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Madrid E, Gonzalez-Miranda I, Muñoz S, Rejas C, Cardemil F, Martinez F, Cortes JP, Berasaluce M, Párraga M. Arsenic concentration in topsoil of central Chile is associated with aberrant methylation of P53 gene in human blood cells: a cross-sectional study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:48250-48259. [PMID: 35188613 DOI: 10.1007/s11356-022-19085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Gene expression can be modified in people who are chronically exposed to high concentrations of heavy metals. The soil surrounding the Ventanas Industrial Complex, located on the coastal zone of Puchuncaví and Quintero townships (Chile), contain heavy metal concentrations (As, Cu, Pb, Zn, among others) that far exceed international standards. The aim of this study was to determine the potential association of the heavy metals in soils, especially arsenic, with the status of methylation of four tumor suppressor genes in permanent residents in those townships. To study the methylation status in genes p53, p16, APC, and RASSF1A, we took blood samples from adults living in areas near the industrial complex for at least 5 years and compared it to blood samples from adults living in areas with normal heavy metal concentrations of soils. Results indicated that inhabitants of an area with high levels of heavy metals in soil have a significantly higher proportion of methylation in the promoter region of the p53 tumor suppressor gene compared with control areas (p-value: 0.0035). This is the first study to consider associations between heavy metal exposure in humans and aberrant DNA methylation in Chile. Our results suggest more research to support consistent decision-making on processes of environmental remediation or prevention of exposure.
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Affiliation(s)
- Eva Madrid
- Interdisciplinary Centre for Health Studies (CIESAL) - Escuela de Medicina, Universidad de Valparaíso, Viña del Mar, Valparaíso, Chile.
| | - Isabel Gonzalez-Miranda
- Centro Regional de Investigación e Innovación para la Sostenibilidad de la Agricultura y los Territorios Rurales (Ceres), Quillota, Valparaíso, Chile
- Pontificia Universidad Católica de Valparaíso, Vicerrectoría de Investigación y Estudios Avanzados, Valparaíso, Chile
| | - Sergio Muñoz
- Department of Public Health-CIGES, Universidad de La Frontera, Temuco, Chile
| | - Carolina Rejas
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Felipe Cardemil
- Department of Basic and Clinical Oncology, School of Medicine, Universidad de Chile, Santiago, Chile
| | - Felipe Martinez
- Facultad de Medicina, Escuela de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | | | - Maite Berasaluce
- Interdisciplinary Centre for Health Studies (CIESAL) - Escuela de Medicina, Universidad de Valparaíso, Viña del Mar, Valparaíso, Chile
| | - Mario Párraga
- Laboratorio de Biología Molecular, Centro de Investigaciones Biomédicas, Universidad de Valparaíso, Valparaíso, Chile
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Liu L, Ying C, Zhao Z, Sui L, Zhang X, Qian C, Wang Q, Chen L, Guo Q, Wu J. Identification of reliable biomarkers of human papillomavirus 16 methylation in cervical lesions based on integration status using high-resolution melting analysis. Clin Epigenetics 2018; 10:10. [PMID: 29410710 PMCID: PMC5781301 DOI: 10.1186/s13148-018-0445-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023] Open
Abstract
Background The dynamic methylation of human papillomavirus (HPV) 16 DNA is thought to be associated with the progression of cervical lesions. Previous studies that did not consider the physical status of HPV 16 may have incorrectly mapped HPV 16 methylomes. In order to identify reliable biomarkers for squamous cervical cancer (SCC), we comprehensively evaluated the methylation of HPV 16 depending on the integration incidence of each sample. Methods Based on the integration status of 115 HPV 16-infected patients (50 SCC, 30 high-grade squamous intraepithelial lesion [HSIL], and 35 low-grade squamous intraepithelial lesion [LSIL]) and HPV 16-infected Caski cell lines by PCR detection of integrated papillomavirus sequences, we designed a series of primers that would not be influenced by breakpoints for a high-resolution melting (HRM) PCR method to detect the genome methylation. Results A few regions with recurrent interruptions were identified in E1, E2/E4, L1, and L2 despite scattering of breakpoints throughout all eight genes of HPV 16. Frequent integration sites often occurred concomitantly with methylated CpG sites. The HRM PCR method showed 100% agreement with pyrosequencing when 3% was set as the cutoff value. A panel of CpG sites such as nt5606, nt5609, nt5615, and nt5378 can be combined in reweighing calculations to distinguish SCC from HSIL and LSIL patients which have high sensitivity and specificity (88% and 92.31%, respectively). Conclusions Our research shows that combination of CpG sites nt5606, nt5609, nt5615, and nt5378 can be used as potential diagnosis biomarkers for SCC, and the HRM PCR method is suitable for clinical methylation analysis. Electronic supplementary material The online version of this article (10.1186/s13148-018-0445-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lu Liu
