1
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Site-specific insertion of endonuclease recognition sites into amplicons to improve post-PCR analysis sensitivity of gene mutation. Biosens Bioelectron 2022; 208:114191. [PMID: 35366426 DOI: 10.1016/j.bios.2022.114191] [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: 01/13/2022] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022]
Abstract
Precise detection of low-frequency gene mutations surrounded by excess wild-type DNA is important in many aspects of medical fields. Most hybridization-based methods for high-resolution mutant allele analysis are hindered by competition of the complementary strand with single-strand probes for the target strand. Here, we demonstrate that site-specific insertion of endonuclease recognition sites into amplicons allows post-PCR generation of short dsDNA or ssDNA, whereby improves the sensitivity of both melting temperature analysis (MTA) and end-point detection following up. Using a three-staged PCR protocol, enrichment of target gene and incorporation of specific restriction sites in amplicons were ensued with hardly any loss in amplification efficiency and specificity. It enables simultaneous discrimination among a panel of totally 11 EGFR 19 exon deletion mutations via MTA after post-PCR digestion by either FokI only or cooperated with CRISPR-Cas12a, using SYBR green I. By replacement of one double-strand cleavage site with a nickase binding domain post-PCR generation of ssDNA of interest via strand displacement amplification (termed as iSDA) is realized. Our preliminary investigation shows that iSDA permits analysis of single nucleotide variants down to 0.1% allelic-frequency using end-point detection. Given the good compatibility with the majority of mutant-enrich PCR methods, we envision it would advance the current gene profiling technologies to a large extent.
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2
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Abstract
Allele-specific competitive blocker PCR (ACB-PCR) is a sensitive and quantitative approach for the selective amplification of a specific base substitution. Using the ACB-PCR technique, hotspot cancer-driver mutations (tumor-relevant mutations in oncogenes and tumor suppressor genes, which confer a selective growth advantage) are being developed as quantitative biomarkers of cancer risk. ACB-PCR employs a mutant-specific primer (with a 3'-penultimate mismatch relative to the mutant DNA sequence, but a double 3'-terminal mismatch relative to the wild-type DNA sequence) to selectively amplify rare mutant DNA molecules. A blocker primer having a non-extendable 3'-end and a 3'-penultimate mismatch relative to the wild-type DNA sequence, but a double 3'-terminal mismatch relative to the mutant DNA sequence is included in ACB-PCR to selectively repress amplification from abundant wild-type molecules. Consequently, ACB-PCR can quantify the level of a single base pair substitution mutation in a DNA population when present at a mutant:wild-type ratio of 1 × 10-5 or greater. Quantification of rare mutant alleles is achieved by parallel analysis of unknown samples and mutant fraction (MF) standards (defined mixtures of mutant and wild-type DNA sequences). The ability to quantify specific mutations with known association to cancer has several important applications in evaluating the carcinogenic potential of chemical exposures in rodent models. Further, the measurement of cancer-driver mutant subpopulations is important for precision cancer treatment (selecting the most appropriate targeted therapy and predicting the development of therapeutic resistance). This chapter provides a step-by-step description of the ACB-PCR methodology as it has been used to measure human PIK3CA codon 1047, CAT→CGT (H1047R) mutation.
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3
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Damin F, Galbiati S, Soriani N, Burgio V, Ronzoni M, Ferrari M, Chiari M. Analysis of KRAS, NRAS and BRAF mutational profile by combination of in-tube hybridization and universal tag-microarray in tumor tissue and plasma of colorectal cancer patients. PLoS One 2018; 13:e0207876. [PMID: 30562355 PMCID: PMC6298683 DOI: 10.1371/journal.pone.0207876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/06/2018] [Indexed: 01/05/2023] Open
Abstract
Microarray technology fails in detecting point mutations present in a small fraction of cells from heterogeneous tissue samples or in plasma in a background of wild-type cell-free circulating tumor DNA (ctDNA). The aim of this study is to overcome the lack of sensitivity and specificity of current microarray approaches introducing a rapid and sensitive microarray-based assay for the multiplex detection of minority mutations of oncogenes (KRAS, NRAS and BRAF) with relevant diagnostics implications in tissue biopsies and plasma samples in metastatic colorectal cancer patients. In our approach, either wild-type or mutated PCR fragments are hybridized in solution, in a temperature gradient, with a set of reporters with a 5' domain, complementary to the target sequences and a 3' domain complementary to a surface immobilized probe. Upon specific hybridization in solution, which occurs specifically thanks to the temperature gradients, wild-type and mutated samples are captured at specific location on the surface by hybridization of the 3' reporter domain with its complementary immobilized probe sequence. The most common mutations in KRAS, NRAS and BRAF genes were detected in less than 90 minutes in tissue biopsies and plasma samples of metastatic colorectal cancer patients. Moreover, the method was able to reveal mutant alleles representing less than 0,3% of total DNA. We demonstrated detection limits superior to those provided by many current technologies in the detection of RAS and BRAF gene superfamily mutations, a level of sensitivity compatible with the analysis of cell free circulating tumor DNA in liquid biopsy.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail:
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Burgio
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Monica Ronzoni
- Dipartimento di Oncologia Medica, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
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4
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Nicholson AM, Olpe C, Hoyle A, Thorsen AS, Rus T, Colombé M, Brunton-Sim R, Kemp R, Marks K, Quirke P, Malhotra S, Ten Hoopen R, Ibrahim A, Lindskog C, Myers MB, Parsons B, Tavaré S, Wilkinson M, Morrissey E, Winton DJ. Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium. Cell Stem Cell 2018; 22:909-918.e8. [PMID: 29779891 PMCID: PMC5989058 DOI: 10.1016/j.stem.2018.04.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/16/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022]
Abstract
We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0.7% of all crypts undergo fission in a single year). Pro-oncogenic mutations subvert both stem cell replacement to accelerate fixation and clonal expansion by crypt fission to achieve high mutant allele frequencies with age. The benchmarking of these behaviors allows the advantage associated with different gene-specific mutations to be compared irrespective of the cellular mechanisms by which they are conferred.
