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Kougioumtsidou N, Vavoulidis E, Nasioutziki M, Symeonidou M, Pratilas GC, Mareti E, Petousis S, Chatzikyriakidou A, Grimbizis G, Theodoridis T, Miliaras D, Dinas K, Zepiridis L. DNA methylation patterns of RAR-β2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions. Diagn Cytopathol 2020; 49:153-164. [PMID: 32530576 DOI: 10.1002/dc.24513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/27/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Promoter hypermethylation is common in Breast Cancer (BC) with studies mainly in histological specimens showing frequent methylation of tumor suppressor genes (TSGs) compared with normal tissues. The aim of this study was to estimate the frequency of promoter methylation of RAR-β2 and RASSF1A genes in breast FNAB material aiming to evaluate the methylation status of these two genes as biomarker for detecting BC in Greek population. METHODS FNAB material from 104 patients was collected for cytological evaluation and epigenetic analysis. DNA was extracted and subjected to bisulfite conversion. A methylation-specific PCR was carried out and the final products were separated with electrophoresis in 2% agarose gels. RESULTS From 104 samples, RASSF1A hypermethylation was observed in 78 (75%) and RAR-β2 hypermethylation in 64 (61.6%). 84% and 78% of the cases diagnosed with breast malignancy (n = 50) were methylated for RASSF1A and RAR-β2, respectively. Methylated RASSF1A and RAR-β2 were also detected in 88.3% and 76.5% in samples diagnosed as suspicious for malignancy (n = 17) and in 57.2% of samples diagnosed with atypia (n = 14). The Odds Ratio for breast malignancy was 4.545 in patients with RASSF1A hypermethylation and 9.167 in patients with RAR-β2 hypermethylation underlying their promoter's methylation positive correlation with breast malignancy. CONCLUSION To optimize the sensitivity and specificity of this epigenetic setting, more TSGs related to BC should be gradually imported in our evaluated methylation panel and be validated in a larger study sample with the aim that the obtained epigenetic profiles will provide clinicians with valuable tools for management of BC patients in Greece.
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Affiliation(s)
- Niki Kougioumtsidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Vavoulidis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Nasioutziki
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Marianthi Symeonidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Georgios Chrysostomos Pratilas
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Mareti
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Stamatios Petousis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Faculty of Medicine, Laboratory of Medical Biology-Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Gregorios Grimbizis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Theodoros Theodoridis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Dimosthenis Miliaras
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Dinas
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Leonidas Zepiridis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
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Chen L, Zhang YH, Lu G, Huang T, Cai YD. Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways. Artif Intell Med 2017; 76:27-36. [PMID: 28363286 DOI: 10.1016/j.artmed.2017.02.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/31/2017] [Accepted: 02/05/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Cancer is a disease that involves abnormal cell growth and can invade or metastasize to other tissues. It is known that several factors are related to its initiation, proliferation, and invasiveness. Recently, it has been reported that long non-coding RNAs (lncRNAs) can participate in specific functional pathways and further regulate the biological function of cancer cells. Studies on lncRNAs are therefore helpful for uncovering the underlying mechanisms of cancer biological processes. METHODS We investigated cancer-related lncRNAs using gene ontology (GO) terms and KEGG pathway enrichment scores of neighboring genes that are co-expressed with the lncRNAs by extracting important GO terms and KEGG pathways that can help us identify cancer-related lncRNAs. The enrichment theory of GO terms and KEGG pathways was adopted to encode each lncRNA. Then, feature selection methods were employed to analyze these features and obtain the key GO terms and KEGG pathways. RESULTS The analysis indicated that the extracted GO terms and KEGG pathways are closely related to several cancer associated processes, such as hormone associated pathways, energy associated pathways, and ribosome associated pathways. And they can accurately predict cancer-related lncRNAs. CONCLUSIONS This study provided novel insight of how lncRNAs may affect tumorigenesis and which pathways may play important roles during it. These results could help understanding the biological mechanisms of lncRNAs and treating cancer.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China; College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Guohui Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China.
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.
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Fang C, Jian ZY, Shen XF, Wei XM, Yu GZ, Zeng XT. Promoter Methylation of the Retinoic Acid Receptor Beta2 (RARβ2) Is Associated with Increased Risk of Breast Cancer: A PRISMA Compliant Meta-Analysis. PLoS One 2015; 10:e0140329. [PMID: 26451736 PMCID: PMC4599915 DOI: 10.1371/journal.pone.0140329] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/24/2015] [Indexed: 12/25/2022] Open
Abstract
Background Epigenetic studies demonstrate that an association may exist between methylation of the retinoic acid receptor beta2 (RARβ2) gene promoter and breast cancer onset risk, tumor stage, and histological grade, however the results of these studies are not consistent. Hence, we performed this meta-analysis to ascertain a more comprehensive and accurate association. Materials and Methods Relevant studies were retrieved from the PubMed, Embase and Chinese National Knowledge Infrastructure databases up to February 28, 2015. After two independent reviewers screened the studies and extracted the necessary data, meta-analysis was performed using Review Manager 5.2 software. Results Nineteen eligible articles, including 20 studies, were included in our analysis. Compared to non-cancerous controls, the frequency of RARβ2 methylation was 7.27 times higher in patients with breast cancer (odds ratio (OR) = 7.27, 95% confidence interval (CI) = 3.01–17.52). Compared to late-stage RARβ2 methylated patients, the pooled OR of early-stage ones was 0.81 (OR = 0.81, 95% CI = 0.55–1.17). The OR of low-grade RARβ2 methylated patients was 0.96 (OR = 0.96, 95% CI = 0.74–1.25) compared to high-grade RARβ2 methylated patients. Conclusion RARβ2 methylation is significantly increased in breast cancer samples when compared to non-cancerous controls. RARβ2 could serve as a potential epigenetic marker for breast cancer detection and management.
