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Cao Y, Gu J, Yan L, Deng S, Mao F, Cai W, Li H, Liu X, Wang J, Wu K, Cai K. The value of haematological parameters and serum tumour markers for predicting KRAS mutations in 784 Chinese colorectal cancer patients: a retrospective analysis. BMC Cancer 2020; 20:1099. [PMID: 33183271 PMCID: PMC7659200 DOI: 10.1186/s12885-020-07551-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Background Identifying the mutation status of KRAS is important for optimizing treatment in patients with colorectal cancer (CRC). The aim of this study was to investigate the predictive value of haematological parameters and serum tumour markers (STMs) for KRAS gene mutations. Methods The clinical data of patients with colorectal cancer from January 2014 to December 2018 were retrospectively collected, and the associations between KRAS mutations and other indicators were analysed. Receiver operating characteristic (ROC) curve analysis was performed to quantify the predictive value of these factors. Univariate and multivariate logistic regression models were applied to identify predictors of KRAS mutations by calculating the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). Results KRAS mutations were identified in 276 patients (35.2%). ROC analysis revealed that age, CA12–5, AFP, SCC, CA72–4, CA15–3, FERR, CYFRA21-1, MCHC, and tumor location could not predict KRAS mutations (P = 0.154, 0.177, 0.277, 0.350, 0.864, 0.941, 0.066, 0.279, 0.293, and 0.053 respectively), although CEA, CA19–9, NSE and haematological parameter values showed significant predictive value (P = 0.001, < 0.001, 0.043 and P = 0.003, < 0.001, 0.001, 0.031, 0.030, 0.016, 0.015, 0.019, and 0.006, respectively) but without large areas under the curve. Multivariate logistic regression analysis showed that CA19–9 was significantly associated with KRAS mutations and was the only independent predictor of KRAS positivity (P = 0.016). Conclusions Haematological parameters and STMs were related to KRAS mutation status, and CA19–9 was an independent predictive factor for KRAS gene mutations. The combination of these clinical factors can improve the ability to identify KRAS mutations in CRC patients.
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Affiliation(s)
- Yinghao Cao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Junnan Gu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Lizhao Yan
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Shenghe Deng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Fuwei Mao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Wentai Cai
- College of life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Hang Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Xinghua Liu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Jiliang Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Ke Wu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China.
| | - Kailin Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China.
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Germetaki T, Nicholls C, Adams RA, Braun M, Rogan J, Moghadam S, Lenfert E, Lukas A, Edelstein DL, Jones FS, Saunders MP. Blood-based RAS mutation testing: concordance with tissue-based RAS testing and mutational changes on progression. Future Oncol 2020; 16:2177-2189. [PMID: 32716216 DOI: 10.2217/fon-2020-0523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: To determine the concordance between plasma and tissue RAS mutation status in metastatic colorectal cancer patients to gauge whether blood-based testing is a viable alternative. We also evaluated the change in mutation status on progression. Materials/methods: RAS testing was performed on plasma from patients commencing first-line therapy (OncoBEAM™ RAS CEIVD kit). Results were then compared with formalin-fixed paraffin embedded tumor samples. Results: The overall percentage agreement (concordance) was 86.0% (86/100), which demonstrates that blood-based testing is an alternative to tissue-based testing. Reproducibility was 100% between three laboratories and 20% showed changes in their RAS mutational status on progression. Conclusion: These results show good concordance between tissue and plasma samples and suggest the need for longitudinal plasma testing during treatment to guide management decisions.
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Affiliation(s)
- Theodora Germetaki
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Camille Nicholls
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Richard A Adams
- Department of Medical Oncology, Velindre Hospital, Velindre Road, Cardiff, Wales CF14 2TL, UK
| | - Michael Braun
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Jane Rogan
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Sharzad Moghadam
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Eva Lenfert
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | - Antje Lukas
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | | | | | - Mark P Saunders
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
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Sensitive, enzyme-free and label-free electrochemical sensor for K-ras G12D point mutation detection based on double cascade amplification reaction. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Swift SL, Duffy S, Lang SH. Impact of tumor heterogeneity and tissue sampling for genetic mutation testing: a systematic review and post hoc analysis. J Clin Epidemiol 2020; 126:45-55. [PMID: 32540382 DOI: 10.1016/j.jclinepi.2020.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The objective of the study was to identify guidelines to assist systematic reviewers or clinical researchers in identifying sampling bias due to tumor heterogeneity (TH) in solid cancers assayed for somatic mutations. We also assessed current reporting standards to determine the impact of TH on sample bias. STUDY DESIGN AND SETTING We conducted a systematic review searching 13 databases (to January 2019) to identify guidelines. A post hoc analysis was performed using 12 prostate tumor somatic mutation data sets from a previous systematic review to assess reporting on TH. RESULTS Searches identified 2,085 records. No formal guidelines were identified. Forty publications contained incidental recommendations across five major themes: using multiple tumor samples (n = 29), sample purity thresholds (n = 14), using specific sequencing methods (n = 8), using liquid biopsies (n = 4), and microdissection (n = 4). In post hoc analyses, 50% (6 of 12) clearly reported pathology methods. Forty-two percent (5 of 12) did not report pathology results. Forty-two percent (5 of 12) confirmed the pathology of the sample by direct diagnosis rather than inference. Forty-two percent (5 of 12) used multiple samples per patient. Fifty-eight percent (7 of 12) reported on tumor purity (reported ranges 10% to 100%). CONCLUSIONS As precision medicine progresses to the clinic, guidelines are required to help evidence-based decision makers understand how TH may impact sample bias. Authors need to clearly report pathology methods and results and tumor purity methods and results.
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Affiliation(s)
| | - Steve Duffy
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Shona H Lang
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK.
