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Feng Z, Yang Y, Liu Z, Zhao W, Huang L, Wu T, Mu Y. Integrated analysis of DNA methylome and transcriptome reveals the differences in biological characteristics of porcine mesenchymal stem cells. BMC Genom Data 2021; 22:56. [PMID: 34922435 PMCID: PMC8684131 DOI: 10.1186/s12863-021-01016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bone marrow (BM) and umbilical cord (UC) are the main sources of mesenchymal stem cells (MSCs). These two MSCs display significant differences in many biological characteristics, yet the underlying regulation mechanisms of these cells remain largely unknown. RESULTS BMMSCs and UCMSCs were isolated from inbred Wuzhishan miniature pigs and the first global DNA methylation and gene expression profiles of porcine MSCs were generated. The osteogenic and adipogenic differentiation ability of porcine BMMSCs is greater than that of UCMSCs. A total of 1979 genes were differentially expressed and 587 genes were differentially methylated at promoter regions in these cells. Integrative analysis revealed that 102 genes displayed differences in both gene expression and promoter methylation. Gene ontology enrichment analysis showed that these genes were associated with cell differentiation, migration, and immunogenicity. Remarkably, skeletal system development-related genes were significantly hypomethylated and upregulated, whereas cell cycle genes were opposite in UCMSCs, implying that these cells have higher cell proliferative activity and lower differentiation potential than BMMSCs. CONCLUSIONS Our results indicate that DNA methylation plays an important role in regulating the differences in biological characteristics of BMMSCs and UCMSCs. Results of this study provide a molecular theoretical basis for the application of porcine MSCs in human medicine.
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Affiliation(s)
- Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong, China
| | - Zhiguo Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weimin Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianwen Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yulian Mu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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2
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Sun B, Zhao H. The bioinformatics analysis of RIOX2 gene in lung adenocarcinoma and squamous cell carcinoma. PLoS One 2021; 16:e0259447. [PMID: 34855761 PMCID: PMC8638848 DOI: 10.1371/journal.pone.0259447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is characterized by high morbidity and mortality rates, and it has become an important public health issue worldwide. The occurrence and development of tumors is a multi-gene and multi-stage complex process. As an oncogene, ribosomal oxygenase 2 (RIOX2) has been associated with a variety of cancers. In this article, we analyzed the correlation between RIOX2 expression and methylation in lung cancer based on the databases including the cancer genome atlas (TCGA) (https://portal.gdc.cancer.gov/) and the gene expression omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). It was found that RIOX2 is highly expressed in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues, whose expression is negatively correlated with its methylation level. In this regard, methylation at cg09716038, cg14773523, cg14941179, and cg22299097 had a significant negative correlation with RIOX2 expression in LUAD, whereas in LUSC, methylation at cg09716038, cg14773523, cg14941179, cg22299097, cg05451573, cg10779801, and cg23629183 is negatively correlated with RIOX2 expression. According to the analysis based on the databases, RIOX2 gene could not be considered as the independent prognostic biomarker in lung adenocarcinoma or squamous cell lung cancer. However, the molecular mechanism of RIOX2 gene in the development of lung cancer may be helpful in improving lung cancer therapy.
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Affiliation(s)
- Bingqing Sun
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hongwen Zhao
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
- * E-mail:
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Li X, Yu B, Wu X, Zhang J, Jia C, Wang Z, Zhou Q, Zhou H, Yi G, Chen X, Fu S. Associations between Placental Insulin-Like Growth Factor-1 Gene Expression, DNA Methylation and Intrauterine Growth Restriction. Health (London) 2020. [DOI: 10.4236/health.2020.123022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chen X, Huang J, Zhang S, Mo F, Su S, Li Y, Fang L, Deng J, Huang H, Luo Z, Zheng J. Electrochemical Biosensor for DNA Methylation Detection through Hybridization Chain-Amplified Reaction Coupled with a Tetrahedral DNA Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2019; 11:3745-3752. [PMID: 30624036 DOI: 10.1021/acsami.8b20144] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is a key factor in the pathogenesis of gene expression diseases or malignancies. Thus, it has become a significant biomarker for the diagnosis and prognosis of these diseases. In this paper, we designed an ultrasensitive and specific electrochemical biosensor for DNA methylation detection. The platform consisted of stem-loop-tetrahedron composite DNA probes anchoring at a Au nanoparticle-coated gold electrode, a restriction enzyme digestion of HpaII, and signal amplification procedures including electrodeposition of Au nanoparticles, hybridization chain reaction, and horseradish peroxidase enzymatic catalysis. Under optimal conditions, the design showed a broad dynamic range from 1 aM to 1 pM and a detection limit of about 0.93 aM. The approach also showed ideal specificity, repeatability, and stability. The recovery test demonstrated that the design is a promising platform for DNA methylation detection under clinical circumstances and could meet the need for cancer diagnosis.
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Affiliation(s)
- Xi Chen
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | | | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
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Mo S, Su Z, Heng B, Chen W, Shi L, Du X, Lai C. SFRP1 Promoter Methylation and Renal Carcinoma Risk: A Systematic Review and Meta-Analysis. J NIPPON MED SCH 2018; 85:78-86. [PMID: 29731501 DOI: 10.1272/jnms.2018_85-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM Epigenetic inactivation of tumor suppressor genes is an important molecular mechanism in the formation and development of human tumors. The purpose of our study was to evaluate the correlation between the methylation level of the secreted frizzled-related protein 1 (SFRP1) gene and the risk of renal cell carcinoma (RCC). METHODS The relevant literature was searched in detail in several electronic databases. The methodological heterogeneity was analyzed by meta-regression and subgroup analyses. The odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were calculated to summarize the dichotomous outcomes of our meta-analysis. RESULTS The ten included articles contained 535 RCC samples and 475 normal controls. The results demonstrated that the methylation level of the SFRP1 promoter region was significantly correlated with an increased incidence of RCC (OR=13.72; 95% CI: 6.01-31.28; P=0.000). Furthermore, the eligible studies that had sufficient clinical data about the RCC cases were included in the analysis, and the results indicated that the frequency of SFRP1 promoter methylation was associated with a higher histological grade (P=0.000), tumor stage (P=0.033), tumor size (≥5 cm; P=0.029), and distant metastasis (P=0.047). CONCLUSION Our results indicate that the methylation level of the SFRP1 promoter region is increased in patients with RCC compared to normal controls and might be involved in the occurrence and development of RCC. Additional well-designed studies are needed to further verify our conclusions.
