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Smeby J, Sveen A, Merok MA, Danielsen SA, Eilertsen IA, Guren MG, Dienstmann R, Nesbakken A, Lothe RA. CMS-dependent prognostic impact of KRAS and BRAFV600E mutations in primary colorectal cancer. Ann Oncol 2019. [PMID: 29518181 PMCID: PMC5961317 DOI: 10.1093/annonc/mdy085] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [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] [Indexed: 12/14/2022] Open
Abstract
Background The prognostic impact of KRAS and BRAFV600E mutations in primary colorectal cancer (CRC) varies with microsatellite instability (MSI) status. The gene expression-based consensus molecular subtypes (CMSs) of CRC define molecularly and clinically distinct subgroups, and represent a novel stratification framework in biomarker analysis. We investigated the prognostic value of these mutations within the CMS groups. Patients and methods Totally 1197 primary tumors from a Norwegian series of CRC stage I-IV were analyzed for MSI and mutation status in hotspots in KRAS (codons 12, 13 and 61) and BRAF (codon 600). A subset was analyzed for gene expression and confident CMS classification was obtained for 317 samples. This cohort was expanded with clinical and molecular data, including CMS classification, from 514 patients in the publically available dataset GSE39582. Gene expression signatures associated with KRAS and BRAFV600E mutations were used to evaluate differential impact of mutations on gene expression among the CMS groups. Results BRAFV600E and KRAS mutations were both associated with inferior 5-year overall survival (OS) exclusively in MSS tumors (BRAFV600E mutation versus KRAS/BRAF wild-type: Hazard ratio (HR) 2.85, P < 0.001; KRAS mutation versus KRAS/BRAF wild-type: HR 1.30, P = 0.013). BRAFV600E-mutated MSS tumors were strongly enriched and associated with metastatic disease in CMS1, leading to negative prognostic impact in this subtype (OS: BRAFV600E mutation versus wild-type: HR 7.73, P = 0.001). In contrast, the poor prognosis of KRAS mutations was limited to MSS tumors with CMS2/CMS3 epithelial-like gene expression profiles (OS: KRAS mutation versus wild-type: HR 1.51, P = 0.011). The subtype-specific prognostic associations were substantiated by differential effects of BRAFV600E and KRAS mutations on gene expression signatures according to the MSI status and CMS group. Conclusions BRAFV600E mutations are enriched and associated with metastatic disease in CMS1 MSS tumors, leading to poor prognosis in this subtype. KRAS mutations are associated with adverse outcome in epithelial (CMS2/CMS3) MSS tumors.
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Affiliation(s)
- J Smeby
- Department of Molecular Oncology, Institute for Cancer Research; Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre; Department of Oncology, Oslo University Hospital, Oslo; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo
| | - A Sveen
- Department of Molecular Oncology, Institute for Cancer Research; Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre
| | - M A Merok
- Department of Molecular Oncology, Institute for Cancer Research; Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - S A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research; Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre
| | - I A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research; Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre
| | - M G Guren
- Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre; Department of Oncology, Oslo University Hospital, Oslo
| | - R Dienstmann
- Oncology Data Science Group, Vall d'Hebron Institute of Oncology, Barcelona; Vall d'Hebron University Hospital, Barcelona; Universitat Autonoma de Barcelona, Barcelona, Spain; Computational Oncology, Sage Bionetworks, Seattle, USA
| | - A Nesbakken
- Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo; Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - R A Lothe
- Department of Molecular Oncology, Institute for Cancer Research; Division of Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo.
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Berg KCG, Sveen A, Høland M, Alagaratnam S, Berg M, Danielsen SA, Nesbakken A, Søreide K, Lothe RA. Gene expression profiles of CMS2-epithelial/canonical colorectal cancers are largely driven by DNA copy number gains. Oncogene 2019; 38:6109-6122. [PMID: 31308487 PMCID: PMC6756070 DOI: 10.1038/s41388-019-0868-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 09/26/2018] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022]
Abstract
About 80% of colorectal cancers (CRCs) have chromosomal instability, which is an integral part of aggressive malignancy development, but the importance of specific copy number aberrations (CNAs) in modulating gene expression, particularly within the framework of clinically relevant molecular subtypes, remains mostly elusive. We performed DNA copy number profiling of 257 stage I-IV primary CRCs and integrative gene expression analysis in 151 microsatellite stable (MSS) tumors, focusing on high-level amplifications and the effect of CNAs on the characteristics of the gene expression-based consensus molecular subtypes (CMS). The results were validated in 323 MSS tumors from TCGA. Novel recurrent high-level amplifications (≥15 additional copies) with a major impact on gene expression were found for TOX3 (16q) at 1.5% frequency, as well as for CCND2 (12p) and ANXA11 (10q) at 1% frequency, in addition to the well-known targets ERBB2 (17q) and MYC (8q). Focal amplifications with ≥15 or ≥5 additional copies of at least one of these regions were associated with a poor overall survival among patients with stage I-III MSS CRCs (multivariable hazard ratio ≥3.2, p ≤ 0.01). All high-level amplifications were focal and had a more consistent relationship with gene expression than lower amplitude and/or broad-range amplifications, suggesting specific targeting during carcinogenesis. Genome-wide, copy number driven gene expression was enriched for pathways characteristic of the CMS2-epithelial/canonical subtype, including DNA repair and cell cycle progression. Furthermore, 50% of upregulated genes in CMS2-epithelial/canonical MSS CRCs were driven by CNAs, an enrichment compared with the other CMS groups, and associated with the stronger correspondence between CNAs and gene expression in malignant epithelial cells than in the cells of the tumor microenvironment (fibroblasts, endothelial cells, leukocytes). In conclusion, we identify novel recurrent amplifications with impact on gene expression in CRC and provide the first evidence that CMS2 may have a stronger copy-number related genetic basis than subtypes more heavily influenced by gene expression signals from the tumor microenvironment.
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Affiliation(s)
- Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Sharmini Alagaratnam
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway
| | - Marianne Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,Gastrointestinal Translational Research Unit, Lab for Molecular Biology, Stavanger University Hospital, P.O. Box 8100, NO-4011, Stavanger, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Lab for Molecular Biology, Stavanger University Hospital, P.O. Box 8100, NO-4011, Stavanger, Norway.,Department of Gastrointestinal Surgery, Stavanger University Hospital, P.O. Box 8100, NO-4011, Stavanger, Norway.,Department of Clinical Medicine, University of Bergen, P.O. Box 7804, NO-5020, Bergen, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424, Oslo, Norway. .,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424, Oslo, Norway.