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5
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CT texture analysis for the prediction of KRAS mutation status in colorectal cancer via a machine learning approach. Eur J Radiol 2019; 118:38-43. [PMID: 31439256 DOI: 10.1016/j.ejrad.2019.06.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/27/2019] [Accepted: 06/30/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE This study aimed to investigate whether a machine learning-based computed tomography (CT) texture analysis could predict the mutation status of V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) in colorectal cancer. METHOD This retrospective study comprised 40 patients with pathologically confirmed colorectal cancer who underwent KRAS mutation testing, contrast-enhancement CT, and 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) before treatment. Of the 40 patients, 20 had mutated KRAS genes, whereas 20 had wild-type KRAS genes. Fourteen CT texture parameters were extracted from portal venous phase CT images of primary tumors, and the maximum standard uptake values (SUVmax) on 18F-FDG PET images were recorded. Univariate logistic regression was used to develop predictive models for each CT texture parameter and SUVmax, and a machine learning method (multivariate support vector machine) was used to develop a comprehensive set of CT texture parameters. The area under the receiver operating characteristic (ROC) curve (AUC) of each model was calculated using five-fold cross validation. In addition, the performance of the machine learning method with the CT texture parameters was compared with that of SUVmax. RESULTS In the univariate analyses, the AUC of each CT texture parameter ranged from 0.4 to 0.7, while the AUC of the SUVmax was 0.58. Comparatively, the multivariate support vector machine with comprehensive CT texture parameters yielded an AUC of 0.82, indicating a superior prediction performance when compared to the SUVmax. CONCLUSIONS A machine learning-based CT texture analysis was superior to the SUVmax for predicting the KRAS mutation status of a colorectal cancer.
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Yang M, Schell MJ, Loboda A, Nebozhyn M, Li J, Teer JK, Pledger WJ, Yeatman TJ. Repurposing EGFR Inhibitor Utility in Colorectal Cancer in Mutant APC and TP53 Subpopulations. Cancer Epidemiol Biomarkers Prev 2019; 28:1141-1152. [PMID: 31015202 PMCID: PMC7845290 DOI: 10.1158/1055-9965.epi-18-1383] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND EGFR is a major therapeutic target for colorectal cancer. Currently, extended RAS/RAF testing identifies only nonresponders to EGFR inhibitors (EGFRi). We aimed to develop a mutation signature that further refines drug-sensitive subpopulations to improve EGFRi outcomes. METHODS A prespecified, 203-gene expression signature score measuring cetuximab sensitivity (CTX-S) was validated with two independent clinical trial datasets of cetuximab-treated patients with colorectal cancer (n = 44 and n = 80) as well as an in vitro dataset of 147 cell lines. The CTX-S score was then used to decipher mutated genes that predict EGFRi sensitivity. The predictive value of the identified mutation signature was further validated by additional independent datasets. RESULTS Here, we report the discovery of a 2-gene (APC+TP53) mutation signature that was useful in identifying EGFRi-sensitive colorectal cancer subpopulations. Mutant APC+TP53 tumors were more predominant in left- versus right-sided colorectal cancers (52% vs. 21%, P = 0.0004), in microsatellite stable (MSS) versus microsatellite instable (MSI) cases (47% vs. 2%, P < 0.0001), and in the consensus molecular subtype 2 versus others (75% vs. 37%, P < 0.0001). Moreover, mutant APC+TP53 tumors had favorable outcomes in two cetuximab-treated patient-derived tumor xenograft (PDX) datasets (P = 0.0277, n = 52; P = 0.0008, n = 98). CONCLUSIONS Our findings suggest that the APC and TP53 combination mutation may account for the laterality of EGFRi sensitivity and provide a rationale for refining treated populations. The results also suggest addition of APC+TP53 sequencing to extended RAS/RAF testing that may directly increase the response rates of EGFRi therapy in selected patients. IMPACT These findings, if further validated through clinical trials, could also expand the utility of EGFRi therapies that are currently underutilized.
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Affiliation(s)
- Mingli Yang
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | | | - Jiannong Li
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - W Jack Pledger
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina
- Department of Molecular Medicine, VCOM, Spartanburg, South Carolina
| | - Timothy J Yeatman
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina.
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García-Foncillas J, Alba E, Aranda E, Díaz-Rubio E, López-López R, Tabernero J, Vivancos A. Incorporating BEAMing technology as a liquid biopsy into clinical practice for the management of colorectal cancer patients: an expert taskforce review. Ann Oncol 2018; 28:2943-2949. [PMID: 28945877 PMCID: PMC5834030 DOI: 10.1093/annonc/mdx501] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The importance of mutation identification for advanced colorectal cancer treatment with anti-epidermal growth factor receptor agents is well established. However, due to delays in turnaround time, low-quality tissue samples, and/or lack of standardization of testing methods a significant proportion of patients are being treated without the information that Kirsten rat sarcoma and neuroblastoma rat sarcoma (RAS) testing can provide. The detection of mutated circulating tumor DNA by BEAMing technology addresses this gap in care and allows these patients to receive international guideline-recommended expanded RAS testing with rapid turnaround times. Furthermore, the overall concordance between OncoBEAM RAS colorectal cancer testing and standard of care tissue testing is very high (93.3%). This article presents an overview of the clinical utility and potential applications of this minimally invasive method, such as early detection of emergent resistance to anti-epidermal growth factor receptor therapy. If appropriately implemented, BEAMing technology holds considerable promise to enhance the quality of patient care and improve clinical outcomes.
