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Hartmann K, Schlombs K, Laible M, Gürtler C, Schmidt M, Sahin U, Lehr HA. Robustness of biomarker determination in breast cancer by RT-qPCR: impact of tumor cell content, DCIS and non-neoplastic breast tissue. Diagn Pathol 2018; 13:83. [PMID: 30342538 PMCID: PMC6195967 DOI: 10.1186/s13000-018-0760-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022] Open
Abstract
Background Tissue heterogeneity in formalin-fixed paraffin-embedded (FFPE) breast cancer specimens may affect the accuracy of reverse transcription quantitative real-time PCR (RT-qPCR). Herein, we tested the impact of tissue heterogeneity of breast cancer specimen on the RT-qPCR-based gene expression assay MammaTyper®. Methods MammaTyper® quantifies the mRNA expression of the four biomarkers ERBB2, ESR1, PGR, and MKI67. Based on pre-defined cut-off values, this molecular in vitro diagnostic assay permits binary marker classification and determination of breast cancer subtypes as defined by St Gallen 2013. In this study, we compared data from whole FFPE sections with data obtained in paired RNA samples after enrichment for invasive carcinoma via macro- or laser-capture micro-dissection. Results Compared to whole sections, removal of surrounding adipose tissue by macrodissection generated mean absolute 40-ddCq differences of 0.28–0.32 cycles for all four markers, with ≥90% concordant binary classifications. The mean raw marker Cq values in the adipose tissue were delayed by 6 to 7 cycles compared with the tumor-enriched sections, adding a trivial linear fold change of 1.0078 to 1.0156. Comparison of specimens enriched for invasive tumor with whole sections with as few as 20% tumor cell content resulted in mean absolute differences that remained on average below 0.59 Cq. The mean absolute difference between whole sections containing up to 60% ductal carcinoma in situ (DCIS) and specimens after dissection of DCIS was only 0.16–0.25 cycles, although there was a tendency for higher gene expression in DCIS. Observed variations were related to small size of samples and proximity of values to the limit of detection. Conclusion Expression of ESR1, PGR, ERBB2 and MKI67 by MammaTyper® is robust in clinical FFPE samples. Assay performance was unaffected by adipose tissue and was stable in samples with as few as 20% tumor cell content and up to 60% DCIS. Electronic supplementary material The online version of this article (10.1186/s13000-018-0760-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kerstin Hartmann
- BioNTech Diagnostics GmbH, An der Goldgrube 12, 55131, Mainz, Germany.
| | - Kornelia Schlombs
- BioNTech Diagnostics GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Mark Laible
- BioNTech Diagnostics GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Claudia Gürtler
- BioNTech Diagnostics GmbH, An der Goldgrube 12, 55131, Mainz, Germany
| | - Marcus Schmidt
- Department of Obstetrics and Gynecology, Johannes Gutenberg University, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Ugur Sahin
- BioNTech AG, An der Goldgrube 12, 55131, Mainz, Germany
| | - Hans-Anton Lehr
- Institute of Pathology, Medizin Campus Bodensee, Röntgenstraße 2, 88048, Friedrichshafen, Germany
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Fasching P, Laible M, Weber K, Wirtz R, Denkert C, Schlombs K, Schmatloch S, Camara O, Lück H, Huober J, Karn T, van Mackelenbergh M, Marme F, Müller V, Schem C, Stickeler E, Sahin U, Loibl S, Untch M. Evaluation of the MammaTyper® as a molecular predictor for pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) and outcome in patients with different breast cancer (BC) subtypes. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy270.222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Fasching P, Laible M, Weber K, Wirtz R, Denkert C, Schlombs K, Schmatloch S, Camara O, Lück H, Huober J, Karn T, van Mackelenbergh M, Marme F, Müller V, Schem C, Stickeler E, Sahin U, Loibl S, Untch M. Validation of the MammaTyper® pathological complete response (pCR)-score as a predictor for response after neoadjuvant chemotherapy (NACT) in patients with early breast cancer (BC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy269.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Gürtler C, Laible M, Schwabe W, Steinhäuser H, Li X, Liu S, Schlombs K, Sahin U. Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms. J Mol Diagn 2018; 20:398-414. [DOI: 10.1016/j.jmoldx.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 12/22/2022] Open
