogeneous biology and present a challenge for determining optimal treatment. In the Neoadjuvant Breast Registry Symphony Trial (NBRST) patients were classified according to MammaPrint/BluePrint subtyping to provide insight into the response to neoadjuvant endocrine therapy (NET) or neoadjuvant chemotherapy (NCT).

OBJECTIVE

The purpose of this predefined substudy was to compare MammaPrint/BluePrint with conventional 'clinical' immunohistochemistry/fluorescence in situ hybridization (IHC/FISH) subtyping in 'clinical luminal' [HR+/human epidermal growth factor receptor 2-negative (HER2-)] breast cancer patients to predict treatment sensitivity.

METHODS

NBRST IHC/FISH HR+/HER2- breast cancer patients (n = 474) were classified into four molecular subgroups by MammaPrint/BluePrint subtyping: Luminal A, Luminal B, HER2, and Basal type. Pathological complete response (pCR) rates were compared with conventional IHC/FISH subtype.

RESULTS

The overall pCR rate for 'clinical luminal' patients to NCT was 11 %; however, 87 of these 474 patients were reclassified as Basal type by BluePrint, with a high pCR rate of 32 %. The MammaPrint index was highly associated with the likelihood of pCR (p < 0.001). Fifty-three patients with BluePrint Luminal tumors received NET with an aromatase inhibitor and 36 (68 %) had a clinical response.

CONCLUSIONS

With BluePrint subtyping, 18 % of clinical 'luminal' patients are classified in a different subgroup, compared with conventional assessment, and these patients have a significantly higher response rate to NCT compared with BluePrint Luminal patients. MammaPrint/BluePrint subtyping can help allocate effective treatment to appropriate patients. In addition, accurate identification of subtype biology is important in the interpretation of neoadjuvant treatment response since lack of pCR in luminal patients does not portend the worse prognosis associated with residual disease in Basal and HER2 subtypes.

Abstract PD7-01: Can surrogate pathological subtyping replace molecular subtyping? Outcome results from the MINDACT trial

Background

Molecular subgroups within early breast cancer (EBC), such as Luminal A, Luminal B, HER-2+, Basal-like may help to best to identify patients for specific treatment regimens. Controversy exists as to which methodology is best at identifying these molecular subgroups. Immunohistochemistry (IHC) may be used as a surrogate method to stratify patients. Molecular subtyping gene expression based tests, such as BluePrint, measure a greater number of genes than pathological criteria. ER, PgR, HER-2 and Ki67 are measured individually at the protein level, while BluePrint is designed to capture the functional underlying biologic pathway regulated by these receptors.

Methods

The MINDACT trial is an international, prospective, randomized, phase III trial which has proventhe clinical utility of MammaPrint in selecting EBC patients who can safely avoid chemotherapy. Here we present the results of a preplanned MINDACT sub-study to compare outcome based on molecular subtyping (MS) to surrogate pathological subtyping (PS) as endorsed by 2013 St. Gallen Consensus. MS data were obtained by MammaPrint (MP) and BluePrint classifying patients in the following subtypes: Luminal A (MP Low Risk); Luminal B (MP High Risk); HER2-type; and Basal-type. ER, PgR, HER2 and Ki67 protein status were centrally assessed by IHC/FISH. The primary hypothesis was that among PS Luminal patients, patients with HER-2+ or Basal-type tumors by MS would have a decreased DMFS compared to MS Luminal patients. At α=5% with 220 events, the study has 80% power to demonstrate this for HR=2.44.

Results

The table depicts classification of tumors according to PS versus MS for all patients (n=5,806).

PS versus MSMSPSLum ALum BHER-2+BasalTotalLum A24562708132747Lum B106979422861971HER-2 enriched1189531826557TN14107500531Total365711693556255806

Most pronounced differences: MS classified 54% as Luminal A among the Luminal B by PS. MS classified 38% as Luminal (A and B) and 5% as Basal-type among the HER-2+ by PS. MS classified 5% as Luminal (A and B) among the TN cases by PS.

MS identifies 63% of patients as Luminal A, while PS identifies 47%; 5yr DMFS for both methods was ≥ 96.0%.

PS Luminal cancers that were classified as HER-2+ or Basal-type by MS had a lower 5yr DMFS (88.0% for HER-2+ and 90.2% for Basal), albeit non-significant, than those who were also Luminal by MS (95.9%): HR= 1.40, 95% CI = 0.75-2.60.

In PS TN cancers, MS identified 24 out of 500 patients (5%) as Luminal-type with excellent prognosis (5yr DMFS of 100% versus 71.4% for MS HER-2+ or 90.1% for MS Basal-type).

Among the PS Luminal patients, Ki67 cut at 20% identified patients with ki67 low (69%), with 5yr DMFS ≥ 96.0% (better compared to the 14% cut-off).

Conclusions

1) MS was able to re-stratify 16% of patients to a low risk Luminal A-type group with an excellent outcome. 2) Among TN EBC, 5% were classified as Luminal by MS and had an excellent outcome. 3) Albeit limited by low numbers of patients in each subgroup, this study suggest that MS is better correlated with outcome. 4) The observed subtype discrepancies may have an impact on treatment decision making. 5) Centrally assessed Ki67 labeling index of 20% may be the best cut-off for surrogate differentiation between Luminal A and B.

Citation Format: Cardoso F, Slaets L, de Snoo F, Bogaerts J, van 't Veer LJ, Rutgers EJ, Piccart-Gebhart MJ, Stork-Sloots L, Russo L, Dell'Orto P, Viale G. Can surrogate pathological subtyping replace molecular subtyping? Outcome results from the MINDACT 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 PD7-01.

Abstract P1-14-05: Three distinct HER2 subtypes identified by BluePrint 80-gene functional subtyping predict treatment-specific response in the prospective neo-adjuvant NBRST registry

Background

Ideally classification by subtype predicts treatment response and overall outcome. BluePrint 80-gene functional molecular subtype is based on mRNA expression (as is intrinsic subtype) associated with intact translation to protein (unlike intrinsic subtype). BluePrint (BP) classifies patients into Luminal, Her2 or Basal-type. Presently subtype is approximated using conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) ("conventional subtype") or assigned by gene expression profiling. The main objective of the prospective neo-adjuvant NBRST study is to compare drug sensitivity as defined by pathological Complete Response (pCR), using 80-gene functional subtype vs. conventional IHC/FISH subtyping. NBRST enrolled over 1,000 US patients between June 2011 and December 2014. In this analysis we present the results for IHC/FISH Her2-positive patients.

Methods

Here we report findings in the 260 NBRST patients who had IHC/FISH Her2+ breast cancer, according to ASCO CAP guidelines at the time of diagnosis. Treatment, including chemotherapy and HER2-targeted agents, was at the discretion of the physician adhering to NCCN approved or other peer-reviewed, established regimens over the course of the study. pCR was defined as T0/isN0. Fisher's exact test was used to compare pCR rates among IHC/FISH and functional subtypes and treatment groups.

Results

The 260 IHC/FISH Her2+ patients had median age 53 (range 23-81) and included T1-4, N0-3 tumors. Of 169 ER+/Her2+ tumors 49% were re-classified as BP Luminal, 43% as BP HER2, and 8% as BP Basal. The median ER% of ER+/Her2+/BP Luminal tumors was 93% (range 3-100), compared to 79% in ER+/Her2+/BP HER2 (range 1-91) and 8% in ER+/Her2+/BP Basal-type (range 2-99).The overall pCR rate in ER+/Her2+/BP Luminal was 17% (4% with chemo/trastuzumab; 39% chemo/trastuzumab/pertuzumab, p&lt;0.0001) and statistically inferior (p&lt;0.0001) to the 59% pCR rate in ER+/Her2+/BP HER2. Of 91 ER-/Her2+ tumors 74% were classified as BP HER2, 25% were re-classified BP Basal and &lt;1% was BP Luminal. NCT pCR rates for ER-/Her2+/BP HER2 was 67% (64% with chemo/trastuzumab; 77% chemo/trastuzumab/pertuzumab, p=0.40) and significantly superior (p=0.026) to the 39% pCR rate in ER-/Her2+/BP Basal (p=0.026).

Conclusions

In the NBRST study, BP 80-gene functional subtype (based on mRNA expression and translation): 1. Re-classifies over half of all IHC/FISH ER+/Her2+ patients; 2. Predicts treatment response or resistance in Her2+ patients not segregated by conventional IHC/FISH classification and 3. Identifies ER+/Her2+ tumors that are sensitive to chemo/trastuzumab/pertuzumab but resistant to chemo/trastuzumab.

Citation Format: Whitworth P, Beitsch P, Baron P, Beatty J, Pellicane JV, Murray MK, Dul CL, Mislowsky AM, Nash CH, Richards PD, Lee LA, Stork-Sloots L, de Snoo F, Untch S, Gittleman M, Akbari S, Rotkis MC. Three distinct HER2 subtypes identified by BluePrint 80-gene functional subtyping predict treatment-specific response in the prospective neo-adjuvant NBRST registry. [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 P1-14-05.

