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Colorectal Cancer Liver Metastases: Genomics and Biomarkers with Focus on Local Therapies. Cancers (Basel) 2023; 15:cancers15061679. [PMID: 36980565 PMCID: PMC10046329 DOI: 10.3390/cancers15061679] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Molecular cancer biomarkers help personalize treatment, predict oncologic outcomes, and identify patients who can benefit from specific targeted therapies. Colorectal cancer (CRC) is the third-most common cancer, with the liver being the most frequent visceral metastatic site. KRAS, NRAS, BRAF V600E Mutations, DNA Mismatch Repair Deficiency/Microsatellite Instability Status, HER2 Amplification, and NTRK Fusions are NCCN approved and actionable molecular biomarkers for colorectal cancer. Additional biomarkers are also described and can be helpful in different image-guided hepatic directed therapies specifically for CRLM. For example, tumors maintaining the Ki-67 proliferation marker after thermal ablation was shown to be particularly resilient to ablation. Ablation margin was also shown to be an important factor in predicting local recurrence, with a ≥10 mm minimal ablation margin being required to attain local tumor control, especially for patients with mutant KRAS CRLM.
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2
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Camargo R, de Castro Moreira Dos Santos A, Cândido Guido B, Lemos Mendanha Cavalcante L, Silva Dias AC, Mendonça de Pontes R, Magalhães Furtado F, Feitosa Salviano C, Tiziani V, Martins Córdoba JC, Quezado Magalhães IM. A sensitive and inexpensive high-resolution melting-based testing algorithm for diagnosis of transient abnormal myelopoiesis and myeloid leukemia of Down syndrome. Pediatr Blood Cancer 2022; 69:e29866. [PMID: 35731576 DOI: 10.1002/pbc.29866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022]
Abstract
Patients with Down syndrome (DS) are commonly affected by a pre-leukemic disorder known as transient abnormal myelopoiesis (TAM). This condition usually undergoes spontaneous remission within the first 2 months after birth; however, in children under 5, 20%-30% of cases evolve to myeloid leukemia of Down syndrome (ML-DS). TAM and ML-DS are caused by co-operation between trisomy 21 and acquired mutations in the GATA1 gene. Currently, only next-generation sequencing (NGS)-based methodologies are sufficiently sensitive for diagnosis in samples with small GATA1 mutant clones (≤10% blasts). Alternatively, this study presents research on a new, fast, sensitive, and inexpensive high-resolution melting (HRM)-based diagnostic approach that allows the detection of most cases of GATA1 mutations, including silent TAM. The algorithm first uses flow cytometry for blast count, followed by HRM and Sanger sequencing to search for mutations on exons 2 and 3 of GATA1. We analyzed 138 samples of DS patients: 110 of asymptomatic neonates, 10 suspected of having TAM, and 18 suspected of having ML-DS. Our algorithm enabled the identification of 33 mutant samples, among them five cases of silent TAM (5/110) and seven cases of ML-DS (7/18) with blast count ≤10%, in which GATA1 alterations were easily detected by HRM. Depending on the type of genetic variation and its location, our methodology reached sensitivity similar to that obtained by NGS (0.3%) at a considerably reduced time and cost, thus making it accessible worldwide.
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Affiliation(s)
- Ricardo Camargo
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil
| | - Agenor de Castro Moreira Dos Santos
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil.,Laboratório Central de Saúde Pública do Distrito Federal, Brasília, Brazil
| | - Bruna Cândido Guido
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil
| | | | - Anna Carolina Silva Dias
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil
| | | | - Felipe Magalhães Furtado
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil
| | | | - Valdenize Tiziani
- Laboratório de Pesquisa Translacional, Hospital da Criança de Brasília José Alencar, Brasília, Brazil
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3
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Satomi K, Yoshida A, Matsushita Y, Sugino H, Fujimoto K, Honda-Kitahara M, Takahashi M, Ohno M, Miyakita Y, Narita Y, Yatabe Y, Shibahara J, Ichimura K. Clinical application of a highly sensitive digital PCR assay to detect a small fraction of IDH1 R132H-mutant alleles in diffuse gliomas. Brain Tumor Pathol 2022; 39:210-217. [PMID: 35902443 DOI: 10.1007/s10014-022-00442-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
The current World Health Organization classification of diffuse astrocytic and oligodendroglial tumors requires the examination of isocitrate dehydrogenase 1 (IDH1) or IDH2 mutations. Conventional analysis tools, including Sanger DNA sequencing or pyrosequencing, fail in detecting these variants of low frequency owing to their limited sensitivity. Digital polymerase chain reaction (dPCR) is a recently developed, highly sensitive, and precise quantitative rare variant assay. This study aimed to establish a robust limit of quantitation of the dPCR assay to detect a small fraction of IDH1 R132H mutation. The dPCR assays with serially diluted IDH1 R132H constructs detected 0.05% or more of mutant IDH1 R132H in samples containing mutant DNA. The measured target/total value of the experiments was proportional to the dilution factors and was almost equal to the actual frequencies of the mutant alleles. Based on the average target/total values, together with a twofold standard deviation of the normal DNA, a limit of quantitation of 0.25% was set to secure a safe margin to judge the mutation status of the IDH1 R132H dPCR assay. In clinical settings, detecting IDH1 R132H using dPCR assays can validate ambiguous immunohistochemistry results even when conventional DNA sequencing cannot detect the mutation and assure diagnostic quality.
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Affiliation(s)
- Kaishi Satomi
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan. .,Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan. .,Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo, 181-8611, Japan.
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yuko Matsushita
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Brain Disease Translational Research, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirokazu Sugino
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kenji Fujimoto
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto-shi, Kumamoto, 860-8555, Japan
| | - Mai Honda-Kitahara
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masamichi Takahashi
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Makoto Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasuji Miyakita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo, 181-8611, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Brain Disease Translational Research, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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4
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Yang L, Shen C, Estrada-Bernal A, Robb R, Chatterjee M, Sebastian N, Webb A, Mo X, Chen W, Krishnan S, Williams TM. Oncogenic KRAS drives radioresistance through upregulation of NRF2-53BP1-mediated non-homologous end-joining repair. Nucleic Acids Res 2021; 49:11067-11082. [PMID: 34606602 PMCID: PMC8565339 DOI: 10.1093/nar/gkab871] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS-activating mutations are oncogenic drivers and are correlated with radioresistance of multiple cancers, including colorectal cancer, but the underlying precise molecular mechanisms remain elusive. Herein we model the radiosensitivity of isogenic HCT116 and SW48 colorectal cancer cell lines bearing wild-type or various mutant KRAS isoforms. We demonstrate that KRAS mutations indeed lead to radioresistance accompanied by reduced radiotherapy-induced mitotic catastrophe and an accelerated release from G2/M arrest. Moreover, KRAS mutations result in increased DNA damage response and upregulation of 53BP1 with associated increased non-homologous end-joining (NHEJ) repair. Remarkably, KRAS mutations lead to activation of NRF2 antioxidant signaling to increase 53BP1 gene transcription. Furthermore, genetic silencing or pharmacological inhibition of KRAS, NRF2 or 53BP1 attenuates KRAS mutation-induced radioresistance, especially in G1 phase cells. These findings reveal an important role for a KRAS-induced NRF2-53BP1 axis in the DNA repair and survival of KRAS-mutant tumor cells after radiotherapy, and indicate that targeting NRF2, 53BP1 or NHEJ may represent novel strategies to selectively abrogate KRAS mutation-mediated radioresistance.
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Affiliation(s)
- Linlin Yang
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Changxian Shen
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Adriana Estrada-Bernal
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Ryan Robb
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Moumita Chatterjee
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Nikhil Sebastian
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Amy Webb
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Xiaokui Mo
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | - Wei Chen
- The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH 43210, USA
| | | | - Terence M Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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5
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Precision Medicine for the Treatment of Colorectal Cancer: the Evolution and Status of Molecular Profiling and Biomarkers. CURRENT COLORECTAL CANCER REPORTS 2021. [DOI: 10.1007/s11888-021-00466-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Zhou S, Sikorski D, Xu H, Zubarev A, Chergui M, Lagacé F, Miller WH, Redpath M, Ghazal S, Butler MO, Petrella TM, Claveau J, Nessim C, Salopek TG, Gniadecki R, Litvinov IV. Defining the Criteria for Reflex Testing for BRAF Mutations in Cutaneous Melanoma Patients. Cancers (Basel) 2021; 13:2282. [PMID: 34068774 PMCID: PMC8126223 DOI: 10.3390/cancers13092282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Targeted therapy has been developed through an in-depth understanding of molecular pathways involved in the pathogenesis of melanoma. Approximately ~50% of patients with melanoma have tumors that harbor a mutation of the BRAF oncogene. Certain clinical features have been identified in BRAF-mutated melanomas (primary lesions located on the trunk, diagnosed in patients <50, visibly pigmented tumors and, at times, with ulceration or specific dermatoscopic features). While BRAF mutation testing is recommended for stage III-IV melanoma, guidelines differ in recommending mutation testing in stage II melanoma patients. To fully benefit from these treatment options and avoid delays in therapy initiation, advanced melanoma patients harboring a BRAF mutation must be identified accurately and quickly. To achieve this, clear definition and implementation of BRAF reflex testing criteria/methods in melanoma should be established so that patients with advanced melanoma can arrive to their first medical oncology appointment with a known biomarker status. Reflex testing has proven effective for a variety of cancers in selecting therapies and driving other medical decisions. We overview the pathophysiology, clinical presentation of BRAF-mutated melanoma, current guidelines, and present recommendations on BRAF mutation testing. We propose that reflex BRAF testing should be performed for every melanoma patient with stages ≥IIB.