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Smeby J, Sveen A, Bergsland CH, Eilertsen IA, Danielsen SA, Eide PW, Hektoen M, Guren MG, Nesbakken A, Bruun J, Lothe RA. Exploratory analyses of consensus molecular subtype-dependent associations of TP53 mutations with immunomodulation and prognosis in colorectal cancer. ESMO Open 2019; 4:e000523. [PMID: 31321083 PMCID: PMC6598553 DOI: 10.1136/esmoopen-2019-000523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 04/01/2019] [Revised: 05/07/2019] [Accepted: 05/25/2019] [Indexed: 12/31/2022] Open
Abstract
Background Accumulating evidence suggests immunomodulatory and context-dependent effects of TP53 mutations in cancer. We performed an exploratory analysis of the transcriptional, immunobiological and prognostic associations of TP53 mutations within the gene expression-based consensus molecular subtypes (CMSs) of colorectal cancer (CRC). Materials and methods In a single-hospital series of 401 stage I–IV primary CRCs, we sequenced the whole coding region of TP53 and analysed CMS-dependent transcriptional consequences of the mutations by gene expression profiling. Immunomodulatory associations were validated by multiplex, fluorescence-based immunohistochemistry of immune cell markers. Prognostic associations of TP53 mutations were analysed in an aggregated series of 635 patients classified according to CMS, including publicly available data from a French multicentre cohort (GSE39582). Results TP53 mutations were found in 60% of the CRCs. However, gene set enrichment analyses indicated that their transcriptional consequences varied among the CMSs and were most pronounced in CMS1-immune and CMS4-mesenchymal. Subtype specificity was primarily seen as an upregulation of gene sets reflecting cell cycle progression in CMS4 and a downregulation of T cell activity in CMS1. The subtype-dependent immunomodulatory associations were reinforced by significant depletion of several immune cell populations in mutated tumours compared with wild-type (wt) tumours exclusively in CMS1, including cytotoxic lymphocytes (adjusted p value in CMS1=0.002 and CMS2−4>0.9, Microenvironment Cell Populations (MCP)-counter algorithm). This was validated by immunohistochemistry-based quantification of tumour infiltrating CD8+ cells. Within CMS1, the immunomodulatory association of TP53 mutations was strongest among microsatellite stable (MSS) tumours, and this translated into a propensity for metastatic disease and poor prognostic value of the mutations specifically in the CMS1/MSS subtype (both series overall survival: TP53 mutation vs wt: HR 5.52, p=0.028). Conclusions Integration of TP53 mutation status with the CMS framework in primary CRC suggested subtype-dependent immunobiological associations with prognostic and potentially immunotherapeutic implications, warranting independent validation.
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Affiliation(s)
- Jørgen Smeby
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christian H Bergsland
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Marianne G Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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4
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Smeby J, Sveen A, Eilertsen IA, Danielsen SA, Hoff AM, Eide PW, Johannessen B, Hektoen M, Skotheim RI, Guren MG, Nesbakken A, Lothe RA. Transcriptional and functional consequences of TP53 splice mutations in colorectal cancer. Oncogenesis 2019; 8:35. [PMID: 31092812 PMCID: PMC6520361 DOI: 10.1038/s41389-019-0141-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 11/01/2018] [Revised: 03/17/2019] [Accepted: 04/05/2019] [Indexed: 01/20/2023] Open
Abstract
TP53 mutations are common in colorectal cancer (CRC). Most TP53 sequencing studies have been restricted to coding regions, but recent studies have revealed that splice mutations can generate transcript variants with distinct tumorigenic and prognostic properties. Here, we performed unrestricted sequencing of all coding sequences and splice regions of TP53 in a single-hospital series of 401 primary CRCs. TP53 splice mutations were detected in 4% of the cases (N = 16), considerably more frequent than reported in major databases, and they were mutually exclusive to exon mutations. RNA sequencing revealed high-level expression of aberrant transcript variants in the majority of splice mutated tumors (75%). Most variants were predicted to produce truncated TP53 proteins, including one sample expressing the potentially oncogenic and druggable p53ψ isoform. Despite heterogeneous transcript structures, downstream transcriptional profiling revealed that TP53 splice mutations had similar effects on TP53 target gene expression and pathway activity as exonic mutations. Intriguingly, TP53 splice mutations were associated with worse 5-year relapse-free survival in stage II disease, compared to both TP53 wild-type and exon mutations (P = 0.007). These data highlight the importance of including splice regions when examining the biological and clinical consequences of TP53 mutations in CRC.
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Affiliation(s)
- Jørgen Smeby
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Marianne G Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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5
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Dienstmann R, Mason MJ, Sinicrope FA, Phipps AI, Tejpar S, Nesbakken A, Danielsen SA, Sveen A, Buchanan DD, Clendenning M, Rosty C, Bot B, Alberts SR, Milburn Jessup J, Lothe RA, Delorenzi M, Newcomb PA, Sargent D, Guinney J. Prediction of overall survival in stage II and III colon cancer beyond TNM system: a retrospective, pooled biomarker study. Ann Oncol 2018; 28:1023-1031. [PMID: 28453697 PMCID: PMC5406760 DOI: 10.1093/annonc/mdx052] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [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] [Indexed: 12/12/2022] Open
Abstract
Background TNM staging alone does not accurately predict outcome in colon cancer (CC) patients who may be eligible for adjuvant chemotherapy. It is unknown to what extent the molecular markers microsatellite instability (MSI) and mutations in BRAF or KRAS improve prognostic estimation in multivariable models that include detailed clinicopathological annotation. Patients and methods After imputation of missing at random data, a subset of patients accrued in phase 3 trials with adjuvant chemotherapy (n = 3016)-N0147 (NCT00079274) and PETACC3 (NCT00026273)-was aggregated to construct multivariable Cox models for 5-year overall survival that were subsequently validated internally in the remaining clinical trial samples (n = 1499), and also externally in different population cohorts of chemotherapy-treated (n = 949) or -untreated (n = 1080) CC patients, and an additional series without treatment annotation (n = 782). Results TNM staging, MSI and BRAFV600E mutation status remained independent prognostic factors in multivariable models across clinical trials cohorts and observational studies. Concordance indices increased from 0.61-0.68 in the TNM alone model to 0.63-0.71 in models with added molecular markers, 0.65-0.73 with clinicopathological features and 0.66-0.74 with all covariates. In validation cohorts with complete annotation, the integrated time-dependent AUC rose from 0.64 for the TNM alone model to 0.67 for models that included clinicopathological features, with or without molecular markers. In patient cohorts that received adjuvant chemotherapy, the relative proportion of variance explained (R2) by TNM, clinicopathological features and molecular markers was on an average 65%, 25% and 10%, respectively. Conclusions Incorporation of MSI, BRAFV600E and KRAS mutation status to overall survival models with TNM staging improves the ability to precisely prognosticate in stage II and III CC patients, but only modestly increases prediction accuracy in multivariable models that include clinicopathological features, particularly in chemotherapy-treated patients.