Abstract P4-14-10: Pertuzumab overcomes chemotherapy/trastuzumab resistance in ER+/Her2+ tumors classified as luminal functional subtype by the 80-gene BluePrint assay in the prospective neo-adjuvant breast registry symphony trial (NBRST)

Background

The prospective Neo-adjuvant Breast Registry Symphony Trial (NBRST) enrolled over 1000 US patients between June 2011 and December 2014. The aim of NBRST study is to compare chemosensitivity as defined by pathological Complete Response (pCR) using the 80-gene BluePrint functional subtype profile vs. conventional IHC/FISH subtyping. Treatment was at the discretion of the physician utilizing standard NCCN regimens. Pertuzumab, a monoclonal antibody, inhibits the dimerization of HER2 with other HER receptors. Pertuzumab received US FDA approval for the neo-adjuvant treatment of HER2-positive breast cancer in September 2013. Essentially all patients with HER2 positive cancers were treated with chemotherapy + trastuzumab and after this date pertuzumab was added, creating 2 distinct groups of Her2 treated patients.

The aim of the current analysis is to compare the pCR rate of trastuzumab (H) vs trastuzumab and pertuzumab (H + P) by conventional and BluePrint functional subtype.

Methods

The current analysis includes women from the NBRST study, with histologically proven breast cancer, who received neo-adjuvant chemotherapy plus H or H + P and who provided written informed consent. Pathological assessment of Her2 was done according to ASCO CAP guidelines at the time of diagnosis. BluePrint (BP) classifies patients into Luminal, HER2 or Basal-type. pCR is defined as T0/isN0. All pCRs were verified with a de-identified copy of the surgical pathology report. Fisher's exact test was used to compare pCR rates within different subgroups.

Results

252 IHC/FISH Her2+ patients received H (166) or H + P (86). The median age was 53 (range 23-81). 8% was stage I, 68% stage II and 24% stage III. 65% were ER positive.

BP classified 55% of patients as HER2, 32% as Luminal, and 14% as Basal-type.

The pCR rates and p-values within different subgroups of clinical Her2+ patients are provided in the table below.

pCR rates and p-values within different subgroups of clinical Her2+ patients(n)H (pCR rate)H + P (pCR rate)p-valueTotal (n=252)40%59%0.005IHC/FISH Her2+/ER+ (163)30%57%0.001IHC/FISH Her2+/ER- (89)69%63%0.82BP HER2 (138)57%78%0.01BP Luminal (80)4%38%0.0002BP Basal (34)47%38%0.69

Conclusions

Addition of pertuzumab to trastuzumab significantly increased response rate in ER+/Her2+, BP HER2 and BP Luminal patients but not in ER-negative and BP Basal patients.

Pertuzumab overcame resistance to NCT/trastuzumab in a substantial proportion of the IHC/FISH Her2+/BP Luminal subgroup; indicated by a significantly increased pCR rate.

Citation Format: Peter B, Pat W, Paul B, Jennifer B, Pellicane JV, Murray MK, Dul CL, Mislowsky AM, Nash CH, Richards PD, Lee LL, Stork-Sloots L, de Snoo F, Untch S, Gittleman M, Akbari S, Rotkis MC. Pertuzumab overcomes chemotherapy/trastuzumab resistance in ER+/Her2+ tumors classified as luminal functional subtype by the 80-gene BluePrint assay in the prospective neo-adjuvant breast registry symphony trial (NBRST). [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 P4-14-10.

Abstract P4-14-29: One-third of HER2 positive patients have 80-gene luminal subtype that is resistant to chemo-trastuzumab but sensitive to chemo-trastuzumab-pertuzumab: Critical implications for the adjuvant setting from the NBRST phase 4 neoadjuvant study

Background

The phase 4 Neo-adjuvant Breast Registry Symphony Trial (NBRST) enrolled over 1,000 US patients between June 2011 and December 2014. The aim of NBRST study is to compare chemo-sensitivity as defined by pathological Complete Response (pCR) using the 80-gene BluePrint (BP) functional subtype profile vs. conventional IHC/FISH subtyping. Treatment was at the discretion of the physician utilizing standard NCCN regimens. Pertuzumab, a monoclonal antibody, inhibits the dimerization of HER2 with other HER receptors. Pertuzumab received US FDA approval for the neo-adjuvant treatment of HER2-positive breast cancer in September 2013. Essentially all patients with HER2 positive cancers were treated with chemotherapy + trastuzumab and after this date pertuzumab was added, creating 2 distinct groups of Her2-treated patients.

The aim of the current analysis is to compare the pCR rate of chemo-trastuzumab (c-t) vs chemo-trastuzumab plus pertuzumab (c-t-p) by conventional and 80-gene BP functional subtype. 80-gene BP functional subtype was derived by supervised cluster analysis for concordant mRNA and protein expression.

Methods

The current analysis includes women from the NBRST study, with histologically proven breast cancer, who received neo-adjuvant treatment, had 80-gene subtyping and provided written informed consent. Pathological assessment of HER2 was performed according to ASCO CAP guidelines at the time of diagnosis. 80-gene BluePrint (BP) classifies patients into Luminal, HER2 or Basal-type. pCR is defined as T0/isN0. All pCRs were verified with a de-identified copy of the surgical pathology report. Fisher's exact test was used to compare pCR rates within different subgroups.

Results

286 IHC/FISH HER2+ patients received c-t (175) or c-t-p (111). Of these 80-gene BP subtype classified 53% as HER2-type, 33% as Luminal-type and 14% as Basal-type. 64% were ER positive.

The pCR rates and p-values within different subgroups of clinical HER2+ patients are provided in the table below.

 c-tc-t-p (n)pCR ratep-valueTotal (n=286)41%57%0.01BP HER2 (153)58%73%0.06 BP Luminal (93) 6% 39% 0.0002BP Basal (40)45%1.0IHC/FISH HER2+/ER+ (183)31%53%0.003IHC/FISH HER2+/ER- (103)59%64%0.68

Conclusions

One-third of ASCO/CAP Her2+ patients had 80-gene BP Luminal subtype and demonstrated resistance to c-t (pCR 6%). Addition of Pertuzumab overcame resistance in this group (pCR 39%). This finding in the neoadjuvant setting suggests a substantial potential benefit in the adjuvant setting and thus an urgent need to consider treatment in at-risk patients as well as confirmatory tissue analysis from independently reported trials.

Citation Format: Beitsch P, Whitworth P, Baron P, Beatty J, Pellicane JV, Murray MK, Dul C, Mislowsky AM, Nash CH, Richards PD, Lee LA, Stork-Sloots L, de Snoo F, Untch S, Gittleman M, Akbari S, Rotkis MC. One-third of HER2 positive patients have 80-gene luminal subtype that is resistant to chemo-trastuzumab but sensitive to chemo-trastuzumab-pertuzumab: Critical implications for the adjuvant setting from the NBRST phase 4 neoadjuvant study. [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 P4-14-29.

Impact of Tumor Size on Probability of Pathologic Complete Response After Neoadjuvant Chemotherapy

BACKGROUND

The prospective Neoadjuvant Breast Symphony Trial (NBRST) study found that MammaPrint/BluePrint functional molecular subtype is superior to conventional immunohistochemistry/fluorescence in situ hybridization subtyping for predicting pathologic complete response (pCR) to neoadjuvant chemotherapy. The purpose of this substudy was to determine if the rate of pCR is affected by tumor size.

METHODS

The NBRST study includes breast cancer patients who received neoadjuvant chemotherapy. MammaPrint/BluePrint subtyping classified patients into four molecular subgroups: Luminal A, Luminal B, HER2 (human epidermal growth factor receptor 2), and Basal type. Probability of pCR (ypT0/isN0) as a function of tumor size and molecular subgroup was evaluated.

RESULTS

A total of 608 patients were evaluable with overall pCR rates of 28.5 %. Luminal A and B patients had significantly lower rates of pCR (6.1 and 8.7 %, respectively) than either basal (37.1 %) or HER2 (55.0 %) patients (p < 0.001). The probability of pCR significantly decreased with tumor size >5 cm [p = 0.022, odds ratio (OR) 0.58, 95 % confidence interval (CI) 0.36, 0.93]. This relationship was statistically significant in the Basal (p = 0.026, OR 0.46, 95 % CI 0.23, 0.91) and HER2 (p = 0.039, OR 0.36, 95 % CI 0.14, 0.95) subgroups. In multivariate logistic regression analyses, the dichotomized tumor size variable was not significant in any of the molecular subgroups.

DISCUSSION

Even though tumor size would intuitively be a clinical determinant of pCR, the current analysis showed that the adjusted OR for tumor size was not statistically significant in any of the molecular subgroups. Factors significantly associated with pCR were PR status, grade, lymph node status, and BluePrint molecular subtyping, which had the strongest correlation.