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Affiliation(s)
- Sarah Zhou
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Daniel Sikorski
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Honghao Xu
- Division of Dermatology, Laval University, Quebec City, QC G1V 0A6, Canada; (H.X.); (J.C.)
| | - Andrei Zubarev
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - May Chergui
- Department of Pathology, McGill University, Montreal, QC H3A 0G4, Canada; (M.C.); (M.R.)
| | - François Lagacé
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Wilson H. Miller
- Departments of Medicine and Oncology, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Margaret Redpath
- Department of Pathology, McGill University, Montreal, QC H3A 0G4, Canada; (M.C.); (M.R.)
| | - Stephanie Ghazal
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
| | - Marcus O. Butler
- Princess Margaret Cancer Centre, Department of Medical Oncology and Hematology, University of Toronto, Toronto, ON M5G 2C1, Canada;
| | - Teresa M. Petrella
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON M4N 3M5, Canada;
| | - Joël Claveau
- Division of Dermatology, Laval University, Quebec City, QC G1V 0A6, Canada; (H.X.); (J.C.)
| | - Carolyn Nessim
- Division of General Surgery, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Thomas G. Salopek
- Division of Dermatology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (T.G.S.); (R.G.)
| | - Robert Gniadecki
- Division of Dermatology, University of Alberta, Edmonton, AB T6G 2R3, Canada; (T.G.S.); (R.G.)
| | - Ivan V. Litvinov
- Division of Dermatology, McGill University, Montreal, QC H3A 0G4, Canada; (S.Z.); (D.S.); (A.Z.); (F.L.); (S.G.)
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7
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Benson AB, Venook AP, Al-Hawary MM, Arain MA, Chen YJ, Ciombor KK, Cohen S, Cooper HS, Deming D, Farkas L, Garrido-Laguna I, Grem JL, Gunn A, Hecht JR, Hoffe S, Hubbard J, Hunt S, Johung KL, Kirilcuk N, Krishnamurthi S, Messersmith WA, Meyerhardt J, Miller ED, Mulcahy MF, Nurkin S, Overman MJ, Parikh A, Patel H, Pedersen K, Saltz L, Schneider C, Shibata D, Skibber JM, Sofocleous CT, Stoffel EM, Stotsky-Himelfarb E, Willett CG, Gregory KM, Gurski LA. Colon Cancer, Version 2.2021, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw 2021; 19:329-359. [PMID: 33724754 DOI: 10.6004/jnccn.2021.0012] [Citation(s) in RCA: 735] [Impact Index Per Article: 245.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This selection from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Colon Cancer focuses on systemic therapy options for the treatment of metastatic colorectal cancer (mCRC), because important updates have recently been made to this section. These updates include recommendations for first-line use of checkpoint inhibitors for mCRC, that is deficient mismatch repair/microsatellite instability-high, recommendations related to the use of biosimilars, and expanded recommendations for biomarker testing. The systemic therapy recommendations now include targeted therapy options for patients with mCRC that is HER2-amplified, or BRAF V600E mutation-positive. Treatment and management of nonmetastatic or resectable/ablatable metastatic disease are discussed in the complete version of the NCCN Guidelines for Colon Cancer available at NCCN.org. Additional topics covered in the complete version include risk assessment, staging, pathology, posttreatment surveillance, and survivorship.
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Affiliation(s)
- Al B Benson
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University
| | - Alan P Venook
- UCSF Helen Diller Family Comprehensive Cancer Center
| | | | | | | | | | - Stacey Cohen
- Fred Hutchinson Cancer Research Center/Seattle Cancer Care Alliance
| | | | | | - Linda Farkas
- UT Southwestern Simmons Comprehensive Cancer Center
| | | | | | | | | | | | | | - Steven Hunt
- Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine
| | | | | | - Smitha Krishnamurthi
- Case Comprehensive Cancer Center/University Hospitals Seidman Cancer Center and Cleveland Clinic Taussig Cancer Institute
| | | | | | - Eric D Miller
- The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
| | - Mary F Mulcahy
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University
| | | | | | | | | | - Katrina Pedersen
- Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine
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8
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Colon Cancer Biomarkers: Implications for Personalized Medicine. J Pers Med 2020; 10:jpm10040167. [PMID: 33066312 PMCID: PMC7711712 DOI: 10.3390/jpm10040167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022] Open
Abstract
The heterogeneity of colon cancers and their reactions presents both a challenge and promise for personalized medicine. The challenge is to develop effective biologically personalized therapeutics guided by predictive and prognostic biomarkers. Presently, there are several classes of candidate biomarkers, including genomic probes, inhibitory RNAs, assays for immunity dysfunction and, not to be forgotten, specific histopathologic and histochemical features. To develop effective therapeutics, candidate biomarkers must be qualified and validated in comparable independent cohorts, no small undertaking. This process and subsequent deployment in clinical practice involves not only the strong association of the biomarker with the treatment but also careful attention to the prosaic aspects of representative tumor site selection, obtaining a fully adequate sample which is preserved and prepared to optimize high quality analysis. In the future, the clinical utility of biomarker analytical results will benefit from associated clinical and basic science data with the assistance of artificial intelligence techniques. By application of an individualized, selected suite of biomarkers, comprehensively interpreted, individualized, more effective and less toxic therapy for colon cancer will be enabled, thereby fulfilling the promise of personalized medicine.
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9
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Houts AC, Ogale S, Sommer N, Satram-Hoang S, Walker MS. Treatment Patterns and Outcomes in Patients with KRAS Wild-Type Metastatic Colorectal Cancer Treated in First Line with Bevacizumab- or Cetuximab-Containing Regimens. J Gastrointest Cancer 2019; 50:69-77. [PMID: 29168112 DOI: 10.1007/s12029-017-0027-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
PURPOSE Patients with Kirsten rat sarcoma viral oncogene wild-type (KRAS WT) metastatic colorectal cancer (mCRC) treated in first line with bevacizumab (B) or cetuximab (C) plus standard chemo backbones had comparable outcomes in phase III Cancer and Leukemia Group B (CALGB) 80405. We examined comparative effectiveness of B and C regimens in real-world community settings. METHODS This retrospective study examined progression-free survival (PFS) and OS in a US community sample of KRAS WT mCRC patients treated with first-line B (n = 254) or C (n = 146) regimens. Medical records from the Vector Oncology Data Warehouse were used. Disease progression was determined from patient charts. OS was measured from the start of first-line treatment until death. RESULTS There were no significant difference in either PFS or OS respectively between B-treated compared to C-treated patients (HR = 1.324, 95% CI 0.901, 1.947; HR = 1.080, 95% CI 0.721, 1.617). More B patients received oxaliplatin backbones (74.8 vs. 36.3%), and more C patients received irinotecan backbones (51.4 vs. 20.1%), ps < 0.001. Multivariate survival analyses showed a significant difference indicating a greater risk for death among C-treated patients with right-sided tumors vs. left-sided tumors (HR = 2.263, 95% CI 1.394, 3.673, p = 0.0009), but not for B-treated patients (HR = 1.209, 95% CI 0.825, 1.771, p = 0.3297). CONCLUSIONS Consistent with CALGB 80405, median PFS and OS for these community oncology KRAS WT mCRC patients treated with first-line B or C regimens did not differ significantly.
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Affiliation(s)
- Arthur C Houts
- Vector Oncology, 6555 Quince, Suite 400, Memphis, TN, 38119, USA.
| | - Sarika Ogale
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Nicolas Sommer
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sacha Satram-Hoang
- Q.D. Research, Inc., 8777 Auburn Folsom Rd., Suite C501, Granite Bay, CA, 95746, USA
| | - Mark S Walker
- Vector Oncology, 6555 Quince, Suite 400, Memphis, TN, 38119, USA
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10
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Guo J, Cao B, Xu X, Wu F, Zhu B. Novel CTCF mutations in Chinese patients with ovarian endometriosis. Mol Med Rep 2018; 18:1031-1036. [PMID: 29845264 DOI: 10.3892/mmr.2018.9049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/01/2018] [Indexed: 11/06/2022] Open
Abstract
Endometriosis is a common gynecological disease characterized by the outgrowth of the endometrium, however, the detailed molecular etiology remains largely uncharacterized. Recent studies have implicated that endometriosis is potentially a precancerous lesion, and that CCCTC‑binding factor (CTCF) mutations may be involved in the pathogenesis of this disorder. However, the detailed CTCF mutation spectrum in Chinese patients with ovarian endometriosis remains largely unknown. In the present study, a cohort of 92 patients with ovarian endometriosis were analyzed for the presence of CTCF mutations by sequencing the entire coding regions. In addition, 67 healthy eutopic endometrial tissues and 46 healthy ovarian tissues from control samples (without endometriosis) were also analyzed. In total, two CTCF missense mutations, p.K206E (c.616A>G) and p.H373L (c.1118A>T), were identified in 2/92 (2.2%) endometriotic lesions. The patient with the p.K206E mutation was 26 years old and diagnosed with primary infertility, whereas the patient with the p.H373L mutation was 37 years old and concurrently diagnosed with uterine leiomyoma. The p.H373L mutation was previously identified in endometrial cancer samples with low frequency, while the p.K206E mutation was novel. In addition, no CTCF mutations were detected in the 67 healthy eutopic endometrial and 46 healthy ovarian tissue samples. In silico prediction and evolutionary conservation analysis suggested that these CTCF mutations may be pathogenic. In summary, the present study identified 2 potential pathogenic CTCF mutations in endometriotic lesions from 2/92 patients with ovarian endometriosis. These results, together with a prior exome‑sequencing based study, suggest that CTCF mutations may be involved in the development of ovarian endometriosis.
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Affiliation(s)
- Jiubai Guo
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Bianna Cao
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaoyun Xu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Fei Wu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Bin Zhu
- Gongqing College of Nanchang University, Gongqingcheng, Jiangxi 332020, P.R. China
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11
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Yoon N, Vander Velde R, Marusyk A, Scott JG. Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs. Bull Math Biol 2018; 80:1776-1809. [PMID: 29736596 DOI: 10.1007/s11538-018-0434-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/17/2018] [Indexed: 12/15/2022]
Abstract
Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown. To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups, [Formula: see text] and [Formula: see text], each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics. Specifically, based on a system of ordinary differential equations for [Formula: see text] and [Formula: see text], we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point, T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e., [Formula: see text]-long for DrugA and [Formula: see text]-long for DrugB with [Formula: see text] and [Formula: see text]). We prove that the optimal duration of the initial stage, in which the first drug is administered, T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition. We further analyzed the relationship between population makeup, [Formula: see text], and the effect of each drug. We determine a critical ratio, which we term [Formula: see text], at which the two drugs are equally effective. As the first stage of the optimal strategy is applied, [Formula: see text] changes monotonically to [Formula: see text] and then, during the second stage, remains at [Formula: see text] thereafter. Beyond our analytic results, we explored an individual-based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.
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Affiliation(s)
- Nara Yoon
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Robert Vander Velde
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andriy Marusyk
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jacob G Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.