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Breyer J, Wirtz RM, Otto W, Laible M, Schlombs K, Erben P, Kriegmair MC, Stoehr R, Eidt S, Denzinger S, Burger M, Hartmann A. Predictive value of molecular subtyping in NMIBC by RT-qPCR of ERBB2, ESR1, PGR and MKI67 from formalin fixed TUR biopsies. Oncotarget 2017; 8:67684-67695. [PMID: 28978063 PMCID: PMC5620203 DOI: 10.18632/oncotarget.18804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 06/02/2017] [Indexed: 12/21/2022] Open
Abstract
Expression of ESR1, PGR, HER2 and Ki67 is important for risk stratification and therapy in breast cancer. Hormone receptor expression can also be found in MIBC, reflecting luminal and basal subtypes of breast cancer. Thus the purpose was to investigate on the mRNA expression of the aforementioned markers and their prognostic value in pT1 bladder cancer. Retrospective analysis of clinical data and Formalin-Fixed Paraffin-Embedded tissues (FFPE) of patients with stage pT1 NMIBC who underwent transurethral resection of the bladder was performed. mRNA expression was measured by single step RT-qPCR. Relative gene expression was determined by normalization to two housekeeping genes (CALM2, B2M) using the 40-ΔΔCT method. Correlation of mRNA expression with outcome was assessed using Kaplan-Meier analysis and multivariate Cox regression analysis. From overall 302 patients, 255 samples could be analyzed with valid measurements. Subtype distribution was Luminal-A in 11.4%, Luminal-B in 38.8%, triple negative in 36.9% and ERBB2 in 12.9%, respectively. Kaplan-Meier analysis revealed molecular subtyping being statistical significant for RFS (p=0.0408) and PFS (p=0.0039). Luminal-A patients did have the best RFS and PFS. Multivariate analysis revealed molecular subtyping to be significant for PFS (L-R Chi2 of 11.89, p=0.0078). Elevated expression of HER2 was statistically significant for PFS (p=0.0025) and discriminated among G3 tumors a high risk group (60% PFS) from a low risk risk group (90% PFS) after 5 year follow-up (p<0.001). Expression of ESR1, PGR and HER2 has predictive value in stage pT1 NMIBC and reveals potential therapeutic targets.
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Affiliation(s)
- Johannes Breyer
- Department of Urology, University of Regensburg, Regensburg, Germany
| | - Ralph Markus Wirtz
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany.,Institute of Pathology at The St Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | - Wolfgang Otto
- Department of Urology, University of Regensburg, Regensburg, Germany
| | | | | | - Philipp Erben
- Department of Urology, University Medical Centre Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maximilian Christian Kriegmair
- Department of Urology, University Medical Centre Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Robert Stoehr
- Institute of Pathology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Eidt
- Institute of Pathology at The St Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | - Stefan Denzinger
- Department of Urology, University of Regensburg, Regensburg, Germany
| | - Maximilian Burger
- Department of Urology, University of Regensburg, Regensburg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University of Erlangen-Nuremberg, Erlangen, Germany
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Varga Z, Lebeau A, Bu H, Hartmann A, Penault-Llorca F, Guerini-Rocco E, Schraml P, Symmans F, Stoehr R, Teng X, Turzynski A, von Wasielewski R, Gürtler C, Laible M, Schlombs K, Joensuu H, Keller T, Sinn P, Sahin U, Bartlett J, Viale G. An international reproducibility study validating quantitative determination of ERBB2, ESR1, PGR, and MKI67 mRNA in breast cancer using MammaTyper®. Breast Cancer Res 2017; 19:55. [PMID: 28490348 PMCID: PMC5426065 DOI: 10.1186/s13058-017-0848-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/27/2017] [Indexed: 02/05/2023] Open
Abstract
