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Rotimi SO, Rotimi OA, Salhia B. A Review of Cancer Genetics and Genomics Studies in Africa. Front Oncol 2021; 10:606400. [PMID: 33659210 PMCID: PMC7917259 DOI: 10.3389/fonc.2020.606400] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the second leading cause of death globally and is projected to overtake infectious disease as the leading cause of mortality in Africa within the next two decades. Cancer is a group of genomic diseases that presents with intra- and inter-population unique phenotypes, with Black populations having the burden of morbidity and mortality for most types. At large, the prevention and treatment of cancers have been propelled by the understanding of the genetic make-up of the disease of mostly non-African populations. By the same token, there is a wide knowledge gap in understanding the underlying genetic causes of, and genomic alterations associated with, cancer among black Africans. Accordingly, we performed a review of the literature to survey existing studies on cancer genetics/genomics and curated findings pertaining to publications across multiple cancer types conducted on African populations. We used PubMed MeSH terms to retrieve the relevant publications from 1990 to December 2019. The metadata of these publications were extracted using R text mining packages: RISmed and Pubmed.mineR. The data showed that only 0.329% of cancer publications globally were on Africa, and only 0.016% were on cancer genetics/genomics from Africa. Although the most prevalent cancers in Africa are cancers of the breast, cervix, uterus, and prostate, publications representing breast, colorectal, liver, and blood cancers were the most frequent in our review. The most frequently reported cancer genes were BRCA1, BRCA2, and TP53. Next, the genes reported in the reviewed publications’ abstracts were extracted and annotated into three gene ontology classes. Genes in the cellular component class were mostly associated with cell part and organelle part, while those in biological process and molecular function classes were mainly associated with cell process, biological regulation, and binding, and catalytic activity, respectively. Overall, this review highlights the paucity of research on cancer genomics on African populations, identified gaps, and discussed the need for concerted efforts to encourage more research on cancer genomics in Africa.
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Affiliation(s)
- Solomon O Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Oluwakemi A Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Norris Comprehensive Cancer Centre, University of Southern California, Los Angeles, CA, United States
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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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de Ruijter TC, van der Heide F, Smits KM, Aarts MJ, van Engeland M, Heijnen VCG. Prognostic DNA methylation markers for hormone receptor breast cancer: a systematic review. Breast Cancer Res 2020; 22:13. [PMID: 32005275 PMCID: PMC6993426 DOI: 10.1186/s13058-020-1250-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In patients with hormone receptor-positive breast cancer, differentiating between patients with a low and a high risk of recurrence is an ongoing challenge. In current practice, prognostic clinical parameters are used for risk prediction. DNA methylation markers have been proven to be of additional prognostic value in several cancer types. Numerous prognostic DNA methylation markers for breast cancer have been published in the literature. However, to date, none of these markers are used in clinical practice. METHODS We conducted a systematic review of PubMed and EMBASE to assess the number and level of evidence of published DNA methylation markers for hormone receptor-positive breast cancer. To obtain an overview of the reporting quality of the included studies, all were scored according to the REMARK criteria that were established as reporting guidelines for prognostic biomarker studies. RESULTS A total of 74 studies were identified reporting on 87 different DNA methylation markers. Assessment of the REMARK criteria showed variation in reporting quality of the studies. Eighteen single markers and one marker panel were studied in multiple independent populations. Hypermethylation of the markers RASSF1, BRCA, PITX2, CDH1, RARB, PCDH10 and PGR, and the marker panel GSTP1, RASSF1 and RARB showed a statistically significant correlation with poor disease outcome that was confirmed in at least one other, independent study. CONCLUSION This systematic review provides an overview on published prognostic DNA methylation markers for hormone receptor-positive breast cancer and identifies eight markers that have been independently validated. Analysis of the reporting quality of included studies suggests that future research on this topic would benefit from standardised reporting guidelines.
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Affiliation(s)
- Tim C. de Ruijter
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Frank van der Heide
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M. Smits
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Maureen J. Aarts
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Manon van Engeland
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C. G. Heijnen
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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Donovan MG, Wren SN, Cenker M, Selmin OI, Romagnolo DF. Dietary fat and obesity as modulators of breast cancer risk: Focus on DNA methylation. Br J Pharmacol 2020; 177:1331-1350. [PMID: 31691272 DOI: 10.1111/bph.14891] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) is the most common cancer and second leading cause of cancer mortality in women worldwide. Validated biomarkers enhance efforts for early detection and treatment, which reduce the risk of mortality. Epigenetic signatures have been suggested as good biomarkers for early detection, prognosis and targeted therapy of BC. Here, we highlight studies documenting the modifying effects of dietary fatty acids and obesity on BC biomarkers associated with DNA methylation. We focus our analysis on changes elicited in writers of DNA methylation (i.e., DNA methyltransferases), global DNA methylation and gene-specific DNA methylation. To provide context, we precede this discussion with a review of the available evidence for an association between BC incidence and both dietary fat consumption and obesity. We also include a review of well-vetted BC biomarkers related to cytosine-guanine dinucleotides methylation and how they influence BC risk, prognosis, tumour characteristics and response to treatment. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Micah G Donovan
- Interdisciplinary Cancer Biology Graduate Program, University of Arizona, Tucson, Arizona
| | - Spencer N Wren
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Mikia Cenker
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Ornella I Selmin
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
| | - Donato F Romagnolo
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
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DNA Methylation Profiles and Their Diagnostic Utility in BC. DISEASE MARKERS 2019; 2019:6328503. [PMID: 31198475 PMCID: PMC6526564 DOI: 10.1155/2019/6328503] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/31/2019] [Accepted: 02/18/2019] [Indexed: 01/02/2023]
Abstract
Biomarkers, including DNA methylation, have shown a great potential for use in personalized medicine for BC and especially for the diagnosis of BC in developing countries. According to the bisulfite sequencing PCR in twelve specimens (BC and matched normal tissues), nine genetic probes were designed to detect the frequency of methylation of the promoters in a total of 302 paired cases of BC and matched normal breast tissues. Finally, a total of 900 serum samples were used to validate the use of these methylation biomarkers for clinical diagnosis of BC. A high frequency of promoter methylation of SFN, HOXA11, P16, RARβ, PCDHGB7, hMLH1, WNT5a, HOXD13, and RASSF1a was observed in BC tissues. The methylation frequencies of HOXD13 and hMLH1 increased with the progression of BC. The methylation frequencies of HOXD13 and WNT5a were significantly higher in BC. We found that methylation modification-positive samples were most consistently associated with luminal BC. Finally, we confirmed that RASSF1a, P16, and PCDHGB7 displayed a significant sensitivity and specificity as diagnostic biomarkers for BC (P < 0.001), and a panel that combined these three genes displayed increased significance (AUC, 0.781; P < 0.001). These data suggest that epigenetic markers in serum can potentially be used to diagnose BC. The identification of additional BC-specific methylated genes would improve the sensitivity and specificity of this approach. This study could also indicate that different molecular subtypes of BC are caused by distinct genetic and epigenetic mechanisms.