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12
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Oh HS, Kwon H, Park S, Kim M, Jeon MJ, Kim TY, Shong YK, Kim WB, Choi J, Kim WG, Song DE. Comparison of Immunohistochemistry and Direct Sanger Sequencing for Detection of the BRAF(V600E) Mutation in Thyroid Neoplasm. Endocrinol Metab (Seoul) 2018; 33:62-69. [PMID: 29388401 PMCID: PMC5874197 DOI: 10.3803/enm.2018.33.1.62] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The BRAF(V600E) mutation is the most common genetic alteration identified in papillary thyroid carcinoma (PTC). Because of its costs effectiveness and sensitivity, direct Sanger sequencing has several limitations. The aim of this study was to evaluate the efficiency of immunohistochemistry (IHC) as an alternative method to detect the BRAF(V600E) mutation in preoperative and postoperative tissue samples. METHODS We evaluated 71 patients who underwent thyroid surgery with the result of direct sequencing of the BRAF(V600E) mutation. IHC staining of the BRAF(V600E) mutation was performed in 49 preoperative and 23 postoperative thyroid specimens. RESULTS Sixty-two patients (87.3%) had PTC, and of these, BRAF(V600E) was confirmed by direct sequencing in 57 patients (91.9%). In 23 postoperative tissue samples, the BRAF(V600E) mutation was detected in 16 samples (70%) by direct sequencing and 18 samples (78%) by IHC. In 24 fine needle aspiration (FNA) samples, BRAF(V600E) was detected in 18 samples (75%) by direct sequencing and 16 samples (67%) by IHC. In 25 core needle biopsy (CNB) samples, the BRAF(V600E) mutation was detected in 15 samples (60%) by direct sequencing and 16 samples (64%) by IHC. The sensitivity and specificity of IHC for detecting the BRAF(V600E) mutation were 77.8% and 66.7% in FNA samples and 99.3% and 80.0% in CNB samples. CONCLUSION IHC could be an alternative method to direct Sanger sequencing for BRAF(V600E) mutation detection both in postoperative and preoperative samples. However, application of IHC to detect the BRAF(V600E) mutation in FNA samples is of limited value compared with direct sequencing.
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Affiliation(s)
- Hye Seon Oh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyemi Kwon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Division of Endocrinology and Metabolism, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Suyeon Park
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Mijin Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Ji Jeon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Yong Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young Kee Shong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won Bae Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won Gu Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Dong Eun Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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13
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A novel high-sensitivity assay to detect a small fraction of mutant IDH1 using droplet digital PCR. Brain Tumor Pathol 2018; 35:97-105. [DOI: 10.1007/s10014-018-0310-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
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14
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Romei C, Ciampi R, Casella F, Tacito A, Torregrossa L, Ugolini C, Basolo F, Materazzi G, Vitti P, Elisei R. RET mutation heterogeneity in primary advanced medullary thyroid cancers and their metastases. Oncotarget 2018. [PMID: 29515777 PMCID: PMC5839408 DOI: 10.18632/oncotarget.23986] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose Medullary Thyroid Cancer (MTC) whose pathogenesis is strictly related to RET proto-oncogene alterations, has been shown to have a heterogenic RET mutation profile in subpopulations of MTC. The aim of our study was to investigate the RET somatic mutation profile in primary MTC and in the corresponding metastatic tissues in a series of advanced metastatic cases. Results This study demonstrated that in about 20% of cases a different RET mutation profile can be found when comparing primary tumor and its corresponding metastases. Furthermore in 8% of tumors, RET intratumor heterogeneity was observed We also showed that in some cases an imbalance of RET copy number was present. We confirmed a high prevalence (90%) of RET somatic mutations in advanced tumors. Materials and Methods Fifty-six MTC patients (50 somatic and 6 hereditary cases) have been included in the study and a total of 209 specimens have been analysed by direct sequencing. Multiplex ligation-dependent probe amplification (MLPA) has been used to investigate amplification/deletion of RET alleles. Conclusions In conclusion, this study showed a genetic intra- and intertumor heterogeneity in MTC, But in only 20% of CASES These results could justify the relatively moderate level of aggressiveness of the disease with respect to more aggressive human tumors that are characterized by a high rate of mutation and heterogeneity.
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Affiliation(s)
- Cristina Romei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Raffaele Ciampi
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Francesca Casella
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Alessia Tacito
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Liborio Torregrossa
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy
| | - Clara Ugolini
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy
| | - Gabriele Materazzi
- Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Pisa, Italy
| | - Paolo Vitti
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Rossella Elisei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
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15
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Kim SJ, Kim E, Rim KT. Non-invasive quantification of cell-free DNA mutations in plasma during lung tumor progression in mice. Cancer Biomark 2017; 20:477-485. [PMID: 28946552 DOI: 10.3233/cbm-170303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Testing carcinogenicity caused by chemicals requires a noninvasive tool that can be used before autopsy because autopsy takes a long time. We investigated whether non-small cell lung cancer related gene mutations could be detected in cell-free DNA in plasma by Insight OncoTM next-generation sequencing, which is a fast and sensitive method. Adenoma formation was confirmed in urethane-injected 17-week-old mice. Seven single nucleotide polymorphisms, such as Cdkn2a and Vegfa, were selected. Mutant-enriched Insight OncoTM NGS and normal NGS were performed on genomic DNA. The results demonstrate that Insight OncoTM NGS detected Cdkn2a and Vegfa SNPs at 0.05%. The sensitivity of Insight OncoTM NGS was twice higher than that of normal NGS. In this analysis, the Cdkn2a gene mutation was detected not only in two genomic DNA samples of lung tissue from the 11th week of urethane injection but also in two cell-free DNA samples. In addition, the Vegfa gene mutation was detected not only in three genomic DNA samples of lung tissue of injection but also in one cell-free DNA sample, showing 33% concordance. Our results confirm that Insight OncoTM NGS is a rapid and sensitive detection method that enables lung cancer-associated gene mutations to be detected in cell-free DNA before the end of the carcinogenicity test.
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Affiliation(s)
- Soo-Jin Kim
- Chemicals Research Bureau, Occupational Safety and Health Research Institute, Korea Occupational Safety and Health Agency, Daejeon 34122, Korea.,Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Eunhee Kim
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Kyung-Taek Rim
- Chemicals Research Bureau, Occupational Safety and Health Research Institute, Korea Occupational Safety and Health Agency, Daejeon 34122, Korea
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16
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Zou Y, Liu FY, Wu J, Wan L, Fang SF, Zhang ZY, Luo Y, Chen MH, Huang MZ, He M, Huang OP. Mutational analysis of the RAS/RAF/MEK/ERK signaling pathway in 260 Han Chinese patients with cervical carcinoma. Oncol Lett 2017; 14:2427-2431. [PMID: 28781678 DOI: 10.3892/ol.2017.6435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Prevalent mutations in the mitogen-activated protein kinase 1 (MAPK1)/extracellular signal-regulated kinase 2 (ERK2) pathway have been identified in cervical squamous cell carcinoma in a large-scale genome sequencing effort. Furthermore, mutations in the rat sarcoma viral oncogene homolog (RAS)/Raf/Mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway have also been revealed to have important roles in the pathogenesis of human cancer. However, whether the potential hotspot mutations in ERK2 and other components of the RAS/RAF/MEK/ERK signaling pathway also exist in Chinese patients with cervical carcinoma remains to be elucidated. In the present study, a total of 260 patients with cervical carcinoma of distinct subtypes were analyzed for the presence of potential hotspot mutations in the RAS/RAF/MEK/ERK signaling pathway. No ERK2 mutations were detected in these samples; however, Kirsten RAS (KRAS) p.G12D (c.35G>A) mutation was identified in 2/26 (7.7%) cervical adenocarcinoma cases, including 1/20 cervical mucinous adenocarcinoma and 1/6 cervical endometrioid carcinoma cases. In addition, no mutations in the ERK1, neuroblastoma RAS, Harvey RAS or B-Raf proto-oncogene serine/threonine kinase genes were detected in the present study. These results indicated that ethnic differences may be a primary reason for the discrepancy in ERK2 mutation frequencies between the current study and previous studies. Furthermore, mutation in the KRAS gene, but not other genes in the RAS/RAF/MEK/ERK signaling pathway, may have an active role in the pathogenesis of cervical carcinoma.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Fa-Ying Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Juan Wu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Lei Wan
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Shu-Fen Fang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Zi-Yu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yong Luo
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Mei-Hong Chen
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Mei-Zhen Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ming He
- Department of Pharmacology and Molecular Therapeutics, Nanchang University School of Pharmaceutical Science, Nanchang 330006, P.R. China
| | - Ou-Ping Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
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17
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Pérez-Báez W, García-Latorre EA, Maldonado-Martínez HA, Coronado-Martínez I, Flores-García L, Taja-Chayeb L. Impact of fixation artifacts and threshold selection on high resolution melting analysis for KRAS mutation screening. Mol Cell Probes 2017. [PMID: 28627450 DOI: 10.1016/j.mcp.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Treatment in metastatic colorectal cancer (mCRC) has expanded with monoclonal antibodies targeting epidermal growth factor receptor, but is restricted to patients with a wild-type (WT) KRAS mutational status. The most sensitive assays for KRAS mutation detection in formalin-fixed paraffin embedded (FFPE) tissues are based on real-time PCR. Among them, high resolution melting analysis (HRMA), is a simple, fast, highly sensitive, specific and cost-effective method, proposed as adjunct for KRAS mutation detection. However the method to categorize WT vs mutant sequences in HRMA is not clearly specified in available studies, besides the impact of FFPE artifacts on HRMA performance hasn't been addressed either. METHODS Avowedly adequate samples from 104 consecutive mCRC patients were tested for KRAS mutations by Therascreen™ (FDA Validated test), HRMA, and HRMA with UDG pre-treatment to reverse FFPE fixation artifacts. Comparisons of KRAS status allocation among the three methods were done. Focusing on HRMA as screening test, ROC curve analyses were performed for HRMA and HMRA-UDG against Therascreen™, in order to evaluate their discriminative power and to determine the threshold of profile concordance between WT control and sample for KRAS status determination. RESULTS Comparing HRMA and HRMA-UDG against Therascreen™ as surrogate gold standard, sensitivity was 1 for both HRMA and HRMA-UDG; and specificity and positive predictive values were respectively 0.838 and 0.939; and 0.777 and 0.913. As evaluated by the McNemar test, HRMA-UDG allocated samples to a WT/mutated genotype in a significatively different way from HRMA (p > 0.001). On the other hand HRMA-UDG did not differ from Therascreen™ (p = 0.125). ROC-curve analysis showed a significant discriminative power for both HRMA and HRMA-UDG against Therascreen™ (respectively, AUC of 0.978, p > 0.0001, CI 95% 0.957-0.999; and AUC of 0.98, p > 0.0001, CI 95% 0.000-1.0). For HRMA as a screening tool, the best threshold (degree of concordance between sample curves and WT control) was attained at 92.14% for HRMA (specificity of 0.887), and at 92.55% for HRMA-UDG (specificity of 0.952). CONCLUSIONS HRMA is a highly sensitive method for KRAS mutation detection, with apparently adequate and statistically significant discriminative power. FFPE sample fixation artifacts have an impact on HRMA results, so for HRMA on FFPE samples pre-treatment with UDG should be strongly suggested. The choice of the threshold for melting curve concordance has also great impact on HRMA performance. A threshold of 93% or greater might be adequate if using HRMA as a screening tool. Further validation of this threshold is required.