Molecular subtyping improves diagnostic stratification of patients with primary breast cancer into prognostically defined risk groups

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. The aim of this study was to evaluate the prognostic value of molecular subtyping using MammaPrint and BluePrint in women with early-stage breast cancer (BC) treated at US institutions following National Comprehensive Cancer Network standard guidelines. Tumor samples were collected from stage 1-2B consecutively diagnosed BC patients (n = 373) who underwent lumpectomy or mastectomy with an axillary staging procedure between 1992 and 2010 at two institutes (NorthShore University HealthSystem and Fox Chase Cancer Center) in the United States of America, with a median follow-up time of 9.5 years. MammaPrint low-risk patients had a 10-year DMFS of 96 % (95 %CI 92.8–99.4), while MammaPrint high-risk patients had a 10-year DMFS of 87 % (95 %CI 81.9–92.1) with a hazard ratio of 3.62 (95 %CI 1.38–9.50) (p = 0.005). Uni- and multivariate analyses included age, tumor size, grade, ER, and Her2; in multivariate analysis, MammaPrint reached near-significance (HR 3.01; p 0.08). When comparing BluePrint molecular subtyping with clinical stratification, the prognosis (10-year DMFS) was significantly different in 10-year DMFS between the different molecular subtypes (p < 0.001). This retrospective study with 10-year follow-up data provides valuable insight into prognosis of patients with primary BC comparing clinical with molecular subtyping. The BluePrint molecular stratification assay identifies patients with significantly different outcomes compared with standard clinical molecular stratification.

Application of a 70-Gene Expression Profile to Japanese Breast Cancer Patients

BACKGROUND

As data on using MammaPrint®, a 70-gene expression profile for molecular subtyping of breast cancer, are limited in Japanese patients, we aimed to determine the gene profiles of Japanese patients using MammaPrint and to investigate its possible clinical application for selecting adjuvant treatments.

PATIENTS AND METHODS

50 women treated surgically at our institution were examined. The MammaPrint results were compared with the St Gallen 2007 and intrinsic subtype risk categorizations.

RESULTS

Of 38 cases judged to be at intermediate risk based on the St Gallen 2007 Consensus, 11 (29%) were in the high-risk group based on MammaPrint. 1 of the 30 luminal A-like tumors (3%) was judged as high risk based on MammaPrint results, whereas 7 of the 20 tumors (35%) categorized as luminal B-like or triple negative were in the low-risk group. There have been no recurrences to date in the MammaPrint group, and this is possibly attributable to most of the high-risk patients receiving chemotherapy that had been recommended on the basis of their MammaPrint results.

CONCLUSIONS

Our results indicate that MammaPrint is applicable to Japanese patients and that it is of potential value in current clinical practice for devising individualized treatments.

Abstract OT3-2-02: MINT I: Multi-Institutional Neo-adjuvant Therapy, MammaPrint Project I

Background:

Women with locally advanced breast cancer (LABC) are often treated with neo-adjuvant chemotherapy to reduce the size of the tumor prior to surgery, to enable breast conserving surgery and to observe the clinical effect of therapy in real time. Studies have shown that the 25–27% of individuals who have a pathologic complete response (pCR) to neoadjuvant therapy have a survival advantage of 80% in 5 years, which is double the expected survival of the remaining patients without pCR. If patients who are likely to show a pCR could be identified prior to initiation of therapy, it would enable more informed treatment decisions – patients likely to respond would be served well by current neoadjuvant chemotherapy protocols, while those unlikely to respond may be better suited to innovative new strategies for drug discovery [von Minckwitz et al. JCO 2006]. Genomic assays, which are widely used to provide prognostic and predictive information in early breast cancer, have the potential to provide information on the likelihood of a patient with LABC responding to neo-adjuvant therapy [Glück et al. BRCRT2013].

Trial design:

MINT I is a prospective study designed to test the ability of molecular profiling, as well as traditional pathologic and clinical prognostic factors, to predict response to neo-adjuvant chemotherapy in patients with LABC. MammaPrint risk profile, BluePrint molecular subtyping profile, TargetPrint estrogen receptor (ER), progesterone receptor (PR) and HER2 single gene readout, and TheraPrint Research Gene Panel will be analyzed on a fresh tumor specimen using the whole genome array. Patients will receive neo-adjuvant chemotherapy pre-specified in the protocol. Response will be measured centrally. pCR is defined as the absence of invasive carcinoma in both the breast and axilla at microscopic examination of the resection specimen, regardless of the presence of carcinoma in situ.

Eligibility:

The study will include women ≥18 years with histologically-proven invasive breast cancer T2 (≥3.5cm)-T4, N0M0 or T2-T4N1M0, adequate bone marrow reserves and normal renal and hepatic function who signed an IRB approved informed consent.

Objectives:

The objectives of the study are to:

1. Determine the predictive power of MammaPrint and BluePrint for sensitivity to neo-adjuvant chemotherapy as measured by pCR.

2. Compare TargetPrint ER, PR and HER2 with local and centralized IHC and/or CISH/FISH assessment.

3. Identify correlations between TheraPrint and response to neo-adjuvant chemotherapy.

4. Identify and/or validate predictive gene expression profiles of clinical response or resistance to neo-adjuvant chemotherapy.

5. Compare BluePrint with IHC-based subtype classification.

Statistical methods:

Standard statistical tests such as the Pearson Chi-square test will be used to characterize and evaluate the relationship between chemoresponsiveness and gene expression patterns.

Accrual:

A total of 226 eligible patients will be enrolled from multiple institutions. To date (June 06, 2014), 103 patients have been enrolled.

Citation Format: Charles E Cox, Peter Blumencranz, Ruben Saez, Robert Wesolowski, William Dooley, Lisette Stork-Sloots, Femke de Snoo, Sarah Untch, Eli Avisar. MINT I: Multi-Institutional Neo-adjuvant Therapy, MammaPrint Project I [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 OT3-2-02.

Genomic classifier ColoPrint predicts recurrence in stage II colorectal cancer patients more accurately than clinical factors

BACKGROUND

Approximately 20% of patients with stage II colorectal cancer will experience a relapse. Current clinical-pathologic stratification factors do not allow clear identification of these high-risk patients. ColoPrint (Agendia, Amsterdam, The Netherlands, http://www.agendia.com) is a gene expression classifier that distinguishes patients with low or high risk of disease relapse.

METHODS

ColoPrint was developed using whole-genome expression data and validated in several independent validation cohorts. Stage II patients from these studies were pooled (n = 416), and ColoPrint was compared with clinical risk factors described in the National Comprehensive Cancer Network (NCCN) 2013 Guidelines for Colon Cancer. Median follow-up was 81 months. Most patients (70%) did not receive adjuvant chemotherapy. Risk of relapse (ROR) was defined as survival until first event of recurrence or death from cancer.

RESULTS

In the pooled stage II data set, ColoPrint identified 63% of patients as low risk with a 5-year ROR of 10%, whereas high-risk patients (37%) had a 5-year ROR of 21%, with a hazard ratio (HR) of 2.16 (p = .004). This remained significant in a multivariate model that included number of lymph nodes retrieved and microsatellite instability. In the T3 microsatellite-stable subgroup (n = 301), ColoPrint classified 59% of patients as low risk with a 5-year ROR of 9.9%. High-risk patients (31%) had a 22.4% ROR (HR: 2.41; p = .005). In contrast, the NCCN clinical high-risk factors were unable to distinguish high- and low-risk patients (15% vs. 13% ROR; p = .55).

CONCLUSION

ColoPrint significantly improved prognostic accuracy independent of microsatellite status or clinical variables, facilitating the identification of patients at higher risk who might be considered for additional treatment.

Chemosensitivity predicted by BluePrint 80-gene functional subtype and MammaPrint in the Prospective Neoadjuvant Breast Registry Symphony Trial (NBRST)

Purpose

The purpose of the NBRST study is to compare a multigene classifier to conventional immunohistochemistry (IHC)/fluorescence in situ hybridization (FISH) subtyping to predict chemosensitivity as defined by pathological complete response (pCR) or endocrine sensitivity as defined by partial response.

Methods

The study includes women with histologically proven breast cancer, who will receive neoadjuvant chemotherapy (NCT) or neoadjuvant endocrine therapy. BluePrint in combination with MammaPrint classifies patients into four molecular subgroups: Luminal A, Luminal B, HER2, and Basal.

Results

A total of 426 patients had definitive surgery. Thirty-seven of 211 (18 %) IHC/FISH hormone receptor (HR)+/HER2− patients were reclassified by Blueprint as Basal (n = 35) or HER2 (n = 2). Fifty-three of 123 (43 %) IHC/FISH HER2+ patients were reclassified as Luminal (n = 36) or Basal (n = 17). Four of 92 (4 %) IHC/FISH triple-negative (TN) patients were reclassified as Luminal (n = 2) or HER2 (n = 2). NCT pCR rates were 2 % in Luminal A and 7 % Luminal B patients versus 10 % pCR in IHC/FISH HR+/HER2− patients. The NCT pCR rate was 53 % in BluePrint HER2 patients. This is significantly superior (p = 0.047) to the pCR rate in IHC/FISH HER2+ patients (38 %). The pCR rate of 36 of 75 IHC/FISH HER2+/HR+ patients reclassified as BPLuminal is 3 %. NCT pCR for BluePrint Basal patients was 49 of 140 (35 %), comparable to the 34 of 92 pCR rate (37 %) in IHC/FISH TN patients.

Conclusions

BluePrint molecular subtyping reclassifies 22 % (94/426) of tumors, reassigning more responsive patients to the HER2 and Basal categories while reassigning less responsive patients to the Luminal category. These findings suggest that compared with IHC/FISH, BluePrint more accurately identifies patients likely to respond (or not respond) to NCT.