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Affiliation(s)
- Anna M Nicholson
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Cora Olpe
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge, UK
| | - Alice Hoyle
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Ann-Sofie Thorsen
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Teja Rus
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mathilde Colombé
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | - Richard Kemp
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Kate Marks
- Pathology and Tumour Biology, Level 4, Wellcome Trust Brenner Building, St. James University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Phil Quirke
- Pathology and Tumour Biology, Level 4, Wellcome Trust Brenner Building, St. James University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | | | | | - Ashraf Ibrahim
- Department of Histopathology, Box 235, CUHFT, Cambridge, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Barbara Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Simon Tavaré
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mark Wilkinson
- Norwich Research Park BioRepository, James Watson Road, Norwich NR4 7UQ, UK
| | - Edward Morrissey
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
| | - Douglas J Winton
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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5
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Grabocka E, Bar-Sagi D. Mutant KRAS Enhances Tumor Cell Fitness by Upregulating Stress Granules. Cell 2017; 167:1803-1813.e12. [PMID: 27984728 DOI: 10.1016/j.cell.2016.11.035] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/23/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023]
Abstract
There is growing evidence that stress-coping mechanisms represent tumor cell vulnerabilities that may function as therapeutically beneficial targets. Recent work has delineated an integrated stress adaptation mechanism that is characterized by the formation of cytoplasmic mRNA and protein foci, termed stress granules (SGs). Here, we demonstrate that SGs are markedly elevated in mutant KRAS cells following exposure to stress-inducing stimuli. The upregulation of SGs by mutant KRAS is dependent on the production of the signaling lipid molecule 15-deoxy-delta 12,14 prostaglandin J2 (15-d-PGJ2) and confers cytoprotection against stress stimuli and chemotherapeutic agents. The secretion of 15-d-PGJ2 by mutant KRAS cells is sufficient to enhance SG formation and stress resistance in cancer cells that are wild-type for KRAS. Our findings identify a mutant KRAS-dependent cell non-autonomous mechanism that may afford the establishment of a stress-resistant niche that encompasses different tumor subclones. These results should inform the design of strategies to eradicate tumor cell communities.
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Affiliation(s)
- Elda Grabocka
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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6
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A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon. Anal Chim Acta 2017; 957:55-62. [DOI: 10.1016/j.aca.2016.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/10/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
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7
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Itonaga M, Matsuzaki I, Warigaya K, Tamura T, Shimizu Y, Fujimoto M, Kojima F, Ichinose M, Murata SI. Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification. PLoS One 2016; 11:e0151654. [PMID: 26999437 PMCID: PMC4801409 DOI: 10.1371/journal.pone.0151654] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid—locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP), for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. PNA-LNA mediated LAMP was applied for cDNA from 4 kinds of pancreatic carcinoma cell lines with or without KRAS point mutation. The amplified DNA products were verified by naked-eye as well as a real-time PCR equipment. By PNA-LNA mediated LAMP, amplification of wild type KRAS DNA was blocked by clamping PNA probe, whereas, mutant type KRAS DNA was significantly amplified within 50 min. Mutant alleles could be detected in samples which diluted until 0.1% of mutant-to-wild type ratio. On the other hand, mutant alleles could be reproducibly with a mutant-to-wild type ratio of 30% by direct sequencing and of 1% by PNA-clamping PCR. The limit of detection (LOD) of PNA-LNA mediated LAMP was much lower than the other conventional methods. Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V) of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. PNA-LNA mediated LAMP is a simple, rapid, specific and sensitive methodology for the detection of KRAS mutation.
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Affiliation(s)
- Masahiro Itonaga
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Ibu Matsuzaki
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Kenji Warigaya
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Takaaki Tamura
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Yuki Shimizu
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masakazu Fujimoto
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Fumiyoshi Kojima
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masao Ichinose
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shin-ichi Murata
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- * E-mail:
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8
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Li Y, Fu XH, Yuan JQ, Yang ZY, Mao C, Dong XM, Tang JL, Wang SY. Colorectal cancer: using blood samples and tumor tissue to detect K-ras mutations. Expert Rev Anticancer Ther 2016; 15:715-25. [PMID: 26035720 DOI: 10.1586/14737140.2015.1037836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We performed a meta-analysis to assess whether blood can be substituted for tumor tissue in K-ras mutation testing. PubMed, EMBASE, MEDLINE, and BIOSIS databases were searched. Twenty-three studies including 1261 patients were included. The pooled overall sensitivity, specificity, and concordance rate were 0.69 (95% CI: 0.59-0.78), 0.96 (95% CI: 0.93-0.97), and 0.86 (95% CI: 0.82-0.89), respectively. Subgroup analysis indicated that plasma (sensitivity: 0.74; mutation rate: 0.34) exhibited superior sensitivity compared with serum (sensitivity: 0.45; mutation rate: 0.24). We conclude that blood is a suitable substitute for tumor tissue in K-ras mutation testing. K-ras mutation positivity in blood can be used to identify patients who should not receive EGFR monoclonal antibody therapy, but the absence of blood positivity does not necessarily imply negativity.
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Affiliation(s)
- Yang Li
- Center of Injury Prevention and Control, Medical College of Jinan University, Guangzhou, China
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9
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Gazzaniga P, Raimondi C, Nicolazzo C, Carletti R, di Gioia C, Gradilone A, Cortesi E. The rationale for liquid biopsy in colorectal cancer: a focus on circulating tumor cells. Expert Rev Mol Diagn 2015; 15:925-32. [PMID: 25959553 DOI: 10.1586/14737159.2015.1045491] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Capturing circulating tumor cells (CTCs) and/or circulating tumor DNA from blood, which represents a precious source of biological material derived from both primary and metastatic tumors, has been named a 'liquid biopsy'. While the circulating tumor DNA might be more representative of the bulk of the metastatic tumor, CTCs are thought to reflect more of the metastases-initiating cells. Consequently, a liquid biopsy made of tumor cells and tumor DNA that is able to track cancer evolution, as a fingerprint of the patient's individual tumor, and is easy to perform at every stage of the disease course, sounds attractive. This article mainly focuses on the applications of CTCs to track tumor dynamics in real time using colorectal cancer as a model system. The analysis of viable CTCs at DNA, RNA and protein levels, as well as their expansion in vitro, may allow deep investigation of the features of metastases-initiating cells.
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Affiliation(s)
- Paola Gazzaniga
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italy
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10
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Ma T, Liu H, Sun X, Gao L, Shi J, Zhao H, Jia B, Wang F, Liu Z. Serial in Vivo Imaging Using a Fluorescence Probe Allows Identification of Tumor Early Response to Cetuximab Immunotherapy. Mol Pharm 2014; 12:10-7. [DOI: 10.1021/mp5002944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Teng Ma
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Hao Liu
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Xianlei Sun
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Liquan Gao
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jiyun Shi
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Interdisciplinary
Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiyun Zhao
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Medical
and Healthy Analytical Center, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Bing Jia
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Fan Wang
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Interdisciplinary
Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaofei Liu
- Medical
Isotopes Research Center, Peking University, Beijing 100191, China
- Department
of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
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11
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Myers MB, McKinzie PB, Wang Y, Meng F, Parsons BL. ACB-PCR quantification of somatic oncomutation. Methods Mol Biol 2014; 1105:345-63. [PMID: 24623241 DOI: 10.1007/978-1-62703-739-6_27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Allele-specific competitive blocker-polymerase chain reaction (ACB-PCR) is a sensitive approach for the selective amplification of an allele. Using the ACB-PCR technique, hotspot point mutations in oncogenes and tumor-suppressor genes (oncomutations) are being developed as quantitative biomarkers of cancer risk. ACB-PCR employs a mutant specific primer (with a 3'-penultimate mismatch relative to the mutant DNA sequence, but a double 3'-terminal mismatch relative to the wild-type DNA sequence) to selectively amplify rare mutant DNA molecules. A blocker primer (having a non-extendable 3'-end and with a 3'-penultimate mismatch relative to the wild-type DNA sequence, but a double 3'-terminal mismatch relative to the mutant DNA sequence) is included in ACB-PCR to selectively repress amplification from the abundant wild-type molecules. Consequently, ACB-PCR is capable of quantifying the level of a single basepair substitution mutation in a DNA population when present at a mutant:wild type ratio of 10(-5) or greater. Quantification of rare mutant alleles is achieved by parallel analysis of unknown samples and mutant fraction (MF) standards (defined mixtures of mutant and wild-type DNA sequences). The ability to quantify specific mutations with known association to cancer has several important applications, including evaluating the carcinogenic potential of chemical exposures in rodent models and in the diagnosis and treatment of cancer. This chapter provides a step-by-step description of the ACB-PCR methodology as it has been used to measure human KRAS codon 12 GGT to GAT mutation.
