Nature or Nurture: Can Prey-Based Diets Influence Species-Specific Physiological Performance Traits of Epidermal Lipid Content and Cutaneous Water Loss?

Epidermal lipids serve as the primary barrier to cutaneous water loss (CWL) and play a significant role in water conservation and homeostasis. Previous studies have shown the correlation between increased aridity of habitats and the amount of epidermal lipids among species. Generally, increased amounts of epidermal lipids lower skin permeability. Species-specific differences in CWL and prey preferences between two sympatric snake species, the Northern Cottonmouth (Agkistrodon piscivorus) and the Eastern Copperhead (Agkistrodon contortrix), motivated us to question if prey-base can result in these observed species-specific differences in CWL. We experimentally controlled the diets for a captive colony of Northern Cottonmouths (A. piscivorus) by feeding either fish (Notemigonus crysoleucas) or mice (Mus musculus) to investigate if diet can affect the quantity and quality of epidermal lipids and the rates of CWL. Snakes fed mice gained consistently more mass, but diet treatments did not affect growth rate. We found no significant differences in quantitative lipid content or rates of CWL between diet treatments. An analysis for qualitative lipid content using infrared spectrophotometry also showed no diet effect, thus suggesting that lipid content and CWL are strong species-specific physiological performance traits not influenced by recent dietary history. While there is some evidence that epidermal permeability may be variable under certain environmental conditions (e.g., humidity), our findings show that diet has no effect and that a shift in prey preference may not influence or enhance physiological performance for decreasing CWL.

Abstract P2-03-03: A multicenter clinical study of Xpert® breast cancer STRAT4 demonstrates high concordance with central lab ER, PgR, HER2, and Ki67 IHC and HER2 FISH tests in FFPE breast tumor tissues

The Xpert® Breast Cancer STRAT4 (STRAT4) is a CE-IVD marked, semi-quantitative, cartridge-based RT-qPCR assay for the detection of ESR1, PGR, ERBB2 (HER2), and MKi67 mRNAs from formalin fixed, paraffin embedded (FFPE) breast tumors. The assay is fast (< 2 hrs), reproducible, robust, and easy to perform.

The aim of this multicenter clinical study was to assess the performance characteristics of the STRAT4 assay relative to central lab immunohistochemistry (IHC) for ER, PgR, HER2, and Ki67 and to fluorescence in situ hybridization (FISH) for HER2 gene amplification.

Methods: A total of 200 archived primary invasive breast cancer FFPE blocks were sourced from Indivumed for this study. From each block, twelve (12) adjacent tissue sections (4-µm thickness) on slides were prepared for pathological H&E confirmation to define tumor area, and for testing by STRAT4, IHC (ER, PgR, HER2,Ki67), and HER2 FISH. Standard STRAT4 lysate preparation using a single unstained slide per specimen and testing on N=84, N=68, and N=48 samples was performed at 3 independent sites, respectively (2 US and 1 EU). A single slide from each specimen was also processed using the recommended concentrated lysate procedure for STRAT4 testing at Cepheid. All IHC and FISH testing was performed by a central academic reference laboratory in the US. For a given sample, STRAT4 data generated using the standard lysate procedure was included for concordance analysis when all target gene test results were valid. In cases where the standard lysate preparation yielded indeterminate test results for any target, data from the concentrated lysate preparation was used for the data analysis. Receiver Operating Characteristic (ROC) analysis, overall percent agreement (OPA), positive percent agreement (PPA), and negative percent agreement (NPA) between STRAT4 and IHC (IHC/FISH for HER2) were determined for ESR1,PGR, ERBB2, and MKi67.

Results: Of the 200 samples tested by STRAT4, all samples generated valid results for ESR1 and ERBB2, 199 of 200 samples were valid for PGR, and 198 of 200 samples were valid for MKi67 using the standard or concentrated lysate preparation protocol. One sample failed to generate results for both ER and PgR IHC. Twelve samples failed to yield HER2 FISH results.

The STRAT4 success rate and results concordance with IHC were comparable across study sites. OPA between STRAT4 and IHC was 97% for ESR1, 88.9% for PGR, 93.3% for HER2 (92.4% for IHC and FISH), and 90.7% for MKi67 (excluding IHC 10-20% staining). Areas under the ROC curves were 0.9922 for ESR1, 0.9509 for PGR, 0.9958 for ERBB2, and 0.9395 for MKi67.

Conclusion: STRAT4 measurements for ESR1, PGR, ERBB2 and MKi67 mRNA expression are robust and highly concordant with IHC (IHC/FISH for HER2). The technical portion of the assay is easily performed in < 2 hrs including hands-on time using standard FFPE tissue sections. Xpert STRAT4 offers local pathology labs an alternative to centralized, subjective IHC/FISH tests that require a higher level of expertise. Further investigations correlating STRAT4 markers directly with clinical outcomes in independent cohorts are in progress.

Citation Format: Wu NC, Wong E, Acca B, Birkmeier J, Tran L, Zhao S, Wong W, Chu VC, Ho K, Malek M, Lu C, Ge G, David K, Quigley NB, Beqaj SS, Davenport S, Weidler J, Bates M, Press M. A multicenter clinical study of Xpert® breast cancer STRAT4 demonstrates high concordance with central lab ER, PgR, HER2, and Ki67 IHC and HER2 FISH tests in FFPE breast tumor tissues [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-03.

Abstract P6-03-07: An automated DNA methylation assay (QM-MSP) for rapid breast cancer diagnosis in underdeveloped countries

BACKGROUND: Underdeveloped countries reported 882,900 new cases of breast cancer and 324,000 deaths in 2012, likely to be a gross underestimation according to recent reports. Often, mammography screening is not available, primary care services are limited, and pathology and treatment services are available only in the regional hospitals. Because of the lack of access to diagnostic and treatment services, it is estimated that more than 90% of patients with breast cancer never present for medical treatment. To address this situation, an accurate, easy-to-perform diagnostic test appropriate for use in remote clinics is desperately needed. Johns Hopkins (JH) and Cepheid partnered to translate a robust Quantitative Multiplex Methylation-Specific PCR (QM-MSP) assay to an automated, cartridge-based system that provides quantitative measures of DNA methylation within hours of fine needle aspiration or core biopsy of image-detected suspicious lesions.

METHODS: With a goal of discriminating malignant from benign breast disease with high sensitivity and specificity, we evaluated 24 breast cancer-specific DNA methylation markers (selected through comprehensive methylome analysis) in 119 invasive ductal carcinomas and 186 benign breast tissues. QM-MSP was performed on sections of formalin-fixed paraffin-embedded (FFPE) tissues to quantify DNA methylation. The dynamic range and performance of quantitative methylation detection was tested using a subset of 9 genes in the cartridge-based system.

RESULTS: QM-MSP was performed in a Training set consisting of 93 tissues [n=43 IDC, n=50 benign lesions (25 usual ductal hyperplasia, UDH, and 25 papilloma)] from the US. We selected 9 DNA markers significantly (p<0.05) more methylated in malignant compared to benign lesions, which had low or no methylation. An independent Test set consisted of benign (n=26) and malignant (n=10) tissues (mostly Caucasian; JH Test Set). As a panel, the 9 markers were significantly more methylated in malignant than benign tissue (p<0.001), revealing a sensitivity of 90% and specificity of 92%, using a laboratory cutoff of 9.5 CMI units (900 unit scale) based on receiver operator characteristic statistics (ROC; p<0.0001, AUC=0.977). To determine if the markers characterized in the JH Test Set could perform as well in samples from a different geography, the panel was tested on 176 tissues from Wuhan, China (China Test Set). In this cohort (66 IDC and 110 benign tissues - 49 fibroadenoma, 19 benign cyst, 12 UDH, 30 papilloma), sensitivity was 89% and specificity was 89% for detection of breast cancer with ROC AUC=0.945. An advanced version of the cartridge with up to 12 methylated DNA markers is under development, thus far showing robust signals in cancer and low background in benign tissues. Current work at JH is focused on optimizing the technical performance of the cartridge.

CONCLUSIONS: We identified a panel of methylated DNA markers that discriminate malignant from benign breast lesions and built a prototype automated cartridge-based assay with promising sensitivity and specificity for breast cancer. Such an assay has the potential to aid in specimen triage in the pathology lab and provide fast, low cost and accurate diagnosis of breast cancer in LMIC settings.

Citation Format: Fackler MJ, Downs BM, Mercado-Rodriguez C, Cimino-Mathews A, Chen C, Yuan J, Cope LM, Kohlway A, Kocmond K, Lai E, Weidler J, Visvanathan K, Umbricht CB, Harvey S, Wolff AC, Bates M, Sukumar S. An automated DNA methylation assay (QM-MSP) for rapid breast cancer diagnosis in underdeveloped countries [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 P6-03-07.

