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Kuilman MM, Ellappalayam A, Barcaru A, Haan JC, Bhaskaran R, Wehkamp D, Menicucci AR, Audeh WM, Mittempergher L, Glas AM. BluePrint breast cancer molecular subtyping recognizes single and dual subtype tumors with implications for therapeutic guidance. Breast Cancer Res Treat 2022; 195:263-274. [PMID: 35984580 PMCID: PMC9464757 DOI: 10.1007/s10549-022-06698-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/28/2022] [Accepted: 07/27/2022] [Indexed: 12/05/2022]
Abstract
Purpose BluePrint (BP) is an 80-gene molecular subtyping test that classifies early-stage breast cancer (EBC) into Basal, Luminal, and HER2 subtypes. In most cases, breast tumors have one dominant subtype, representative of a single activated pathway. However, some tumors show a statistically equal representation of more than one subtype, referred to as dual subtype. This study aims to identify and examine dual subtype tumors by BP to understand their biology and possible implications for treatment guidance. Methods The BP scores of over 15,000 tumor samples from EBC patients were analyzed, and the differences between the highest and the lowest scoring subtypes were calculated. Based upon the distribution of the differences between BP scores, a threshold was determined for each subtype to identify dual versus single subtypes. Results Approximately 97% of samples had one single activated BluePrint molecular subtype, whereas ~ 3% of samples were classified as BP dual subtype. The most frequently occurring dual subtypes were the Luminal-Basal-type and Luminal-HER2-type. Luminal-Basal-type displays a distinct biology from the Luminal single type and Basal single type. Burstein’s classification of the single and dual Basal samples showed that the Luminal-Basal-type is mostly classified as ‘luminal androgen receptor’ and ‘mesenchymal’ subtypes, supporting molecular evidence of AR activation in the Luminal-Basal-type tumors. Tumors classified as Luminal-HER2-type resemble features of both Luminal-single-type and HER2-single-type. However, patients with dual Luminal-HER2-type have a lower pathological complete response after receiving HER2-targeted therapies in addition to chemotherapy in comparison with patients with a HER2-single-type. Conclusion This study demonstrates that BP identifies tumors with two active functional pathways (dual subtype) with specific transcriptional characteristics and highlights the added value of distinguishing BP dual from single subtypes as evidenced by distinct treatment response rates. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-022-06698-x.
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Affiliation(s)
- Midas M Kuilman
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Architha Ellappalayam
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Andrei Barcaru
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Josien C Haan
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Rajith Bhaskaran
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Diederik Wehkamp
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands
| | - Andrea R Menicucci
- Department of Medical Affairs, Agendia Inc, 22 Morgan, Irvine, CA, 92618, USA
| | - William M Audeh
- Department of Medical Affairs, Agendia Inc, 22 Morgan, Irvine, CA, 92618, USA
| | - Lorenza Mittempergher
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands.
| | - Annuska M Glas
- Department of Research and Development, Agendia N.V, Radarweg 60, 1043 NT, Amsterdam, The Netherlands.
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Kuilman M, Ellappalayam A, Mittempergher L, Wehkamp D, Chan B, Bhaskaran R, Glas A. BluePrint molecular subtyping recognizes single and dual subtype tumors with consequences for therapeutic guidance. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)30821-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jacob L, Witteveen A, Beumer I, Delahaye L, Wehkamp D, van den Akker J, Snel M, Chan B, Floore A, Bakx N, Brink G, Poncet C, Bogaerts J, Delorenzi M, Piccart M, Rutgers E, Cardoso F, Speed T, van 't Veer L, Glas A. Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial. Commun Biol 2020; 3:397. [PMID: 32719399 PMCID: PMC7385160 DOI: 10.1038/s42003-020-1111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Gene expression data obtained in large studies hold great promises for discovering disease signatures or subtypes through data analysis. It is also prone to technical variation, whose removal is essential to avoid spurious discoveries. Because this variation is not always known and can be confounded with biological signals, its removal is a challenging task. Here we provide a step-wise procedure and comprehensive analysis of the MINDACT microarray dataset. The MINDACT trial enrolled 6693 breast cancer patients and prospectively validated the gene expression signature MammaPrint for outcome prediction. The study also yielded a full-transcriptome microarray for each tumor. We show for the first time in such a large dataset how technical variation can be removed while retaining expected biological signals. Because of its unprecedented size, we hope the resulting adjusted dataset will be an invaluable tool to discover or test gene expression signatures and to advance our understanding of breast cancer.