Background Accurate determination of the predictive markers human epidermal growth factor receptor 2 (HER2/ERBB2), estrogen receptor (ER/ESR1), progesterone receptor (PgR/PGR), and marker of proliferation Ki67 (MKI67) is indispensable for therapeutic decision making in early breast cancer. In this multicenter prospective study, we addressed the issue of inter- and intrasite reproducibility using the recently developed reverse transcription-quantitative real-time polymerase chain reaction-based MammaTyper® test. Methods Ten international pathology institutions participated in this study and determined messenger RNA expression levels of ERBB2, ESR1, PGR, and MKI67 in both centrally and locally extracted RNA from formalin-fixed, paraffin-embedded breast cancer specimens with the MammaTyper® test. Samples were measured repeatedly on different days within the local laboratories, and reproducibility was assessed by means of variance component analysis, Fleiss’ kappa statistics, and interclass correlation coefficients (ICCs). Results Total variations in measurements of centrally and locally prepared RNA extracts were comparable; therefore, statistical analyses were performed on the complete dataset. Intersite reproducibility showed total SDs between 0.21 and 0.44 for the quantitative single-marker assessments, resulting in ICC values of 0.980–0.998, demonstrating excellent agreement of quantitative measurements. Also, the reproducibility of binary single-marker results (positive/negative), as well as the molecular subtype agreement, was almost perfect with kappa values ranging from 0.90 to 1.00. Conclusions On the basis of these data, the MammaTyper® has the potential to substantially improve the current standards of breast cancer diagnostics by providing a highly precise and reproducible quantitative assessment of the established breast cancer biomarkers and molecular subtypes in a decentralized workup. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0848-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zsuzsanna Varga
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.
| | - Annette Lebeau
- Private Group Practice for Pathology and PathoPlan GbR, Lübeck, Germany
| | - Hong Bu
- Department of Pathology and Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Arndt Hartmann
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Peter Schraml
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Stoehr
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Andreas Turzynski
- Private Group Practice for Pathology and PathoPlan GbR, Lübeck, Germany
| | | | | | | | | | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Peter Sinn
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ugur Sahin
- BioNTech Diagnostics GmbH, Mainz, Germany
| | - John Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research (OICR), Toronto, ON, Canada
| | - Giuseppe Viale
- European Institute of Oncology, University of Milan, Milan, Italy
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Sinn HP, Schneeweiss A, Keller M, Schlombs K, Laible M, Seitz J, Lakis S, Veltrup E, Altevogt P, Eidt S, Wirtz RM, Marmé F. Comparison of immunohistochemistry with PCR for assessment of ER, PR, and Ki-67 and prediction of pathological complete response in breast cancer. BMC Cancer 2017; 17:124. [PMID: 28193205 PMCID: PMC5307758 DOI: 10.1186/s12885-017-3111-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 02/04/2017] [Indexed: 12/23/2022] Open
Abstract
Background Proliferation may predict response to neoadjuvant therapy of breast cancer and is commonly assessed by manual scoring of slides stained by immunohistochemistry (IHC) for Ki-67 similar to ER and PgR. This method carries significant intra- and inter-observer variability. Automatic scoring of Ki-67 with digital image analysis (qIHC) or assessment of MKI67 gene expression with RT-qPCR may improve diagnostic accuracy. Methods Ki-67 IHC visual assessment was compared to the IHC nuclear tool (AperioTM) on core biopsies from a randomized neoadjuvant clinical trial. Expression of ESR1, PGR and MKI67 by RT-qPCR was performed on RNA extracted from the same formalin-fixed paraffin-embedded tissue. Concordance between the three methods (vIHC, qIHC and RT-qPCR) was assessed for all 3 markers. The potential of Ki-67 IHC and RT-qPCR to predict pathological complete response (pCR) was evaluated using ROC analysis and non-parametric Mann-Whitney Test. Results Correlation between methods (qIHC versus RT-qPCR) was high