Abstract P2-03-02: Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer

Background: An on-demand, closed system RT-qPCR (the GeneXpert system, Cepheid, Sunnyvale, CA) has the potential to provide biomarker information in low resourced settings. The system consists of an inexpensive, single-use, disposable, macrofluidic cartridge and an instrument that automates RT-qPCR. Here we use it with a research use only cartridge (STRAT4) that measures the mRNA expression levels of ESR1, PGR, ERBB2, and MKi67 using a single 5uM thick FFPE tissue section from an excisional or core biopsy specimen containing invasive carcinoma of the breast. The assay, results are expressed as a delta cycle threshold (dCt) value, defined as the Ct of a control gene (CYFIP1) minus the Ct of the target gene (ESR1, PGR, ERBB2, or MKi67). We determine whether the dCt result for each marker is equivalent using the entire non-macrodissected section (non m-d) to the dCt results obtained following tumor macro-dissection (m-d) to eliminate non-tumor elements from the assay.

Methods: We evaluated the impact of m-d versus non m-d using STRAT4 on a cohort of 62 formalin-fixed paraffin-embedded (FFPE) tumor core needle biopsy specimens with a range of HER2 expression determined by clinical immunohistochemistry and fluorescence in situ hybridization (IHC/FISH). Concordance (sensitivity and specificity) of the STRAT4 ESR1 and HER2 mRNA versus ER and HER2 IHC/FISH measurements were also assessed.

Results: We observed excellent agreement of the resulting dCt between the paired samples, m-d versus non m-d, for ESR1 (R2=0.92), PGR (R2=0.90), ERBB2 (R2=0.94) and MKi67 (R2=0.90). No significant difference (P value > 0.99) was observed when we compared the dCt between the paired samples m-d versus non m-d. In addition, using the predefined STRAT4 dCt cutoff for ESR and ERBB2 positivity, we found a significant concordance between RT-qPCR and IHC/FISH for ESR-positivity for the paired samples, m-d (P value < 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) versus non m-d (P value < 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) and HER2-positivity for the paired samples, m-d (P value < 0.001; sensitivity = 0.85; specificity = 0.98; PPV = 0.92; NPV = 0.96) versus non m-d (P value < 0.001; sensitivity = 0.71; specificity = 0.98; PPV = 0.90; NPV = 0.92), respectively.

Conclusion: These data suggest that mRNA for ESR and ERBB2 is sufficiently low in surrounding tissues that m-d of whole sections is not required for accurate assessment of key breast cancer mRNA markers in a closed system RT-qPCR assay. The simplicity of the assay workflow may be particularly valuable in low resourced settings where routine access to pathology expertise and to high quality IHC/FISH is challenging.

Citation Format: Gupta S, Carvajal-Hausdorf DE, Wasserman BE, Ho K, Weidler J, Wong W, Rhees B, Bates M, Rimm DL. Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-02.

Abstract P1-03-03: High concordance of ER, PR, HER2 and Ki67 by central IHC and FISH with mRNA measurements by GeneXpert® breast cancer stratifier assay

Current methods for the assessment of ER, PR, Her2, and Ki67 using FFPE tissues are hard to standardize and difficult to perform in Low and Middle Income Countries (LMIC). The GeneXpert® breast cancer stratifier assay (RUO) (BC Strat) is a cartridge-based, RT-qPCR assay of ESR1, PGR, ERBB2, and MKi67 mRNAs using FFPE specimens. The assay is fast (<2 hours, including <10 minutes of hands-on time) and easy to perform.

The aims of this study were: 1) to evaluate the concordance of BC Strat using different IHC antibodies and scoring methods in a preliminary dataset (Part I); and 2) to assess concordance between BC Strat and high quality standard methods in an expanded dataset (Part II).

Methods

Part I: IHC Antibody Variability

To assess BC Strat concordance with various IHC antibodies, 155 invasive ductal carcinoma blocks were sourced from 3 sites. Twenty-four adjacent slide sections from each block were prepared and shipped to different labs for BC Strat analysis(Cepheid) or IHC and FISH testing. Table 1 summarizes the IHC antibodies and scoring methods used in each reference lab.

Table 1:IHC antibodies and scoring methods used in reference labs Antibody for IHClabIHC scoringERSP1MPLNAutomated (Aperio)ER6F11Path IncAutomated (Aperio)ER6F11USCManualPRIE2MPLNAutomated (Aperio)PR16Path IncAutomated (Aperio)PRPGR636USCManualHer2*4B5MPLNAutomated (Aperio)Her2*HercepTestUSCManualKi6730-9MPLNAutomated (Aperio)Ki67MIB1Path IncAutomated (Aperio)Ki67MIB1USCManual*HER2 FISH (all with PathVysion kit) was performed at USC

Part II: Concordance Study

522 invasive ductal carcinoma FFPE samples were sourced from 5 sites. All BC Strat analysis was performed at Cepheid and all IHC and FISH was performed in the Press laboratory at USC. Overall percent agreement (OPA), positive percent agreement (PPA), and negative percent agreement (NPA) between BC Strat and IHC were determined.

Results

Part I: IHC Antibody Variability

Table 2 summarizes the OPA for BC Strat analysis and IHC performed with different IHC antibodies and scoring methods. Slightly better concordance for ER and PR was observed between the BC Strat and the IHC methods performed at USC. Discordant IHC results were also observed among the reference labs' standard methodologies.

Table 2: Overall Percent Agreement between IHC and BC Strat Reference LabOPA with BC StratERMPLN92%ERPath Inc96%ERUSC98%PRMPLN84%PRPath Inc83%PRUSC87%Her2*MPLN*93%Her2*USC*91%Ki67MPLN75%Ki67Path Inc67%Ki67USC81%*for IHC 2+(equivocal), FISH HER2/CEP17 ratio was examined

Part II: Concordance Study

Of the 522 samples tested, 499 (96%) yielded valid results for both BC Strat and IHC (IHC and FISH for Her2). OPA between BC Strat and IHC was 98% for ESR1, 91% for PGR, 93% for ERBB2 (IHC and FISH, 97% for Her2 IHC excluding IHC2+), and 81% for MKi67.

Conclusion

BC Strat assay measurements for ESR1, PGR, ERBB2 and MKi67 mRNA expression in FFPE breast tumor tissues are highly concordant with IHC and FISH performed by high quality reference labs. Further investigations using clinical outcomes from independent studies including prospective-retrospective clinical trials are in progress.

Citation Format: Wu NC, Wong W, Ho KE, Chu VC, Rizo A, Davonport S, Kelly D, Makar R, Jassem J, Duchnowska R, Biernat W, Radecka B, Fujita T, Klein JL, Stonecypher M, Ohta S, Juhl H, Weidler JM, Bates M, Press MF. High concordance of ER, PR, HER2 and Ki67 by central IHC and FISH with mRNA measurements by GeneXpert® breast cancer stratifier assay [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 P1-03-03.

Abstract P1-03-11: Analytical validation for the RT-qPCR based multiplex mRNA measurements of ER, PgR, HER2, and Ki67 from FFPE tumor tissue using the GeneXpert breast cancer stratifier assay

BACKGROUND: Accurate assessment of ER, PgR, HER2 and Ki67 status is crucial for breast cancer therapy and patient management. Immunohistochemistry (IHC) assays have been standard diagnostic tools but they are complex and time-consuming to perform and may not be readily available in decentralized laboratories, particularly in low-to-middle income countries. Molecular diagnostics can be a sensitive and accurate alternative to the traditional IHC, and the GeneXpert Breast Cancer Stratifier assay RUO (BC Strat), a single use cartridge-based assay performed on the broadly distributed GeneXpert® Instrument (GX) platform, streamlines a technically demanding RT-qPCR process to provide easy, robust, and reproducible ESR1, PGR, ERBB2, and MKi67 mRNA measurements from a 4 µm thick, formalin-fixed paraffin embedded (FFPE) breast tumor section in less than 2 hours.

METHODS: Analytical validation of the BC Strat assay included studies of Linearity/Dynamic Range, Analytical Sensitivity (Minimum Assay Input), Specificity (Potential Interfering Substances), Carryover Contaminations, and Kit and Specimen Slide Stabilities. Both in-vitro RNA transcript (IVT) and/or clinical breast cancer tissues were used as sample input materials. Assay results for each analyte were generated from cycle threshold (Ct) values, and final positive/negative test results for each target were also reported as delta Ct values, where dCt = Ct [CYFIP1 Reference] – Ct [Target], using dCt cutoffs previously derived from a clinical sample cohort.