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Affiliation(s)
- Wendy Pérez-Báez
- Immunology Department and CQB Post-graduate Program, National School of Biological Sciences, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala s/n, Colonia Santo Tomás, Delegación Miguel Hidalgo, Ciudad de México, Mexico City, CP 11340, México; Molecular Pathology and Immunopathology Department, Pathology Department, Instituto Nacional de Cancerología, San Fernando 2 piso 1, Colonia Barrio del Niño Jesús, Delegación Tlalpan, Ciudad de México, Mexico City, CP 14080, México
| | - Ethel A García-Latorre
- Immunology Department and CQB Post-graduate Program, National School of Biological Sciences, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala s/n, Colonia Santo Tomás, Delegación Miguel Hidalgo, Ciudad de México, Mexico City, CP 11340, México.
| | - Héctor Aquiles Maldonado-Martínez
- Molecular Pathology and Immunopathology Department, Pathology Department, Instituto Nacional de Cancerología, San Fernando 2 piso 1, Colonia Barrio del Niño Jesús, Delegación Tlalpan, Ciudad de México, Mexico City, CP 14080, México
| | - Iris Coronado-Martínez
- Molecular Pathology and Immunopathology Department, Pathology Department, Instituto Nacional de Cancerología, San Fernando 2 piso 1, Colonia Barrio del Niño Jesús, Delegación Tlalpan, Ciudad de México, Mexico City, CP 14080, México
| | - Leonardo Flores-García
- Blood Bank, Instituto Nacional de Cancerología, San Fernando 22, Colonia Sección XVI, Delegación Tlalpan, Ciudad de México, Mexico City, CP 14080, México
| | - Lucía Taja-Chayeb
- Pharmacogenetics Laboratory, Instituto Nacional de Cancerología, San Fernando 22, Colonia Sección XVI, Delegación Tlalpan, Ciudad de México, Mexico City, CP 14080, México
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18
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Malgulwar PB, Nambirajan A, Pathak P, Faruq M, Suri V, Sarkar C, Jagdevan A, Sharma BS, Sharma MC. Study of β-catenin and BRAF alterations in adamantinomatous and papillary craniopharyngiomas: mutation analysis with immunohistochemical correlation in 54 cases. J Neurooncol 2017; 133:487-495. [DOI: 10.1007/s11060-017-2465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 05/06/2017] [Indexed: 01/03/2023]
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19
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Breton Q, Plouhinec H, Prunier‐Mirebeau D, Boisselier B, Michalak S, Menei P, Rousseau A. BRAF-V600E immunohistochemistry in a large series of glial and glial-neuronal tumors. Brain Behav 2017; 7:e00641. [PMID: 28293477 PMCID: PMC5346524 DOI: 10.1002/brb3.641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/18/2016] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Some glial-neuronal tumors (GNT) (pleomorphic xantho-astrocytoma [PXA], ganglioglioma [GG]) display BRAF-V600E mutation, which represents a diagnostic clue to these entities. Targeted therapies against BRAF-V600 protein have shown promising results in GNT. The aim of this study was to assess the utility of BRAF-V600E immunohistochemistry (IHC, clone VE1) in daily practice in a series of 140 glial, and GNT compared to molecular biology (MB) techniques. METHODS We performed BRAF-V600E IHC on all 140 cases. We used Sanger sequencing and allele-specific quantitative PCR (ASQ-PCR) to detect BRAF-V600E mutation when sufficient amount of materiel was available. RESULTS BRAF-V600E immunostaining was detected in 29.5% of cases (41/140 cases; 61.5% GG/GC/AGG (32/52), 33% PXA, 6.6% pilocytic astrocytomas). In 47 cases, MB could be performed: Sanger sequencing and ASQ-PCR in 34 cases, ASQ-PCR only in 11 cases, and Sanger sequencing only in two cases. In initial tumors, Sanger sequencing identified BRAF-V600E mutation in 19.5% tumors (seven of 36 tested cases). ASQ-PCR showed mutation in 48.5% tumors (17/35 tested cases). In six cases (5 GG, one PXA), the results were discordant between IHC and MB; the five GG cases were immunopositive for BRAF-V600E but wild type with both MB techniques. In another 7 GG, the percentage of mutated (ganglion) cells was low, and Sanger sequencing failed to detect the mutation, which was detected by IHC and ASQ-PCR. CONCLUSIONS In tumors with few mutated cells (e.g., GG), anti-BRAF-V600E IHC appears more sensitive than Sanger sequencing. The latter, although considered as the gold standard, is not to be used up-front to detect BRAF mutation in GG. The combination of IHC and ASQ-PCR appears more efficient to appraise the indication of targeted therapies in these glioneuronal tumors.
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Affiliation(s)
- Quentin Breton
- Pathology DepartmentAngers University HospitalAngersFrance
| | | | | | - Blandine Boisselier
- Pathology DepartmentAngers University HospitalAngersFrance
- INSERM UMR‐1066, Micro‐ and Nanomedicine Biomimetics (MINT)Angers University HospitalAngersFrance
| | | | - Philippe Menei
- INSERM UMR‐1066, Micro‐ and Nanomedicine Biomimetics (MINT)Angers University HospitalAngersFrance
- Neurosurgery DepartmentAngers University HospitalAngersFrance
| | - Audrey Rousseau
- Pathology DepartmentAngers University HospitalAngersFrance
- INSERM UMR‐1066, Micro‐ and Nanomedicine Biomimetics (MINT)Angers University HospitalAngersFrance
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20
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Schirosi L, Strippoli S, Gaudio F, Graziano G, Popescu O, Guida M, Simone G, Mangia A. Is immunohistochemistry of BRAF V600E useful as a screening tool and during progression disease of melanoma patients? BMC Cancer 2016; 16:905. [PMID: 27863476 PMCID: PMC5116153 DOI: 10.1186/s12885-016-2951-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 10/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In clinical practice the gold standard method to assess BRAF status in patients with metastatic melanoma is based on molecular assays. Recently, a mutation-specific monoclonal antibody (VE1), which detects the BRAF V600E mutated protein, has been developed. With this study we aimed to confirm the clinical value of the VE1 Ventana® antibody, as today a univocal validated and accredited immunohistochemical procedure does not exist, to preliminary detect BRAF status in our routine diagnostic procedures. Moreover, we explored the biological meaning of BRAF immunohistochemical labeling both as a predictor marker of response to target therapy and, for the first time, as a player of acquired tumor drug resistance. METHODS We analyzed a retrospective series of 64 metastatic melanoma samples, previously investigated for molecular BRAF status, using a fully automatized immunohistochemical method. We correlated the data to the clinicopathologic characteristics of patients and their clinical outcome. RESULTS The sensitivity and the specificity of the Ventana® VE1 antibody were 89.2 and 96.2% respectively, while the positive predictive value and negative predictive value were 97.1 and 86.2%, respectively. For six mutated patients the histological sample before treatment and when disease progressed was available. The immunohistochemical BRAF V600E expression in the specimens when disease progressed was less intense and more heterogeneous compared to the basal expression. Multivariate analysis revealed that a less intense grade of positive expression is an independent predictor of a less aggressive stage at diagnosis (p = 0.0413). CONCLUSIONS Our findings encourage the introduction of immunohistochemistry as a rapid screening tool for the assessment of BRAF status in melanoma patients in routine diagnostic procedures and prepare the ground for other studies to highlight the role of immunohistochemical BRAF V600E expression in patients at the time of progression.
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Affiliation(s)
- Laura Schirosi
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Sabino Strippoli
- Medical Oncology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Francesca Gaudio
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Giusi Graziano
- Scientific Direction, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Ondina Popescu
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Michele Guida
- Medical Oncology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Giovanni Simone
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy
| | - Anita Mangia
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124, Bari, Italy.
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21
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Targeted sequencing with enrichment PCR: a novel diagnostic method for the detection of EGFR mutations. Oncotarget 2016; 6:13742-9. [PMID: 25915533 PMCID: PMC4537046 DOI: 10.18632/oncotarget.3807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/18/2015] [Indexed: 01/01/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is an important mediator of tumor cell survival and proliferation. The detection of EGFR mutations can predict prognoses and indicate when treatment with EGFR tyrosine kinase inhibitors should be used. As such, the development of highly sensitive methods for detecting EGFR mutations is important. Targeted next-generation sequencing is an effective method for diagnosing mutations. We compared the abilities of enrichment PCR followed by ultra-deep pyrosequencing (UDP), UDP alone, and PNA-mediated RT-PCR clamping to detect low-frequency EGFR mutations in tumor cell lines and tissue samples. Using enrichment PCR-UDP, we were able to detect the E19del and L858R mutations at minimum frequencies of 0.01% and 0.05%, respectively, in the PC-9 and H197 tumor cell lines. We also confirmed the sensitivity of detecting the E19del mutation by performing a titration analysis in FFPE tumor samples. The lowest mutation frequency detected was 0.0692% in tissue samples. EGFR mutations with frequencies as low as 0.01% were detected using enrichment PCR-UDP, suggesting that this method is a valuable tool for detecting rare mutations, especially in scarce tissue samples or those with small quantities of DNA.