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Affiliation(s)
- R Dienstmann
- Computational Oncology, Sage Bionetworks, Seattle, USA.,Oncology Data Science Group, Vall d´Hebron Institute of Oncology and Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - M J Mason
- Computational Oncology, Sage Bionetworks, Seattle, USA
| | - F A Sinicrope
- Division of Medical Oncology, Mayo Clinic and Mayo Comprehensive Cancer Center, Rochester
| | - A I Phipps
- Epidemiology Department, University of Washington and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - S Tejpar
- Molecular Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - A Nesbakken
- Department of Gastrointestinal Surgery, Institute of Clinical Medicine, and K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - S A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, and K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - A Sveen
- Department of Molecular Oncology, Institute for Cancer Research, and K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - D D Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Australia.,Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, Australia
| | - M Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - C Rosty
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.,Envoi Specialist Pathologists, Herston, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Australia
| | - B Bot
- Computational Oncology, Sage Bionetworks, Seattle, USA
| | - S R Alberts
- Division of Medical Oncology, Mayo Clinic and Mayo Comprehensive Cancer Center, Rochester
| | - J Milburn Jessup
- Diagnostics Evaluation Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, Rockville, USA
| | - R A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, and K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - M Delorenzi
- SIB Swiss Institute Bioinformatics, Lausanne, Switzerland.,Department of Oncology, Ludwig Center for Cancer Research, University Lausanne, Lausanne, Switzerland
| | - P A Newcomb
- Epidemiology Department, University of Washington and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - D Sargent
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, USA
| | - J Guinney
- Computational Oncology, Sage Bionetworks, Seattle, USA
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6
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Sveen A, Bruun J, Eide PW, Eilertsen IA, Ramirez L, Murumägi A, Arjama M, Danielsen SA, Kryeziu K, Elez E, Tabernero J, Guinney J, Palmer HG, Nesbakken A, Kallioniemi O, Dienstmann R, Lothe RA. Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies. Clin Cancer Res 2017; 24:794-806. [PMID: 29242316 DOI: 10.1158/1078-0432.ccr-17-1234] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/26/2017] [Accepted: 12/06/2017] [Indexed: 01/27/2023]
Abstract
Purpose: Response to standard oncologic treatment is limited in colorectal cancer. The gene expression-based consensus molecular subtypes (CMS) provide a new paradigm for stratified treatment and drug repurposing; however, drug discovery is currently limited by the lack of translation of CMS to preclinical models.Experimental Design: We analyzed CMS in primary colorectal cancers, cell lines, and patient-derived xenografts (PDX). For classification of preclinical models, we developed an optimized classifier enriched for cancer cell-intrinsic gene expression signals, and performed high-throughput in vitro drug screening (n = 459 drugs) to analyze subtype-specific drug sensitivities.Results: The distinct molecular and clinicopathologic characteristics of each CMS group were validated in a single-hospital series of 409 primary colorectal cancers. The new, cancer cell-adapted classifier was found to perform well in primary tumors, and applied to a panel of 148 cell lines and 32 PDXs, these colorectal cancer models were shown to recapitulate the biology of the CMS groups. Drug screening of 33 cell lines demonstrated subtype-dependent response profiles, confirming strong response to EGFR and HER2 inhibitors in the CMS2 epithelial/canonical group, and revealing strong sensitivity to HSP90 inhibitors in cells with the CMS1 microsatellite instability/immune and CMS4 mesenchymal phenotypes. This association was validated in vitro in additional CMS-predicted cell lines. Combination treatment with 5-fluorouracil and luminespib showed potential to alleviate chemoresistance in a CMS4 PDX model, an effect not seen in a chemosensitive CMS2 PDX model.Conclusions: We provide translation of CMS classification to preclinical models and uncover a potential for targeted treatment repurposing in the chemoresistant CMS4 group. Clin Cancer Res; 24(4); 794-806. ©2017 AACR.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Lorena Ramirez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mariliina Arjama
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Kushtrim Kryeziu
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Elena Elez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Justin Guinney
- SAGE Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Hector G Palmer
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Arild Nesbakken
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Rodrigo Dienstmann
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.,SAGE Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
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7
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Kolberg M, Bruun J, Murumägi A, Mpindi JP, Bergsland CH, Høland M, Eilertsen IA, Danielsen SA, Kallioniemi O, Lothe RA. Drug sensitivity and resistance testing identifies PLK1 inhibitors and gemcitabine as potent drugs for malignant peripheral nerve sheath tumors. Mol Oncol 2017; 11:1156-1171. [PMID: 28556483 PMCID: PMC5579334 DOI: 10.1002/1878-0261.12086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 02/27/2017] [Revised: 04/24/2017] [Accepted: 05/16/2017] [Indexed: 12/13/2022] Open
Abstract
Patients with malignant peripheral nerve sheath tumor (MPNST), a rare soft tissue cancer associated with loss of the tumor suppressor neurofibromin (NF1), have poor prognosis and typically respond poorly to adjuvant therapy. We evaluated the effect of 299 clinical and investigational compounds on seven MPNST cell lines, two primary cultures of human Schwann cells, and five normal bone marrow aspirates, to identify potent drugs for MPNST treatment with few side effects. Top hits included Polo-like kinase 1 (PLK1) inhibitors (volasertib and BI2536) and the fluoronucleoside gemcitabine, which were validated in orthogonal assays measuring viability, cytotoxicity, and apoptosis. DNA copy number, gene expression, and protein expression were determined for the cell lines to assess pharmacogenomic relationships. MPNST cells were more sensitive to BI2536 and gemcitabine compared to a reference set of 94 cancer cell lines. PLK1, RRM1, and RRM2 mRNA levels were increased in MPNST compared to benign neurofibroma tissue, and the protein level of PLK1 was increased in the MPNST cell lines compared to normal Schwann cells, indicating an increased dependence on these drug targets in malignant cells. Furthermore, we observed an association between increased mRNA expression of PLK1, RRM1, and RRM2 in patient samples and worse disease outcome, suggesting a selective benefit from inhibition of these genes in the most aggressive tumors.
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Affiliation(s)
- Matthias Kolberg
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Jarle Bruun
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Astrid Murumägi
- Institute for Molecular Medicine FinlandFIMMUniversity of HelsinkiFinland
| | - John P. Mpindi
- Institute for Molecular Medicine FinlandFIMMUniversity of HelsinkiFinland
| | - Christian H. Bergsland
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Maren Høland
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Ina A. Eilertsen
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Stine A. Danielsen
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
| | - Olli Kallioniemi
- Institute for Molecular Medicine FinlandFIMMUniversity of HelsinkiFinland
- Science for Life LaboratorySolnaSweden
- Department of Oncology and PathologyKarolinska InstitutetSolnaSweden
| | - Ragnhild A. Lothe
- Department of Molecular OncologyInstitute for Cancer Researchthe Norwegian Radium HospitalOslo University HospitalNorway
- Centre for Cancer BiomedicineUniversity of OsloNorway
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8
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Berg KCG, Eide PW, Eilertsen IA, Johannessen B, Bruun J, Danielsen SA, Bjørnslett M, Meza-Zepeda LA, Eknæs M, Lind GE, Myklebost O, Skotheim RI, Sveen A, Lothe RA. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol Cancer 2017; 16:116. [PMID: 28683746 PMCID: PMC5498998 DOI: 10.1186/s12943-017-0691-y] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [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: 04/05/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Colorectal cancer (CRC) cell lines are widely used pre-clinical model systems. Comprehensive insights into their molecular characteristics may improve model selection for biomedical studies. Methods We have performed DNA, RNA and protein profiling of 34 cell lines, including (i) targeted deep sequencing (n = 612 genes) to detect single nucleotide variants and insertions/deletions; (ii) high resolution DNA copy number profiling; (iii) gene expression profiling at exon resolution; (iv) small RNA expression profiling by deep sequencing; and (v) protein expression analysis (n = 297 proteins) by reverse phase protein microarrays. Results The cell lines were stratified according to the key molecular subtypes of CRC and data were integrated at two or more levels by computational analyses. We confirm that the frequencies and patterns of DNA aberrations are associated with genomic instability phenotypes and that the cell lines recapitulate the genomic profiles of primary carcinomas. Intrinsic expression subgroups are distinct from genomic subtypes, but consistent at the gene-, microRNA- and protein-level and dominated by two distinct clusters; colon-like cell lines characterized by expression of gastro-intestinal differentiation markers and undifferentiated cell lines showing upregulation of epithelial-mesenchymal transition and TGFβ signatures. This sample split was concordant with the gene expression-based consensus molecular subtypes of primary tumors. Approximately ¼ of the genes had consistent regulation at the DNA copy number and gene expression level, while expression of gene-protein pairs in general was strongly correlated. Consistent high-level DNA copy number amplification and outlier gene- and protein- expression was found for several oncogenes in individual cell lines, including MYC and ERBB2. Conclusions This study expands the view of CRC cell lines as accurate molecular models of primary carcinomas, and we present integrated multi-level molecular data of 34 widely used cell lines in easily accessible formats, providing a resource for preclinical studies in CRC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0691-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Merete Bjørnslett
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mette Eknæs
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ola Myklebost
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway. .,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.