RESULTS: The BC Strat assay demonstrated ≥3 log Linear Dynamic Range covering 5-7 logs sample input for all 4 Target dCts with R2≥0.95 independently. The assay currently requires minimal sample input equivalent to CYFIP1 Ct≤35 (Ct=33.5 ±1.5Ct SD) from 20 replicates of 5-level serial sample dilutions using two independent assay lot materials. It is acceptably robust against non-tumor tissues, DCIS, necrotic and/or hemorrhagic cells, lymphocytes, and genomic DNA contaminants. No carryover contamination from the same GeneXpert module was observed over 20 repeat tests during 9 consecutive days. Current real-time data supports assay stability at 5, 30, 37, 45 and 50°C for at least 3 months with minimal performance impact. Sectioned FFPE breast tumor tissues generated consistent dCt results when stored at 4°C and 30°C for up to 1 month before BC Strat assay testing.

CONCLUSIONS: The analytical validations of the BC Strat assay demonstrate an easy and robust mRNA detection with high sensitivity, specificity, reproducibility, and stability in order to aid medical pathologists and clinicians to more rapidly and objectively determine ESR1, PGR, ERBB2, and MKi67 mRNA status in breast cancer. Although stability studies out to 37 months are ongoing, current data suggest the assay is stable for at least 3 months over a wide range of temperatures. The GeneXpert Breast Cancer Stratifier assay potentially offers a rapid, standardized, and cost-effective solution to streamlining complex molecular diagnostics available for use in local pathology laboratories worldwide.

Citation Format: Chu VC, Wu N, Ho KE, Rizo A, Malek M, Weidler JM, Bates M, Wong W. Analytical validation for the RT-qPCR based multiplex mRNA measurements of ER, PgR, HER2, and Ki67 from FFPE tumor tissue using the GeneXpert breast cancer stratifier assay [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 P1-03-11.

Abstract P1-03-09: Highly reproducible decentralized gene expression analysis of ESR1, PGR, ERBB2 and MKi67 on an automated, standardized molecular diagnostics platform, GeneXpert

Background: Accurate assessment of ER, PgR, HER2, and Ki67 status using FFPE samples from patients with breast cancer is critical for appropriate patient management, yet immunohistochemistry (IHC), the most common method of assessing these markers, suffers from inherent variability due to pre-analytical/analytical factors and subjective interpretation by pathologists. Here we describe the GeneXpert (GX) Breast Cancer Stratifier RUO Assay (BC Strat), a real time quantitative PCR assay (RT-qPCR) kit which exhibits robust, highly reproducible mRNA measures of ESR1, PGR, ERBB2 (HER2) and MKi67.

The aims of this study were: 1) To assess the impact of variability contributed by pathologist-to-pathologist differences in the selection of the tumor area to be assayed, inter-laboratory assay performance, and macrodissection (MAC) vs. no macrodissection (nonMAC) on decentralized BC Strat results; and 2) to assess preliminary concordance of BC Strat with central IHC and FISH results.

Materials & Methods: The GX BC Strat is a cartridge-based RT-qPCR assay performed on the GeneXpert® Instrument (Cepheid) that automates RNA purification, RT-qPCR amplification and detection of mRNA of target genes (ESR1, PGR, ERBB2, and MKi67) and a control gene (CYFIP1) after sample preparation. Results are reported as delta cycle threshold (dCt) measurements (CYFIP1 Ct - target gene Ct) in less than 2 hrs.

Thirty-two invasive ductal carcinoma FFPE blocks were sourced based on varying levels of ER, PgR, HER2, and Ki67 expression and % tumor cell content/tumor area. Adjacent sections from each block were prepared as slides and sent to 3 external GX testing sites and a reference lab. Each site used its own pathologists/technicians to determine the % tumor cell content/tumor area, perform MAC or nonMAC, prepare lysates, and perform GX testing. Reference IHC/FISH was performed by Geneuity/MPLN (Maryville, TN, USA). Site-to-site concordance in GX results for MAC or nonMAC samples using pre-defined assay cutoffs per marker were analyzed, as were % tumor cell content/tumor area assessments between pathologists.

Results: BC Strat testing of 32 FFPE breast cancer samples with MAC demonstrated excellent GX site-to-site concordance in positive/negative status calls for ESR1 (100%), PGR (100%), ERBB2 (97%), and MKi67 (97%). In most cases, MAC vs. nonMAC had minimal impact on final positive/negative calls for GX, resulting in high overall concordance for MAC vs. nonMAC for ESR1 (91%), PGR (99%), ERBB2 (99%), and MKi67 (95%). The assay also demonstrated a strong overall concordance with IHC for ESR1 (97%), PGR (81%), ERBB2 (98%, IHC/FISH), and MKi67 (89%).

Conclusion: Decentralized performance of the GX BC Strat Assay is feasible and minimally affected by differences in tumor area selection and MAC techniques across tumors with a range of sizes, invasive tumor cell contents, and expression levels of ER, PgR, HER2, and Ki67. GX BC Strat dCt results across sites are highly reproducible and show good concordance of results with central lab IHC and HER2 FISH results. These results suggest standardized, decentralized testing of ESR1, PGR, ERBB2 and MKi67 by the GX BC Strat in local pathology labs is feasible.

Citation Format: Wong W, Ho KE, Wu N, Chu VC, Lalli P, Longshore JW, Klein J, Stonecypher M, Lykke C, Sherwood T, Davenport S, Weidler J, Bates M, Press MF. Highly reproducible decentralized gene expression analysis of ESR1, PGR, ERBB2 and MKi67 on an automated, standardized molecular diagnostics platform, GeneXpert [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 P1-03-09.

Abstract P1-03-07: High concordance of a closed system, near point of care, RT-qPCR breast cancer assay for HER2 (ERBB2) mRNA compared to both IHC/FISH and quantitative immunofluorescence

Background

Reliable assessment of HER2 receptor status in breast cancer by either IHC or FISH does not unequivocally define receptor expression, due to their semi-quantitative nature, and as many as 10-15% of cases fall into the ASCO/CAP “equivocal” category. Historically, RNA measurements by PCR, including using several commercially available platforms, have been tested, but have not gained broad acceptance for assessment of HER2. However, RNA measurement, as a continuous value, has potential for use for adjudication of the equivocal category. In the current study, we used a real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay (GeneXpert® Breast Cancer Stratifier RUO Assay, Cepheid, Sunnyvale, CA, USA) for ERBB2 (HER2) mRNA on the GeneXpert® (GX) platform (Cepheid), which utilizes a closed-system, single-use cartridge, automated system. The RT-qPCR results from GX were then compared with results from clinical HER2 IHC/FISH assays following ASCO/CAP 2013 HER2 testing guidelines (Wolff et al JCO 2013) and quantitative immunofluorescence (QIF).

Methods

Multiple cores (1mm in diameter) were retrospectively collected from 80 formalin-fixed paraffin-embedded (FFPE) tissue blocks with invasive breast cancer seen by Yale Pathology Labs between 1998 and 2011. Tissue cores were processed as lysates for testing at Yale in the automated GX assay. Briefly, gene-specific reverse transcription was performed, followed by RT-qPCR (TaqMan) and ERBB2 mRNA results were expressed as the difference in cycle threshold values (delta Ct) between the endogenous control transcript (CYFIP1) and the ERBB2 mRNA transcript. Results from IHC and FISH were extracted from the pathology reports for the Yale CLIA lab and QIF for each case was measured as previously described (Carvajal et al, JNCI 2015).

Results

Quality control testing showed that the GX platform shows no case to case cross contamination on material from routine histology practices. Concordance between RT-qPCR and IHC/FISH was 91.25% (sensitivity = 0.87; specificity = 0.94; PPV = 0.89; NPV = 0.92) using a pre-defined delta Ct cut-off (dCt ≥ -1) for HER2 (+) based on prior concordance studies with HER2 IHC/FISH. Concordance between RT-qPCR and QIF was 99% (sensitivity = 0.97; specificity = 1.0; PPV = 1.0; NPV = 0.98) using dCt ≥ -1 and the pre-defined cut-point for positivity by QIF.

Conclusions

The GX closed system RT-qPCR assay shows greater than 90% concordance with the ASCO/CAP 2013 HER2 IHC/FISH scoring. Additionally, the GX RT-qPCR assay is highly concordant (99%) with the continuous variable HER2 QIF assay, and may better reflect the true continuum of HER2 receptor status in invasive breast cancer. These initial results suggest that rapid, closed system molecular assays may have future value for the adjudication of the ASCO/CAP HER2 equivocal category. This pilot study did not include ASCO/CAP 2013 “equivocal” cases, but that effort is underway.

Citation Format: Wasserman B, Carvajal-Hausdorf D, Ho K, Wong W, Wu N, Chu VC, Lai EW, Weidler JM, Bates M, Neumenister V, Rimm DL. High concordance of a closed system, near point of care, RT-qPCR breast cancer assay for HER2 (ERBB2) mRNA compared to both IHC/FISH and quantitative immunofluorescence [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 P1-03-07.

