Abstract P2-08-57: A biologic signature to predict ipsilateral breast event risk at 10 years for early breast cancer

Background

Outcomes for women with early breast cancer have continually improved. A biologic signature to identify those patients that have elevated ipsilateral breast event (IBE) risk after breast conserving surgery (BCS) treated with or without radiation therapy (RT) is needed. More aggressive systemic or surgical options may be warranted for patients with elevated risk while BCS alone may be an option for very low risk patients. We report early results for a biologic signature interrogating critical pathways.

Material and Methods

This study includes patients from Uppsala University Hospital and Västerås Hospital diagnosed with early breast cancer, 20mm or less, treated surgically between 1987 and 2004. Women with lymph node metastases or treated with mastectomy or chemotherapy were excluded. A panel of biomarkers (HER2, PR, Ki67, COX2, p16/INK4A, FOXA1 and SIAH2) were assayed and scored in PreludeDx's CLIA lab by board-certified pathologists. There were 171 eligible patients with biomarker data; 131 received RT and 9 received hormone therapy.

Risk groups were calculated using biomarkers and clinical factors age and size. Absolute 10-year IBE risk was assessed using Kaplan-Meier survival analysis. Hazard ratios (HR) were determined using Cox proportional hazards analysis.

Results

There were 49 IBEs recorded. The biologic signature classified 41% of women into a low risk group. Patients in the elevated risk group had a significantly increased risk of 10-year IBE compared to those in the low risk group (Table 1). The HR for elevated vs. low risk group was 5.0 [2.2-11], p<0.001, in a multivariate analysis of risk group and RT. Patients in the elevated risk group treated with BCS and RT had an 18% apparent risk difference in 10-year IBE. Patients in the low risk group had similar low 10-year risks of IBE, when treated with BCS, with or without RT. The low risk women had somewhat increased prevalence of low grade tumors (58% vs. 41%). Women with low grade and small tumors (up to 10mm) were classified into both risk groups (54% low vs. 38% elevated risk).

Table 1:10-year Risks of Local Recurrence by Risk GroupBCS without RTBCS plus RTN10-Yr local IBE Risk, 95%CIn10-Yr local IBE Risk, 95%CIBaseline4028%, [11% – 31%]13122% [12% – 24%]Low Risk Group196% [0%-14%]516% [0%-12%]Elevated Risk Group2149% [20%-68%]8031% [21% - 41%]

Discussion

A biologic risk signature identified early breast cancer patients with low and elevated 10-year IBE risks for women treated with BCS with or without RT and no chemotherapy. Approximately 40% of women were classified into a low risk group with a 0.5% IBE risk per year. Women in the elevated risk group had 3% to 5% IBE risks per year depending on treatment. Treatment for women in this observational study was neither randomized nor strictly rules based. With further prospective validation, the biologic signature identified herein may provide a tool enabling improved management for women diagnosed with early breast cancer.

Citation Format: Bremer T, Savala J, Leesman G, Wärnberg F, Sund M, Wadsten C, Whitworth PW. A biologic signature to predict ipsilateral breast event risk at 10 years for early breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-57.

Abstract GS5-08: A validation of DCIS biological risk profile in a randomised study for radiation therapy with 20 year follow-up (SweDCIS)

Background: Women diagnosed with ductal carcinoma in situ (DCIS) and their physicians need tools that assess individualized risk and predict treatment benefit. A DCIS biologic signature was previously validated in an observational study at Kaiser Permanente NW. We evaluated the results of the signature for predictive utility in a national randomized clinical trial (SweDCIS) by assessing the 10-year benefit of adjuvant radiotherapy (RT) on ipsilateral breast event (IBE) and invasive breast cancer (IBC) risks.

Methods: The signature was validated in a prospective-retrospective study in women from the SweDCIS trial (n=1046) performed by the Swedish Breast Cancer Group. Women were treated with breast conserving surgery (BCS) between 1987-1999 and randomized to RT or no RT. A central pathology review of paraffin embedded tissue blocks (n=873) was performed at Uppsala University (UU). Freshly cut slides were provided to PreludeDx for biomarker testing. Extended follow-up of SweDCIS was published in 2014.