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Yari K, Rahimi Z. Promoter Methylation Status of the Retinoic Acid Receptor-Beta 2 Gene in Breast Cancer Patients: A Case Control Study and Systematic Review. Breast Care (Basel) 2019; 14:117-123. [PMID: 31798384 DOI: 10.1159/000489874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background We aimed to determine the promoter methylation status of the retinoic acid receptor-beta 2 (RARβ2) gene among breast cancer patients and to review relevant studies in this field in various populations. Methods We analyzed 400 samples which comprised blood specimens from 102 breast cancer patients, 102 first-degree female relatives of patients, 100 cancer-free females, 48 breast cancer tissues, and 48 adjacent normal breast tissues from the same patients. The RARβ2 methylation status was determined using methylation-specific polymerase chain reaction (MSP) and DNA sequencing methods. Results The presence of combined partially methylated (MU) and fully methylated (MM) forms of the RARβ2 gene (MU+MM) in the blood of patients was associated with susceptibility to breast cancer (odds ratio = 4.7, p = 0.05). A significantly higher frequency of the MM genotype was observed in cancer tissue (10.4%) compared to matched adjacent normal breast tissue (0%) (p = 0.02). Conclusion We found a higher frequency of RARβ2 gene methylation in the blood and cancer tissues of patients compared to the blood of controls and adjacent normal breast tissues. The survey of studies on various populations demonstrated a higher RARβ2 methylation frequency in breast cancer patients compared to normal individuals, and many reports suggest a significant association between hypermethylation of the gene and susceptibility to breast cancer.
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Affiliation(s)
| | - Zohreh Rahimi
- Medical Biology Research Center.,Department of Clinical Biochemistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Alhudiri IM, Nolan CC, Ellis IO, Elzagheid A, Rakha EA, Green AR, Chapman CJ. Expression of Lamin A/C in early-stage breast cancer and its prognostic value. Breast Cancer Res Treat 2019; 174:661-668. [DOI: 10.1007/s10549-018-05092-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 10/27/2022]
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Lerner L, Winn R, Hulbert A. Lung cancer early detection and health disparities: the intersection of epigenetics and ethnicity. J Thorac Dis 2018; 10:2498-2507. [PMID: 29850158 DOI: 10.21037/jtd.2018.04.07] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lung cancer is the most prominent cause of cancer-related mortality. Significant disparities in incidence and outcome characterize the disease's manifestations among ethnically and racially diverse populations. Complete surgical resection is the most effective curative treatment. However, success relies on early tumor detection. The National Lung Cancer Screening trial showed that lung cancer related mortality can be reduced by the use of low-dose CT (LDCT) screening. However, this test is plagued by a high false positive rate of 97% and the device itself is limited to designated cancer centers due to its expense and size. This restriction makes it difficult for underserved groups to access LDCT screening, the current standard of care. Highly sensitive and specific epigenetic DNA methylation-based biomarkers have the potential to work independently or in conjunction with LDCT screening to identify early-stage tumors. These tests could reduce unnecessary invasive confirmatory diagnostic tests and their associated morbidity and mortality. These tests also have the opportunity to bring lung cancer screening to the community thereby reducing unequal accessibility. However, epigenetic alterations are closely linked to the interplay between hereditary and environmental factors such as diet, lifestyle, ethnic ancestry, toxin exposure, residential segregation, and disparate community support structures. Despite this, the overwhelming number of early detection DNA methylation biomarker studies to date have either failed to control for ethnicity or have employed heavily Caucasian-biased patient cohorts. This review seeks to summarize the literature related to the early detection of lung cancer through molecular biomarkers among different ethnicities. Ethnical specific epigenetic biomarkers have the potential to be the first step towards an accessible, available personalized medicine approach to cancer through liquid biopsy.