Abstract P3-07-09: Quantitative p95HER2 protein expression is predictive of trastuzumab response in HER2-positive metastatic breast cancer

Background: Expression of p95HER2 (p95), a truncated form of the HER2 receptor that lacks the trastuzumab binding site but retains kinase activity, has been reported as a prognostic biomarker for poor outcome in trastuzumab-treated HER2-positive metastatic breast cancer (MBC). However, the ability of p95 to predict trastuzumab benefit has not been demonstrated due to the difficulty in obtaining the appropriate control group, namely HER2+ MBC patients not treated with trastuzumab. In the current study, the predictive value of p95 expression was tested in a cohort comprised of HER2-positive MBC patients treated before the availability of trastuzumab and trastuzumab-treated HER2-positive MBC patients.

Methods: The current cohort was derived from 206 HER2-positive MBC patients in the Munich Cancer Registry with a median follow up of 64 months. Cases were divided between those that received trastuzumab (n=115) and those that were treated before the availability of trastuzumab (n=91). Quantitative p95 protein expression was measured in formalin-fixed paraffin-embedded samples using the p95 VeraTag® assay (Monogram Biosciences), which is specific for the active M611 form of p95. Quantitative total HER2 protein expression was measured using the HERmark® assay (Monogram Biosciences). p95 and HERmark cutoffs were pre-specified (Duchnowska, Clin Cancer Res, 20:2805, 2014 and Huang, Am J Clin Pathol, 134:303, 2010). Analyses with p95 were restricted to samples with confirmed HER2 overexpression by HERmark. All hazard ratios (HR) were stratified by estrogen receptor status and grade.

Results: Consistent with previous training (Sperinde, Clin Cancer Res, 16:4226, 2010) and validation (Duchnowska, Clin Cancer Res, 20:2805, 2014) datasets, subjects treated with trastuzumab experienced a shorter time to progression (TTP) when p95 expression levels were above the cutoff versus below the cutoff (HR = 3.8, p = 0.019). However, only a trend was observed between p95 expression levels and overall survival (HR = 2.2, p = 0.20), possibly due to a lower frequency of events and relatively small sample size. The predictive value of p95 was assessed by determining the benefit of adding trastuzumab to chemotherapy treatment in subsets below and above the p95 cutoff. As expected, patients with p95 below the cutoff experienced significant benefit in TTP from adding trastuzumab (HR = 0.13, p<0.001), whereas patients with p95 above the cutoff experienced less benefit (HR = 0.70, p=0.47). p95 expression level was predictive of trastuzumab response with an interaction p-value of 0.015. The results for OS were similar, however trastuzumab benefit was less distinct between the two groups (interaction p = 0.18); HR = 0.23, p = 0.0013 below the p95 cutoff versus HR = 0.50, p = 0.14 above the p95 cutoff.

Conclusions: In this dataset, quantitative p95 expression was predictive of trastuzumab treatment benefit in MBC. Patients with high p95 expression may be particularly good candidates for dual HER2 blockade, as reported in the NeoALTTO trial (Scaltriti, Clin Cancer Res, 21:569, 2015), or other additional therapies.

Citation Format: Sperinde J, Bachmeier B, Weidler JM, Lie Y, Chenna A, Winslow J, Engel J, Schubert-Fritschle G, Sommerhoff C, Petropoulos C, Bates M, Huang W, Nerlich A. Quantitative p95HER2 protein expression is predictive of trastuzumab response in HER2-positive metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-09.

Abstract P6-11-07: Quantitative p95HER2 levels in primary breast cancers and in matched brain metastases

Background: Patients with HER2-positive breast cancer are at high risk for brain metastases. A large number of HER2-positive tumors also express p95HER2 (p95), a truncated form of HER2 that lacks the trastuzumab binding site but retains kinase activity. Although p95 expression in primary breast tumors is well studied, the prevalence and significance of p95 expression in brain metastases is unknown. In the current study we examined expression of p95 in brain metastases and in matched primary breast tumors.

Methods: Seventy-five pairs of formalin-fixed paraffin-embedded samples from matched primary breast cancers and brain metastases were assayed for quantitative p95 protein expression using the p95 VeraTag® assay (Clin Cancer Res, 16:4226, 2010) specific for the M611 form of p95. Sufficient material to obtain p95 data in both primary and matched brain metastasis samples was available in 52 cases. In the remaining 23 cases, a p95 measurement was obtained in either the primary or brain metastasis sample. Estrogen (ER) and progesterone (PR) receptor status were scored using immunohistochemistry. Hormone receptor positivity was defined as either ER or PR positive. Quantitative HER2 protein expression was measured using the HERmark® assay. Both the p95 VeraTag assay and the HERmark assay measure tumor-averaged protein expression in units of relative fluorescence per mm2 tumor (RF/mm2). Measurements of p95 > 2.8 RF/mm2 and HER2 > 17.8 RF/mm2 were considered as positive results.

Results: There was a net increase in p95 expression in brain metastases relative to the matched primary tumor with a median increase of 1.5-fold (p = 0.001, range 0.2-fold to 35-fold). The increase in p95 expression was only weakly correlated with the increase in quantitative HER2 expression (R2 = 0.18; p = 0.0018). Cases with HERmark-positive tumors were more likely to have the largest (≥ 5-fold) increase in p95 expression compared to those with lower HER2 expression (odds ratio = 6.3; p = 0.018). Changes in p95 levels from primary to brain metastasis were unrelated to hormone receptor status (p = 0.59). P95 positivity in the primary tumor correlated with time from breast cancer diagnosis to first progression (HR = 2.2; p = 0.012) when stratified by hormone receptor status and tumor grade. Although there was a trend towards correlation of p95 positivity in the brain metastasis with time from diagnosis to brain metastasis (HR = 1.7; p = 0.058, stratified as above), p95 positivity did not correlate with overall survival from the time of brain metastasis diagnosis (HR = 1.3; p = 0.42, stratified as above).

Conclusions: This is the first study of quantitative p95 expression in matched primary tumors and brain metastases. Brain metastases of breast cancer show significant increases in p95 protein expression compared to matched primary tumors. These data provide a rationale for future correlative studies on p95 levels in brain metastases.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-11-07.

Abstract P2-10-31: Correlation of quantitative p95HER2 and total HER2 levels with clinical outcomes in a combined analysis of two cohorts of trastuzumab-treated metastatic breast cancer patients

Background: Expression of p95HER2 (p95), a truncated form of HER2 also known as p110 or M611-CTF, is a possible trastuzumab resistance mechanism and has been associated with poor prognosis in trastuzumab-treated HER2-positive metastatic breast cancer (MBC). Previously we reported on optimal clinical cutoffs for quantitative p95 (Clin Cancer Res, 16:4226, 2010) and quantitative HER2 protein expression (H2T) by HERmark® (Cancer, 116:5168, 2010) that defined patient subsets with different progression-free survival (PFS). These cutoffs were confirmed in an independent trastuzumab-treated MBC cohort (ASCO 2011, #586). Here, using individual patient data, we performed an analysis on the combined data set of 243 cases from the discovery and validation cohorts to derive optimal cutoffs for quantitative p95 and H2T.

Methods: Both quantitative H2T (HERmark, Monogram Biosciences) and p95 assays employed the VeraTag® method to quantify protein expression in formalin-fixed, paraffin-embedded tumor samples from two cohorts of 101 and 142 cases of trastuzumab-treated MBC with 7.4 and 9.2 months median PFS, respectively. All analyses were stratified by hormone receptor status, tumor grade (3 vs. 1+2) and cohort. H2T measurements were compared to pre-specified cutoffs for HERmark negative (H2T<10.5 Relative Fluorescence/mm2 tumor [RF/mm2]) and HERmark positive (H2T>17.8 RF/mm2), derived from the <5th percentile of centrally determined HER2-positives and the >95th percentile of centrally determined HER2-negatives, respectively, within a reference database of 1,090 breast cancer patient samples.

Results: Patients classified as HERmark-positive had longer PFS than those classified as HERmark-negative (HR = 0.52; p = 0.0006; medians 10.0 and 5.9 months). The previously determined optimal H2T cutoff of 13.8 RF/mm2 in the center of the HERmark-equivocal zone, gave a similar result (HR = 0.54; p = 0.0005). This was close to the optimal cutoff of 12.75 RF/mm2 (HR = 0.48; p < 0.0001, unadjusted) for the combined data set. The PFS for the small group of patients in the HERmark-equivocal zone (n = 20) was more similar to the HERmark-negatives (equivocal vs. negative: HR=0.98; p = 0.9) than the HERmark-positives (positive vs. equivocal: HR=0.57; p = 0.057). The pre-specified p95 cutoff at 2.8 RF/mm2 separated the 174 HERmark-positive cases into two groups of longer (p95<2.8 RF/mm2) vs. shorter PFS (HR = 1.9; p = 0.0014; medians 13.1 and 7.4 months). Increasing continuous p95 also correlated with shorter PFS (HR = 1.9/log; p = 0.022) in the HERmark-positive subset. An optimal p95 cutoff was identified at 2.7 RF/mm2 (HR = 2.0; p = 0.0009, unadjusted), although a slightly higher local HR maximum was found at 1.55 RF/mm2 (HR = 2.3; p = 0.0004, unadjusted).

