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Puppe J, Liu X, Ratz L, Bartke L, van de Ven M, Vliet MH, Wientjes E, van der Gulden H, Zevenhoven J, Hahnen E, Malter W, Wessels LFA, Schmutzler R, Mallmann P, Reinhardt C, Linn S, Jonkers J. Double BRCA1 and BRCA2 inactivation is epistatic in mammary tumorigenesis and treatment response to PARP-inhibition and platinum drugs. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1717868] [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: 10/23/2022] Open
Affiliation(s)
- J Puppe
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | - X Liu
- Netherlands Cancer Institute
| | - L Ratz
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | - L Bartke
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | | | | | | | | | - E Hahnen
- Zentrum Familiärer Brust- und Eierstockkrebs, Uniklinik Köln
| | - W Malter
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | - R Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Uniklinik Köln
| | - P Mallmann
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | - S Linn
- Netherlands Cancer Institute
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2
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van der Vos KE, Vis DJ, Nevedomskaya E, Kim Y, Choi W, McConkey D, Wessels LFA, van Rhijn BWG, Zwart W, van der Heijden MS. Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer. Sci Rep 2020; 10:10952. [PMID: 32616859 PMCID: PMC7331601 DOI: 10.1038/s41598-020-67850-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease that often recurs despite aggressive treatment with neoadjuvant chemotherapy and (radical) cystectomy. Basal and luminal molecular subtypes have been identified that are linked to clinical characteristics and have differential sensitivities to chemotherapy. While it has been suggested that epigenetic mechanisms play a role in defining these subtypes, a thorough understanding of the biological mechanisms is lacking. This report details the first genome-wide analysis of histone methylation patterns of human primary bladder tumours by chromatin immunoprecipitations and next-generation sequencing (ChIP-seq). We profiled multiple histone marks: H3K27me3, a marker for repressed genes, and H3K4me1 and H3K4me3, which are indicators of active enhancers and active promoters. Integrated analysis of ChIP-seq data and RNA sequencing revealed that H3K4 mono-methylation demarcates MIBC subtypes, while no association was found for the other two histone modifications in relation to basal and luminal subtypes. Additionally, we identified differentially methylated H3K4me1 peaks in basal and luminal tumour samples, suggesting that active enhancers play a role in defining subtypes. Our study is the first analysis of histone modifications in primary bladder cancer tissue and provides an important resource for the bladder cancer community.
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Affiliation(s)
- K E van der Vos
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D J Vis
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E Nevedomskaya
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Y Kim
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - W Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - D McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - B W G van Rhijn
- Department of Surgical Oncology (Urology), The Netherlands Cancer Institute, Antoni Van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - W Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M S van der Heijden
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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3
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Abstract
Cancer is a complex disease in which cells progressively accumulate mutations disrupting their cellular processes. A fraction of these mutations drive tumourigenesis by affecting oncogenes or tumour suppressor genes, but many mutations are passengers with no clear contribution to tumour development. The advancement of DNA and RNA sequencing technologies has enabled in-depth analysis of thousands of human tumours from various tissues to perform systematic characterization of their (epi)genomes and transcriptomes in order to identify (epi)genetic changes associated with cancer. Combined with considerable progress in algorithmic development, this expansion in scale has resulted in the identification of many cancer-associated mutations, genes and pathways that are considered to be potential drivers of tumour development. However, it remains challenging to systematically identify drivers affected by complex genomic rearrangements and drivers residing in non-coding regions of the genome or in complex amplicons or deletions of copy-number driven tumours. Furthermore, functional characterization is challenging in the human context due to the lack of genetically tractable experimental model systems in which the effects of mutations can be studied in the context of their tumour microenvironment. In this respect, mouse models of human cancer provide unique opportunities for pinpointing novel driver genes and their detailed characterization. In this review, we provide an overview of approaches for complementing human studies with data from mouse models. We also discuss state-of-the-art technological developments for cancer gene discovery and validation in mice.
