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Pancreatic ductal adenocarcinoma: tumor microenvironment and problems in the development of novel therapeutic strategies. Clin Exp Med 2022:10.1007/s10238-022-00886-1. [DOI: 10.1007/s10238-022-00886-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 12/19/2022]
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2
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Kuznetsova AV, Popova OP, Astakhov DA, Ivanov YV, Panchenkov DN, Ivanov AA. [Epithelial-stromal interactions in pancreatic adenocarcinoma: the role of stroma in disease progression]. Arkh Patol 2022; 84:65-70. [PMID: 36178225 DOI: 10.17116/patol20228405165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common and difficult to treat form of pancreas cancer. PDAC and other solid cancers contain both tumor cells and normal connective tissue cells called stromal cells, which are responsible for the excess production of extracellular matrix. It is known that in more than 90% of PDAC tumors and in many other types of cancer, mutations of the KRAS gene are observed, the reciprocal signaling of which has been shown between tumor and stromal cells in vitro. Pancreatic stromal stellate cells are considered precursors of activated or tumor-associated fibroblasts (CAFs), which are an increasing population of cells that proliferate in situ or are recruited into the tumor. CAFs are a heterogeneous population of stromal fibroblasts with different molecular profiles that change during tumorigenesis. Both immunosuppressive and immunosuppressive subsets of CAFs can coexist in the stroma of a single tumor. Based on the heterogeneity of the intertumor stroma, attempts are being made to classify PDAC and predict the course of the disease.
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Affiliation(s)
- A V Kuznetsova
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
- Koltzov Institute of Developmental Biology, Moscow, Russia
| | - O P Popova
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - D A Astakhov
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - Y V Ivanov
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - D N Panchenkov
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - A A Ivanov
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
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3
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Avery JT, Zhang R, Boohaker RJ. GLI1: A Therapeutic Target for Cancer. Front Oncol 2021; 11:673154. [PMID: 34113570 PMCID: PMC8186314 DOI: 10.3389/fonc.2021.673154] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
GLI1 is a transcriptional effector at the terminal end of the Hedgehog signaling (Hh) pathway and is tightly regulated during embryonic development and tissue patterning/differentiation. GLI1 has low-level expression in differentiated tissues, however, in certain cancers, aberrant activation of GLI1 has been linked to the promotion of numerous hallmarks of cancer, such as proliferation, survival, angiogenesis, metastasis, metabolic rewiring, and chemotherapeutic resistance. All of these are driven, in part, by GLI1’s role in regulating cell cycle, DNA replication and DNA damage repair processes. The consequences of GLI1 oncogenic activity, specifically the activity surrounding DNA damage repair proteins, such as NBS1, and cell cycle proteins, such as CDK1, can be linked to tumorigenesis and chemoresistance. Therefore, understanding the underlying mechanisms driving GLI1 dysregulation can provide prognostic and diagnostic biomarkers to identify a patient population that would derive therapeutic benefit from either direct inhibition of GLI1 or targeted therapy towards proteins downstream of GLI1 regulation.
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Affiliation(s)
- Justin T Avery
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
| | - Ruowen Zhang
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States
| | - Rebecca J Boohaker
- Oncology Department, Drug Discovery Division, Southern Research, Birmingham, AL, United States
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4
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Genotyping data of routinely processed matched primary/metastatic tumor samples. Data Brief 2020; 34:106646. [PMID: 33365374 PMCID: PMC7749371 DOI: 10.1016/j.dib.2020.106646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/05/2023] Open
Abstract
Genotypic and phenotypic comparisons of tumors in multiple tissue samples from the same patient are important for understanding disease evolution and treatment possibilities. Panel NGS genotyping is currently widely used in this context, whereby NGS variant filtering and final evaluation constitute the basis for meaningful comparisons. Here, we present the genotype data used for genotype / phenotype comparisons between matched primary / metastatic colorectal tumors in the work by Chatzopoulos et al (doi: 10.1016/j.humpath.2020.10.009), as well as the process followed for obtaining these data. We describe key issues while processing routinely formalin-fixed paraffin-embedded (FFPE) tumors for genotyping, NGS application (Ion Torrent), a stringent variant filtering algorithm for genotype analyses in FFPE tissues and particularly in matched tumor samples, and provide the respective datasets. Apart from research, tumor NGS genotyping is currently applied for clinical diagnostic purposes in Oncology. The datasets and method description provided herein (a) are important for comprehending the peculiarities of FFPE tumor genotyping, which is still mostly based on principles of germline DNA genotyping; (b) can be used in pooled analyses, e.g., of primary / metastatic tumors for the investigation of tumor evolution.
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5
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Linardou H, Kotoula V, Kouvatseas G, Mountzios G, Karavasilis V, Samantas E, Kalogera-Fountzila A, Televantou D, Papadopoulou K, Mavropoulou X, Daskalaki E, Zaramboukas T, Efstratiou I, Lampaki S, Rallis G, Res E, Syrigos KN, Kosmidis PA, Pectasides D, Fountzilas G. Genotyping KRAS and EGFR Mutations in Greek Patients With Non-small-cell Lung Cancer: Incidence, Significance and Implications for Treatment. Cancer Genomics Proteomics 2020; 16:531-541. [PMID: 31659106 DOI: 10.21873/cgp.20155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/15/2019] [Accepted: 09/18/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND/AIM KRAS mutations are reported in 20-25% of non-small cell lung cancer (NSCLC) and their prognostic role is unclear. We studied KRAS and EGFR genotyping in Greek NSCLC patients. PATIENTS AND METHODS KRAS and EGFR genotypes were centrally evaluated in 421 NSCLC patients (diagnosed September 1998 -June 2013) and associated with clinicopathological parameters. Outcome comparisons were performed in 288 patients receiving first line treatment. RESULTS Most patients were male (78.6%), >60 years old (63.9%), current smokers (51.1%), with adenocarcinoma histology (63.9%). EGFR and KRAS mutations were found in 10.7% and 16.6% of all histologies, respectively, and in 14.9% and 21.9% of adenocarcinomas. At 4.5 years median follow-up, KRAS status was an independent negative prognostic factor for overall survival (OS, p=0.016). KRAS mutations conferred 80% increased risk of death in patients receiving first-line treatment (p=0.002). CONCLUSION The presence of KRAS mutations is an independent negative prognosticator among Greek NSCLC patients and an independent response predictor to first line treatment.
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Affiliation(s)
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Giannis Mountzios
- Second Oncology Department, Henry Dunant Hospital Center, Athens, Greece
| | - Vasilios Karavasilis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, Aristotle University of Thessaloniki, School of Health Sciences, Thessaloniki, Greece
| | - Epaminondas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Anna Kalogera-Fountzila
- Department of Radiology, AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Despina Televantou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Xanthipi Mavropoulou
- Department of Radiology, AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Emily Daskalaki
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Thomas Zaramboukas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | | | - Sofia Lampaki
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, Aristotle University of Thessaloniki, School of Health Sciences, Thessaloniki, Greece
| | - Grigorios Rallis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, Aristotle University of Thessaloniki, School of Health Sciences, Thessaloniki, Greece
| | - Eleni Res
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Konstantinos N Syrigos
- Oncology Unit GPP, Sotiria General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Paris A Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
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6
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Pentheroudakis G, Mavroeidis L, Papadopoulou K, Koliou GA, Bamia C, Chatzopoulos K, Samantas E, Mauri D, Efstratiou I, Pectasides D, Makatsoris T, Bafaloukos D, Papakostas P, Papatsibas G, Bombolaki I, Chrisafi S, Kourea HP, Petraki K, Kafiri G, Fountzilas G, Kotoula V. Angiogenic and Antiangiogenic VEGFA Splice Variants in Colorectal Cancer: Prospective Retrospective Cohort Study in Patients Treated With Irinotecan-Based Chemotherapy and Bevacizumab. Clin Colorectal Cancer 2019; 18:e370-e384. [DOI: 10.1016/j.clcc.2019.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/07/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
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7
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Dufraing K, van Krieken JH, De Hertogh G, Hoefler G, Oniscu A, Kuhlmann TP, Weichert W, Marchiò C, Ristimäki A, Ryška A, Scoazec JY, Dequeker E. Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study. Histopathology 2019; 75:312-319. [PMID: 31054167 PMCID: PMC6851675 DOI: 10.1111/his.13891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
Abstract
AIMS Results from external quality assessment revealed considerable variation in neoplastic cell percentages (NCP) estimation in samples for biomarker testing. As molecular biology tests require a minimal NCP, overestimations may lead to false negative test results. We aimed to develop recommendations to improve the NCP determination in a prototypical entity - colorectal carcinoma - that can be adapted for other cancer types. METHODS AND RESULTS A modified Delphi study was conducted to reach consensus by 10 pathologists from 10 countries with experience in determining the NCP for colorectal adenocarcinoma. This study included two online surveys and a decision-making meeting. Consensus was defined a priori as an agreement of > 80%. All pathologists completed both surveys. Consensus was reached for 8 out of 19 and 2 out of 13 questions in the first and second surveys, respectively. Remaining issues were resolved during the meeting. Twenty-four recommendations were formulated. Major recommendations resulted as follows: only pathologists should conduct the morphological evaluation; nevertheless molecular biologists/technicians may estimate the NCP, if specific training has been performed and a pathologist is available for feedback. The estimation should be determined in the area with the highest density of viable neoplastic cells and lowest density of inflammatory cells. Other recommendations concerned: the determination protocol itself, needs for micro- and macro-dissection, reporting and interpreting, referral practices and applicability to other cancer types. CONCLUSION We believe these recommendations may lead to more accurate NCP estimates, ensuring the correct interpretation of test results, and might help in validating digital algorithms in the future.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Anca Oniscu
- Department of Molecular Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Tine P Kuhlmann
- Department of Pathology, Herlev Hospital, Copenhagen, Denmark
| | - Wilko Weichert
- Department of Pathology, Technical University Munich, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin and Pathology Unit, Torino, Italy.,FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aleš Ryška
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | | | - Elisabeth Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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8
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Papaxoinis G, Kotoula V, Giannoulatou E, Koliou GA, Karavasilis V, Lakis S, Koureas A, Bobos M, Chalaralambous E, Daskalaki E, Chatzopoulos K, Tsironis G, Pazarli E, Chrisafi S, Samantas E, Kaklamanos IG, Varthalitis I, Konstantara A, Syrigos KN, Pentheroudakis G, Pectasides D, Fountzilas G. Phase II study of panitumumab combined with capecitabine and oxaliplatin as first-line treatment in metastatic colorectal cancer patients: clinical results including extended tumor genotyping. Med Oncol 2018; 35:101. [PMID: 29855806 DOI: 10.1007/s12032-018-1160-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/27/2018] [Indexed: 12/12/2022]
Abstract
This clinical trial assessed the efficacy and toxicity of panitumumab combined with oxaliplatin and capecitabine as first-line treatment in KRAS exon 2 wild-type metastatic colorectal cancer (mCRC) patients. Patients with exon 2 KRAS wild-type mCRC received panitumumab 9 mg/Kg, oxaliplatin 130 mg/m2, and capecitabine 2000 mg/m2 repeated every 3 weeks. The primary endpoint was objective response rate (ORR, minimum 42 responses). We retrospectively assessed mutations in genes implicated in CRC with massively parallel sequencing; ERBB2 and EGFR amplification with fluorescence in situ hybridization, and tumor-infiltrating lymphocyte density. Among 78 patients enrolled, 45 (57.7%) completed 6 cycles. Most common grade 3-4 toxicities were skin rash (19.2%), diarrhea (18%), and neuropathy (6.4%). Among 5 (6.4%) potentially treatment-related deaths, 2 (2.6%) were characterized toxic. Objective response occurred in 43 (55.1%) of the patients (complete 6.4% and partial response 48.7%; stable 17.9% and progressive disease 7.7%), while 3.8% were non-evaluable and 15% discontinued their treatment early. Additional mutations in KRAS/NRAS/BRAF were found in 11/62 assessable (18%) tumors. After 51 months median follow-up, median progression-free (PFS) was 8.1 and overall survival 20.2 months, independently of KRAS/NRAS/BRAF or PI3K-pathway mutation status. Patients with TP53 mutations (n = 34; 55%), as well as those with left colon primary tumors (n = 66; 85%), had significantly better PFS, also confirmed in multivariate analysis. Although the clinical trial met its primary endpoint, according to the current standards, the efficacy and tolerability of the drug combination are considered insufficient. Extended genotyping yielded interesting results regarding the significance of TP53 mutations.ClinicalTrials.gov identifier: NCT01215539, Registration date: Sep 29, 2010.