- 1Department of Clinical Laboratory, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Chunmei Ying
- 1Department of Clinical Laboratory, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Zhen Zhao
- 2Department of Clinical Laboratory, Minhang District Central Hospital, Shanghai, China
| | - Long Sui
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Xinyan Zhang
- 4The Research Institute of Obstetrics and Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunyan Qian
- 5Yuhang Branch, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Qing Wang
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Limei Chen
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Qisang Guo
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Jiangnan Wu
- 6Department of Clinical Statistics, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Targeting the Epigenome as a Novel Therapeutic Approach for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:287-313. [DOI: 10.1007/978-981-10-6020-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Li SR, Wang ZM, Wang YH, Wang XB, Zhao JQ, Xue HB, Jiang FG. Value of PAX1 Methylation Analysis by MS-HRM in the Triage of Atypical Squamous Cells of Undetermined Significance. Asian Pac J Cancer Prev 2016; 16:5843-6. [PMID: 26320460 DOI: 10.7314/apjcp.2015.16.14.5843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of cervical high grade lesions in patients with atypical squamous cells of undetermined significance (ASCUS) is still a challenge. Our study tested the efficacy of the paired boxed gene 1 (PAX1) methylation analysis by methylation-sensitive high-resolution melting (MS-HRM) in the detection of high grade lesions in ASCUS and compared performance with the hybrid capture 2 (HC2) human papillomavirus (HPV) test. MATERIALS AND METHODS A total of 463 consecutive ASCUS women from primary screening were selected. Their cervical scrapings were collected and assessed by PAX1 methylation analysis (MS-HRM) and high-risk HPV-DNA test (HC2). All patients with ASCUS were admitted to colposcopy and cervical biopsies. The Chi- square test was used to test the differences of PAX1 methylation or HPV infection between groups. RESULTS The specificity, sensitivity, and accuracy for detecting CIN2 + lesions were: 95.6%, 82.4%, and 94.6%, respectively, for the PAX1 MS-HRM test; and 59.7%, 64.7%, and 60.0% for the HC2 HPV test. CONCLUSIONS The PAX1 methylation analysis by MS-HRM demonstrated a better performance than the high-risk HPV-DNA test for the detection of high grade lesions (CIN2 +) in ASCUS cases. This approach could screen out the majority of low grade cases of ASCUS, and thus reduce the referral rate to colposcopy.
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Affiliation(s)
- Shi-Rong Li
- Department of Clinical Laboratory, Weifang City People's Hospital, Weifang, China E-mail :
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An improved fluorescence polarization assay in 5'-nuclease reaction for gene promoter methylation detection. J Biotechnol 2015. [PMID: 26197420 DOI: 10.1016/j.jbiotec.2015.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The detection of gene promoter methylation plays increasing roles in personalized medicine. In this study, an improved gene promoter methylation assay based on fluorescence polarization in 5'-nuclease reaction was developed. The novel assay offered a homogeneous annealing and cleavage reaction fully integrated with PCR which used a probe labeled with fluorescence without quencher to obtain the decreased fluorescence polarization values. In this platform, gene promoter methylated and unmethylated alleles were detected simultaneously in a tube. O(6)-methylguanine-DNA methyltransferase gene promoter methylation in 103 glioma tissue samples and epidermal growth factor receptor gene promoter methylation in 116 primary non-small-cell lung carcinoma tissue samples were detected by the novel assay and sequencing, absolute quantitative analysis of methylated allele in parallel. The accuracy of the results measured by the improved fluorescence polarization assay was evaluated using the paired-samples t test. No significant difference was found ( P>0.05). Therefore, the improved fluorescence polarization assay in 5'-nuclease reaction demonstrated a homogeneous, reliable and cost-effective method for gene promoter methylation analysis in clinic. That would provide a scientific basis for applying a reasonable therapeutic regimen in future treatment.