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Affiliation(s)
- Shijie Mo
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Zexuan Su
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Baoli Heng
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Weijun Chen
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Liping Shi
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Xinghua Du
- Department of Urology, The First Affiliated Hospital, Jinan University
| | - Caiyong Lai
- Department of Urology, The First Affiliated Hospital, Jinan University
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6
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Qiao MX, Li C, Zhang AQ, Hou LL, Yang J, Hu HG. Regulation of DEK expression by AP-2α and methylation level of DEK promoter in hepatocellular carcinoma. Oncol Rep 2016; 36:2382-90. [PMID: 27499261 DOI: 10.3892/or.2016.4984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/23/2016] [Indexed: 11/06/2022] Open
Abstract
DEK is overexpressed in multiple invasive tumors. However, the transcriptional regulatory mechanism of DEK remains unclear. In the present study, progressive-type truncation assay indicated that CpG2-2 (-167 bp/+35 bp) was the DEK core promoter, whose methylation inhibited DEK expression. Bisulfite genomic sequencing analysis indicated that the methylation levels of the DEK promoter in normal hepatic cells and tissues were higher than those in hepatocellular carcinoma (HCC) cells. TFSEARCH result revealed transcription factor binding sites in CpG2-2. Among the sites, the AP-2α binding site showed the most significant methylation difference; hence, AP-2α is a key transcription factor that regulates DEK expression. Point or deletion mutation of the AP-2α binding site significantly reduced the promoter activity. Chromatin immunoprecipitation assay demonstrated the binding of AP-2α to the core promoter. Furthermore, knock down of endogenous AP-2α downregulated DEK expression, whereas overexpression of AP-2α upregulated DEK expression. Thus, AP-2α is an important transcription factor of DEK expression, which is correlated with the methylation level of the DEK core promoter in HCC.
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Affiliation(s)
- Ming-Xu Qiao
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, P.R. China
| | - Chun Li
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, P.R. China
| | - Ai-Qun Zhang
- Institute of Hepatobiliary Surgery, PLA General Hospital, Beijing 100853, P.R. China
| | - Ling-Ling Hou
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, P.R. China
| | - Juan Yang
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, P.R. China
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing 100044, P.R. China
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Toren P, Ozgur E, Bayindir M. Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges. LAB ON A CHIP 2016; 16:2572-2595. [PMID: 27306702 DOI: 10.1039/c6lc00521g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.
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Affiliation(s)
- Pelin Toren
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Erol Ozgur
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Mehmet Bayindir
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey and Department of Physics, Bilkent University, 06800 Ankara, Turkey
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8
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Clinical potential of DNA methylation in organ transplantation. J Heart Lung Transplant 2016; 35:843-50. [DOI: 10.1016/j.healun.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/18/2016] [Accepted: 02/26/2016] [Indexed: 01/17/2023] Open
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10
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Li Y, Pan P, Qiao P, Liu R. Downregulation of N-myc downstream regulated gene 1 caused by the methylation of CpG islands of NDRG1 promoter promotes proliferation and invasion of prostate cancer cells. Int J Oncol 2015. [PMID: 26202882 DOI: 10.3892/ijo.2015.3086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Current studies tend to consider N-myc downstream regulated gene 1 (NDRG1) as a tumor suppressor gene, inhibiting cell proliferation and invasion. NDRG1 expression in cancer cells is generally low, but the molecular mechanism is unclear. Aberrant methylation of CpG islands (CGIs) in gene promoter was able to inactivate tumor suppressor genes and activate oncogenes, disordering cell proliferation and apoptosis, playing a promotion role in tumor occurrence and progression. The present study was performed to investigate the effect of epigenetic modification of NDRG1 on prostate cancer (PCa) cells. The protein expression in human specimens was measured by immunohistochemical staining. The expression level of NDRG1 was changed by plasmid vectors in PCa cells. These cells were used to study proliferation and invasiveness. NDRG1 expression in normal prostate cells was higher than that in PCa cells. Downregulation of NDRG1 expression enhanced cell proliferation and invasiveness. In contrast, its upregulation could reduce cell proliferation and invasiveness. In PCa cells, the methylation rate of CGIs in the promoter region of NDRG1 was higher than that in normal prostate cells. 5-Aza-CdR, a methylation inhibitor, was able to effectively reverse the aberrant methylation of NDRG1, enhancing its expression, inhibiting cell growth. NDRG1 can inhibit the cell proliferation and invasion of PCa, but its expression level is low. The aberrant methylation of NDRG1 promoter is an important mechanism for gene silencing, playing an important role in tumor occurrence and progression. Therefore, reversing the aberrant methylation of NDRG1 may be used for PCa treatment.
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Affiliation(s)
- Yalin Li
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Pan Pan
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Pengfei Qiao
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Ranlu Liu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
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Chen J, Kwong DL, Cao T, Hu Q, Zhang L, Ming X, Chen J, Fu L, Guan X. Esophageal squamous cell carcinoma (ESCC): advance in genomics and molecular genetics. Dis Esophagus 2015; 28:84-9. [PMID: 23796192 DOI: 10.1111/dote.12088] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal cancer is aggressive and has poor prognosis. Esophageal squamous cell carcinoma (ESCC) is histologically the most prevalent type of esophageal cancer and ranked as the sixth leading cause of cancer death worldwide. In recent years, cancer has been widely regarded as genetic disease, as well as epigenetic abnormalities including DNA methylation, histone deacetylation, chromatin remodeling, gene imprinting and noncoding RNA regulation. In this review, we will provide a general overview of genes, proteins and microRNAs that are involved in the development of ESCC, which aims to enhance our understanding of molecular mechanisms implicated in ESCC development and progression.