High concordance of protein (by IHC), gene (by FISH; HER2 only), and microarray readout (by TargetPrint) of ER, PgR, and HER2: results from the EORTC 10041/BIG 03-04 MINDACT trial

BACKGROUND

To investigate the correlation of TargetPrint with local and central immunohistochemistry/fluorescence in situ hybridization assessment of estrogen (ER), progesterone (PgR), and human epidermal growth factor receptor 2 (HER2) in the first 800 patients enrolled in the MINDACT trial.

PATIENTS AND METHODS

Data from local (N = 800) and central (N = 626) assessments of receptor status were collected and compared with TargetPrint results.

RESULTS

For ER, the positive agreement (the percentage of central pathology positive assessments that were also TargetPrint/local laboratory positive) for TargetPrint in comparison to centralized assessment was 98% with a negative agreement (the percentage of central pathology negative assessments that were also TargetPrint/local laboratory negative) of 96%. For PgR, the positive agreement was 83% with a negative agreement of 92%. For HER2, the positive agreement was 75% with a negative agreement of 99%. Even though the local assessment showed higher positive agreement for PgR (89%) and higher positive agreement for HER2 (85%), the range of discordant local versus central assessments were as high as 6.7% for ER, 12.9% for PgR, and 4.3% for HER2.

CONCLUSION

TargetPrint and local assessment of ER, PgR, and HER2 show high concordance with central assessment in the first 800 MINDACT patients. However, there are concerns about the higher discordance rates for some local sites. TargetPrint can improve the reliability of hormone receptor and HER2 testing for those centers with a lower rate of concordance with the reference laboratory, with the limitation of a positive agreement of 75% for HER2. TargetPrint consequently has important implications for treatment decisions in clinical practice and is a reliable alternative to local assessment for ER.

CLINICAL TRIALS NUMBER

NCT00433589.

Abstract OT1-2-02: PROMIS: Prospective study of MammaPrint in breast cancer patients with an intermediate recurrence score (PROMIS)

Background: Gene expression profiling offers the potential to improve prognostic accuracy, treatment choice, and health outcomes in women diagnosed with early-stage breast cancer. Numerous gene-profiling assays are now available, which can be applied to a single tumor specimen to provide physicians with a more complete basis for treatment decisions.

· MammaPrint is a 70-gene profile to estimate whether patients are at high or low risk of developing metastases within the first 10 years after curative surgery

· BluePrint is an 80-gene molecular subtyping profile that discriminates between three breast cancer subtypes: Luminal, HER2, and Basal

· TargetPrint provides a quantitative measurement of estrogen receptor (ER), progesterone receptor (PR), and HER2

· Oncotype DX measures expression of five reference genes and 16 cancer-related genes, quantifying the risk of distant recurrence in patients with ER+ early breast cancer who are treated with adjuvant hormonal therapy, and predicting clinical benefit with adjuvant chemotherapy

Trial design: PROMIS is a prospective study that will investigate the additional value of MammaPrint, BluePrint and TargetPrint in women with an intermediate Oncotype DX score. An initial CRF – capturing baseline patient characteristics, pathology information, Oncotype DX score and the recommended treatment plan – will be completed before receiving the MammaPrint result. A second CRF – capturing the actual treatment – will be completed within 4 weeks after receiving the MammaPrint result.

Eligibility: Women aged ≥18 years with histologically proven invasive stage I-II, node negative or node positive (N1), hormone receptor positive, HER2 negative breast cancer, who received an Oncotype DX intermediate score (18-30) and who signed informed consent.

Objectives:

Primary objective:

Assess the impact of MammaPrint on chemotherapy + endocrine versus endocrine alone treatment decisions in lymph node negative, hormone receptor positive, HER2 negative breast cancer patients, who received an Oncotype DX intermediate score

Secondary objectives:

Assess the impact of MammaPrint on chemotherapy + endocrine versus endocrine alone treatment decisions in lymph node positive (N1), hormone receptor positive, HER2 negative breast cancer patients, who received an Oncotype DX intermediate score

Assess the distribution of MammaPrint Low and High Risk in patients with an intermediate recurrence score

Assess concordance of TargetPrint ER, PR and HER2 results with Oncotype DX ER, PR and Her2 and with locally assessed IHC/FISH ER, PR and HER2

Compare clinical subtype based on IHC/FISH ER, PR, HER2 and Ki-67 (if available) with BluePrint molecular subtype

Statistical methods: A sample size of 820 lymph node negative, hormone receptor positive, HER2 negative breast cancer patients is required to detect a 20% overall treatment change (5% significance and 90% power). A McNemars test will be performed for the comparison of the two proportions treated (before and after), both expressed as a percentage.

Accrual: A total of 150 out of 820 have been enrolled from multiple institutions in the US.

Clinical trial registry number: NCT01617954.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr OT1-2-02.

Abstract OT1-2-01: MINT I: Multi-institutional neo-adjuvant therapy, MammaPrint project I

Background: Women with locally advanced breast cancer (LABC) are often treated with neo-adjuvant chemotherapy to reduce the size of the tumor prior to surgery, to enable breast conserving surgery and to observe the clinical effect of therapy in real time. Studies have shown that the 25–27% of individuals who have a pathologic complete response (pCR) to neoadjuvant therapy have a survival advantage of 80% in 5 years, which is double the expected survival of the remaining patients without pCR. If patients who are likely to show a pCR could be identified prior to initiation of therapy, it would enable more informed treatment decisions – patients likely to respond would be served well by current neoadjuvant chemotherapy protocols, while those unlikely to respond may be better suited to innovative new strategies for drug discovery [von Minckwitz et al. JCO 2006]. Genomic assays, which are widely used to provide prognostic and predictive information in early breast cancer, have the potential to provide information on the likelihood of a patient with LABC responding to neo-adjuvant therapy [Glück et al. ASCO 2012].

Trial design: MINT I is a prospective study designed to test the ability of molecular profiling, as well as traditional pathologic and clinical prognostic factors, to predict response to neo-adjuvant chemotherapy in patients with LABC. MammaPrint risk profile, BluePrint molecular subtyping profile, TargetPrint estrogen receptor (ER), progesterone receptor (PR) and HER2 single gene readout, and TheraPrint Research Gene Panel will be analyzed on a fresh tumor specimen using the whole genome array. Patients will receive neo-adjuvant chemotherapy pre-specified in the protocol. Response will be measured centrally. pCR is defined as the absence of invasive carcinoma in both the breast and axilla at microscopic examination of the resection specimen, regardless of the presence of carcinoma in situ.

Eligibility: The study will include women ≥18 years with histologically-proven invasive breast cancer T2 (≥3.5cm)-T4, N0M0 or T2-T4N1M0, adequate bone marrow reserves and normal renal and hepatic function who signed an IRB approved informed consent.

Objectives: The objectives of the study are to:

1. Determine the predictive power of MammaPrint and BluePrint for sensitivity to neo-adjuvant chemotherapy as measured by pCR.

2. Compare TargetPrint ER, PR and HER2 with local and centralized IHC and/or CISH/FISH assessment.

3. Identify correlations between TheraPrint and response to neo-adjuvant chemotherapy.

4. Identify and/or validate predictive gene expression profiles of clinical response or resistance to neo-adjuvant chemotherapy.

5. Compare BluePrint with IHC-based subtype classification.

Statistical methods: Standard statistical tests such as the Pearson Chi-square test will be used to characterize and evaluate the relationship between chemoresponsiveness and gene expression patterns.

Accrual: A total of 226 eligible patients will be enrolled from multiple institutions. To date (June 06, 2013), 57 patients have been enrolled.

Clinical trial registry number: NCT01501487.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr OT1-2-01.

Abstract P1-02-02: Concordance of microarray based determination of ER, PR and HER2 receptor status and local IHC/FISH assessment in the prospective neo-adjuvant breast registry symphony trial (NBRST)

Background

The level of estrogen receptor (ER), progesterone receptor (PR) and HER2 expression is predictive for prognosis and/or treatment response in breast cancer patients. However, differences in fixation and IHC and subjective interpretation can substantially affect the accuracy and reproducibility of the results. The commercially available TargetPrint test measures the mRNA expression level of ER, PR and HER2. Previously TargetPrint was shown to be strongly correlated with high quality IHC/FISH assessment, especially for ER and HER2. Concordance rates were 98% (k = 0.90) for ER; 85% (k = 0.62) for PR and 96% for HER2 (k = 0.78) in 619 patients (Viale et al., SABCS 2011).

This study compares results from the microarray-based TargetPrint with IHC and FISH conducted according to local standard procedures in the prospective NBRST study.

Methods

The NBRST study includes women aged 18–90 with histologically proven breast cancer, who are scheduled to start neo-adjuvant chemotherapy (CT) or neo-adjuvant endocrine therapy (ET), and who provide written informed consent. The mRNA level of ER, PR and HER2 (TargetPrint) was assessed at the Agendia laboratory (Agendia Inc, Irvine, CA) in fresh and formalin fixed paraffin embedded tumor samples submitted from 40 institutes in the US. The results of the IHC/FISH assessments conducted according to local standard procedures were compared to the quantitative gene expression readouts.