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Affiliation(s)
- Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, HFT-120, Jefferson, AR, 72079, USA,
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12
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Electrochemical biosensor based on functional composite nanofibers for detection of K-ras gene via multiple signal amplification strategy. Anal Biochem 2014; 466:51-8. [PMID: 25173509 DOI: 10.1016/j.ab.2014.08.023] [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: 06/03/2014] [Revised: 08/10/2014] [Accepted: 08/20/2014] [Indexed: 12/16/2022]
Abstract
An electrochemical biosensor based on functional composite nanofibers for hybridization detection of specific K-ras gene that is highly associated with colorectal cancer via multiple signal amplification strategy has been developed. The carboxylated multiwalled carbon nanotubes (MWCNTs) doped nylon 6 (PA6) composite nanofibers (MWCNTs-PA6) was prepared using electrospinning, which served as the nanosized backbone for thionine (TH) electropolymerization. The functional composite nanofibers [MWCNTs-PA6-PTH, where PTH is poly(thionine)] used as supporting scaffolds for single-stranded DNA1 (ssDNA1) immobilization can dramatically increase the amount of DNA attachment and the hybridization sensitivity. Through the hybridization reaction, a sandwich format of ssDNA1/K-ras gene/gold nanoparticle-labeled ssDNA2 (AuNPs-ssDNA2) was fabricated, and the AuNPs offered excellent electrochemical signal transduction. The signal amplification was further implemented by forming network-like thiocyanuric acid/gold nanoparticles (TA/AuNPs). A significant sensitivity enhancement was obtained; the detection limit was down to 30fM, and the discriminations were up to 54.3 and 51.9% between the K-ras gene and the one-base mismatched sequences including G/C and A/T mismatched bases, respectively. The amenability of this method to the analyses of K-ras gene from the SW480 colorectal cancer cell lysates was demonstrated. The results are basically consistent with those of the K-ras Kit (HRM: high-resolution melt). The method holds promise for the diagnosis and management of cancer.
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13
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Liu Y, Gudnason H, Li YP, Bang DD, Wolff A. An oligonucleotide-tagged microarray for routine diagnostics of colon cancer by genotyping KRAS mutations. Int J Oncol 2014; 45:1556-64. [PMID: 25018048 DOI: 10.3892/ijo.2014.2541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/14/2014] [Indexed: 11/06/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent types of cancer, causing significant morbidity and mortality worldwide. CRC is curable if diagnosed at an early stage. Mutations in the oncogene KRAS play a critical role in early development of CRC. Detection of activated KRAS is of diagnostic and therapeutic importance. In this study, KRAS gene fragments containing mutations in codon 12 were amplified by multiplex PCR using a 5'-Cy5-labeled reverse primer in combination with 3'-mutation-specific forward primers that were linked with four unique nucleotide-sequence tags at the 5'-end. The Cy5-labeled reverse primer was extended under PCR amplification to the 5'-end of the mutation-specific forward primers and thus included the complimentary sequence of the tag. PCR products were hybridized to tag-probes immobilized on various substrates and detected by a scanner. Our results indicate that all mutations at codon 12 of KRAS derived from cancer cells and clinical samples could be unambiguously detected. KRAS mutations were accurately detected when the mutant DNA was present only in 10% of the starting mixed materials including wild-type genomic DNA, which was isolated from either cancer cells or spiked fecal samples. The immobilized tag-probes were stable under multiple thermal cycling treatments, allowing re-use of the tag-microarray and further optimization to solid PCR. Our results demonstrated that a novel oligonucleotide-tagged microarray system has been developed which would be suitable to be used for detection of KRAS mutations and clinical diagnosis of CRC.
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Affiliation(s)
- Yuliang Liu
- DTU Veterinary Laboratory of Applied Micro-Nanotechnology, Department of Poultry, Fish and Fur Animals, National Veterinary Institute, Technical University of Denmark, DK-8200, Aarhus N, Denmark
| | - Haukur Gudnason
- DTU Nanotech. BioLabchip, Department of Micro and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Yi-Ping Li
- DTU Veterinary Laboratory of Applied Micro-Nanotechnology, Department of Poultry, Fish and Fur Animals, National Veterinary Institute, Technical University of Denmark, DK-8200, Aarhus N, Denmark
| | - Dang Duong Bang
- DTU Veterinary Laboratory of Applied Micro-Nanotechnology, Department of Poultry, Fish and Fur Animals, National Veterinary Institute, Technical University of Denmark, DK-8200, Aarhus N, Denmark
| | - Anders Wolff
- DTU Nanotech. BioLabchip, Department of Micro and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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14
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Real-time bidirectional pyrophosphorolysis-activated polymerization for quantitative detection of somatic mutations. PLoS One 2014; 9:e96420. [PMID: 24769870 PMCID: PMC4000192 DOI: 10.1371/journal.pone.0096420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/07/2014] [Indexed: 12/24/2022] Open
Abstract
Detection of somatic mutations for targeted therapy is increasingly used in clinical settings. However, due to the difficulties of detecting rare mutations in excess of wild-type DNA, current methods often lack high sensitivity, require multiple procedural steps, or fail to be quantitative. We developed real-time bidirectional pyrophosphorolysis-activated polymerization (real-time Bi-PAP) that allows quantitative detection of somatic mutations. We applied the method to quantify seven mutations at codons 12 and 13 in KRAS, and 2 mutations (L858R, and T790M) in EGFR in clinical samples. The real-time Bi-PAP could detect 0.01% mutation in the presence of 100 ng template DNA. Of the 34 samples from the colon cancer patients, real-time Bi-PAP detected 14 KRAS mutant samples whereas the traditional real-time allele-specific PCR missed two samples with mutation abundance <1% and DNA sequencing missed nine samples with mutation abundance <10%. The detection results of the two EGFR mutations in 45 non-small cell lung cancer samples further supported the applicability of the real-time Bi-PAP. The real-time Bi-PAP also proved to be more efficient than the real-time allele-specific PCR in the detection of templates prepared from formalin-fixed paraffin-embedded samples. Thus, real-time Bi-PAP can be used for rapid and accurate quantification of somatic mutations. This flexible approach could be widely used for somatic mutation detection in clinical settings.