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Affiliation(s)
- George Papaxoinis
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, 11527, Athens, Greece.
| | - Vassiliki Kotoula
- Department of Pathology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | | | - Vasilios Karavasilis
- Department of Medical Oncology, Faculty of Medicine, School of Health Sciences, Papageorgiou Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotirios Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Koureas
- Department of Radiology, Aretaieio Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elpida Chalaralambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Emily Daskalaki
- Department of Pathology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George Tsironis
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Elisavet Pazarli
- Department of Pathology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Epaminontas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Ioannis G Kaklamanos
- Department of Surgery, School of Health Sciences, General Oncologic Hospital of Kifisia, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Konstantinos N Syrigos
- Oncology Unit GPP, Sotiria General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, 11527, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
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9
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Papadopoulou K, Murray S, Manousou K, Tikas I, Dervenis C, Sgouros J, Rontogianni D, Lakis S, Bobos M, Poulios C, Pervana S, Lazaridis G, Fountzilas G, Kotoula V. Genotyping and mRNA profiling reveal actionable molecular targets in biliary tract cancers. Am J Cancer Res 2018; 8:2-15. [PMID: 29416916 PMCID: PMC5794717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/13/2017] [Indexed: 06/08/2023] Open
Abstract
Biliary tract cancer (BTC) represents a heterogeneous disease with dismal outcome. Herein, we examined genotype and angiogenesis features in BTC. We applied genotyping (Sanger, qPCR, 101-gene panel NGS), mRNA relative quantification methods, and β-catenin immunohistochemistry in 84 FFPE BTC (55 gallbladder [GBC], 14 intrahepatic [ICC], 15 extrahepatic [ECC] carcinomas). We identified 541 mutations in 68 (81%) tumors. Top mutated genes were CTNNB1 (36%); PTEN (33%); TP53 (31%); PIK3R1 (29%); PIK3CA (13%); BRCA2 and KRAS (12%); BRCA1 (11%). Six GBCs were hypermutated [hm] displaying a distinct mutational pattern. Mutations in TP53 and PI3K, Wnt and RAS components were prevalent among non-hypermutated tumors. All hmGBCs carried mutations in BRCA2 and other homologous recombination repair (HRR) genes, in PD1, but not in CTNNB1 and KRAS. None of the pathogenic BRCA2 p.D2723G and BRCA1 p.Q563* and c.5266dupC was present at frequencies expected for germline mutations. We observed copy gains (>6 copies) in EGFR (9% of informative tumors), PRKAR1A (7%), PIK3CA (6%), ERBB2 (5%) and MET (4%). TP53 mutations were prevalent in GBC (P<0.001) and PRKAR1A copy gains in ICC (P=0.007). PTEN was frequently co-mutated with CTNNB1 (P<0.001). Unrelated to CTNNB1 mutations, nuclear β-catenin was detected in 45% of tumors, among them in 5/6 hmGBC. We observed strong mRNA expression correlation of the two neuropilins (NRP1 and NRP2) with each other (Spearman's rho 0.59) and with the endothelin receptor (NRP2 rho 0.66; NRP2 rho 0.51), and between VEGFA and its receptors (FLT1 rho 0.49; KDR rho 0.45). All PIK3CA mutated tumors expressed endothelin 1 mRNA (P=0.010). Most tumors expressing nuclear β-catenin were negative for VEGFC (P=0.009) and FLT4 (P=0.002) mRNA expression. In conclusion, we confirmed the presence of known genomic aberrations in BTC and different genotypes between BTC subsets. Novel findings are the coexistence of PI3K and WNT pathway gene alterations in BTC, their association with angiogenesis, and the hypermutated GBCs with HRR gene mutations, all of which may be considered for new treatment options in this difficult to treat disease.
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Affiliation(s)
- Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | | | - Kyriaki Manousou
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data OfficeAthens, Greece
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Christos Dervenis
- First Department of Surgery, General Hospital Konstantopouleio Agia OlgaAthens, Greece
| | - Joseph Sgouros
- Third Department of Medical Oncology, Agii Anargiri Cancer HospitalAthens, Greece
| | | | - Sotirios Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | | | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
- Aristotle University of ThessalonikiThessaloniki, Greece
| | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
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10
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Fountzilas G, Giannoulatou E, Alexopoulou Z, Zagouri F, Timotheadou E, Papadopoulou K, Lakis S, Bobos M, Poulios C, Sotiropoulou M, Lyberopoulou A, Gogas H, Pentheroudakis G, Pectasides D, Koutras A, Christodoulou C, Papandreou C, Samantas E, Papakostas P, Kosmidis P, Bafaloukos D, Karanikiotis C, Dimopoulos MA, Kotoula V. TP53 mutations and protein immunopositivity may predict for poor outcome but also for trastuzumab benefit in patients with early breast cancer treated in the adjuvant setting. Oncotarget 2017; 7:32731-53. [PMID: 27129168 PMCID: PMC5078047 DOI: 10.18632/oncotarget.9022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/28/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We investigated the impact of PIK3CA and TP53 mutations and p53 protein status on the outcome of patients who had been treated with adjuvant anthracycline-taxane chemotherapy within clinical trials in the pre- and post-trastuzumab era. RESULTS TP53 and PIK3CA mutations were found in 380 (21.5%) and 458 (25.9%) cases, respectively, including 104 (5.9%) co-mutated tumors; p53 immunopositivity was observed in 848 tumors (53.5%). TP53 mutations (p < 0.001) and p53 protein positivity (p = 0.001) were more frequent in HER2-positive and triple negative (TNBC) tumors, while PIK3CA mutations were more frequent in Luminal A/B tumors (p < 0.001). TP53 mutation status and p53 protein expression but not PIK3CA mutation status interacted with trastuzumab treatment for disease-free survival; patients with tumors bearing TP53 mutations or immunopositive for p53 protein fared better when treated with trastuzumab, while among patients treated with trastuzumab those with the above characteristics fared best (interaction p = 0.017 for mutations; p = 0.015 for IHC). Upon multivariate analysis the above interactions remained significant in HER2-positive patients; in the entire cohort, TP53 mutations were unfavorable in patients with Luminal A/B (p = 0.003) and TNBC (p = 0.025); p53 immunopositivity was strongly favorable in patients treated with trastuzumab (p = 0.009). MATERIALS AND METHODS TP53 and PIK3CA mutation status was examined in 1766 paraffin tumor DNA samples with informative semiconductor sequencing results. Among these, 1585 cases were also informative for p53 protein status assessed by immunohistochemistry (IHC; 10% positivity cut-off). CONCLUSIONS TP53 mutations confer unfavorable prognosis in patients with Luminal A/B and TNBC tumors, while p53 immunopositivity may predict for trastuzumab benefit in the adjuvant setting.
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Affiliation(s)
- George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, NSW, Australia
| | - Zoi Alexopoulou
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, "Alexandra" Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Eleni Timotheadou
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | | | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Helen Gogas
- First Department of Medicine, "Laiko" General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, "Hippokration" Hospital, Athens, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | | | - Christos Papandreou
- Department of Medical Oncology, University Hospital of Larissa, University of Thessaly School of Medicine, Larissa, Greece
| | - Epaminontas Samantas
- Third Department of Medical Oncology, "Agii Anargiri" Cancer Hospital, Athens, Greece
| | | | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | | | | | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
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Teerapakpinyo C, Wanthong P, Aumchaaumchaya M, Chankate P, Kaikeaw W, Tosakorn W, Shaungshoti S. Pyrosequencing analysis of KRAS codon 61 mutations in Thai patients with advanced colorectal cancer. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0901.369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background
KRAS, coding for a small G-protein downstream of epidermal growth factor receptor (EGFR) plays an important role in the EGFR signaling network. Mutation in KRAS is associated with resistance to anti-EGFR in patients with advanced colorectal cancer (CRC). According to the American Society of Clinical Oncology (ASCO) guidelines, screening for mutations in KRAS codons 12 and 13 in tumor samples is mandatory for all CRC patients who are candidates for anti-EGFR targeted therapy. However, some patients with undetectable mutations in codons 12/13 do not benefit from anti-EGFR treatment, and this might be because of mutations in codon 61, which is not currently recommended for screening.
Objectives
To develop an in-house pyrosequencing method to screen for KRAS codon 61 mutations, and examine the prevalence of mutations in Thai patients with advanced CRC with no detectable mutation in codons 12/13.
Materials and Methods
DNA extracted from FFPE specimens was screened for KRAS codon 61 mutations using pyrosequencing. Our method was suitable for routine clinical samples (formalin-fixed, paraffin-embedded tissue), and was able to detect 5 common mutations in codon 61 of the KRAS gene, including c.182AT (p.Q61L), c.182AG (p.Q61R), c.182AC (p.Q61P), c.183AC (p.Q61H), and c.183AT (p.Q61H).
Results
Of the 74 samples with undetectable codon 12/13 mutation examined, two (2.7%) were found to harbor mutation in codon 61.
Conclusion
Despite the low prevalence of KRAS codon 61 mutation in our population with advanced CRC, adding the mutation test into the routine molecular service deserves consideration because the cost of treatment is very expensive.
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Affiliation(s)
- Chinachote Teerapakpinyo
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Phanni Wanthong
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Mathawee Aumchaaumchaya
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Piyamai Chankate
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Warisa Kaikeaw
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Warunya Tosakorn
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
| | - Shanop Shaungshoti
- Chula GenePRO Center, Research Affairs , Faculty of Medicine , Chulalongkorn University , Bangkok 10330 , Thailand
- Department of Pathology , Faculty of Medicine, Chulalongkorn University , Bangkok 10330 , Thailand
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12
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Skougaard K, Nielsen D, Jensen BV, Pfeiffer P, Hendel HW. Early 18F-FDG-PET/CT as a predictive marker for treatment response and survival in patients with metastatic colorectal cancer treated with irinotecan and cetuximab. Acta Oncol 2016; 55:1175-1182. [PMID: 27548393 DOI: 10.3109/0284186x.2016.1170197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND To clarify if early reduction in standard uptake value (SUV) could predict metabolic response, radiologic response and overall survival (OS) in patients with metastatic colorectal cancer receiving third-line treatment. MATERIAL AND METHODS Patients were regardless of KRAS status, included in this phase II trial. They were treated with the monoclonal antibody, cetuximab, and the chemotherapeutic drug, irinotecan, every second week. A F18-fluorodeoxy glucose positron emission tomography/computed tomography (FDG-PET/CT) was scheduled before the first and second treatment, respectively, and then after every fourth treatment. Early metabolic response after one treatment and best overall metabolic response was calculated according to EORTC criteria (responders: ≥15% decrease in ∑SUVmax) and PERCIST (responders: ≥30% decrease in SULpeak). Best overall radiologic response was calculated according to RECIST 1.0. RESULTS By EORTC criteria, early metabolic response predicted partial metabolic response (PMR) with a high positive predictive value (PPV) of 0.875 and a high negative predictive value (NPV) of 0.714. Partial radiologic response was predicted with a low PPV of 0.368 but a high NPV of 1.0. By PERCIST, PMR was predicted with a high PPV of 0.826 and an intermediate NPV of 0.667 and partial radiologic response was predicted with a low PPV of 0.5 but a high NPV of 1.0. Median OS was nearly the same with the two criteria sets; 14.1 months for early metabolic responders and 9.9 months for non-responders using EORTC criteria and 13.5 and 10.1 months, respectively, using PERCIST. CONCLUSIONS With both EORTC criteria and PERCIST, early reduction in FDG uptake was predictive of a later partial metabolic and partial radiologic response to treatment. It was also predictive of significantly longer survival of early metabolic responders compared to non-responders. However, the sensitivities and specificities were not high enough to support clinical routine use.