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22
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Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
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Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Digitally guided microdissection aids somatic mutation detection in difficult to dissect tumors. Cancer Genet 2015; 209:42-9. [PMID: 26767919 DOI: 10.1016/j.cancergen.2015.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023]
Abstract
Molecular genetic testing on formalin fixed, paraffin embedded (FFPE) tumors frequently requires dissection of tumor from tissue sections mounted on glass slides. In a process referred to as "manual macrodissection," the pathologist reviews an H&E stained slide at the light microscope and marks areas for dissection, and then the laboratory performs manual dissection from adjacent sections without the aid of a microscope, using the marked reference H&E slide as a guide. Manual macrodissection may be inadequate for tissue sections with low tumor content. We compared manual macrodissection to a new method, digitally guided microdissection, on a series of 32 FFPE pancreatic cancer samples. KRAS hotspot mutation profiling was performed using the Sequenom MassARRAY system (Agena Bioscience). Digitally guided microdissection was performed on multiple smaller areas of high tumor content selected from within the larger areas marked for manual macrodissection. The KRAS mutant allele fraction and estimated neoplastic cellularity were significantly higher in samples obtained by digitally guided microdissection (p < 0.01), and 7 of the 32 samples (22%) showed a detectable mutation only with digitally guided microdissection. DNA quality and yield per cubic millimeter of dissected tissue were similar for both dissection methods. These results indicate a significant improvement in tumor content achievable with digitally guided microdissection.
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Davari M, Ashrafi F, Maracy M, Aslani A, Tabatabaei M. Cost-effectiveness Analysis of Cetuximab in Treatment of Metastatic Colorectal Cancer in Iranian Pharmaceutical Market. Int J Prev Med 2015; 6:63. [PMID: 26288707 PMCID: PMC4521302 DOI: 10.4103/2008-7802.161068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 03/19/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cetuximab is a monoclonal antibody which acts against the epidermal growth-factor receptor. Randomized controlled trials show that the addition of cetuximab to folinic acid, 5-flourouracil, irinotecan (FOLFIRI), folinic acid, 5-flourouracil, oxaliplatin (FOLFOX) and capecitabin + oxaliplatin (CAPOX) regimens, as the first-line treatment for metastatic colorectal cancer (CRC), increases the overall survival (OS) and progression-free survival (PFS) compared to FOLFIRI, FOLFOX and CAPOX regimens alone. The aim of this study was to analyze the cost-effectiveness of different treatment programs for managing metastatic CRC with and without cetuximab in the first-line treatment of unresectable metastatic CRC in Iran. METHODS A systematic search of the literature was performed in PubMed, Centre for Reviews and Dissemination Databases and Cochrane Library to assess the effectiveness of the drug in the context of PFS, OS and the adverse events. The incremental cost-effectiveness ratio of each treatment program was calculated. An extensive sensitivity analysis was conducted on the results regarding the effectiveness. RESULTS The addition of cetuximab to FOLFIRI, FOLFOX and CAPOX programs increased PFS by 0.1, 0.042 and 0.042 years, respectively. Similarly, the addition of cetuximab to FOLFIRI, FOLFOX and CAPOX increased OS by 0.325, 0.442 and 0.442 years and also cost $212825, $202484 and $204198 individually. Whereas, based on the World Health Organisation (WHO) suggested threshold for cost-effectiveness analysis, even FOLFOX + cetuximab was very higher than the threshold in Iran (37.4 times higher). CONCLUSIONS The FOLFOX regimen + cetuximab provides lower costs per additional life years gained (more cost-effective) compared with its alternatives in the treatment of patients with unresectable metastatic CRC. However, according to the WHO indicator, none of the cetuximab regimens could be considered as cost effective for the Iranian health care market.
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Affiliation(s)
- Majid Davari
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Ashrafi
- Department of Hematology and Medical Oncology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammadreza Maracy
- Department of Statistic and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abolfazl Aslani
- Department of Pharmaceutics, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammadreza Tabatabaei
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Wang Y, Lei F, Rong W, Zeng Q, Sun W. Positive feedback between oncogenic KRAS and HIF-1α confers drug resistance in colorectal cancer. Onco Targets Ther 2015; 8:1229-37. [PMID: 26060408 PMCID: PMC4454194 DOI: 10.2147/ott.s80017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Approximately 30%-50% of colorectal cancers (CRCs) harbor the somatic mutated KRAS gene. KRAS G12V, one of the most common KRAS mutations in CRCs, is linked to increased tumor aggressiveness, less response to anti-epidermal growth factor receptor (EGFR) therapy, and poor survival rate. In this study, we sought to determine whether resistance to EGFR inhibitors in colorectal cancer cells harboring KRAS G12V mutation is associated with hypoxia. Our data indicated that HIF-1α was induced by KRAS G12V signaling at transcription level. Hypoxia or HIF-1α overexpression could increase KRAS G12V activity. Therefore, a positive feedback between hypoxia and KRAS G12V activation was formed. Cetuximab, an EGFR inhibitor, which has a minor effect on KRAS-mutant CRCs, could effectively inhibit the proliferation of CRC cells harboring KRAS G12V mutation when combined with HIF-1α inhibitor PX-478. Our data indicated that hypoxia was involved in resistance to anti-EGFR therapy, and a combination therapy might be necessary for CRC patients with KRAS mutation.
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Affiliation(s)
- Yanzhao Wang
- Department of Hepatobiliary Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Fuming Lei
- Department of General Surgery, Peking University Shougang Hospital, Beijing, People's Republic of China
| | - Wanshui Rong
- Department of General Surgery, Peking University Shougang Hospital, Beijing, People's Republic of China
| | - Qingmin Zeng
- Department of General Surgery, Peking University Shougang Hospital, Beijing, People's Republic of China
| | - Wenbing Sun
- Department of Hepatobiliary Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
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26
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Carter GC, Landsman-Blumberg PB, Johnson BH, Juneau P, Nicol SJ, Li L, Shankaran V. KRAS testing of patients with metastatic colorectal cancer in a community-based oncology setting: a retrospective database analysis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:29. [PMID: 25888436 PMCID: PMC4380249 DOI: 10.1186/s13046-015-0146-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/16/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND In 2009, treatment guidelines were updated to recommend KRAS testing at diagnosis for patients with metastatic colorectal cancer (mCRC). We investigated KRAS testing rates over time and compared characteristics of KRAS-tested and not-tested patients in a community-based oncology setting. METHODS Adult patients with a diagnosis of mCRC from 2008-2011 were selected from the ACORN Data Warehouse (ACORN Research LLC, Memphis, TN). Text mining of physician progress notes and full chart reviews identified KRAS-tested patients, test dates, and test results (KRAS status). The overall proportion of eligible patients KRAS-tested in each calendar year was calculated. Among KRAS-tested patients, the proportion tested at diagnosis (within 60 days) was calculated by year. Univariate and multivariate analyses were used to compare patient characteristics at diagnosis between tested and not-tested cohorts, and to identify factors associated with KRAS testing. RESULTS Among 1,363 mCRC patients seen from 2008-2011, 648 (47.5%) were KRAS-tested. Among newly diagnosed mCRC patients, the rate of KRAS testing increased from 5.9% prior to 2008, to 13.9% in 2008, and then jumped dramatically to 32.3% in 2009, after which a modest yearly increase continued. The proportions of KRAS-tested patients who had been diagnosed in previous years but not tested previously increased from 17.7% in 2008 to 27.0% in 2009, then decreased to 19.0% in 2010 and 17.6% in 2011. Among patients who were KRAS-tested, the proportions tested at the time of diagnosis increased annually (to 78.4% in 2011). Patients more likely to have been tested included those with lung metastases, poor performance status, more comorbidities, and mCRC diagnosis in 2009 or later. CONCLUSIONS The frequency of KRAS testing increased over time, corresponding to changes in treatment guidelines and epidermal growth factor receptor inhibitor product labels; however, approximately 50% of eligible patients were untested during the study period.
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Affiliation(s)
- Gebra Cuyun Carter
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA.
| | | | | | | | - Steven J Nicol
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA.
| | - Li Li
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA.
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Ilm K, Kemmner W, Osterland M, Burock S, Koch G, Herrmann P, Schlag PM, Stein U. High MACC1 expression in combination with mutated KRAS G13 indicates poor survival of colorectal cancer patients. Mol Cancer 2015; 14:38. [PMID: 25742883 PMCID: PMC4335361 DOI: 10.1186/s12943-015-0316-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/05/2015] [Indexed: 12/28/2022] Open
Abstract
Background The metastasis-associated in colon cancer 1 (MACC1) gene has been identified as prognostic biomarker for colorectal cancer (CRC). Here, we aimed at the refinement of risk assessment by separate and combined survival analyses of MACC1 expression with any of the markers KRAS mutated in codon 12 (KRAS G12) or codon 13 (KRAS G13), BRAF V600 mutation and MSI status in a retrospective study of 99 CRC patients with tumors UICC staged I, II and III. Findings We showed that only high MACC1 expression (HR: 6.09, 95% CI: 2.50-14.85, P < 0.001) and KRAS G13 mutation (HR: 5.19, 95% CI: 1.06-25.45, P = 0.042) were independent prognostic markers for shorter metastasis-free survival (MFS). Accordingly, Cox regression analysis revealed that patients with high MACC1 expression and KRAS G13 mutation exhibited the worst prognosis (HR: 14.48, 95% CI: 3.37-62.18, P < 0.001). Patients were classified based on their molecular characteristics into four clusters with significant differences in MFS (P = 0.003) by using the SPSS 2-step cluster function and Kaplan-Meier survival analysis. Conclusion According to our results, patients with high MACC1 expression and mutated KRAS G13 exhibited the highest risk for metachronous metastases formation. Moreover, we demonstrated that the “Traditional pathway” with an intermediate risk for metastasis formation can be further subdivided by assessing MACC1 expression into a low and high risk group with regard to MFS prognosis. This is the first report showing that identification of CRC patients at high risk for metastasis is possible by assessing MACC1 expression in combination with KRAS G13 mutation. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0316-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katharina Ilm
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany.
| | - Wolfgang Kemmner
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany.
| | - Marc Osterland
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany.
| | - Susen Burock
- Charité Comprehensive Cancer Center, Berlin, Germany.
| | - Gudrun Koch
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany.
| | - Pia Herrmann
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany.
| | | | - Ulrike Stein
- Experimental and Clinical Research Center, Charité University Medicine Berlin and Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str.10, 13125, Berlin, Germany. .,German Cancer Consortium, Heidelberg, Germany.