A panel of biomarkers (HER2, PR, Ki67, COX2, p16/INK4A, FOXA1 and SIAH2) were assayed and scored in PreludeDx's CLIA lab by board-certified pathologists. Continuous Decision Scores (DS) were calculated with the biologic signature using the biomarker and clinical factors (age, size, margin, and palpability) blinded to patient outcome. The DS results were provided to the Uppsala Regional Cancer Center for analysis. A predefined and co-developed statistical analysis plan was executed. Absolute 10-year RT benefit was assessed using Kaplan-Meier survival analysis. Hazard ratios (HR) were determined using Cox proportional hazards analysis and the interaction of the DS and RT benefit was assessed.

Results: Complete biomarker and clinical information was available in 584 women. In women with clear margins (n=506), 78 IBEs, including 31 IBCs, were recorded within 10 years of diagnosis. The multivariate analysis of DS (0-10 unit scale) and the RT interaction was significant for risk of IBC (p=0.048) and IBE (p<0.001) at 10 years. The DS defined an elevated risk group (>3) for which there was pronounced 10-year benefit of RT (p=0.01) with an absolute risk reduction of 9% for IBC (Table 1). The corresponding low risk group (≤3), which included 48% of all patients, demonstrated no significant RT benefit (p=0.70) with an absolute risk reduction of 1%. The continuous DS variable was correlated with IBE risk, HR 1.49/per 5 units 95%CI[1.02,2.18] (p=0.038), in addition to the RT benefit for IBE in low (p=0.04) and elevated (p<0.001) risk groups.

Table 1. 10-year RT benefit in women from the SweDCIS trial.DS Risk GroupsIBC eventsIn Situ or IBC eventsnAbsolute RT-benefitHR [95%CI] Absolute RT-benefit HR [95%CI]Low Risk Group (DS≤3)2431%0.83 [0.32, 2.16]9%0.48 [0.24-0.97]Elevated Risk Group (DS>3)2639%0.24 [0.08, 0.73]17%0.31 [0.17-0.59]

Discussion: Evaluation of the SweDCIS trial validated prognostic and RT predictive utility of the biologic signature. Women diagnosed with DCIS and treated with BCS±RT were stratified into clinically relevant low and elevated risk groups (≤3 vs >3). Women in the elevated risk group had twice the treatment benefit for IBC from RT compared to prior randomized trials, while the low risk group had no benefit from RT.

Citation Format: Wärnberg F, Garmo H, Folkvaljon Y, Holmberg L, Karlsson P, Sandelin K, Linke S, Lyle S, Simin K, Leesman G, Barry T, Savala J, Whitworth P, Bremer T. A validation of DCIS biological risk profile in a randomised study for radiation therapy with 20 year follow-up (SweDCIS) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS5-08.

Abstract S5-01: DCIS biological risk profile predicts risk of recurrence after breast conserving surgery in a Kaiser Permanente NW population

Background: Patients with DCIS and their physicians need tools that provide better information about the individual patient's biological risk profile to help make treatment decisions. Prelude and the Kaiser Permanente Northwest Center for Health Research (KPCHR) validated a biological risk signature based test to assess ipsilateral breast event (IBE) risk after breast conserving surgery (BCS) with radiation (+RT) or without radiation therapy (-RT).

Methods: The Prelude DCIS test was independently validated in a retrospective cohort from the Kaiser Permanente Northwest (KPNW) integrated healthcare system in patients diagnosed with DCIS from 1990- 2007 and treated with BCS±RT(n=608). KPCHR performed central pathology review to identify patients meeting study eligibility criteria with formalin fixed paraffin embedded (FFPE) tissue samples (n=475); KPCHR also reviewed medical records to collect patient, treatment, and outcome data. FFPE patient samples were provided to Prelude for testing. REMARK guidelines were followed.

A panel of biomarkers (HER2, PR, Ki-67, COX2, p16/INK4A, FOXA1 and SIAH2) were assayed by the Prelude CLIA lab and scored by board-certified pathologists (n=455). Prelude's DCIS test was executed independently using biomarker and clinicopathologic data while blinded to patient outcome data. The risk results were provided to KPCHR under a Data Transfer Authority. KPCHR biostatisticians executed a predefined and co-developed statistical analysis plan. IBE rates were assessed using Kaplan-Meier survival analysis. Hazard ratios (HR) were determined using Cox proportional hazards analysis, with RT as a covariate.