for ER and PgR (spearman´s r = 0.82, p < 0.0001 and r = 0.86, p < 0.0001, respectively) resulting in high levels of concordance using predefined cut-offs. When comparing qIHC of ER and PgR with RT-qPCR of ESR1 and PGR the overall agreement was 96.6 and 91.4%, respectively, while overall agreement of visual IHC with RT-qPCR was slightly lower for ER/ESR1 and PR/PGR (91.2 and 92.9%, respectively). In contrast, only a moderate correlation was observed between qIHC and RT-qPCR continuous data for Ki-67/MKI67 (Spearman’s r = 0.50, p = 0.0001). Up to now no predictive cut-off for Ki-67 assessment by IHC has been established to predict response to neoadjuvant chemotherapy. Setting the desired sensitivity at 100%, specificity for the prediction of pCR (ypT0ypN0) was significantly higher for mRNA than for protein (68.9% vs. 22.2%). Moreover, the proliferation levels in patients achieving a pCR versus not differed significantly using MKI67 RNA expression (Mann-Whitney p = 0.002), but not with qIHC of Ki-67 (Mann-Whitney p = 0.097) or vIHC of Ki-67 (p = 0.131). Conclusion Digital image analysis can successfully be implemented for assessing ER, PR and Ki-67. IHC for ER and PR reveals high concordance with RT-qPCR. However, RT-qPCR displays a broader dynamic range and higher sensitivity than IHC. Moreover, correlation between Ki-67 qIHC and RT-qPCR is only moderate and RT-qPCR with MammaTyper® outperforms qIHC in predicting pCR. Both methods yield improvements to error-prone manual scoring of Ki-67. However, RT-qPCR was significantly more specific. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3111-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans-Peter Sinn
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220-221, 69120, Heidelberg, Germany.
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, University-Hospital Heidelberg, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Marius Keller
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220-221, 69120, Heidelberg, Germany
| | | | - Mark Laible
- BioNTech Diagnostics GmbH, 55131, Mainz, Germany
| | - Julia Seitz
- National Center for Tumor Diseases, University-Hospital Heidelberg, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Sotirios Lakis
- STRATIFYER Molecular Pathology GmbH, Werthmannstr. 1c, 50935, Köln, Germany
| | - Elke Veltrup
- STRATIFYER Molecular Pathology GmbH, Werthmannstr. 1c, 50935, Köln, Germany
| | - Peter Altevogt
- German Cancer Research Center, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sebastian Eidt
- Department of Pathology, St. Elisabeth-Krankenhaus, Werthmannstr. 1c, 50935, Köln, Germany
| | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, Werthmannstr. 1c, 50935, Köln, Germany.,Department of Pathology, St. Elisabeth-Krankenhaus, Werthmannstr. 1c, 50935, Köln, Germany
| | - Frederik Marmé
- National Center for Tumor Diseases, University-Hospital Heidelberg, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
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Breyer J, Otto W, Wirtz RM, Wullich B, Keck B, Erben P, Kriegmair MC, Stoehr R, Eckstein M, Laible M, Schlombs K, Eidt S, Denzinger S, Burger M, Hartmann A. ERBB2 Expression as Potential Risk-Stratification for Early Cystectomy in Patients with pT1 Bladder Cancer and Concomitant Carcinoma in situ. Urol Int 2016; 98:282-289. [DOI: 10.1159/000453670] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/21/2016] [Indexed: 11/19/2022]
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9
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Breyer J, Wirtz RM, Laible M, Schlombs K, Erben P, Kriegmair MC, Stoehr R, Eidt S, Denzinger S, Burger M, Hartmann A, Otto W. ESR1, ERBB2, and Ki67 mRNA expression predicts stage and grade of non-muscle-invasive bladder carcinoma (NMIBC). Virchows Arch 2016; 469:547-552. [PMID: 27514658 DOI: 10.1007/s00428-016-2002-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/24/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
Abstract