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Affiliation(s)
- J R de Ruiter
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - J Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
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4
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Stelloo S, Nevedomskaya E, Kim Y, Hoekman L, Bleijerveld OB, Mirza T, Wessels LFA, van Weerden WM, Altelaar AFM, Bergman AM, Zwart W. Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis. Oncogene 2017; 37:313-322. [PMID: 28925401 DOI: 10.1038/onc.2017.330] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/10/2017] [Accepted: 08/06/2017] [Indexed: 12/13/2022]
Abstract
Androgen receptor (AR) is a key player in prostate cancer development and progression. Here we applied immunoprecipitation mass spectrometry of endogenous AR in LNCaP cells to identify components of the AR transcriptional complex. In total, 66 known and novel AR interactors were identified in the presence of synthetic androgen, most of which were critical for AR-driven prostate cancer cell proliferation. A subset of AR interactors required for LNCaP proliferation were profiled using chromatin immunoprecipitation assays followed by sequencing, identifying distinct genomic subcomplexes of AR interaction partners. Interestingly, three major subgroups of genomic subcomplexes were identified, where selective gain of function for AR genomic action in tumorigenesis was found, dictated by FOXA1 and HOXB13. In summary, by combining proteomic and genomic approaches we reveal subclasses of AR transcriptional complexes, differentiating normal AR behavior from the oncogenic state. In this process, the expression of AR interactors has key roles by reprogramming the AR cistrome and interactome in a genomic location-specific manner.
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Affiliation(s)
- S Stelloo
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E Nevedomskaya
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Y Kim
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L Hoekman
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - O B Bleijerveld
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - T Mirza
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - W M van Weerden
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A F M Altelaar
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, The Netherlands Proteomics Centre, Utrecht University, Utrecht, The Netherlands
| | - A M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - W Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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5
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Vis DJ, Lewin J, Liao RG, Mao M, Andre F, Ward RL, Calvo F, Teh BT, Camargo AA, Knoppers BM, Sawyers CL, Wessels LFA, Lawler M, Siu LL, Voest E. Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape. Ann Oncol 2017; 28:1145-1151. [PMID: 28453708 PMCID: PMC5406763 DOI: 10.1093/annonc/mdx037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. METHODS A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally. Additionally, respondents were asked as to provide the primary intent of their initiative (clinical diagnostic, research or combination). RESULTS Of 107 initiatives invited to participate, 59 responded (response rate = 55%). Whole exome sequencing (P = 0.03) and whole genome sequencing (P = 0.01) were utilized less frequently in clinical diagnostic than in research initiatives. Procedures to identify cancer-specific variants were heterogeneous, with bioinformatics pipelines employing different mutation calling/variant annotation algorithms. Measurement of treatment efficacy varied amongst initiatives, with time on treatment (57%) and RECIST (53%) being the most common; however, other parameters were also employed. Whilst 72% of initiatives indicated data sharing, its scope varied, with a number of restrictions in place (e.g. transfer of raw data). The largest perceived barriers to data harmonization were the lack of financial support (P < 0.01) and bioinformatics concerns (e.g. lack of interoperability) (P = 0.02). Capturing clinical data was more likely to be perceived as a barrier to data sharing by larger initiatives than by smaller initiatives (P = 0.01). CONCLUSIONS These results identify the main barriers, as perceived by the cancer sequencing community, to effective sharing of cancer genomic and clinical data. They highlight the need for greater harmonization of technical, ethical and data capture processes in cancer sample sequencing worldwide, in order to support effective and responsible data sharing for the benefit of patients.
