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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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McKinzie PB, McKim KL, Pearce MG, Bishop ME, Parsons BL. Lifespan Kras mutation levels in lung and liver of B6C3F 1 mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:715-721. [PMID: 30255594 DOI: 10.1002/em.22198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Somatic mutations accumulate in the human genome and are correlated with increased cancer incidence as humans age. The standard model for studying the carcinogenic effects of exposures for human risk assessment is the rodent 2-year carcinogenicity assay. However, there is little information regarding the effect of age on cancer-driver gene mutations in these models. The mutant fraction (MF) of Kras codon 12 GGT to GAT and GGT to GTT mutations, oncogenic mutations orthologous between humans and rodents, was quantified over the lifespan of B6C3F1 mice. MFs were measured in lung and liver tissue, organs that frequently develop tumors following carcinogenic exposures. The MFs were evaluated at 4, 6, 8, 12, 21, and 85 weeks, with the 12-week and 21-week time points being coincident with the conclusion of 28-day and 90-day exposure durations used in short-term toxicity testing. The highly sensitive and quantitative Allele-specific Competitive Blocker PCR (ACB-PCR) assay was used to quantify the number of mutant Kras codon 12 alleles. The mouse lung showed a slight, but significant trend increase in the Kras codon 12 GAT mutation over the 85-week period. The trend with age can be equally well-fit by several non-linear functions, but not by a linear function. In contrast, the liver GAT mutation did not increase, and the GTT mutation did not increase for either organ. Even with the slight increase in the lung GAT MFs, our results indicate that the future use of Kras mutation as a biomarker of carcinogenic effect will not be confounded by animal age. Environ. Mol. Mutagen. 59:715-721, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Karen L McKim
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Mason G Pearce
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Michelle E Bishop
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, Arkansas
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Parsons BL, McKim KL, Myers MB. Variation in organ-specific PIK3CA and KRAS mutant levels in normal human tissues correlates with mutation prevalence in corresponding carcinomas. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:466-476. [PMID: 28755461 PMCID: PMC5601221 DOI: 10.1002/em.22110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 05/27/2023]
Abstract
Large-scale sequencing efforts have described the mutational complexity of individual cancers and identified mutations prevalent in different cancers. As a complementary approach, allele-specific competitive blocker PCR (ACB-PCR) is being used to quantify levels of hotspot cancer driver mutations (CDMs) with high sensitivity, to elucidate the tissue-specific properties of CDMs, their occurrence as tumor cell subpopulations, and their occurrence in normal tissues. Here we report measurements of PIK3CA H1047R mutant fraction (MF) in normal colonic mucosa, normal lung, colonic adenomas, colonic adenocarcinomas, and lung adenocarcinomas. We report PIK3CA E545K MF measurements in those tissues, as well as in normal breast, normal thyroid, mammary ductal carcinomas, and papillary thyroid carcinomas. We report KRAS G12D and G12V MF measurements in normal colon. These MF measurements were integrated with previously published ACB-PCR data on KRAS G12D, KRAS G12V, and PIK3CA H1047R. Analysis of these data revealed a correlation between the degree of interindividual variability in these mutations (as log10 MF standard deviation) in normal tissues and the frequencies with which the mutations are detected in carcinomas of the corresponding organs in the COSMIC database. This novel observation has important implications. It suggests that interindividual variability in mutation levels of normal tissues may be used as a metric to identify mutations with critical early roles in tissue-specific carcinogenesis. Additionally, it raises the possibility that personalized cancer therapeutics, developed to target specifically activated oncogenic products, might be repurposed as prophylactic therapies to reduce the accumulation of cells carrying CDMs and, thereby, reduce future cancer risk. Environ. Mol. Mutagen. 58:466-476, 2017. © 2017 This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