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Affiliation(s)
- Cheng Fang
- Center for Evidence-Based Medicine and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhi-Yuan Jian
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xian-Feng Shen
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xue-Mei Wei
- Department of Nursing, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, P.R. China
| | - Guo-Zheng Yu
- Center for Evidence-Based Medicine and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xian-Tao Zeng
- Center for Evidence-Based Medicine and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- * E-mail:
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Monoallelic chromatin conformation flanking long-range silenced domains in cancer-derived and normal cells. PLoS One 2013; 8:e63190. [PMID: 23696799 PMCID: PMC3655995 DOI: 10.1371/journal.pone.0063190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/27/2013] [Indexed: 11/25/2022] Open
Abstract
Epigenetic inactivation of chromatin plays an important role in determining cell phenotype in both normal and cancer cells, but our knowledge is still incomplete with respect to any potential monoallelic nature of the phenomenon. We have genotyped DNA isolated from chromatin of two colorectal cancer-derived lines and a culture of normal human intestinal epithelial cells (HIEC), which was immunoprecipitated with antibodies to acetylated vs. methylated histone H3K9, and presented the data as B allele frequency differences over multiple single-nucleotide polymorphism (SNP) moving window averages. [B allele is an arbitrary term defined as one of the two alleles at any given SNP, named A and B]. Three different validation tests confirmed that peaks exhibiting differences represented monoallelic domains. These complementary tests confirmed the following: 1) genes in the regions of high B allele frequency difference were expressed monoallelically; 2) in normal cells all five imprinting control regions which carried heterozygous SNPs were characterized by B allele difference peaks; and 3) the haplotypes in the B allele difference peaks were faithfully maintained in the chromatin immunoprecipitated with the respective antibodies. In both samples most of the monoallelic domains were found at the boundaries between regions of open and closed chromatin. With respect to the cancer line, this supports the established concept of conformation spreading, but the results from the normal cells were unexpected. Since these cells were polyclonal, the monoallelic structures were probably not determined by random choice as occurs in X-inactivation, so we propose that epigenetic inactivation in some domains may be heritable and polymorphic in normal human cells.
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Pappas JJ, Toulouse A, Basik M, Lévesque L, Bradley W. Knockdown of RARB2 identifies a dual role in cancer. Genes Chromosomes Cancer 2011; 50:700-14. [DOI: 10.1002/gcc.20892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/26/2011] [Indexed: 01/16/2023] Open
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Pirouzpanah S, Taleban FA, Atri M, Abadi AR, Mehdipour P. The effect of modifiable potentials on hypermethylation status of retinoic acid receptor-beta2 and estrogen receptor-alpha genes in primary breast cancer. Cancer Causes Control 2010; 21:2101-11. [PMID: 20711807 DOI: 10.1007/s10552-010-9629-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 07/30/2010] [Indexed: 02/08/2023]
Abstract
Epigenetic silencing of retinoic acid receptor-beta2 (RARbeta2) and estrogen receptor-alpha (ERalpha) expressions have been revealed to be important in the development of approaches for diagnosis and therapy of breast cancer. We aimed to explore the correlation of some potential factors with the hypermethylation status of RARbeta2 and ERalpha genes among Iranian breast cancer patients. The hypermethylation status was investigated in 137 dissected tissues from primary breast cancer patients through methylation-specific PCR. Overall, the methylation frequencies of RARbeta2 and ERalpha genes were observed in 36.5 and 51.1% of participants, respectively. The hypermethylated RARbeta2 was associated with younger age at diagnosis and negative family history of breast cancer. The hypermethylation of ERalpha was correlated positively with smoking, duration of estradiol exposure, ER-negativity in tumors and body mass index (at 5 years ago). The plasma levels of folate and vitamin B(12) were inversely related to the hypermethylation status of ERalpha, after controlling for covariates. The risk of ERalpha hypermethylation was increased with high plasma level of total homocysteine. In conclusion, our data provide new insights into the possible effect of some lifestyle-related factors on the aberrant methylation drift of ERalpha and RARbeta2 genes in breast cancer.
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Affiliation(s)
- Saeed Pirouzpanah
- Department of Human Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University M.C., Tehran 19395-4741, Iran.
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A modified protocol for bisulfite genomic sequencing of difficult samples. Biol Proced Online 2009; 11:99-112. [PMID: 19551458 PMCID: PMC3055914 DOI: 10.1007/s12575-009-9010-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 05/21/2009] [Indexed: 10/28/2022] Open
Abstract
The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED) designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes.
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DNA methylation, epimutations and cancer predisposition. Int J Biochem Cell Biol 2008; 41:34-9. [PMID: 18835361 DOI: 10.1016/j.biocel.2008.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 12/11/2022]
Abstract
Hereditary cancer syndromes caused by germline mutations give rise to distinct spectra of cancers with characteristic clinico-pathological features. Many of these hereditary cancer genes are silenced by methylation in a similar spectrum of sporadic cancers. It is likely that the initiating event in some of those cases of sporadic cancer is the somatic epigenetic inactivation (epimutation) of the same hereditary cancer gene. Recently, it has been shown that epimutations of certain hereditary cancer genes can be constitutional i.e. present throughout the soma. These epimutations may be inherited or arise very early in the germline. The heritability of these epimutations is very low as in most cases they are erased by passage through the germline. In other cases, predisposition to epimutations rather than the epimutations themselves can be inherited. These cases are characterised by Mendelian inheritance and are likely to be associated with sequence variants. Other sequence variants and environmental influences may also affect methylation propensity at a global level.
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