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Wu J, Huang THM. Applications of chromatin immunoprecipitation-based epigenomic tools in nutritional studies. Nutr Rev 2008; 66 Suppl 1:S49-53. [PMID: 18673491 DOI: 10.1111/j.1753-4887.2008.00068.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jiejun Wu
- The Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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52
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Hansen RR, Avens HJ, Shenoy R, Bowman CN. Quantitative evaluation of oligonucleotide surface concentrations using polymerization-based amplification. Anal Bioanal Chem 2008; 392:167-75. [PMID: 18661123 PMCID: PMC2517095 DOI: 10.1007/s00216-008-2259-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 06/17/2008] [Accepted: 06/18/2008] [Indexed: 01/10/2023]
Abstract
Quantitative evaluation of minimal polynucleotide concentrations has become a critical analysis among a myriad of applications found in molecular diagnostic technology. Development of high-throughput, nonenzymatic assays that are sensitive, quantitative and yet feasible for point-of-care testing are thus beneficial for routine implementation. Here, we develop a nonenzymatic method for quantifying surface concentrations of labeled DNA targets by coupling regulated amounts of polymer growth to complementary biomolecular binding on array-based biochips. Polymer film thickness measurements in the 20–220 nm range vary logarithmically with labeled DNA surface concentrations over two orders of magnitude with a lower limit of quantitation at 60 molecules/μm2 (∼106 target molecules). In an effort to develop this amplification method towards compatibility with fluorescence-based methods of characterization, incorporation of fluorescent nanoparticles into the polymer films is also evaluated. The resulting gains in fluorescent signal enable quantification using detection instrumentation amenable to point-of-care settings. Polymerization-based amplification for quantitative evaluation of 3’ biotinylated oligonucleotide surface concentrations ![]()
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Affiliation(s)
- Ryan R Hansen
- Department of Chemical and Biological Engineering, ECCH 111 CB 424, University of Colorado, Boulder, CO 80309, USA
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53
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Abstract
For years, head and neck squamous cell carcinomas (HNSCC) have been among the leading cancers worldwide. Despite considerable efforts, the 5-year survival rate for HNSCC has not changed significantly. To improve this situation, it is necessary to understand the fundamental biological processes leading to the disease and its progression. In addition to known genetic changes in HNSCC, molecular cytogenetic investigations have identified chromosomal regions of gains and losses, but many of the responsible candidate genes have yet to be identified. Furthermore, recent results indicate the importance of epigenetic modifications in HNSCC, such as DNA methylation. Several genes, including the tumor suppressor CDKN2A and other candidates such as DAPK1, MGMT, TIMP3, TCF21, and C/EBPalpha, have been found to harbor hypermethylated regulatory sequences that lead to reduced expression or gene silencing. Hypermethylation in such genes could be used not only as biomarkers for the early detection of HNSCC but also to improve prevention strategies and therapy outcomes.
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Affiliation(s)
- P Schmezer
- Abteilung Toxikologie und Krebsrisikofaktoren, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg
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54
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Board RE, Knight L, Greystoke A, Blackhall FH, Hughes A, Dive C, Ranson M. DNA Methylation in Circulating Tumour DNA as a Biomarker for Cancer. Biomark Insights 2008. [DOI: 10.1177/117727190700200003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Free circulating DNA, which is thought to be derived from the primary tumour, can be detected in the blood of patients with cancer. Detection of genetic and epigenetic alteration in this tumour DNA offers a potential source of development of prognostic and predictive biomarkers for cancer. One such change is DNA methylation of the promotor region of tumour suppressor genes. This causes down regulation of tumour suppressor gene expression, a frequent event in carcinogenesis. Hypermethylation of the promotor region of a number of genes has been detected in many tumour types and more recently these changes have been detected in circulating tumour DNA. This review will summarise the literature detailing DNA methylation in circulating tumour DNA and discuss some of the current controversies and technical challenges facing its use as a potential biomarker for cancer.