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Affiliation(s)
- Lane Lerner
- 1University of Illinois at Chicago Cancer Center, 2Department of Surgery/Cancer Center University of Illinois at Chicago Cancer Center, University of Illinois Hospital and Health Sciences System, Chicago, USA
| | - Robert Winn
- 1University of Illinois at Chicago Cancer Center, 2Department of Surgery/Cancer Center University of Illinois at Chicago Cancer Center, University of Illinois Hospital and Health Sciences System, Chicago, USA
| | - Alicia Hulbert
- 1University of Illinois at Chicago Cancer Center, 2Department of Surgery/Cancer Center University of Illinois at Chicago Cancer Center, University of Illinois Hospital and Health Sciences System, Chicago, USA
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Niu H, Yang J, Yang K, Huang Y. The relationship between RASSF1A promoter methylation and thyroid carcinoma: A meta-analysis of 14 articles and a bioinformatics of 2 databases (PRISMA). Medicine (Baltimore) 2017; 96:e8630. [PMID: 29145283 PMCID: PMC5704828 DOI: 10.1097/md.0000000000008630] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. METHODS We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility. The data from the Cancer Genome Atlas project (TCGA) database was used to analyze the relationship between RASSF1A promoter methylation and thyroid carcinoma susceptibility, clinical characteristics, prognosis. Odds ratios were estimated for thyroid carcinoma susceptibility and hazard ratios were estimated for thyroid carcinoma prognosis. The heterogeneity between studies of meta-analysis was explored using H, I values, and meta-regression. We adopted quality criteria to classify the studies of meta-analysis. Subgroup analyses were done for thyroid carcinoma susceptibility according to ethnicity, methods, and primers. RESULTS Result of meta-analysis indicated that RASSF1A promoter methylation is associated with higher susceptibility to thyroid carcinoma with small heterogeneity. Similarly, the result from GEO database also showed that a significant association between RASSF1A gene promoter methylation and thyroid carcinoma susceptibility. For the results of TCGA database, we found that RASSF1A promoter methylation is associated with susceptibility and poor disease-free survival (DFS) of thyroid carcinoma. In addition, we also found a close association between RASSF1A promoter methylation and patient tumor stage and age, but not in patients of different genders. CONCLUSIONS The methylation status of RASSF1A promoter is strongly associated with thyroid carcinoma susceptibility and DFS. The RASSF1A promoter methylation test can be applied in the clinical diagnosis of thyroid carcinoma.
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Affiliation(s)
- Heng Niu
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
| | - Jingyu Yang
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
| | - Kunxian Yang
- Chest Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan
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Das M, Sharma SK, Sekhon GS, Mahanta J, Phukan RK, Jalan BK. p16 gene silencing along with p53 single-nucleotide polymorphism and risk of esophageal cancer in Northeast India. Tumour Biol 2017; 39:1010428317698384. [PMID: 28459370 DOI: 10.1177/1010428317698384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The high incidence of esophageal cancer in Northeast India and the unique ethnic background and dietary habits provide a great opportunity to study the molecular genetics behind esophageal squamous cell carcinoma in this part of the region. We hypothesized that in addition to currently known environmental risk factors for esophageal cancer, genetic and epigenetic factors are also involved in esophageal carcinogenesis in Northeast India. Therefore, in this study, we explored the possible association between the two important G1 cell cycle regulatory genes p16 and p53 and environmental risk factors and risk of esophageal carcinogenesis. A total of 100 newly diagnosed esophageal cancer cases along with equal number of age-, sex-, and ethnicity-matched controls were included in this study. Methylation-specific polymerase chain reaction was used to determine the p16 promoter methylation status. Single-nucleotide polymorphism at codon 72 of p53 gene was assessed by the polymerase chain reaction-restriction fragment length polymorphism method. Aberrant methylation of p16 gene was seen in 81% of esophageal cancer cases. Hypermethylation of p16 gene was not found in healthy controls. p53 Pro/Pro genotype was found to be a risk genotype in Northeast India compared with Arg/Pro and Arg/Arg. p53 variant/polymorphism was significantly associated with esophageal cancer risk in the study population under all three genetic models, namely, dominant model (Arg/Pro + Pro/Pro vs Arg/Arg odds ratio = 2.25, confidence interval = 1.19-4.26; p = 0.012), recessive model (Arg/Arg + Arg/Pro vs Pro/Pro odds ratio = 2.35, confidence interval = 1.24-4.44; p = 0.008), and homozygous model (Pro/Pro vs Arg/Arg odds ratio = 3.33, confidence interval = 1.54-7.20; p = 0.002). However, p53 variant/polymorphism was not statistically associated with esophageal cancer risk under the heterozygous model (Pro/Pro vs Arg/Pro). In the case-only analysis based on p16 methylation, the p53 variant/polymorphism (Pro/Pro or Arg/Pro) showed significant association for esophageal cancer risk (odds ratio = 3.33, confidence interval = 1.54-7.20; p = 0.002). Gene-gene and gene-environment interaction using the case-only approach revealed a strong association between p16 methylation, p53 single-nucleotide polymorphism, and environmental factors and esophageal cancer risk. Cases with p16 methylation and p53 variant/polymorphism (Pro/Pro or Arg/Pro) along with both betel quid and tobacco chewing habit (odds ratio = 8.29, confidence interval = 1.14-60.23; p = 0.037) conferred eightfold increased risk toward esophageal cancer development. This study reveals a synergistic interaction between epigenetic, genetic, and environmental factors and risk of esophageal cancer in this high-incidence region of Northeast India. The inactivation of either p16 or p53 in a majority of esophageal cancer cases in this study suggests the possible crosstalk between the important cell cycle genes.
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Affiliation(s)
- Mandakini Das
- 1 Regional Medical Research Centre, NE Region (ICMR), Dibrugarh, India
| | | | | | - Jagadish Mahanta
- 1 Regional Medical Research Centre, NE Region (ICMR), Dibrugarh, India
| | - Rup Kumar Phukan
- 1 Regional Medical Research Centre, NE Region (ICMR), Dibrugarh, India
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Zhan L, Zhang B, Tan Y, Yang C, Huang C, Wu Q, Zhang Y, Chen X, Zhou M, Shu A. Quantitative assessment of the relationship between RASSF1A gene promoter methylation and bladder cancer (PRISMA). Medicine (Baltimore) 2017; 96:e6097. [PMID: 28207521 PMCID: PMC5319510 DOI: 10.1097/md.0000000000006097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Methylation of the Ras-association domain family 1 isoform A (RASSF1A) gene promoter region is thought to participate in the initiation and development of many different cancers. However, in bladder cancer the role of RASSF1A methylation was unclear. To evaluate the relationship between RASSF1A methylation and bladder cancer, a quantitative assessment of an independent meta-analysis was performed. In addition, a DNA methylation microarray database from the cancer genome atlas (TCGA) project was used to validate the results of the meta-analysis. METHODS We searched published articles from computerized databases, and DNA methylation data were extracted from TCGA project. All data were analyzed by R software. RESULTS The results of the meta-analysis indicated that the frequency of RASSF1A gene methylation in bladder cancer patients is significantly higher than in healthy controls. The hazard ratio (HR) was 2.24 (95% CI = [1.45; 3.48], P = 0.0003) for overall survival (OS), and the RASSF1A gene promoter methylation status was strongly associated with the TNM stage and differentiation grade of the tumor. The similar results were also found by the data from TCGA project. CONCLUSION There was a significant relationship between the methylation of the RASSF1A gene promoter and bladder cancer. Therefore, RASSF1A gene promoter methylation will be a potential biomarker for the clinical diagnosis of bladder cancer.