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Affiliation(s)
- J García-Foncillas
- Cancer Institute, University Hospital Fundacion Jimenez Diaz, Autonomous University, Madrid
| | - E Alba
- Medical Oncology Unit, Regional University Hospital Virgen de la Victoria, IBIMA, Málaga
| | - E Aranda
- Biomedical Research Institute (IMIBIC), Hospital Reina Sofía, Faculty of Medicine, Universidad de Córdoba, Cordoba, Spain (CIBERONC)
| | - E Díaz-Rubio
- Research Institute IdISSC, Hospital Clínico San Carlos, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain (CIBERONC)
| | - R López-López
- Medical Oncology Department and Translational Medical Oncology Group, University Clinical Hospital & Health Research Institute (IDIS); CIBERONC, Santiago de Compostela, University School of Medicine, Santiago de Compostela, Spain
| | - J Tabernero
- Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAM), Barcelona, Spain (CIBERONC)
| | - A Vivancos
- Vall d'Hebron Institute of Oncology (VHIO), Cancer Genomics Lab., Barcelona, Spain
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Della Corte CM, Malapelle U, Vigliar E, Pepe F, Troncone G, Ciaramella V, Troiani T, Martinelli E, Belli V, Ciardiello F, Morgillo F. Efficacy of continuous EGFR-inhibition and role of Hedgehog in EGFR acquired resistance in human lung cancer cells with activating mutation of EGFR. Oncotarget 2018; 8:23020-23032. [PMID: 28416737 PMCID: PMC5410282 DOI: 10.18632/oncotarget.15479] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/08/2017] [Indexed: 01/09/2023] Open
Abstract
Purpose The aim of this work was to investigate the efficacy of sequential treatment with first-, second- and third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and the mechanisms of acquired resistance occurring during the sequential use of these inhibitors. Experimental design We developed an in vivo model of acquired resistance to EGFR-inhibitors by treating nude mice xenografted with HCC827, a human non-small-cell lung cancer (NSCLC) cell line harboring EGFR activating mutation, with a sequence of first-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs) (erlotinib and gefitinib), of second-generation EGFR-TKI (afatinib) plus/minus the anti-EGFR monoclonal antibody cetuximab, and of third-generation EGFR-TKI (osimertinib). Results HCC827-derived xenografts and with acquired resistance to EGFR-inhibitors were sensitive to the sequential use of first-, second- and third-generation EGFR-TKIs. Continuous EGFR inhibition of first-generation resistant tumors by sequential treatment with afatinib plus/minus cetuximab, followed by osimertinib, represented an effective therapeutic strategy in this model. Whereas T790M resistance mutation was not detected, a major mechanism of acquired resistance was the activation of components of the Hedgehog (Hh) pathway. This phenomenon was accompanied by epithelial-to-mesenchymal transition. Cell lines established in vitro from gefitinib-, or afatinib- or osimertinib-resistant tumors showed metastatic properties and maintained EGFR-TKIs resistance in vitro, that was reverted by the combined blockade of Hh, with the selective SMO inhibitor sonidegib, and EGFR. Conclusions EGFR-mutant NSCLC can benefit from continuous treatment with EGFR-inhibitors, indepenently from mechanisms of resistance. In a complex and heterogenous scenario, Hh showed an important role in mediating resistance to EGFR-inhibitors through the induction of mesenchymal properties.
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Affiliation(s)
- Carminia Maria Della Corte
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Umberto Malapelle
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Elena Vigliar
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Francesco Pepe
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Giancarlo Troncone
- Dipartimento di Sanità Pubblica, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Vincenza Ciaramella
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Teresa Troiani
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Martinelli
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Valentina Belli
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Fortunato Ciardiello
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Floriana Morgillo
- Oncologia Medica, Dipartimento Medico-Chirurgico di Internistica Clinica e Sperimentale "F. Magrassi e A. Lanzara," Università degli studi della Campania "Luigi Vanvitelli", Naples, Italy
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Kafatos G, Niepel D, Lowe K, Jenkins-Anderson S, Westhead H, Garawin T, Traugottová Z, Bilalis A, Molnar E, Timar J, Toth E, Gouvas N, Papaxoinis G, Murray S, Mokhtar N, Vosmikova H, Fabian P, Skalova A, Wójcik P, Tysarowski A, Barugel M, van Krieken JH, Trojan J. RAS mutation prevalence among patients with metastatic colorectal cancer: a meta-analysis of real-world data. Biomark Med 2017; 11:751-760. [PMID: 28747067 PMCID: PMC6367778 DOI: 10.2217/bmm-2016-0358] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/06/2017] [Indexed: 02/06/2023] Open
Abstract
AIM A confirmed wild-type RAS tumor status is commonly required for prescribing anti-EGFR treatment for metastatic colorectal cancer. This noninterventional, observational research project estimated RAS mutation prevalence from real-world sources. MATERIALS & METHODS Aggregate RAS mutation data were collected from 12 sources in three regions. Each source was analyzed separately; pooled prevalence estimates were then derived from meta-analyses. RESULTS The pooled RAS mutation prevalence from 4431 tumor samples tested for RAS mutation status was estimated to be 43.6% (95% CI: 38.8-48.5%); ranging from 33.7% (95% CI: 28.4-39.3%) to 54.1% (95% CI: 51.7-56.5%) between sources. CONCLUSION The RAS mutation prevalence estimates varied among sources. The reasons for this are not clear and highlight the need for further research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jozsef Timar
- Semmelweis Medical University, Budapest, Hungary
| | - Erika Toth
- National Institute of Oncology, Budapest, Hungary
| | - Nikolaos Gouvas
- Gastrointestinal Cancer Study Group, Heraklion, Crete, Greece
| | - George Papaxoinis
- Hellenic Cooperative Oncology Group, University of Athens, Athens, Greece
| | | | - Nadia Mokhtar
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hana Vosmikova
- University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Pavel Fabian
- Masaryk Memorial Cancer Institute, Brno, Czech Republic
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10
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Yang M, Yeatman TJ. Molecular stratification of colorectal cancer populations and its use in directing precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2017.1362316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mingli Yang
- Gibbs Research Institute, Gibbs Cancer Center & Research Institute, Spartanburg, SC 29303, USA
| | - Timothy J Yeatman
- Gibbs Research Institute, Gibbs Cancer Center & Research Institute, Spartanburg, SC 29303, USA
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11
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Lee SH, Chung AM, Lee A, Oh WJ, Choi YJ, Lee YS, Jung ES. KRAS Mutation Test in Korean Patients with Colorectal Carcinomas: A Methodological Comparison between Sanger Sequencing and a Real-Time PCR-Based Assay. J Pathol Transl Med 2016; 51:24-31. [PMID: 28013534 PMCID: PMC5267542 DOI: 10.4132/jptm.2016.10.03] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/23/2016] [Accepted: 10/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. Methods We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. Results KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. Conclusions The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
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Affiliation(s)
- Sung Hak Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Arthur Minwoo Chung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo Jin Oh
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeong Jin Choi
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn-Soo Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun Sun Jung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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12