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Vedeld HM, Merok M, Jeanmougin M, Danielsen SA, Honne H, Presthus GK, Svindland A, Sjo OH, Hektoen M, Eknaes M, Nesbakken A, Lothe RA, Lind GE. CpG island methylator phenotype identifies high risk patients among microsatellite stable BRAF mutated colorectal cancers. Int J Cancer 2017; 141:967-976. [PMID: 28542846 PMCID: PMC5518206 DOI: 10.1002/ijc.30796] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 02/17/2017] [Accepted: 05/08/2017] [Indexed: 12/26/2022]
Abstract
The prognostic value of CpG island methylator phenotype (CIMP) in colorectal cancer remains unsettled. We aimed to assess the prognostic value of this phenotype analyzing a total of 1126 tumor samples obtained from two Norwegian consecutive colorectal cancer series. CIMP status was determined by analyzing the 5‐markers CAGNA1G, IGF2, NEUROG1, RUNX3 and SOCS1 by quantitative methylation specific PCR (qMSP). The effect of CIMP on time to recurrence (TTR) and overall survival (OS) were determined by uni‐ and multivariate analyses. Subgroup analyses were conducted according to MSI and BRAF mutation status, disease stage, and also age at time of diagnosis (<60, 60‐74, ≥75 years). Patients with CIMP positive tumors demonstrated significantly shorter TTR and worse OS compared to those with CIMP negative tumors (multivariate hazard ratio [95% CI] 1.86 [1.31‐2.63] and 1.89 [1.34‐2.65], respectively). In stratified analyses, CIMP tumors showed significantly worse outcome among patients with microsatellite stable (MSS, P < 0.001), and MSS BRAF mutated tumors (P < 0.001), a finding that persisted in patients with stage II, III or IV disease, and that remained significant in multivariate analysis (P < 0.01). Consistent results were found for all three age groups. To conclude, CIMP is significantly associated with inferior outcome for colorectal cancer patients, and can stratify the poor prognostic patients with MSS BRAF mutated tumors. What's new? As many as one‐fifth of colorectal cancers have a CpG island methylator phenotype (CIMP) involving widespread promoter DNA methylation. CIMP is associated with key factors related to disease outcome, including microsatellite instability and BRAF mutations. In this study, CIMP was found to be significantly associated with worse prognosis in colorectal cancer patients, particularly those with microsatellite stable (MSS) BRAF‐mutated tumors. In stratified analyses, trends toward worse survival were identified for CIMP‐positive stage III and stage IV patients in the MSS BRAF‐mutated group. The findings suggest that CIMP status should be included in prognostic analyses at time of diagnosis.
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Affiliation(s)
- Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marianne Merok
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hilde Honne
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gro Kummeneje Presthus
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Aud Svindland
- Department of Pathology, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ole H Sjo
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Merete Hektoen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Eknaes
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital - Aker, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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10
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Sveen A, Johannessen B, Tengs T, Danielsen SA, Eilertsen IA, Lind GE, Berg KCG, Leithe E, Meza-Zepeda LA, Domingo E, Myklebost O, Kerr D, Tomlinson I, Nesbakken A, Skotheim RI, Lothe RA. Multilevel genomics of colorectal cancers with microsatellite instability-clinical impact of JAK1 mutations and consensus molecular subtype 1. Genome Med 2017; 9:46. [PMID: 28539123 PMCID: PMC5442873 DOI: 10.1186/s13073-017-0434-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 01/06/2017] [Accepted: 05/03/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations-the microsatellite instability (MSI) phenotype. We investigated molecular heterogeneity and tumor immunogenicity in relation to clinical endpoints within this distinct subtype of colorectal cancers. METHODS A total of 333 primary MSI+ colorectal tumors from multiple cohorts were analyzed by multilevel genomics and computational modeling-including mutation profiling, clonality modeling, and neoantigen prediction in a subset of the tumors, as well as gene expression profiling for consensus molecular subtypes (CMS) and immune cell infiltration. RESULTS Novel, frequent frameshift mutations in four cancer-critical genes were identified by deep exome sequencing, including in CRTC1, BCL9, JAK1, and PTCH1. JAK1 loss-of-function mutations were validated with an overall frequency of 20% in Norwegian and British patients, and mutated tumors had up-regulation of transcriptional signatures associated with resistance to anti-PD-1 treatment. Clonality analyses revealed a high level of intra-tumor heterogeneity; however, this was not associated with disease progression. Among the MSI+ tumors, the total mutation load correlated with the number of predicted neoantigens (P = 4 × 10-5), but not with immune cell infiltration-this was dependent on the CMS class; MSI+ tumors in CMS1 were highly immunogenic compared to MSI+ tumors in CMS2-4. Both JAK1 mutations and CMS1 were favorable prognostic factors (hazard ratios 0.2 [0.05-0.9] and 0.4 [0.2-0.9], respectively, P = 0.03 and 0.02). CONCLUSIONS Multilevel genomic analyses of MSI+ colorectal cancer revealed molecular heterogeneity with clinical relevance, including tumor immunogenicity and a favorable patient outcome associated with JAK1 mutations and the transcriptomic subgroup CMS1, emphasizing the potential for prognostic stratification of this clinically important subtype. See related research highlight by Samstein and Chan 10.1186/s13073-017-0438-9.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Torstein Tengs
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Stine A. Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Ina A. Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Guro E. Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Kaja C. G. Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Edward Leithe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Leonardo A. Meza-Zepeda
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
| | - Enric Domingo
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Ola Myklebost
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
| | - David Kerr
- Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Arild Nesbakken
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Rolf I. Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
| | - Ragnhild A. Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- K. G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Norwegian Cancer Genomics Consortium, Oslo University Hospital, P.O. Box 4953, Nydalen, NO-0424 Oslo Norway
- Centre for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, P.O. Box 4950, Nydalen, NO-0424 Oslo Norway