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Affiliation(s)
- Kristin Skougaard
- Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Dorte Nielsen
- Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | | | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
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13
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Cernomaz AT, Macovei II, Pavel I, Grigoriu C, Marinca M, Baty F, Peter S, Zonda R, Brutsche M, Grigoriu BD. Comparison of next generation sequencing, SNaPshot assay and real-time polymerase chain reaction for lung adenocarcinoma EGFR mutation assessment. BMC Pulm Med 2016; 16:88. [PMID: 27215400 PMCID: PMC4877937 DOI: 10.1186/s12890-016-0250-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The epidermal growth factor receptor (EGFR) mutation status assessment has become increasingly important given the significant impact of tyrosine kinase inhibitors in lung cancer management. Our aim was to compare real life operational characteristics for three EGFR mutation assays - two targeted approaches and a next generation sequencing (NGS) technique. METHODS EGFR mutation status was assessed for lung adenocarcinoma samples (formalin fixed- paraffin embedded samples) using qPCR, SNaPshot and NGS (Ion Torrent™) techniques. RESULTS A total of 15 high clinical significance mutations were identified by at least one technique from the total of 64 samples. All mutations were identified by the TaqMan qPCR technique while SNaPshot in conjunction with fragment analysis identified 11 EGFR mutations. The NGS approach followed by an automatic analysis using the default calling parameters identified 10 mutations from the SNaPshot/qPCR panel and other three insertions, five point mutations and 58 silent variants; manual data review identified all 15 high significance mutations. CONCLUSIONS Performance was similar for high tumor content samples but careful data analysis and post hoc variant calling filter alterations were necessary in order to obtain robust results from low tumor content samples by NGS. NGS is able to generate a comprehensive mutational profile albeit at a higher cost and workload. Result interpretation should take into account not only general run parameters such as mean read depth but also relative coverage and read distribution; currently there is an acute need to define firm recommendations/standards concerning NGS data interpretation and quality control.
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Affiliation(s)
- Andrei-Tudor Cernomaz
- Department of Thoracic Oncology, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Str. Gen. Berthelot, 2-4, Iasi, 700384, Romania
| | - Ina Iuliana Macovei
- Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Ionut Pavel
- Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Carmen Grigoriu
- Pathology Department, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Mihai Marinca
- Oncology Department, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Florent Baty
- Department of Pulmonary Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Simona Peter
- Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Radu Zonda
- Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania
| | - Martin Brutsche
- Department of Pulmonary Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Bogdan- Dragos Grigoriu
- Department of Thoracic Oncology, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Str. Gen. Berthelot, 2-4, Iasi, 700384, Romania. .,Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania.
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14
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High-throughput RNAi screening of human kinases identifies predictors of clinical outcome in colorectal cancer patients treated with oxaliplatin. Oncotarget 2016; 6:16774-85. [PMID: 25904054 PMCID: PMC4599307 DOI: 10.18632/oncotarget.3736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/01/2015] [Indexed: 12/15/2022] Open
Abstract
The purpose of this study is to identify protein kinase genes that modulate oxaliplatin cytotoxicity in vitro and evaluate the roles of these genes in predicting clinical outcomes in CRC patients receiving oxaliplatin-based adjuvant chemotherapy. A high-throughput RNAi screening targeting 626 human kinase genes was performed to identify kinase genes whose inhibition potentiates oxaliplatin sensitivity in CRC cells. The associations between copy numbers of the candidate genes and recurrence-free survival and overall survival were analyzed in 142 stage III CRC patients receiving first-line oxaliplatin-based adjuvant chemotherapy who were enrolled from two independent hospitals. HT-RNAi screening identified 40 kinase genes whose inhibition potentiated oxaliplatin cytotoxicity in DLD1 cells. The relative copy number (RCN) of MAP4K1 and CDKL4 were associated with increased risks of both recurrence and death. Moreover, significant genes-based risk score and the ratios of RCN of different genes can further categorize patients into subgroups with distinctly differing outcomes. The estimated AUC for the prediction models including clinical variables plus kinase biomarkers was 0.77 for the recurrence and 0.82 for the survival models. The copy numbers of MAP4K1 and CDKL4 can predict clinical outcomes in CRC patients treated with oxaliplatin-based chemotherapy.
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KRAS G12D Mutation Subtype Is A Prognostic Factor for Advanced Pancreatic Adenocarcinoma. Clin Transl Gastroenterol 2016; 7:e157. [PMID: 27010960 PMCID: PMC4822095 DOI: 10.1038/ctg.2016.18] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/12/2016] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES There is no molecular biomarker available in the clinical practice to assess the prognosis of advanced pancreatic carcinoma. This multicenter prospective study aimed to investigate the role of KRAS mutation subtypes within the primary tumor to determine the prognosis of advanced pancreatic cancer. METHODS The exon-2 KRAS mutation status was tested on endoscopic ultrasound-guided fine-needle aspiration biopsy material (primary tumor; restriction fragment-length polymorphism plus sequencing and TaqMan allelic discrimination) of patients with proven locally advanced and/or metastatic pancreatic ductal carcinoma. We used the Kaplan-Meier method, log-rank test, and Cox's model to evaluate the impact of KRAS status on the overall survival (OS), adjusting for age, stage of disease, clinical performance status, CA 19-9 levels, and treatment. RESULTS A total of 219 patients (men: 116; mean age: 67±9.4 years) were included: 147 harbored a codon-12 KRAS mutation (G12D: 73; G12V: 53; G12R: 21) and 72 had a wild-type KRAS. There was no difference in the OS between patients with a mutant KRAS (8 months; 95% confidence interval (95% CI): 8.7-12.3) and the wild-type (9 months; 95% CI: 8.7-12.8; hazard ratio (HR): 1.03; P=0.82). However, the patients with a G12D mutation had a significantly shorter OS (6 months; 95% CI: 6.4-9.7) compared with the other patients (OS: 9 months; 95% CI: 10-13; HR: 1.47; P=0.003; i.e., wild type: 9 months, G12V: 9 months, G12R: 14 months). Similar results were observed in the subgroup of 162 patients who received chemotherapy (HR: 1.66; P=0.0013; G12D (n=49): 8 months, wild type (n=56): 10 months, G12V (n=38): 10 months, G12R (n=19): 14 months). Multivariate analyses identified KRAS G12D as an independent predictor for worse prognosis within the entire series (HR: 1.44; P=0.01) and in the subgroup of patients that received chemotherapy (HR: 1.84; P=0.02). CONCLUSIONS The KRAS G12D mutation subtype is an independent prognostic marker for advanced pancreatic ductal carcinoma. Codon and amino-acid-specific mutations of KRAS should be considered when evaluating the prognoses as well as in trials testing drugs that target RAS and downstream RAS pathways.
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Bournet B, Buscail C, Muscari F, Cordelier P, Buscail L. Targeting KRAS for diagnosis, prognosis, and treatment of pancreatic cancer: Hopes and realities. Eur J Cancer 2016; 54:75-83. [DOI: 10.1016/j.ejca.2015.11.012] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/08/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023]
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Assessment of the total cfDNA and HPV16/18 detection in plasma samples of head and neck squamous cell carcinoma patients. Oral Oncol 2016; 54:36-41. [PMID: 26786940 DOI: 10.1016/j.oraloncology.2015.12.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 12/08/2015] [Accepted: 12/21/2015] [Indexed: 01/08/2023]
Abstract
OBJECTIVES The advantages of the circulating cell-free DNA (cfDNA) methodology are quick results and the possibility of repeated analysis. The main aim of our study was to establish the relationship of the total cfDNA with patients' clinical characteristics and circulating HPV DNA detection in the blood of patients with head and neck squamous cell carcinoma (HNSCC). METHODS The cfDNA level of 200 HNSCC patients in plasma was quantified using TaqMan-based TERT amplification. TaqMan technology was also used for HPV16/18 detection. Additionally, mutations in KRAS and EGFR were investigated. RESULTS A higher level (p=0.011) of the total cfDNA was found in patients with oropharyngeal squamous cell carcinoma (OPSCC) (9.60 ± 6.23 ng/ml) in comparison with other HNSCC (7.67 ± 4.44 ng/ml). The level of cfDNA in patients with clinical N2-N3 disease (9.28 ± 6.34 ng/ml) was (p=0.015) higher than in patients with a clinical N0-N1 disease (7.50 ± 3.69 ng/ml). It was also higher in patients with stage IV (9.16 ± 6.04 ng/ml) compared with stages I-III of cancer (7.26 ± 3.63 ng/ml) (p=0.011). Analysis of HPV16/18 in plasma revealed that 14% of patients were HPV-positive, the majority of whom had the type HPV16 (96.4%). CfDNA level was comparable in HPV-positive and HPV-negative HNSCC patients, as well in the OPSCC subgroup. Somatic mutations in EGFR and KRAS were not found. CONCLUSIONS A high level of cfDNA is specific for patients with OPSCC. HPV detection in cfDNA does not depend on the cfDNA concentration. Our results prove the diagnostic potential of plasma-based HPV cfDNA tests for the early detection and monitoring of HPV-positive HNSCC.
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Kriegsmann M, Arens N, Endris V, Weichert W, Kriegsmann J. Detection of KRAS, NRAS and BRAF by mass spectrometry - a sensitive, reliable, fast and cost-effective technique. Diagn Pathol 2015; 10:132. [PMID: 26220423 PMCID: PMC4518505 DOI: 10.1186/s13000-015-0364-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND According to current clinical guidelines mutational analysis for KRAS and NRAS is recommended prior to EGFR-directed therapy of colorectal cancer (CRC) in the metastatic setting. Therefore, reliable, fast, sensitive and cost-effective methods for routine tissue based molecular diagnostics are required that allow the assessment of the CRC mutational status in a high throughput fashion. METHODS We have developed a custom designed assay for routine mass-spectrometric (MS) (MassARRAY, Agena Bioscience) analysis to test the presence/absence of 18 KRAS, 14 NRAS and 4 BRAF mutations. We have applied this assay to 93 samples from patients with CRC and have compared the results with Sanger sequencing and a chip hybridization assay (KRAS LCD-array Kit, Chipron). In cases with discordant results, next-generation sequencing (NGS) was performed. RESULTS MS detected a KRAS mutation in 46/93 (49%), a NRAS mutation in 2/93 (2%) and a BRAF mutation in 1/93 (1%) of the cases. MS results were in agreement with results obtained by combination of the two other methods in 92 (99%) of 93 cases. In 1/93 (1%) of the cases a G12V mutation has been detected by Sanger sequencing and MS, but not by the chip assay. In this case, NGS has confirmed the G12V mutation in KRAS. CONCLUSIONS Mutational analysis by MS is a reliable method for routine diagnostic use, which can be easily extended for testing of additional mutations.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | | | - Volker Endris
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | - Wilko Weichert
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
- National Center of Tumor Diseases, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Jörg Kriegsmann
- Institute of Molecular Pathology, Trier, Germany.
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany.
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Kotoula V, Lyberopoulou A, Papadopoulou K, Charalambous E, Alexopoulou Z, Gakou C, Lakis S, Tsolaki E, Lilakos K, Fountzilas G. Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA. PLoS One 2015; 10:e0128818. [PMID: 26039550 PMCID: PMC4454570 DOI: 10.1371/journal.pone.0128818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AIM Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. METHODS Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. RESULTS Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman's rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8-99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1-95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3-76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. CONCLUSIONS Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.