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Qiu C, Zhi Y, Shen Y, Gong J, Li Y, Rong S, Okunieff P, Zhang L, Li X. Performance of the HPV-16 L1 methylation assay and HPV E6/E7 mRNA test for the detection of squamous intraepithelial lesions in cervical cytological samples. J Virol Methods 2015; 224:35-41. [PMID: 26297960 DOI: 10.1016/j.jviromet.2015.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 08/07/2015] [Accepted: 08/14/2015] [Indexed: 01/19/2023]
Abstract
HPV-16 L1 methylation and E6/E7 mRNA have suggested that they had close relationship with cervical neoplastic progression. This study aimed to evaluate the clinical performance of the HPV-16 L1 methylation assay and E6/E7 mRNA test for detecting high-grade cervical lesions (CIN2+). A total of 81 women with liquid-based cytology (LBC) samples, histological results, and positive HPV-DNA test for HPV type 16 only were included in this study. HPV-16 L1 methylation and E6/E7 mRNA levels were measured using methylation-sensitive high resolution melting (MS-HRM) analysis and Quantivirus®HPV E6/E7 RNA 3.0 assay (bDNA), respectively, in the same residue of LBC samples. The current date showed a positive correlation between the HPV-16 L1 methylation and the E6/E7 mRNA levels. The L1 methylation and mRNA levels both increased with disease severity. The mRNA test method showed higher sensitivity and NPV (98.0 and 91.7% vs. 89.8 and 80.8%), while lower specificity and PPV (34.4 and 69.6% vs. 65.6 and 80.0%), than the L1 methylation assay for detecting histology-confirmed CIN2+. When using the detection method of mRNA test combined with L1 methylation assay, we obtained a sensitivity of 89.8% and a specificity of 71.9%. These findings suggest that assessment of HPV-16 L1 methylation testing combined with E6/E7 mRNA testing may be a promising method for the triage of women with HPV type 16 only.
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Affiliation(s)
- Cui Qiu
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yanfang Zhi
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yong Shen
- The Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Street, Jinshui District, Zhengzhou 450008, China
| | - Jiaomei Gong
- The Second Affiliated Hospital of Zhengzhou University, No. 2 Jingba Street, Guancheng Hui District, Zhengzhou 450014, China
| | - Ya Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Shouhua Rong
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Paul Okunieff
- University of Florida Shands Cancer Center, Gainesville, FL, USA
| | - Lulu Zhang
- Engineering Research Center of Microbial Tumer Marker and Drug Sensitive Test, Xinxiang, Henan, 453400, China
| | - Xiaofu Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China.
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Capper RL, Jin YK, Lundgren PB, Peplow LM, Matz MV, van Oppen MJH. Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples. BMC Genet 2015; 16:62. [PMID: 26070466 PMCID: PMC4465018 DOI: 10.1186/s12863-015-0222-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Background The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs. Conclusions Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxana L Capper
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Young K Jin
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. .,Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Petra B Lundgren
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Mikhail V Matz
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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Qiu C, Zhi Y, Shen Y, Gong J, Li Y, Li X. High-resolution melting analysis of HPV-16L1 gene methylation: A promising method for prognosing cervical cancer. Clin Biochem 2015; 48:855-9. [PMID: 25982893 DOI: 10.1016/j.clinbiochem.2015.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for DNA methylation analysis, but it is rarely used for the detection of viral DNA methylation. In this study, we investigated the HPV-16L1 gene methylation that is detected by MS-HRM as a potential biomarker for prognosing cervical dysplasia and cancer. DESIGN AND METHODS A total of 114 HPV-16 infected patients (normal (17), CIN1 (25), CIN2 (29), CIN3 (32), SCC (11)) who underwent liquid-based cytology test and biopsy were included in this study. 17 cases with HPV-16 infection and negative cytologic and histologic results served as the control group. The HPV-16L1 gene methylation statuses of these samples were investigated using a methylation-sensitive high-resolution melting (MS-HRM) assay after bisulfite modification. RESULTS The HPV-16L1 gene methylation statuses of all the 114 specimens were successfully detected by MS-HRM, and we observed increasing methylation levels in severe lesions, as determined using histologic assays. In addition, the methylation levels of CIN2+ (CIN2, CIN3 and SCC) were significantly higher than that of CIN2- (normal and CIN1, P<0.001). When taking CIN2+ as the reference, our HPV-16L1 DNA methylation assay achieved 91.7% sensitivity and 59.5% specificity, respectively. CONCLUSIONS The results of the present work demonstrated that HPV-16L1 gene methylation was closely associated with cervical precancerosis and cancer. Moreover, using MS-HRM to detect HPV-16L1 gene methylation may be a powerful assay for the triage of HPV-16-positive females, which could identify patients with high risk of invasive cancer.
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Affiliation(s)
- Cui Qiu
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yanfang Zhi
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yong Shen
- The Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Street, Jinshui District, Zhengzhou 450008, China
| | - Jiaomei Gong
- The Second Affiliated Hospital of Zhengzhou University, No. 2 Jingba Street, Guancheng Hui District, Zhengzhou 450014, China
| | - Ya Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Xiaofu Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China.