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Affiliation(s)
- D. J. Vis
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J. Lewin
- Princess Margaret Cancer Centre, Toronto, Canada
| | - R. G. Liao
- Global Alliance for Genomics and Health, Broad Institute, Cambridge, USA
| | - M. Mao
- Yonsei Cancer Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - F. Andre
- INSERM U981, Université Paris Sud, Institut Gustave Roussy, Villejuif, France
| | - R. L. Ward
- Research, University of Queensland, Brisbane, Australia
| | - F. Calvo
- Cancer Core Europe, Gustave Roussy, Villejuif, France
| | | | | | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - C. L. Sawyers
- Memorial Sloan Kettering Cancer Centre, New York, USA
| | - L. F. A. Wessels
- Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Bioinformatics & Statistics, Delft University of Technology, Delft, The Netherlands
| | - M. Lawler
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK
| | - L. L. Siu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - E. Voest
- Netherlands Cancer Institute, Amsterdam, The Netherlands
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6
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Lips EH, Hoogstraat M, Mulder L, Nederlof PM, Sonke GS, Rodenhuis S, Wesseling J, Wessels LFA. Abstract PD1-07: Comprehensive characterization of matched pre-treatment biopsies and residual disease of doxorubicin treated breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-pd1-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Neoadjuvant chemotherapy is standard of care for locally advanced breast cancer. Unfortunately not all patients benefit from this treatment. Even after decades of research, we still cannot predict which tumor will or will not respond. This may in part be due to tumor heterogeneity, as the sample taken before treatment not necessarily represents the tumor cell population that causes therapy resistance.
Methods
To test this hypothesis, we collected pre-treatment biopsies, resection specimens, and matched blood from 21 breast cancer patients treated with doxorubicin and cyclophosphamide in a neoadjuvant setting. Specifically, tumors were selected with a tumor percentage >50% after chemotherapy to enrich for resistant samples and ensure high quality data. RNA and whole exome sequencing were performed to characterize somatic mutations, copy number alterations and gene expression profiles. Histopathological characteristics were determined to obtain a comprehensive profile of all tumor samples.
Results
The comparisons of somatic variants and copy number alterations revealed a very diverse image: in several cases, high-level amplifications, large genomic gains or losses, and mutations in known oncogenes or tumor suppressors such as MAP3K1 and RUNX1 were either lost or gained during treatment, while in other cases no such changes were detected. We observed a remarkable number of genetic alterations involved in cell cycle progression and DNA damage checkpoints, including amplification of MDM2, CCND1 and CDK4, and copy number loss or mutations in CDKN1B and ATM. Strikingly, both cases of CDKN1B loss were identified in pre-treatment biopsies and no longer detectable in the surgery specimen. In contrast, CCND1, CDK4 and MDM2 amplifications were retained, although CCND1 expression decreased significantly in CCND1 amplified tumors.
In addition, eighty percent of tumors showed a decreased cell proliferation after chemotherapy, where the high-proliferative ER+ (Luminal B) tumors were most strongly affected. This trend was also visible in a validation cohort of 94 ER+ samples, but the prognosis of Luminal B tumors that showed a decrease in proliferation was still significantly worse than that of Luminal A tumors that did not show an altered proliferation rate.
Conclusion
Our results confirm that biologically relevant genomic alterations can differ between pre- and post-treatment samples, which greatly impacts biomarker discovery. In addition, our findings emphasize the chemotherapy insensitivity of CCND1 amplified ER+ breast cancers, and stress the need for better treatment regimens for these patients. In contrast, genomic loss of CDKN1B may be a marker for sensitivity to doxorubicin.
Citation Format: Lips EH, Hoogstraat M, Mulder L, Nederlof PM, Sonke GS, Rodenhuis S, Wesseling J, Wessels LFA. Comprehensive characterization of matched pre-treatment biopsies and residual disease of doxorubicin treated breast cancer [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 PD1-07.