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Domingo E, Freeman-Mills L, Rayner E, Glaire M, Briggs S, Vermeulen L, Fessler E, Medema JP, Boot A, Morreau H, van Wezel T, Liefers GJ, Lothe RA, Danielsen SA, Sveen A, Nesbakken A, Zlobec I, Lugli A, Koelzer VH, Berger MD, Castellví-Bel S, Muñoz J, de Bruyn M, Nijman HW, Novelli M, Lawson K, Oukrif D, Frangou E, Dutton P, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church DN. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study. Lancet Gastroenterol Hepatol 2016; 1:207-216. [PMID: 28404093 DOI: 10.1016/s2468-1253(16)30014-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/26/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Precision cancer medicine depends on defining distinct tumour subgroups using biomarkers that may occur at very modest frequencies. One such subgroup comprises patients with exceptionally mutated (ultramutated) cancers caused by mutations that impair DNA polymerase epsilon (POLE) proofreading. METHODS We examined the association of POLE proofreading domain mutation with clinicopathological variables and immune response in colorectal cancers from clinical trials (VICTOR, QUASAR2, and PETACC-3) and colorectal cancer cohorts (Leiden University Medical Centre 1 and 2, Oslo 1 and 2, Bern, AMC-AJCC-II, and Epicolon-1). We subsequently investigated its association with prognosis in stage II/III colorectal cancer by Cox regression of pooled individual patient data from more than 4500 cases from these studies. FINDINGS Pathogenic somatic POLE mutations were detected in 66 (1·0%) of 6517 colorectal cancers, and were mutually exclusive with mismatch repair deficiency (MMR-D) in the 6277 cases for whom both markers were determined (none of 66 vs 833 [13·4%] of 6211; p<0·0001). Compared with cases with wild-type POLE, cases with POLE mutations were younger at diagnosis (median 54·5 years vs 67·2 years; p<0·0001), were more frequently male (50 [75·8%] of 66 vs 3577 [55·5%] of 6445; p=0·0010), more frequently had right-sided tumour location (44 [68·8%] of 64 vs 2463 [39·8%] of 6193; p<0·0001), and were diagnosed at an earlier disease stage (p=0·006, χ2 test for trend). Compared with mismatch repair proficient (MMR-P) POLE wild-type tumours, POLE-mutant colorectal cancers displayed increased CD8+ lymphocyte infiltration and expression of cytotoxic T-cell markers and effector cytokines, similar in extent to that observed in immunogenic MMR-D cancers. Both POLE mutation and MMR-D were associated with significantly reduced risk of recurrence compared with MMR-P colorectal cancers in multivariable analysis (HR 0·34 [95% CI 0·11-0·76]; p=0·0060 and 0·72 [0·60-0·87]; p=0·00035), although the difference between the groups was not significant. INTERPRETATION POLE proofreading domain mutations identify a subset of immunogenic colorectal cancers with excellent prognosis. This association underscores the importance of rare biomarkers in precision cancer medicine, but also raises important questions about how to identify and implement them in practice. FUNDING Cancer Research UK, Academy of Medical Sciences, Health Foundation, EU, ERC, NIHR, Wellcome Trust, Dutch Cancer Society, Dutch Digestive Foundation.
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Affiliation(s)
- Enric Domingo
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Emily Rayner
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Mark Glaire
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK
| | - Sarah Briggs
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - Louis Vermeulen
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Evelyn Fessler
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Jan Paul Medema
- Academic Medical Center Amsterdam, Center for Experimental Molecular Medicine, Amsterdam, Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden, Netherlands
| | | | | | | | - Ragnhild A Lothe
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Stine A Danielsen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K G Jebsen Colorectal Cancer Research Centre, Oslo, Norway; Department of Gastrointestinal Surgery, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Institute of Pathology, University of Bern, Bern, Switzerland
| | - Martin D Berger
- Department of Medical Oncology, University Hospital of Bern, Bern, Switzerland
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Kay Lawson
- Department of Histopathology, UCL, London, UK
| | | | - Eleni Frangou
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Peter Dutton
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sabine Tejpar
- Department of Molecular Digestive Oncology, University of Leuven, Leuven, Belgium
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute Bioinformatics, Lausanne, Switzerland
| | - Rachel Kerr
- Department of Oncology, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK
| | - David Kerr
- Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford Centre for Cancer Gene Research and NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David N Church
- Cancer Genomics and Immunology Group, University of Oxford, Oxford, UK; Oxford Cancer Centre, Churchill Hospital, Oxford Radcliffe Hospitals NHS Trust, University of Oxford, Oxford, UK.
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Berg KG, Eilertsen IA, Alagaratnam S, Danielsen SA, Nesbakken A, Sveen A, Lothe RA. Abstract 103: Gene expression based subtypes of colorectal cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-103] [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
Colorectal cancer is a heterogeneous disease and improved molecular stratification of patients is warranted for precise treatment. Several gene expression classification systems are reported in the literature, albeit many have shown low reproducibility in external validation. A robust random forest classification system based on gene expression profiles was recently proposed, suggesting the existence of four biologically different subtypes with associations to prognosis (CMS1, CMS2, CMS3 and CMS4) (Guinney,J., et al., Nat Med, 2015). By applying the CMS classifier to high-quality gene expression profiles from a consecutive series of >400 stage I-IV primary colorectal cancers we are able to reproduce results from Guinney et al in an independent cohort. Analyses of mutational hotspots in BRAF / KRAS and the complete coding sequence of TP53 confirms enrichment of BRAF mutations in CMS1 (p<0.001), TP53 mutations in CMS2 and KRAS mutations in CMS4 (p<0.001). We further validate high levels of somatic copy number aberrations (SCNAs) in CMS2 and CMS4 compared to CMS1 and CMS3 (pair-wise comparisons, fraction of genome affected by SCNAs: CMS1 vs CMS2: p<0.001; CMS1 vs CMS4: p<0.01; CMS2 vs CMS3: p<0.001; CMS3 vs CMS4: p<0.01). Additionally we explore within-subtype variations with respect to SCNAs in the CMS2 and CMS4 subtypes. Altogether our results validate the CMS system as a robust classification system for colorectal cancer.
Citation Format: Kaja G. Berg, Ina A. Eilertsen, Sharmini Alagaratnam, Stine A. Danielsen, Arild Nesbakken, Anita Sveen, Ragnhild A. Lothe. Gene expression based subtypes of colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 103.