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Combaret V, Iacono I, Bellini A, Bréjon S, Bernard V, Marabelle A, Coze C, Pierron G, Lapouble E, Schleiermacher G, Blay JY. Detection of tumor ALK status in neuroblastoma patients using peripheral blood. Cancer Med 2015; 4:540-50. [PMID: 25653133 PMCID: PMC4402069 DOI: 10.1002/cam4.414] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/04/2014] [Accepted: 12/23/2014] [Indexed: 12/24/2022] Open
Abstract
New protocols based on ALK-targeted therapy by crizotinib or other ALK-targeting molecules have opened for the treatment of patients with neuroblastoma (NB) if their tumors showed mutation and/or amplification of the ALK gene. However, tumor samples are not always available for analysis of ALK mutational status in particular at relapse. Here, we evaluated the ALK mutational status of NB samples by analysis of circulating DNA, using the droplet digital PCR (ddPCR) system. ddPCR assays was developed for the detection of ALK mutations at F1174 and R1275 hotspots found in NB tumors and was applied for the analysis of circulating DNA obtained from 200 μL of serum or plasma samples collected from 114 patients with NB. The mutations F1174L (exon 23 position 3520, T>C and position 3522, C>A) and the mutation R1275Q (exon 25 position 3824, G>A) were detected in circulating DNA. The sensitivity of our test was 100%, 85%, and 92%, respectively, and the specificity was 100%, 91%, and 98%, respectively. In conclusion, the assay that we have developed offers a reliable, noninvasive blood test to assess ALK mutational status at F1174 and R1275 hotspots and should help clinicians to identify patients showing an ALK mutation in particular when no tumor tissue is available.
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Affiliation(s)
- Valérie Combaret
- Centre Léon-Bérard, Laboratoire de Recherche Translationnelle, 28 rue Laennec, 69373, Lyon Cedex 08, France
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29
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Lozano MD, Labiano T, Echeveste J, Gurpide A, Martín-Algarra S, Zhang G, Sharma A, Palma JF. Assessment of EGFR and KRAS mutation status from FNAs and core-needle biopsies of non-small cell lung cancer. Cancer Cytopathol 2014; 123:230-6. [PMID: 25529460 DOI: 10.1002/cncy.21513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 11/25/2014] [Accepted: 12/01/2014] [Indexed: 11/11/2022]
Abstract
BACKGROUND Molecular testing to determine gene mutation status is now the recommended standard of care for patients with advanced or metastatic Non-small cell lung cancer (NSCLC). Because the majority of patients with NSCLC present with metastatic disease, minimally invasive procedures are necessary for diagnosis, staging, and molecular analysis. However, the resulting samples have perceived limitations in the oncology community, and most commercially available tests have not been validated for these sample types. The current study was undertaken to assess the feasibility of determining epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation status in fine-needle aspirates (FNAs) and core-needle biopsies (CNBs) after staining with Papanicolaou or hematoxylin and eosin, respectively. METHODS Gene mutation status was determined in 140 NSCLC tumor samples with proprietary tests for EGFR and KRAS mutations (cobas tests) followed by Sanger sequencing of exons 18 through 21 of the EGFR gene and exon 2 of the KRAS gene. The results were analyzed based on FNA (n = 91) or CNB (n = 49) sampling. RESULTS The cobas tests yielded valid results in the majority of FNA and CNB samples for both EGFR (97.9%) and KRAS (93.6%). Moreover, valid results were obtained for 90% of samples that had DNA concentrations below the values recommended by the manufacturer. For samples with valid results from both cobas testing and Sanger sequencing, 95.7% and 93% agreement were observed for EGFR status and KRAS status, respectively. CONCLUSIONS Gene mutation testing can be successfully performed on cytology and CNB samples, expanding the potential of personalized cancer treatment to patients who have limited tissue samples.
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Affiliation(s)
- Maria D Lozano
- Department of Pathology, Clinical University of Navarra-University of Navarra, Pamplona, Spain
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Schleiermacher G, Javanmardi N, Bernard V, Leroy Q, Cappo J, Rio Frio T, Pierron G, Lapouble E, Combaret V, Speleman F, de Wilde B, Djos A, Øra I, Hedborg F, Träger C, Holmqvist BM, Abrahamsson J, Peuchmaur M, Michon J, Janoueix-Lerosey I, Kogner P, Delattre O, Martinsson T. Emergence of New ALK Mutations at Relapse of Neuroblastoma. J Clin Oncol 2014; 32:2727-34. [DOI: 10.1200/jco.2013.54.0674] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose In neuroblastoma, the ALK receptor tyrosine kinase is activated by point mutations. We investigated the potential role of ALK mutations in neuroblastoma clonal evolution. Methods We analyzed ALK mutations in 54 paired diagnosis–relapse neuroblastoma samples using Sanger sequencing. When an ALK mutation was observed in one paired sample, a minor mutated component in the other sample was searched for by more than 100,000× deep sequencing of the relevant hotspot, with a sensitivity of 0.17%. Results All nine ALK-mutated cases at diagnosis demonstrated the same mutation at relapse, in one case in only one of several relapse nodules. In five additional cases, the mutation seemed to be relapse specific, four of which were investigated by deep sequencing. In two cases, no mutation evidence was observed at diagnosis. In one case, the mutation was present at a subclonal level (0.798%) at diagnosis, whereas in another case, two different mutations resulting in identical amino acid changes were detected, one only at diagnosis and the other only at relapse. Further evidence of clonal evolution of ALK-mutated cells was provided by establishment of a fully ALK-mutated cell line from a primary sample with an ALK-mutated cell population at subclonal level (6.6%). Conclusion In neuroblastoma, subclonal ALK mutations can be present at diagnosis with subsequent clonal expansion at relapse. Given the potential of ALK-targeted therapy, the significant spatiotemporal variation of ALK mutations is of utmost importance, highlighting the potential of deep sequencing for detection of subclonal mutations with a sensitivity 100-fold that of Sanger sequencing and the importance of serial samplings for therapeutic decisions.
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Affiliation(s)
- Gudrun Schleiermacher
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Niloufar Javanmardi
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Virginie Bernard
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Quentin Leroy
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Julie Cappo
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Thomas Rio Frio
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Gaelle Pierron
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Eve Lapouble
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Valérie Combaret
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Frank Speleman
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Bram de Wilde
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Anna Djos
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Ingrid Øra
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Fredrik Hedborg
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Catarina Träger
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Britt-Marie Holmqvist
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Jonas Abrahamsson
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Michel Peuchmaur
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Jean Michon
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Isabelle Janoueix-Lerosey
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Per Kogner
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Olivier Delattre
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
| | - Tommy Martinsson
- Gudrun Schleiermacher, Julie Cappo, Isabelle Janoueix-Lerosey, and Olivier Delattre, L'Institut National de la Santé et de la Recherche Médicale U830, Laboratoire de Génétique et Biologie des Cancers; Gudrun Schleiermacher, Virginie Bernard, Quentin Leroy, Thomas Rio Frio, Gaelle Pierron, Eve Lapouble, and Jean Michon, Institut Curie; Michel Peuchmaur, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Robert Debré, Service de Pathologie; Michel Peuchmaur, Université Diderot Paris 7, Sorbonne
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Bilbao-Sieyro C, Santana G, Moreno M, Torres L, Santana-Lopez G, Rodriguez-Medina C, Perera M, Bellosillo B, de la Iglesia S, Molero T, Gomez-Casares MT. High resolution melting analysis: a rapid and accurate method to detect CALR mutations. PLoS One 2014; 9:e103511. [PMID: 25068507 PMCID: PMC4113452 DOI: 10.1371/journal.pone.0103511] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/30/2014] [Indexed: 01/23/2023] Open
Abstract
Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.
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Affiliation(s)
- Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Morfology Department, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Guillermo Santana
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Melania Moreno
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Laura Torres
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Gonzalo Santana-Lopez
- Preventive Medicine Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodriguez-Medina
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - María Perera
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Beatriz Bellosillo
- Laboratori de Biologia Molecular Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Silvia de la Iglesia
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Teresa Molero
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Medical Sciences Department, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Maria Teresa Gomez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- * E-mail:
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Ogino S, Lochhead P, Giovannucci E, Meyerhardt JA, Fuchs CS, Chan AT. Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology. Oncogene 2014; 33:2949-55. [PMID: 23792451 PMCID: PMC3818472 DOI: 10.1038/onc.2013.244] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 12/18/2022]
Abstract
Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research. Experimental and clinical studies support a carcinogenic role for PTGS2 (cyclooxygenase-2), which is an important enzymatic mediator of inflammation, and a target of aspirin. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation as a molecular biomarker that predicts response to aspirin therapy. The PI3K (phosphatidylinositol-4,5-bisphosphonate 3-kinase) enzyme has a pivotal role in the PI3K-AKT signaling pathway. Activating PIK3CA oncogene mutations are observed in various malignancies including breast cancer, ovarian cancer, brain tumor, hepatocellular carcinoma, lung cancer and colon cancer. The prevalence of PIK3CA mutations increases continuously from rectal to cecal cancers, supporting the 'colorectal continuum' paradigm, and an important interplay of gut microbiota and host immune/inflammatory reaction. MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'. As exposome and interactome vary from person to person and influence disease process, each disease process is unique (the unique disease principle). Therefore, MPE concept and paradigm can extend to non-neoplastic diseases including diabetes mellitus, cardiovascular diseases, metabolic diseases, and so on. MPE research opportunities are currently limited by paucity of tumor molecular data in the existing large-scale population-based studies. However, genomic, epigenomic and molecular pathology testings (for example, analyses for microsatellite instability, MLH1 promoter CpG island methylation, and KRAS and BRAF mutations in colorectal tumors) are becoming routine clinical practices. In order for integrative molecular and population science to be routine practice, we must first reform education curricula by integrating both population and molecular biological sciences. As consequences, next-generation hybrid molecular biological and population scientists can advance science, moving closer to personalized precision medicine and health care.