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Rankin A, Klempner SJ, Erlich R, Sun JX, Grothey A, Fakih M, George TJ, Lee J, Ross JS, Stephens PJ, Miller VA, Ali SM, Schrock AB. Broad Detection of Alterations Predicted to Confer Lack of Benefit From EGFR Antibodies or Sensitivity to Targeted Therapy in Advanced Colorectal Cancer. Oncologist 2016; 21:1306-1314. [PMID: 27682134 PMCID: PMC5189622 DOI: 10.1634/theoncologist.2016-0148] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/20/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION A KRAS mutation represented the first genomic biomarker to predict lack of benefit from anti-epidermal growth factor receptor (EGFR) antibody therapy in advanced colorectal cancer (CRC). Expanded RAS testing has further refined the treatment approach, but understanding of genomic alterations underlying primary and acquired resistance is limited and further study is needed. MATERIALS AND METHODS We prospectively analyzed 4,422 clinical samples from patients with advanced CRC, using hybrid-capture based comprehensive genomic profiling (CGP) at the request of the individual treating physicians. Comparison with prior molecular testing results, when available, was performed to assess concordance. RESULTS We identified a RAS/RAF pathway mutation or amplification in 62% of cases, including samples harboring KRAS mutations outside of the codon 12/13 hotspot region in 6.4% of cases. Among cases with KRAS non-codon 12/13 alterations for which prior test results were available, 79 of 90 (88%) were not identified by focused testing. Of 1,644 RAS/RAF wild-type cases analyzed by CGP, 31% harbored a genomic alteration (GA) associated with resistance to anti-EGFR therapy in advanced CRC including mutations in PIK3CA, PTEN, EGFR, and ERBB2. We also identified other targetable GA, including novel kinase fusions, receptor tyrosine kinase amplification, activating point mutations, as well as microsatellite instability. CONCLUSION Extended genomic profiling reliably detects alterations associated with lack of benefit to anti-EGFR therapy in advanced CRC, while simultaneously identifying alterations potentially important in guiding treatment. The use of CGP during the course of clinical care allows for the refined selection of appropriate targeted therapies and clinical trials, increasing the chance of clinical benefit and avoiding therapeutic futility. IMPLICATIONS FOR PRACTICE Comprehensive genomic profiling (CGP) detects diverse genomic alterations associated with lack of benefit to anti-epidermal growth factor receptor therapy in advanced colorectal cancer (CRC), as well as targetable alterations in many other genes. This includes detection of a broad spectrum of activating KRAS alterations frequently missed by focused molecular hotspot testing, as well as other RAS/RAF pathway alterations, mutations shown to disrupt antibody binding, RTK activating point mutations, amplifications, and rearrangements, and activating alterations in downstream effectors including PI3K and MEK1. The use of CGP in clinical practice is critical to guide appropriate selection of targeted therapies for patients with advanced CRC.
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Affiliation(s)
- Andrew Rankin
- Foundation Medicine Inc., Cambridge, Massachusetts, USA
| | - Samuel J Klempner
- The Angeles Clinic & Research Institute, Los Angeles, California, USA
| | - Rachel Erlich
- Foundation Medicine Inc., Cambridge, Massachusetts, USA
| | - James X Sun
- Foundation Medicine Inc., Cambridge, Massachusetts, USA
| | - Axel Grothey
- Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Marwan Fakih
- City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Thomas J George
- College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jeeyun Lee
- Department of Hematology and Oncology, Samsung Medical Center, SungKyunKwan University School of Medicine, Seoul, Republic of Korea
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | | | | | - Siraj M Ali
- Foundation Medicine Inc., Cambridge, Massachusetts, USA
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13
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Boleij A, Tack V, Taylor A, Kafatos G, Jenkins-Anderson S, Tembuyser L, Dequeker E, van Krieken JH. RAS testing practices and RAS mutation prevalence among patients with metastatic colorectal cancer: results from a Europe-wide survey of pathology centres. BMC Cancer 2016; 16:825. [PMID: 27784278 PMCID: PMC5080758 DOI: 10.1186/s12885-016-2810-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 09/23/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Treatment options for patients with metastatic colorectal cancer (mCRC) include anti-epithelial growth factor therapies, which, in Europe, are indicated in patients with RAS wild-type tumours only and require prior mutation testing of "hot-spot" codons in exons 2, 3 and 4 of KRAS and NRAS. The aim of this study was to evaluate the implementation of RAS testing methods and estimate the RAS mutation prevalence in mCRC patients. METHODS Overall, 194 pathology laboratories were invited to complete an online survey. Participating laboratories were asked to provide information on their testing practices and aggregated RAS mutation data from 20 to 30 recently tested patients with mCRC. RESULTS A total of 96 (49.5 %) laboratories across 24 European countries completed the survey. All participants tested KRAS exon 2, codons 12 and 13. Seventy (72.9 %) laboratories reported complete testing of all RAS hot-spot codons, and three (3.1 %) reported only testing KRAS exon 2. Sixty-nine (71.9 %) laboratories reported testing >80 patients yearly for RAS mutation status. Testing was typically performed within the reporting institution (93.8 %, n = 90), at the request of a treating oncologist (89.5 %, n = 85); testing methodology varied by laboratory and by individual codon tested. For laboratory RAS testing, turnaround times were ≤10 working days for the majority of institutions (90.6 %, n = 87). The overall crude RAS mutation prevalence was 48.5 % (95 % confidence interval: 46.4-50.6) for laboratories testing all RAS hot-spot codons. Prevalence estimates varied significantly by primary tumour location, approximate number of patients tested yearly and indication given for RAS testing. CONCLUSION Our findings indicate a rapid uptake of RAS testing in the majority of European pathology laboratories.
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Affiliation(s)
- Annemarie Boleij
- Department of Pathology, Radboud University Medical Centre, Geert Grooteplein-Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Véronique Tack
- Department of Public Health and Primary Care, University of Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Aliki Taylor
- Centre for Observational Research, Amgen Ltd, 1 Uxbridge Business Park, Uxbridge, UB8 1DH, UK
| | - George Kafatos
- Centre for Observational Research, Amgen Ltd, 1 Uxbridge Business Park, Uxbridge, UB8 1DH, UK
| | | | - Lien Tembuyser
- Department of Public Health and Primary Care, University of Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Els Dequeker
- Department of Public Health and Primary Care, University of Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.
| | - J Han van Krieken
- Department of Pathology, Radboud University Medical Centre, Geert Grooteplein-Zuid 10, 6525 GA, Nijmegen, The Netherlands
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14
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Omolo B, Yang M, Lo FY, Schell MJ, Austin S, Howard K, Madan A, Yeatman TJ. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer. BMC Med Genomics 2016; 9:65. [PMID: 27756306 PMCID: PMC5069826 DOI: 10.1186/s12920-016-0225-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 10/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60 % of patients with a wild type KRAS fail to respond to EGFRi combination therapies, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. METHODS In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter™ (NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq (t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA). RESULTS Using Affy_FF as the "gold" standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE (r = 0.233, p = 0.090); (2) NanoS_FFPE (r = 0.608, p < 0.0001); (3) RNA-Acc_FFPE (r = 0.175, p = 0.21); (4) t-RNA_FFPE (r = -0.237, p = 0.085); (5) and t-RNA (r = -0.012, p = 0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified "problematic" samples (n = 15) and genes (n = 2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r = 0.672, p < 0.0001); NanoS_FFPE (r = 0.738, p < 0.0001); and RNA-Acc_FFPE (r = 0.483, p = 0.002). CONCLUSIONS Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix GeneChip and multiple RNASeq technologies. Moreover, NanoString was the most forgiving technology in the analysis of samples with presumably poor RNA quality. Using this approach, the RAS signature score may now be reasonably applied to FFPE clinical samples.