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Affiliation(s)
- Leyun Zhan
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Bingyi Zhang
- Ultrasound department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Yaojun Tan
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Chengliang Yang
- Cardiothoracic surgery, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Chenhong Huang
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Qiongya Wu
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Yulin Zhang
- Department of science and education, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Xiaobo Chen
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Mi Zhou
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
| | - Aihua Shu
- Anesthesia department, People's Hospital of China Three Gorges University, The First People's Hospital of Yichang, Yichang, Hubei, P.R. China
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Wu L, Shen Y, Peng X, Zhang S, Wang M, Xu G, Zheng X, Wang J, Lu C. Aberrant promoter methylation of cancer-related genes in human breast cancer. Oncol Lett 2016; 12:5145-5155. [PMID: 28105221 PMCID: PMC5228392 DOI: 10.3892/ol.2016.5351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
The clinical relevance of aberrant DNA methylation is being increasingly recognized in breast cancer. The present study aimed to evaluate the promoter methylation status of seven candidate genes and to explore their potential use as a biomarker for the diagnosis of breast cancer. A total of 70 Chinese patients with breast cancer were recruited, and matched with 20 patients with benign breast disease (BBD). Methylation-specific polymerase chain reaction was performed to measure the methylation status of selected genes. The protein expression of candidate genes was determined by immunohistochemistry. Hypermethylation of Breast cancer 1, early onset; DNA repair associated (BRCA1), glutathione S-transferase pi 1 (GSTP1), cyclin dependent kinase inhibitor 2A, O-6-methylguanine-DNA methyltransferase, phosphatase and tensin homolog, retinoic acid receptor beta 2 and cyclin D2 was observed to be more common in cancerous tissues (24.3, 31.4, 40.0, 27.1, 48.6, 55.7 and 67.1%, respectively) as compared with BBD controls (0.0, 0.0, 20.0, 25.0, 40.0, 40.0 and 45.0%, respectively). Immunohistochemical analysis demonstrated a correlation between the methylation of the target gene and downregulation of protein expression. When BRCA1 and GSTP1 were combined as the biomarker, the area under the receiver operating characteristic curve reached 0.721 (95% confidence interval, 0.616–0.827). The present findings indicated that promoter methylation of cancer-related genes was frequently observed in patients with breast cancer and was associated with various clinical features. Hypermethylation of BRCA1 and GSTP1 may be used as promising biomarkers for breast cancer.
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Affiliation(s)
- Liang Wu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Ye Shen
- Department of Gastrointestinal Surgery, Aoyoung Hospital, Zhangjiagang, Jiangsu 215617, P.R. China
| | - Xianzhen Peng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Simin Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Ming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Guisheng Xu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Xianzhi Zheng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Jianming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China; Department of Social Medicine and Health Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P.R. China; The Innovation Center for Social Risk Governance in Health, Nanjing, Jiangsu, 211166, P.R. China
| | - Cheng Lu
- Department of Breast, Nanjing Maternity and Child Health Hospital of Nanjing Medical University, Nanjing, Jiangsu 210004, P.R. 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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14
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Huang R, Ding P, Yang F. Clinicopathological significance and potential drug target of CDH1 in breast cancer: a meta-analysis and literature review. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:5277-85. [PMID: 26425077 PMCID: PMC4583122 DOI: 10.2147/dddt.s86929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CDH1, as a tumor suppressor gene, contributes sporadic breast cancer (BC) progression. However, the association between CDH1 hypermethylation and BC, and its clinicopathological significance remains unclear. We conducted a meta-analysis to investigate the relationship between the CDH1 methylation profile and the major clinicopathological features. A detailed literature was searched through the electronic databases PubMed, Web of Science™, and EMBASE™ for related research publications. The data were extracted and assessed by two reviewers independently. Odds ratios (ORs) with corresponding confidence intervals (CIs) were calculated and summarized respectively. The frequency of CDH1 methylation was significantly higher in invasive ductal carcinoma than in normal breast tissues (OR =5.83, 95% CI 3.76-9.03, P<0.00001). CDH1 hypermethylation was significantly higher in estrogen receptor (ER)-negative BC than in ER-positive BC (OR =0.62, 95% CI 0.43-0.87, P=0.007). In addition, we found that the CDH1 was significantly methylated in HER2-negative BC than in HER2-positive BC (OR =0.26, 95% CI 0.15-0.44, P<0.00001). However, CDH1 methylation frequency was not associated with progesterone receptor (PR) status, or with grades, stages, or lymph node metastasis of BC patients. Our results indicate that CDH1 hypermethylation is a potential novel drug target for developing personalized therapy. CDH1 hypermethylation is strongly associated with ER-negative and HER2-negative BC, respectively, suggesting CDH1 methylation status could contribute to the development of novel therapeutic approaches for the treatment of ER-negative or HER2-negative BC with aggressive tumor biology.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, School of Public Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Ping Ding
- Department of Occupational and Environmental Health, School of Public Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Fei Yang