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Danielsen SA, Lind GE, Kolberg M, Høland M, Bjerkehagen B, Sundby Hall K, van den Berg E, Mertens F, Smeland S, Picci P, Lothe RA. Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis. Neuro Oncol 2014; 17:63-9. [PMID: 25038505 PMCID: PMC4416132 DOI: 10.1093/neuonc/nou140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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] [Indexed: 12/03/2022] Open
Abstract
Background Malignant peripheral nerve sheath tumor (MPNST) is a rare and highly aggressive disease with no evidence of effect from adjuvant therapy. It is further associated with the hereditary syndrome neurofibromatosis type 1 (NF1). Silencing of the tumor suppressor gene RASSF1A through DNA promoter hypermethylation is known to be involved in cancer development, but its impact in MPNSTs remains unsettled. Methods The RASSF1A promoter was analyzed by methylation-specific PCR in 113 specimens, including 44 NF1-associated MPNSTs, 47 sporadic MPNSTs, 21 benign neurofibromas, and 1 nonneoplastic nerve sheath control. Results RASSF1A methylation was found only in the malignant samples (60%) and identified a subgroup among patients with NF1-associated MPNST with a poor prognosis. These patients had a mean 5-year disease-specific survival of 27.3 months (95% CI: 17.2–37.4) versus 47.4 months (95% CI: 37.5–57.2) for NF1 patients with unmethylated promoters, P = 0.014. In multivariate Cox regression analysis, methylated RASSF1A remained an adverse prognostic factor independent of clinical risk factors, P = .013 (hazard ratio: 5.2; 95% CI: 1.4–19.4). Conclusion A considerable number of MPNST samples display hypermethylation of the RASSF1A gene promoter, and for these tumors, this is the first molecular marker that if validated can characterize a subgroup of patients with inferior prognosis, restricted to individuals with NF1.
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Affiliation(s)
- Stine A Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Matthias Kolberg
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Maren Høland
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Bodil Bjerkehagen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Kirsten Sundby Hall
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Eva van den Berg
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Fredrik Mertens
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Sigbjørn Smeland
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Piero Picci
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
| | - Ragnhild A Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (S.A.D., G.E.L., M.K., M.H., R.A.L.); Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (M.H., S.S.); Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway (S.A.D., G.E.L., R.A.L.); Department of Pathology (B.B), Division of Diagnostics and Intervention and Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway (K.S.H., S.S.); Department of Medical Genetics, University Hospital of Groningen, The Netherlands (E.v.d.B.); Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden (F.M.); Laboratory of Oncologic Research of the Istituto Ortopedico Rizzoli, Bologna, Italy (P.P.)
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Ahmed D, Danielsen SA, Aagesen TH, Bretthauer M, Thiis-Evensen E, Hoff G, Rognum TO, Nesbakken A, Lothe RA, Lind GE. A tissue-based comparative effectiveness analysis of biomarkers for early detection of colorectal tumors. Clin Transl Gastroenterol 2012; 3:e27. [PMID: 23324654 PMCID: PMC3535074 DOI: 10.1038/ctg.2012.21] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES: We recently identified a six-gene methylation-based biomarker panel suitable for early detection of colorectal cancer (CRC). In this study, we compared the performance of this novel epi-panel with that of previously identified DNA methylation markers in the same clinical tissue sample sets. METHODS: Quantitative methylation-specific PCR was used to analyze the promoter region of SEPT9 and VIM in a total of 485 tissue samples, divided into test and validation sets. ITGA4, NTRK2, OSMR, and TUBG2 were also included in the analyses. Receiver operating characteristic (ROC) curves were used to compare the performances of the individual biomarkers with that of the novel epi-panel. RESULTS: SEPT9 and VIM were methylated in 82 and 67% of CRCs (n=169) and in 88 and 54% of the adenomas (n=104). Only 3% of the normal mucosa samples (n=107) were methylated for these genes, confirming that the methylation was highly cancer-specific. Areas under the ROC curve (AUC), distinguishing CRCs from normal mucosa, were 0.94 for SEPT9 and 0.81 for VIM. AUC values for separating adenomas from normal mucosa samples were 0.96 and 0.81 for the same genes. In comparison, the novel epi-panel achieved an AUC of 0.98 (CRC) and 0.97 (adenomas). ITGA4, OSMR, NTRK2, and TUBG2 were methylated in 90, 78, 7, and 1% of the CRCs, and in 76, 77, 3, and 0% of the adenomas. Between 0 and 2% of the normal mucosa samples were methylated for the same genes. ITGA4 and OSMR achieved an AUC of 0.96 and 0.92 (CRC vs. normal mucosa), and 0.93 and 0.92 (adenomas vs. normal mucosa). CONCLUSIONS: We have confirmed the high performance of some of the previously identified DNA methylation markers. Furthermore, we showed that a recently reported epi-panel performed better than the individual DNA methylation biomarkers when analyzed in the same tissue samples. This observation was also true for VIM and SEPT9, which are included in commercially available noninvasive tests for CRC. These results further underscore the value of combining a manageable number of individual markers into a panel, which in addition to having a higher sensitivity and specificity might provide a more profound robustness to a noninvasive test compared with single markers.
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Affiliation(s)
- Deeqa Ahmed
- 1] Department of Cancer Prevention, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway [2] Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
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Danielsen SA, Cekaite L, Ågesen TH, Sveen A, Nesbakken A, Thiis-Evensen E, Skotheim RI, Lind GE, Lothe RA. Phospholipase C isozymes are deregulated in colorectal cancer--insights gained from gene set enrichment analysis of the transcriptome. PLoS One 2011; 6:e24419. [PMID: 21909432 PMCID: PMC3164721 DOI: 10.1371/journal.pone.0024419] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [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: 05/20/2011] [Accepted: 08/10/2011] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancer types in developed countries. To identify molecular networks and biological processes that are deregulated in CRC compared to normal colonic mucosa, we applied Gene Set Enrichment Analysis to two independent transcriptome datasets, including a total of 137 CRC and ten normal colonic mucosa samples. Eighty-two gene sets as described by the Kyoto Encyclopedia of Genes and Genomes database had significantly altered gene expression in both datasets. These included networks associated with cell division, DNA maintenance, and metabolism. Among signaling pathways with known changes in key genes, the “Phosphatidylinositol signaling network”, comprising part of the PI3K pathway, was found deregulated. The downregulated genes in this pathway included several members of the Phospholipase C protein family, and the reduced expression of two of these, PLCD1 and PLCE1, were successfully validated in CRC biopsies (n = 70) and cell lines (n = 19) by quantitative analyses. The repression of both genes was found associated with KRAS mutations (P = 0.005 and 0.006, respectively), and we observed that microsatellite stable carcinomas with reduced PLCD1 expression more frequently had TP53 mutations (P = 0.002). Promoter methylation analyses of PLCD1 and PLCE1 performed in cell lines and tumor biopsies revealed that methylation of PLCD1 can contribute to reduced expression in 40% of the microsatellite instable carcinomas. In conclusion, we have identified significantly deregulated pathways in CRC, and validated repression of PLCD1 and PLCE1 expression. This illustrates that the GSEA approach may guide discovery of novel biomarkers in cancer.