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Affiliation(s)
- Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- Department of Pathology, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- * E-mail:
| | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | | | - Chryssa Gakou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Konstantinos Lilakos
- Department of Haematology, “Laikon” General Hospital, University of Athens Medical School, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
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Park YS, Na YS, Ryu MH, Lee CW, Park HJ, Lee JK, Park SR, Ryoo BY, Kang YK. FGFR2 Assessment in Gastric Cancer Using Quantitative Real-Time Polymerase Chain Reaction, Fluorescent In Situ Hybridization, and Immunohistochemistry. Am J Clin Pathol 2015; 143:865-72. [PMID: 25972329 DOI: 10.1309/ajcpnflsmwwpp8dr] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES Fibroblast growth factor receptor 2 (FGFR2) amplification has been reported to be a target for treatment in gastric cancer. However, an optimal tissue source and method for evaluating FGFR2 have yet to be established. METHODS Copy numbers were compared by quantitative polymerase chain reaction (qPCR) using frozen vs formalin-fixed, paraffin-embedded (FFPE) tissue and biopsy vs surgical specimens. We correlated the results of qPCR and immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) using stage IV gastric cancer biopsy specimens and validated the results in surgical specimens. RESULTS FFPE tissues were suitable for qPCR, and biopsy specimens were equivalent to or better than surgical specimens. qPCR and IHC results exhibited an excellent correlation with FISH at eight or more copies by qPCR in any kind of tissue, 5% or more by IHC in biopsy specimens, and 10% or more by IHC in surgical specimens. FGFR2 amplification was 6.6% in stage IV gastric cancers, and 42% of these showed heterogeneous amplification and overexpression. IHC indicated a good correlation with FISH even in the heterogeneous cases. CONCLUSIONS FFPE biopsy tissues are an adequate source for FGFR2 evaluation in gastric carcinomas, and a qPCR-based copy number assay can be used for screening. IHC is also a valid and practical method for evaluating FGFR2, considering frequent heterogeneity.
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Affiliation(s)
- Young Soo Park
- Department of Pathology, University of Ulsan College of Medicine, Republic of Korea
| | - Young-Soon Na
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Chae-Won Lee
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Hye Jin Park
- Department of Pathology, University of Ulsan College of Medicine, Republic of Korea
| | - Ju-Kyung Lee
- Asan Institute for Life Science, University of Ulsan College of Medicine, Republic of Korea
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Baek-Yeol Ryoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
| | - Yoon-Koo Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Republic of Korea
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Lu R, Shao J, Zhou M, Zhang H, Wu Y. Accurate Detection of Hepatitis B Virus G1896A Mutant by Developed Taqman-ARMS Followed a Strict Control System. J Clin Lab Anal 2015; 30:315-8. [PMID: 25968238 DOI: 10.1002/jcla.21857] [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: 02/12/2014] [Accepted: 04/07/2015] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) G1896A mutation was associated with HBeAg seronegativity and hepatitis B related acute-on-chronic liver failure. In this study, we developed Taqman amplification refractory mutation system (Taqman-ARMS) and established a strict control system to detect HBV G1896A mutant. METHODS HBV viral DNA was isolated from 60 patient serum samples, and full-length HBV genome was cloned. Then, Taqman-ARMS was used to detect HBV G1896A mutant. RESULTS The assay has the sensitivity of 1E+3 IU/ml G1896A template, and 0.1% weak population virus with G1896A could be found in mixtures. Total of all 60 clinical samples random collected were detected by Taqman-ARMS, the results were consistent with those by DNA sequencing. CONCLUSION The proposed Taqman-ARMS real-time PCR method for the detection of G1896A mutation of HBV was rapid, simple, sensitive, specific, and applicable in the clinical setting.
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Affiliation(s)
- Renfei Lu
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
| | - Jianguo Shao
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
| | - Min Zhou
- Nantong Center for Disease Control and Prevention, Nantong, Jiangsu, P. R., China
| | - Hongping Zhang
- Nantong Center for Disease Control and Prevention, Nantong, Jiangsu, P. R., China
| | - Yueping Wu
- Department of Laboratory, The Third People's Hospital of Nantong, Nantong, Jiangsu, P. R., China
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Automated objective determination of percentage of malignant nuclei for mutation testing. Appl Immunohistochem Mol Morphol 2015; 22:363-71. [PMID: 24162261 DOI: 10.1097/pai.0b013e318299a1f6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Detection of DNA mutations in tumor tissue can be a critical companion diagnostic test before prescription of a targeted therapy. Each method for detection of these mutations is associated with an analytic sensitivity that is a function of the percentage of tumor cells present in the specimen. Currently, tumor cell percentage is visually estimated resulting in an ordinal and highly variant result for a biologically continuous variable. We proposed that this aspect of DNA mutation testing could be standardized by developing a computer algorithm capable of accurately determining the percentage of malignant nuclei in an image of a hematoxylin and eosin-stained tissue. Using inForm software, we developed an algorithm, to calculate the percentage of malignant cells in histologic specimens of colon adenocarcinoma. A criterion standard was established by manually counting malignant and benign nuclei. Three pathologists also estimated the percentage of malignant nuclei in each image. Algorithm #9 had a median deviation from the criterion standard of 5.4% on the training set and 6.2% on the validation set. Compared with pathologist estimation, Algorithm #9 showed a similar ability to determine percentage of malignant nuclei. This method represents a potential future tool to assist in determining the percent of malignant nuclei present in a tissue section. Further validation of this algorithm or an improved algorithm may have value to more accurately assess percentage of malignant cells for companion diagnostic mutation testing.
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Dudley JC, Gurda GT, Tseng LH, Anderson DA, Chen G, Taube JM, Gocke CD, Eshleman JR, Lin MT. Tumor cellularity as a quality assurance measure for accurate clinical detection of BRAF mutations in melanoma. Mol Diagn Ther 2015; 18:409-18. [PMID: 24604154 DOI: 10.1007/s40291-014-0091-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Detection of BRAF mutations is an established standard of care to predict small-molecule inhibitor (vemurafenib) response in metastatic melanoma. Molecular assays should be designed to detect not only the most common p.V600E mutation, but also p.V600K and other non-p.V600E mutations. OBJECTIVE The purpose of this study was to assess if tumor cellularity can function as a quality assurance (QA) measure in molecular diagnostics. Potential causes of discrepancy between the observed and predicted mutant allele percentage were also explored. METHODS We correlated pathologist-generated estimates of tumor cellularity versus mutant allele percentage via pyrosequencing as a QA measure for BRAF mutation detection in formalin-fixed, paraffin-embedded melanoma specimens. RESULTS BRAF mutations were seen in 27/62 (44 %) specimens, with 93 % p.V600E and 7 % non-p.V600E. Correlation between p.V600E mutant percentage and tumor cellularity was poor-moderate (r = -0.02; p = 0.8), primarily because six samples showed a low p.V600E signal despite high tumor cellularity. A QA investigation revealed that our initial pyrosequencing assay showed a false positive, weak p.V600E signal in specimens with a p.V600K mutation. A redesigned assay detected BRAF mutations in 50/131 (38 %) specimens, including 30 % non-p.V600E. This revised assay showed strong correlation between p.V600E BRAF mutant percentage and tumor cellularity (r = 0.76; p ≤ 0.01). Re-evaluation of the previously discordant samples by the revised assay confirmed a high level of p.V600K mutation in five specimens. CONCLUSIONS Pathologists play important roles in molecular diagnostics, beyond identification of correct cells for testing. Accurate evaluation of tumor cellularity not only ensures sufficient material for required analytic sensitivity, but also provides an independent QA measure of the molecular assays.
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Affiliation(s)
- Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Park SB202, 600 North Wolfe St., Baltimore, MD, 21287, USA
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Li A, Chen H, Lin M, Zhang C, Tang E, Peng J, Wei Q, Li H, Yin L. PIK3C2G copy number is associated with clinical outcomes of colorectal cancer patients treated with oxaliplatin. Int J Clin Exp Med 2015; 8:1137-1143. [PMID: 25785104 PMCID: PMC4358559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
PURPOSE To investigate whether the copy number of PIK3C2G is associated with clinical outcomes for stage III colorectal cancer (CRC) patients treated with oxaliplatin-based chemotherapy. METHODS A total of 142 CRC patients who received first-line oxaliplatin-based chemotherapy after curative surgery in Ruijin Hospital and The Tenth People's Hospital were recruited in this study. Patients were enrolled between June 2006 and December 2011, with follow-up to January 2014. Quantitative real-time PCR method was used to detect the copy number of PIK3C2G. Cox proportional hazards model and Kaplan-Meier curves were used to analyze the association between PIK3C2G copy number and clinical outcome. RESULTS In patients with stage III disease, low copy number of PIK3C2G was associated with increased risk of both recurrence (HR, 2.44, 95% CI, 1.33-4.47, P=0.004) and death (HR, 2.89, 95% CI, 1.49-5.60, P=0.002). Multivariate analysis also indicated that low PIK3C2G copy number was a significant and independent predictor of OS and RFS of stage III CRC. CONCLUSIONS PIK3C2G is capable of predicting the recurrence and overall survival of stage III CRC patients receiving oxaliplatin-based therapy.
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Affiliation(s)
- Ajian Li
- Department of General Surgery, Ruijin Hospital Affiliated Shanghai Jiaotong University School of MedicineShanghai 200025, China
| | - Hui Chen
- Department of General Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 200437, China
| | - Moubin Lin
- Department of General Surgery, Ruijin Hospital Affiliated Shanghai Jiaotong University School of MedicineShanghai 200025, China
| | - Chenbo Zhang
- Department of General Surgery, Ruijin Hospital Affiliated Shanghai Jiaotong University School of MedicineShanghai 200025, China
| | - Erjiang Tang
- Department of General Surgery, Yangpu Hospital Affiliated to Shanghai Tongji University School of MedicineShanghai 200090, China
| | - Jian Peng
- Center for Translational Medicine, Yangpu Hospital Affiliated to Shanghai Tongji University School of MedicineShanghai 200090, China
| | - Qing Wei
- Department of Pathology, The Tenth People’s Hospital Affiliated to Shanghai Tongji University School of MedicineShanghai 200072, China
| | - Huaguang Li
- Department of General Surgery, Yangpu Hospital Affiliated to Shanghai Tongji University School of MedicineShanghai 200090, China
| | - Lu Yin
- Department of General Surgery, Ruijin Hospital Affiliated Shanghai Jiaotong University School of MedicineShanghai 200025, China
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Dufresne A, Alberti L, Brahmi M, Kabani S, Philippon H, Pérol D, Blay JY. Impact of KIT exon 10 M541L allelic variant on the response to imatinib in aggressive fibromatosis: analysis of the desminib series by competitive allele specific Taqman PCR technology. BMC Cancer 2014; 14:632. [PMID: 25174682 PMCID: PMC4161827 DOI: 10.1186/1471-2407-14-632] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aggressive fibromatosis (AF) is a rare fibroblastic proliferative disease with a locally aggressive behavior and no distant metastasis, characterized by driver mutations in CTNNB1 or the APC gene. When progressive and/or symptomatic AF is not amenable to local management, a variety of medical treatments may be efficient, including imatinib mesylate. The phase II "Desminib trial" included 40 patients with AF to evaluate the toxicity and efficacy of imatinib resulting in a 65% tumor control rate at 1 year. We investigated a potential predictive value of KIT exon 10 M541L variant (KITL541) on this prospective series. METHODS DNA was extracted in sufficient quantity from 33 patients included in the Desminib trial. The detection of KITL541 was performed by Competitive Allele-Specific Taqman® PCR technology. Chi-2 analyses were performed to search for a correlation between KIT status and tumor response. Progression free (PFS) and overall survival (OS) were compared by log-rank test after Kaplan-Meier analysis. RESULTS In 6 out of 33 cases (18%), the technique failed to determine the mutational status; 5 patients (19%) harboured KITL541 and 22 patients (81%) were classified as KIT wild type. Compared with total cohort, KITL541 frequency did not distinguish between different clinical characteristics. In the KITL541 and the KITWT subgroups, the tumor control rate at 1 year was 100% and 68%, respectively (p = 0.316). The median PFS of patients harboring KITL541 or not is 29.9 and 24.5 months, respectively (p = 0.616), and the median OS is not reached, in any of the groups. CONCLUSION Our results do not support a predictive effect of KITL541 on the efficacy of imatinib for patients with AF.
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Affiliation(s)
- Armelle Dufresne
- Cancer Research Center of Lyon, INSERM UMR 1052, CNRS UMR 5286, Centre Leon Berard, 28 rue Laënnec, Lyon, France.