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Affiliation(s)
- Ruth E Board
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Lucy Knight
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Alastair Greystoke
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Fiona H Blackhall
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
| | - Andrew Hughes
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Caroline Dive
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Malcolm Ranson
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
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55
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Melnikov AA, Scholtens DM, Wiley EL, Khan SA, Levenson VV. Array-based multiplex analysis of DNA methylation in breast cancer tissues. J Mol Diagn 2007; 10:93-101. [PMID: 18165279 DOI: 10.2353/jmoldx.2008.070077] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Abnormal DNA methylation is well established for cancer cells, but a methylation-based diagnostic test is yet to be developed. One of the problems is insufficient accuracy of cancer detection in heterogeneous clinical specimens when only a single gene is analyzed. A new technique was developed to produce a multigene methylation signature in each sample, and its potential for selection of informative genes was tested using DNA from formalin-fixed, paraffin-embedded breast cancer tissues. Fifty-six promoters were analyzed in each of 138 clinical specimens by a microarray-based modification of the previously developed technique. Specific methylation signatures were identified for atypical ductal hyperplasia, ductal carcinoma in situ, and invasive ductal carcinoma. Informative promoters selected by Fisher's exact test were used for composite biomarker design using naïve Bayes algorithm. All informative promoters were unmethylated in disease compared with normal tissue. Cross-validation showed 72.4% sensitivity and 74.7% specificity for detection of ductal carcinoma in situ and invasive ductal carcinoma, and 87.5% sensitivity and 95% specificity for detection of atypical ductal hyperplasia. These results indicate that informative cancer-specific methylation signatures can be detected in heterogeneous tissue specimens, suggesting that a diagnostic assay can then be developed.
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Affiliation(s)
- Anatoliy A Melnikov
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago Illinois, USA
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56
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Abstract
Pyrosequencing is a sequencing-by-synthesis method that quantitatively monitors the real-time incorporation of nucleotides through the enzymatic conversion of released pyrophosphate into a proportional light signal. Quantitative measures are of special importance for DNA methylation analysis in various developmental and pathological situations. Analysis of DNA methylation patterns by pyrosequencing combines a simple reaction protocol with reproducible and accurate measures of the degree of methylation at several CpGs in close proximity with high quantitative resolution. After bisulfite treatment and PCR, the degree of each methylation at each CpG position in a sequence is determined from the ratio of T and C. The process of purification and sequencing can be repeated for the same template to analyze other CpGs in the same amplification product. Quantitative epigenotypes are obtained using this protocol in approximately 4 h for up to 96 DNA samples when bisulfite-treated DNA is already available as the starting material.
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Affiliation(s)
- Jörg Tost
- Laboratory for Epigenetics, CEA-Institut de Génomique, Centre National de Génotypage, Evry Cedex, France.
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57
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Nafee TM, Farrell WE, Carroll WD, Fryer AA, Ismail KMK. Review article: Epigenetic control of fetal gene expression. BJOG 2007; 115:158-68. [DOI: 10.1111/j.1471-0528.2007.01528.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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58
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Vineis P, Perera F. Molecular Epidemiology and Biomarkers in Etiologic Cancer Research: The New in Light of the Old. Cancer Epidemiol Biomarkers Prev 2007; 16:1954-65. [DOI: 10.1158/1055-9965.epi-07-0457] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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59
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Abstract
Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.
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Affiliation(s)
- Daniel Zilberman
- University of California, 211 Koshland Hall, Berkeley, CA 94720, USA
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60
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Fernander AF, Shavers VL, Hammons GJ. A biopsychosocial approach to examining tobacco-related health disparities among racially classified social groups. Addiction 2007; 102 Suppl 2:43-57. [PMID: 17850613 DOI: 10.1111/j.1360-0443.2007.01954.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
AIMS To articulate a broader, multi-causal model that incorporates psychosocial and environmental factors that can differ systematically across racially classified social groups (RCSGs) and impact biological pathways related to the development of tobacco-related diseases. METHODS This paper is built upon a review of the existing scientific literature on selected biopsychosocial factors (diet/nutrition, obesity, alcoholic intake, psychosocial stress, occupational/environmental exposures and exposure to other diseases and illnesses) and tobacco use in examining the biological contributions to differences in tobacco-related health outcomes among RCSGs. FINDINGS Recent work has focused on RCSG genetic variations as a possible explanation for differences in tobacco-related health disparities. It is argued in this paper that, given the genetic heterogeneity 'within' RCSGs, it is unlikely that across RCSG genetic variations are likely to be the major source of differences impacting biological pathways in tobacco-related health outcomes. The evidence shows that results, even at the level of within-population genetic variations, have been limited and often inconsistent. A conceptual framework is proposed to account for biological pathways related to the development of tobacco-related diseases. CONCLUSIONS Determinants of tobacco-related health disparities are not understood clearly. The contribution of biological factors may be important. Current efforts to determine biological differences in tobacco use and related diseases among RCSGs have focused primarily on genetic variations. However, this approach has limitations. An alternative biopsychosocial framework that examines the potential biological mechanisms through which life experiences and behavior might affect tobacco use and health outcomes in these population groups is needed, including those of life-style (e.g. diet/nutrition, obesity, physical exercise, alcohol consumption), psychosocial (e.g. stress and coping), occupational/environmental exposures and the presence of other diseases/illnesses.