Pathological staging and grading are crucial for risk assessment in non-muscle-invasive bladder cancer (NMIBC). Molecular grading might support pathological evaluation and minimize interobserver variability. In this study, the well-established breast cancer markers ESR1, PGR, ERBB2, and MKI67 were evaluated as potential molecular markers to support grading and staging in NMIBC. We retrospectively analyzed clinical data and formalin-fixed paraffin-embedded tissues (FFPE) of patients with NMIBC. Messenger RNA (mRNA) expression of the aforementioned markers was measured by single-step reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) using RNA-specific TaqMan assays. Relative gene expression was determined by normalization to two reference genes (CALM2 and B2M) using the 40-ΔΔCT method and correlated to histopathological stage and grade. Pathological assessment was performed by an experienced uropathologist. Statistical analysis was performed using the SAS software JMP 9.0.0 version and GraphPad Prism 5.04. Of 381 cases of NMIBC, samples of 100 pTa and 255 pT1 cases were included in the final study. Spearman rank correlation revealed significant correlations between grade and expression of MKI67 (r = 0.52, p < 0.0001), ESR1 (r = 0.25, p < 0.0001), and ERBB2 (r = 0.18, p = 0.0008). In Mann-Whitney tests, MKI67 was significantly different between all grades (p < 0.0001), while ESR1 (p = 0.0006) and ERBB2 (p = 0.027) were significantly different between G2 and G3. Higher expression of MKI67 (r = 0.49; p < 0.0001), ERBB2 (r = 0.22; p < 0.0001), and ESR1 (r = 0.18; p = 0.0009) mRNA was positively correlated with higher stage. MKI67 (p < 0.0001), ERBB2 (p = 0.0058), and PGR (p = 0.0007) were significantly different between pTa and pT1. In NMIBC expression of ESR1, ERBB2 and MKI67 are significantly different between stage and grade. This potentially provides objective parameters for pathological evaluation.
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Affiliation(s)
- Johannes Breyer
- Department of Urology, University of Regensburg, Caritas Krankenhaus St. Josef, Landshuter Str. 65, 93053, Regensburg, Germany.
| | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany.,Institute of Pathology at the St Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | | | | | - Philipp Erben
- Department of Urology, University of Mannheim, Mannheim, Germany
| | | | - Robert Stoehr
- Institute of Pathology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Eidt
- Institute of Pathology at the St Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | - Stefan Denzinger
- Department of Urology, University of Regensburg, Caritas Krankenhaus St. Josef, Landshuter Str. 65, 93053, Regensburg, Germany
| | - Maximilian Burger
- Department of Urology, University of Regensburg, Caritas Krankenhaus St. Josef, Landshuter Str. 65, 93053, Regensburg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Wolfgang Otto
- Department of Urology, University of Regensburg, Caritas Krankenhaus St. Josef, Landshuter Str. 65, 93053, Regensburg, Germany
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Laible M, Schlombs K, Kaiser K, Veltrup E, Herlein S, Lakis S, Stöhr R, Eidt S, Hartmann A, Wirtz RM, Sahin U. Technical validation of an RT-qPCR in vitro diagnostic test system for the determination of breast cancer molecular subtypes by quantification of ERBB2, ESR1, PGR and MKI67 mRNA levels from formalin-fixed paraffin-embedded breast tumor specimens. BMC Cancer 2016; 16:398. [PMID: 27389414 PMCID: PMC4936300 DOI: 10.1186/s12885-016-2476-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023] Open
Abstract
Background MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative), HER2 positive (non-luminal) and Triple negative (ductal) according to the mRNA expression of ERBB2, ESR1, PGR and MKI67 and the St Gallen consensus surrogate clinical definition. Until now and regarding formalin-fixed, paraffin-embedded material (FFPE), this has been a task mostly accomplished by immunohistochemistry (IHC). However the discrepancy rates of IHC for the four breast cancer biomarkers are frequently under debate, especially for Ki-67 which carries the highest degree of inter- and even intra-observer variability. Herein we describe a series of studies in FFPE specimens which aim to fully validate the analytical performance of the MammaTyper assay, including the site to site reproducibility of the individual marker measurements. Methods Tumor RNA was extracted with the novel RNXtract RNA extraction kit. Synthetic RNA was used to assess the sensitivity of the RNXtract kit. DNA and RNA specific qPCR assays were used so as to