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Affiliation(s)
- Laurent Jacob
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France
| | | | - Inès Beumer
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | | | | | | | | | - Bob Chan
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Arno Floore
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Niels Bakx
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Guido Brink
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | | | | | - Mauro Delorenzi
- University Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Emiel Rutgers
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Terence Speed
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Laura van 't Veer
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands.
- Helen Diller Family Comprehensive Cancer Center, University California San Francisco, San Francisco, CA, USA.
| | - Annuska Glas
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands.
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Bhaskaran R, Griffioen C, Wehkamp D, Mittempergher L, Glas A. Unravelling the biological characteristics of MammaPrint extreme risk subgroups. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz240.064] [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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Mittempergher L, Delahaye LJMJ, Witteveen AT, Spangler JB, Hassenmahomed F, Mee S, Mahmoudi S, Chen J, Bao S, Snel MHJ, Leidelmeijer S, Besseling N, Bergstrom Lucas A, Pabón-Peña C, Linn SC, Dreezen C, Wehkamp D, Chan BY, Bernards R, van 't Veer LJ, Glas AM. MammaPrint and BluePrint Molecular Diagnostics Using Targeted RNA Next-Generation Sequencing Technology. J Mol Diagn 2019; 21:808-823. [PMID: 31173928 DOI: 10.1016/j.jmoldx.2019.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/21/2019] [Accepted: 04/16/2019] [Indexed: 01/31/2023] Open
Abstract
Next-generation DNA sequencing is rapidly becoming an indispensable tool for genome-directed cancer diagnostics, but next-generation RNA sequencing (RNA-seq) is currently not standardly used in clinical diagnostics for expression assessment. However, multigene RNA diagnostic assays are used increasingly in the routine diagnosis of early-stage breast cancer. Two of the most widely used tests are currently available only as a central laboratory service, which limits their clinical use. We evaluated the use of RNA-seq as a decentralized method to perform such tests. The MammaPrint and BluePrint RNA-seq tests were found to be equivalent to the clinically validated microarray tests. The RNA-seq tests were highly reproducible when performed in different locations and were stable over time. The MammaPrint RNA-seq test was clinically validated. Our data demonstrate that RNA-seq can be used as a decentralized platform, yielding results substantially equivalent to results derived from the predicate diagnostic device.
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Affiliation(s)
| | | | - Anke T Witteveen
- Research and Development, Agendia NV, Amsterdam, the Netherlands
| | | | | | - Sammy Mee
- Product Support, Agendia Inc., Irvine, California
| | | | - Jiang Chen
- Product Support, Agendia Inc., Irvine, California
| | - Simon Bao
- Product Support, Agendia Inc., Irvine, California
| | | | | | - Naomi Besseling
- Research and Development, Agendia NV, Amsterdam, the Netherlands
| | | | - Carlos Pabón-Peña
- Diagnostics and Genomics Group, Agilent Technologies, Santa Clara, California
| | - Sabine C Linn
- Division of Molecular Pathology and Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christa Dreezen
- Research and Development, Agendia NV, Amsterdam, the Netherlands
| | - Diederik Wehkamp
- Research and Development, Agendia NV, Amsterdam, the Netherlands
| | - Bob Y Chan
- Product Support, Agendia Inc., Irvine, California
| | - René Bernards
- Research and Development, Agendia NV, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laura J van 't Veer
- Research and Development, Agendia NV, Amsterdam, the Netherlands; Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California
| | - Annuska M Glas
- Research and Development, Agendia NV, Amsterdam, the Netherlands.