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Affiliation(s)
- Bernard Omolo
- Division of Mathematics and Computer Science, University of South Carolina-Upstate, 800 University Way, Spartanburg, SC, 29303, USA
| | - Mingli Yang
- Gibbs Cancer Center and Research Institute, 101 E Wood Street, Spartanburg, SC 29303, USA
| | - Fang Yin Lo
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Sharon Austin
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Kellie Howard
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Anup Madan
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center and Research Institute, 101 E Wood Street, Spartanburg, SC 29303, USA.
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15
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Waters AM, Bagni R, Portugal F, Hartley JL. Single Synonymous Mutations in KRAS Cause Transformed Phenotypes in NIH3T3 Cells. PLoS One 2016; 11:e0163272. [PMID: 27684555 PMCID: PMC5042562 DOI: 10.1371/journal.pone.0163272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/05/2016] [Indexed: 12/29/2022] Open
Abstract
Synonymous mutations in the KRAS gene are clustered at G12, G13, and G60 in human cancers. We constructed 9 stable NIH3T3 cell lines expressing KRAS, each with one of these synonymous mutations. Compared to the negative control cell line expressing the wild type human KRAS gene, all the synonymous mutant lines expressed more KRAS protein, grew more rapidly and to higher densities, and were more invasive in multiple assays. Three of the cell lines showed dramatic loss of contact inhibition, were more refractile under phase contrast, and their refractility was greatly reduced by treatment with trametinib. Codon usage at these glycines is highly conserved in KRAS compared to HRAS, indicating selective pressure. These transformed phenotypes suggest that synonymous mutations found in driver genes such as KRAS may play a role in human cancers.
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Affiliation(s)
- Andrew M. Waters
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
- Biology Department, Catholic University of America, Washington, District of Columbia, United States of America
| | - Rachel Bagni
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Franklin Portugal
- Biology Department, Catholic University of America, Washington, District of Columbia, United States of America
| | - James L. Hartley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
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16
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Li C, Chen M, Zhao P, Ayana DA, Wang L, Jiang Y. Expression of MCRS1 and MCRS2 and their correlation with serum carcinoembryonic antigen in colorectal cancer. Exp Ther Med 2016; 12:589-596. [PMID: 27446248 PMCID: PMC4950148 DOI: 10.3892/etm.2016.3424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 03/03/2016] [Indexed: 12/16/2022] Open
Abstract
Cancer-associated genes serve a crucial role in carcinogenesis. The present study aimed to investigate the mRNA expression levels of microspherule protein 1 (MCRS1) and MCRS2 in colorectal cancer (CRC) and their association with clinical variables. The mRNA expression levels of MCRS1 and MCRS2 were assessed by semi-quantitative reverse transcription polymerase chain reaction in the tumor and corresponding non-tumor tissues of 54 newly-diagnosed CRC patients, as well as in the normal colonic mucosa tissue of 19 age/gender-matched healthy controls. Immunofluorescence was also employed to identify the expression of MCRS1 in CRC tissues, while the concentration of serum carcinoembryonic antigen (CEA) was determined by an enzyme-linked immunoassay. The results identified a negative correlation between MCRS1 and MCRS2 expression levels (r=-0.3018, P=0.0266). MCRS1 mRNA expression was significantly increased and MCRS2 mRNA expression was decreased in CRC tissues compared with the levels in the corresponding normal tissues (both P<0.001). An increase in MCRS1 expression and a decrease in MCRS2 expression was detected in advanced stage when compared with early stage CRC patients. Immunofluorescence analysis revealed increased expression of MCRS1 in CRC patients. Furthermore, the expression levels of MCRS1 displayed positive correlation, whilst those of MCRS2 displayed negative correlation, with the serum CEA level in patients with CRC. The results suggest that increased MCRS1 and decreased MCRS2 expression appeared to be involved in the pathogenesis of CRC. The present study provides evidence suggesting that MCRS1 and MCRS2 may identify CRC patients at a risk of disease relapse, and thus, may be potential tools for monitoring disease activity and act as novel diagnostic markers in the treatment of CRC.
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Affiliation(s)
- Chenguang Li
- Department of Colorectal and Anal Surgery, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China; Key Laboratory of Zoonosis Research, Ministry of Education, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China
| | - Mingxiao Chen
- Department of Colorectal and Anal Surgery, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China
| | - Pingwei Zhao
- Department of Colorectal and Anal Surgery, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China
| | - Desalegn Admassu Ayana
- Department of Medical Laboratory Sciences, Haramaya University, Dire Dawa 3000, Ethiopia
| | - Lei Wang
- Department of Colorectal and Anal Surgery, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China
| | - Yanfang Jiang
- Key Laboratory of Zoonosis Research, Ministry of Education, The First Hospital, Jilin University, Changchun, Jilin 130032, P.R. China
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17
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Zhang T, Boominathan R, Foulk B, Rao C, Kemeny G, Strickler JH, Abbruzzese JL, Harrison MR, Hsu DS, Healy P, Li J, Pi C, Prendergast KM, Hobbs C, Gemberling S, George DJ, Hurwitz HI, Connelly M, Garcia-Blanco MA, Armstrong AJ. Development of a Novel c-MET-Based CTC Detection Platform. Mol Cancer Res 2016; 14:539-47. [PMID: 26951228 DOI: 10.1158/1541-7786.mcr-16-0011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/25/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED Amplification of the MET oncogene is associated with poor prognosis, metastatic dissemination, and drug resistance in many malignancies. We developed a method to capture and characterize circulating tumor cells (CTC) expressing c-MET using a ferromagnetic antibody. Immunofluorescence was used to characterize cells for c-MET, DAPI, and pan-CK, excluding CD45(+) leukocytes. The assay was validated using appropriate cell line controls spiked into peripheral blood collected from healthy volunteers (HV). In addition, peripheral blood was analyzed from patients with metastatic gastric, pancreatic, colorectal, bladder, renal, or prostate cancers. CTCs captured by c-MET were enumerated, and DNA FISH for MET amplification was performed. The approach was highly sensitive (80%) for MET-amplified cells, sensitive (40%-80%) for c-MET-overexpressed cells, and specific (100%) for both c-MET-negative cells and in 20 HVs. Of 52 patients with metastatic carcinomas tested, c-MET CTCs were captured in replicate samples from 3 patients [gastric, colorectal, and renal cell carcinoma (RCC)] with 6% prevalence. CTC FISH demonstrated that MET amplification in both gastric and colorectal cancer patients and trisomy 7 with gain of MET gene copies in the RCC patient. The c-MET CTC assay is a rapid, noninvasive, sensitive, and specific method for detecting MET-amplified tumor cells. CTCs with MET amplification can be detected in patients with gastric, colorectal, and renal cancers. IMPLICATIONS This study developed a novel c-MET CTC assay for detecting c-MET CTCs in patients with MET amplification and warrants further investigation to determine its clinical applicability. Mol Cancer Res; 14(6); 539-47. ©2016 AACR.