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26
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Schou JV, Rossi S, Jensen BV, Nielsen DL, Pfeiffer P, Høgdall E, Yilmaz M, Tejpar S, Delorenzi M, Kruhøffer M, Johansen JS. miR-345 in metastatic colorectal cancer: a non-invasive biomarker for clinical outcome in non-KRAS mutant patients treated with 3rd line cetuximab and irinotecan. PLoS One 2014; 9:e99886. [PMID: 24940606 PMCID: PMC4062472 DOI: 10.1371/journal.pone.0099886] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/20/2014] [Indexed: 01/06/2023] Open
Abstract
Introduction MicroRNAs (miRNAs) have important regulatory functions in cellular processes and have shown promising potential as prognostic markers for disease outcome in patients with cancer. The aim of the present study was to find miRNA expression profiles in whole blood that were prognostic for overall survival (OS) in patients with metastatic colorectal cancer (mCRC) treated with cetuximab and irinotecan. Methods From 138 patients with mCRC in 3rd line therapy with cetuximab and irinotecan in a prospective phase II study, 738 pretreatment miRNAs were isolated and profiled from whole blood using the TaqMan MicroRNA Array v2.0. Mutation status of KRAS, BRAF, and PI3KCA was known. Results After Bonferroni adjustment, 6 miRNAs: (miR-345, miR-143, miR-34a*, miR-628-5p, miR-886-3p and miR-324-3p), were found associated with short OS. miR-345 was the strongest prognostic miRNA, significant in the full cohort and in the non-KRAS mutant population. miR-345, as a continuous variable in the full cohort, resulted in a hazard ratio (HR) of 2.38 per IQR (CI 95%: 1.8–3.1, P-value = 2.86e−07, Bonferroni adjusted, univariable analysis) and a HR = 1.75 per IQR (CI 95%: 1.24–2.48, P-Wald = 1.45e-03) in the multivariable analysis adjusted for gender, age, KRAS, PI3KCA and performance status. miR-345 was prognostic in progression-free survival (PFS) with a HR = 1.63 per IQR (CI 95%: 1.25–2.114, P-Wald = 2.92e-4) in the multivariable analysis. In addition, high miR-345 expression was associated with lack of response to treatment with cetuximab and irinotecan. Conclusion We identified miR-345 in whole blood as a potential biomarker for clinical outcome. MiR-345 was a single prognostic biomarker for both OS and PFS in all patients and also in the non-KRAS mutant population.
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Affiliation(s)
- Jakob V. Schou
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
- * E-mail:
| | - Simona Rossi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benny V. Jensen
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
| | - Dorte L. Nielsen
- Department of Oncology, Herlev University Hospital, Herlev, Denmark
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Mette Yilmaz
- Department of Oncology, Aalborg University Hospital, Aalborg, Denmark
| | - Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
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Skougaard K, Johannesen HH, Nielsen D, Schou JV, Jensen BV, Høgdall EVS, Hendel HW. CT versus FDG-PET/CT response evaluation in patients with metastatic colorectal cancer treated with irinotecan and cetuximab. Cancer Med 2014; 3:1294-301. [PMID: 24941936 PMCID: PMC4302679 DOI: 10.1002/cam4.271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 04/21/2014] [Accepted: 04/30/2014] [Indexed: 12/26/2022] Open
Abstract
We compared morphologic computed tomography (CT)-based to metabolic fluoro-deoxy-glucose (FDG) positron emission tomography (PET)/CT-based response evaluation in patients with metastatic colorectal cancer and correlated the findings with survival and KRAS status. From 2006 to 2009, patients were included in a phase II trial and treated with cetuximab and irinotecan every second week. They underwent FDG-PET/CT examination at baseline and after every fourth treatment cycle. Response evaluation was performed prospectively according to Response Evaluation Criteria in Solid Tumors (RECIST 1.0) and retrospectively according to Positron Emission Tomography Response Criteria in Solid Tumors (PERCIST). Best overall responses were registered. Sixty-one patients were eligible for response evaluation. Partial response (PR) rate was 18%, stable disease (SD) rate 64%, and progressive disease (PD) rate 18%. Partial metabolic response (PMR) rate was 56%, stable metabolic disease rate 33%, and progressive metabolic disease (PMD) rate 11%. Response agreement was poor, κ-coefficient 0.19. Hazard ratio for overall survival for responders (PR/PMR) versus nonresponders (PD/PMD) was higher for CT- than for FDG-PET/CT evaluation. Within patients with KRAS mutations, none had PR but 44% had PMR. In conclusion, morphologic and metabolic response agreement was poor primarily because a large part of the patients shifted from SD with CT evaluation to PMR when evaluated with FDG-PET/CT. Furthermore, a larger fraction of the patients with KRAS mutations had a metabolic treatment response.
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Affiliation(s)
- Kristin Skougaard
- Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
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28
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Wang YZ, Zhu Z, Zhang HY, Zhu MZ, Xu X, Chen CH, Liu LG. Detection of hepatitis B virus A1762T/G1764A mutant by amplification refractory mutation system. Braz J Infect Dis 2014; 18:261-5. [PMID: 24389280 PMCID: PMC9427444 DOI: 10.1016/j.bjid.2013.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/03/2013] [Accepted: 09/11/2013] [Indexed: 01/25/2023] Open
Affiliation(s)
- Yong-Zhong Wang
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Zhen Zhu
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Hong-Yu Zhang
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Min-Zhi Zhu
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Xin Xu
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Chun-Hua Chen
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Long-Gen Liu
- Institute for the Study of Liver Diseases, The Third People's Hospital of Changzhou, Changzhou, China.
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Clinical validation of a PCR assay for the detection of EGFR mutations in non-small-cell lung cancer: retrospective testing of specimens from the EURTAC trial. PLoS One 2014; 9:e89518. [PMID: 24586842 PMCID: PMC3934888 DOI: 10.1371/journal.pone.0089518] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/21/2014] [Indexed: 01/21/2023] Open
Abstract
The EURTAC trial demonstrated that the tyrosine kinase inhibitor (TKI) erlotinib was superior to chemotherapy as first-line therapy for advanced non-small cell lung cancers (NSCLC) that harbor EGFR activating mutations in a predominantly Caucasian population. Based on EURTAC and several Asian trials, anti-EGFR TKIs are standard of care for EGFR mutation-positive NSCLC. We sought to validate a rapid multiplex EGFR mutation assay as a companion diagnostic assay to select patients for this therapy. Samples from the EURTAC trial were prospectively screened for EGFR mutations using a combination of laboratory-developed tests (LDTs), and tested retrospectively with the cobas EGFR mutation test (EGFR PCR test). The EGFR PCR test results were compared to the original LDT results and to Sanger sequencing, using a subset of specimens from patients screened for the trial. Residual tissue was available from 487 (47%) of the 1044 patients screened for the trial. The EGFR PCR test showed high concordance with LDT results with a 96.3% overall agreement. The clinical outcome of patients who were EGFR-mutation detected by the EGFR PCR test was very similar to the entire EURTAC cohort. The concordance between the EGFR PCR test and Sanger sequencing was 90.6%. In 78.9% of the discordant samples, the EGFR PCR test result was confirmed by a sensitive deep sequencing assay. This retrospective study demonstrates the clinical utility of the EGFR PCR test in the accurate selection of patients for anti-EGFR TKI therapy. The EGFR PCR test demonstrated improved performance relative to Sanger sequencing.
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KRAS mutations: analytical considerations. Clin Chim Acta 2014; 431:211-20. [PMID: 24534449 DOI: 10.1016/j.cca.2014.01.049] [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: 12/16/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second most common cause of cancer death globally. Significant improvements in survival have been made in patients with metastasis by new therapies. For example, Cetuximab and Panitumumab are monoclonal antibodies that inhibit the epidermal growth receptor (EGFR). KRAS mutations in codon 12 and 13 are the recognized biomarkers that are analyzed in clinics before the administration of anti-EGFR therapy. Genetic analyses have revealed that mutations in KRAS predict a lack of response to Panitumumab and Cetuximab in patients with metastatic CRC (mCRC). Notably, it is estimated that 35-45% of CRC patients harbor KRAS mutations. Therefore, KRAS mutation testing should be performed in all individuals with the advanced CRC in order to identify the patients who will not respond to the monoclonal EGFR antibody inhibitors. New techniques for KRAS testing have arisen rapidly, and each technique has advantages and disadvantages. Herein, we review the latest published literature specific to KRAS mutation testing techniques. Since reliability and feasibility are important issues in clinical analyses. Therefore, this review also summarizes the effectiveness and limitations of numerous KRAS mutation testing techniques.
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A Multicenter Blinded Study Evaluating EGFR and KRAS Mutation Testing Methods in the Clinical Non–Small Cell Lung Cancer Setting—IFCT/ERMETIC2 Project Part 1. J Mol Diagn 2014; 16:45-55. [DOI: 10.1016/j.jmoldx.2013.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 07/04/2013] [Accepted: 07/30/2013] [Indexed: 11/22/2022] Open
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Lewandowska MA, Jóźwicki W, Żurawski B. KRAS and BRAF mutation analysis in colorectal adenocarcinoma specimens with a low percentage of tumor cells. Mol Diagn Ther 2013; 17:193-203. [PMID: 23606169 PMCID: PMC3663254 DOI: 10.1007/s40291-013-0025-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background and Objective The rapid development of molecular biology techniques allows for the introduction of real-time polymerase chain reaction (PCR) methods with a limit of mutation detection at 1 % in a background of wild-type DNA. Analysis of KRAS mutations in codons 12, 13, and 61, together with analysis of BRAF mutations in codon 600, are predictive biomarkers for anti-epidermal growth factor receptor (EGFR) treatment in colorectal cancer. Our aim was to compare PCR methods for KRAS mutations and BRAF mutation analysis using DNA isolated from tissue samples previously evaluated for presence of tumor cells using a quantitative scale and the percentage of tumor cells (PTC) scale. We addressed the question of whether a low number of tumor cells can be qualified for somatic mutation testing. Results Our study showed that PTC as low as 10 % was good enough to detect KRAS G12D, G13D, and Q61L mutations in formalin-fixed paraffin-embedded (FFPE) material. Furthermore, our results indicate that up to 20 % of colorectal cancer may carry mutations in the KRAS codon 61 and BRAF codon 600, which suggests the value of these mutation analyses because patients carrying them are unlikely to respond to cetuximab or panitumumab. A low level of KRAS somatic mutation detection has not been studied in depth in the context of clinical outcomes in patients; therefore, we compared new PCR methods, (KRBR-RT 50 Entrogen; ViennaLab StripAssay) and re-evaluated KRAS and BRAF status in patients with relapse after targeted therapy. Conclusions The importance of molecular results was confirmed by clinical observation of a patient with relapse who had qualified for targeted therapy with KRAS WT status (but was diagnosed by less sensitive single-stranded conformation polymorphisms method). Interestingly, during anti-EGFR treatment, it came to the selection of cells with KRAS G12C mutation which were present from the beginning in the tumor but at a low level (detected by PCR methods) only and led consequently to the metastasis. Taking into consideration the limit of detection, labor time, and assay cost, the real-time PCR method seems to be very promising especially for FFPE material with the PTC below 15 %.
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Affiliation(s)
- Marzena Anna Lewandowska
- Molecular Oncology and Genetics Unit, Department of Tumor Pathology and Pathomorphology, Franciszek Lukaszczyk Oncology Center, ul. dr I. Romanowskiej 2, 85-796, Bydgoszcz, Poland.