- Department of Occupational and Environmental Health, School of Public Health, Central South University, Changsha, Hunan, People's Republic of China
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15
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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Braga EA, Khodyrev DS, Loginov VI, Pronina IV, Senchenko VN, Dmitriev AA, Kubatiev AA, Kushlinskii NE. Methylation in the regulation of the expression of chromosome 3 and microRNA genes in clear-cell renal cell carcinomas. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tamkovich SN, Voytsitskiy VE, Laktionov PP. Modern methods in breast cancer diagnostics. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s1990750814040106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Zhang CY, Zhao YX, Xia RH, Han J, Wang BS, Tian Z, Wang LZ, Hu YH, Li J. RASSF1A promoter hypermethylation is a strong biomarker of poor survival in patients with salivary adenoid cystic carcinoma in a Chinese population. PLoS One 2014; 9:e110159. [PMID: 25302792 PMCID: PMC4193867 DOI: 10.1371/journal.pone.0110159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/08/2014] [Indexed: 11/18/2022] Open
Abstract
In addition to the clinicopathological parameters, molecular biomarkers are becoming increasingly important in the prognostic evaluation of cancer patients. This study aimed to determine the molecular alterations in the RAS association domain family protein1A gene (RASSF1A) in salivary adenoid cystic carcinoma (ACC) and to evaluate the potential of such alterations as prognostic markers. One hundred and sixty-seven ACC tumor tissues and 50 samples of matched normal salivary gland tissues from the same patients were analyzed for RASSF1A promoter methylation status by bisulfite sequencing PCR (BSP) and/or methylation-specific PCR (MSP). Fifty ACC tumor tissues and matched normal salivary gland tissues were analyzed for loss of heterozygosity (LOH) by examining two microsatellite markers (D3S1478, D3S1621) at 3p21. RASSF1A gene mutations were detected by direct sequencing of all six exons in 50 tumor and normal tissue specimens. Over-all, RASSF1A promoter hypermethylation was detected in 35.3% (59/167) of ACC tissues and was associated with histologically solid tumor pattern (P = 0.002) and advanced TNM stage (P = 0.014). RASSF1A LOH was observed in 18.0% (9/50) of cases, and no somatic mutation of RASSF1A was detected in any cases. RASSF1A promoter methylation was associated with the poor over-all survival (Log-rank test, P <0.001) and disease-free survival (Log-rank test, P <0.001) and identified as an independent predicator of over-all patient survival (P = 0.009) and disease-free survival (P <0.001). It was concluded that RASSF1A methylation is involved in the development, differentiation and progression of ACC and is a strong independent biomarker of poor survival in ACC patients in a Chinese population.
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Affiliation(s)
- Chun-Ye Zhang
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Yang-Xing Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, P. R. China
| | - Rong-Hui Xia
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Jing Han
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Bing-Shun Wang
- Department of Biostatistics, Shanghai Jiao Tong University, School of Medicine, Shanghai, P. R. China
| | - Zhen Tian
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Li-Zhen Wang
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Yu-Hua Hu
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
| | - Jiang Li
- Department of Oral Pathology, 9th People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, P. R. China
- * E-mail:
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19
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Naushad SM, Reddy CA, Kumaraswami K, Divyya S, Kotamraju S, Gottumukkala SR, Digumarti RR, Kutala VK. Impact of hyperhomocysteinemia on breast cancer initiation and progression: epigenetic perspective. Cell Biochem Biophys 2014; 68:397-406. [PMID: 23934182 DOI: 10.1007/s12013-013-9720-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Our recent study showing association of hyperhomocysteinemia and hypomethioninemia in breast cancer and other studies indicating association of hyperhomocysteinemia with metastasis and development of drug resistance in breast cancer cells treated with homocysteine lead us to hypothesize that homocysteine might modulate the expression of certain tumor suppressors, i.e., RASSF1, RARβ1, CNND1, BRCA1, and p21, and might influence prognostic markers such as BNIP3 by inducing epigenetic alteration. To demonstrate this hypothesis, we have treated MCF-7 and MDA-MB-231 cells with different doses of homocysteine and observed dose-dependent inhibition of BRCA1 and RASSF1, respectively. In breast cancer tissues, we observed the following expression pattern: BNIP3 > BRCA1 > RARβ1 > CCND1 > p21 > RASSF1. Hyperhomocysteinemia was positively associated with BRAC1 hypermethylation both in breast cancer tissue and corresponding peripheral blood. Peripheral blood CpG island methylation of BRCA1 in all types of breast cancer and methylation of RASSF1 in ER/PR-negative breast cancers showed positive correlation with total plasma homocysteine. The methylation of RASSF1 and BRCA1 was associated with breast cancer initiation as well as progression, while BRCA1 methylation was associated with DNA damage. Vitamin B12 showed inverse association with the methylation at both the loci. RFC1 G80A and cSHMT C1420T variants showed positive association with methylation at both the loci. Genetic variants influencing remethylation step were associated positively with BRCA1 methylation and inversely with RASSF1 methylation. GCPII C1561T variant showed inverse association with BRCA1 methylation. We found good correlation of BRAC1 (r = 0.90) and RASSF1 (0.92) methylation pattern between the breast cancer tissue and the corresponding peripheral blood. To conclude, elevated homocysteine influences methionine dependency phenotype of breast cancer cells and is associated with breast cancer progression by epigenetic modulation of RASSF1 and BRCA1.