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Affiliation(s)
- Tian Zhang
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Rengasamy Boominathan
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Brad Foulk
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Chandra Rao
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Gabor Kemeny
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - John H Strickler
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - James L Abbruzzese
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Michael R Harrison
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - David S Hsu
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Patrick Healy
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Jing Li
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Cinthia Pi
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Katherine M Prendergast
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Carey Hobbs
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Sarah Gemberling
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Daniel J George
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Herbert I Hurwitz
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Mark Connelly
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Mariano A Garcia-Blanco
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Andrew J Armstrong
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina. Department of Pharmacology and Cancer Biology, Duke University, Durham, NC.
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18
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Malapelle U, Pisapia P, Sgariglia R, Vigliar E, Biglietto M, Carlomagno C, Giuffrè G, Bellevicine C, Troncone G. Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases. J Clin Pathol 2016; 69:767-71. [PMID: 26797410 PMCID: PMC5036215 DOI: 10.1136/jclinpath-2015-203403] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/29/2015] [Indexed: 12/20/2022]
Abstract
AIMS The incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers. METHODS Following a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes. RESULTS A total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%). CONCLUSIONS In a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Chiara Carlomagno
- Department of Surgical and Clinical Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Giuffrè
- Department of "Patologia Umana dell'Adulto e dell'età evolutiva, G.Barresi", University of Messina, Messina, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Lazure P, Marshall JL, Hayes SM, Murray S. Challenges That Hinder the Translation of Clinical Advances Into Practice: Results From an International Assessment in Colorectal Cancer. Clin Colorectal Cancer 2015; 15:54-66. [PMID: 26341411 DOI: 10.1016/j.clcc.2015.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/20/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Over the past decade, individualization of treatment for colorectal cancer (CRC) has been improved by: (1) approval of several new agents by national agencies such as the US Food and Drug Administration (FDA); and (2) rapid advances in mutation analysis. However, data are sparse on the clinical challenges experienced by oncologists as they address the increased complexity created by the growing potential for individualization of CRC treatment. MATERIALS AND METHODS To identify clinical challenges experienced by oncologists regarding CRC treatment, an international assessment was conducted. A mixed methods approach was used, with the collection and analysis of qualitative (semistructured telephone interviews) and quantitative (online survey) data. Participants were oncologists actively practicing in 1 of 7 targeted countries with a minimum caseload of 10 CRC patients per year. RESULTS The sample included 358 oncologists from China (n = 68), France (n = 44), Germany (n = 44), Italy (n = 45), Spain (n = 44), the United Kingdom (n = 45), and the United States (n = 68). Mixed methods findings indicated that oncologists' treatment selection is hindered by practice challenges in: (1) mutation analysis and subsequent adaptation of treatment; (2) optimal sequential use of treatment choices; (3) treatment individualization based on patient and tumor profile; (4) management of side effects and toxicities; (5) chemoresistance, cross-resistance, and combinations to overcome resistance; and (6) access to new emerging treatments. CONCLUSION In the context of increased complexity created by the approval of new agents and advances in mutation analysis, challenges are experienced by practicing oncologists in the individualization of treatment for CRC patients. Details of these challenges should stimulate dialogue among oncologists, and development of interventions to improve clinical practice.
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20
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Cacciola NA, Calabrese C, Malapelle U, Pellino G, De Stefano A, Sepe R, Sgariglia R, Quintavalle C, Federico A, Bianco A, Uchimura Bastos A, Milone M, Bellevicine C, Milone F, Carlomagno C, Selvaggi F, Troncone G, Fusco A, Pallante P. UbcH10 expression can predict prognosis and sensitivity to the antineoplastic treatment for colorectal cancer patients. Mol Carcinog 2015; 55:793-807. [PMID: 25917796 DOI: 10.1002/mc.22322] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 03/10/2015] [Accepted: 03/16/2015] [Indexed: 01/13/2023]
Abstract
Colorectal cancer (CRC) is one of the most frequent and deadly malignancies worldwide. Despite the progresses made in diagnosis and treatment, the identification of tumor markers is still a strong clinical need, because current treatments are efficacious only in a subgroup of patients. UbcH10 represents a potential candidate biomarker, whose expression levels could be employed to predict response or resistance to chemotherapy or targeted agents. UbcH10 mRNA and protein expression levels have been evaluated in a large group of CRC patients and correlated with clinico-pathological characteristics, including KRAS mutations. Moreover, the endogenous levels of UbcH10 and its role on cell growth have been evaluated in CRC cells. Finally, to investigate the impact of UbcH10 protein expression on the response to irinotecan, its active metabolite SN-38 and cetuximab treatment, UbcH10 silencing experiments were carried-out on two colon carcinoma cell lines, Caco-2, and DLD1. Overexpression of UbcH10 mRNA and protein was observed in the vast majority of patients analyzed. UbcH10 suppression decreased CRC cell growth rate (at least in part through deregulation of Cyclin B and ERK1) and sensitized them to pharmacological treatments with irinotecan, SN-38 and cetuximab (at least in part through a down-regulation of AKT). Taken together, these findings indicate that UbcH10 expression regulates CRC growth and could play an important role in the personalization of the therapy of CRC patients.