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Malapelle U, Carlomagno C, de Luca C, Bellevicine C, Troncone G. KRAS testing in metastatic colorectal carcinoma: challenges, controversies, breakthroughs and beyond. J Clin Pathol 2013; 67:1-9. [DOI: 10.1136/jclinpath-2013-201835] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Blons H, Rouleau E, Charrier N, Chatellier G, Côté JF, Pages JC, de Fraipont F, Boyer JC, Merlio JP, Morel A, Gorisse MC, de Cremoux P, Leroy K, Milano G, Ouafik L, Merlin JL, Le Corre D, Aucouturier P, Sabourin JC, Nowak F, Frebourg T, Emile JF, Durand-Zaleski I, Laurent-Puig P. Performance and cost efficiency of KRAS mutation testing for metastatic colorectal cancer in routine diagnosis: the MOKAECM study, a nationwide experience. PLoS One 2013; 8:e68945. [PMID: 23935912 PMCID: PMC3723748 DOI: 10.1371/journal.pone.0068945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022] Open
Abstract
Purpose Rapid advances in the understanding of cancer biology have transformed drug development thus leading to the approval of targeted therapies and to the development of molecular tests to select patients that will respond to treatments. KRAS status has emerged as a negative predictor of clinical benefit from anti-EGFR antibodies in colorectal cancer, and anti-EGFR antibodies use was limited to KRAS wild type tumors. In order to ensure wide access to tumor molecular profiling, the French National Cancer Institute (INCa) has set up a national network of 28 regional molecular genetics centers. Concurrently, a nationwide external quality assessment for KRAS testing (MOKAECM) was granted to analyze reproducibility and costs. Methods 96 cell-line DNAs and 24 DNA samples from paraffin embedded tumor tissues were sent to 40 French laboratories. A total of 5448 KRAS results were collected and analyzed and a micro-costing study was performed on sites for 5 common methods by an independent team of health economists. Results This work provided a baseline picture of the accuracy and reliability of KRAS analysis in routine testing conditions at a nationwide level. Inter-laboratory Kappa values were >0.8 for KRAS results despite differences detection methods and the use of in-house technologies. Specificity was excellent with only one false positive in 1128 FFPE data, and sensitivity was higher for targeted techniques as compared to Sanger sequencing based methods that were dependent upon local expertise. Estimated reagent costs per patient ranged from €5.5 to €19.0. Conclusion The INCa has set-up a network of public laboratories dedicated to molecular oncology tests. Our results showed almost perfect agreements in KRAS testing at a nationwide level despite different testing methods ensuring a cost-effective equal access to personalized colorectal cancer treatment.
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Affiliation(s)
- Hélène Blons
- UMR-S775, INSERM, Paris, France
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris Department of biology, Hôpital Européen Georges Pompidou, Paris, France
| | | | - Nathanaël Charrier
- Assistance Publique Hôpitaux de Paris, Henri Mondor-Albert Chenevier Hospitals, Department of Public Health, Creteil; URCEco Ile de France, Paris, France
| | - Gilles Chatellier
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, URC Paris, France
| | - Jean-François Côté
- EA4340, Université de Versailles St Quentin en Yvelines; Assistance Publique Hôpitaux de Paris Hôpital Ambroise Paré, Department of Pathology; Boulogne-Billancourt, France
| | - Jean-Christophe Pages
- INSERM U966, Université François Rabelais de Tours, Faculté de Médecine, Tours, France
| | | | | | - Jean Philippe Merlio
- Bordeaux University Hospital Segalene Department of Tumor Biology, Pessac; Bordeaux University EA 2406, Bordeaux, France
| | - Alain Morel
- Cancer Center Paul Papin; INSERM U892; University of Angers, Angers, France
| | | | - Patricia de Cremoux
- Assistance Publique Hôpitaux de Paris, Saint Louis Hospital, Molecular oncology unit, Department of biochemistry, Paris, France
| | - Karen Leroy
- Assistance Publique Hôpitaux de Paris Department of pathology Henri Mondor Hospital, Creteil, France
| | | | - L’Houcine Ouafik
- Aix-Marseille Université, Inserm-CRO2 UMR911, AP-HM, CHU Nord, Service de Transfert d’Oncologie Biologique, Marseille, France
| | | | | | - Pascaline Aucouturier
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, URC Paris, France
| | - Jean-Christophe Sabourin
- Rouen University Hospital Department of surgical and molecular pathology; Inserm U1079, Rouen, France
| | | | - Thierry Frebourg
- Rouen University Hospital Department of Genetics, Inserm U614, Rouen, France
| | - Jean-François Emile
- EA4340, Université de Versailles St Quentin en Yvelines; Assistance Publique Hôpitaux de Paris Hôpital Ambroise Paré, Department of Pathology; Boulogne-Billancourt, France
| | - Isabelle Durand-Zaleski
- Assistance Publique Hôpitaux de Paris, Henri Mondor-Albert Chenevier Hospitals, Department of Public Health, Creteil; URCEco Ile de France, Paris, France
| | - Pierre Laurent-Puig
- UMR-S775, INSERM, Paris, France
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris Department of biology, Hôpital Européen Georges Pompidou, Paris, France
- * E-mail:
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Kang SY, Ahn S, Lee SM, Jeong JY, Sung JY, Oh YL, Kim KM. Shifted termination assay (STA) fragment analysis to detect BRAF V600 mutations in papillary thyroid carcinomas. Diagn Pathol 2013; 8:121. [PMID: 23883275 PMCID: PMC3751688 DOI: 10.1186/1746-1596-8-121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/11/2013] [Indexed: 11/28/2022] Open
Abstract
Background BRAF mutation is an important diagnostic and prognostic marker in patients with papillary thyroid carcinoma (PTC). To be applicable in clinical laboratories with limited equipment, diverse testing methods are required to detect BRAF mutation. Methods A shifted termination assay (STA) fragment analysis was used to detect common V600 BRAF mutations in 159 PTCs with DNAs extracted from formalin-fixed paraffin-embedded tumor tissue. The results of STA fragment analysis were compared to those of direct sequencing. Serial dilutions of BRAF mutant cell line (SNU-790) were used to calculate limit of detection (LOD). Results BRAF mutations were detected in 119 (74.8%) PTCs by STA fragment analysis. In direct sequencing, BRAF mutations were observed in 118 (74.2%) cases. The results of STA fragment analysis had high correlation with those of direct sequencing (p < 0.00001, κ = 0.98). The LOD of STA fragment analysis and direct sequencing was 6% and 12.5%, respectively. In PTCs with pT3/T4 stages, BRAF mutation was observed in 83.8% of cases. In pT1/T2 carcinomas, BRAF mutation was detected in 65.9% and this difference was statistically significant (p = 0.007). Moreover, BRAF mutation was more frequent in PTCs with extrathyroidal invasion than tumors without extrathyroidal invasion (84.7% versus 62.2%, p = 0.001). To prepare and run the reactions, direct sequencing required 450 minutes while STA fragment analysis needed 290 minutes. Conclusions STA fragment analysis is a simple and sensitive method to detect BRAF V600 mutations in formalin-fixed paraffin-embedded clinical samples. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5684057089135749
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Kitano S, Myers J, Nakamura J, Yamane A, Yamashita M, Nakayama M, Tsukahara Y, Ushida H, Liu W, Ratain MJ, Amano M. A novel fully automated molecular diagnostic system (AMDS) for colorectal cancer mutation detection. PLoS One 2013; 8:e62989. [PMID: 23671647 PMCID: PMC3650034 DOI: 10.1371/journal.pone.0062989] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/27/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND KRAS, BRAF and PIK3CA mutations are frequently observed in colorectal cancer (CRC). In particular, KRAS mutations are strong predictors for clinical outcomes of EGFR-targeted treatments such as cetuximab and panitumumab in metastatic colorectal cancer (mCRC). For mutation analysis, the current methods are time-consuming, and not readily available to all oncologists and pathologists. We have developed a novel, simple, sensitive and fully automated molecular diagnostic system (AMDS) for point of care testing (POCT). Here we report the results of a comparison study between AMDS and direct sequencing (DS) in the detection of KRAS, BRAF and PI3KCA somatic mutations. METHODOLOGY/PRINCIPAL FINDING DNA was extracted from a slice of either frozen (n = 89) or formalin-fixed and paraffin-embedded (FFPE) CRC tissue (n = 70), and then used for mutation analysis by AMDS and DS. All mutations (n = 41 among frozen and 27 among FFPE samples) detected by DS were also successfully (100%) detected by the AMDS. However, 8 frozen and 6 FFPE samples detected as wild-type in the DS analysis were shown as mutants in the AMDS analysis. By cloning-sequencing assays, these discordant samples were confirmed as true mutants. One sample had simultaneous "hot spot" mutations of KRAS and PIK3CA, and cloning assay comfirmed that E542K and E545K were not on the same allele. Genotyping call rates for DS were 100.0% (89/89) and 74.3% (52/70) in frozen and FFPE samples, respectively, for the first attempt; whereas that of AMDS was 100.0% for both sample sets. For automated DNA extraction and mutation detection by AMDS, frozen tissues (n = 41) were successfully detected all mutations within 70 minutes. CONCLUSIONS/SIGNIFICANCE AMDS has superior sensitivity and accuracy over DS, and is much easier to execute than conventional labor intensive manual mutation analysis. AMDS has great potential for POCT equipment for mutation analysis.
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Affiliation(s)
- Shiro Kitano
- Technical Research Institute, Toppan Printing Co., Ltd., Chiba, Japan.
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Brotto K, Malisic E, Cavic M, Krivokuca A, Jankovic R. The usability of allele-specific PCR and reverse-hybridization assays for KRAS genotyping in Serbian colorectal cancer patients. Dig Dis Sci 2013; 58:998-1003. [PMID: 23108567 DOI: 10.1007/s10620-012-2469-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/16/2012] [Indexed: 12/09/2022]
Abstract
BACKGROUND Colorectal cancers (CRCs) with wild-type KRAS respond to EGFR-targeted antibody treatment. Analysis of the hotspot clustered mutations in codons 12 and 13 is compulsory before therapy and no standardized methodology for that purpose has been established so far. Since these mutations may have different biological effects and clinical outcome, reliable frequency and types of KRAS mutations need to be determined for individual therapy. AIMS The purpose of this study was to describe the KRAS mutation spectrum in a group of 481 Serbian mCRC patients and to compare the general performances of allele-specific PCR and reverse-hybridization assays. METHODS KRAS testing was performed with two diagnostic analyses, DxS TheraScreen K-RAS PCR Kit and KRAS StripAssay™. RESULTS KRAS mutations in codons 12 and 13 were present in 37.6 % of analyzed formalin-fixed paraffin-embedded (FFPE) DNA samples. The seven most frequent mutation types were observed with both assays: p.G12D 34.6 %, p.G12V 24.9 %, p.G12A 10.3 %, p.G12C 8.1 %, p.G12S 5.4 %, p.G12R 1.6 %, and p.G13D 15.1 %. Regarding double mutants, 0.8 % of them were present among all tested samples and 2.2 % among KRAS mutated ones. CONCLUSIONS Two screening approaches that were used in this study have been shown as suitable tests for detecting KRAS mutations in diagnostic settings. In addition, they appear to be good alternatives to methods presently in use. In our experience, both methods showed capacity to detect and identify double mutations which may be important for potential further subgrouping of CRC patients.
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Affiliation(s)
- Ksenija Brotto
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia.
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Kriegshäuser G, Auner V, Zeillinger R. New and potential clinical applications of KRAS as a cancer biomarker. ACTA ACUST UNITED AC 2013; 4:383-95. [PMID: 23496197 DOI: 10.1517/17530059.2010.510512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
IMPORTANCE OF THE FIELD KRAS mutation is the most common oncogenic alteration in various human cancers. Recently, KRAS has emerged as an important predictive biomarker in common malignancies such as metastatic colorectal cancer (mCRC) and non-small cell lung cancer (NSCLC). This work aims to discuss the clinical impact of the KRAS mutation status on state-of-the-art treatment approaches, including epidermal growth factor receptor (EGFR)-targeted therapies. AREAS COVERED IN THIS REVIEW This review considers the potential of KRAS to serve as a diagnostic, prognostic or predictive biomarker in various cancers, including those of the lung, colon/rectum, pancreas, ovary and endometrium. WHAT THE READER WILL GAIN KRAS mutations in mCRC and NSCLC primary tumors predict resistance to EGFR-targeted therapy. In pancreatic cancer, KRAS may prove useful as a diagnostic biomarker to screen for early neoplasia. Furthermore, quantitative KRAS mutation analysis could have the potential to distinguish pancreatic cancer from other conditions such as chronic pancreatitis. With respect to ovarian and endometrial cancer, further studies should focus on determining reliable biomarkers for predicting response to EGFR-targeted therapy. Besides EGFR inhibition, KRAS may also serve as a diagnostic and predictive biomarker for evolving therapies directed against mutant RAS proteins. TAKE HOME MESSAGE KRAS has been recognized as an outstanding predictive biomarker to select mCRC and NSCLC patients for EGFR-targeted therapies; however, multi-determinant approaches including other molecular markers should facilitate the identification of patients likely to respond to such therapies.