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Affiliation(s)
- Shaik Mohammad Naushad
- Department of Clinical Pharmacology and Therapeutics, Nizam's Institute of Medical Sciences (NIMS), Panjagutta, Hyderabad, 500082, Andhra Pradesh, India
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Eng A, McCormack V, dos-Santos-Silva I. Receptor-defined subtypes of breast cancer in indigenous populations in Africa: a systematic review and meta-analysis. PLoS Med 2014; 11:e1001720. [PMID: 25202974 PMCID: PMC4159229 DOI: 10.1371/journal.pmed.1001720] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/29/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Breast cancer is the most common female cancer in Africa. Receptor-defined subtypes are a major determinant of treatment options and disease outcomes but there is considerable uncertainty regarding the frequency of poor prognosis estrogen receptor (ER) negative subtypes in Africa. We systematically reviewed publications reporting on the frequency of breast cancer receptor-defined subtypes in indigenous populations in Africa. METHODS AND FINDINGS Medline, Embase, and Global Health were searched for studies published between 1st January 1980 and 15th April 2014. Reported proportions of ER positive (ER+), progesterone receptor positive (PR+), and human epidermal growth factor receptor-2 positive (HER2+) disease were extracted and 95% CI calculated. Random effects meta-analyses were used to pool estimates. Fifty-four studies from North Africa (n=12,284 women with breast cancer) and 26 from sub-Saharan Africa (n=4,737) were eligible. There was marked between-study heterogeneity in the ER+ estimates in both regions (I2>90%), with the majority reporting proportions between 0.40 and 0.80 in North Africa and between 0.20 and 0.70 in sub-Saharan Africa. Similarly, large between-study heterogeneity was observed for PR+ and HER2+ estimates (I2>80%, in all instances). Meta-regression analyses showed that the proportion of ER+ disease was 10% (4%-17%) lower for studies based on archived tumor blocks rather than prospectively collected specimens, and 9% (2%-17%) lower for those with ≥ 40% versus those with <40% grade 3 tumors. For prospectively collected samples, the pooled proportions for ER+ and triple negative tumors were 0.59 (0.56-0.62) and 0.21 (0.17-0.25), respectively, regardless of region. Limitations of the study include the lack of standardized procedures across the various studies; the low methodological quality of many studies in terms of the representativeness of their case series and the quality of the procedures for collection, fixation, and receptor testing; and the possibility that women with breast cancer may have contributed to more than one study. CONCLUSIONS The published data from the more appropriate prospectively measured specimens are consistent with the majority of breast cancers in Africa being ER+. As no single subtype dominates in the continent availability of receptor testing should be a priority, especially for young women with early stage disease where appropriate receptor-specific treatment modalities offer the greatest potential for reducing years of life lost. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Amanda Eng
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Valerie McCormack
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Isabel dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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21
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Si JG, Su YY, Han YH, Chen RH. Role of RASSF1A promoter methylation in the pathogenesis of ovarian cancer: a meta-analysis. Genet Test Mol Biomarkers 2014; 18:394-402. [PMID: 24665911 DOI: 10.1089/gtmb.2014.0022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE The aim of the current meta-analysis was to comprehensively assess the role of RASSF1A promoter methylation in the pathogenesis of ovarian cancer. METHOD A range of electronic databases were searched: Web of Science (1945-2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966-2013), EMBASE (1980-2013), CINAHL (1982-2013), and the Chinese Biomedical Database (1982-2013) without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. The crude odds ratio (OR) with its corresponding 95% confidence interval (CI) was calculated. RESULTS Twelve clinical cohort studies with a total of 739 ovarian cancer patients were included in the current meta-analysis. The results of our meta-analysis suggested that the frequency of RASSF1A promoter methylation in cancer tissues was higher compared with benign, adjacent, and normal tissues (cancer tissues vs. benign tissues: OR=9.92, 95% CI: 7.67-12.82, p<0.001; cancer tissues vs. adjacent tissues: OR=68.15, 95% CI: 39.30-118.18, p<0.001; cancer tissues vs. normal tissues: OR=30.71, 95% CI: 23.12-40.80, p<0.001; respectively). Subgroup analysis based on ethnicity and sample types revealed that RASSF1A gene methylation was closely associated with the pathogenesis of ovarian cancer in all subgroups (all p<0.05). CONCLUSION Our findings indicated that abnormal RASSF1A promoter methylation may be strongly correlated with the pathogenesis of ovarian cancer.
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Affiliation(s)
- Jin-Ge Si
- Department of Obstetrics and Gynecology, The People's Hospital of Zhongshan City , Zhongshan, People's Republic of China
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22
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Hagrass HA, Pasha HF, Shaheen MA, Abdel Bary EH, Kassem R. Methylation status and protein expression of RASSF1A in breast cancer patients. Mol Biol Rep 2013; 41:57-65. [PMID: 24253900 DOI: 10.1007/s11033-013-2837-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 10/26/2013] [Indexed: 12/31/2022]
Abstract
Recently genetics and epigenetics alterations have been found to be characteristic of malignancy and hence can be used as targets for detection of neoplasia. RAS association domain family protein 1A (RASSF1A) gene hypermethylation has been a subject of interest in recent researches on cancer breast patients. The aim of the present study was to evaluate whether RASSF1A methylation status and RASSF1A protein expression are associated with the major clinico-pathological parameters. One hundred and twenty breast cancer Egyptian patients and 100-control subjects diagnosed with benign lesions of the breast were enrolled in this study. We evaluated RASSF1A methylation status in tissue and serum samples using Methyl specific PCR together with RASSF1A protein expression in tissues by immunohistochemistry. Results were studied in relation to known prognostic clinicopathological features in breast cancer. Frequency of RASSF1A methylation in tissues and serum were 70 and 63.3 % respectively and RASSF1A protein expression showed frequency of 46.7 %. There was an association between RASSF1A methylation in tissues, serum and loss of protein expression in tissues with invasive carcinoma, advanced stage breast cancer, L.N. metastasis, ER/PR and HER2 negativity. RASSF1A methylation in serum showed high degree of concordance with methylation in tissues (Kappa = 0.851, P < 0.001). RASSF1A hypermethylation in tissues and serum and its protein expression may be a valid, reliable and sensitive tool for detection and follow up of breast cancer patients.