Conclusions: HERmark positive and negative categories, defined by analytical comparison with centrally determined HER2 status, were confirmed to have significantly different PFS in trastuzumab-treated MBC patients. The optimal H2T clinical cutoff for this combined analysis was centered in the HERmark analytical equivocal zone. An optimal p95 clinical cutoff of 2.7 RF/mm2 derived from this combined analysis was nearly identical to the previously established cutoff of 2.8 RF/mm2.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-10-31.

Abstract P2-05-06: Quantitative measurement of HER2 expression in breast cancers: comparison with “real world” HER2 testing in a multi-center Collaborative Biomarker Study (CBS) and correlation with clinicopathological features

Background: Accurate determination of HER2 status is critical in determining appropriate therapy for breast cancer patients. The HERmark® assay is a novel method to quantitatively measure HER2 total protein expression (H2T) in breast cancer. In this study, we compared HERmark H2T with central laboratory HER2 retesting and local (site reported) HER2 testing of formalin-fixed, paraffin-embedded (FFPE) breast cancer tissues. The quantitative total HER2 measurements (H2T) by HERmark and results of local HER2 tests were correlated with tumor pathohistological characteristics and overall survival of breast cancer patients.

Methods: 232 FFPE breast cancer tissues were provided by 11 CBS study sites for HER2 testing by the HERmark assay and central laboratory IHC re-testing performed in blinded fashion. Local HER2 immunohistochemistry and/or fluorescence in situ hybridization (FISH) results and valid HERmark H2T and central HER2 IHC results were obtained in 192 cases for analysis.

Results: H2T showed a significant correlation with central HER2 IHC staining intensity (P < 0.0001). The concordance rates of positive and negative HERmark status (excluding equivocal) with those of local HER2 status determined by the CBS sites, and with those of central HER2 IHC status were 84% (Kappa = 0.68) and 96% (Kappa = 0.91), respectively. Higher H2T levels significantly correlated with higher tumor grade (p = 0.007) and negative ER/PR status (p = 0.002). Twenty-six (14%) cases showed discordant (conversion of negative and positive) results between local HER2 status and HERmark status. Of the discordant cases, HERmark significantly agreed with H-score of central HER2 IHC retesting (p = 0.014), as compared with local HER2 status. The concordant negative group (local HER2 negative/H2T low) demonstrated better overall survival (OS) (HR = 0.198, p = 0.0001), compared to that of concordant positive group (local HER2 positive/H2T high). The concordant negative group also showed better OS than that of discordant local HER2 negative/H2T high group (HR = 0.065, p = 0.0003), but showed no significant difference in OS as compared to that of discordant local HER2 positive/H2T low group (HR = 1.774, p = 0.499).). In 24 cases (13%) considered to be “triple negative” by local HER2, ER and PR testing, HERmark re-classified 4 cases (17%) as HER2 positive.

Conclusions: H2T by HERmark yields a continuum of quantitative HER2 protein measurements that shows an excellent correlation with central HER2 IHC retesting and confirms the known correlations between HER2 expression with tumor grade and ER/PR status. OS results of concordant HER2 positive or negative groups (between local HER2 testing and HERmark H2T) confirmed that HER2 positive patients (excluding adjuvant trastuzumab therapy) have worse OS than patients with HER2 negative disease. However, in the HERmark and local HER2 discordant groups, OS appeared to track better with H2T by HERmark and not with the local HER2 status. Novel quantitative HER2 measurements may identify patients with false (+) and (−) HER2 status by local HER2 testing and may provide added clinical value to routine “real world” HER2 testing.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-05-06.

Abstract P2-10-16: Quantitative HER3 protein expression and PIK3CA mutation status in matched samples from primary and metastatic breast cancer tissues and correlation with time to recurrence

Background: HER3 is thought to play a prominent role in resistance to HER2-directed breast cancer therapies. Recent data suggest that HER3 levels also influence HER2-normal breast tumor biology. HER3 and PI3K signaling are linked in that in HER3 signaling activates PI3K and inhibition of PI3K activity can upregulate HER3 expression. Here, we measured quantitative HER3 protein expression levels and PIK3CA mutation status in matched tissues from the primary tumor and site of metastasis to assess correlations with time to recurrence.

Methods: 44 pairs (8 HER2+ by HERmark®) of matched tissues from the primary tumor and the site of metastasis were evaluated for HER3 protein expression using a sensitive, quantitative assay for HER3 protein expression in FFPE tissue sections (VeraTag®). Matched samples were also evaluated for quantitative HER2 expression (HERmark) and for PIK3CA mutations at exon 9 (E542K and E545K) and exon 20 (H1047R).

Results: HER3 protein expression at the metastatic site was largely independent of HER3 levels at the primary site (Spearman p = 0.50) in contrast to HER2 expression (Spearman p = 0.0004). HER3 expression in the primary tumor correlated with time to recurrence (TTR) (HR = 2.0 per 2-fold increase in HER3; p < 0.0001). Conversely, HER3 expression measured at the site of metastasis was not correlated with TTR (p = 0.55). Estrogen receptor negative tumors were less likely to have PIK3CA mutations (p = 0.023). In cases of primary tumors with PIK3CA mutations, no reversions to wild-type PIK3CA were observed in the metastatic sites. In metastatic tumors, mutations detected in the primary tumor as well as new mutations were observed. A gain of an exon 9 mutation at the metastatic site correlated with shorter TTR (HR = 2.5; p = 0.043). Excluding the 8 samples that were HER2+ by HERmark, longer TTR was observed for patients with PIK3CA mutations in the primary tumor (HR = 0.47; p = 0.042), which is consistent with previous reports. Interestingly, the longer TTR for those with PIK3CA mutations appeared to be dependent on quantitative HER3 protein level (interaction p = 0.065).

Conclusions: HER3 protein expression in matched primary and metastatic breast cancer tissues were unrelated. This may indicate that HER3 protein is influenced by the different tumor microenvironments of the primary and metastatic sites. PIK3CA mutations were either maintained or acquired at metastatic sites. Both low HER3 protein expression and the presence of PIK3CA mutations in the primary tumor but not the metastatic tumor were associated with longer TTR. These observations suggest that HER3 protein expression may be an important prognostic factor for breast cancer progression.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-10-16.

Predictive value of HIV-1 replication capacity and phenotypic susceptibility scores in antiretroviral treatment-experienced patients

OBJECTIVES

The aim of the study was to determine the prognostic value of HIV replication capacity (RC) for subsequent antiretroviral (ARV) treatment response in ARV-experienced patients.

METHODS

RC and phenotypic resistance testing were performed at baseline and week 12 on plasma samples from patients randomized to undergo a 12-week ARV drug-free period (ARDFP) or initiate immediate salvage therapy (no-ARDFP group) in the Options in Management with Antiretrovirals (OPTIMA) trial. Dichotomous and incremental phenotypic susceptibility scores (dPSSs and iPSSs, respectively) were calculated. The predictive value of RC and PSS for ARV therapy response and/or ARDFP was evaluated using multivariate regression analysis and Pearson correlations.

RESULTS

In 146 no-ARDFP subjects, baseline RC (50.8%) did not change at week 12 and was not correlated with CD4 cell count or viral load changes at week 12 (P=0.33 and P=0.79, respectively) or at week 24 (P=0.96 and P=0.14, respectively). dPSS predicted virological but not CD4 cell count response to ARV therapy at weeks 12, 24 and 48 (P=0.002, P<0.001 and P=0.005, respectively). RC was significantly correlated with dPSS and iPSS at baseline, but did not increase their predictive value. In the 137 ARDFP patients, RC increased significantly (from 52.4 to 85.8%), but did not predict CD4 cell count and viral load changes during ARDFP (P=0.92 and P=0.26, respectively). RC after ARDFP did not predict subsequent CD4 cell count and viral load changes 12 weeks following ARV treatment reinitiation (P=0.90 and P=0.29, respectively).

CONCLUSIONS

We found no additional predictive value of replication capacity for virological or immunological responses (above what PSS provides) in patients undergoing salvage ARV treatment.

P2-12-05: Correlation between Quantitative HER2 Protein Expression and Risk of Brain Metastases in HER2−Positive Advanced Breast Cancer Patients Receiving Trastuzumab-Containing Therapy

Background. Patients with HER2−positive breast cancer are at particularly high risk for brain metastases; however, the biological basis is not fully understood. Within HER2−positive breast cancer tumors, it is possible to resolve a ∼1.5-log range of HER2 protein expression using a novel quantitative HER2 assay (HERmark®). We investigated the correlation between quantitative HER2 protein expression in primary breast cancers and the time to brain metastases (TTBM) in HER2−positive advanced breast cancer patients treated with trastuzumab.