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Affiliation(s)
- Gernot Kriegshäuser
- ViennaLab Diagnostics GmbH, Gaudenzdorfer Gürtel 43-45, 1120 Vienna, Austria +43 1 812015642 ; +43 1 812015619 ;
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Schildgen V, Schulz C, Lüsebrink J, Tillmann RL, Engel-Riedel W, Stoelben E, Schildgen O, Brockmann M. Combination of Pyrosequencing® and Sanger sequencing reveals alleged novel mutation in exon 18 of EGFR. Per Med 2013; 10:201-209. [DOI: 10.2217/pme.12.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background:EGFR sequencing is crucial for therapeutic decisions in treatment regimens of lung cancer patients. Several mutations have been identified in the past, of which some were confirmed as activating or resistance mutations by in vitro phenotyping. In this study, novel mutations of so far unknown relevance were identified by a combination of Sanger and Pyrosequencing®. Materials & methods: Formalin-fixed paraffin-embedded lung biopsies from 20 randomly selected patients suffering from non-small-cell lung cancer with previous external EGFR mutation analyses were reanalyzed by Sanger sequencing according to a previous study, and Pyrosequencing with the EGFR Pyro Kit (Qiagen, Hilden, Germany). Sensitivity and specificity were determined in comparison with the results of an external supplier for all relevant mutations in exons 18, 19, 20 and 21. Results: Our analyses revealed that Pyrosequencing is faster and more sensitive for the common mutations compared with Sanger sequencing and the results of the external supplier. A new mutation, c.2160delC, in exon 18 in 40% of patients leading to a frameshift was identified. Another two frameshift mutations were detected in exon 18 in 10% of patients; c.2168delT in combination with c.2160delC, and c.2163insG alone. Conclusion: Divergences regarding the detection of the common mutations could be traced back to inhomogeneous or insufficient tumor material. Surprisingly, none of the newly identified mutations have been previously described, although they occurred in total in up to 40% of randomly selected cases. A possible explanation may be that commercial assays did not cover these deletions that are located nearby but not in the known mutation hotspot of exon 18, or that Sanger sequencing produced serious artifacts.
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Affiliation(s)
- Verena Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany
| | - Carolin Schulz
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany
| | - Jessica Lüsebrink
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany
| | - Ramona-Liza Tillmann
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany
| | | | - Erich Stoelben
- Lungenklinik, Kliniken der Stadt Köln gGmbH, Köln, Germany
| | - Oliver Schildgen
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany.
| | - Michael Brockmann
- Institut für Pathologie, Kliniken der Stadt Köln gGmbH, Krankenhaus Merheim, Klinikum der Privaten Universität Witten/Herdecke, Institut für Pathologie, Ostmerheimer Str. 200, D-51109 Köln (Cologne), Germany
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Abd El Kader Y, Emera G, Safwat E, Kassem HA, Kassem NM. The KRAS StripAssay for detection of KRAS mutation in Egyptian patients with colorectal cancer (CRC): a pilot study. J Egypt Natl Canc Inst 2013; 25:37-41. [PMID: 23499205 DOI: 10.1016/j.jnci.2012.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/14/2012] [Accepted: 12/31/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. PURPOSE Detection of KRAS mutation in Egyptian colorectal cancer (CRC) patients by the KRAS StripAssay. METHODS Examination of 20 colorectal cancer (CRC) patients is done to detect KRAS mutations by KRAS StripAssay. For the StripAssay, a mutant-enriched PCR was followed by hybridization to KRAS-specific probes bound to a nitrocellulose strip. RESULTS Among 20 patients, KRAS mutations were identified in 80% of patients by the KRAS StripAssay. CONCLUSIONS Our preliminary results suggest that KRAS StripAssay is an alternative to protocols currently in use for KRAS mutation detection.
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Affiliation(s)
- Yasser Abd El Kader
- Kasr El-Aini Centre of Clinical Oncology and Nuclear Medicine (NEMROCK), Faculty of Medicine, Cairo University, Cairo, Egypt
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Dejmek A, Zendehrokh N, Tomaszewska M, Edsjö A. Preparation of DNA from cytological material: effects of fixation, staining, and mounting medium on DNA yield and quality. Cancer Cytopathol 2013; 121:344-53. [PMID: 23408720 DOI: 10.1002/cncy.21276] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/14/2012] [Accepted: 12/04/2012] [Indexed: 12/22/2022]
Abstract
BACKGROUND Personalized oncology requires molecular analysis of tumor cells. Several studies have demonstrated that cytological material is suitable for DNA analysis, but to the authors' knowledge there are no systematic studies comparing how the yield and quality of extracted DNA is affected by the various techniques used for the preparation of cytological material. METHODS DNA yield and quality were compared using cultured human lung cancer cells subjected to different preparation techniques used in routine cytology, including fixation, mounting medium, and staining. The results were compared with the outcome of epidermal growth factor receptor (EGFR) genotyping of 66 clinical cytological samples using the same DNA preparation protocol. RESULTS All tested protocol combinations resulted in fragment lengths of at least 388 base pairs. The mounting agent EcoMount resulted in higher yields than traditional xylene-based medium. Spray and ethanol fixation resulted in both a higher yield and better DNA quality than air drying. In liquid-based cytology (LBC) methods, CytoLyt solution resulted in a 5-fold higher yield than CytoRich Red. Papanicolaou staining provided twice the yield of hematoxylin and eosin staining in both liquid-based preparations. Genotyping outcome and quality control values from the clinical EGFR genotyping demonstrated a sufficient amount and amplifiability of DNA in both spray-fixed and air-dried cytological samples. CONCLUSIONS Reliable clinical genotyping can be performed using all tested methods. However, in the cell line experiments, spray- or ethanol-fixed, Papanicolaou-stained slides provided the best results in terms of yield and fragment length. In LBC, the DNA recovery efficiency of the preserving medium may differ considerably, which should be taken into consideration when introducing LBC. Cancer (Cancer Cytopathol) 2013;121:344-353. © 2013 American Cancer Society.
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Affiliation(s)
- Annika Dejmek
- Department of Clinical Pathology, University and Regional Laboratories Region Skåne, Malmo, Sweden
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Peeters M, Oliner KS, Parker A, Siena S, Van Cutsem E, Huang J, Humblet Y, Van Laethem JL, André T, Wiezorek J, Reese D, Patterson SD. Massively parallel tumor multigene sequencing to evaluate response to panitumumab in a randomized phase III study of metastatic colorectal cancer. Clin Cancer Res 2013; 19:1902-12. [PMID: 23325582 DOI: 10.1158/1078-0432.ccr-12-1913] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate whether EGF receptor (EGFR) pathway mutations predicted response to monotherapy with panitumumab, an anti-EGFR monoclonal antibody, in a randomized phase III study of metastatic colorectal cancer. EXPERIMENTAL DESIGN Using massively parallel multigene sequencing, we analyzed 320 samples for 9 genes, with multigene sequence data from 288 (90%) samples. RESULTS Mutation rates were: KRAS (45%), NRAS (5%), BRAF (7%), PIK3CA (9%), PTEN (6%), TP53 (60%), EGFR (1%), AKT1 (<1%), and CTNNB1 (2%). In the randomized study and open-label extension, 22 of 138 (16%) wild-type KRAS (codons 12/13/61) patients versus 0 of 103 mutant KRAS (codons 12/13) patients had objective responses. Of 6 mutant KRAS (codon 61) patients, 1 with a Q61H mutation achieved partial response during the extension. Among wild-type KRAS (codons 12/13/61) patients, 0 of 9 patients with NRAS mutations, 0 of 13 with BRAF mutations, 2 of 10 with PIK3CA mutations, 1 of 9 with PTEN mutations, and 1 of 2 with CTNNB1 mutations responded to panitumumab. No patients responded to best supportive care alone. Panitumumab treatment was associated with longer progression-free survival (PFS) among wild-type KRAS (codons 12/13/61) patients [HR, 0.39; 95% confidence interval (CI), 0.28-0.56]. Among wild-type KRAS patients, a treatment effect for PFS favoring panitumumab occurred in patients with wild-type NRAS (HR, 0.39; 95% CI, 0.27-0.56) and wild-type BRAF (HR, 0.37; 95% CI, 0.24-0.55) but not mutant NRAS (HR, 1.94; 95% CI, 0.44-8.44). CONCLUSIONS These results show the feasibility and potential clinical use of next-generation sequencing for evaluating predictive biomarkers.
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Affiliation(s)
- Marc Peeters
- Department of Oncology, Antwerp University Hospital, Edegem, Belgium.
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Tougeron D, Lecomte T, Pagès JC, Villalva C, Collin C, Ferru A, Tourani JM, Silvain C, Levillain P, Karayan-Tapon L. Effect of low-frequency KRAS mutations on the response to anti-EGFR therapy in metastatic colorectal cancer. Ann Oncol 2013; 24:1267-73. [PMID: 23293113 DOI: 10.1093/annonc/mds620] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Only patients with wild-type (WT) KRAS tumors benefit from anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (Mabs) in metastatic colorectal cancer (mCRC). Pyrosequencing is now widely used for the determination of KRAS mutation burden and a conservative cut-off point of 10% has been defined. Up until now, the impact of low-frequency KRAS mutations (<10%) on the response to anti-EGFR Mabs has yet to be evaluated. PATIENTS AND METHODS Tumors from patients receiving anti-EGFR Mabs based on a WT genotype for KRAS, as determined using direct sequencing, have been retrospectively analyzed by pyrosequencing. Patients were categorized as WT (no KRAS mutation) or low-frequency mutation when KRAS mutation was <10% (KRAS low MT). RESULTS A total of 168 patients treated by anti-EGFR Mabs for mCRC were analyzed. According to pyrosequencing, 138 tumors remained KRAS WT, while 30 tumors were KRAS low MT. In the KRAS low MT and KRAS WT groups, the response rates were 6.7% and 37.0%, respectively, while stabilization amounted to 23.3% versus 32.6% and progression to 70% versus 29% (P < 0.01). Progression-free survival (PFS) was 2.7 ± 0.5 months for KRAS low MT and was 6.0 ± 0.3 months for KRAS WT (P < 0.01). CONCLUSIONS These results appear to validate consideration of low-frequency KRAS mutation tumors as positive, and justify a large-scale prospective study.
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Affiliation(s)
- D Tougeron
- Department of Gastroenterology, Poitiers University Hospital, 2 rue de la Milétrie, 86000 Poitiers Cedex, France.
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Kotoula V, Kalogeras KT, Kouvatseas G, Televantou D, Kronenwett R, Wirtz RM, Fountzilas G. Sample parameters affecting the clinical relevance of RNA biomarkers in translational breast cancer research. Virchows Arch 2012; 462:141-54. [PMID: 23262785 PMCID: PMC3568476 DOI: 10.1007/s00428-012-1357-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/28/2012] [Accepted: 11/30/2012] [Indexed: 12/21/2022]
Abstract
In the frame of translational breast cancer research, eligibility criteria for formalin-fixed paraffin-embedded tissue (FFPE) material processing for gene expression studies include tumor cell content (TCC) and sample site (primary vs metastatic tumors). Herein we asked whether the observed differences in gene expression between paired samples with respect to TCC and sample site also have different clinical significance. We assessed ESR1, ERBB2, MAPT, MMP7, and RACGAP1 mRNA expression with real time PCR in paired samples before (NMD) and after macrodissection (MD) from 98 primary tumors (PMD, PNMD) and 72 metastatic lymph nodes (LNMD, LNNMD), as well as from 93 matched P (mP) and LN (mLN). TCC range was 2.5–75 % in the NMD series and 28–98 % in the MD and in the mP/mLN series. The prognostic effect of these markers, individually or in clusters, remained stable between paired PMD/NMD. In comparison, cluster classification failed in the LNNMD group with lower TCC. In the mP/mLN cohort, RACGAP1 mRNA expression was of prognostic significance when tested in mLN samples (p < 0.001). Similarly, luminal B, HER2, and triple negative tumors were of dismal prognosis when classified in the LN component of the same series (mLN, overall survival: p = 0.013, p = 0.034, and p = 0.007, respectively). In conclusion, the clinical relevance of the RNA markers examined may be affected by TCC in metastatic LN samples but not in primary tumors, while it differs between primary tumors and matched metastases. These data will facilitate the design of translational studies involving FFPE sample series.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki School of Medicine, University Campus, 54006 Thessaloniki, Greece.