Results

There were 355 eligible patients enrolled. 67% of patients are IHC ER positive and 25% Her2 IHC/FISH positive. 11 patients were IHC/FISH HER2 equivocal (all TargetPrint HER2 negative). Comparison of IHC and gene expression read out by TargetPrint showed a concordance of 88% (k = 0.75)for ER; 83% (k = 0.66) for PR and 89% (k = 0.70) for HER2. The discordance range for institutes who submitted more than 10 samples was 0-30% for ER, 0-47% for PR and 0-28% for HER2. 16% of all IHC ER+ samples were classified negative by microarray. In contrast, 4% of IHC ER- samples were classified positive by microarray. However for HER2, as many as 33% of IHC/FISH HER2+ samples were classified negative by microarray; 3% of IHC/FISH HER2- samples were classified positive by microarray.

Conclusions

Microarray based readout of ER, PR and HER2 status using TargetPrint is comparable to local IHC and FISH analysis in 355 analyzed samples from 40 US institutes but the discordance range for individual institutes was up to 30% for ER and 28% for Her2.

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

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 P3-05-02: Pathological assessment of discordant cases for molecular (BluePrint and MammaPrint) versus clinical subtypes for breast cancer among 621 patients from the EORTC 10041/BIG 3–04 (MINDACT) trial

Background: Biology has become the main driver of breast cancer therapy. Intrinsic biological subtypes by gene expression profiling have been identified. Pathology can be used to define surrogates of these subtypes but these are not always concordant, which may lead to different treatment plans. We investigated the concordance between BluePrint and MammaPrint (microarray-based) breast cancer subtypes and pathological surrogates (based on ER, PR, HER2 & Ki67).

Methods: Using available data (centrally assessed pathology and genomics) from the MINDACT pilot phase [Rutgers et al. EJC 2011] 621 tumors were analyzed. Patients were classified according to 4-category based pathology (ER, PR, HER2 and Ki67); additionally, classification was performed adhering to the recent St. Gallen recommendations [Goldhirsch et al. 2011], which recognizes an additional category (Luminal B HER2+). Based on BluePrint and MammaPrint 4 subtypes are formed: Luminal A (Luminal-type/MammaPrint Low Risk); Luminal B (Luminal-type/MammaPrint High Risk); HER2-type; and Basal-type. This study is an analysis of discordant patient groups (i.e. clinical HER2+/BluePrint Luminal-type; clinical Hormone Receptor (HR)-positive/BluePrint Basal-type) providing comparison of centrally assessed tumor heterogeneity as well as comparison of quantified ER, PR and HER2 results.

Results: Ki67 is often used as biomarker to distinguish Luminal A from Luminal B subgroups. The concordance between MammaPrint and centrally assessed Ki67 in Luminal-type patients is 71%, with a κ score of 0.35 (95% CI 0.26–0.45) indicating that Ki67 and MammaPrint cannot reliably substitute for each other. There is a relatively large group of clinical HER2+ cases that are BluePrint Luminal-type (29 out of 76; 38%) indicating that tumor expression of the Luminal profile is dominant compared with expression of the HER2 profile. These patients have high IHC ER results and fall into the group that St Gallen separately defines as Luminal B HER2-type. These patients may have lower response to trastuzumab [von Minckwitz et al. JCO 2012]. 12 out of 76 BluePrint Basal-type patients are clinical HR+. These patients have low centrally assessed IHC ER and PR expression (≥1% and &lt;10%).

Conclusions: Marked differences are observed between BluePrint and MammaPrint (microarray based) breast cancer subtypes and centrally re-assessed pathological surrogates (based on ER, PR, HER2 & Ki67). The greatest discordance is seen in the sub-stratification of Luminal patients, and in the HR+/HER2+ patients. The observed subtype discrepancies may have an important impact on treatment decision making.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-05-02.

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

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 OT3-4-01: PROMIS: Prospective Registry Of MammaPrint in breast cancer patients with an Intermediate recurrence Score

Background: Gene expression profiling in breast cancer offers the potential to improve prognostic accuracy, treatment choice, and health outcomes in women diagnosed with early-stage breast cancer. Numerous gene-profiling assays are now available, which can be applied to a single tumor specimen to provide physicians with a more complete basis for treatment decisions.

MammaPrint is a DNA microarray-based in vitro diagnostic that measures the activity of 70 genes to estimate whether patients are at high risk or low risk of developing metastases within the first 10 years after curative surgery. BluePrint is an 80-gene molecular subtyping profile that discriminates between three breast cancer subtypes: Luminal, HER2, and Basal. TargetPrint provides a quantitative measurement of estrogen receptor (ER), progesterone receptor (PR), and HER2, and can serve as a reliable second pathology assessment for locally-assessed parameters. Oncotype DX measures expression of five reference genes and 16 cancer-related genes, quantifying the risk of distant recurrence in patients with ER+ early breast cancer who are treated with adjuvant hormonal therapy, and predicting clinical benefit with additional adjuvant chemotherapy.

Trial design: PROMIS is a prospective, observational, case-only study that will investigate the additional value of MammaPrint, BluePrint and TargetPrint in women with an intermediate Oncotype DX score. An initial CRF – capturing baseline patient characteristics, pathology information, Oncotype DX score and the recommended treatment plan – will be completed before receiving the MammaPrint result. A second CRF – capturing the recommended treatment – will be completed within 4 weeks after receiving the MammaPrint result.

Eligibility: The study will include women aged ≥18 years with histologically proven invasive stage I-II, node-negative, hormone receptor-positive, HER2-negative breast cancer and Oncotype DX score of 18–30 who signed informed consent.

Objectives: The objectives of the study are to: 1. Describe the frequency of chemotherapy + endocrine versus endocrine-alone decisions in Oncotype DX intermediate score patients.2. Assess the impact of MammaPrint on chemotherapy + endocrine versus endocrine-alone treatment decisions.3. Assess the distribution of MammaPrint Low and High Risk in patients with an intermediate recurrence score.4. Assess concordance of TargetPrint ER, PR and HER2 results with Oncotype DX ER, PR and HER2 and with locally assessed IHC/FISH ER, PR and HER2.5. Compare clinical subtype based on IHC/FISH ER, PR, HER2 and Ki-67 (if available) with BluePrint molecular subtype.

Statistical methods: As the project is exploratory, sample size calculations do not apply as only descriptive statistics will be used. The frequency of chemotherapy + endocrine versus endocrine-alone decisions in Oncotype DX intermediate score patients will be calculated before and after receiving the MammaPrint result. A Chi-square test will be performed for the comparison of the two proportions.

Accrual: A total of ∼300 eligible patients will be enrolled from multiple institutions.

Clinical trial registry number: NCT01617954

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr OT3-4-01.

Abstract OT3-4-02: MINT I: Multi-Institutional Neo-adjuvant Therapy, MammaPrint Project I

Background: Women with locally advanced breast cancer (LABC) are often treated with neo-adjuvant chemotherapy to reduce the size of the tumor prior to surgery, to enable breast conserving surgery and to observe the clinical effect of therapy in real time. Studies have shown that the 25–27% of individuals who have a pathologic complete response (pCR) to neoadjuvant therapy have a survival advantage of 80% in 5 years, which is double the expected survival of the remaining patients without pCR. If patients who are likely to show a pCR could be identified prior to initiation of therapy, it would enable more informed treatment decisions – patients likely to respond would be served well by current neoadjuvant chemotherapy protocols, while those unlikely to respond may be better suited to innovative new strategies for drug discovery [von Minckwitz et al. JCO 2006]. Genomics assays, which are widely used to provide prognostic and predictive information in early breast cancer, have the potential to provide information on the likelihood of a patient with LABC responding to neo-adjuvant therapy [Glück et al. ASCO 2012].

Trial design: MINT I is a prospective study designed to test the ability of molecular profiling, as well as traditional pathologic and clinical prognostic factors, to predict responsiveness to neo-adjuvant chemotherapy in patients with LABC. MammaPrint risk profile, BluePrint molecular subtyping profile, TargetPrint estrogen receptor (ER), progesterone receptor (PR) and HER2 single gene readout, and the 56-gene TheraPrint Research Gene Panel will be analyzed on a fresh tumor specimen using the whole genome array. Patients will receive neo-adjuvant chemotherapy pre-specified in the protocol. Response will be measured centrally. pCR is defined as the absence of invasive carcinoma in both the breast and axilla at microscopic examination of the resection specimen, regardless of the presence of carcinoma in situ.

Eligibility: The study will include women ≥18 years with histologically-proven invasive breast cancer T2 (≥3.5cm)-T4, N0M0 or T2-T4N1M0, adequate bone marrow reserves and normal renal and hepatic function who signed an IRB approved informed consent.

Objectives: The objectives of the study are to: 1. Determine the predictive power of MammaPrint and BluePrint for sensitivity to neo-adjuvant chemotherapy as measured by pCR.2. Compare TargetPrint ER, PR and HER2 with local and centralized IHC and/or CISH/FISH assessment.3. Identify correlations between TheraPrint and response to neo-adjuvant chemotherapy.4. Identify and/or validate predictive gene expression profiles of clinical response or resistance to neo-adjuvant chemotherapy.5. Compare BluePrint with IHC-based subtype classification.

Statistical methods: Standard statistical tests such as the Pearson Chi-square test will be used to characterize and evaluate the relationship between chemoresponsiveness and gene expression patterns.

Accrual: A total of 226 eligible patients will be enrolled from multiple institutions. To date (June 06, 2012), 31 patients have been enrolled.

Clinical trial registry number: NCT01501487.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr OT3-4-02.

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.