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Affiliation(s)
- J Chen
- Departments of Clinical Oncology, The University of Hong Kong, Hong Kong; Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Lee TY, Shin Y, Park MK. A simple, low-cost, and rapid device for a DNA methylation-specific amplification/detection system using a flexible plastic and silicon complex. LAB ON A CHIP 2014; 14:4220-9. [PMID: 25184832 DOI: 10.1039/c4lc00804a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Abnormal DNA methylation has been associated with the development and progression of several human cancers and is a potential target for treatment. Thus, myriad technologies for the analysis of DNA methylation have been developed over the past few decades. However, most of these technologies are still far from ideal because they are time-consuming, labor-intensive, and complex, and there is the risk of contamination of samples. Here, we present an innovative DNA methylation-specific amplification/detection device for analysis of DNA methylation in cancer-related DNA biomarkers. The assay is based on a microfluidic system that is coupled to a flexible plastic-based on-chip endonuclease digestion device with optimized magnetic field effect and a methylation-specific isothermal solid-phase amplification/detection technique to allow a low-cost, simple, and rapid analysis of DNA methylation status in a label-free and real-time manner. This flexible plastic/silicon-based microfluidic device is relatively simple to fabricate with a flexible thin film and a magnet array by using a laser machine that can overcome the limitations of a PDMS-based microfluidic device. We demonstrated the ability of the methylation analysis based on the proposed flexible device to detect the methylated RARβ gene, which is a common DNA methylation biomarker in several human cancers. The simple platform detected the methylated gene in genomic DNA from human cancer cell lines within 65 min, whereas other methods required at least several hours. Therefore, this simple, low-cost, and rapid methylation analysis platform will be useful for the detection of DNA methylation in point-of-care applications.
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Affiliation(s)
- Tae Yoon Lee
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, Singapore 117685.
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Iglesias T, Espina M, Montes-Bayón M, Sierra LM, Blanco-González E. Anion exchange chromatography for the determination of 5-methyl-2'-deoxycytidine: application to cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. Anal Bioanal Chem 2014; 407:2423-31. [PMID: 25142048 DOI: 10.1007/s00216-014-8070-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/30/2022]
Abstract
Epigenetic alterations are increasingly implicated in the initiation and progression of cancer. Genome-wide (global) hypomethylation seems to occur in early neoplasia and is a feature of genomic DNA derived from solid tumour tissues like ovarian cancer. Thus, analytical methods that provide sensitive and quantitative information about cytosine methylation in DNA are currently required. In this work, we compare two different anion-exchange columns for the separation of methylated cytosine from the other DNA nucleotides: a silica-based (Tracer Extrasil SAX) column and a polystyrene/divinyl benzene-based (Mono-Q™) column. Under the optimised conditions, linearity range, precision and detection limits of the developed high-performance liquid chromatography (HPLC) method were evaluated and compared using conventional ultraviolet (UV) absorbance detection at 270 nm. Good separation of the five target nucleotides, including 5-methyl-2'-deoxycytidine monophosphate (5mdCMP) and 2'-deoxycytidine monophosphate (dCMP) was achieved on the Mono-Q™ column with a gradient elution of ammonium acetate buffer (1 M, pH 6.9) at a flow rate of 1 mL min(-1). The coupling of this column to inductively coupled plasma mass spectrometry (ICP-MS) permitted also phosphorous ((31)P) specific detection of the nucleotides. Both detection systems offered adequate analytical performance characteristics, with detection limits of 30 and 40 μg L(-1) for 5mdCMP by HPLC-UV and HPLC-ICP-MS, respectively. However, the latter method allowed the determination of the global DNA methylation level (%) without the need for external calibration. Different genomic DNA samples were analysed including calf thymus DNA and DNA from two human cancer cell lines (adenocarcinoma epithelial A549 and ovarian carcinoma A2780) using the proposed strategy. In the line A2780, the cisplatin-sensitive and cisplatin-resistant variants were analysed, finding no significant differences in the methylation percentage after treatment with cisplatin.
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Affiliation(s)
- Tamara Iglesias
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, C/ Julián Clavería 8, 33006, Oviedo, Spain
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Kamiyama H, Noda H, Konishi F, Rikiyama T. Molecular biomarkers for the detection of metastatic colorectal cancer cells. World J Gastroenterol 2014; 20:8928-8938. [PMID: 25083065 PMCID: PMC4112864 DOI: 10.3748/wjg.v20.i27.8928] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/29/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
Approximately half of all patients with colorectal cancer develop local recurrence or distant metastasis during the course of their illness. Recently, the molecular detection of metastatic cancer cells in various types of clinical samples, such as lymph nodes, bone marrow, peripheral blood, and peritoneal lavage fluid, has been investigated as a potential prognostic marker. The prognostic value of molecular tumor cell detection was independent of the type of detection method used. As assays become more sensitive and quantitative, a more thorough assessment of the cancer status of patients will be based on molecular markers alone. At present, it is difficult to conclude that one specific molecular marker is superior to others. Comparative analyses are recommended to assess the prognostic impact of molecular analyses in the same patient and determine the biomarkers that provide the most accurate prognostic information.
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Ye QQ, Lu HN, Zhang X, Wang DP, Huang ZG. Analysis of GATA5 and Vimentin methylation in fecal DNA for detection of colorectal cancer. Shijie Huaren Xiaohua Zazhi 2014; 22:2971-2976. [DOI: 10.11569/wcjd.v22.i20.2971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the possibility of using GATA binding protein 5 (GATA5) and Vimentin promoter methylation as markers for the noninvasive detection of colorectal cancer (CRC).
METHODS: Stool samples were collected from 49 patients with CRC and 37 endoscopically normal subjects who underwent colonoscopy at our hospital from February 2012 to December 2012, and DNA was isolated from all samples. Methylation-specific polymerase chain reaction (MSP) was then utilized to analyze promoter CpG methylation of GATA5 and Vimentin.