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Affiliation(s)
- EH Lips
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - M Hoogstraat
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - L Mulder
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - PM Nederlof
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - GS Sonke
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - S Rodenhuis
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - J Wesseling
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - LFA Wessels
- The Netherlands Cancer Institute- Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
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7
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Lips EH, Mulder L, de Ronde
JJ, Mandjes IAM, Koolen BB, Wessels LFA, Rodenhuis S, Wesseling J. Breast cancer subtyping by immunohistochemistry and histological grade outperforms breast cancer intrinsic subtypes in predicting neoadjuvant chemotherapy response. Breast Cancer Res Treat 2013; 140:63-71. [PMID: 23828499 PMCID: PMC3706735 DOI: 10.1007/s10549-013-2620-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [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: 03/22/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Abstract
Intrinsic subtypes are widely accepted for the classification of breast cancer. Lacking gene expression data, surrogate classifications based on immunohistochemistry (IHC) have been proposed. A recent St. Gallen consensus meeting recommends to use this "surrogate intrinsic subtypes" for predicting adjuvant chemotherapy resistance, implying that "Surrogate Luminal A" breast cancers should only receive endocrine therapy. In this study we assessed both gene expression based intrinsic subtypes as well as surrogate intrinsic subtypes regarding their power to predict neoadjuvant chemotherapy benefit. Single institution data of 560 breast cancer patients were reviewed. Gene expression data was available for 247 patients. Subtypes were determined on the basis of IHC, Ki67, histological grade, endocrine responsiveness, and gene expression, and were correlated with chemotherapy response and recurrence-free survival. In ER+/HER2- tumors, a high histological grade was the best predictor for chemotherapy benefit, both in terms of pCR (p = 0.004) and recurrence-free survival (p = 0.002). The gene expression based and surrogate intrinsic subtype based on Ki67 had no predictive or prognostic value in ER+/HER2- tumors. Histological grade, ER, PR, and HER2 were the best predictive factors for chemotherapy response in breast cancer. We propose to continue the conventional use of these markers.
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Affiliation(s)
- E. H. Lips
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - L. Mulder
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - J. J. de Ronde
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Bioinformatics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - I. A. M. Mandjes
- Data Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - B. B. Koolen
- Department of Nuclear Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Surgical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L. F. A. Wessels
- Department of Bioinformatics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - S. Rodenhuis
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J. Wesseling
- Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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8
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Wesseling J, Lips EH, Oonk AMM, Smits RM, van Rijn CCM, Mulder L, Laddach N, Savola SS, Wessels LFA, Nederlof PM, Rodenhuis S, Imholz ALT. PD03-08: BRCA1-Like Triple Negative Tumors: Clinicopathological Variables and Chemosensitivity to Alkylating Agents. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-pd03-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Our group has previously employed array Comparative Genomic Hybridization (aCGH) to assess the genomic patterns of BRCA1-mutated breast cancers. It is reasonable to assume that this pattern indicates ‘BRCAness’ and thus serves as a marker for homologous recombination deficiency. This BRCA1-like aCGH profile is also present in about half of all triple negative sporadic breast cancers and has been shown to be predictive for benefit from intensive chemotherapy with DNA crosslinking agents. To study BRCA1-like tumors and conventional dose chemotherapy sensitivity in more detail, we compared clinical factors and survival rates in a uniform cohort of triple negative breast tumors treated with alkylating agents.
Patients and methods
103 patients with triple negative tumors received conventional dose adjuvant chemotherapy with doxorubicin/cyclophosphamide. DNA was extracted from tumor samples and BRCA1-like profiles were assessed. Tumors were classified as BRCA1 -like or non-BRCA1-like. Standard clinical and histopathological factors were determined and compared between both groups. Relapse free survival (RFS), disease specific survival (DSS) and overall survival (OS) after diagnosis were compared between BRCA1-like and non-BRCA1-like tumors.
Results
66 tumors (65%) had a BRCA1-like profile, while 35 tumors (35%) did not show such a profile. Patients with BRCA1-like tumors tended to be younger and had more often node-negative disease compared to the patients with non-BRCA1-like tumors (p=0.058 and p=0.034, respectively). There was no significant difference in survival between BRCA1-like and non BRCA1-like patients after treatment with alkylating agents: the median RFS was 121 vs. 109 months, median DSS was 129 vs. 114 months and OS was 127 vs. 110 months, for BRCA1-like versus non-BRCA1-like tumors. T-stage was the only variable significantly associated with survival.
Conclusion
BRCA1-like tumors occurred in younger patients and were more often node negative, which are features shared with tumors in BRCA1-mutation carriers. We did not observe a difference in survival between BRCA1-like and non-BRCA1-like triple negative breast cancers after treatment with conventional dose chemotherapy with alkylating agents. These results confirm our previous findings that BRCA1-like tumors have similar sensitivity to anthracycline-based adjuvant chemotherapy as other triple-negative tumors. It will be important to establish whether BRCA1-like tumors also share the exquisite sensitivity of BRCA-mutated tumors to PARP-inhibitors.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-08.