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Kizys MML, Cardoso MG, Lindsey SC, Harada MY, Soares FA, Melo MCC, Montoya MZ, Kasamatsu TS, Kunii IS, Giannocco G, Martins JRM, Cerutti JM, Maciel RMB, Dias-da-Silva MR. Optimizing nucleic acid extraction from thyroid fine-needle aspiration cells in stained slides, formalin-fixed/paraffin-embedded tissues, and long-term stored blood samples. ACTA ACUST UNITED AC 2012; 56:618-26. [DOI: 10.1590/s0004-27302012000900004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/22/2012] [Indexed: 11/22/2022]
Abstract
OBJECTIVE: Adequate isolation of nucleic acids from peripheral blood, fine-needle aspiration cells in stained slides, and fresh and formalin-fixed/paraffin-embedded tissues is crucial to ensure the success of molecular endocrinology techniques, especially when samples are stored for long periods, or when no other samples can be collected from patients who are lost to follow-up. Here, we evaluate several procedures to improve current methodologies for DNA (salting-out) and RNA isolation. MATERIALS AND METHODS: We used proteinase K treatment, heat shock, and other adaptations to increase the amount and quality of the material retrieved from the samples. RESULTS: We successfully isolated DNA and RNA from the samples described above, and this material was suitable for PCR, methylation profiling, real-time PCR and DNA sequencing. CONCLUSION: The techniques herein applied to isolate nucleic acids allowed further reliable molecular analyses. Arq Bras Endocrinol Metab. 2012;56(9):618-26
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gisele Giannocco
- Universidade Federal de Sao Paulo, Brazil; Faculdade de Medicina do ABC, Brazil
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Kristensen LS, Kjeldsen TE, Hager H, Hansen LL. Competitive amplification of differentially melting amplicons (CADMA) improves KRAS hotspot mutation testing in colorectal cancer. BMC Cancer 2012; 12:548. [PMID: 23173730 PMCID: PMC3517778 DOI: 10.1186/1471-2407-12-548] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/12/2012] [Indexed: 11/11/2022] Open
Abstract
Background Cancer is an extremely heterogeneous group of diseases traditionally categorized according to tissue of origin. However, even among patients with the same cancer subtype the cellular alterations at the molecular level are often very different. Several new therapies targeting specific molecular changes found in individual patients have initiated the era of personalized therapy and significantly improved patient care. In metastatic colorectal cancer (mCRC) a selected group of patients with wild-type KRAS respond to antibodies against the epidermal growth factor receptor (EGFR). Testing for KRAS mutations is now required prior to anti-EGFR treatment, however, less sensitive methods based on conventional PCR regularly fail to detect KRAS mutations in clinical samples. Methods We have developed sensitive and specific assays for detection of the seven most common KRAS mutations based on a novel methodology named Competitive Amplification of Differentially Melting Amplicons (CADMA). The clinical applicability of these assays was assessed by analyzing 100 colorectal cancer samples, for which KRAS mutation status has been evaluated by the commercially available TheraScreen® KRAS mutation kit. Results The CADMA assays were sensitive to at least 0.5% mutant alleles in a wild-type background when using 50 nanograms of DNA in the reactions. Consensus between CADMA and the TheraScreen kit was observed in 96% of the colorectal cancer samples. In cases where disagreement was observed the CADMA result could be confirmed by a previously published assay based on TaqMan probes and by fast COLD-PCR followed by Sanger sequencing. Conclusions The high analytical sensitivity and specificity of CADMA may increase diagnostic sensitivity and specificity of KRAS mutation testing in mCRC patients.
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Affiliation(s)
- Lasse Sommer Kristensen
- Department of Biomedicine, University of Aarhus, Bartholin Building, Wilhelm Meyers Allé 4, DK-8000 Aarhus C, Denmark.
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Anderson S, Bloom KJ, Vallera DU, Rueschoff J, Meldrum C, Schilling R, Kovach B, Lee JRJ, Ochoa P, Langland R, Halait H, Lawrence HJ, Dugan MC. Multisite Analytic Performance Studies of a Real-Time Polymerase Chain Reaction Assay for the Detection of BRAF V600E Mutations in Formalin-Fixed, Paraffin-Embedded Tissue Specimens of Malignant Melanoma. Arch Pathol Lab Med 2012; 136:1385-91. [DOI: 10.5858/arpa.2011-0505-oa] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—A polymerase chain reaction–based companion diagnostic (cobas 4800 BRAF V600 Mutation Test) was recently approved by the US Food and Drug Administration to select patients with BRAF-mutant metastatic melanoma for treatment with the BRAF inhibitor vemurafenib.
Objectives.—(1) To compare the analytic performance of the cobas test to Sanger sequencing by using screening specimens from phase II and phase III trials of vemurafenib, and (2) to assess the reproducibility of the cobas test at different testing sites.
Design.—Specimens from 477 patients were used to determine positive and negative percent agreements between the cobas test and Sanger sequencing for detecting V600E (1799T>A) mutations. Specimens were evaluated with a massively parallel pyrosequencing method (454) to resolve discordances between polymerase chain reaction and Sanger results. Reproducibility of the cobas test was assessed at 3 sites by using 3 reagent lots and an 8-member panel of melanoma samples.
Results.—A valid cobas result was obtained for all eligible patients. Sanger sequencing had a failure rate of 9.2% (44 of 477). For the remaining 433 specimens, positive percent agreement was 96.4% (215 of 223) and negative percent agreement, 80% (168 of 210). Among 42 cobas mutation-positive/Sanger V600E-negative specimens, 17 were V600E positive and 24 were V600K positive by 454. The cobas test detected 70% of V600K mutations. In the reproducibility study, a correct interpretation was made for 100% of wild-type specimens and specimens with greater than 5% mutant alleles; V600E mutations were detected in 90% of specimens with less than 5% mutant alleles.
Conclusions.—The cobas test (1) had a lower assay failure rate than that of Sanger, (2) was more sensitive in detecting V600E mutations, (3) detected most V600K mutations, and (4) was highly reproducible.
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Ross JS. Clinical Implementation of KRAS Testing in Metastatic Colorectal Carcinoma: The Pathologist's Perspective. Arch Pathol Lab Med 2012; 136:1298-307. [DOI: 10.5858/arpa.2011-0478-ra] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—Mutation status of the KRAS gene identifies a distinct disease subtype of metastatic colorectal carcinoma that does not respond to antibody therapeutics targeting the epidermal growth factor receptor. This is currently the only validated marker in metastatic colorectal carcinoma with a clear implication in treatment selection. KRAS testing is widely accepted in clinical practice to guide metastatic colorectal carcinoma therapeutic decisions, and there are many commercially available platforms to perform the test.
Objective.—To evaluate the critical role of pathologists in the full implementation of KRAS testing by optimizing tumor tissue collection and fixation procedures and by choosing testing technologies and reliable Clinical Laboratory Improvement Amendments of 1988–certified laboratories to perform the tests.
Data Sources.—Prospective clinical trials, retrospective studies, and quality assessment and survey reports were identified in the following databases: PubMed, American Society of Clinical Oncology Proceedings (American Society of Clinical Oncology Annual Meeting and Gastrointestinal Cancer Symposium) and European Society for Medical Oncology Proceedings (Annals of Oncology European Society for Medical Oncology Congress and Annals of Oncology World Congress on Gastrointestinal Cancers).
Conclusions.—More bona fide standards are needed to address the variety of available test methods, which have different performance characteristics including speed, sensitivity to detect rare mutations, and technical requirements. Refined standards addressing timing of KRAS testing, laboratory performance and accuracy, quality assurance and control, proper tissue collection, and appropriate result reporting would also be greatly beneficial. Pathologists should be aware that the amount of information they need to manage will increase, because future trends and technological advances will enhance the predictive power of diagnostic tests or the scope of the biomarker panels tested routinely across tumor types.
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Affiliation(s)
- Jeffrey S. Ross
- From the Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York
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Malapelle U, Bellevicine C, Salatiello M, de Luca C, Rispo E, Riccio P, Sparano L, De Stefano A, Carlomagno C, Maiello FM, Vita G, Nappi O, Troncone G. Sanger sequencing in routine KRAS testing: a review of 1720 cases from a pathologist's perspective. J Clin Pathol 2012; 65:940-4. [PMID: 22872705 PMCID: PMC3461636 DOI: 10.1136/jclinpath-2012-200773] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background Sanger sequencing (SS) of PCR products is still the most frequent method to test colorectal cancer for KRAS mutations in routine practice. Methods An audit of SS on 1720 routine cases was carried out, taking into account age, gender, specimen type (resection vs biopsies), tumour site (primary vs metastasis), tumour stage, neoplastic cells abundance (>30% vs <30%) and fixation type (buffered formalin vs simple formalin). In a subset of 50 wild-type (WT) patients correlations between SS findings and response rate (RR), progression-free survival (PFS) and overall survival (OS) were also evaluated. Results The tests were informative in 1691 cases (98.3%). Mutations were detected in 671 cases (39.6%). No significant differences in mutation rates were observed with respect to age (p=0.2), gender (p=0.2), specimen type (p=0.3) and formalin fixation (p=0.08). Conversely, KRAS mutant rate was higher in metastatic tissue (50% vs 39%, p=0.02), in samples with over 30% of neoplastic cells (43.4% vs 26.6%, p=0.02) and in tumours tested in stage IV (p=0.05). The RR of SS KRAS WT patients was 26% (one complete and 12 partial responses). The disease control rate (objective responses plus stable disease) was 56%. Median PFS was 4.4 months and median OS was 10.4 months. Conclusions Pathological criteria that make SS a more robust method for KRAS testing and treatment response prediction are neoplastic cell abundance, metastatic tissue sample and stage IV primary tumour.
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Affiliation(s)
- Umberto Malapelle
- Scienze Biomorfologiche e Funzionali, Universitá degli Studi di Napoli Federico II, Napoli, Italy
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KRAS mutation detection by high-resolution melting analysis significantly predicts clinical benefit of cetuximab in metastatic colorectal cancer. Br J Cancer 2012; 107:626-31. [PMID: 22805329 PMCID: PMC3419946 DOI: 10.1038/bjc.2012.275] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Anti-epidermal growth factor receptor (EGFR) monoclonal antibodies are restricted to KRAS wild-type (WT) metastatic colorectal cancers (mCRCs), usually identified by direct sequencing, that may yield false negative results because of genetic heterogeneity within the tumour. We evaluated the efficiency of high-resolution melting analysis (HRMA) in identifying KRAS-mutant (MUT) tumours. Methods: We considered 50 mCRC patients scored as KRAS-WT by direct sequencing and treated with cetuximab-containing chemotherapy, and tested the correlations between HRMA findings and response rate (RR), progression-free (PFS) and overall survival (OS). Results: Aberrant melting curves were detected in four (8%) cases; gene cloning confirmed these mutations. Response rate (RR) of HRMA KRAS-WT patients was 28.3%. There was no response in HRMA KRAS-MUT patients. Disease control rate (responsive plus stable disease) was 58.7% in HRMA KRAS-WT patients and 25% in HRMA KRAS-MUT patients. There was no correlation between HRMA KRAS status and RR (P=0.287) or disease control (P=0.219). Median PFS (4.8 vs 2.3 months; hazard ratio (HR)=0.29, P=0.02) and OS (11.0 vs 2.7 months; HR=0.11, P=0.03) were significantly longer for the HRMA KRAS-WT than for HRMA KRAS-MUT patients. Conclusions: High-resolution melting analysis identified 8% more KRAS-MUT patients not responding to cetuximab-containing regimens, suggesting that HRMA may be more effective than direct sequencing in selecting patients for anti-EGFR antibodies.
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