RESULTS: The sensitivity and specificity of GATA5 gene methylation assay for detection of colorectal cancer were 81.63% and 86.49%, respectively. The sensitivity and specificity of Vimentin gene methylation were 44.90% and 86.49%, respectively. The overall sensitivity of detection of fecal DNA with at least one methylated gene was 95.1% in patients with CRC. In contrast, only 10 of the 37 (27.0%) normal individuals exhibited methylated DNA in the above promoter regions. GATA5 and Vimentin promoter methylation showed no significant correlation with gender, age, tumor-node-metastasis (TNM) stage or tumor location.
CONCLUSION: The abnormal methylation of GATA5 and Vimentin occurs frequently in fecal samples of patients with colorectal cancer. Detection of aberrantly methylated GATA5 and Vimentin in fecal samples may be a promising, noninvasive screening method for colorectal cancer, and the combined detection of multiple gene methylation for colorectal neoplasia screening is superior to single gene detection.
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Zhang Y, Guo J, Gao Y, Niu S, Yang C, Bai C, Yu X, Zhao Z. Genome-wide methylation changes are associated with muscle fiber density and drip loss in male three-yellow chickens. Mol Biol Rep 2014; 41:3509-16. [DOI: 10.1007/s11033-014-3214-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
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Huang RL, Chang CC, Su PH, Chen YC, Liao YP, Wang HC, Yo YT, Chao TK, Huang HC, Lin CY, Chu TY, Lai HC. Methylomic analysis identifies frequent DNA methylation of zinc finger protein 582 (ZNF582) in cervical neoplasms. PLoS One 2012; 7:e41060. [PMID: 22815913 PMCID: PMC3397950 DOI: 10.1371/journal.pone.0041060] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/16/2012] [Indexed: 12/26/2022] Open
Abstract
Background Despite of the trend that the application of DNA methylation as a biomarker for cancer detection is promising, clinically applicable genes are few. Therefore, we looked for novel hypermethylated genes for cervical cancer screening. Methods and Findings At the discovery phase, we analyzed the methylation profiles of human cervical carcinomas and normal cervixes by methylated DNA immunoprecipitation coupled to promoter tiling arrays (MeDIP-on-chip). Methylation-specific PCR (MSP), quantitative MSP and bisulfite sequencing were used to verify the methylation status in cancer tissues and cervical scrapings from patients with different severities. Immunohistochemical staining of a cervical tissue microarray was used to confirm protein expression. We narrowed to three candidate genes: DBC1, PDE8B, and ZNF582; their methylation frequencies in tumors were 93%, 29%, and 100%, respectively. At the pre-validation phase, the methylation frequency of DBC1 and ZNF582 in cervical scraping correlated significantly with disease severity in an independent cohort (n = 330, both P<0.001). For the detection of cervical intraepithelial neoplasia 3 (CIN3) and worse, the area under the receiver operating characteristic curve (AUC) of ZNF582 was 0.82 (95% confidence interval = 0.76–0.87). Conclusions Our study shows ZNF582 is frequently methylated in CIN3 and worse lesions, and it is demonstrated as a potential biomarker for the molecular screening of cervical cancer.
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Affiliation(s)
- Rui-Lan Huang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Po-Hsuan Su
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Chih Chen
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Ping Liao
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hui-Chen Wang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Yi-Te Yo
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ching-Yu Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tang-Yuan Chu
- Center for Cervical Cancer Prevention, Department of Obstetrics and Gynecology, Graduate Institute of Clinical Medicine, Tzu Chi Medical Center, Tzu Chi University, Hualien, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- * E-mail:
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Li JS, Ying JM, Wang XW, Wang ZH, Tao Q, Li LL. Promoter methylation of tumor suppressor genes in esophageal squamous cell carcinoma. CHINESE JOURNAL OF CANCER 2012; 32:3-11. [PMID: 22572016 PMCID: PMC3845589 DOI: 10.5732/cjc.011.10381] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a prevalent and fatal cancer in China and other Asian countries. Epigenetic silencing of key tumor suppressor genes (TSGs) is critical to ESCC initiation and progression. Recently, many novel TSGs silenced by promoter methylation have been identified in ESCC, and these genes further serve as potential tumor markers for high-risk group stratification, early detection, and prognosis prediction. This review summarizes recent discoveries on aberrant promoter methylation of TSGs in ESCC, providing better understanding of the role of disrupted epigenetic regulation in tumorigenesis and insight into diagnostic and prognostic biomarkers for this malignancy.
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Affiliation(s)
- Ji-Sheng Li
- Department of Chemotherapy, Shandong University, Jinan, Shandong, People's Republic of China
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19
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Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR. Biotechniques 2011; 49:xiii-xvii. [PMID: 20964632 DOI: 10.2144/000113494] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We describe a new method that is well-suited for the determination of the methylation level of repetitive sequences such as human Alu elements. We have applied the method to the analysis of cell and tissue DNAs and expect it to have wide utility in studies of DNA methylation in cancer and other disease states, in monitoring response to epigenetic cancer therapies and in epidemiological studies. Only 1 ng DNA is needed for a duplex, one-tube real-time PCR in which methylation level and the amount of input DNA are concurrently measured. The relative cutting by the methylation-sensitive enzyme BstUI is compared with that of the methylation-insensitive enzyme DraI to give a measure of DNA methylation. The method depends upon the use of 5'-tailed, 3'-blocked oligonucleotides called facilitator oligonucleotides (Foligos). Only cut DNAs with specific matching sequences at their 3' ends can copy the tails of the Foligos and thus become tagged and available for subsequent PCR. Both the tagging and PCR are carried out by the same enzyme, Taq DNA polymerase. Because amplification only occurs if suitable ends have been generated in the target DNA, we have called this method end-specific PCR (ESPCR). ESPCR avoids the bisulfite treatment step that is usually required to measure methylation.