Central review of discordant samples for microarray-based ER, PR, and HER2 and local IHC/FISH assessment worldwide from 827 patients

11

Background: Differences in fixation and IHC and subjective interpretation can substantially affect the accuracy and reproducibility of estrogen receptor (ER), progesterone receptor (PR) and HER2 expression. The commercially available TargetPrint test measures the mRNA expression level of ER, PR and HER2 and is 98% concordant with centrally assessed ER as presented by Viale et al, SABCS 2011. This study compares results from the microarray-based TargetPrint with IHC and FISH (for HER2 IHC2+) generated by local standard procedures. Methods: Fresh tumor samples (core needle biopsies or surgical) were collected for 831 patients diagnosed with breast cancer stage I to IV (Feb 2008 - Jan 2011) from 22 hospitals from Europe, New Zealand, Japan and US. The results of the IHC/FISH assessments performed according to the local standards at the hospitals were compared to the quantitative gene expression readouts with TargetPrint. Discordant cases were centrally reviewed for IHC/FISH assessment. Results: Of the 831 samples, IHC assessment was unknown for 4 ER/ PR samples; HER2 was unknown for 12 samples. Comparison of IHC and gene expression read out by TargetPrint showed a concordance of 95% for ER; 83% for PR and 94% for HER2. In this study, 3% of all IHC ER positive samples were classified negative by microarray, and 11% of IHC PR positive samples were classified negative by microarray. For HER2, 4% of IHC/FISH HER2 positive samples were classified negative by microarray and 2% of IHC/FISH HER2 negative samples were classified positive by microarray. Most notably, all available 5 ER IHC negative/TargetPrint positive samples turned out to be positive with central re-assessment. HER2 IHC2+ samples with discordant classifications for TargetPrint and local assessment are currently being reviewed for FISH/SISH assessment. Conclusions: Microarray based readout of ER, PR and HER2 status using TargetPrint is fairly comparable to local IHC and FISH analysis in 827 analyzed samples in various hospitals worldwide. However, re-assessment of discordant cases–especially IHC ER-/TargetPrint ER+ cases- confirms TargetPrint to be a useful high quality second opinion for local IHC/FISH assessment.

Comparison of molecular (BluePrint and MammaPrint) and pathological subtypes for breast cancer among the first 800 patients from the EORTC 10041/BIG 3-04 (MINDACT) trial

32

Background: Biology has become the main driver of breast cancer therapy. Intrinsic biological subtypes by gene expression profiling have been identified. Pathology can be used to define surrogates of these subtypes but these are not always concordant, which may lead to different treatment plans. We investigated the concordance between BluePrint (BP) + MammaPrint (MP) (micro array based) breast cancer subtypes and pathological surrogates (based on ER, PR, HER2 and Ki67). Contrary to the Perou gene set (evolved into PAM50), BluePrint was trained using pathological data. Methods: Using available data (centrally assessed pathology and genomic) from the MINDACT pilot phase (Rutgers et al 2011) 621 tumors were analyzed. Two pathology classifications were used: one with 4 categories and one with 5 categories (Goldhirsch et al 2011). Based on BP 3 subtypes are formed: Luminal, HER2 and Basal. The Luminal subtype is further split into Luminal A (MP low risk) and Luminal B (MP high risk). Results: See table. Conclusions: All pathological Basal cases are BP Basal, apart from 1 BP HER2 case. Of the BP Basal cases, 15 are not pathological Basal: 1 is Luminal A, 11 are Luminal B (of which 8 are IHC ER/PR borderline (≥1% and < 10%)) and 3 are HER2. All pathological Luminal (A & B) that are BP HER2 are HER2- by TargetPrint. 25 of the 26 pathological HER2+ that are BP Luminal A are ER+. Most discordant cases are seen within the Luminal subtype, indicating that Ki67 discriminates Luminal A vs. B differently than MammaPrint does. The observed subtype discrepancies reveal potential important impact for treatment-decision making. MINDACT will provide important information. [Table: see text]

Gene expression panel (TheraPrint) analyzed as predictors of response to neoadjuvant chemotherapy (NCT) in patients (pts) with stage II-III and inflammatory breast cancer (BC)

8

Background: TheraPrint is a microarray-based gene expression panel of 125 genes identified as potential targets for prognosis and therapeutic response. These genes may hold the key to a greater level of personalized prognosis and therapy for BC pts. The aim of the current study was to assess the clinical relevance of the TheraPrint genes for either predictive and/or prognostic value in two patient cohorts treated with NCT. Methods: The 1st patient cohort are 68 Stage II-III BC pts treated with NCT. Expression data from Agilent full genome arrays, containing the MammaPrint, BluePrint and TheraPrint diagnostic profiles/probes (Somlo et al, 2009). Median FU 2.3 years. The 2nd patient cohort are 230 Stage I-III BC pts treated with NCT. Expression data from Affymetrix probe sets was publically available (Iwamoto et al, 2011). Median FU 5.2 years. To identify genes that are differentially expressed between responders (pCR/RCBI) and non-responders, a supervised analysis was performed. The analysis was performed across all pts and also within groups of HER2+ and HER2-. Univariate t-tests were performed, with results filtered by permutation p-value (p<0.05) and fold change of >1.5. Global test was also reported. In addition, survival data analysis was performed across all pts. Results: Overlapping genes between the 2 datasets that were significantly differentially expressed between responders and non-responders include: BCL2 (down-regulated) and CDH3, GRB7, KRT6B, KRT17 (up-regulated). When analysing the HER2- subgroup, 3 genes turned out to be differentially expressed between responders and non-responders in the 2 datasets: FLT1, PIK3R1 (down-regulated) and KRT6B (up-regulated). For the HER2+ subgroup, only one gene overlapped for the 2 datasets: IL2RA (up-regulated). The top canonical pathways for the significant genes have been analyzed, and in addition correlation of the TheraPrint gene expression with survival for these pt groups. Conclusions: This study has identified several genes from a panel of 125 TheraPrint genes with statistically significant correlation between expression and response to NCT.

Response and long-term outcomes after neoadjuvant chemotherapy: Pooled dataset of patients stratified by molecular subtyping by MammaPrint and BluePrint

10

Background: Classification of breast cancers into molecular subtypes may be important for the proper selection of therapy for patients with early breast cancer. Previous analyses had shown that breast cancer subtypes have distinct clinical outcome (Sorlie, PNAS, 2001; Esserman, BCRT, 2011). Herein, we analyze using MammaPrint together with an 80-gene molecular subtyping profile (BluePrint) the response to neo-adjuvant chemotherapy and long term outcomes. Methods: This study was carried out on data from 144 patients from the I-SPY I trial; 232 patients from biomarker discovery program at MD Anderson (133 and 99 respectively; Hess, 2006, JCO; Iwamoto, 2011, BCRT); and 68 patients from City of Hope (Somlo, ASCO, 2010). All patients were treated in the neo-adjuvant setting with standard chemotherapy. MammaPrint and BluePrint were determined on 44K Agilent arrays run at Agendia or available through the I-SPY 1 data portal, or from Affymetrix U133A arrays. MammaPrint and BluePrint 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: The overall pCR of this patient cohort was 22% but differed substantially among the subgroups. pCR was observed in 5% of the Luminal-A samples and 10% of Luminal-B, in 39% of the HER2-type samples and in 33% of the Basal-type samples. Patients with Basal-type tumors had a 5-year DFS of 71%; HER2-type had a 5-year DFS of 67% (n=71); 69% in HER2-type subgroup not treated with HER2-targeted therapy (n=45); Luminal-B type had a 5-year DFS of 77% and Luminal-A type showed 5-year DFS of 95%. Conclusions: We observed marked differences in response and DFS to neo-adjuvant treatment in groups stratified by MammaPrint and BluePrint. These findings confirm differences in chemotherapy response among molecular subgroups and indicate that the BluePrint and MP profile used for this analysis helps to further establish a clinical correlation between molecular subtyping and treatment outcomes.

The PARSC trial, a prospective study for the assessment of recurrence risk in stage II colon cancer patients using ColoPrint

TPS10632

Background: An 18-gene expression profile, ColoPrint, has been developed for identifying colon cancer patients more likely to develop recurrent disease and who would be candidates for adjuvant chemotherapy. The gene signature was validated in public datasets and independent patient cohorts (stage II and III patients). Uni-and multivariate analysis was performed on the pooled stage II patient set (n=320) (median follow-up 70 months). ColoPrint classifies 65% of stage II patients as Low Risk. The 3-year RFS was 91% for Low Risk and 74% for High Risk patients with a HR of 2.9 (p=0.001). ColoPrint was the only significant prognostic marker in the subgroup of patients with T3-MSS phenotype (Tabernero, ASCO GI 2012). Methods: A blinded prospective trial, PARSC (Prospective study for the Assessment of Recurrence risk in Stage II colon cancer patients) using ColoPrint has been initiated. Objectives are: (1)To validate the performance of ColoPrint in estimating the 3-year relapse rate in patients with stage II colon cancer. (2) To compare the risk assessment in stage II patients using the ColoPrint profile vs a clinical risk assessment based on Investigator’s assessment of risk and ASCO high-risk recommendations. (3) To investigate therapy as a potential confounding factor for ColoPrint results. (4) To assess the performance of ColoPrint in estimating the 3-year relapse rate in patients with stage III colon cancer. Inclusion criteria: age ≥ 18 years, adenocarcinoma of the colon, stage II and III, no prior neo-adjuvant therapy, no synchronous tumors, fresh tumor sample, and written informed consent. The treatment of the patient is at the discretion of the physician adhering to National Comprehensive Cancer Network (NCCN)-approved regimens or a recognized alternative (blinded for ColoPrint result). The trial started in Sept. 2008 with currently 32 participating sites in 11 countries. Thus far, 340 eligible stage II and 280 stage III patients have been enrolled. The aim is to enroll 575 stage II patients. Clinical trial registry number: NCT00903565.