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Parsons BL, Myers MB. KRAS mutant tumor subpopulations can subvert durable responses to personalized cancer treatments. Per Med 2013; 10:191-199. [PMID: 27867401 DOI: 10.2217/pme.13.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
KRAS mutations in colorectal and lung cancers predict failure to respond to therapies that target the EGFR. Significant percentages of patients with KRAS wild-type tumors also fail to respond to these therapies. Relapse occurs in patients with KRAS wild-type and mutant tumors, with moderately longer progression-free survival in patients with KRAS wild-type tumors. Colon and lung tumors frequently carry KRAS mutant tumor subpopulations not detected by DNA sequencing. This suggests detected and undetected KRAS mutant subpopulations in colon and lung tumors are undermining the efficacy of anti-EGFR therapies. Therefore, consideration should be given to combining therapies that target KRAS mutant cells with those that downregulate EGFR signaling. As tumors are frequently polyclonal in origin and comprised of distinct clonal populations carrying complementing genetic and/or epigenetic lesions, preclinical models that assess the efficacy of combination therapies in the context of heterogeneous tumor cell populations will be essential for progress in this area.
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Affiliation(s)
- Barbara L Parsons
- US FDA, National Center for Toxicological Research, Division of Genetic & Molecular Toxicology, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Meagan B Myers
- US FDA, National Center for Toxicological Research, Division of Genetic & Molecular Toxicology, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
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Myers MB, Wang Y, McKim KL, Parsons BL. Hotspot oncomutations: implications for personalized cancer treatment. Expert Rev Mol Diagn 2012; 12:603-20. [PMID: 22845481 DOI: 10.1586/erm.12.51] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding the extent to which specific tumor mutations impact or mediate patient response to particular cancer therapies has become a rapidly increasing area of research. Recent research findings regarding four predominant mutational targets (KRAS, BRAF, EGFR and PIK3CA) show that these tumor mutations have predictive power for identifying which patients are likely to respond to particular therapies, and have prognostic significance irrespective of treatment. However, in this regard, the literature is frequently nuanced and sometimes contradictory. This lack of clarity may be due, at least in part, to the utilization of mutation detection methods with varying sensitivities across studies of different patient populations. Nevertheless, considerable evidence suggests minor tumor subpopulations may be contributing to inappropriate patient stratification, development of resistance to treatment, and the relapse that often follows treatment with molecularly targeted therapies. Consequently, mutant tumor subpopulations need to be considered in order to improve strategies for personalized cancer treatment.
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Affiliation(s)
- Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA.
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17
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Laghi L, Bianchi P, Delconte G, Celesti G, Di Caro G, Pedroni M, Chiaravalli AM, Jung B, Capella C, de Leon MP, Malesci A. MSH3 protein expression and nodal status in MLH1-deficient colorectal cancers. Clin Cancer Res 2012; 18:3142-53. [PMID: 22496206 DOI: 10.1158/1078-0432.ccr-12-0175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with colorectal cancers (CRC) and high microsatellite instability (MSI) have a better outcome than their chromosome-unstable counterpart. Given the heterogeneity of microsatellite-unstable CRCs, we wanted to see whether any MSI-associated molecular features are specifically associated with prognosis. EXPERIMENTAL DESIGN One hundred and nine MSI-high CRCs were typed for primary mismatch repair (MMR) defect and for secondary loss of MMR proteins. Frameshifts at seven target genes, mutations in the RAS pathway, and methylation at MLH1/CDKN2A promoters were also searched. The interplay of molecular findings with clinicopathologic features and patient survival was analyzed. RESULTS Of 84 MLH1-deficient CRCs, 31 (36.9%) had MSH3 and 11 (13.1%) had MSH6 loss (P < 0.001), biallelic frameshift mutations at mononucleotide repeats accounting for most (78%) MSH3 losses. As compared with MSH3-retaining cancers, MLH1-deficient tumors with MSH3 loss showed a higher number of mutated target genes (3.94 ± 1.56 vs. 2.79 ± 1.75; P = 0.001), absence of nodal involvement at pathology [N0; OR, 0.11; 95% confidence interval (CI), 0.04-0.43, P < 0.001], and better disease-free survival (P = 0.06). No prognostic value was observed for KRAS status and for MLH1/CDKN2A promoter methylation. The association between MSH3 loss and N0 was confirmed in an independent cohort of 71 MLH1-deficient CRCs (OR, 0.23; 95% CI, 0.06-0.83, P = 0.02). CONCLUSIONS MLH1-deficient CRCs not expressing MSH3 have a more severe MSI, a lower rate of nodal involvement, and a better postsurgical outcome.
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Affiliation(s)
- Luigi Laghi
- Laboratory of Molecular Gastroenterology, Department of Gastroenterology, IRCCS Istituto Clinico Humanitas - Rozzano, Milano, Italy.
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Dijkstra JR, Opdam FJM, Boonyaratanakornkit J, Schönbrunner ER, Shahbazian M, Edsjö A, Hoefler G, Jung A, Kotsinas A, Gorgoulis VG, López-Ríos F, de Stricker K, Rouleau E, Biesmans B, van Krieken JHJM. Implementation of formalin-fixed, paraffin-embedded cell line pellets as high-quality process controls in quality assessment programs for KRAS mutation analysis. J Mol Diagn 2012; 14:187-91. [PMID: 22414609 DOI: 10.1016/j.jmoldx.2012.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/14/2011] [Accepted: 01/04/2012] [Indexed: 11/17/2022] Open
Abstract
In recent years, the mutational status of the KRAS oncogene has become incorporated into standard medical care as a predictive marker for therapeutic decisions related to patients with metastasized colorectal cancer. This is necessary, because these patients benefit from epidermal growth factor receptor (EGFR)-targeted therapy with increased progression-free survival only if the tumor does not carry a mutation in KRAS. Many different analytical platforms, both those commercially available and those developed in house, have been used within pathology laboratories to assess KRAS mutational status. For a testing laboratory to become accredited to perform such tests, it is essential that they perform reliability testing, but it has not previously been possible to perform this kind of testing on the complete workflow on a large scale without compromising reproducibility or the mimicry of the control sample. We assessed a novel synthetic control for formalin-fixed, paraffin-embedded (FFPE) tumor samples in a blind study conducted within nine laboratories across Europe. We show that FFPE material can, at least in part, mimic clinical samples and we demonstrate this control to be a valuable tool in the assessment of platforms used in testing for KRAS mutational status.