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20
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Corrie SR, Sova P, Feng Q, Blair T, Kiviat NB, Trau M. Bisulfite-free analysis of 5MeC-binding proteins and locus-specific methylation density using a microparticle-based flow cytometry assay. Analyst 2011; 136:688-91. [DOI: 10.1039/c0an00790k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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21
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Promoter hypermethylation of KiSS-1 gene in gastric cancer. Chin J Cancer Res 2010. [DOI: 10.1007/s11670-010-0280-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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22
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Wang H, Chen X. [Advances of DNA methylation in lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2010; 13:1074-8. [PMID: 21081052 PMCID: PMC6000490 DOI: 10.3779/j.issn.1009-3419.2010.11.15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Haibing Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to Tongji University, Shanghai 200433, China
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23
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Suzuki M, Yoshino I. Aberrant methylation in non-small cell lung cancer. Surg Today 2010; 40:602-7. [DOI: 10.1007/s00595-009-4094-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 02/16/2009] [Indexed: 01/15/2023]
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24
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p15INK4b methylation correlates with thrombocytopenia, blast percentage, and survival in myelodysplastic syndromes in a dose dependent manner: Quantitation using pyrosequencing study. Leuk Res 2010; 34:718-22. [DOI: 10.1016/j.leukres.2009.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/02/2009] [Accepted: 09/06/2009] [Indexed: 11/19/2022]
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25
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Duan X, Liu L, Feng F, Wang S. Cationic conjugated polymers for optical detection of DNA methylation, lesions, and single nucleotide polymorphisms. Acc Chem Res 2010; 43:260-70. [PMID: 19954139 DOI: 10.1021/ar9001813] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Simple, rapid, and sensitive technologies to detect nucleic acid modifications have important applications in genetic analysis, clinical diagnosis, and molecular biology. Because genetic modifications such as single nucleotide polymorphisms (SNP), DNA methylation, and other lesions can serve as hallmarks of human disease, interest in such methods has increased in recent years. This Account describes a new strategy for the optical detection of these DNA targets using cationic conjugated polymers (CCPs). Because of their unique signal amplification properties, researchers have extensively investigated conjugated polymers as optical transducers in highly sensitive biosensors. Recently, we have shown that cationic polyfluorene can detect SNPs within the DNA of clinical samples. When we incorporated deoxyguanosine triphosphate (dGTP-Fl) into the DNA chain at an SNP site where the target/probe pair is complementary, we observed higher fluorescence resonance energy transfer (FRET) efficiency between cationic polyfluorene and fluorescein label on the dGTP. By monitoring the change in emission intensity of cationic polyfluorene or fluorescein, we identified the homozygous or heterozygous SNP. The high sensitivity of this assay results from the 10-fold enhancement of fluorescein emission intensity by the FRET from polyfluorene. This method can detect allele frequencies (the proportion of all copies of a gene that is made up of a particular gene variant) as low as 2%. Using this novel method, we clearly discriminated among the SNP genotypes of 76 individuals of Chinese ancestry. Improving on this initial system, we designed a method for multicolor and one-tube SNP genotyping assays based on cationic polyfluorene using fluorescein-labeled deoxyuridine triphosphate (dUTP-Fl) and Cy3-labeled deoxycytidine triphosphate (dCTP-Cy3) in extension reactions. We also developed a one-step method for direct detection of SNP genotypes from genomic DNA by combining allele-specific PCR with CCPs. In 2008, we developed a new method for DNA methylation detection based on single base extension reaction and CCPs. Treatment of DNA with bisulfite followed by PCR amplification converts unmethylated DNA into a C/T polymorphism, which allows us to characterize the methylation status of the target DNA. Furthermore, we used CCPs to detect DNA lesions caused by ultraviolet light irradiation for the first time. By monitoring the color change of cationic polythiophene before and after DNA cleavage, we also detected oxidative damage to DNA by hydroxyl radical. These CCP-based new assays avoid primer labeling, cumbersome workups, and sophisticated instruments, leading to simpler procedures and improved sensitivity. We expect that these features could lead to major advances in human disease diagnostics and genomic study in the near future.
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Affiliation(s)
- Xinrui Duan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fude Feng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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26
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Affiliation(s)
- Tomasz K Wojdacz
- Human Genetics Institute, University of Aarhus, Wilhelm Meyers Alle 240, DK-8000 Aarhus C, Denmark
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Kamiyama H, Noda H, Takata O, Suzuki K, Kawamura Y, Konishi F. Promoter hypermethylation of tumor-related genes in peritoneal lavage and the prognosis of patients with colorectal cancer. J Surg Oncol 2009; 100:69-74. [PMID: 19384904 DOI: 10.1002/jso.21291] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND OBJECTIVES The predictive value of free cancer cells in the peritoneal fluid of patients with colorectal cancer (CRC) remain to be elucidated. The aim of this study was to determine the prognostic relevance of the methylation of tumor-related genes detected in the peritoneal lavage fluid (PLF) of patients undergoing a resection for CRC. METHODS The promoter methylation pattern of four target genes, CDH1, CDKN2A (p16), MGMT, and APC, was examined in 51 primary CRC and corresponding matched PLF DNA. The relative methylation levels of these genes in primary CRC tissue and paired PLF were assessed by quantitative methylation-specific polymerase chain reaction (QMSP). RESULTS An aberrant methylation of at least one gene was found in 45 of 51 (88%) primary tumors. In matched PLF specimens, the frequencies of aberrant promoter methylation detected for each marker were 16% for CDH1, 2% for p16, 4% for MGMT and 24% for APC. Patients with PLF demonstrating the methylation of more than one of these four target genes demonstrated significantly shorter relapse-free survival. CONCLUSIONS These findings suggest that disseminated tumor cells in PLF detected by QMSP may correlate with the postoperative clinical course of patients undergoing curative surgery for CRC.