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Affiliation(s)
- J Wesseling
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - EH Lips
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - AMM Oonk
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - RM Smits
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - CCM van Rijn
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - L Mulder
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - N Laddach
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - SS Savola
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - LFA Wessels
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - PM Nederlof
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - S Rodenhuis
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
| | - ALT Imholz
- 1Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands; Deventer Hospital, Deventer, Netherlands; MRC-Holland, Amsterdam, Netherlands
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9
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Vollebergh MA, Lips EH, Nederlof PM, Wessels LFA, Schmidt MK, van Beers EH, Cornelissen S, Holtkamp M, Froklage FE, de Vries EGE, Schrama JG, Wesseling J, van de Vijver MJ, van Tinteren H, de Bruin M, Hauptmann M, Rodenhuis S, Linn SC. An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients. Ann Oncol 2011; 22:1561-1570. [PMID: 21135055 PMCID: PMC3121967 DOI: 10.1093/annonc/mdq624] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/07/2010] [Accepted: 09/14/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Breast cancer cells deficient for BRCA1 are hypersensitive to agents inducing DNA double-strand breaks (DSB), such as bifunctional alkylators and platinum agents. Earlier, we had developed a comparative genomic hybridisation (CGH) classifier based on BRCA1-mutated breast cancers. We hypothesised that this BRCA1-like(CGH) classifier could also detect loss of function of BRCA1 due to other causes besides mutations and, consequently, might predict sensitivity to DSB-inducing agents. PATIENTS AND METHODS We evaluated this classifier in stage III breast cancer patients, who had been randomly assigned between adjuvant high-dose platinum-based (HD-PB) chemotherapy, a DSB-inducing regimen, and conventional anthracycline-based chemotherapy. Additionally, we assessed BRCA1 loss through mutation or promoter methylation and immunohistochemical basal-like status in the triple-negative subgroup (TN subgroup). RESULTS We observed greater benefit from HD-PB chemotherapy versus conventional chemotherapy among patients with BRCA1-like(CGH) tumours [41/230 = 18%, multivariate hazard ratio (HR) = 0.12, 95% confidence interval (CI) 0.04-0.43] compared with patients with non-BRCA1-like(CGH) tumours (189/230 = 82%, HR = 0.78, 95% CI 0.50-1.20), with a significant difference (test for interaction P = 0.006). Similar results were obtained for overall survival (P interaction = 0.04) and when analyses were restricted to the TN subgroup. Sixty-three percent (20/32) of assessable BRCA1-like(CGH) tumours harboured either a BRCA1 mutation (n = 8) or BRCA1 methylation (n = 12). CONCLUSION BRCA1 loss as assessed by CGH analysis can identify patients with substantially improved outcome after adjuvant DSB-inducing chemotherapy when compared with standard anthracycline-based chemotherapy in our series.
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Affiliation(s)
- M A Vollebergh
- Division of Molecular Biology; Division of Medical Oncology
| | - E H Lips
- Division of Experimental Therapy
| | - P M Nederlof
- Division of Experimental Therapy; Division of Molecular Pathology
| | - L F A Wessels
- Department of Bioinformatics and Statistics, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam; Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft
| | - M K Schmidt
- Division of Experimental Therapy; Department of Epidemiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam
| | | | | | | | | | - E G E de Vries
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen
| | | | | | - M J van de Vijver
- Department of Epidemiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam; Department of Pathology, Academic Medical Center
| | - H van Tinteren
- Department of Biometrics, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | - M Hauptmann
- Department of Bioinformatics and Statistics, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam
| | | | - S C Linn
- Division of Molecular Biology; Division of Medical Oncology.