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Sobral-Leite M, Van de Vijver K, Michaut M, van der Linden R, Hooijer GK, Horlings HM, Severson TM, Mulligan AM, Weerasooriya N, Sanders J, Glas AM, Wehkamp D, Mittempergher L, Kersten K, Cimino-Mathews A, Peters D, Hooijberg E, Broeks A, van de Vijver MJ, Bernards R, Andrulis IL, Kok M, de Visser KE, Schmidt MK. Assessment of PD-L1 expression across breast cancer molecular subtypes, in relation to mutation rate, BRCA1-like status, tumor-infiltrating immune cells and survival. Oncoimmunology 2018; 7:e1509820. [PMID: 30524905 PMCID: PMC6279322 DOI: 10.1080/2162402x.2018.1509820] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 01/28/2023] Open
Abstract
To better understand the expression pattern of programmed death-ligand 1 (PD-L1) expression in different breast cancer types, we characterized PD-L1 expression in tumor and tumor-infiltrating immune cells, in relation to mutation rate, BRCA1-like status and survival. We analyzed 410 primary treatment-naive breast tumors comprising 162 estrogen receptor-positive (ER+) and HER2-, 101 HER2+ and 147 triple-negative (TN) cancers. Pathologists quantified tumor-infiltrating lymphocytes (TILs) and PD-L1 expression in tumor cells and TILs using whole slides and tissue microarray. Mutation rate was assessed by DNA sequencing, BRCA1-like status using multiplex ligation-dependent probe amplification, and immune landscape by multiplex image analyses of CD4, CD68, CD8, FOXP3, cytokeratin, and PD-L1. Half of PD-L1 scores evaluated by tissue microarray were false negatives compared to whole slide evaluations. We observed at least 1% of PD-L1-positive (PD-L1+) cells in 53.1% of ER+HER2-, 73.3% of HER2+, and 84.4% of TN tumors. PD-L1 expression was higher in ductal compared to lobular carcinomas, also within ER+HER2- tumors (p = 0.04). High PD-L1+ TILs score (> 50%) was independently associated with better outcome in TN tumors (HR = 0.27; 95%CI = 0.10-0.69). Within TN tumors, PD-L1 and TIL scores showed a modest but significant positive association with the number of silent mutations, but no association with BRCA1-like status. Multiplex image analyses indicated that PD-L1 is expressed on multiple immune cells (CD68+ macrophages, CD4+, FOXP3+, and CD8+ T cells) in the breast tumor microenvironment, independent of the PD-L1 status of the tumor cells. We found no evidence that levels of PD-L1+ TILs in TN breast cancer are driven by high mutation rate or BRCA1-like status.
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Affiliation(s)
- Marcelo Sobral-Leite
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil
| | - Koen Van de Vijver
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Gerrit K.J. Hooijer
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Hugo M. Horlings
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M. Severson
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Joyce Sanders
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Kelly Kersten
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Dennis Peters
- Core Facility Molecular Pathology and Biobanking, Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Erik Hooijberg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Irene L. Andrulis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marleen Kok
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marjanka K. Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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In 't Veld SGJG, Duong KN, Snel M, Witteveen A, Beumer IJ, Delahaye LJMJ, Wehkamp D, Bernards R, Glas AM, Tian S. A Computational Workflow Translates a 58-Gene Signature to a Formalin-Fixed, Paraffin-Embedded Sample-Based Companion Diagnostic for Personalized Treatment of the BRAF-Mutation-Like Subtype of Colorectal Cancers. High Throughput 2017; 6:ht6040016. [PMID: 29479053 PMCID: PMC5748595 DOI: 10.3390/ht6040016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 10/12/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer patients with the BRAF(p.V600E) mutation have poor prognosis in metastatic setting. Personalized treatment options and companion diagnostics are needed to better treat these patients. Previously, we developed a 58-gene signature to characterize the distinct gene expression pattern of BRAF-mutation-like subtype (accuracy 91.1%). Further experiments repurposed drug Vinorelbine as specifically lethal to this BRAF-mutation-like subtype. The aim of this study is to translate this 58-gene signature from a research setting to a robust companion diagnostic that can use formalin-fixed, paraffin-embedded (FFPE) samples to select patients with the BRAF-mutation-like subtype. BRAF mutation and gene expression data of 302 FFPE samples were measured (mutants = 57, wild-type = 245). The performance of the 58-gene signature in FFPE samples showed a high sensitivity of 89.5%. In the identified BRAF-mutation-like subtype group, 50% of tumours were known BRAF mutants, and 50% were BRAF wild-type. The stability of the 58-gene signature in FFPE samples was evaluated by two control samples over 40 independent experiments. The standard deviations (SD) were within the predefined criteria (control 1: SD = 0.091, SD/Range = 3.0%; control 2: SD = 0.169, SD/Range = 5.5%). The fresh frozen version and translated FFPE version of this 58-gene signature were compared using 170 paired fresh frozen and FFPE samples and the result showed high consistency (agreement = 99.3%). In conclusion, we translated this 58-gene signature to a robust companion diagnostic that can use FFPE samples.
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Affiliation(s)
- Sjors G J G In 't Veld
- Department of Neurosurgery, VU University Medical Center, 1081HV Amsterdam, The Netherlands.
| | - Kim N Duong
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | - Mireille Snel
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | - Anke Witteveen
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | - Inès J Beumer
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | | | - Diederik Wehkamp
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | - René Bernards
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
| | - Annuska M Glas
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
| | - Sun Tian
- Agendia NV, Science Park 406, 1098XH Amsterdam, The Netherlands.