Methods. The study group included 142 consecutive patients who were administered trastuzumab-based therapy for HER2−positive metastatic breast cancer, defined as 3+ categorical staining by immunohistochemistry (IHC). HER-2/neu gene copy number was subsequently quantified as HER2/CEP17 ratio by central laboratory fluorescence in situ hybridization (FISH). HER2 protein was quantified as total HER2 protein expression (H2T) by the HERmark assay in formalin-fixed, paraffin-embedded primary tumor samples. HER2 variables were correlated with clinical features and TTBM measured from the initiation of trastuzumab-containing therapy.

Results. H2T level (continuous variable) was correlated with shorter TTBM (HR=2.3; p=0.013), whereas HER2 gene amplification by FISH (p=0.28) and continuous HER2/CEP17 ratio (p=0.25) had no significant prognostic impact. The correlation between continuous H2T level and TTBM was confirmed in a multivariate analysis (HR=3.2; p=0.021). Controlling for the competing risk of death from causes other than brain metastases, continuous H2T remained a strong correlate of TTBM (HR=2.7; p=0.0009). In the subset of patients that was centrally-determined HER2 positive by FISH (117 patients), above-median H2T level was significantly associated with shorter TTBM (HR=2.4; p=0.005), whereas this was not true for median FISH/CEP17 ratio (p=0.4). In a multivariate analysis of this subset, continuous H2T (p=0.021) and a time dependent covariate capturing time to non-brain metastases (p=0.0044) were prognostic for TTBM, whereas FISH/CEP17, ER, PgR and grade were not.

Conclusions. These data reveal a strong relationship between quantitative HER2 protein expression levels and the risk of brain relapse in HER2−positive advanced breast cancer patients. Consequently, quantitative assessment of HER2 protein expression may inform and facilitate refinements in therapeutic treatment strategies for selected subpopulations of patients in this group.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-12-05.

P1-07-12: Assessment of Real World HER2 Status by Immunohistochemistry (IHC) and Fluorescence In Situ Hybridization (FISH) in Breast Cancers: Comparison with HERmark®, a Validated Quantitative Measure of HER2 Protein Expression

Background: Accurate assessment of the HER2 status is critical in determining appropriate therapy for patients with invasive breast cancer. ASCO/CAP HER2 testing guidelines caution that up to 20% of routine HER2 testing by IHC/FISH may be unreliable (Wolff et al. JCO 2007;25:118). The HERmark assay is a novel quantitative HER2 protein measurement for determining HER2 status in breast cancer. Central HER2 testing showed high concordance (96-98%) with HERmark for positive and negative categories when equivocal subsets were excluded (Huang et al. Am J Clin Pathol 2010;134:303; Joensuu et al, 2008 SABCS, abstract 2071). In this study, we examined concordance between HERmark and routine HER2 testing by IHC and FISH from “real world” formalin-fixed, paraffin-embedded (FFPE) breast cancers submitted commercially for HERmark testing.

Methods: 717 HERmark results on FFPE breast cancers tested from 2008 to 2010 and corresponding HER2 IHC/FISH results were reviewed. The IHC and FISH results, per pathology reports submitted at the time of HERmark testing, were compared to HERmark categorical (negative, equivocal, positive) results.

Results: 590 (419) samples had IHC (FISH) and HERmark results available. Of these cases, 92% (94%) were either negative or equivocal by IHC (FISH). The HERmark testing reported 33% HERmark negative, 33% HERmark equivocal and 34% HERmark positive. Comparisons of HER2 status by IHC and FISH vs. HERmark are detailed in Table 1.

P1-07-01: Comparison of Four HER2 Testing Methods in the Detection of HER2−Positive Breast Cancer: Results from the FinHer Study Cohort

Background: Accurate assessment of the HER2 status is essential for identifying patients who may benefit from HER2 targeted therapy. The current methods, immunohistochemistry (IHC) and in situ hybridization (ISH), determine HER2 status semi-quantitatively as positive (+), equivocal (+/−) and negative (−) with predefined cutoff values. Recent studies have suggested that current HER2 cutoffs may not be optimal for all clinical settings of HER2 targeted therapy. In a small subset of adjuvant NCCTG N9831 patients confirmed as HER2−normal by round-robin review of HER2 testing, trastuzumab benefit was observed (Perez et al, SABCS 2010). Quantification of HER2 as continuous variable may enable a more accurate optimization of HER2 cutoffs for various HER2 targeted therapies. In this study, we measured continuous HER2 protein expression by the HERmark™ assay and continuous mRNA expression by quantitative real time polymerase chain reaction (qPCR), and compared these results with central IHC and central chromogenic in situ hybridization (CISH) results of FinHer.

Methods: Total HER2 protein expression (H2T) was quantified using the HERmark assay as previously described (Huang et al. Am J Clin Pathol 2010;134:303). HER2 mRNA expression (H2N) was measured by qPCR as previously published (Noske et al. Br Cancer Res Treat 2011;126:109). The results of H2T and H2N as continuous variables and as predefined categories were compared with central CISH results from FinHer (Joensuu et al, N Engl J Med 2006;354), and central IHC retesting.

Results: H2T in 899 evaluable samples described a continuum of 0.4 to 721.2 (relative HERmark unit); while H2N in 915 evaluable samples showed a continuum of 31.4 to 42.8 (delta-Ct). Significant correlation between H2T and H2N as continuous variable was found (R2= 0.56, P&lt; .0001). Paired method comparison was performed for samples with valid results in any two of the four testing methods. Overall concordance of H2T and H2N with predefined categories (+, +/−, -) was 81%, and concordance of (+) and (−) subsets was 95% when (+/−) cases (H2T 11%; H2N 6%) were excluded. Overall concordance of central IHC and H2T categories (+, +/−, -) was 75%, and concordance of (+) and (−) subsets was 96% when (+/−) cases (IHC 16%; H2T 11%) were excluded. Overall concordance of IHC and H2N categories (+, +/−, -) was 84%, and concordance of (+) and (−) subsets was 99% when (+/−) cases (IHC 16%; H2N 6%) were excluded. Concordance of central CISH (+, -) with H2T and H2N categories (+, -) was 89% and 91%, respectively, when (+/−) cases were excluded from H2T (13%) and H2N (8%), respectively.

Conclusions: All four methods identified HER2−positive breast cancers. The discordance rate between the methods tested was approximately 10 to 20% despite careful delineation of cancerous tissue in the sample and analysis of adjacent tumor sections. No combination of assays could be identified with concordance rate &gt;95% when the equivocal subsets were included in comparisons. Exclusion of the equivocal subsets (about 10% of samples) yielded high concordance rates of approximately 95% or higher. H2T and H2N showed comparable continuous distribution patterns and significant concordance with standard HER2 status by central IHC and CISH.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-01.

Identification of a subpopulation of metastatic breast cancer patients with very high HER2 expression levels and possible resistance to trastuzumab

BACKGROUND

Patients with metastatic breast cancer (MBC) overexpressing HER2 (human epidermal growth factor receptor 2) are currently selected for treatment with trastuzumab, but not all patients respond.

PATIENTS AND METHODS

Using a novel assay, HER2 protein expression (H2T) was measured in formalin-fixed, paraffin-embedded primary breast tumors from 98 women treated with trastuzumab-based therapy for MBC. Using subpopulation treatment effect pattern plots, the population was divided into H2T low (H2T < 13.8), H2T high (H2T ≥ 68.5), and H2T intermediate (13.8 ≤ H2T < 68.5) subgroups. Kaplan-Meier (KM) analyses were carried out comparing the groups for time to progression (TTP) and overall survival (OS). Cox multivariate analyses were carried out to identify correlates of clinical outcome. Bootstrapping analyses were carried out to test the robustness of the results.

RESULTS

TTP improved with increasing H2T until, at the highest levels of H2T, an abrupt decrease in the TTP was observed. KM analyses demonstrated that patients with H2T low tumors [median TTP 4.2 months, hazard ratio (HR) = 3.7, P < 0.0001] or H2T high tumors (median TTP 4.6 months, HR = 2.7, P = 0.008) had significantly shorter TTP than patients whose tumors were H2T intermediate (median TTP 12 months). OS analyses yielded similar results.

CONCLUSIONS

MBC patients with very high levels of H2T may represent a subgroup with de novo resistance to trastuzumab. These results are preliminary and require confirmation in larger controlled clinical cohorts.