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Affiliation(s)
- Hoda A Hagrass
- Clinical Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt,
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Locke WJ, Clark SJ. Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis. Breast Cancer Res 2012; 14:215. [PMID: 23168266 PMCID: PMC4053120 DOI: 10.1186/bcr3237] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic gene regulation has influence over a diverse range of cellular functions, including the maintenance of pluripotency, differentiation, and cellular identity, and is deregulated in many diseases, including cancer. Whereas the involvement of epigenetic dysregulation in cancer is well documented, much of the mechanistic detail involved in triggering these changes remains unclear. In the current age of genomics, the development of new sequencing technologies has seen an influx of genomic and epigenomic data and drastic improvements in both resolution and coverage. Studies in cancer cell lines and clinical samples using next-generation sequencing are rapidly delivering spectacular insights into the nature of the cancer genome and epigenome. Despite these improvements in technology, the timing and relationship between genetic and epigenetic changes that occur during the process of carcinogenesis are still unclear. In particular, what changes to the epigenome are playing a driving role during carcinogenesis and what influence the temporal nature of these changes has on cancer progression are not known. Understanding the early epigenetic changes driving breast cancer has the exciting potential to provide a novel set of therapeutic targets or early-disease biomarkers or both. Therefore, it is important to find novel systems that permit the study of initial epigenetic events that potentially occur during the first stages of breast cancer. Non-malignant human mammary epithelial cells (HMECs) provide an exciting in vitro model of very early breast carcinogenesis. When grown in culture, HMECs are able to temporarily escape senescence and acquire a pre-malignant breast cancer-like phenotype (variant HMECs, or vHMECs). Cultured HMECs are composed mainly of cells from the basal breast epithelial layer. Therefore, vHMECs are considered to represent the basal-like subtype of breast cancer. The transition from HMECs to vHMECs in culture recapitulates the epigenomic phenomena that occur during the progression from normal breast to pre-malignancy. Therefore, the HMEC model system provides the unique opportunity to study the very earliest epigenomic aberrations occurring during breast carcinogenesis and can give insight into the sequence of epigenomic events that lead to breast malignancy. This review provides an overview of epigenomic research in breast cancer and discusses in detail the utility of the HMEC model system to discover early epigenomic changes involved in breast carcinogenesis.
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Jiang Y, Cui L, Chen WD, Shen SH, Ding LD. The prognostic role of RASSF1A promoter methylation in breast cancer: a meta-analysis of published data. PLoS One 2012; 7:e36780. [PMID: 22615811 PMCID: PMC3355150 DOI: 10.1371/journal.pone.0036780] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/06/2012] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Epigenetic alterations have been investigated as prognostic indicators in breast cancer but their translation into clinical practice has been impeded by a lack of appropriate validation. We present the results of a meta-analysis of the associations between RASSF1A promoter methylation status and both disease free survival (DFS) and overall survival (OS) in female breast cancer. METHODS Eligible studies were identified through searching the PubMed, Web of Science and Embase databases. Studies were pooled and summary hazard ratios (HR) with corresponding confidence intervals (CIs) were calculated. Funnel plots were also carried out to evaluate publication bias. RESULTS A total of 1795 patients from eight studies were included in the meta-analysis. There are eight studies which investigated DFS in 1795 cases. The relative hazard estimates ranged from 1.77-5.64 with a combined HR of 2.75 (95%CI 1.96-3.84). The HR of RASSF1A promoter methylation on DFS adjusted for other potential prognostic factors was 2.54 (95%CI 1.77-3.66). There has been five trials which analyzed the associations of RASSF1A promoter methylation status with OS in 1439 patients. The hazard estimates ranged from 1.21-6.90 with a combined random-effects estimates of 3.47 (95%CI 1.44-8.34). OS reported in multivariate analysis was evaluated in four series comprising 1346 cases and the summarized random-effects HR estimate was 3.35 (95%CI 1.14-9.85). Additionally, no publication bias was detected for both OS and DFS. CONCLUSION The results of this meta-analysis suggest that RASSF1A promoter hypermethylation confers a higher risk of relapse and a worse survival in patients with breast cancer. Large prospective studies are now needed to establish the clinical utility of RASSF1A promoter methylation.
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Affiliation(s)
- Yong Jiang
- Department of Oncology, Jiangyan People’s Hospital, the Affiliated Hospital of Yangzhou University, Jiangyan, China
| | - Lin Cui
- Department of Oncology, Jiangyan People’s Hospital, the Affiliated Hospital of Yangzhou University, Jiangyan, China
| | - Wen-de Chen
- Department of Scientific Research, Jiangyan People’s Hospital, the Affiliated Hospital of Yangzhou University, Jiangyan, China
| | - Shi-hai Shen
- Department of Scientific Research, Jiangyan People’s Hospital, the Affiliated Hospital of Yangzhou University, Jiangyan, China
| | - Li-dong Ding
- Department of Scientific Research, Jiangyan People’s Hospital, the Affiliated Hospital of Yangzhou University, Jiangyan, China
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Gil EY, Jo UH, Jeong H, Whang YM, Woo OH, Cho KR, Seo JH, Kim A, Lee ES, Koh I, Kim YH, Park KH. Promoter methylation of RASSF1A modulates the effect of the microtubule-targeting agent docetaxel in breast cancer. Int J Oncol 2012; 41:611-20. [PMID: 22581300 DOI: 10.3892/ijo.2012.1470] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/12/2012] [Indexed: 02/05/2023] Open
Abstract
Docetaxel is one of the most commonly used chemotherapeutic agents in breast cancer. To avert from significant toxicities with no clinical benefit, identification of predictive markers for response is one of the most important unsolved clinical needs. Therefore, the potential associations of RASSF1A hypermethylation and response to docetaxel-based chemotherapy were evaluated, and the underlying mechanism was studied. The expression of RASSF1A in breast cancer cell lines and tissues of normal breast, ductal carcinoma in situ (DCIS), and breast cancer (n=45) was analyzed by immunohistochemistry and western blot analysis. Immunohistochemical staining showed that the expression of RASSF1A was frequently lost in primary breast cancers and human breast cancer cell lines, while normal breast tissues or DCIS displayed moderate to strong expression. Furthermore, quantitative methylation analysis of the RASSF1A promoter region in 45 primary breast cancers revealed that RASSF1A was frequently methylated in primary breast cancers (≥20% methylation in 53% of the patients), and prospective analysis in patients with locally advanced or recurrent breast cancer showed that the mean level of methylation of RASSF1A was significantly higher in patients who did not respond to docetaxel-based chemotherapy (30.6±8.5%) than patients with partial or complete response (20.1±11.2%, p=0.042). Finally, in vitro studies showed that RASSF1A had cooperative activity in suppression of cancer cell growth and proliferation by enhancing docetaxel-induced cell cycle arrest. Our results suggest that hypermethylated RASSF1A is an important modulating factor for the efficacy of docetaxel-based chemotherapy in breast cancer.