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Affiliation(s)
- Jeroen R Dijkstra
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Emelyanova MA, Amossenko FA, Chudinov AV, Surzhikov SA, Kazubskaya TP, Lubchenko LN, Nasedkina TV. Detection of KRAS mutations in tumor cells using biochips. Mol Biol 2011; 45:797-803. [DOI: 10.1134/s0026893311040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
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20
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Kitano S, Nakayama M, Yamane A, Tsukahara Y, Amano M. Detection of DNA mutations by fluorescence resonance energy transfer-based preferential homoduplex formation assay. Anal Biochem 2011; 408:197-205. [DOI: 10.1016/j.ab.2010.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/18/2010] [Accepted: 09/08/2010] [Indexed: 11/25/2022]
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21
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El-Serafi MM, Bahnassy AA, Ali NM, Eid SM, Kamel MM, Abdel-Hamid NA, Zekri ARN. The prognostic value of c-Kit, K-ras codon 12, and p53 codon 72 mutations in Egyptian patients with stage II colorectal cancer. Cancer 2010; 116:4954-64. [PMID: 20652953 DOI: 10.1002/cncr.25417] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND The prognosis for patients with colorectal cancer (CRC) depends mainly on standard clinicopathologic factors. However, patients with similar disease characteristics exhibit various outcomes, especially in stage II. Therefore, the identification of molecular prognostic markers is needed to predict patient outcomes. METHODS The authors assessed the prognostic value of c-Kit (also called cluster of differentiation 117 [CD117] or KIT), cyclooxygenase-2 (COX-2), tumor protein 53 (p53), and Kirsten rat sarcoma viral oncogene homolog (K-ras) aberrations in 90 patients with stage II CRC using immunohistochemistry and molecular techniques. The results were correlated with standard clinicopathologic prognostic factors, overall survival (OS), and disease-free survival (DFS). RESULTS COX2 and c-Kit overexpression was detected in 54.6% and 59.3% of patients, respectively. Overexpression of p53 was detected in 47 patients, including 29 who had mutations, and a unique mutation pattern was detected with 3 hotspots at codons 72, 245, and 273. Overexpression of ras was detected in 44 patients, including 37 who had mutations. On multivariate analysis, c-Kit overexpression, p53 codon 72 mutations, perforation, and performance status were independent prognostic factors for DFS (P=.054, P=.015, P<.0001, and P=.043, respectively); whereas codon 12 K-ras mutation, performance status, and perforation were independent prognostic factors for OS (P=.033, P=.006, and P<.0001, respectively). CONCLUSIONS The current results provide evidence for the prognostic value of c-Kit overexpression in patients with stage II CRC. The high p53 mutation rate and the unique hotspot in codon 72 have not been reported previously in CRC. This may be related to environmental or racial features that are unique to the studied population.
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Affiliation(s)
- Mostafa M El-Serafi
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
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22
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Parsons BL, Meng F. K-RAS mutation in the screening, prognosis and treatment of cancer. Biomark Med 2010; 3:757-69. [PMID: 20477713 DOI: 10.2217/bmm.09.95] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The potential use of K-RAS mutation as a cancer screening biomarker has been investigated for many years. Numerous associations between K-RAS mutation and various cancers have been established, but these associations have not been translated into effective, cost-efficient cancer screening strategies. This lack of progress may be due to the existence of K-RAS mutation in nontumor tissues and/or using detection, rather than quantitation, of K-RAS mutation as the endpoint for cancer risk categorization. K-RAS mutation appears to be a useful prognostic biomarker for colon cancer. Recent progress toward sensitive and quantitative mutation characterization and the successful use of K-RAS mutation in a personalized medicine approach to targeted biological therapy selection are likely to re-direct and expand the use of K-RAS mutation as a cancer biomarker in the near future.
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Affiliation(s)
- Barbara L Parsons
- US Food and Drug Administration, National Center for Toxicological Research, Division of Genetic & Reproductive Toxicology, HFT-120, 3900 NCTR Rd. Jefferson, AR 72079, USA.
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Detection of Occult Metastases in Sentinel Lymph Nodes From Colon Cancer Patients by K-ras Mutation Peptide Nucleic Acid Clamp PCR. Ann Surg 2010; 251:1087-91. [DOI: 10.1097/sla.0b013e3181dae1bc] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Parsons BL, Marchant-Miros KE, Delongchamp RR, Verkler TL, Patterson TA, McKinzie PB, Kim LT. ACB-PCR Quantification of K-RASCodon 12 GAT and GTT Mutant Fraction in Colon Tumor and Non-Tumor Tissue. Cancer Invest 2010. [DOI: 10.1080/07357901003630975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Affiliation(s)
- Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Zhu D, Xing D, Tang Y, Zhang L. A novel mutant allele specific amplification and electrochemiluminescence method for the detection of point mutation in clinical samples. Biosens Bioelectron 2009; 24:3306-10. [DOI: 10.1016/j.bios.2009.04.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 04/17/2009] [Accepted: 04/17/2009] [Indexed: 11/25/2022]
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Hu Y, Le Leu RK, Young GP. Detection of K-ras mutations in azoxymethane-induced aberrant crypt foci in mice using LNA-mediated real-time PCR clamping and mutant-specific probes. Mutat Res 2009; 677:27-32. [PMID: 19442760 DOI: 10.1016/j.mrgentox.2009.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 04/23/2009] [Accepted: 05/03/2009] [Indexed: 10/20/2022]
Abstract
Azoxymethane, a rodent colon-specific carcinogen, induce DNA damage, and causes proto-oncogene K-ras point mutations and subsequent tumor formation if DNA damage is not repaired or removed. The present study was designed to detect and characterize K-ras mutations in azoxymethane (AOM)-induced aberrant crypt foci (ACF) in mice, and determine whether dietary supplementation of selenium influences K-ras mutations frequency in ACF using a new PCR technique of locked nucleic acid-mediated real-time PCR clamping combined with mutant-specific probes. K-ras mutations were identified in 33% of AOM-induced ACF. In addition to G to A transition mutation, specific G to T transversion mutation was also identified for the first time in mouse ACF. Furthermore, selenium intake was associated with reduced ACF formation and reduced K-ras mutations rate, respectively, from 112 and 37% in mice fed control diet to 65 and 14% in mice fed selenium-containing diet (p < 0.05). This is the first report of the use of one-step LNA-mediated real-time PCR clamping to detect K-ras mutations in AOM-induced colon cancer model. It is highly sensitive and can be applied to the detection of early genetic alterations in carcinogen-based animal models.
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Affiliation(s)
- Ying Hu
- Department of Medicine, Flinders Centre for Cancer Prevention and Control, Flinders University of South Australia, Adelaide, Australia.