Multiple Subtypes of HER-2/Neu-Positive Metastatic Breast Cancer

Background: Using IHC or FISH to select patients for trastuzumab-based therapy, only half of HER2-positive patients show evidence of response. In vitro data implicate HER2:HER3 heterodimers and p95HER2 (p95), the truncated 95-kilodalton C-terminal fragment of HER-2 lacking the trastuzumab binding site, as mediators of resistance to trastuzumab at the receptor level. We have previously reported that central FISH-positive patients with low HER2 protein expression by VeraTag had significantly reduced response to trastuzumab compared to patients who had FISH-positive tumors with high HER2 protein expression (Lipton, SABCS 2008). Adding quantitative measurements of HER3 and p95, we offer evidence for the existence of multiple sub-types of HER2-positive tumors that respond differently to trastuzumab.Methods: Using the VeraTag assay, quantitative protein measurements of HER2, HER3, and p95 were made in FFPE specimens from a cohort of patients with metastatic breast cancer (MBC) and correlated with time to progression (TTP) and overall survival (OS) following treatment with first-line trastuzumab using Kaplan-Meier (KM) and Cox proportional hazards regression analyses.Results: Measurements of HER2 (H2T), HER3 (H3T) and p95 were made in FFPE tumor samples from 95 patients treated with first-line trastuzumab for metastatic breast cancer. Within the group that overexpressed HER2 by the VeraTag Assay (n=60), a group with highly overexpressed HER2 (n=15) had shorter TTP and OS than those that had moderate HER2 overexpression (median TTP 4.6 vs. 12 mos, HR=2.1; p=0.011; median OS 29 vs. 40 mos, HR=2.0; p=0.047). Within the subgroup with moderate H2T overexpression (n=45), bivariate Cox analyses demonstrated that p95 and H3T were independent predictors of TTP (p95 HR=2.1; p=0.031; H3T HR=3.5; p=0.0037). For OS, p95 was significant and H3T showed a strong trend (p95 HR=2.5; p=0.025, H3T HR=2.2; p=0.089). Univariate KM analysis with the p95+ and H3T+ groups combined, gives the results in the table below. These data suggest that HER2-positive breast cancer patients can be classified into at least 4 sub-groups with different outcomes following trastuzumab treatment.Conclusions: These data suggest the existence of multiple subgroups of HER2-positive patients expressing varying HER2, p95, and HER3 levels that experience different clinical outcomes following treatment with trastuzumab. Furthermore, the association of HER3 and p95 overexpression with poor response to trastuzumab in otherwise HER2-positive tumors suggests possible treatment approaches with combinations of targeted therapies.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2030.

Breast Cancer Patients with Very High Tumor HER2 Expression Levels Might Not Benefit from Treatment with Trastzumab Plus Chemotherapy: A Retrospective Exploratory Analysis of the FinHer Trial

Background: FinHer (NEJM 2006) is one of the several prospective randomized clinical trials that show a clinical benefit from trastuzumab added to adjuvant chemotherapy. We have previously reported that patients with metastatic breast cancer who had very high levels of HER2 protein expression as measured by the HERmark assay and who were treated with trastuzumab had similar time-to-progression (TTP) compared to a group of patients who had FISH-negative and HER2 normal cancer suggesting reduced efficacy of trastuzumab when tumor HER2 content is very high (Sperinde, ASCO 2009). Here we investigate the relationship between clinical benefit from trastuzumab and quantitative HER2 protein expression (H2T) as determined by the HERmark assay.Methods: H2T was quantitated by the HERmark assay in 899 formalin-fixed paraffin-embedded specimens from patients enrolled in the FinHer trial; 196 of the samples were HER2-positive by chromogenic in situ hybridization (CISH). Focusing on the HER2-positive patients who were randomized to trastuzumab treatment or control, Cox proportional hazards analyses, sub-population treatment effect pattern plots (STEPP analyses), positional scanning analyses, and Kaplan-Meier analyses were used to identify sub-populations of HER2 over-expressing patients who experienced different clinical outcomes on trastuzumab.Results: Using time to distant recurrence (TDR) and overall survival (OS) as endpoints, Cox proportional hazards analyses treating H2T as a continuous variable failed to show a relationship between HER2 expression levels and clinical benefit from trastuzumab (HR=1, p=ns for both). STEPP analyses were performed to look for non-linear relationships between H2T and clinical outcome. At the highest levels of H2T, the hazard ratio comparing trastuzumab treatment to control approached and exceeded 1. Positional scanning analyses were conducted to identify the optimal cutoff discriminating the very high H2T group. Patients with very high H2T values (&gt;= 125.9) did not benefit from trastuzumab plus chemotherapy treatment relative to controls (HR=1.23, p=0.75 for TDR, HR=1.05, p=0.95 for OS), while those with H2T values &lt;125.9 did (HR=0.52, p=0.05 for TDR, HR=0.48, p=0.1 for OS). The very high H2T group represented 13% of the HER2-positive population compared with 16% in the prior study from Sperinde et al.Discussion: In this exploratory analysis of a prospectively randomized controlled trial of trastuzumab in the adjuvant setting, the 13% of patients with the highest H2T values showed no evidence of clinical benefit from trastuzumab. Potential explanations include insufficient trastuzumab dose, steric hindrance preventing access of trastuzumab to its epitope target under conditions of HER2 over-crowding, or the existence of trastuzumab-resistant forms of HER2 at the highest levels of over-expression (e.g. p95/HER2, HER2:HER3 heterodimers). Although these results are in agreement with prior observations from the metastatic setting, they need to be confirmed in larger randomized trials of trastuzumab in early breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5083.

Discordant HER2 Total and HER2 Homodimer Levels by HERmark Analysis in Matched Primary and Metastatic Breast Cancer FFPE Specimens

Background: HER-2/neu is over-expressed in approximately 25% of primary invasive breast cancers and selection of patients for consideration of trastuzumab is a critical step in defining the treatment plan. We have previously reported that quantitative measurements of HER2 protein expression (H2T) and HER2 homodimers (H2D) using the HERmark assay identifies sub-populations of “HER2-positive” patients (by IHC and/or FISH) that have different clinical outcomes on trastuzumab (Leitzel, ASCO 2008; Lipton, SABCS 2008). Previous studies report up to a 20 % discordance in HER2 status using conventional IHC or FISH analysis between the primary and metastatic breast tumors. Here we correlate HER2 total and homodimer levels in matched primary and metastatic tissue from the same patient.Methods: 27 patients had matched primary and metastatic FFPE (formalin-fixed, paraffin-embedded) specimens tested in the HERmark assay to quantitate and compare their H2T and H2D expression levels.Results: FFPE tissue was available from 27 primary breast cancers and metachronous metastatic sites. Metastatic lesions included 7 skin, 5 lymph node, 3 bone, 3 pleura, 2 brain, 2 chest wall, and 5 other soft tissue lesions. The median elapsed time between matched primary and metastatic sites was 71 mo. (range 9-137 mo). During the time period between the primary specimen harvest and the metastatic biopsy, 6 patients were treated with chemotherapy alone, 10 received hormonal therapy without trastuzumab, 3 patients received trastuzumab, and 3 received no treatment. Treatment was not known for 5 patients. For the whole population, there was a weak to moderate positive correlation between primary and metastatic cancers with H2T (r2=0.36, p&lt;0.001) and for H2D (r2=0.27, p&lt;0.006). Using the optimized time to progression (TTP) positional scanning cutpoints for H2T and H2D defined in our previous reports, 4/20 patients (20%) converted from low to high, and 1/7 (14%) converted from high to low H2T. Using the H2D cutpoint, 7/15 patients (47%) converted from low to high, and 3/12 (25%) converted from high to low H2D. Overall discordance between primary and metastatic sites was 19% for H2T, and 37% for H2D.Conclusions: HERmark analysis of matching primary and metastatic breast cancers revealed 19% discordance for H2T, and 37% for H2D. The most frequent conversion was from low HER2 in the primary tissue to high HER2 in the metastatic site.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2131.