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A rapid and accurate closed-tube Methylation-Sensitive High Resolution Melting Analysis assay for the semi-quantitative determination of SOX17 promoter methylation in clinical samples. Clin Chim Acta 2015; 444:303-9. [DOI: 10.1016/j.cca.2015.02.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/11/2015] [Accepted: 02/19/2015] [Indexed: 12/23/2022]
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10
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Rawłuszko-Wieczorek AA, Horbacka K, Krokowicz P, Misztal M, Jagodziński PP. Prognostic potential of DNA methylation and transcript levels of HIF1A and EPAS1 in colorectal cancer. Mol Cancer Res 2014; 12:1112-27. [PMID: 24825851 DOI: 10.1158/1541-7786.mcr-14-0054] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Hypoxic conditions during the formation of colorectal cancer may support the development of more aggressive tumors. Hypoxia-inducible factor (HIF) is a heterodimeric complex, composed of oxygen-induced HIFα and constitutively expressed HIFβ subunits, which mediates the primary transcriptional response to hypoxic stress. Among HIFα isoforms, HIF1α (HIF1A) and endothelial PAS domain-containing protein 1 (EPAS1) are able to robustly activate hypoxia-responsive gene signatures. Although posttranslational regulation of HIFα subunits is well described, less is known about their transcriptional regulation. Here, molecular analysis determined that EPAS1 mRNA was significantly reduced in primary colonic adenocarcinoma specimens compared with histopathologically nonneoplastic tissue from 120 patients. In contrast, no difference in HIF1A mRNA levels was observed between cancerous and noncancerous tissue. Bisulfite DNA sequencing and high-resolution melting analysis identified significant DNA hypermethylation in the EPAS1 regulatory region from cancerous tissue compared with nonneoplastic tissue. Importantly, multivariate Cox regression analysis revealed a high HR for patients with cancer with low EPAS1 transcript levels (HR, 4.91; 95% confidence interval, CI, 0.42-56.15; P = 0.047) and hypermethylated EPAS1 DNA (HR, 33.94; 95% CI, 2.84-405.95; P = 0.0054). Treatment with a DNA methyltransferase inhibitor, 5-Aza-2'-deoxycytidine (5-aza-dC/Decitabine), upregulated EPAS1 expression in hypoxic colorectal cancer cells that were associated with DNA demethylation of the EPAS1 regulatory region. In summary, EPAS1 is transcriptionally regulated by DNA methylation in colorectal cancer. IMPLICATIONS DNA methylation and mRNA status of EPAS1 have novel prognostic potential for colorectal cancer.
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Affiliation(s)
| | - Karolina Horbacka
- General and Colorectal Surgery, Poznań University of Medical Sciences, Poland
| | - Piotr Krokowicz
- General and Colorectal Surgery, Poznań University of Medical Sciences, Poland
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Xing L, Quist TS, Stevenson TJ, Dahlem TJ, Bonkowsky JL. Rapid and efficient zebrafish genotyping using PCR with high-resolution melt analysis. J Vis Exp 2014:e51138. [PMID: 24561516 PMCID: PMC4116811 DOI: 10.3791/51138] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Zebrafish is a powerful vertebrate model system for studying development, modeling disease, and performing drug screening. Recently a variety of genetic tools have been introduced, including multiple strategies for inducing mutations and generating transgenic lines. However, large-scale screening is limited by traditional genotyping methods, which are time-consuming and labor-intensive. Here we describe a technique to analyze zebrafish genotypes by PCR combined with high-resolution melting analysis (HRMA). This approach is rapid, sensitive, and inexpensive, with lower risk of contamination artifacts. Genotyping by PCR with HRMA can be used for embryos or adult fish, including in high-throughput screening protocols.