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Manjanatha MG, Shelton SD, Chen Y, Parsons BL, Myers MB, McKim KL, Gollapudi BB, Moore NP, Haber LT, Allen B, Moore MM. Dose and temporal evaluation of ethylene oxide-induced mutagenicity in the lungs of male big blue mice following inhalation exposure to carcinogenic concentrations. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:122-134. [PMID: 28326610 DOI: 10.1002/em.22080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Ethylene oxide (EO) is a direct acting alkylating agent; in vitro and in vivo studies indicate that it is both a mutagen and a carcinogen. However, it remains unclear whether the mode of action (MOA) for cancer for EO is a mutagenic MOA, specifically via point mutation. To investigate the MOA for EO-induced mouse lung tumors, male Big Blue (BB) B6C3F1 mice (10/group) were exposed to EO by inhalation, 6 hr/day, 5 days/week for 4 (0, 10, 50, 100, or 200 ppm EO), 8, or 12 weeks (0, 100, or 200 ppm EO). Lung DNA samples were analyzed for cII mutant frequency (MF) at 4, 8 and 12 weeks of exposure; the mutation spectrum was analyzed for mutants from control and 200 ppm EO treatments. Although EO-induced cII MFs were 1.5- to 2.7-fold higher than the concurrent controls at 4 weeks, statistically significant increases in the cII MF were found only after 8 and 12 weeks of exposure and only at 200 ppm EO (P ≤ 0.05), which is twice the highest concentration used in the cancer bioassay. Consistent with the positive response, DNA sequencing of cII mutants showed a significant shift in the mutational spectra between control and 200 ppm EO following 8 and 12 week exposures (P ≤ 0.035), but not at 4 weeks. Thus, EO mutagenic activity in vivo was relatively weak and required higher than tumorigenic concentrations and longer than 4 weeks exposure durations. These data do not follow the classical patterns for a MOA mediated by point mutations. Environ. Mol. Mutagen. 58:122-134, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mugimane G Manjanatha
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - Sharon D Shelton
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - Karen L McKim
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
| | - B Bhaskar Gollapudi
- Toxicology and Environmental Research and Consulting, Dow Chemical Company, Midland, Michigan
| | - Nigel P Moore
- Toxicology and Environmental Research and Consulting, Dow Europe GmbH, Horgen, Switzerland
| | - Lynne T Haber
- Environmental Health, Toxicology Excellence for Risk Assessment, Cincinnati, Ohio
| | - Bruce Allen
- Independent Consultant, Chapel Hill, North Carolina
| | - Martha M Moore
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas
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Laulicht-Glick F, Wu F, Zhang X, Jordan A, Brocato J, Kluz T, Sun H, Costa M. Tungsten exposure causes a selective loss of histone demethylase protein. Mol Carcinog 2017; 56:1778-1788. [PMID: 28218462 DOI: 10.1002/mc.22634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/08/2017] [Accepted: 02/16/2017] [Indexed: 01/20/2023]
Abstract
In the course of our investigations into the toxicity of tungstate, we discovered that cellular exposure resulted in the loss of the histone demethylase protein. We specifically investigated the loss of two histone demethylase dioxygenases, JARID1A and JMJD1A. Both of these proteins were degraded in the presence of tungstate and this resulted in increased global levels of H3K4me3 and H3K9me2, the substrates of JARID1A and JMJD1A, respectively. Treatment with MG132 completely inhibited the loss of the demethylase proteins induced by tungstate treatment, suggesting that tungstate activated the proteasomal degradation of these proteins. The changes in global histone marks and loss of histone demethylase protein persisted for at least 48 h after removing sodium tungstate from the culture. The increase in global histone methylation remained when cells were cultured in methionine-free media, indicating that the increased histone methylation did not depend upon any de novo methylation process, but rather was due to the loss of the demethylase protein. Similar increases of H3K4me3 and H3K9me2 were observed in the livers of the mice that were acutely exposed to tungstate via their drinking water. Taken together, our results indicated that tungstate exposure specifically reduced histone demethylase JARID1A and JMJD1A via proteasomal degradation, leading to increased histone methylation.