determine analyte specificity of RNXtract. For the assessment of limit of blank, limit of detection, analytical measurement range and PCR efficiency of the MammaTyper kit serial dilutions of samples were used. Analytical precision studies of MammaTyper were built around two different real time PCR platforms and involved breast tumor samples belonging to different subtypes analyzed across multiple sites and under various stipulated conditions. The MammaTyper assay robustness was tested against RNA input variations, alternative extraction methods and tumor cell content. Results Individual assays were linear up to at least 32.33 and 33.56 Cqs (quantification cycles) for the two qPCR platforms tested. PCR efficiency ranged from 99 to 109 %. In qPCR platform 1, estimates for assay specific inter-site standard deviations (SD) were between 0.14 and 0.20 Cqs accompanied by >94 % concordant single marker assignments for all four markers. In platform 2, the inter-site SD estimates were between 0.40 and 0.66 Cqs while the concordance for single marker assignments was >94 % for all four markers. The agreement reached between the two qPCR systems located in one site was 100 % for ERBB2, 96.9 % for ESR1, 97.2 % for PGR and 98.6 % for MKI67. RT-qPCR for individual markers was stable up to a 64-fold dilution for a typical clinical sample. There was no change in assay performance detected at the level of individual markers or subtypes after using different RNA isolation methods. The presence of up to 80 % of surrounding non-tumor tissue including in situ carcinoma did not affect the assay output. Sixteen out of 20 RNXtract eluates yielded more than 50 ng/μl of RNA (average RNA output: 233 ng/μl), whereas DNA contamination per sample was restricted to less than 15 ng/μl. Median recovery rate of RNA extraction was 91.0 %. Conclusions In this study the performance characteristics of MammaTyper were successfully validated. The various sources of analytical perturbations resulted in negligible variations in individual marker assessments. Therefore, MammaTyper may serve as a technical improvement to current standards for decentralized FFPE-based routine assessment of the commonly used breast cancer biomarkers and for molecular subtyping of breast cancer specimens. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2476-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Elke Veltrup
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany
| | - Stefanie Herlein
- Institute of Pathology, University of Erlangen, Erlangen, Germany
| | - Sotiris Lakis
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany
| | - Robert Stöhr
- Institute of Pathology, University of Erlangen, Erlangen, Germany
| | - Sebastian Eidt
- Institut für Pathologie am St. Elisabeth-Krankenhaus, Cologne, Germany
| | - Arndt Hartmann
- Institute of Pathology, University of Erlangen, Erlangen, Germany
| | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, Cologne, Germany
| | - Ugur Sahin
- BioNTech Diagnostics GmbH, Mainz, Germany
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11
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Wirtz RM, Sihto H, Isola J, Heikkilä P, Kellokumpu-Lehtinen PL, Auvinen P, Turpeenniemi-Hujanen T, Jyrkkiö S, Lakis S, Schlombs K, Laible M, Weber S, Eidt S, Sahin U, Joensuu H. Biological subtyping of early breast cancer: a study comparing RT-qPCR with immunohistochemistry. Breast Cancer Res Treat 2016; 157:437-46. [PMID: 27220750 PMCID: PMC4903103 DOI: 10.1007/s10549-016-3835-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/13/2016] [Indexed: 12/23/2022]
Abstract
The biological subtype of breast cancer influences the selection of systemic therapy. Distinction between luminal A and B cancers depends on consistent assessment of Ki-67, but substantial intra-observer and inter-observer variability exists when immunohistochemistry (IHC) is used. We compared RT-qPCR with IHC in the assessment of Ki-67 and other standard factors used in breast cancer subtyping. RNA was extracted from archival breast tumour tissue of 769 women randomly assigned to the FinHer trial. Cancer ESR1, PGR, ERBB2 and MKI67 mRNA content was quantitated with an RT-qPCR assay. Local pathologists assessed ER, PgR and Ki-67 expression using IHC. HER2 amplification was identified with chromogenic in situ hybridization (CISH) centrally. The results were correlated with distant disease-free survival (DDFS) and overall survival (OS). qPCR-based and IHC-based assessments of ER and PgR showed good concordance. Both low tumour MKI67 mRNA (RT-qPCR) and Ki-67 protein (IHC) levels were prognostic for favourable DDFS [hazard ratio (HR) 0.42, 95 % CI 0.25–0.71, P = 0.001; and HR 0.56, 0.37–0.84, P = 0.005, respectively] and OS. In multivariable analyses, cancer MKI67 mRNA content had independent influence on DDFS (adjusted HR 0.51, 95 % CI 0.29–0.89, P = 0.019) while Ki-67 protein expression had not any influence (P = 0.266) whereas both assessments influenced independently OS. Luminal B patients treated with docetaxel-FEC had more favourable DDFS and OS than those treated with vinorelbine-FEC when the subtype was defined by RT-qPCR (for DDFS, HR 0.52, 95 % CI 0.29–0.94, P = 0.031), but not when defined using IHC. Breast cancer subtypes approximated with RT-qPCR and IHC show good concordance, but cancer MKI67 mRNA content correlated slightly better with DDFS than Ki-67 expression. The findings based on MKI67 mRNA content suggest that patients with luminal B cancer benefit more from docetaxel-FEC than from vinorelbine-FEC.
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Affiliation(s)
- Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, Werthmannstr. 1c, 50935, Cologne, Germany.
| | - Harri Sihto
- Laboratory of Molecular Oncology, Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Jorma Isola
- Laboratory of Cancer Biology, Institute of Medical Technology, Tampere, Finland
| | - Päivi Heikkilä
- Department of Pathology, HUSLAB, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | | | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | | | - Sirkku Jyrkkiö
- Department of Oncology, Turku University Hospital, Turku, Finland
| | - Sotiris Lakis
- STRATIFYER Molecular Pathology GmbH, Werthmannstr. 1c, 50935, Cologne, Germany
| | | | | | | | - Sebastian Eidt
- Institute of Pathology at the St-Elisabeth-Hospital, Cologne, Germany
| | - Ugur Sahin
- BioNTech Diagnostics GmbH, Mainz, Germany
| | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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12
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Wirtz RM, Scheffen I, Marme F, Laible M, Schlombs K, Hake R, Schumacher C, Schneeweiss A, Eidt S, Sinn HP. Predictive value of ultra-high ESR1 mRNA expression in early breast cancer. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e12045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Iris Scheffen
- St. Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | - Frederik Marme
- National Center for Tumor disease/Department of Gynecology, University of Heidelberg, Heidelberg, Germany
| | | | | | - Roland Hake
- Department of Pathology, St. Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
| | | | | | - Sebastian Eidt
- Department of Pathology, St. Elisabeth Hospital Köln-Hohenlind, Cologne, Germany
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13
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Abstract
gonzo (goz) is a zebrafish mutant with defects in cartilage formation. The goz phenotype comprises cartilage matrix defects and irregular chondrocyte morphology. Expression of endoderm, mesoderm, and cartilage marker genes is, however, normal, indicating a defect in chondrocyte morphogenesis. The mutated gene responsible for the goz phenotype, identified by positional cloning and confirmed by phosphomorpholino knockdown, encodes zebrafish site-1 protease (s1p). S1P has been shown to process and activate sterol regulatory element-binding proteins (SREBPs), which regulate expression of key enzymes of lipid biosynthesis or transport. This finding is consistent with the abnormal distribution of lipids in goz embryos. Knockdown of site-2 protease, which is also involved in activation of SREBPs, results in similar lipid and cartilage phenotypes as S1P knockdown. However, knockdown of SREBP cleavage-activating protein, which forms a complex with SREBP and is essential for S1P cleavage, results only in lipid phenotypes, whereas cartilage appears normal. This indicates that the cartilage phenoptypes of goz are caused independently of the lipid defects.
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