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Affiliation(s)
- Lingyan Xing
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine; Department of Neurobiology and Anatomy, University of Utah School of Medicine; Interdepartmental Program in Neurosciences, University of Utah School of Medicine
| | - Tyler S Quist
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine
| | - Tamara J Stevenson
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine
| | - Timothy J Dahlem
- Mutation Generation and Detection Core, HSC Core Research Facility, University of Utah School of Medicine
| | - Joshua L Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine; Department of Neurobiology and Anatomy, University of Utah School of Medicine; Interdepartmental Program in Neurosciences, University of Utah School of Medicine; Department of Neurology, University of Utah School of Medicine; ;
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Wang ZM. PAX1 Methylation Analysis by MS-HRM is Useful in Triage of High-grade Squamous Intraepithelial Lesions. Asian Pac J Cancer Prev 2014; 15:891-4. [DOI: 10.7314/apjcp.2014.15.2.891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Yamagata Y, Nishino K, Takaki E, Sato S, Maekawa R, Nakai A, Sugino N. Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells. PLoS One 2014; 9:e83612. [PMID: 24465385 PMCID: PMC3900404 DOI: 10.1371/journal.pone.0083612] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to characterize the genome-wide DNA methylation profiles of isolated endometrial stromal cells obtained from eutopic endometria with (euESCa) and without endometriosis (euESCb) and ovarian endometrial cysts (choESC). Three samples were analyzed in each group. The infinium methylation array identified more hypermethylated and hypomethylated CpGs in choESC than in euESCa, and only a few genes were methylated differently in euESCa and euESCb. A functional analysis revealed that signal transduction, developmental processes, immunity, etc. were different in choESC and euESCa. A clustering analysis and a principal component analysis performed based on the methylation levels segregated choESC from euESC, while euESCa and euESCb were identical. A transcriptome analysis was then conducted and the results were compared with those of the DNA methylation analysis. Interestingly, the hierarchical clustering and principal component analyses showed that choESC were segregated from euESCa and euESCb in the DNA methylation analysis, while no segregation was recognized in the transcriptome analysis. The mRNA expression levels of the epigenetic modification enzymes, including DNA methyltransferases, obtained from the specimens were not significantly different between the groups. Some of the differentially methylated and/or expressed genes (NR5A1, STAR, STRA6 and HSD17B2), which are related with steroidogenesis, were validated by independent methods in a larger number of samples. Our findings indicate that different DNA methylation profiles exist in ectopic ESC, highlighting the benefits of genome wide DNA methylation analyses over transcriptome analyses in clarifying the development and characterization of endometriosis.
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Affiliation(s)
- Yoshiaki Yamagata
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Eiichi Takaki
- Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryo Maekawa
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Norihiro Sugino
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
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Expression and DNA methylation levels of prolyl hydroxylases PHD1, PHD2, PHD3 and asparaginyl hydroxylase FIH in colorectal cancer. BMC Cancer 2013; 13:526. [PMID: 24195777 PMCID: PMC3828400 DOI: 10.1186/1471-2407-13-526] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common and comprehensively studied malignancies. Hypoxic conditions during formation of CRC may support the development of more aggressive cancers. Hypoxia inducible factor (HIF), a major player in cancerous tissue adaptation to hypoxia, is negatively regulated by the family of prolyl hydroxylase enzymes (PHD1, PHD2, PHD3) and asparaginyl hydroxylase, called factor inhibiting HIF (FIH). Methods PHD1, PHD2, PHD3 and FIH gene expression was evaluated using quantitative RT-PCR and western blotting in primary colonic adenocarcinoma and adjacent histopathologically unchanged colonic mucosa from patients who underwent radical surgical resection of the colon (n = 90), and the same methods were used for assessment of PHD3 gene expression in HCT116 and DLD-1 CRC cell lines. DNA methylation levels of the CpG island in the promoter regulatory region of PHD1, PHD2, PHD3 and FIH were assessed using bisulfite DNA sequencing and high resolution melting analysis (HRM) for patients and HRM analysis for CRC cell lines. Results We found significantly lower levels of PHD1, PHD2 and PHD3 transcripts (p = 0.00026; p < 0.00001; p < 0.00001) and proteins (p = 0.004164; p = 0.0071; p < 0.00001) in primary cancerous than in histopathologically unchanged tissues. Despite this, we did not observe statistically significant differences in FIH transcript levels between cancerous and histopathologically unchanged colorectal tissue, but we found a significantly increased level of FIH protein in CRC (p = 0.0169). The reduced PHD3 expression was correlated with significantly increased DNA methylation in the CpG island of the PHD3 promoter regulatory region (p < 0.0001). We did not observe DNA methylation in the CpG island of the PHD1, PHD2 or FIH promoter in cancerous and histopathologically unchanged colorectal tissue. We also showed that 5-Aza-2’-deoxycytidine induced DNA demethylation leading to increased PHD3 transcript and protein level in HCT116 cells. Conclusion We demonstrated that reduced PHD3 expression in cancerous tissue was accompanied by methylation of the CpG rich region located within the first exon and intron of the PHD3 gene. The diminished expression of PHD1 and PHD2 and elevated level of FIH protein in cancerous tissue compared to histopathologically unchanged colonic mucosa was not associated with DNA methylation within the CpG islands of the PHD1, PHD2 and FIH genes.
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