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Affiliation(s)
- Hidenori Kamiyama
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama, Japan
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28
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Tan JX, Sun YJ. [Progresses of methods for epigenomics study]. YI CHUAN = HEREDITAS 2009; 31:3-12. [PMID: 19138896 DOI: 10.3724/sp.j.1005.2009.00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epigenetics refers to the heritable changes in gene expression without any alteration in DNA sequence, including DNA methylation, histone modification and chromatin conformation. Epigenomics deals with global analyses of epigenetic changes across the entire genome. In the fields of epigenetics and epigenomics, DNA methylation has been drawn a special attention because of its close correlation to human development and carcinogenesis. In recent years, a variety of methods have been developed to study DNA methylation and other epigenetic modification. This review introduces and compares the new methods for epigenomics study and provides useful information for the researcher in this area.
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Affiliation(s)
- Jian-Xin Tan
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
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29
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Jordà M, Rodríguez J, Frigola J, Peinado MA. Analysis of DNA methylation by amplification of intermethylated sites (AIMS). Methods Mol Biol 2009; 507:107-16. [PMID: 18987810 DOI: 10.1007/978-1-59745-522-0_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in the control of gene expression and chromosome structure in plants and mammalian cells. Multiple types of DNA fingerprinting techniques have been developed and applied to investigate DNA methylation profiles in different experimental settings. One of these techniques, the amplification of intermethylated sites (AIMS) is a simple approach appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. This method is appropriate to compare large series of samples and the simultaneous identification of hypo- and hypermethylation events. Applications of AIMS include the study of DNA methylation changes in cancer and aging, and the discovery of DNA methylation in a social insect.
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Affiliation(s)
- Mireia Jordà
- Institut de Medicina Predictiva i Personalitzada del Càncer(IMPPC), Barcelona, Spain
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30
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Corrie S, Sova P, Lawrie G, Battersby B, Kiviat N, Trau M. Development of a multiplexed bead-based assay for detection of DNA methylation in cancer-related genes. MOLECULAR BIOSYSTEMS 2008; 5:262-8. [PMID: 19225617 DOI: 10.1039/b813077a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report a method for the detection of methylated CpG dinucleotides located within CpG islands in genomic DNA using multiplexed bead-based assays and standard flow cytometry instrumentation. Four CpG "clusters" were identified in the TFPI2 and SPARC CpG islands whose methylation status was highly correlated with the incidence of invasive cervical cancer in our previous studies. Eight probes in total were designed for both the methylated and unmethylated forms of each cluster and attached to different fluorescently-encoded organosilica bead sets. Probe design was investigated by changing either the length of probes whilst keeping the melting temperature constant, or changing the melting temperature and keeping the probe length constant. Asymmetric polymerase chain reaction (PCR) methods designed without methylation-specific primers were used to prepare fluorescently-labelled targets based on bisulfite-converted genomic DNA. After investigating the specificity of the probes in a model system using fluorescently-labelled synthetic oligonucleotides, cancer cell-line DNA was analysed and the constant length probe design facilitated the correct genotyping of all clusters with respect to negative controls.
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Affiliation(s)
- Simon Corrie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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31
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Galectin-3 in urine of cancer patients: stage and tissue specificity. J Cancer Res Clin Oncol 2008; 135:355-63. [PMID: 18836743 DOI: 10.1007/s00432-008-0481-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
Abstract
PURPOSE Galectin-3 has been implicated in advanced stage of cancer disease. In the current study we examined the possibility of urinary galectin-3 levels to stage cancer disease and to follow up therapy. EXPERIMENTAL DESIGN Urine was collected from all types of cancer patients at different stages including patients undergoing radio/chemotherapy. Galectin-3 level was determined by anti-galectin-3 based ELISA and agglutination assays. Immunoblotting and purification on lactosyl affinity column further confirmed the presence of galectin-3. RESULTS Cancer samples exhibited stage dependent expression of galectin-3 approx. ranging from 1.0 to 3.3, 4.4 to 5.4, 5.4 to 24.7, 13.1 to 31.9, 13.9 to 32.9 ng/mg C (creatinine) for stage I-V, respectively, at P approximately <0.05 level. Galectin-3 levels were decreased by approx. threefolds after 5th day of therapy. CONCLUSIONS Sample collection being simple and non-invasive, urinary galectin-3 may be used as a potential diagnostic tool for monitoring or follow up of the stage of cancer disease.
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32
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Zhang D, Bai Y, Wang Y, Luo J, Ge Q, Qiao Y, Jia C, Lu Z. Detailed methylation patterns and protein expression profiles of MGMT in colorectal carcinoma surgical margins. Clin Biochem 2008; 41:19-25. [DOI: 10.1016/j.clinbiochem.2007.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2007] [Revised: 08/12/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
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Rodriguez J, Vives L, Jordà M, Morales C, Muñoz M, Vendrell E, Peinado MA. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Nucleic Acids Res 2007; 36:770-84. [PMID: 18084025 PMCID: PMC2241897 DOI: 10.1093/nar/gkm1105] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Methylation of the cytosine is the most frequent epigenetic modification of DNA in mammalian cells. In humans, most of the methylated cytosines are found in CpG-rich sequences within tandem and interspersed repeats that make up to 45% of the human genome, being Alu repeats the most common family. Demethylation of Alu elements occurs in aging and cancer processes and has been associated with gene reactivation and genomic instability. By targeting the unmethylated SmaI site within the Alu sequence as a surrogate marker, we have quantified and identified unmethylated Alu elements on the genomic scale. Normal colon epithelial cells contain in average 25 486 ± 10 157 unmethylated Alu's per haploid genome, while in tumor cells this figure is 41 995 ± 17 187 (P = 0.004). There is an inverse relationship in Alu families with respect to their age and methylation status: the youngest elements exhibit the highest prevalence of the SmaI site (AluY: 42%; AluS: 18%, AluJ: 5%) but the lower rates of unmethylation (AluY: 1.65%; AluS: 3.1%, AluJ: 12%). Data are consistent with a stronger silencing pressure on the youngest repetitive elements, which are closer to genes. Further insights into the functional implications of atypical unmethylation states in Alu elements will surely contribute to decipher genomic organization and gene regulation in complex organisms.