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10
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Didraga MA, van Beers EH, Joosse SA, Brandwijk KIM, Oldenburg RA, Wessels LFA, Hogervorst FBL, Ligtenberg MJ, Hoogerbrugge N, Verhoef S, Devilee P, Nederlof PM. A non-BRCA1/2 hereditary breast cancer sub-group defined by aCGH profiling of genetically related patients. Breast Cancer Res Treat 2011; 130:425-36. [PMID: 21286804 DOI: 10.1007/s10549-011-1357-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [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: 07/07/2010] [Accepted: 01/17/2011] [Indexed: 02/04/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 explain approximately 25% of all familial breast cancers. Despite intense efforts to find additional high-risk breast cancer genes (BRCAx) using linkage analysis, none have been reported thus far. Here we explore the hypothesis that BRCAx breast tumors from genetically related patients share a somatic genetic etiology that might be revealed by array comparative genomic hybridization (aCGH) profiling. As BRCA1 and BRCA2 tumors can be identified on the basis of specific genomic profiles, the same may be true for a subset of BRCAx families. Analyses used aCGH to compare 58 non-BRCA1/2 familial breast tumors (designated BRCAx) to sporadic (non-familiar) controls, BRCA1 and BRCA2 tumors. The selection criteria for BRCAx families included at least three cases of breast cancer diagnosed before the age of 60 in the family, and the absence of ovarian or male breast cancer. Hierarchical cluster analysis was performed to determine sub-groups within the BRCAx tumor class and family heterogeneity. Analysis of aCGH profiles of BRCAx tumors indicated that they constitute a heterogeneous class, but are distinct from both sporadic and BRCA1/2 tumors. The BRCAx class could be divided into sub-groups. One subgroup was characterized by a gain of chromosome 22. Tumors from family members were classified within the same sub-group in agreement with the hypothesis that tumors from the same family would harbor a similar genetic background. This approach provides a method to target a sub-group of BRCAx families for further linkage analysis studies.
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Affiliation(s)
- M A Didraga
- Department of Experimental Therapy, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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11
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Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LFA, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR, Futreal PA. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011; 469:539-42. [PMID: 21248752 PMCID: PMC3030920 DOI: 10.1038/nature09639] [Citation(s) in RCA: 965] [Impact Index Per Article: 74.2] [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: 07/28/2010] [Accepted: 11/02/2010] [Indexed: 11/24/2022]
Abstract
The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ~3500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (KDM6A)1, JARID1C (KDM5C) and SETD22. These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control3. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodeling complex gene PBRM14 as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.
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Affiliation(s)
- Ignacio Varela
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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12
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Weigelt B, Horlings HM, Kreike B, Hayes MM, Hauptmann M, Wessels LFA, de Jong D, Van de Vijver MJ, Van't Veer LJ, Peterse JL. Refinement of breast cancer classification by molecular characterization of histological special types. J Pathol 2008; 216:141-50. [PMID: 18720457 DOI: 10.1002/path.2407] [Citation(s) in RCA: 411] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Most invasive breast cancers are classified as invasive ductal carcinoma not otherwise specified (IDC NOS), whereas about 25% are defined as histological 'special types'. These special-type breast cancers are categorized into at least 17 discrete pathological entities; however, whether these also constitute discrete molecular entities remains to be determined. Current therapy decision-making is increasingly governed by the molecular classification of breast cancer (luminal, basal-like, HER2+). The molecular classification is derived from mainly IDC NOS and it is unknown whether this classification applies to all histological subtypes. We aimed to refine the breast cancer classification systems by analysing a series of 11 histological special types [invasive lobular carcinoma (ILC), tubular, mucinous A, mucinous B, neuroendocrine, apocrine, IDC with osteoclastic giant cells, micropapillary, adenoid cystic, metaplastic, and medullary carcinoma] using immunohistochemistry and genome-wide gene expression profiling. Hierarchical clustering analysis confirmed that some histological special types constitute discrete entities, such as micropapillary carcinoma, but also revealed that others, including tubular and lobular carcinoma, are very similar at the transcriptome level. When classified by expression profiling, IDC NOS and ILC contain all molecular breast cancer types (ie luminal, basal-like, HER2+), whereas histological special-type cancers, apart from apocrine carcinoma, are homogeneous and only belong to one molecular subtype. Our analysis also revealed that some special types associated with a good prognosis, such as medullary and adenoid cystic carcinomas, display a poor prognosis basal-like transcriptome, providing strong circumstantial evidence that basal-like cancers constitute a heterogeneous group. Taken together, our results imply that the correct classification of breast cancers of special histological type will allow a more accurate prognostication of breast cancer patients and facilitate the identification of optimal therapeutic strategies.