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Hong YS, Kim TW. Chemotherapy for Colorectal Cancer. THE KOREAN JOURNAL OF GASTROENTEROLOGY 2009; 54:355-63. [DOI: 10.4166/kjg.2009.54.6.355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Gilje B, Heikkilä R, Oltedal S, Tjensvoll K, Nordgård O. High-fidelity DNA polymerase enhances the sensitivity of a peptide nucleic acid clamp PCR assay for K-ras mutations. J Mol Diagn 2008; 10:325-31. [PMID: 18556764 DOI: 10.2353/jmoldx.2008.070183] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sensitive detection of tumor-specific point mutations is of interest in both the early detection of cancer and the monitoring of treatment at a molecular level. Recently, peptide nucleic acid (PNA) clamp real-time PCR has provided a time-sparing and sensitive method for the detection of mutations in the presence of a large excess of wild-type DNA. We present the first report that the sensitivity of PNA clamp PCR is limited by the low fidelity of TaqDNA polymerase. Replication errors introduced by Taq polymerase in the PNA-binding site were amplified during PCR due to the resulting mismatches between PNA and DNA. To reduce the frequency of polymerase-induced errors, we developed a PNA clamp PCR assay for the detection of mutations in codons 12 and 13 of the K-ras gene based on a high-fidelity DNA polymerase. The sensitivity of our assay increased approximately 10-fold, significantly detecting mutant DNA diluted 20,000-fold in wild-type DNA (P = 0.025), compared with its detection at 2000-fold dilution (P = 0.039) when Taq polymerase was used. Our data suggest that the replication errors caused by Taq polymerase must be taken into consideration for PNA clamp PCR and for other methods based on selective PCR amplification, and that these assays can be enhanced by high-fidelity DNA polymerases.
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Affiliation(s)
- Bjørnar Gilje
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway.
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Vladimirova V, Denkhaus D, Soerensen N, Wagner S, Wolff JEA, Pietsch T. Low level of microsatellite instability in paediatric malignant astrocytomas. Neuropathol Appl Neurobiol 2007; 34:547-54. [PMID: 18053027 DOI: 10.1111/j.1365-2990.2007.00919.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM Microsatellite instability (MSI) has been proposed as a possible mechanism in the development of cancer. The aim of the current study was to determine whether MSI is involved in the pathogenesis of paediatric malignant astrocytomas. METHODS We screened a cohort of 126 high-grade astrocytoma samples for MSI using a sensitive and precise method of DNA analysis including a panel of five mononucleotide repeats, in combination with immunohistochemistry for DNA mismatch repair (MMR) proteins. RESULTS We identified low level of MSI (MSI-L) in four of 126 (3.2%) paediatric malignant astrocytic tumours. To analyse the molecular profile associated with MSI-L positive tumours, we performed immunohistochemistry for protein expression of hMSH6 and p53 as well as mutational analysis of the K-ras gene. In MSI-L paediatric malignant astrocytic tumours we detected retained nuclear expression of hMSH6 protein and strong nuclear accumulation of p53 protein indicating possible mutations of TP53. There was no correlation between K-ras mutational status and frequency of MSI in this patient population. CONCLUSION Our results suggest that the MSI-L phenotype is associated with p53 accumulation and/or mutations. However, this represents only a small subgroup of paediatric gliomas with possible distinct biological features, and the deficiencies of DNA MMR genes do not play a main role in the tumourigenesis of the majority of paediatric malignant astrocytomas.
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Affiliation(s)
- V Vladimirova
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany.
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Chiou CC, Luo JD, Chen TL. Single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe for the detection of rare mutations. Nat Protoc 2007; 1:2604-12. [PMID: 17406515 DOI: 10.1038/nprot.2006.428] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The detection of rare mutant DNA from a background of wild-type alleles usually requires laborious manipulations, such as restriction enzyme digestion and gel electrophoresis. Here, we describe a protocol for homogeneous detection of rare mutant DNA in a single tube. The protocol uses a peptide nucleic acid (PNA) as both PCR clamp and sensor probe. The PNA probe binds tightly to perfectly matched wild-type DNA template but not to mismatched mutant DNA sequences, which specifically inhibits the PCR amplification of wild-type alleles without interfering with the amplification of mutant DNA. A fluorescein tag (which undergoes fluorescence resonance energy transfer with the adjacent fluorophore of an anchor probe when both are annealed to the template DNA) also allows the PNA probe to generate unambiguous melting curves to detect mutant DNA during real-time fluorescent monitoring. The whole assay takes about only 1 h. This protocol has been used for detecting mutant K-ras DNA and could be applied to the detection of other rare mutant DNAs.
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Affiliation(s)
- Chiuan-Chian Chiou
- Graduate Institute of Medical Biotechnology, Chang Gung University, KweiShan, TaoYuan 333, Taiwan.
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Klebig F, Fischer C, Petri S, Gerull H, Wagener C, Tschentscher P. Limitations in Molecular Detection of Lymph Node Micrometastasis From Colorectal Cancer. ACTA ACUST UNITED AC 2007; 16:91-5. [PMID: 17525678 DOI: 10.1097/pdm.0b013e31803278ee] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer patients with lymph node metastasis have a shorter survival and may require adjuvant therapy after surgery of the primary tumor. It is supposed that a more reliable diagnosis can be achieved using tumor-specific DNA mutations for the detection of metastasizing cells. To design a practical approach for a molecular diagnosis of micrometastasis, we applied direct DNA sequencing to screen 48 early stage colorectal carcinomas for the most frequent mutations of the KRAS, P53, and APC tumor genes. KRAS mutations were detected as frequently as described earlier. In contrast, the frequency of P53 and APC hot spot mutations was unexpectedly low, compared with previous studies using other screening methods or including advanced tumor stages. Not more than 31% of early stage tumors showed a mutation in at least 1 of the selected hot spot codons. Applying mutant-enriched polymerase chain reaction (PCR), the mutation of the primary tumor was detected in lymph node DNA from 2 of the KRAS-positive patients. In 1 patient, the result was not verified by subtractive iterative PCR, a principally different molecular method with high sensitivity and specificity. Our data suggest that screening for suitable markers for a molecular detection of occult lymph node metastasis cannot be restricted to small-sized hot spot regions of a few tumor genes and possibly must include tumor-specific epigenetic changes. Furthermore, restriction enzyme-based methods such as mutant-enriched PCR are not suitable to detect any mutation with equal efficiency and they should be carefully controlled to avoid false-positive detection of marker mutations in lymph node DNA.