Correlation of quantitative total HER2 expression and HER2 homodimers with histopathologic characteristics of breast cancers in the FinHer study

11061

Background: We recently reported that the HERmark assay (Monogram Biosciences) accurately measures continua of total HER2 expression (H2T) and HER2 homodimers (H2D) over a wide (∼3 logs) dynamic range, and that a higher concordance was observed between H2T and HER2 status with more stringent central tests as compared with IHC tests performed locally (Joensuu et al, 2008 SABCS,abstract 2071). H2D/H2T ratio was reported as a marker of activated HER2 and a prognosticator of disease progression in HER2+ patients not treated with trastuzumab in the adjuvant setting (Bates et al, 2008 SABCS,abstract 1074). In this follow-up analysis, H2T, H2D, and H2D/H2T ratio were correlated with histopathologic characteristics of breast cancers in the FinHer study. Methods: The HERmark assay was used to measure H2T and H2D in 899 formalin-fixed, paraffin-embedded FinHer specimens. The results were correlated with histopathologic characteristics of breast cancers in the FinHer study (Joensuu et al, N Engl J Med2006;354), including estrogen receptor/progesterone receptor (ER/PR), tumor grade, tumor size, lymph node metastasis, and stage. Results: Higher H2T and H2D levels correlated with ER/PR negativity and high tumor grade (P<0.0001). 42% (102/244) of ER- and 37% (137/374) of PR- cases were HERmark Positive; while 17% (110/655) of ER+ and 14% (75/524) of PR+ cases were HERmark Positive. 10% (13/136) of grade 1, 18% (65/353) of grade 2, and 35% (131/375) of grade 3 tumors were HERmark Positive. No significant association was found between H2T or H2D and tumor size, lymph node metastasis or stage. ER/PR negative and poorly differentiated cancers had higher H2D/H2T ratios (P=0.013), and H2D/H2T ratios >0.6 were associated with smaller primary tumor diameters at the time of cancer detection (P=0.009). Conclusions: The quantitative H2T measurement confirms the known correlations between HER2 expression and histopathologic characteristics of breast cancer. The novel H2D measurement and H2D/H2T ratio may provide further insights into HER2 activation and better diagnostic tests for targeted HER2 therapy.

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Identification of a subpopulation of metastatic breast cancer patients with very high HER2 expression levels and possible resistance to trastuzumab

1059

Background: Many HER2-positive patients with metastatic breast cancer (MBC) fail to respond to trastuzumab. We previously reported that precise quantitation of HER2 expression (H2T) by the HERmark assay identified a sub-population of IHC 3+, FISH(+) (positive) patients with low H2T levels that responded poorly to trastuzumab (Lipton, San Antonio Breast Cancer Symposium 2008, abs #32). Here we identify a sub-population of FISH(+) patients with very high H2T levels, that experience clinical outcomes that are indistinguishable from those of FISH(-) (negative) patients with low H2T levels. Methods: The HERmark assay was used to measure H2T in formalin-fixed, paraffin-embedded (FFPE) primary breast tumor specimens from 99 women treated with trastuzumab for MBC. Specimens were also tested by central FISH. A sub-population treatment effect pattern plot (STEPP) was generated to examine the progression-free survival (PFS) rate at 12 months after treatment with trastuzumab across the distribution of H2T. Kaplan-Meier (KM) analyses were performed comparing the PFS of FISH(-), H2T low (log10H2T < 1.25) patients with those of FISH(+), H2T high (log10H2T ≥ 1.95) and FISH(+), H2T intermediate (1.25 < log10H2T < 1.95) groups. Cutoffs were identified by lowest p-value in a positional scanning analysis. Results: The PFS rate improved gradually with increasing H2T in STEPP analyses. At the highest levels of H2T, an abrupt decrease in the PFS rate was observed, consistent with a reduction in susceptibility to trastuzumab. KM analyses demonstrated that patients who were FISH(+), H2T intermediate had a significantly longer PFS than patients who were FISH(-), H2T low (median PFS 12.6 vs. 4.5 mos; HR = 0.34; p < 0.0001). Patients that were FISH(+), H2T high experienced a PFS that was no better than patients that were FISH(-), H2T low (median PFS 4.6 vs. 4.5 mos; HR = 0.87; p = 0.68). Conclusions: Precise quantitation of HER2 expression levels allows the identification of multiple sub-populations of HER2(+) patients that have different clinical outcomes on trastuzumab. MBC patients with very high levels of H2T could represent a sub-group with de novo resistance to trastuzumab who may benefit from combined therapy.

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Quantitative measurements of HER2 expression and HER2 homodimer using a novel proximity based assay: comparison with HER2 status by immunohistochemistry and chromogenic in situ hybridization in the FinHer study

Abstract #2071

Background: The accuracy and reliability of current methods, immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), to assess HER2 status has recently been a subject of debate. The best method to assess HER2 status remains controversial. We developed a novel assay (HERmark, Monogram Biosciences) that provides precise quantification of HER2 expression (H2T) and HER2 homodimer (H2D) in formalin-fixed paraffin-embedded (FFPE) tissues. We compared H2T and H2D to local IHC, central chromogenic in situ hybridization (CISH) and central IHC retesting of breast cancers from the FinHer study.&#x2028; Methods: H2T and H2D were detected through light-dependent release of fluorescent tags (VeraTag reporters) conjugated to a HER2 antibody, requiring proximity to a second HER2 “scissors” antibody. The VeraTag signal was quantified by capillary electrophoresis and normalized to tumor area. Assay comparisons correlated H2T and H2D with HER2 testing by local IHC and central CISH from FinHer (Joensuu et al, N Engl J Med 2006;354), as well as central HER2 status reassessment by combination of externally performed central IHC retesting (PhenoPath labs, Seattle, WA) and central CISH (FinHer) according to ASCO/CAP guideline for HER2 testing in breast cancer (Wolff et al, Arch Pathol Lab Med 2007;131).&#x2028; Results: H2T and H2D in 899 evaluable FinHer samples described a continuum over a wide dynamic range (∼ 3 logs), in contrast with conventional IHC categories (0-3+). The correlation between H2T and IHC categories was significant (P &lt; .0001). Overlap of H2T among the IHC categories was observed. H2D showed a similar correlation with IHC and a general correlation with H2T (P &lt; .0001). A H2T cutoff value, based on its ability to distinguish high and low responders in a cohort of metastatic breast cancer patients treated with trastuzumab-based regimens (log10 H2T= 1.14, Leitzel et al, 2008 ASCO, abstract 1002), was used to define HERmark negative (-) and positive (+), which were then compared with IHC and CISH results. The concordances between HERmark (-) and local IHC (-), central CISH (-), and central HER2 reassessment (-) were 89%, 84%, and 91%, respectively. The concordances between HERmark (+) and local IHC (+), central CISH (+), and central HER2 reassessment (+) were 71%, 89%, and 92%, respectively. The HERmark test showed greater overall concordance with central HER2 reassessment (91%) than with local IHC (84%) and central CISH (87%)&#x2028; Conclusions: HERmark reliably measures H2T and H2D in FFPE tissues. H2T showed excellent concordance with central HER2 status according to ASCO/CAP guideline for HER2 testing. The precise quantification of H2T and H2D may provide novel, quantifiable, predictive tests for targeted HER2 therapy.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2071.

Quantitative HER2 homodimer levels correlate with time to first recurrence in HER2-positive breast cancer patients who did not receive trastuzumab in the adjuvant setting

Abstract #1074

BACKGROUND: HER2-positive breast cancer patients are currently treated with trastuzumab in the adjuvant setting, but prior to 2005 these patients were not routinely offered trastuzumab, creating an opportunity to examine the relationship between HER2 expression and disease progression. The VeraTag technology is a proximity-based assay system that permits quantitative measurements of total HER2 protein expression (H2T) as well as HER2 homodimers (H2D) in formalin-fixed paraffin-embedded (FFPE) tissues. We measured H2T and H2D in a cohort of patients who were HER2-positive but did not receive trastuzumab in the adjuvant setting, and correlated those measurements with time to first recurrence of disease.&#x2028; METHODS: Patients were selected for study because they were treated with a trastuzumab-containing regimen for HER2+ metastatic breast cancer. HER2-positivity was defined as IHC (Herceptest) 3+ or 2+, FISH+ (Vysis). 96 HER2+ patients who had been treated (but not with trastuzumab) in the adjuvant setting were identified. The VeraTag assay was used to quantitate H2T and H2D. Kaplan-Meier and Cox proportional hazards analyses were employed.&#x2028; RESULTS: The distribution of H2T ranged over approximately 135-fold, and H2D varied over approximately 100-fold. In univariate Cox proportional hazards regression analysis, H2T trended toward significance (HR=1.44, p= 0.088) while both H2D (HR=1.39, p=0.022) and the ratio H2D/H2T (HR=2.01, p=0.03) were significantly correlated with time to first recurrence. Kaplan-Meier analysis of the H2T distribution divided into tertiles showed no significant difference in time to first recurrence among the tertiles (HR=0.7, p=0.16 for low vs. high comparison) and no trend was observed (Log Rank test for trend p=0.2). However, the same analyses performed using H2D (HR=0.59, p=0.03) or H2D/H2T (HR=0.56, p=0.01) demonstrated significantly longer time to first recurrence for the lowest tertile compared with the highest tertile respectively. A trend was observed in both cases (H2D: Log Rank p=0.048; H2D/H2T: Log Rank p=0.026)&#x2028; CONCLUSION: In a population of HER2+ patients who did not receive trastuzumab in the adjuvant setting, and who subsequently developed metastatic disease, higher levels of HER2 homodimers and the ratio of homodimers to HER2 total expression correlated with time to first recurrence while total HER2 expression levels did not. These data suggest that measures of the activated forms of HER2 (dimers) may be better predictors of disease progression than simple quantitation of HER2 alone.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 1074.