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Affiliation(s)
- Stine A. Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Lina Cekaite
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Trude H. Ågesen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Arild Nesbakken
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Espen Thiis-Evensen
- Department of Organ Transplantation, Gastroenterology, and Nephrology, Oslo University Hospital, Oslo, Norway
| | - Rolf I. Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Guro E. Lind
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild A. Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- * E-mail:
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16
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Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, Bretthauer M, Thiis-Evensen E, Nesbakken A, Lothe RA. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011; 10:85. [PMID: 21777459 PMCID: PMC3166273 DOI: 10.1186/1476-4598-10-85] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [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: 03/24/2011] [Accepted: 07/21/2011] [Indexed: 12/16/2022] Open
Abstract
Background The presence of cancer-specific DNA methylation patterns in epithelial colorectal cells in human feces provides the prospect of a simple, non-invasive screening test for colorectal cancer and its precursor, the adenoma. This study investigates a panel of epigenetic markers for the detection of colorectal cancer and adenomas. Methods Candidate biomarkers were subjected to quantitative methylation analysis in test sets of tissue samples from colorectal cancers, adenomas, and normal colonic mucosa. All findings were verified in independent clinical validation series. A total of 523 human samples were included in the study. Receiver operating characteristic (ROC) curve analysis was used to evaluate the performance of the biomarker panel. Results Promoter hypermethylation of the genes CNRIP1, FBN1, INA, MAL, SNCA, and SPG20 was frequent in both colorectal cancers (65-94%) and adenomas (35-91%), whereas normal mucosa samples were rarely (0-5%) methylated. The combined sensitivity of at least two positives among the six markers was 94% for colorectal cancers and 93% for adenoma samples, with a specificity of 98%. The resulting areas under the ROC curve were 0.984 for cancers and 0.968 for adenomas versus normal mucosa. Conclusions The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.
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Affiliation(s)
- Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
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17
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Lind GE, Raiborg C, Danielsen SA, Rognum TO, Thiis-Evensen E, Hoff G, Nesbakken A, Stenmark H, Lothe RA. SPG20, a novel biomarker for early detection of colorectal cancer, encodes a regulator of cytokinesis. Oncogene 2011; 30:3967-78. [PMID: 21499309 PMCID: PMC3174365 DOI: 10.1038/onc.2011.109] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [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] [Indexed: 12/16/2022]
Abstract
Colorectal cancer is a common disease with high mortality. Suitable biomarkers for detection of tumors at an early curable stage would significantly improve patient survival. Here, we show that the SPG20 (spastic paraplegia-20) promoter, encoding the multifunctional Spartin protein, is hypermethylated in 89% of colorectal carcinomas, 78% of adenomas and only 1% of normal mucosa samples. SPG20 methylation was also present in a pilot series of stool samples and corresponding tumors from colorectal cancer patients. SPG20 promoter hypermethylation resulted in loss of mRNA expression in various cancer types and subsequent depletion of Spartin. We further showed that Spartin downregulation in cancer cells resulted in cytokinesis arrest, which was reversed when SPG20 methylation was inhibited. The present study identifies SPG20 promoter hypermethylation as a biomarker suitable for non-invasive detection of colorectal cancer, and a possible mechanism for cytokinesis arrest in colorectal tumorigenesis.
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Affiliation(s)
- G E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Radiumhospitalet, Oslo University Hospital, Oslo, Norway
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18
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Berg M, Danielsen SA, Ahlquist T, Merok MA, Ågesen TH, Vatn MH, Mala T, Sjo OH, Bakka A, Moberg I, Fetveit T, Mathisen Ø, Husby A, Sandvik O, Nesbakken A, Thiis-Evensen E, Lothe RA. DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset. PLoS One 2010; 5:e13978. [PMID: 21103049 PMCID: PMC2980471 DOI: 10.1371/journal.pone.0013978] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [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: 06/21/2010] [Accepted: 10/14/2010] [Indexed: 12/12/2022] Open
Abstract
The incidence of colorectal cancer (CRC) increases with age and early onset indicates an increased likelihood for genetic predisposition for this disease. The somatic genetics of tumor development in relation to patient age remains mostly unknown. We have examined the mutation status of five known cancer critical genes in relation to age at diagnosis, and compared the genomic complexity of tumors from young patients without known CRC syndromes with those from elderly patients. Among 181 CRC patients, stratified by microsatellite instability status, DNA sequence changes were identified in KRAS (32%), BRAF (16%), PIK3CA (4%), PTEN (14%) and TP53 (51%). In patients younger than 50 years (n = 45), PIK3CA mutations were not observed and TP53 mutations were more frequent than in the older age groups. The total gene mutation index was lowest in tumors from the youngest patients. In contrast, the genome complexity, assessed as copy number aberrations, was highest in tumors from the youngest patients. A comparable number of tumors from young (<50 years) and old patients (>70 years) was quadruple negative for the four predictive gene markers (KRAS-BRAF-PIK3CA-PTEN); however, 16% of young versus only 1% of the old patients had tumor mutations in PTEN/PIK3CA exclusively. This implies that mutation testing for prediction of EGFR treatment response may be restricted to KRAS and BRAF in elderly (>70 years) patients. Distinct genetic differences found in tumors from young and elderly patients, whom are comparable for known clinical and pathological variables, indicate that young patients have a different genetic risk profile for CRC development than older patients.
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Affiliation(s)
- Marianne Berg
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Stine A. Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Terje Ahlquist
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Marianne A. Merok
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Aker, Oslo, Norway
| | - Trude H. Ågesen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Morten H. Vatn
- Department of Organ Transplantation, Gastroenterology and Nephrology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Epigen, Akershus University Hospital, Lørenskog, Norway
| | - Tom Mala
- Department of Gastrointestinal Surgery, Oslo University Hospital, Aker, Oslo, Norway
| | - Ole H. Sjo
- Department of Gastrointestinal Surgery, Oslo University Hospital, Aker, Oslo, Norway
| | - Arne Bakka
- Department of Digestive Surgery, Akershus University Hospital, Lørenskog, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ingvild Moberg
- Department of Digestive Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Torunn Fetveit
- Department of Surgery, Sørlandet Hospital, Arendal, Norway
| | - Øystein Mathisen
- Department of Liver, Gastrointestinal and Pediatric Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anders Husby
- Department of Surgery, Diakonhjemmet Hospital, Oslo, Norway
| | - Oddvar Sandvik
- Department of Gastrointestinal Surgery, Sørlandet Hospital, Kristiansand, Norway
| | - Arild Nesbakken
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Gastrointestinal Surgery, Oslo University Hospital, Aker, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Espen Thiis-Evensen
- Department of Organ Transplantation, Gastroenterology and Nephrology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ragnhild A. Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
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19
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Pinheiro M, Ahlquist T, Danielsen SA, Lind GE, Veiga I, Pinto C, Costa V, Afonso L, Sousa O, Fragoso M, Santos L, Henrique R, Lopes P, Lopes C, Lothe RA, Teixeira MR. Colorectal carcinomas with microsatellite instability display a different pattern of target gene mutations according to large bowel site of origin. BMC Cancer 2010; 10:587. [PMID: 20979647 PMCID: PMC2984429 DOI: 10.1186/1471-2407-10-587] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [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: 12/12/2009] [Accepted: 10/27/2010] [Indexed: 11/10/2022] Open
Abstract
Background Only a few studies have addressed the molecular pathways specifically involved in carcinogenesis of the distal colon and rectum. We aimed to identify potential differences among genetic alterations in distal colon and rectal carcinomas as compared to cancers arising elsewhere in the large bowel. Methods Constitutional and tumor DNA from a test series of 37 patients with rectal and 25 patients with sigmoid carcinomas, previously analyzed for microsatellite instability (MSI), was studied for BAX, IGF2R, TGFBR2, MSH3, and MSH6 microsatellite sequence alterations, BRAF and KRAS mutations, and MLH1 promoter methylation. The findings were then compared with those of an independent validation series consisting of 36 MSI-H carcinomas with origin from each of the large bowel regions. Immunohistochemical and germline mutation analyses of the mismatch repair system were performed when appropriate. Results In the test series, IGFR2 and BAX mutations were present in one and two out of the six distal MSI-H carcinomas, respectively, and no mutations were detected in TGFBR2, MSH3, and MSH6. We confirmed these findings in the validation series, with TGFBR2 and MSH3 microsatellite mutations occurring less frequently in MSI-H rectal and sigmoid carcinomas than in MSI-H colon carcinomas elsewhere (P = 0.00005 and P = 0.0000005, respectively, when considering all MSI-carcinomas of both series). No MLH1 promoter methylation was observed in the MSI-H rectal and sigmoid carcinomas of both series, as compared to 53% found in MSI-H carcinomas from other locations (P = 0.004). KRAS and BRAF mutational frequencies were 19% and 43% in proximal carcinomas and 25% and 17% in rectal/sigmoid carcinomas, respectively. Conclusion The mechanism and the pattern of genetic changes driving MSI-H carcinogenesis in distal colon and rectum appears to differ from that occurring elsewhere in the colon and further investigation is warranted both in patients with sporadic or hereditary disease.