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Beumer I, Witteveen A, Delahaye L, Wehkamp D, Snel M, Dreezen C, Zheng J, Floore A, Brink G, Chan B, Linn S, Bernards R, van 't Veer L, Glas A. Equivalence of MammaPrint array types in clinical trials and diagnostics. Breast Cancer Res Treat 2016; 156:279-87. [PMID: 27002507 PMCID: PMC4819553 DOI: 10.1007/s10549-016-3764-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 01/28/2023]
Abstract
MammaPrint is an FDA-cleared microarray-based test that uses expression levels of the 70 MammaPrint genes to assess distant recurrence risk in early-stage breast cancer. The prospective RASTER study proved that MammaPrint Low Risk patients can safely forgo chemotherapy, which is further subject of the prospective randomized MINDACT trial. While MammaPrint diagnostic results are obtained from mini-arrays, clinical trials may be performed on whole-genome arrays. Here we demonstrate the equivalence and reproducibility of the MammaPrint test. MammaPrint indices were collected for breast cancer samples: (i) on both customized certified array types (n = 1,897 sample pairs), (ii) with matched fresh and FFPE tissues (n = 552 sample pairs), iii) for control samples replicated over a period of 10 years (n = 11,333), and iv) repeated measurements (n = 280). The array type indicated a near perfect Pearson correlation of 0.99 (95 % CI: 0.989-0.991). Paired fresh and FFPE samples showed an excellent Pearson correlation of 0.93 (95 % CI 0.92-0.94), in spite of the variability introduced by intratumoral tissue heterogeneity. Control samples showed high consistency over 10 year's time (overall reproducibility of 97.4 %). Precision and repeatability are overall 98.2 and 98.3 %, respectively. Results confirm that the combination of the near perfect correlation between array types, excellent equivalence between tissue types, and a very high stability, precision, and repeatability demonstrate that results from clinical trials (such as MINDACT and I-SPY 2) are equivalent to current MammaPrint FFPE and fresh diagnostics, and can be used interchangeably.
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Affiliation(s)
- Inès Beumer
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Anke Witteveen
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Leonie Delahaye
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Diederik Wehkamp
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Mireille Snel
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Christa Dreezen
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - John Zheng
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Arno Floore
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Guido Brink
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Bob Chan
- Agendia Inc, 22 Morgan, Irvine, CA 92618, USA
| | - Sabine Linn
- Divisions of Molecular Pathology and Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Rene Bernards
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | | | - Annuska Glas
- Agendia NV, Science Park 406, 1098 XH, Amsterdam, The Netherlands.
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Delahaye LJ, Wehkamp D, Floore AN, Bernards R, Van't Veer LJ, Glas AM. Performance characteristics of the MammaPrint ® breast cancer diagnostic gene signature. Per Med 2013; 10:801-811. [PMID: 29776281 DOI: 10.2217/pme.13.88] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND The analytical performance of multigene signatures depends on many parameters, including precision, repeatability, reproducibility and intratumor heterogeneity. Indicators such as sensitivity, specificity, positive predictive value and negative predictive value are typically used to define the clinical performance of a diagnostic test. AIM Here we study these performance characteristics of the MammaPrint® (Agendia NV, Amsterdam, The Netherlands) 70-gene signature using the US FDA-recommended guidelines, as well as predetermined acceptance criteria. RESULTS The clinical and analytical performance characteristics show that MammaPrint is a robust, reproducible, precise test, with a maximum variation of 5% in multiple samplings of the same tissue. CONCLUSION MammaPrint is a reliable indicator of distant metastasis in early-stage breast cancer patients of all ages and is well suited for personalized medical care.
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Affiliation(s)
- Leonie Jm Delahaye
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Diederik Wehkamp
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Arno N Floore
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Rene Bernards
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Laura J Van't Veer
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Annuska M Glas
- Department of Product Development & Support, Agendia NV, Science Park 406, 1098 XH Amsterdam, The Netherlands.