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Affiliation(s)
- B Weigelt
- Division of Experimental Therapy, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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13
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Abstract
Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in unraveling these transcription regulation networks, the actual environmental signals are often not incorporated into the model, simply because they have not been measured. The unquantified heterogeneity of the environmental parameters across microarray experiments frustrates regulatory network inference. Results: We propose an inference algorithm that models the influence of environmental parameters on gene expression. The approach is based on a yeast microarray compendium of chemostat steady-state experiments. Chemostat cultivation enables the accurate control and measurement of many of the key cultivation parameters, such as nutrient concentrations, growth rate and temperature. The observed transcript levels are explained by inferring the activity of TFs in response to combinations of cultivation parameters. The interplay between activated enhancers and repressors that bind a gene promoter determine the possible up- or downregulation of the gene. The model is translated into a linear integer optimization problem. The resulting regulatory network identifies the combinatorial effects of environmental parameters on TF activity and gene expression. Availability: The Matlab code is available from the authors upon request. Contact:t.a.knijnenburg@tudelft.nl Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- T A Knijnenburg
- Information and Communication Theory Group, Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.
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14
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Weigelt B, Wessels LFA, Bosma AJ, Glas AM, Nuyten DSA, He YD, Dai H, Peterse JL, van't Veer LJ. No common denominator for breast cancer lymph node metastasis. Br J Cancer 2005; 93:924-32. [PMID: 16189523 PMCID: PMC2361648 DOI: 10.1038/sj.bjc.6602794] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The axillary lymph node status is the most powerful prognostic factor for breast cancer patients to date. The molecular mechanisms that control lymph node metastasis, however, remain poorly understood. To define patterns of genes or gene regulatory pathways that drive breast cancer lymph node metastasis, we compared the gene expression profiles of 15 primary breast carcinomas and their matching lymph node metastases using microarrays. In general, primary breast carcinomas and lymph node metastases do not differ at the transcriptional level by a common subset of genes. No classifier or single gene discriminating the group of primary tumours from those of the lymph node metastases could be identified. Also, in a series of 295 breast tumours, no classifier predicting lymph node metastasis could be developed. However, subtle differences in the expression of genes involved in extracellular-matrix organisation and growth factor signalling are detected in individual pairs of matching primary and metastatic tumours. Surprisingly, however, different sets of these genes are either up- or downregulated in lymph node metastases. Our data suggest that breast carcinomas do not use a shared gene set to accomplish lymph node metastasis.
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Affiliation(s)
- B Weigelt
- Division of Experimental Therapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Information and Communication Theory Group, Delft University of Technology, 2600 GA Delft, The Netherlands
| | - A J Bosma
- Division of Experimental Therapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - A M Glas
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - D S A Nuyten
- Division of Radiotherapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Y D He
- Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
| | - H Dai
- Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
| | - J L Peterse
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - L J van't Veer
- Division of Experimental Therapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Diagnostic Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. E-mail: Division of Experimental Therapy, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands,
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15
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Broeks A, de Kemp SR, Bakker W, Braaf LM, van Leeuwen FE, Stovall M, Schmidt MK, Russell NS, Wessels LFA, van 't Veer LJ. Breast tumors induced by high-dose radiation display similar genetic profiles. Breast Cancer Res 2005. [PMCID: PMC4233574 DOI: 10.1186/bcr1153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Kok M, van den Berg TMC, Delahaye LJ, Floore A, Glas AM, Peterse JL, Wessels LFA, van 't Veer LJ, Linn SC. Molecular prediction of tamoxifen resistance in breast cancer. Breast Cancer Res 2005. [PMCID: PMC4233539 DOI: 10.1186/bcr1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Nederlof PM, van Beers E, Joosse S, Hogervorst FBL, Wessels LFA, Devilee P, Cornelisse C, Oldenburg R, Verhoef S, van 't Veer LJ. Discovering genetic profiles by array-CGH in familial breast tumors. Breast Cancer Res 2005. [PMCID: PMC4233587 DOI: 10.1186/bcr1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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18