Results: The Prelude DCIS test score was statistically associated with total IBE as a continuous linear variable (0-10 unit scale) on a per unit basis, HR of 1.12, 95% CI [1.03,1.23], p=0.01. The DCIS test score (0-10) corresponded to recurrence risks ranging from 10% to 42% (≤2, >7) for patients treated with BCS-RT and ranging from 4% to 11% (≤2, >7) for patients treated with BCS+RT. Patients treated with BCS ±RT with an elevated test score (≤3 vs >3) had a higher recurrence risk, n=455, HR=1.87 [1.03 - 3.38], p=0.04. In patients treated with BCS-RT in this sample, patients with a higher DCIS signature had an elevated recurrence risk, n=78, HR=2.37, 95% CI [0.82, 6.85], p=0.11. The 10-year contralateral breast event rate was 4%, 95% CI [2%, 6%]. Median follow-up time was 10.4 years.

Discussion: Patients diagnosed with DCIS and treated with BCS ±RT, were stratified into clinically relevant low and elevated risk groups (≤3 vs >3) in an independent validation of the Prelude DCIS test. Patients in the elevated risk group had substantially higher likelihood of 10-year total IBE. The number of patients treated with BCS -RT was limited and while the stratification by risk group for BCS -RT was in the expected direction, it did not reach statistical significance. Two additional validation studies are scheduled to be completed in 2016.

10-YEAR IBE RISKBCS –RTBCS +RTRisk, [95% CI]PrevalenceNRisk, [95% CI]PrevalenceNBaseline Total Risk20%, [12%, 32%]100%788%, [5%, 11%]100%377Low Risk Group (≤3)10% [3%, 29%]53%415%, [2%, 10%]40%149Elevated Risk Group (>3)30%, [17%, 51%]47%3710%, [6%, 15%]60%228

Citation Format: Bremer T, Whitworth P, Leo M, Barry T, Goldstein N, Ganders C, Francisco M, Leesman G, Linke S, Patel R, Pellicane J, Weinmann S. DCIS biological risk profile predicts risk of recurrence after breast conserving surgery in a Kaiser Permanente NW population [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 S5-01.

P3-18-04: Pathway Guided Selection of Targeted Inhibitors for Breast Cancer Treatment

Background: The ability to functionally profile a whole spectrum of pathway proteins in tumor may provide valuable information about the likelihood of drug response and potential mechanisms for drug resistance in breast cancer (BCA) patients. Here we report a comprehensive pathway analysis of membrane associated kinases such as HER1, HER2, HER3, cMET, IGF1R, PI3K and downstream signal transduction proteins including Shc, AKT, ERK, MEK, PDK1, PRAS40, p70S6K and eIF4e in breast cancer cell lines and xenografts as in response to inhibitors targeting the Her1/Her2 and PI3K/AKT and MAPK pathways. For comparison we also analyzed NSCLC lines driven by other receptor tyrosine kinases like EGFR and MET. Methods: Lysates prepared from KPL4 cells and MCF7 cells both harboring PIK3CA mutations (with HER2−amplification and low level HER2 expression, respectively) treated with 6 inhibitors (an allosteric AKT inhibitor, Lapatinib, Regorafenib, MET inhibitor, an allosteric MEK inhibitor or PI3K inhibitor) targeting PI3K/AKT and MAPK pathways were analyzed for modulations of pathway protein phosphorylation using a multiplexed immuno-micorarray.

Tissue lysates prepared from KPL4 xenografts treated with AKT inhibitor were analyzed for pathway modulation in response to the drug treatment. The pathway activation profile shift in response to drug treatments in BCA models are compared to other tumor type models with diverse oncogenic backgrounds.