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Affiliation(s)
- S Ogino
- 1] Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - P Lochhead
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - E Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - C S Fuchs
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A T Chan
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
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High-resolution melting analysis is a sensitive diagnostic tool to detect imatinib-resistant and imatinib-sensitive PDGFRA exon 18 mutations in gastrointestinal stromal tumors. Hum Pathol 2014; 45:573-82. [DOI: 10.1016/j.humpath.2013.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/10/2013] [Accepted: 10/19/2013] [Indexed: 01/01/2023]
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Ihle MA, Fassunke J, König K, Grünewald I, Schlaak M, Kreuzberg N, Tietze L, Schildhaus HU, Büttner R, Merkelbach-Bruse S. Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations. BMC Cancer 2014; 14:13. [PMID: 24410877 PMCID: PMC3893431 DOI: 10.1186/1471-2407-14-13] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/08/2014] [Indexed: 01/11/2023] Open
Abstract
Background The approval of vemurafenib in the US 2011 and in Europe 2012 improved the therapy of not resectable or metastatic melanoma. Patients carrying a substitution of valine to glutamic acid at codon 600 (p.V600E) or a substitution of valine to leucine (p.V600K) in BRAF show complete or partial response. Therefore, the precise identification of the underlying somatic mutations is essential. Herein, we evaluate the sensitivity, specificity and feasibility of six different methods for the detection of BRAF mutations. Methods Samples harboring p.V600E mutations as well as rare mutations in BRAF exon 15 were compared to wildtype samples. DNA was extracted from formalin-fixed paraffin-embedded tissues by manual micro-dissection and automated extraction. BRAF mutational analysis was carried out by high resolution melting (HRM) analysis, pyrosequencing, allele specific PCR, next generation sequencing (NGS) and immunohistochemistry (IHC). All mutations were independently reassessed by Sanger sequencing. Due to the limited tumor tissue available different numbers of samples were analyzed with each method (82, 72, 60, 72, 49 and 82 respectively). Results There was no difference in sensitivity between the HRM analysis and Sanger sequencing (98%). All mutations down to 6.6% allele frequency could be detected with 100% specificity. In contrast, pyrosequencing detected 100% of the mutations down to 5% allele frequency but exhibited only 90% specificity. The allele specific PCR failed to detect 16.3% of the mutations eligible for therapy with vemurafenib. NGS could analyze 100% of the cases with 100% specificity but exhibited 97.5% sensitivity. IHC showed once cross-reactivity with p.V600R but was a good amendment to HRM. Conclusion Therefore, at present, a combination of HRM and IHC is recommended to increase sensitivity and specificity for routine diagnostic to fulfill the European requirements concerning vemurafenib therapy of melanoma patients.
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Gudipudi G, Sagurthi SR, Perugu S, Achaiah G, David Krupadanam GL. Rational design and synthesis of novel 2-(substituted-2H-chromen-3-yl)-5-aryl-1H-imidazole derivatives as an anti-angiogenesis and anti-cancer agent. RSC Adv 2014. [DOI: 10.1039/c4ra09945a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Based on the earlier proven pharmacophore analogues of cancer a novel 2-(substituted-2H-chromen-3-yl)-5-aryl-1H-imidazoles were rationally designed, synthesized and used for competitive biological activity against cancer cell lines.
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Affiliation(s)
| | | | - Shyam Perugu
- Department of Biochemistry
- Osmania University
- Hyderabad, India 500 007
| | - G. Achaiah
- Medicinal Chemistry Division
- University College of Pharmaceutical Sciences
- Kakatiya University
- Warangal, India 500 009
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K-RAS mutation profile in Puerto Rican patients with colorectal cancer: trends from April 2009 to January 2011. Int J Biol Markers 2013; 28:e393-7. [PMID: 23999847 DOI: 10.5301/jbm.5000043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2013] [Indexed: 02/08/2023]
Abstract
The frequency of K-RAS mutations ranges between 30% and 48% among the Caucasian, Asian, and European populations and these mutations are predictors of response to EGFR therapies. We sought to determine the expression of K-RAS gene mutations among colorectal cancer patients in PuertoRico. A retrospective study was conducted to determine the expression of mutant K-RAS among colorectal cancer patients in Puerto Rico between April 2009 and January 2011. The mutant expression of K-RAS was found in 39% (n=195) of the Puerto Rican population, and was more common in the age group of 51-69 years (53.8%) and in males (55.4%, p>0.05). Moreover, mutant K-RAS was more commonly found in tumors of the proximal area (43.8%; p=0.03), with distant metastasis (43.3%, p=0.018), with a mucinous histotype (31.7% p>0.05), and in ulcerated tumors (38.8%, p>0.05). K-RAS mutations were observed on codon 12 (87.7%) and codon 13 (12.3%). The most frequent mutation on codon 12 was 12 ASP (39.5%), followed by 12 VAL (25.4%) that is associated with a significant decrease in overall cancer survival. The mutant expression of K-RAS in cases of rectum carcinoma was 39.5%, where the most common mutation was 12 VAL (37.5%). The frequency of K-RAS mutations in the Puerto Rican population here studied was 39% and mutant K-RAS was associated with advanced colorectal cancer stage, mucinous histotype, and ulcerated tumors.
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Bellevicine C, Vita GD, Malapelle U, Troncone G. Applications and limitations of oncogene mutation testing in clinical cytopathology. Semin Diagn Pathol 2013; 30:284-97. [DOI: 10.1053/j.semdp.2013.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Bellizzi AM. Contributions of molecular analysis to the diagnosis and treatment of gastrointestinal neoplasms. Semin Diagn Pathol 2013; 30:329-61. [DOI: 10.1053/j.semdp.2013.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mutational Analysis of Circulating Tumor Cells Using a Novel Microfluidic Collection Device and qPCR Assay. Transl Oncol 2013; 6:528-38. [PMID: 24151533 DOI: 10.1593/tlo.13367] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/19/2013] [Accepted: 04/24/2013] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cells (CTCs) provide a readily accessible source of tumor material from patients with cancer. Molecular profiling of these rare cells can lead to insight on disease progression and therapeutic strategies. A critical need exists to isolate CTCs with sufficient quantity and sample integrity to adapt to conventional analytical techniques. We present a microfluidic platform (IsoFlux) that uses flow control and immunomagnetic capture to enhance CTC isolation. A novel cell retrieval mechanism ensures complete transfer of CTCs into the molecular assay. Improved sensitivity to the capture antigen was demonstrated by spike-in experiments for three cell lines of varying levels of antigen expression. We obtained spike-in recovery rates of 74%, 75%, and 85% for MDA-MB-231 (low), PC3 (middle), and SKBR3 (high) cell lines. Recovery using matched enumeration protocols and matched samples (PC3) yielded 90% and 40% recovery for the IsoFlux and CellSearch systems, respectively. In matched prostate cancer samples (N = 22), patients presenting more than four CTCs per blood draw were 95% and 36% using IsoFlux and CellSearch, respectively. An assay for detecting KRAS mutations was described along with data from patients with colorectal cancer, of which 87% presented CTCs above the assay's limit of detection (four CTCs). The CTC KRAS mutant rate was 50%, with 46% of patients displaying a CTC KRAS mutational status that differed from the previously acquired tissue biopsy data. The microfluidic system and mutation assay presented here provide a complete workflow to track oncogene mutational changes longitudinally with high success rates.
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Cushman-Vokoun AM, Crowley AM, Rapp SA, Greiner TC. Comparison study of the performance of the QIAGEN EGFR RGQ and EGFR pyro assays for mutation analysis in non-small cell lung cancer. Am J Clin Pathol 2013; 140:7-19. [PMID: 23765529 DOI: 10.1309/ajcpmf26abeoychz] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES To compare 2 laboratory assays commonly used in the evaluation of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC). METHODS Fifty-three formalin-fixed, paraffin-embedded NSCLC specimens were selected. Extracted DNA was analyzed using the EGFR RGQ Amplification Refractory Mutation System Scorpions probe-based real-time polymerase chain reaction (PCR) assay and the EGFR Pyro pyrosequencing assay. RESULTS Fourteen EGFR mutations were identified in 13 specimens using at least 1 of the assays, with a mutation concordance rate of 92.9%. Using dideoxy sequencing as the gold standard, clinical sensitivity was 73.7% and 68.4% by the RGQ and Pyro assays, respectively, but 100% by both for common drug sensitivity mutations. Performance observations included the following: the RGQ system requires higher DNA input, the RGQ system is a single-step procedure, the EGFR Pyro assay is a 2-step procedure, only the RGQ system can identify exon 20 insertions, the RGQ system is more sensitive, and the Pyro system can specify exact mutations for all interrogated sites. CONCLUSIONS Both the RGQ real-time PCR and Pyro assays adequately detect common EGFR mutations; however, the RGQ system is more clinically and analytically sensitive. Performance characteristics should be considered when evaluating these EGFR mutation assays for clinical adoption.
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Affiliation(s)
| | - Ann M. Crowley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Sharleen A. Rapp
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Timothy C. Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
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Smith DL, Lamy A, Beaudenon-Huibregtse S, Sesboüé R, Laosinchai-Wolf W, Sabourin JC, Labourier E. A multiplex technology platform for the rapid analysis of clinically actionable genetic alterations and validation for BRAF p.V600E detection in 1549 cytologic and histologic specimens. Arch Pathol Lab Med 2013; 138:371-8. [PMID: 23808402 DOI: 10.5858/arpa.2013-0002-oa] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information. OBJECTIVE To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens. DESIGN Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates. RESULTS Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%-100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%-99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%-99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451-48 078). CONCLUSIONS The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.
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Affiliation(s)
- David L Smith
- From Asuragen Inc, Austin, Texas, (Drs Smith, Beaudenon-Huibregtse, Laosinchai-Wolf, and Labourier); the Department of Pathology, Rouen University Hospital, Rouen, France (Drs Lamy and Sabourin); and INSERM U1079, Faculty of Medicine, Rouen University, Rouen, France (Dr Sesboüé)
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Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie WR, Dimitrova N, Harris LN. Translating next generation sequencing to practice: opportunities and necessary steps. Mol Oncol 2013; 7:743-55. [PMID: 23769412 DOI: 10.1016/j.molonc.2013.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 04/21/2013] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) approaches for measuring RNA and DNA benefit from greatly increased sensitivity, dynamic range and detection of novel transcripts. These technologies are rapidly becoming the standard for molecular assays and represent huge potential value to the practice of oncology. However, many challenges exist in the transition of these technologies from research application to clinical practice. This review discusses the value of NGS in detecting mutations, copy number changes and RNA quantification and their applications in oncology, the challenges for adoption and the relevant steps that are needed for translating this potential to routine practice.