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van Laar RK, Ma XJ, de Jong D, Wehkamp D, Floore AN, Warmoes MO, Simon I, Wang W, Erlander M, van't Veer LJ, Glas AM. Implementation of a novel microarray-based diagnostic test for cancer of unknown primary. Int J Cancer 2009; 125:1390-7. [DOI: 10.1002/ijc.24504] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Sokolović M, Sokolović A, Wehkamp D, Ver Loren van Themaat E, de Waart DR, Gilhuijs-Pederson LA, Nikolsky Y, van Kampen AHC, Hakvoort TBM, Lamers WH. The transcriptomic signature of fasting murine liver. BMC Genomics 2008; 9:528. [PMID: 18990241 PMCID: PMC2588605 DOI: 10.1186/1471-2164-9-528] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 11/06/2008] [Indexed: 12/17/2022] Open
Abstract
Background The contribution of individual organs to the whole-body adaptive response to fasting has not been established. Hence, gene-expression profiling, pathway, network and gene-set enrichment analysis and immunohistochemistry were carried out on mouse liver after 0, 12, 24 and 72 hours of fasting. Results Liver wet weight had declined ~44, ~5, ~11 and ~10% per day after 12, 24, 48 and 72 hours of fasting, respectively. Liver structure and metabolic zonation were preserved. Supervised hierarchical clustering showed separation between the fed, 12–24 h-fasted and 72 h-fasted conditions. Expression profiling and pathway analysis revealed that genes involved in amino-acid, lipid, carbohydrate and energy metabolism responded most significantly to fasting, that the response peaked at 24 hours, and had largely abated by 72 hours. The strong induction of the urea cycle, in combination with increased expression of enzymes of the tricarboxylic-acid cycle and oxidative phosphorylation, indicated a strong stimulation of amino-acid oxidation peaking at 24 hours. At this time point, fatty-acid oxidation and ketone-body formation were also induced. The induction of genes involved in the unfolded-protein response underscored the cell stress due to enhanced energy metabolism. The continuous high expression of enzymes of the urea cycle, malate-aspartate shuttle, and the gluconeogenic enzyme Pepck and the re-appearance of glycogen in the pericentral hepatocytes indicate that amino-acid oxidation yields to glucose and glycogen synthesis during prolonged fasting. Conclusion The changes in liver gene expression during fasting indicate that, in the mouse, energy production predominates during early fasting and that glucose production and glycogen synthesis become predominant during prolonged fasting.
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Affiliation(s)
- Milka Sokolović
- AMC Liver Center, Academic Medical Center, University of Amsterdam, The Netherlands.
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Sokolović M, Wehkamp D, Sokolović A, Vermeulen J, Gilhuijs-Pederson LA, van Haaften RIM, Nikolsky Y, Evelo CTA, van Kampen AHC, Hakvoort TBM, Lamers WH. Fasting induces a biphasic adaptive metabolic response in murine small intestine. BMC Genomics 2007; 8:361. [PMID: 17925015 PMCID: PMC2148066 DOI: 10.1186/1471-2164-8-361] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 10/09/2007] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The gut is a major energy consumer, but a comprehensive overview of the adaptive response to fasting is lacking. Gene-expression profiling, pathway analysis, and immunohistochemistry were therefore carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting. RESULTS Intestinal weight declined to 50% of control, but this loss of tissue mass was distributed proportionally among the gut's structural components, so that the microarrays' tissue base remained unaffected. Unsupervised hierarchical clustering of the microarrays revealed that the successive time points separated into distinct branches. Pathway analysis depicted a pronounced, but transient early response that peaked at 12 hours, and a late response that became progressively more pronounced with continued fasting. Early changes in gene expression were compatible with a cellular deficiency in glutamine, and metabolic adaptations directed at glutamine conservation, inhibition of pyruvate oxidation, stimulation of glutamate catabolism via aspartate and phosphoenolpyruvate to lactate, and enhanced fatty-acid oxidation and ketone-body synthesis. In addition, the expression of key genes involved in cell cycling and apoptosis was suppressed. At 24 hours of fasting, many of the early adaptive changes abated. Major changes upon continued fasting implied the production of glucose rather than lactate from carbohydrate backbones, a downregulation of fatty-acid oxidation and a very strong downregulation of the electron-transport chain. Cell cycling and apoptosis remained suppressed. CONCLUSION The changes in gene expression indicate that the small intestine rapidly looses mass during fasting to generate lactate or glucose and ketone bodies. Meanwhile, intestinal architecture is maintained by downregulation of cell turnover.
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Affiliation(s)
- Milka Sokolović
- AMC Liver Centre, Academic Medical Centre, Amsterdam, The Netherlands
| | - Diederik Wehkamp
- Bioinformatics Laboratory, Academic Medical Centre, Amsterdam, The Netherlands
| | | | | | | | | | | | - Chris TA Evelo
- BiGCaT Bioinformatics, University of Maastricht, Maastricht, The Netherlands
| | | | | | - Wouter H Lamers
- AMC Liver Centre, Academic Medical Centre, Amsterdam, The Netherlands
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