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Weigelt B, Wessels LFA, Bosma AJ, Glas AM, Nuyten DSA, He YD, Dai H, Peterse JL, van 't Veer LJ. Lymph node metastases display gene expression profiles of their primary breast carcinomas. Breast Cancer Res 2005. [PMCID: PMC4233579 DOI: 10.1186/bcr1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Staal FJT, van der Burg M, Wessels LFA, Barendregt BH, Baert MRM, van den Burg CMM, Van Huffel C, Langerak AW, van der Velden VHJ, Reinders MJT, van Dongen JJM. Erratum: DNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers. Leukemia 2004. [DOI: 10.1038/sj.leu.2403373] [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: 11/09/2022]
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20
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Staal FJT, van der Burg M, Wessels LFA, Barendregt BH, Baert MRM, van den Burg CMM, van Huffel C, Langerak AW, van der Velden VHJ, Reinders MJT, van Dongen JJM. DNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers. Leukemia 2003; 17:1324-32. [PMID: 12835720 DOI: 10.1038/sj.leu.2402974] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microarrays for gene expression profiling are rapidly becoming important research tools for the identification of novel markers, for example, for novel classification of leukemias and lymphomas. Here, we review the considerations and infrastructure for microarray experiments. These considerations are illustrated via a microarray-based comparison of gene expression profiles of paired diagnosis-relapse samples from patients with precursor-B acute lymphoblastic leukemia (ALL), who relapsed during therapy or after completion of treatment. Initial experiments showed that several seemingly differentially expressed genes were actually derived from contaminating non-leukemic cells, particularly myeloid cells and T-lymphocytes. Therefore, we purified the ALL cells of the diagnosis and relapse samples if their frequency was lower than 95%. Furthermore, we observed in earlier studies that extra RNA amplification leads to skewing of particular gene transcripts. Sufficient (non-amplified) RNA of purified and paired diagnosis-relapse samples was obtained from only seven cases. The gene expression profiles were evaluated with Affymetrix U95A chips containing 12 600 human genes. These diagnosis-relapse comparisons revealed only a small number of genes (n=6) that differed significantly in expression: mostly signaling molecules and transcription factors involved in cell proliferation and cell survival were highly upregulated at relapse, but we did not observe any increase in drug-resistance markers. This finding fits with the observation that tumors with a high proliferation index have a poor prognosis. The genes that changed between diagnosis and relapse are currently not in use as diagnostic or disease progression markers, but represent potential new markers for such applications. Leukemia (2003) 17, 1324-1332. doi:10.1038/sj.leu.2402974
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Affiliation(s)
- F J T Staal
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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21
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Abstract
The inference of genetic interactions from measured expression data is one of the most challenging tasks of modern functional genomics. When successful, the learned network of regulatory interactions yields a wealth of useful information. An inferred genetic network contains information about the pathway to which a gene belongs and which genes it interacts with. Furthermore, it explains the function of the gene in terms of how it influences other genes and indicates which genes are pathway initiators and therefore potential drug targets. Obviously, such wealth comes at a price and that of genetic network modeling is that it is an extremely complex task. Therefore, it is necessary to develop sophisticated computational tools that are able to extract relevant information from a limited set of microarray measurements and integrate this with different information sources, to come up with reliable hypotheses of a genetic regulatory network. Thus far, a multitude of modeling approaches have been proposed for discovering genetic networks. However, it is unclear what the advantages and disadvantages of each of the different approaches are and how their results can be compared. In this review, genetic network models are put in a historical perspective that explains why certain models were introduced. Various modeling assumptions and their consequences are also highlighted. In addition, an overview of the principal differences and similarities between the approaches is given by considering the qualitative properties of the chosen models and their learning strategies.
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Affiliation(s)
- E P van Someren
- Information and Communication Theory Group, Department of Mediametics, Faculty of Information Technology and Systems, Delft University of Technology, Mekelweg 4, Delft, The Netherlands.
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