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Affiliation(s)
- Anita F Fernander
- Behavioral Science Department, College of Medicine, University of Kentucky, Lexington, KY, USA
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61
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Dejeux E, Audard V, Cavard C, Gut IG, Terris B, Tost J. Rapid identification of promoter hypermethylation in hepatocellular carcinoma by pyrosequencing of etiologically homogeneous sample pools. J Mol Diagn 2007; 9:510-20. [PMID: 17690210 PMCID: PMC1975099 DOI: 10.2353/jmoldx.2007.060209] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aberrant DNA methylation patterns have been identified in a variety of human diseases, particularly cancer. Pyrosequencing has evolved in recent years as a sensitive and accurate method for the analysis and quantification of the degree of DNA methylation in specific target regions. However, the number of candidate genes that can be analyzed in clinical specimens is often restricted by the limited amount of sample available. Here, we present a novel screening approach that enables the rapid identification of differentially methylated regions such as promoters by pyrosequencing of etiologically homogeneous sample pools after bisulfite treatment. We exemplify its use by the analysis of five genes (CDKN2A, GSTP1, MLH1, IGF2, and CTNNB1) involved in the pathogenesis of human hepatocellular carcinoma using pools stratified for different parameters of clinical importance. Results were confirmed by the individual analysis of the samples. The screening identified all genes displaying differential methylation successfully, and no false positives occurred. Quantitative comparison of the pools and the samples in the pool analyzed individually showed a deviation of approximately 1.5%, making the method ideally suited for the identification of diagnostic markers based on DNA methylation while saving precious DNA material.
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Affiliation(s)
- Emelyne Dejeux
- Laboratory for Epigenetics, Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, CP 5721, 91057 Evry Cedex, France
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Brena RM, Auer H, Kornacker K, Plass C. Quantification of DNA methylation in electrofluidics chips (Bio-COBRA). Nat Protoc 2007; 1:52-8. [PMID: 17406211 DOI: 10.1038/nprot.2006.8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alterations of normal gene expression patterns are a hallmark of human cancers. It is now clear that the dysregulation of epigenetic modifications of the DNA and surrounding histones contributes to aberrant gene silencing, thus being major participants not only in the progression but also the initiation of the disease phenotype. The best-studied epigenetic modification is DNA methylation, which converts cytosine to 5-methylcytosine. Aberrant hypermethylation of the promoter is frequently observed in cancer and is generally associated with gene silencing. Currently, accurate and reproducible quantification of DNA methylation remains challenging. Here, we describe Bio-COBRA, a modified protocol for Combined Bisulfite Restriction Analysis (COBRA), that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. In the life sciences, microfluidics usually entails the scaling down of at least one application, such as electrophoresis, to chip format, which often results in increased efficiency and reliability. Bio-COBRA provides a platform for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. Its sensitivity and reproducibility also makes it a tool for the analysis of DNA methylation in clinical samples. The Bio-COBRA assay can be performed on 12 samples in less than 1 h. If the protocol is started at the DNA isolation step, however, approximately 48 h would be required to complete the entire procedure.