Results: The level of phosphorylated AKT (pAKT) was reduced when MCF7 cells were treated with AKT inhibitor as well as PI3K inhibitor. However, compensatory AKT activation was observed when these cells were treated with BRAF or MEK inhibitor. KPL4 cells also showed reduction of pAKT when treated with Lapatinib, AKT inhibitor or PI3K inhibitor. Compensatory hyper-phosphorylation of ERK (pERK) was observed in both cell lines and KPL4 xenografts with AKT inhibitor treatment while PI3K inhibition did not induce hyper-ERK phosphorylation. Reduction of pERK level was observed when both cell lines were treated with MEK inhibitor. Downstream analytes like PRAS40 and RPS6 summarize PI3K/AKT pathway activity and correlate well with response to treatment whereas eIF4e is a good final readout for activity in the RAS/RAF/MEK/ERK pathway. Treatment with single agents often even shows adverse profile shift through feedback or pathway cross-talk. The comparative analysis of pathway modulation in BCA models to other tumor types in response to drug treatments revealed several adaptive drug resistance mechanism with different oncogenic backgrounds.

Discussion: Evaluation of drug specific pathway modulations in cancer cells provided comprehensive information on efficacy of specific agents on target protein and pathway inhibition. Multiplexed pathway analysis provides valuable information for drug resistance mechanisms due to either redundant pathway activation, cross-talk or through feedback mechanism and may guide appropriate selection of targeted drug-combinations or drug-sequencing in clinical setting. For example, the observed increase in ERK phosphorylation due to AKT inhibition could be blocked by combination therapy with a MEK inhibitor.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-18-04.

Abstract P2-06-13: Pathway Profiling of Signal Transduction Proteins in Paired Tumor and Adjacent Normal Tissues Obtained from Breast Cancer Patients

Background: Targeted therapeutic strategies are currently limited to patients with hormone receptors and/or HER2 positive disease in breast cancer (BCA) treatment. However, patients often develop resistance to these therapies. The ability to functionally profile a whole spectrum of pathway proteins (and their variants) in tumor may provide valuable information about the potential mechanism for drug resistance and evidence for rational selection of suitable targeted therapies. Here we report a comprehensive profile of HER1, HER2, p95HER2, HER3, cMET, IGF1R, PI3K, Shc, AKT and other signal transduction pathway proteins in BCA tissues and their matched adjacent normal tissues (ANTs). Methods: A multiplexed Collaborative Proximity ImmunoAssay (COPIA), antibody-microarray platform requiring co-localization of 2 detector antibodies on captured biomarker proteins has been used for comprehensive pathway analysis. Channeling events between 2 detector enzymes (glucose oxidase & horse radish peroxidase) in proximity enabled the profiling of the target biomarkers with extreme sensitivity and specificity, and a direct comparison to electrochemiluminescence based immunoassay platform (MSD) was performed for pathway proteins in tumor vs. ANTs for their expression and activation in samples collected from 20 BCA patients. Results: Three dilutions of lysate (10ug, 1ug, 0.1ug) were analyzed for quantitative differential pathway modulation for COPIA.

- Substantially higher cytokeratin (CK) levels were found in 16/20 tumor samples when compared to paired-ANT; 3/20 samples showed high levels of CK in ANTs. Substantial levels of HER3 and IGF1R expression was detected in 9 and 5 tumor samples respectively.

- Over-expression of HER2 with high degree of activation was found in 2 patients. In one of the HER2-overexpressing patients, HER3 was also highly expressed and moderately phosphorylated. Co-expression of cMET and IGF1R was evident as well.

- A significant degree of HER2 phosphorylation was found in many patients with low level HER2 expression; this may be due to co-expression of high level of HER3 and other RTKs with trans-activational potential. Evidence of activated PI3K complex will be reported.

- In direct comparison to MSD, COPIA detected activated pathway proteins in samples that were not detectable with MSD. MSD was sensitive enough to detect the very extreme cases. COPIA appeared to be a more desirable method for detection of protein expression and activation for samples with limited availability. The distinct pathway modulation in each patient (detected by COPIA) will be reported.

Discussion: COPIA was used to detect the differential expression and phosphorylation of HER2, other RTKs and pathway proteins in 20 paired tumor and matched ANTs. As this platform requires magnitudes lower amounts of specimen, it can be used to profile tumors at different metastatic sites and could provide comprehensive metastatic profiles. The comprehensive functional pathway profiling of tumor specimen may provide insightful information for potential drug-resistant mechanisms and may guide appropriate selection of targeted drug-combinations or drug-sequencing.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-06-13.