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Affiliation(s)
- Jairo Rodriguez
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Catalonia, Spain
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Wu Z, Luo J, Ge Q, Zhang D, Wang Y, Jia C, Lu Z. Allele-specific extension on microarray for DNA methylation analysis. Anal Chim Acta 2007; 603:199-204. [DOI: 10.1016/j.aca.2007.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 09/04/2007] [Accepted: 09/05/2007] [Indexed: 11/30/2022]
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Rivenbark AG, Coleman WB. Practical applications for epigenetic biomarkers in cancer diagnostics. ACTA ACUST UNITED AC 2007; 1:17-30. [PMID: 23489266 DOI: 10.1517/17530059.1.1.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cancer represents a major global health problem and improvement of cancer treatment requires the development of new and useful molecular diagnostic tests that enable the detection of occult tumors, direction of personalized treatments, monitoring of patients during therapeutic intervention and prediction of long-term clinical outcomes. The ideal molecular diagnostic for cancer testing will be based upon non-invasive sources of DNA and will employ biomarkers that have excellent sensitivity, specificity and overall predictive value. Numerous genes are known to be hypermethylated during cancer development and progression. These methylation-sensitive genes represent potentially valuable epigenetic biomarkers for development of practical cancer molecular diagnostics. In fact, many epigenetic biomarkers have proven to possess excellent predictive value in assays designed to detect occult (or developing) neoplasms and/or forecast clinical course/outcome. The progress to date in this emerging area of cancer diagnostics suggests that we are not far away from a time when testing for epigenetic biomarkers will represent an integral part of cancer screening protocols that can be effectively applied to the general population and/or to groups of people with defined risk factors for specific cancer types.
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Affiliation(s)
- Ashley G Rivenbark
- University of North Carolina School of Medicine, Department of Biochemistry and Biophysics, Chapel Hill, North Carolina 27599, USA
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36
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Ahmed FE. Colorectal cancer epigenetics: the role of environmental factors and the search for molecular biomarkers. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2007; 25:101-54. [PMID: 17558783 DOI: 10.1080/10590500701399184] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This review presents an evenhanded evaluation of the role of epigenetics in the development of colorectal cancer, and investigates the extent of environmental influences on modulating this disease. Advances in our understanding of chromatin structure, histone modification, transcriptional activity and DNA methylation have lead to an integrated approach to the role of epigenetics in carcinogenesis. Epigenetic mechanisms appear to permit response of individuals to environment through change in gene expression and are involved in inactivating one of the two X chromosomes in women. Epigenetic changes play an important role in development and can also arise stochastically as individuals age. Because epigenetic alterations are potentially reversible, thereby allowing malignant cells to revert to the normal state, there is potential to develop effective strategies to prevent or even reverse this curable cancer. Moreover, because the methylation status of a specific sequence or the pattern of methylation across the genome can now be measured accurately, molecular biomarkers of screening, diagnosis, prognosis, prediction of treatment and those related to risk assessment can be developed using sophisticated molecular genetic technologies. Although in many cases a high sensitivity and specificity of the detection assays has been achieved, there still remains ample room for improvement in areas of sample preparation, assay design and marker selection.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine, East Carolina University, Greenville, North Carolina 27858, USA.
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Abstract
Imprinting is defined as the parental allele-specific expression of a very limited set of genes (about 50-80). This regulation depends upon an epigenetic marking of parental alleles during gametogenesis. Monoallelic expression ensures that the levels of the proteins encoded by imprinted genes, important factors of embryonic growth, placental growth or adult metabolism, are assured. Without precise control of their expression, developmental abnormalities result, as is shown by a number of hereditary over-growth syndromes, including Beckwith-Wiedemann syndrome. The regulation of imprinted genes is largely dependent on methylation marks, which are laid down during embryological development of germ cells. Once in place, the methylation status of precise chromosomal regions, Imprinting Control Regions (ICRs), is read by either of two mechanisms, chromatin barrier formation or untranslated RNAs, thereby ensuring that only the maternal or paternal allele is expressed. Each imprinted gene is classified as maternal or paternal according to the expressed allele. The stability of the marked regions in somatic cells is maintained through each cellular replication by a methylation enzyme complex containing Dnmt1. Although the major reading mechanisms of imprinted status are known, chromatin boundary formation by CTCF and untranslated RNAs, the molecules elaborating the initial ICR methylation, are just being uncovered. Mis-regulation of imprinted gene expression (loss of imprinting [LOI]) is seen frequently and precociously in a large variety of human tumours, making LOI a potentially valuable tool for both diagnosis and treatment. In fact, LOI is presently considered the most abundant and most precocious alteration in cancer. The present review proposes a mechanism responsible for LOI, as well as its eventual value in tumour diagnosis and prognosis.
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Affiliation(s)
- P Jelinic
- Division of Experimental Pathology, University Institute of Pathology, Lausanne, Switzerland
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38
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Paluszczak J, Baer-Dubowska W. Epigenetic diagnostics of cancer--the application of DNA methylation markers. J Appl Genet 2007; 47:365-75. [PMID: 17132902 DOI: 10.1007/bf03194647] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In recent years it has become apparent that epigenetic events are potentially equally responsible for cancer initiation and progression as genetic abnormalities. DNA methylation is the main epigenetic modification in humans. Two DNA methylation lesions coexist in human neoplasms: hypermethylation of promoter regions of specific genes within a context of genomic hypomethylation. Aberrant methylation is found at early stages of carcinogenesis and distinct types of cancer exhibit specific patterns of methylation changes. Tumor specific DNA is readily obtainable from different clinical samples and methylation status analysis often permits sensitive disease detection. Methylation markers may also serve for prognostic and predictive purposes as they often reflect the metastatic potential and sensitivity to therapy. As current findings show a great potential of recently characterised methylation markers, more studies in the field are needed in the future. Large clinical studies of newly developed markers are especially needed. The review describes the diagnostic potential of DNA methylation markers.