Central review of discordant samples for microarray based on ER, PR, and HER2 and local IHC/FISH assessment worldwide from 827 patients

10554

Background: Differences in fixation and IHC and subjective interpretation can substantially affect the accuracy and reproducibility of estrogen receptor (ER), progesterone receptor (PR) and HER2 expression. The commercially available TargetPrint test measures the mRNA expression level of ER, PR and HER2 and is 98% concordant with centrally assessed ER as presented by Viale et al, SABCS 2011. This study compares results from the microarray-based TargetPrint with IHC and FISH (for HER2 IHC2+) generated by local standard procedures. Methods: Fresh tumor samples (core needle biopsies or surgical) were collected for 831 patients diagnosed with breast cancer stage I to IV (Feb 2008 - Jan 2011) from 22 hospitals from Europe, New Zealand, Japan and US. The results of the IHC/FISH assessments performed according to the local standards at the hospitals were compared to the quantitative gene expression readouts with TargetPrint. Discordant cases were centrally reviewed for IHC/FISH assessment. Results: Of the 831 samples, IHC assessment was unknown for 4 ER/ PR samples; HER2 was unknown for 12 samples. Comparison of IHC and gene expression read out by TargetPrint showed a concordance of 95% for ER; 83% for PR and 94% for HER2. In this study, 3% of all IHC ER positive samples were classified negative by microarray, and 11% of IHC PR positive samples were classified negative by microarray. For HER2, 4% of IHC/FISH HER2 positive samples were classified negative by microarray and 2% of IHC/FISH HER2 negative samples were classified positive by microarray. Most notably, all available 5 ER IHC negative/TargetPrint positive samples turned out to be positive with central re-assessment. HER2 IHC2+ samples with discordant classifications for TargetPrint and local assessment are currently being reviewed for FISH/SISH assessment. Conclusions: Microarray based readout of ER, PR and HER2 status using TargetPrint is fairly comparable to local IHC and FISH analysis in 827 analyzed samples in various hospitals worldwide. However, re-assessment of discordant cases –especially IHC ER-/TargetPrint ER+ cases- confirms TargetPrint to be a useful high quality second opinion for local IHC/FISH assessment.

Gene expression panel (TheraPrint) analyzed as predictors of response to neoadjuvant chemotherapy (NCT) in patients (pts) with stage II-III and inflammatory breast cancer (BC)

e21013

Background: TheraPrint is a microarray-based gene expression panel of 125 genes identified as potential targets for prognosis and therapeutic response. These genes may hold the key to a greater level of personalized prognosis and therapy for BC pts. The aim of the current study was to assess the clinical relevance of the TheraPrint genes for either predictive and/or prognostic value in 2 patient cohorts treated with NCT. Methods: The 1st patient cohort are 68 Stage II-III BC pts treated with NCT. Expression data from Agilent full genome arrays, containing the MammaPrint, BluePrint and TheraPrint diagnostic profiles/probes (Somlo et al, 2009). Median FU 2.3 years. The 2nd patient cohort are 230 Stage I-III BC pts treated with NCT. Expression data from Affymetrix probe sets was publically available (Iwamoto et al, 2011). Median FU 5.2 years. To identify genes that are differentially expressed between responders (pCR/RCBI) and non-responders, a supervised analysis was performed. The analysis was performed across all pts and also within groups of HER2+ and HER2-. Univariate t-tests were performed, with results filtered by permutation p-value (p<0.05) and fold change of >1.5. Global test was also reported. In addition, survival data analysis was performed across all pts. Results: Overlapping genes between the 2 datasets that were significantly differentially expressed between responders and non-responders include: BCL2 (down-regulated) and CDH3, GRB7, KRT6B, KRT17 (up-regulated). When analysing the HER2- subgroup, 3 genes turned out to be differentially expressed between responders and non-responders in the 2 datasets: FLT1, PIK3R1 (down-regulated) and KRT6B (up-regulated). For the HER2+ subgroup, only one gene overlapped for the 2 datasets: IL2RA (up-regulated). The top canonical pathways for the significant genes have been analyzed, and in addition correlation of the TheraPrint gene expression with survival for these pt groups. Conclusions: This study has identified several genes from a panel of 125 TheraPrint genes with statistically significant correlation between expression and response to NCT.

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.

The PARSC trial, a prospective study for the assessment of recurrence risk in stage II colon cancer (CC) patients using ColoPrint

678

Background: An 18-gene expression profile, ColoPrint, has been developed for identifying CC patients more likely to develop recurrent disease and who would be candidates for adjuvant chemotherapy. The gene signature was validated in in-silico datasets and independent patient cohorts of stage II and III patients. Uni-and multivariate analysis was performed on the pooled stage II patient set (n=320) who had a median follow-up of 70 months. ColoPrint identified two-third of the stage II patients (209/320) as low risk. The 3-year relapse-free survival was 94% for Low Risk patients and 79% for High Risk patients with a HR of 2.74 (95% CI 1.54 - 4.88; p=0.006). Moreover, the profile stratified patients independent of ASCO clinical risk factors.

Methods: A prospective trial, PARSC (Prospective study for the Assessment of Recurrence risk in Stage II CC patients) using ColoPrint has been initiated. Objectives are: (1) to validate the performance of ColoPrint in estimating the 3-year relapse rate in patients with stage II colon cancer; (2) to compare the risk assessment in stage II patients using the ColoPrint profile vs. a clinical risk assessment based on Investigator’s assessment of risk and ASCO high-risk recommendations; (3) to investigate therapy as a potential confounding factor for ColoPrint results; and (4) to assess the performance of ColoPrint in estimating the 3-year relapse rate in patients with stage III colon cancer. Inclusion criteria: age ≥ 18 years, adenocarcinoma of the colon, stage II and III, no prior neo-adjuvant therapy, no synchronous tumors, fresh tumor sample, and written informed consent. The treatment of the patient is at the discretion of the physician adhering to National Comprehensive Cancer Network (NCCN)-approved regimens or a recognized alternative.

Results: The trial started in Sept. 2008 with currently 30 participating sites in 11 countries. Thus far, 288 eligible stage 2 and 251 stage 3 patients have been enrolled.

Conclusions: The aim is to enroll 575 stage II patients to differentiate between 3 year RFS predicted by ColoPrint and clinical factors.

Comparison of MammaPrint, BluePrint, and TargetPrint with clinical parameters in patients with breast cancer: Findings from a prospective United States cohort

47

Background: MammaPrint (MP) is a powerful predictor of disease outcome in early stage breast cancer. In addition, TargetPrint (TP), a microarray-based test that measures the mRNA expression level of ER, PR and HER2 and an 80 gene expression Molecular Subtyping profile BluePrint (BP) were developed. In the present study, MP, BP and TP were measured in a prospective U.S. breast cancer patient cohort.

Methods: MP results were evaluated in fresh tumor samples from 127 breast cancer patients (T1-4N0-2; median age 62 [39-97 yr]) collected by core needle biopsy or from a surgical specimen between July 2008 and January 2011. We compared treatment advice as recommended by NCCN guidelines and classification according to MP. In addition, we compared IHC/FISH ER, PR and HER2 assessments with TP. The MP and BP results were used to subtype the patients into molecular subgroups.

Results: For the group of patients (n=59) for which NCCN recommends the use of a multi-gene signature for determining chemotherapy treatment recommendations, 42 patients were classified as High Risk and 17 as Low Risk by MP. Comparison of TP with IHC/FISH indicated a concordance of 98% for ER, 94% for PR, and 98% for HER2. For a subgroup of 53 patients combined MP and BP results were available; 18 patients were Luminal-type/MP Low Risk, 27 patients were Luminal-type/MP High risk, 1 patient was Her2-type/MP Low Risk, 1 patient was Her2-type/MP High Risk and 6 patients were Basal-type/MP High Risk.

Conclusions: Adding the multi-gene signature MammaPrint, as well as BluePrint and TargetPrint provides additional information for treatment guidance. By combining MammaPrint with the BluePrint molecular subtyping profile, specific groups of patients can be recognized that are at high risk of recurrence and that would possibly benefit from specific treatment. This study shows that TargetPrint provides high quality second opinion for local IHC/FISH assessment.

Combined use of MammaPrint and molecular subtyping profile (BluePrint) to identify subgroups with marked differences in response to neoadjuvant treatment

42

Background: Concordance between the IHC receptor status and the molecular subtype suggests that molecular profiles represent oncogenic processes that are driven by pathways in which ER, PR and HER2 play pivotal roles. It is, therefore, likely that the use of gene expression arrays will enable the identification of previously unappreciated subtypes of breast cancer that differ in clinical outcomes.