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Grumbt B, Eck SH, Hinrichsen T, Hirv K. Diagnostic applications of next generation sequencing in immunogenetics and molecular oncology. ACTA ACUST UNITED AC 2013; 40:196-206. [PMID: 23922545 DOI: 10.1159/000351267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/19/2013] [Indexed: 12/23/2022]
Abstract
SUMMARY With the introduction of the next generation sequencing (NGS) technologies, remarkable new diagnostic applications have been established in daily routine. Implementation of NGS is challenging in clinical diagnostics, but definite advantages and new diagnostic possibilities make the switch to the technology inevitable. In addition to the higher sequencing capacity, clonal sequencing of single molecules, multiplexing of samples, higher diagnostic sensitivity, workflow miniaturization, and cost benefits are some of the valuable features of the technology. After the recent advances, NGS emerged as a proven alternative for classical Sanger sequencing in the typing of human leukocyte antigens (HLA). By virtue of the clonal amplification of single DNA molecules ambiguous typing results can be avoided. Simultaneously, a higher sample throughput can be achieved by tagging of DNA molecules with multiplex identifiers and pooling of PCR products before sequencing. In our experience, up to 380 samples can be typed for HLA-A, -B, and -DRB1 in high-resolution during every sequencing run. In molecular oncology, NGS shows a markedly increased sensitivity in comparison to the conventional Sanger sequencing and is developing to the standard diagnostic tool in detection of somatic mutations in cancer cells with great impact on personalized treatment of patients.
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Affiliation(s)
- Barbara Grumbt
- Center for Human Genetics and Laboratory Medicine, Martinsried, Germany
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Huang T, Zhuge J, Zhang WW. Sensitive detection of BRAF V600E mutation by Amplification Refractory Mutation System (ARMS)-PCR. Biomark Res 2013; 1:3. [PMID: 24252159 PMCID: PMC3776245 DOI: 10.1186/2050-7771-1-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/09/2012] [Indexed: 12/28/2022] Open
Abstract
Background BRAF mutations occur in approximately 8% of all human cancers and approach 50% in melanoma and papillary carcinoma of thyroid. These mutations provide potentially valuable diagnostic, prognostic and treatment response prediction markers. A sensitive, specific, low-cost assay to detect these mutations is needed. Results To detect BRAF V600E mutation in formalin-fixed, paraffin-embedded (FFPE) tissue, we developed a method using Amplification Refractory Mutation System (ARMS)-PCR. This method was designed to amplify three products in a single reaction tube: a 200 bp common product serving as an amplification control, a 144 bp BRAF V600E specific product, and a 97 bp wild-type (wt) specific product. The sensitivity of this method was determined to be as low as 0.5% for the BRAF V600E allele in a wild-type background. This method was successfully validated in 72 thyroid tumors. It detected V600E mutation in 22 out of 33 (67%) of the conventional papillary thyroid carcinoma (PTC), 8 out of 12 (75%) of the tall-cell variant of PTC, whereas none of the 10 follicular variant of PTC showed BRAF V600E mutation. In addition, none of the 14 follicular adenomas and 3 follicular carcinomas had BRAF V600E mutation. As a comparison method, direct dideoxy sequencing found only 27 out of 30 (90%) mutations detected by ARMS-PCR method, suggesting that this ARMS-PCR method has higher sensitivity. Conclusions Our ARMS-PCR method provides a new tool for rapid detection of BRAF V600E mutation. Our results indicate that ARMS-PCR is more sensitive than automated dideoxy sequencing in detecting low BRAF V600E allele burdens in FFPE tumor specimen. The strategy of this ARMS-PCR design may be adapted for early detection of point mutations of a variety of biomarker genes.
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Affiliation(s)
- Tiangui Huang
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
| | - Jian Zhuge
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
| | - Wenyong W Zhang
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
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Zhang J, Zhang LL, Shen L, Xu XM, Yu HG. Regulation of AKT gene expression by cisplatin. Oncol Lett 2013; 5:756-760. [PMID: 23426872 PMCID: PMC3576191 DOI: 10.3892/ol.2013.1132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 12/05/2012] [Indexed: 11/21/2022] Open
Abstract
The use of chemotherapy drugs for the treatment of cancer is an effective therapeutic measure. However, chemoresistance affects the effectiveness of the treatment. AKT overexpression has been observed in chemoresistance. AKT expression in colon cells induced cisplatin resistance. The present study demonstrated the role of reactive oxygen species (ROS) in the induction of AKT regulation by cisplatin through the activation of JAK2/STAT3 at the transcriptional level in colon cancer cells. HCT-116 cells treated with cisplatin exhibited increased JAK2 and STAT3 activities. Reducing the expression of JAK2 in colon cancer cells using small interfering RNA (siRNA) decreased AKT expression. The present study demonstrated that AKT activation is closely associated with chemoresistance in human tumors. The inhibition of ROS decreased the levels of AKT in colon cancer cell lines. The JAK2/STAT3 pathway was also shown to mediate AKT expression and represents a potential target for overcoming cisplatin resistance in human tumors.
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Affiliation(s)
- Jun Zhang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan 430060
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Kaneko Y, Kuramochi H, Nakajima G, Inoue Y, Yamamoto M. Degraded DNA may induce discordance of KRAS status between primary colorectal cancer and corresponding liver metastases. Int J Clin Oncol 2013; 19:113-20. [PMID: 23299277 DOI: 10.1007/s10147-012-0507-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 12/02/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND KRAS mutation is widely accepted as a strong, negative predictive marker for anti-epidermal growth factor receptor antibodies, including cetuximab and panitumumab. Previous reports demonstrated approximately 100 % concordance of KRAS status between primary colorectal cancer and liver metastases; however, mismatched KRAS status still occurs. METHODS KRAS status was evaluated in 105 pairs of formalin-fixed primary colorectal cancer and corresponding liver metastases specimens by direct sequencing. DNA quality of patients displaying mismatched KRAS status between primary tumors and metastases was assessed using a Bioanalyzer. RESULTS KRAS status was successfully analyzed in 90/105 patients (85.7 %). The concordance rate between primary tumors and metastases was 88.2 % in synchronous metastases (n = 76) and 100 % in metachronous metastases (n = 14). Discordance in KRAS status was observed in nine patients. Independent method validation revealed only five samples showed the same KRAS status between the two methods. DNA quality assessment by a Bioanalyzer revealed that the median length of DNA samples in the peak concentration of the mismatched group was significantly shorter than those in the control group (153.5 vs 276.5 bp, P = 0.0059). In addition, the median value of the percentage of degraded DNA (0-200 bp) in each sample in the mismatched group was significantly higher than the control group (35.5 vs 22 %, P = 0.020). These data suggest that the discordant results for these nine patients (18 samples) were due to low quality DNA, which may obscure polymerase chain reaction analysis, affecting sequencing reliability. CONCLUSION Quality control and assurance of KRAS genotyping is critical, and standardization of the methodology is warranted.
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Affiliation(s)
- Yuka Kaneko
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, 8-1 Kawadacho, Shinjuku-ku, Tokyo, Japan
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Ogino S, Fuchs CS, Giovannucci E. How many molecular subtypes? Implications of the unique tumor principle in personalized medicine. Expert Rev Mol Diagn 2012; 12:621-8. [PMID: 22845482 DOI: 10.1586/erm.12.46] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cancers are complex multifactorial diseases. For centuries, conventional organ-based classification system (i.e., breast cancer, lung cancer, colon cancer, colorectal cancer, prostate cancer, lymphoma, leukemia, and so on) has been utilized. Recently, molecular diagnostics has become an essential component in clinical decision-making. However, tumor evolution and behavior cannot accurately be predicted, despite numerous research studies reporting promising tumor biomarkers. To advance molecular diagnostics, a better understanding of intratumor and intertumor heterogeneity is essential. Tumor cells interact with the extracellular matrix and host non-neoplastic cells in the tumor microenvironment, which is influenced by genomic variation, hormones, and dietary, lifestyle and environmental exposures, implicated by molecular pathological epidemiology. Essentially, each tumor possesses its own unique characteristics in terms of molecular make-up, tumor microenvironment and interactomes within and between neoplastic and host cells. Starting from the unique tumor concept and paradigm, we can better classify tumors by molecular methods, and move closer toward personalized cancer medicine and prevention.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
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KRAS mutation analysis in a complex molecular diagnostic referral practice: the need for test redundancy. Pathology 2012; 44:655-7. [PMID: 23172084 DOI: 10.1097/pat.0b013e328359d5ae] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Azizi E, Kittai A, Kozuch P. Antiepidermal growth factor receptor monoclonal antibodies: applications in colorectal cancer. CHEMOTHERAPY RESEARCH AND PRACTICE 2012; 2012:198197. [PMID: 23091721 PMCID: PMC3472558 DOI: 10.1155/2012/198197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/12/2012] [Indexed: 01/19/2023]
Abstract
Patients with metastatic colorectal cancer have a poor prognosis and present a challenge to clinicians. The role of the antiepidermal growth factor receptor (EGFR) pathway in tumorogenesis and tumor progression has been well defined. This paper will review the use of anti-EGFR monoclonal antibodies in the treatment of operable, as well as metastatic colorectal cancer both in the setting of KRAS mutation unselected patients and later in KRAS wild-type patients. Active investigations designed to further identify predictive biomarkers that may be potentially druggable are reviewed as well.
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Affiliation(s)
- Efat Azizi
- Beth Israel Medical Center, Phillips Ambulatory Care Center, Continuum Cancer Centers of New York, 10 Union Square East, Suite 4C, New York, NY, USA ; Section of Hematology/Oncology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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Tan C, Du X. KRAS mutation testing in metastatic colorectal cancer. World J Gastroenterol 2012; 18:5171-80. [PMID: 23066310 PMCID: PMC3468848 DOI: 10.3748/wjg.v18.i37.5171] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/06/2012] [Accepted: 08/04/2012] [Indexed: 02/06/2023] Open
Abstract
The KRAS oncogene is mutated in approximately 35%-45% of colorectal cancers, and KRAS mutational status testing has been highlighted in recent years. The most frequent mutations in this gene, point substitutions in codons 12 and 13, were validated as negative predictors of response to anti-epidermal growth factor receptor antibodies. Therefore, determining the KRAS mutational status of tumor samples has become an essential tool for managing patients with colorectal cancers. Currently, a variety of detection methods have been established to analyze the mutation status in the key regions of the KRAS gene; however, several challenges remain related to standardized and uniform testing, including the selection of tumor samples, tumor sample processing and optimal testing methods. Moreover, new testing strategies, in combination with the mutation analysis of BRAF, PIK3CA and loss of PTEN proposed by many researchers and pathologists, should be promoted. In addition, we recommend that microsatellite instability, a prognostic factor, be added to the abovementioned concomitant analysis. This review provides an overview of KRAS biology and the recent advances in KRAS mutation testing. This review also addresses other aspects of status testing for determining the appropriate treatment and offers insight into the potential drawbacks of mutational testing.
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