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Affiliation(s)
- Jaroslaw Paluszczak
- Department of Pharmaceutical Biochemistry, Poznań University of Medical Sciences, Grunwaldzka 6, 60-780 Poznań, Poland
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Laprise SL, Gray MR. Covalent genomic DNA modification patterns revealed by denaturing gradient gel blots. Gene 2006; 391:45-52. [PMID: 17276628 PMCID: PMC1924925 DOI: 10.1016/j.gene.2006.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 11/10/2006] [Accepted: 12/01/2006] [Indexed: 10/23/2022]
Abstract
Several approaches are used to survey genomic DNA methylation patterns, including Southern blot, PCR, and microarray strategies. All of these methods are based on the use of methylation-sensitive isoschizomer restriction enzyme pairs and/or sodium bisulfite treatment of genomic DNA. They have many limitations, including PCR bias, lack of comprehensive assessment of methylated sites, labor-intensive protocols, and/or the need for expensive equipment. Since the presence of 5-methylcytosine alters the melting properties of DNA molecules, denaturing gradient gel blots (DGG blots), a gene scanning technique which detects differences in DNA fragments based on differential melting behavior, were used to examine genomic modification patterns in normal tissues. Variations in melting behavior, observed as restriction fragment melting polymorphisms (RFMPs), were detected in various tissues from single individuals in all human and mouse genes tested, suggesting the presence of widespread differential cell type-specific DNA modification. Additional DGG blot experiments comparing genomic DNA to unmethylated cloned DNA suggested that the melting variants were most likely caused by DNA methylation differences. The results suggest that the use of DGG blots can provide a comprehensive and rapid method for comparing complex in vivo DNA modification patterns in normal adult somatic cells.
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Affiliation(s)
- Shari L Laprise
- Math/Science Division, Babson College, Forest Street, Babson Park, MA 02457, USA.
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Tetzner R, Dietrich D, Distler J. Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA. Nucleic Acids Res 2006; 35:e4. [PMID: 17135186 PMCID: PMC1747185 DOI: 10.1093/nar/gkl955] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, we adapted the well known uracil DNA glycosylase (UNG) carry-over prevention system for PCR, and applied it to the analysis of DNA methylation based on sodium bisulfite conversion. As sodium bisulfite treatment converts unmethylated cytosine bases into uracil residues, bisulfite treated DNA is sensitive to UNG treatment. Therefore, UNG cannot be used for carry-over prevention of PCR using bisulfite treated template DNA, as not only contaminating products of previous PCR, but also the actual template will be degraded. We modified the bisulfite treatment procedure and generated DNA containing sulfonated uracil residues. Surprisingly, and in contrast to uracil, 6-sulfonyl uracil containing DNA (SafeBis DNA) is resistant to UNG. We showed that the new procedure removes up to 10 000 copies of contaminating PCR product in a closed PCR vessel without significant loss of analytical or clinical sensitivity of the DNA methylation analysis.
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Affiliation(s)
- Reimo Tetzner
- Epigenomics AG, Kleine Praesidentenstrasse 1, 10178 Berlin, Germany
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Brakensiek K, Wingen LU, Länger F, Kreipe H, Lehmann U. Quantitative high-resolution CpG island mapping with Pyrosequencing reveals disease-specific methylation patterns of the CDKN2B gene in myelodysplastic syndrome and myeloid leukemia. Clin Chem 2006; 53:17-23. [PMID: 17095538 DOI: 10.1373/clinchem.2007.072629] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Gene silencing through aberrant CpG island methylation is the most extensively analyzed epigenetic event in human tumorigenesis and has huge diagnostic and prognostic potential. Methylation patterns are often very heterogeneous, however, presenting a serious challenge for the development of methylation assays for diagnostic purposes. METHODS We used Pyrosequencing technology to determine the methylation status of 68 CpG sites in the CpG island of the CDKN2B gene [cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)], frequently hypermethylated in myeloid malignancies, in a series of bone marrow samples from patients with myelodysplasia and myeloid leukemia (n = 82) and from 32 controls. A total of 7762 individual methylation sites were quantitatively evaluated. Precision and reproducibility of the quantification was evaluated with several overlapping primers. RESULTS The use of optimized sequencing primers and the new Pyro Q-CpG software enabled precise and reproducible quantification with a single sequencing primer of up to 15 CpG sites distributed over approximately 100 bp. Extensive statistical analyses of the whole CpG island revealed for the first time disease-specific methylation patterns of the CDKN2B gene in myeloid malignancies and small regions of differential methylation with high discriminatory power that enabled differentiation of even low-grade myelodysplastic syndrome samples from the controls, a result that was confirmed in an independent group of 9 control and 36 patient samples. CONCLUSION The precise quantitative methylation mapping of whole CpG islands is now possible with Pyrosequencing software in combination with optimized sequencing primers. This method reveals disease-specific methylation patterns and enables the development of specific diagnostic assays.
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Affiliation(s)
- Kai Brakensiek
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
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Tost J, El abdalaoui H, Gut IG. Serial pyrosequencing for quantitative DNA methylation analysis. Biotechniques 2006; 40:721-2, 724, 726. [PMID: 16774114 DOI: 10.2144/000112190] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jörg Tost
- Centre National de Génotypage, Evry, France.
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Rodenhiser D, Mann M. Epigenetics and human disease: translating basic biology into clinical applications. CMAJ 2006; 174:341-8. [PMID: 16446478 PMCID: PMC1373719 DOI: 10.1503/cmaj.050774] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders and pediatric syndromes as well as contributing factors in autoimmune diseases and aging. In this review, we examine the basic principles of epigenetic mechanisms and their contribution to human health as well as the clinical consequences of epigenetic errors. In addition, we address the use of epigenetic pathways in new approaches to diagnosis and targeted treatments across the clinical spectrum.
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Affiliation(s)
- David Rodenhiser
- EpiGenWestern Research Group, Children's Health Research Institute, London, Ont.
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