Methods: The cohort consists of 133 (T1-4, N0-3) breast cancer patients treated with T/FAC neoadjuvant chemotherapy. Genome wide expression data was publicly available and downloaded from bioinformatics.mdanderson.org/pubdata.html. The data was used to determine the response to T/FAC neoadjuvant chemotherapy for patients stratified by MammaPrint and molecular subtype (BluePrint). The MammaPrint and BluePrint result were used to subtype the patients into 4 groups: MammaPrint Low-risk/Luminal-type, MammaPrint High-risk/Luminal-type, Basal-type and ERBB2-type.

Results: Within this patient cohort, 20% (n=27) were classified as Basal-type, 62% (n=82) as Luminal-type, and 18% (n=24) as ERBB2-type. The overall pCR of this patient cohort was 26% and differed substantially among the subgroups. pCR was observed in 9% of all Luminal-type samples (i.e. 3% of MammaPrint Low Risk/Luminal-type and 11% of MammaPrint High Risk/Luminal-type), in 50% of the ERBB2-type samples and in 56% of the Basal-type samples. The pCR rates observed for the ERBB2-type and Basal-type patient groups were higher compared to classification based on IHC/CISH assessed ER and HER2 receptor status: 50% for ERBB2-type versus 39% for HER2+ and 56% for Basal-type versus 47% for ER-/HER2- samples.

Conclusions: We observed marked differences in response to neo-adjuvant treatment in groups stratified by MammaPrint and BluePrint. These findings confirm differences in chemotherapy response among molecular subgroups and indicate that the BluePrint profile described here will help to further establish a clinical correlation between molecular subtyping and treatment response.

The PARSC trial: A prospective study for the assessment of recurrence risk in stage II colon cancer (CC) patients using ColoPrint

602

Background: Clinical trials have not yet shown convincingly if adjuvant chemotherapy is justified for stage II CC patients of whom 25% are at risk of recurrence. An 18-gene expression profile, ColoPrint, has been developed for identifying CC cancer patients more likely to develop recurrent disease and who would be candidates for adjuvant chemotherapy. The gene signature has been validated in independent cohorts of 206 CC patients and in in-silico datasets (Salazar et al, JCO in press). The profile classified 63.2% of the stage II patients (n=134) as low risk. The HR for relapse free survival (RFS) was 3.34 (p=0.017) with a 5-year RFS rate of 90.9% (95%CI, 84.0 -97.8%) for low risk patients and 73.9% (95%CI, 59.2-88.6%) for high risk patients. Moreover, the profile stratified patients independent of ASCO clinical risk factors.

Methods: A prospective trial, PARSC (Prospective Study for the Assessment of Recurrence Risk in Stage II CC Patients Using ColoPrint) has been initiated. The main objectives are: (1) determine risk assessment by ColoPrint profile versus clinical parameters based on local protocol and ASCO high-risk recommendations in stage II patients; (2) establish proportion of ′good prognosis′ and ′poor prognosis profile′ in various countries; and (3) validate the power of risk assessment and compare performance of ColoPrint and clinical risk assessment in estimating 3 year relapse rate. Inclusion criteria: age ≥ 18 years, adenocarcinoma of the colon, stage II,no neoadjuvant systemic therapy, no synchronous tumors, fresh tumor sample, and written informed consent. The treatment of the patient is at the discretion of the physician.

Results: The trial started in Sept. 2008 with currently 26 participating sites in 11 countries. So far, 223 stage II patients have been enrolled of whom 183 are eligible. 11 patients were rejected because of prior malignancies; 24 patients were rejected based on low tumor content of the sample (< 30% tumor cells), 3 patients had rectal cancer and 2 synchronous tumor.

Conclusions: The aim is to enroll 600 stage II patients to differentiate between 3 year relapse- free survival predicted by ColoPrint versus clinical factors.

[Table: see text]

Basal-, Luminal-, and HER2- Molecular Subtype, and the MammaPrint 70-Gene Signature as Predictors of Response to Neoadjuvant Chemotherapy (NCT) with Docetaxel, Doxorubicin, Cyclophosphamide (TAC), or AC and Nab-Paclitaxel and Carboplatin +/- Trastuzumab in Patients (Pts) with Stage II-III and Inflammatory Breast Cancer (BC)

Background: Pathologic complete response (pCR) and minimal residual cancer burden (RCB scores of 0 [pCR]-1[near CR]) after NCT may predict for improved survival (Symmans et al. J Clin Oncol 25:4414-22, 2007). Hence, improved NCT regimens in conjunction with molecular markers that predict for both response and/or resistance are needed. Materials and Methods: 115 pts with stages II-III BC were to be prospectively randomized to receive 6 cycles of docetaxel 75 mg/m2, doxorubicin 50 mg/m2, cyclophosphamide 500 mg/m2 with filgrastim support (TAC, arm A) versus a novel regimen of A 60 mg/m2 and C 600 mg/m2 given every 2 weeks x 4, followed by 3 weekly doses of carboplatin (AUC 2) and nab-paclitaxel 100 mg/m2 repeated as 28 day cycles x 3 (arm B). Pts with HER2 + BC received NCT similar to arm B, but with the addition of 12 weekly doses of trastuzumab given together with carboplatin and nab-paclitaxel (arm C). Core biopsies were performed prior to NCT and were preserved fresh frozen. 70-gene (MammaPrint™) profiling and 80-gene profiling (van de Vijver et al. NEJM 347:1999-2009, 2002) to categorize all tumors for basal-, HER2-, and luminal subtypes were carried out. We set out to assess the predictive value of Mammaprint scores (poor vs. good), as well as basal, vs. luminal, vs. HER2 molecular subtype profiling, for response to treatment on arms A vs. B vs. C. Responses were dichotomized as complete or near complete response (Symmans RCB scores of 0-1) vs. suboptimal response (RCB score &gt; 1). Results: Sufficient amount of BC tissue and good quality RNA for gene array assessment were procured in 64% of the first 90 patients who have undergone pre-treatment core biopsies, and then proceeded to NCT, followed by definitive surgery. Here we report on the first 50 pts with complete set of data analyzed. The median age was 50 years (range:31-69). Pts were treated for stage II (49%) and III locally advanced (41%), and inflammatory BC (10%). By gene profiling, 28% of the tumors were HER2-type (vs. 38% by IHC 3+, or FISH, representing all pts treated on arm C), 26% basal-type, 42% luminal-type, and 4% borderline luminal-type. Poor-prognosis signature by the 70-gene (MammaPrint) assay was observed in 74% of pts: 92% of HER2-type, 100% of basal-type, and 52% of luminal-type tumors were characterized as poor-risk by the 70-gene assay. Following NCT, Symmans RCB scores of 0-1 were observed in 71% of pts with HER2-type, in 38% with basal-type, and 28% of pts with luminal-type molecular subtype characteristics. Conclusion: BC with HER2- and basal-molecular subtypes are more likely to respond to NCT and is frequently associated with poor-risk characteristics as determined by the 70-gene assay. The complete analysis of correlations among response to specific sets of NCT, molecular subtype, and 70-gene assay results in the entire pt population will be presented.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2026.

Outcome prediction by the 70-gene profile in the context of the National Comprehensive Cancer Network (NCCN) guidelines

535

Background: According to the NCCN consensus guidelines molecular profiling for breast cancer prognosis may be used in patients with ER-positive, Her2-negative and LN-negative disease. Current proposed NCCN clinical risk assessment suggests adjuvant treatment for the majority of these patients. The 70-gene profile (MammaPrint) is validated as an independent prognostic indicator for patients with lymph node-negative and positive disease. Prognosis prediction by MammaPrint may be more suitable to indicate who needs adjuvant chemotherapy in addition to endocrine therapy. Methods: 566 tumor samples of women with ER-positive, Her2-negative and LN- negative breast cancer from 5 previously reported studies were analyzed and classified by MammaPrint as good or poor prognosis. 10-year breast cancer-specific survival (BCSS) was analyzed according to MammaPrint and the NCCN guidelines. Results: Median follow-up was 3.5 years (range 0.1–21.1). 380 of 566 patients (67%) were classified as good and 186 (33%) as poor prognosis by MammaPrint. Using the NCCN guidelines, 7% were classified as low and 93% as high risk respectively. 349 patients (62%) received no adjuvant treatment, 17% received hormonal treatment only, 2% chemotherapy only and 20% both respectively. At 10 years, BCSS was 91% vs. 67% for the good and poor prognosis groups (HR 4.0 [95%CI 2.0–7.9], p<0.001) whith MammaPrint risk assessment. If the NCCN guidelines were used, BCSS was 86% vs. 83% for the low and high risk groups (HR 1.11 [0.3–4.6), p=0.888). In multivariate analysis, adjusted for known prognostic factors and adjuvant therapy, only MammaPrint and histological grade were independent predictors for 10-year-BCSS with HRs of 2.8 (1.3–6.1, p=0.008) and 1.9 (1.1–3.1, p=0.015), respectively. Conclusions: MammaPrint is a strong and independent prognostic indicator in ER-positive, Her2-negative, LN-negative breast cancer and is discordant in 62% of cases when compared with the NCCN guidelines. MammaPrint identifies approximately 66% of NCCN high risk patients as having a good prognosis. Integration of MammaPrint into clinical risk assessment and adjuvant treatment selection can provide a large benefit for management of patients with endocrine-responsive early breast cancer.

[Table: see text]