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Affiliation(s)
- Felix Klebig
- Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany
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Chien CC, Chen SH, Liu CC, Lee CL, Yang RN, Yang SH, Huang CJ. Correlation of K-ras codon 12 mutations in human feces and ages of patients with colorectal cancer (CRC). Transl Res 2007; 149:96-102. [PMID: 17240321 DOI: 10.1016/j.trsl.2006.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 07/13/2006] [Accepted: 09/04/2006] [Indexed: 11/20/2022]
Abstract
Colorectal cancer (CRC) is the predominant gastrointestinal malignancy and constitutes a major medical and economic burden worldwide. A thorough understanding of the oncogenes or genes related to tumorigenesis is the key to developing successful therapeutic strategies. Molecular analysis of feces constitutes a potentially potent and noninvasive method for detection of CRC. Using nested reverse transcription-polymerase chain reaction (RT-PCR) and amplified restriction fragment length polymorphism analysis, sloughed cells from the entire length of the colon and rectum were analyzed for expression of activating K-ras codon 12 mutants, which are becoming attractive targets for antisense treatment. K-ras codon 12 mutant sequences were detected in feces of 5% (1/20) of healthy controls, in feces of 41% (12/29) of CRC patients, in 10% (3/29) of isolates of tissue complementary DNA (cDNA), and in 14% (4/29) of isolates of genomic DNA. Age of patient was significantly associated with K-ras codon 12 sequences in feces: Patients with wild-type K-ras codon 12 sequences were significantly younger than those with mutated forms of K-ras codon 12. Fecal ribonucleic acid (RNA) analysis was demonstrated to be a useful for diagnosis of CRC. This technique may be suitable for screening and determining the clinical significance of active mutations of the K-ras gene in feces and would possibly be useful for identifying patients that would benefit from antisense therapy.
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Affiliation(s)
- Chih-Cheng Chien
- Department of Anesthesiology, Cathay General Hospital, Neihu, and School of Medicine, Fu Jen Catholic University, Hsin-chuang, Taiwan
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Mori S, Sugahara K, Uemura A, Akamatsu N, Tutsumi R, Kuroki T, Hirakata Y, Atogami S, Hasegawa H, Yamada Y, Kamihira S. Rapid, Simple, and Accurate Detection of K-ras Mutations From Body Fluids Using Real-Time PCR and DNA Melting Curve Analysis. Lab Med 2006. [DOI: 10.1309/6507kah8ev592mj4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Luo JD, Chan EC, Shih CL, Chen TL, Liang Y, Hwang TL, Chiou CC. Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe. Nucleic Acids Res 2006; 34:e12. [PMID: 16432256 PMCID: PMC1345699 DOI: 10.1093/nar/gnj008] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The major problem of using somatic mutations as markers of malignancy is that the clinical samples are frequently containing a trace amounts of mutant allele in a large excess of wild-type DNA. Most methods developed thus far for the purpose of tickling this difficult problem require multiple procedural steps that are laborious. We report herein the development of a rapid and simple protocol for detecting a trace amounts of mutant K-ras in a single tube, one-step format. In a capillary PCR, a 17mer peptide nucleic acid (PNA) complementary to the wild-type sequence and spanning codons 12 and 13 of the K-ras oncogene was used to clamp-PCR for wild-type, but not mutant alleles. The designated PNA was labeled with a fluorescent dye for use as a sensor probe, which differentiated all 12 possible mutations from the wild-type by a melting temperature (T(m)) shift in a range of 9 to 16 degrees C. An extension temperature of 60 degrees C and an opposite primer 97 nt away from the PNA were required to obtain full suppression of wild-type PCR. After optimization, the reaction detected mutant templates in a ratio of 1:10,000 wild-type alleles. Using this newly devised protocol, we have been able to detect 19 mutants in a group of 24 serum samples obtained from patients with pancreatic cancer. Taken together, our data suggest that this newly devised protocol can serve as an useful tool for cancer screening as well as in the detection of rare mutation in many diseases.
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Affiliation(s)
- Ji-Dung Luo
- Department of Medical Biotechnology and Laboratory Science, Chang Gung UniversityTaoyuan 333, Taiwan
| | - Err-Cheng Chan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung UniversityTaoyuan 333, Taiwan
| | - Chun-Liang Shih
- Department of Medical Biotechnology and Laboratory Science, Chang Gung UniversityTaoyuan 333, Taiwan
| | - Tai-Long Chen
- Department of Medical Biotechnology and Laboratory Science, Chang Gung UniversityTaoyuan 333, Taiwan
| | - Ying Liang
- Department of Surgery, Chang Gung Memorial HospitalTaoyuan 333, Taiwan
| | - Tsann-Long Hwang
- Department of Surgery, Chang Gung Memorial HospitalTaoyuan 333, Taiwan
| | - Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung UniversityTaoyuan 333, Taiwan
- To whom correspondence should be addressed: Tel: +886 3 2118800, ext. 5204; Fax: +886 3 2118035;
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Conzelmann M, Linnemann U, Berger MR. Detection of disseminated tumour cells in the liver of cancer patients. Eur J Surg Oncol 2005; 31:977-85. [PMID: 16126360 DOI: 10.1016/j.ejso.2005.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 07/18/2005] [Accepted: 07/18/2005] [Indexed: 12/18/2022] Open
Abstract
AIMS The liver is a common site of metastasis from a variety of solid malignancies. This is due to disseminated tumour cells (DTC) that have spread prior to or during surgery from the primary carcinoma. This article gives a short overview of the data published on the detection of DTC in the liver and describes the commonly used detection methods and respective markers. METHODS A literature survey was performed in public medical databases comprising the last 15 years with focus on DTC detection in liver tissue of cancer patients. KEY FINDINGS Although the liver is a preferred site of metastasis, only a few studies have analysed the DTC incidence in inconspicuous liver tissue. The available reports include only patients with pancreatic and colorectal carcinomas. In patients with pancreatic cancer the DTC incidence varied from 5 to 76%. No follow-up data has been reported so far. In patients with colorectal carcinoma hepatic DTC were found in 5-69% of cases. A negative prognostic influence of hepatic DTC was reported in all but one studies with follow-up information. CONCLUSIONS The detection of DTC in the liver can contribute to identify patients with increased risk who could benefit from an intensified follow-up or new treatment strategies.
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Affiliation(s)
- M Conzelmann
- Unit of Toxicology and Chemotherapy, German Cancer Research Center, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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Luu HH, Kang Q, Park JK, Si W, Luo Q, Jiang W, Yin H, Montag AG, Simon MA, Peabody TD, Haydon RC, Rinker-Schaeffer CW, He TC. An Orthotopic Model of Human Osteosarcoma Growth and Spontaneous Pulmonary Metastasis. Clin Exp Metastasis 2005; 22:319-29. [PMID: 16170668 DOI: 10.1007/s10585-005-0365-9] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 06/28/2005] [Indexed: 10/25/2022]
Abstract
Osteosarcoma is the most common primary malignancy of bone and patients often develop pulmonary metastases. In order to investigate the pathogenesis of human osteosarcoma, there is a great need to develop a clinically relevant animal model. Here we report the development of an osteosarcoma animal model using three related human osteosarcoma lines, the parental TE-85 and two derivative lines MNNG/HOS and 143B. In vitro characterization demonstrated that the 143B line had the greatest cell migration and the least cell adhesion activities among the three lines. The 143B line also exhibited the greatest ability for anchorage independent growth. When GFP-tagged osteosarcoma cells were injected into the proximal tibia of athymic mice, we found that 143B cells were highly tumorigenic and metastatic, and MNNG/HOS cells were tumorigenic but significantly less metastatic. TE85 cells were neither tumorigenic nor metastatic. The number of pulmonary metastases was found 50-fold higher in 143B injected animals than that in MNNG/HOS injected mice. No pulmonary metastases were detected in TE85 injected animals for up to 8 weeks. Primary tumors formed by MNNG/HOS and 143B cells could be visualized by whole body fluorescence imaging, while the pulmonary metastases were visualized on the necropsied samples. The GFP tagged 143B cells (and to a lesser extent, MNNG/HOS cells) were readily recovered from lung metastases. This clinically relevant model of human osteosarcoma provides varying degrees of tumor growth at the primary site and metastatic potential. Thus, this orthotopic model should be a valuable tool to investigate factors that promote or inhibit osteosarcoma growth and/or metastasis.