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Affiliation(s)
- Freda Laulicht-Glick
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Feng Wu
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Ashley Jordan
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Jason Brocato
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Thomas Kluz
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Hong Sun
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Max Costa
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
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Yang J, Zhang Z, Jiang S, Zhang M, Lu J, Huang L, Zhang T, Gong K, Yan S, Yang Z, Shao G. Vanadate-induced antiproliferative and apoptotic response in esophageal squamous carcinoma cell line EC109. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:864-868. [PMID: 27599232 DOI: 10.1080/15287394.2016.1193115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Vanadate is a transition element that present in nature and was shown to be a nonspecific inhibitor of protein tyrosine phosphatases. It was reported that vanadium (Vd) compounds exhibit antitumor actions in several cancer cell lines. This study aimed to examine the antiproliferative and apoptotic actions of different concentrations of sodium vanadate (NaVd) (+5) in esophageal squamous carcinoma cell line EC109 by determining the protein expression levels of cyclin D1 and caspase-3 following incubation for various times from 15 min up to 4 h. In addition, cell proliferation of EC109 treated with different concentrations (NaVd) was also measured using the MTT assay at 4, 12, 24, and 48 h. The cell cycle of EC109 cells exposed to different concentrations of NaVd was detected using flow cytometry determination at 24 h. Data showed that NaVd greater than 100 µM significantly increased cyclin D1. In contrast, reduced caspase-3 protein expression levels occurred at 50 µM. Cellular proliferation was significantly decreased at 50uM. The cell cycle was arrested at S phase with 100 µM NaVd. Taken together, data indicate that NaVd produced concentration- and time-dependent antitumor actions in EC109 cell line.
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Affiliation(s)
- Jie Yang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Zhuxia Zhang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Shuyuan Jiang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Ming Zhang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Jun Lu
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Lihua Huang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Tao Zhang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Kerui Gong
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Shaochun Yan
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Zhanjun Yang
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
| | - Guo Shao
- a Biomedicine Research Center and Basic Medical College , Baotou Medical College , Inner Mongolia , P. R. China
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Manjanatha MG, Shelton SD, Haber L, Gollapudi B, MacGregor JA, Rajendran N, Moore MM. Evaluation of cII mutations in lung of male Big Blue mice exposed by inhalation to vanadium pentoxide for up to 8 weeks. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 789-790:46-52. [DOI: 10.1016/j.mrgentox.2015.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
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Black MB, Dodd DE, McMullen PD, Pendse S, MacGregor JA, Gollapudi BB, Andersen ME. Using gene expression profiling to evaluate cellular responses in mouse lungs exposed to V2O5 and a group of other mouse lung tumorigens and non-tumorigens. Regul Toxicol Pharmacol 2015. [PMID: 26210822 DOI: 10.1016/j.yrtph.2015.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many compounds test positive for lung tumors in two-year NTP carcinogenicity bioassays in B6C3F1 mice. V2O5 was identified as a lung carcinogen in this assay, leading to its IARC (International Agency for Research on Cancer) classification as group 2b or a "possible" human carcinogen. To assess potential tumorigenic mode of action of V2O5, we compared gene expression and gene ontology enrichment in lung tissue of female B6C3F1 mice exposed for 13 weeks to a V2O5 particulate aerosol at a tumorigenic level (2.0 mg/m(3)). Relative to 12 other compounds also tested for carcinogenicity in 2-year bioassays in mice, there were 1026 differentially expressed genes with V2O5, of which 483 were unique to V2O5. Ontology analysis of the 1026 V2O5 differentially expressed genes showed enrichment for hyaluronan and sphingolipid metabolism, adenylate cyclase functions, c-AMP signaling and PKA activation/signaling. Enrichment of lipids/lipoprotein metabolism and inflammatory pathways were consistent with previously reported clinical findings. Enrichment of c-AMP and PKA signaling pathways may arise due to inhibition of phosphatases, a known biological action of vanadate. We saw no enrichment for DNA-damage, oxidative stress, cell cycle, or apoptosis pathway signaling in mouse lungs exposed to V2O5 which is in contrast with past studies evaluating in vivo gene expression in target tissues of other carcinogens (arsenic, formaldehyde, naphthalene and chloroprene).
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Affiliation(s)
- Michael B Black
- The Hamner Institutes for Health Sciences, Six Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA.
| | - Darol E Dodd
- The Hamner Institutes for Health Sciences, Six Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA.
| | - Patrick D McMullen
- The Hamner Institutes for Health Sciences, Six Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA.
| | - Salil Pendse
- The Hamner Institutes for Health Sciences, Six Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA.
| | - Judith A MacGregor
- Toxicology Consulting Services, 26881 Wedgewood Dr., Bonita Springs, FL 34134, USA.
| | | | - Melvin E Andersen
- The Hamner Institutes for Health Sciences, Six Davis Drive, PO Box 12137, Research Triangle Park, NC 27709, USA.
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