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Affiliation(s)
- Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute - Porto, Rua Dr, António Bernardino Almeida, 4200-072 Porto, Portugal
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20
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Costa VL, Henrique R, Danielsen SA, Duarte-Pereira S, Eknaes M, Skotheim RI, Rodrigues A, Magalhães JS, Oliveira J, Lothe RA, Teixeira MR, Jerónimo C, Lind GE. Three epigenetic biomarkers, GDF15, TMEFF2, and VIM, accurately predict bladder cancer from DNA-based analyses of urine samples. Clin Cancer Res 2010; 16:5842-51. [PMID: 20975101 DOI: 10.1158/1078-0432.ccr-10-1312] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE To identify a panel of epigenetic biomarkers for accurate bladder cancer (BlCa) detection in urine sediments. EXPERIMENTAL DESIGN Gene expression microarray analysis of BlCa cell lines treated with 5-aza-2'-deoxycytidine and trichostatin A as well as 26 tissue samples was used to identify a list of novel methylation candidates for BlCa. Methylation levels of candidate genes were quantified in 4 BlCa cell lines, 50 BlCa tissues, 20 normal bladder mucosas (NBM), and urine sediments from 51 BlCa patients and 20 healthy donors, 19 renal cancer patients, and 20 prostate cancer patients. Receiver operator characteristic curve analysis was used to assess the diagnostic performance of the gene panel. RESULTS GDF15, HSPA2, TMEFF2, and VIM were identified as epigenetic biomarkers for BlCa. The methylation levels were significantly higher in BlCa tissues than in NBM (P < 0.001) and the cancer specificity was retained in urine sediments (P < 0.001). A methylation panel comprising GDF15, TMEFF2, and VIM correctly identified BlCa tissues with 100% sensitivity and specificity. In urine samples, the panel achieved a sensitivity of 94% and specificity of 100% and an area under the curve of 0.975. The gene panel could discriminate BlCa from both healthy individuals and renal or prostate cancer patients (sensitivity, 94%; specificity, 90%). CONCLUSIONS By using a genome-wide approach, we have identified a biomarker panel that allows for early and accurate noninvasive detection of BlCa using urine samples.
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Affiliation(s)
- Vera L Costa
- Cancer Epigenetics Group, Portuguese Oncology Institute - Porto, Porto, Portugal
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21
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Danielsen SA, Lind GE, Bjørnslett M, Meling GI, Rognum TO, Heim S, Lothe RA. Novel mutations of the suppressor gene PTENin colorectal carcinomas stratified by microsatellite instability- and TP53mutation- status. Hum Mutat 2009. [DOI: 10.1002/humu.21048] [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: 11/10/2022]
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22
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Bottillo I, Ahlquist T, Brekke H, Danielsen SA, van den Berg E, Mertens F, Lothe RA, Dallapiccola B. Germline and somaticNF1mutations in sporadic and NF1-associated malignant peripheral nerve sheath tumours. J Pathol 2009; 217:693-701. [DOI: 10.1002/path.2494] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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23
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Danielsen SA, Lind GE, Bjørnslett M, Meling GI, Rognum TO, Heim S, Lothe RA. Novel mutations of the suppressor gene PTEN in colorectal carcinomas stratified by microsatellite instability- and TP53 mutation- status. Hum Mutat 2008; 29:E252-62. [PMID: 18781614 DOI: 10.1002/humu.20860] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PTEN regulates cell homeostasis by inhibiting growth signals transduced through PI3-kinases. The gene is mutated in several cancer types, but so far, only a limited number of mutations have been reported in colorectal cancer. In the present study, direct sequencing was used to analyze the whole coding region and exon-intron boundaries of PTEN in a series of microsatellite stable (n=34) and microsatellite unstable (n=30) colorectal carcinomas with known TP53 mutation status. We detected 21 PTEN mutations in altogether 13 tumors (20%), including 19 mutations in the coding sequence and two in the exon-intron boundaries. Sixteen of these alterations have not been previously reported in colorectal cancer. Furthermore, seven out of the 13 altered tumors harbored more than one mutation, potentially leading to loss of gene function. Finally, all PTEN mutations found were in tumors harboring wild-type TP53. In conclusion, PTEN is mutated in a significant subgroup of colorectal carcinomas, and our findings further extend the previously small spectrum of reported PTEN changes. Additionally, it seems that mutations in PTEN and TP53 are mutually exclusive for this cancer type.
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Affiliation(s)
- Stine A Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
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Braun-Howland EB, Danielsen SA, Nierzwicki-Bauer SA. Development of a rapid method for detecting bacterial cells in situ using 16S rRNA-targeted probes. Biotechniques 1992; 13:928-34. [PMID: 1282348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A rapid method for the identification of bacterial cells using 16S rRNA-directed, fluorescently tagged oligonucleotide probes has been developed. The parameters evaluated for their effect on labeling intensity included storage time, type of fixative, time of fixation, treatment time with methanol:formaldehyde and treatment time with borohydride. The results of tests using a variety of microorganisms, both Gram-positive and Gram-negative, are presented. Using this method, cells are spotted onto slides and stored desiccated until hybridized. This method may be especially applicable to environmental samples, which comprise diverse cell types and frequently require storage prior to examination.
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Affiliation(s)
- E B Braun-Howland
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180-3590
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