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Affiliation(s)
- Nunzio Antonio Cacciola
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Chiara Calabrese
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Gianluca Pellino
- Unit of General Surgery, Second University of Naples, Piazza Miraglia 2, Naples, Italy
| | - Alfonso De Stefano
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Romina Sepe
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Cristina Quintavalle
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy.,Institute of Pathology, Molecular Pathology Division, University of Basel, Schonbeinstrasse 40, Basel, Switzerland
| | - Antonella Federico
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Antonio Bianco
- Department of Public Health, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - André Uchimura Bastos
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy.,Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Federal University of São Paulo, São Paulo, Brazil
| | - Marco Milone
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Francesco Milone
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Chiara Carlomagno
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Francesco Selvaggi
- Unit of General Surgery, Second University of Naples, Piazza Miraglia 2, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
| | - Alfredo Fusco
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy.,National Cancer Institute-INCA, Rua André Cavalcanti, 37-Centro, CEP 20231-050, Rio de Janeiro, Brazil
| | - Pierlorenzo Pallante
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples "Federico II", Via S. Pansini 5, Naples, Italy
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21
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Malapelle U, Sgariglia R, De Stefano A, Bellevicine C, Vigliar E, de Biase D, Sepe R, Pallante P, Carlomagno C, Tallini G, Troncone G. KRAS mutant allele-specific imbalance (MASI) assessment in routine samples of patients with metastatic colorectal cancer. J Clin Pathol 2015; 68:265-9. [PMID: 25609577 DOI: 10.1136/jclinpath-2014-202761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AIMS Patients with colorectal cancer harbouring KRAS mutations do not respond to antiepidermal growth factor receptor (anti-EGFR) therapy. Community screening for KRAS mutation selects patients for treatment. When a KRAS mutation is identified by direct sequencing, mutant and wild type alleles are seen on the sequencing electropherograms. KRAS mutant allele-specific imbalance (MASI) occurs when the mutant allele peak is higher than the wild type one. The aims of this study were to verify the rate and tissue distribution of KRAS MASI as well as its clinical relevance. METHODS A total of 437 sequencing electropherograms showing KRAS exon 2 mutation was reviewed and in 30 cases next generation sequencing (NGS) was also carried out. Five primary tumours were extensively laser capture microdissected to investigated KRAS MASI tissue spatial distribution. KRAS MASI influence on the overall survival was evaluated in 58 patients. In vitro response to anti-EGFR therapy in relation to different G13D KRAS MASI status was also evaluated. RESULTS On the overall, KRAS MASI occurred in 58/436 cases (12.8%), being more frequently associated with G13D mutation (p=0.05) and having a heterogeneous tissue distribution. KRAS MASI detection by Sanger Sequencing and NGS showed 94% (28/30) concordance. The longer overall survival of KRAS MASI negative patients did not reach statistical significance (p=0.08). In cell line model G13D KRAS MASI conferred resistance to cetuximab treatment. CONCLUSIONS KRAS MASI is a significant event in colorectal cancer, specifically associated with G13D mutation, and featuring a heterogeneous spatial distribution, that may have a role to predict the response to EGFR inhibitors. The foreseen implementation of NGS in community KRAS testing may help to define KRAS MASI prognostic and predictive significance.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Alfonso De Stefano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoles, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario de Biase
- Department of Medicine (DIMES)-Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Romina Sepe
- CNR/IEOS, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples, Italy
| | - Pierlorenzo Pallante
- CNR/IEOS, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples, Italy
| | - Chiara Carlomagno
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoles, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES)-Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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22
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Atsumi J, Hanami T, Enokida Y, Ogawa H, Delobel D, Mitani Y, Kimura Y, Soma T, Tagami M, Takase Y, Ichihara T, Takeyoshi I, Usui K, Hayashizaki Y, Shimizu K. Eprobe-mediated screening system for somatic mutations in the KRAS locus. Oncol Rep 2015; 33:2719-27. [PMID: 25823645 PMCID: PMC4431451 DOI: 10.3892/or.2015.3883] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/03/2015] [Indexed: 12/21/2022] Open
Abstract
Activating mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) loci are largely predictive of resistance to epidermal growth factor receptor (EGFR) therapy in colorectal cancer (CRC). A highly sensitive detection system for the KRAS gene mutations is urgently needed; however, conventional methods have issues with feasibility and cost performance. Here, we describe a novel detection system using a fluorescence ‘Eprobe’ capable of detecting low level KRAS gene mutations, via real-time PCR, with high sensitivity and simple usability. We designed our Eprobes to be complementary to wild-type (WT) KRAS or to the commonly mutated codons 12 and 13. The WT Eprobe binds strongly to the WT DNA template and suppresses amplification by blocking annealing of the primer during PCR. Eprobe-PCR with WT Eprobe shows high sensitivity (0.05–0.1% of plasmid DNA, 1% of genomic DNA) for the KRAS mutation by enrichment of the mutant type (MT) amplicon. Assay performance was compared to Sanger sequencing using 92 CRC samples. Discrepancies were analyzed by mutation genotyping via Eprobe-PCR with full match Eprobes for 7 prevalent mutations and the next generation sequencing (NGS). Significantly, the Eprobe system had a higher sensitivity for detecting KRAS mutations in CRC patient samples; these mutations could not be identified by Sanger sequencing. Thus, the Eprobe approach provides for highly sensitive and convenient mutation detection and should be useful for diagnostic applications.