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Affiliation(s)
- Hue H Luu
- Molecular Oncology Laboratory, Department of Surgery, The University of Chicago Medical Center, 5841 South Maryland Avenue, Chicago, IL 60637, USA
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Conzelmann M, Linnemann U, Berger MR. Detection of disseminated tumour cells in the liver of colorectal cancer patients. Eur J Surg Oncol 2005; 31:38-44. [PMID: 15642424 DOI: 10.1016/j.ejso.2004.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2004] [Indexed: 11/25/2022] Open
Abstract
AIMS The aim of this study was to assess the incidence and lobar distribution of three surrogate tumour cell markers in biopsies from both liver lobes. PATIENTS AND METHODS This study comprised 189 patients for whom DNA and/or RNA was available from both liver lobes and who showed at least one positive marker in one liver lobe. Detection of cytokeratin 20 (CK20) and guanylylcyclase C (GCC) was performed by nested reverse transcription-PCR. For detection of K-ras mutations in codons 12 and 13, a PCR-restriction-fragment-length-polymorphism assay was used. RESULTS The incidence of all markers and their combinations was higher in the smaller left lobe than in the larger right lobe (CK20: 62 vs 38%; GCC: 52 vs 48%; K-ras: 61 vs 39%; CK20+GCC: 61 vs 39%; CK20+GCC and/or K-ras: 61 vs 39%). The marker incidence in the two liver lobes was independent from the location of the respective primary colorectal carcinoma. CONCLUSIONS The markers CK20, GCC, and K-ras indicating cells shed from the primary CRC were detected more often individually and in combination in biopsies from the smaller left lobe than from the larger right lobe. The site of the primary tumour did not influence the marker incidence in both liver lobes.
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Affiliation(s)
- M Conzelmann
- Unit of Toxicology and Chemotherapy, German Cancer Research Center, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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Conzelmann M, Linnemann U, Berger MR. Molecular detection of clinical colorectal cancer metastasis: how should multiple markers be put to use? Int J Colorectal Dis 2005; 20:137-46. [PMID: 15459772 DOI: 10.1007/s00384-004-0640-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2004] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Up to 45% of colorectal cancer (CRC) patients will develop local recurrence or metastasis following curative resection. The latter is due to cells shed from the primary carcinoma prior to or during surgery. The aim of this study was to contribute toward a "rational"-approach for detecting these disseminated tumor cells (DTC) using a combination of independent markers and detection methods. PATIENTS/METHODS Liver, lymph node, and bone marrow samples from 246 CRC patients were screened for DTC using three markers: mutated K-ras was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and cytokeratin 20 (CK20) and guanylylcyclase C (GCC), indicating circulating epithelial cells, were tracked by nested reverse-transcription (RT) PCR. RESULTS The rate of positive findings of the individual markers (CK20: 88%; GCC: 88%; K-ras: 67%) and their combinations (88-50%) was significantly higher in biopsies from liver metastases than in liver samples from patients without evident distant metastasis (M0; p<0.03). The detection rate of individual markers (except GCC) was also significantly elevated in inconspicuous liver tissue adjacent to metastasis compared with specimens from M0 patients. When using the concomitant detection of all three markers as criterion for DTC in the liver of M0 patients, however, no patient was DTC-positive. Therefore, the concomitant presence of the two CEC markers (CK20 plus GCC) and/or the presence of mutated K-ras were preferred for a combined evaluation, which resulted in a 24% detection rate for biopsies from both liver lobes. This translates into 39% of M0 patients with at least one positive liver biopsy. CONCLUSION Our results suggest that the concomitant detection of CK20 plus GCC and/or the presence of mutated K-ras are a rational approach for tracking CEC/DTC in CRC patients.
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Affiliation(s)
- Michael Conzelmann
- Unit of Toxicology and Chemotherapy, German Cancer Research Center, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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Smakman N, Kranenburg O, Vogten JM, Bloemendaal AL, van Diest P, Borel Rinkes IH. Cyclooxygenase-2 Is a Target of KRASD12, Which Facilitates the Outgrowth of Murine C26 Colorectal Liver Metastases. Clin Cancer Res 2005. [DOI: 10.1158/1078-0432.41.11.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: Mutational activation of the KRAS oncogene and overexpression of cyclooxygenase-2 (COX-2) contribute to colorectal carcinoma (CRC) development, but the relationship between these two events is unclear. This study was designed to clarify that relationship and to assess the contribution of KRAS-dependent COX-2 to the seeding of CRC cells in the liver and to their outgrowth as liver metastases in an experimental mouse model.
Experimental Design: The effect of RNA interference–mediated KRAS knockdown on COX-2 expression and activity was tested in murine C26 CRC cells. The contribution of KRAS-dependent COX-2 to early metastatic tumor cell seeding (by intravital microscopy) and outgrowth of metastases in the liver (by bioluminescence imaging) was studied by using parecoxib, a novel and highly selective liver-activated COX-2 inhibitor. Intratumoral cell proliferation, apoptosis, and tumor-associated angiogenesis were assessed by immunohistochemistry on liver tissue sections.
Results: Stable knockdown of mutant KRASD12 in murine C26 CRC cells by RNA interference lead to a dramatic reduction of COX-2 synthesis and prostaglandin E2 production. Inhibition of host or tumor cell COX-2 activity had no effect on early metastatic cell seeding in the liver but greatly reduced intrahepatic tumor cell proliferation and the rate of liver metastasis outgrowth. COX-2 inhibition had no effect on early tumor vascularization or on tumor cell apoptosis.
Conclusions: The high levels of COX-2 enzyme and prostaglandin production in C26 CRC cells are primarily caused by the presence of endogenous mutant KRASD12. Furthermore, COX-2 inhibition affects the tumoral rather than the vascular compartment during the early stages of C26 liver metastasis outgrowth.
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Affiliation(s)
| | | | | | | | - Paul van Diest
- 2Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
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