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Affiliation(s)
- Romulo M Brena
- Department of Molecular Genetics, The Ohio State University, 420 West 12th Ave, Room 435, Columbus, Ohio 43210, USA
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63
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Kagan J, Srivastava S, Barker PE, Belinsky SA, Cairns P. Towards Clinical Application of Methylated DNA Sequences as Cancer Biomarkers: A Joint NCI's EDRN and NIST Workshop on Standards, Methods, Assays, Reagents and Tools. Cancer Res 2007; 67:4545-9. [PMID: 17510378 DOI: 10.1158/0008-5472.can-06-2888] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The workshop report, entitled Towards Clinical Application of Methylated DNA Sequences as Cancer Biomarkers: A Joint National Cancer Institute's Early Detection Research Network and National Institute of Standards and Technology Workshop, presents a summary of the main issues, current challenges, outcomes, and recommendations toward application of methylated DNA sequences as cancer biomarkers.
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Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Bethesda, Maryland, USA.
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64
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Brena RM, Morrison C, Liyanarachchi S, Jarjoura D, Davuluri RV, Otterson GA, Reisman D, Glaros S, Rush LJ, Plass C. Aberrant DNA methylation of OLIG1, a novel prognostic factor in non-small cell lung cancer. PLoS Med 2007; 4:e108. [PMID: 17388669 PMCID: PMC1831740 DOI: 10.1371/journal.pmed.0040108] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 01/31/2007] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide. Currently, tumor, node, metastasis (TNM) staging provides the most accurate prognostic parameter for patients with non-small cell lung cancer (NSCLC). However, the overall survival of patients with resectable tumors varies significantly, indicating the need for additional prognostic factors to better predict the outcome of the disease, particularly within a given TNM subset. METHODS AND FINDINGS In this study, we investigated whether adenocarcinomas and squamous cell carcinomas could be differentiated based on their global aberrant DNA methylation patterns. We performed restriction landmark genomic scanning on 40 patient samples and identified 47 DNA methylation targets that together could distinguish the two lung cancer subgroups. The protein expression of one of those targets, oligodendrocyte transcription factor 1 (OLIG1), significantly correlated with survival in NSCLC patients, as shown by univariate and multivariate analyses. Furthermore, the hazard ratio for patients negative for OLIG1 protein was significantly higher than the one for those patients expressing the protein, even at low levels. CONCLUSIONS Multivariate analyses of our data confirmed that OLIG1 protein expression significantly correlates with overall survival in NSCLC patients, with a relative risk of 0.84 (95% confidence interval 0.77-0.91, p < 0.001) along with T and N stages, as indicated by a Cox proportional hazard model. Taken together, our results suggests that OLIG1 protein expression could be utilized as a novel prognostic factor, which could aid in deciding which NSCLC patients might benefit from more aggressive therapy. This is potentially of great significance, as the addition of postoperative adjuvant chemotherapy in T2N0 NSCLC patients is still controversial.
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Affiliation(s)
- Romulo M Brena
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Carl Morrison
- Department of Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Sandya Liyanarachchi
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - David Jarjoura
- Division of Biostatistics, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Ramana V Davuluri
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Gregory A Otterson
- Department of Internal Medicine, Division of Hematology and Oncology, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - David Reisman
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Selina Glaros
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Laura J Rush
- Department of Veterinary Biosciences and the Comprehensive Cancer Center, The Ohio State University Columbus, Ohio, United States of America
| | - Christoph Plass
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, United States of America
- * To whom correspondence should be addressed. E-mail:
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65
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Abstract
PURPOSE OF REVIEW The accumulation of somatic mutations is the major driving force for tumorigenesis. These mutations uniquely differentiate tumor cells from their normal counterparts. Mutations within tumor cells and mutant DNA released by tumor cells into blood, lymph, stool, tissues and other bodily compartments can thereby be used for cancer detection. Here we discuss technologies available for the detection and quantification of mutant DNA in clinical samples and the value of such measurements for patient management. RECENT FINDINGS Conventional mutation detection technologies are either qualitative or only roughly estimate the abundance of mutant DNA molecules. Recently-developed approaches, however, use single molecule counting to determine the genotype of each individual member of a DNA population, providing a more accurate and precise digital output. SUMMARY In this review, we discuss the clinical utility of mutant DNA quantification in cancer patients in the context of recent technical advances made in digital mutation detection.
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Affiliation(s)
- Frank Diehl
- The Ludwig Center for Cancer Genetics and Therapeutics, The Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street, Room 590, Baltimore, MD 21231, USA.
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66
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Current World Literature. Curr Opin Oncol 2007; 19:65-9. [PMID: 17133115 DOI: 10.1097/cco.0b013e328012d5fa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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