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Affiliation(s)
- Jun Atsumi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takeshi Hanami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasuaki Enokida
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hiroomi Ogawa
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Diane Delobel
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Mitani
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yasumasa Kimura
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Takahiro Soma
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Michihira Tagami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshiaki Takase
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tatsuo Ichihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Izumi Takeyoshi
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kengo Usui
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Kimihiro Shimizu
- Departments of Thoracic and Visceral Organ Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
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23
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Dolatkhah R, Somi MH, Bonyadi MJ, Asvadi Kermani I, Farassati F, Dastgiri S. Colorectal cancer in iran: molecular epidemiology and screening strategies. J Cancer Epidemiol 2015; 2015:643020. [PMID: 25685149 PMCID: PMC4312646 DOI: 10.1155/2015/643020] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/05/2014] [Accepted: 12/15/2014] [Indexed: 12/22/2022] Open
Abstract
Purpose. The increasing incidence of colorectal cancer (CRC) in the past three decades in Iran has made it a major public health burden. This study aimed to report its epidemiologic features, molecular genetic aspects, survival, heredity, and screening pattern in Iran. Methods. A comprehensive literature review was conducted to identify the relevant published articles. We used medical subject headings, including colorectal cancer, molecular genetics, KRAS and BRAF mutations, screening, survival, epidemiologic study, and Iran. Results. Age standardized incidence rate of Iranian CRCs was 11.6 and 10.5 for men and women, respectively. Overall five-year survival rate was 41%, and the proportion of CRC among the younger age group was higher than that of western countries. Depending on ethnicity, geographical region, dietary, and genetic predisposition, mutation genes were considerably diverse and distinct among CRCs across Iran. The high occurrence of CRC in records of relatives of CRC patients showed that family history of CRC was more common among young CRCs. Conclusion. Appropriate screening strategies for CRC which is amenable to early detection through screening, especially in relatives of CRCs, should be considered as the first step in CRC screening programs.
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Affiliation(s)
- Roya Dolatkhah
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Iraj Asvadi Kermani
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faris Farassati
- Department of Medicine, The University of Kansas Medical School, Molecular Medicine Laboratory, KUMC, Kansas City, KS, USA
| | - Saeed Dastgiri
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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24
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Kothari N, Schell MJ, Teer JK, Yeatman T, Shibata D, Kim R. Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing. J Clin Pathol 2014; 67:764-7. [PMID: 25004944 DOI: 10.1136/jclinpath-2014-202405] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIMS Based on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods. METHODS In this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing. RESULTS Out of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing. CONCLUSIONS Overall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.
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25
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Malapelle U, Vigliar E, Sgariglia R, Bellevicine C, Colarossi L, Vitale D, Pallante P, Troncone G. Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients. J Clin Pathol 2014; 68:64-8. [PMID: 25378536 DOI: 10.1136/jclinpath-2014-202691] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AIMS To evaluate the accuracy, consumable cost and time around testing (TAT) of a next-generation sequencing (NGS) assay, the Ion Torrent AmpliSeq Colon and Lung Cancer Panel, as an alternative to Sanger sequencing to genotype KRAS, NRAS and BRAF in colorectal cancer patients. METHODS The Ion Torrent panel was first verified on cell lines and on control samples and then prospectively applied to routine specimens (n=114), with Sanger sequencing as reference. RESULTS The Ion Torrent panel detected mutant alleles at the 5% level on cell lines and correctly classified all control tissues. The Ion Torrent assay was successfully carried out on most (95.6%) routine diagnostic samples. Of these, 12 (11%) harboured mutations in the BRAF gene and 47 (43%) in either of the two RAS genes, in two cases with a low abundance of RAS mutant allele which was missed by Sanger sequencing. The mean TAT, from sample receipt to reporting, was 10.4 (Sanger) and 13.0 (Ion Torrent) working days. The consumable cost for genotyping KRAS, NRAS and BRAF was €196 (Sanger) and €187 (Ion Torrent). CONCLUSIONS Ion Torrent AmpliSeq Colon and Lung Cancer Panel sequencing is as robust as Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor (EGFR) therapy for metastatic colorectal cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
| | - Lorenzo Colarossi
- Mediterranean Institute of Oncology (IOM), Catania, Italy PhD Programme in Biotechnology and Clinical Medicine, Sapienza University, Rome, Italy
| | | | - Pierlorenzo Pallante
- CNR/IEOS, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
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26
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Wong NACS, Gonzalez D, Salto-Tellez M, Butler R, Diaz-Cano SJ, Ilyas M, Newman W, Shaw E, Taniere P, Walsh SV. RAS testing of colorectal carcinoma—a guidance document from the Association of Clinical Pathologists Molecular Pathology and Diagnostics Group. J Clin Pathol 2014; 67:751-7. [PMID: 24996433 DOI: 10.1136/jclinpath-2014-202467] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Analysis of colorectal carcinoma (CRC) tissue for KRAS codon 12 or 13 mutations to guide use of anti-epidermal growth factor receptor (EGFR) therapy is now considered mandatory in the UK. The scope of this practice has been recently extended because of data indicating that NRAS mutations and additional KRAS mutations also predict for poor response to anti-EGFR therapy. The following document provides guidance on RAS (i.e., KRAS and NRAS) testing of CRC tissue in the setting of personalised medicine within the UK and particularly within the NHS. This guidance covers issues related to case selection, preanalytical aspects, analysis and interpretation of such RAS testing.
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27
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Scott RJ, Fox SB, Desai J, Grieu F, Amanuel B, Garrett K, Harraway J, Cheetham G, Pattle N, Haddad A, Byron K, Rudzki B, Waring P, Iacopetta B. KRASmutation testing of metastatic colorectal cancer in Australia: Where are we at? Asia Pac J Clin Oncol 2014; 10:261-5. [DOI: 10.1111/ajco.12201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Rodney J. Scott
- Hunter Area Pathology Service; Newcastle New South Wales Australia
| | - Stephen B. Fox
- Peter MacCallum Cancer Centre; Melbourne Victoria Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre; Melbourne Victoria Australia
| | - Fabienne Grieu
- Department of Molecular Anatomic Pathology, PathWest QEII; Nedlands Western Australia Australia
| | - Benhur Amanuel
- Department of Molecular Anatomic Pathology, PathWest QEII; Nedlands Western Australia Australia
| | - Kerryn Garrett
- St John of God Pathology; Subiaco Western Australia Australia
| | - James Harraway
- Sullivan Nicolaides Pathology; Brisbane Queensland Australia
| | | | | | - Afaf Haddad
- Dorevitch Pathology; Melbourne Victoria Australia
| | - Keith Byron
- Healthscope Pathology; Clayton Victoria Australia
| | - Barney Rudzki
- Department of Pathology, University of Melbourne; Melbourne Victoria Australia
| | - Paul Waring
- Department of Pathology, University of Melbourne; Melbourne Victoria Australia
| | - Barry Iacopetta
- School of Surgery; University of Western Australia; Nedlands Western Australia Australia
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