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Affiliation(s)
- Eun Young Gil
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
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Pronina IV, Loginov VI, Khodyrev DS, Kazubskaya TP, Braga EA. RASSF1A expression level in primary epithelial tumors of various locations. Mol Biol 2012. [DOI: 10.1134/s0026893312010189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Alvarez C, Tapia T, Cornejo V, Fernandez W, Muñoz A, Camus M, Alvarez M, Devoto L, Carvallo P. Silencing of tumor suppressor genes RASSF1A, SLIT2, and WIF1 by promoter hypermethylation in hereditary breast cancer. Mol Carcinog 2012; 52:475-87. [PMID: 22315090 DOI: 10.1002/mc.21881] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 10/26/2011] [Accepted: 01/10/2012] [Indexed: 01/12/2023]
Abstract
Promoter hypermethylation is gaining strength as one of the main mechanisms through which tumor suppressor genes are silenced during tumor progression. Three tumor suppressor genes are frequently found methylated in their promoter, in concordance with absence of expression, RASSF1A, SLIT2, and WIF1. In addition, a previous array-CGH analysis from our group showed that these genes are found in deleted genomic regions observed in hereditary breast cancer tumors. In the present work we analyzed the methylation status of these three tumor suppressor gene promoters in 47 hereditary breast cancer tumors. Promoter methylation status analysis of hereditary breast tumors revealed high methylation frequencies for the three genes (67% RASSF1A, 80% SLIT2, and 72% WIF1). Additionally, the presence of methylated PCR products was associated with absence of protein expression for the three genes and statistically significant for RASSF1A and WIF1. Interestingly, methylation of all the three genes was found in 4 out of 6 grade I invasive ductal carcinoma tumors. Association between RASSF1A methylation and DCIS tumors was found. These results suggest that silencing of these tumor suppressor genes is an early event in hereditary breast cancer, and could be a marker for pre-malignant phenotypes.
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Affiliation(s)
- Carolina Alvarez
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Abstract
Cancer disparities in incidence and death rates exist among various racial and ethnic groups. These disparities are thought to be due to socioeconomic status, culture, diet, stress, the environment, and biology. Biological functions, such as epigenetic processes, are affected by all these causal factors and extend throughout the life course. Epigenetic processes, in particular DNA methylation, may play a role in the induction of phenotypes with increased cancer risk due to exposure to these multiple factors. DNA methylation is known to cause changes in gene expression of key regulatory genes in cancer. There are limited studies in which epigenetic changes have been explored to address cancer disparities in various racial and ethnic populations. These few studies have reported significant epigenetic differences in various racial and ethnic groups that could account for the differences seen in tumor initiation, progression, aggressiveness, and outcome of these cancers. Genes differentially methylated among these racially and ethnically diverse populations were involved in important cellular functions, such as tumor growth, tumor suppression, hormone receptors, and genes involved in tumor metastasis. Epigenetic research with the advancement in technology has helped identify biomarkers, therapeutic targets, and understand cancer causation in the general population. Unfortunately, these advances in technology have not been applied to explore the basis for cancer health disparities. More research in epigenetics is needed that will enhance our understanding of the determinants of cancer across various diverse populations and ultimately reduce cancer health disparities.
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Affiliation(s)
- Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
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Methylation status of genes in non-neoplastic mucosa from patients with ulcerative colitis-associated colorectal cancer. Am J Gastroenterol 2010; 105:1610-9. [PMID: 20160714 DOI: 10.1038/ajg.2010.22] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Patients with ulcerative colitis (UC) are at increased risk for developing colorectal cancer (CRC). Surveillance in this at-risk population remains challenging. We assessed the methylation status of genes in the non-neoplastic mucosa of UC-CRC patients and controls to identify potential biomarkers of CRC. METHODS We evaluated the methylation status of 10 genes (p16, p14, runt-related transcript factor-3 (RUNX3), cyclooxygenase-2 (COX-2), E-cadherin, methylated-in-tumor-1 (MINT1), MINT31, HPP1, estrogen receptor, SLC5A8) in UC-CRC tumors and non-neoplastic sections from both UC-CRC cases and UC controls (n=114 for each) using methylation-specific PCR. RESULTS Amplification was successful for 96 UC controls, 83 tumors, and 66 non-adjacent, non-neoplastic samples. The prevalence of methylation was significantly greater in UC-CRC tumors for p16, RUNX3, MINT1, MINT31, and HPP1. Methylation of COX-2 and E-cadherin was greater in UC controls than in tumors. Univariate testing of these genes using non-adjacent, non-neoplastic sections from UC-CRC cases indicated that associations between p16, RUNX3, MINT1, MINT31, E-cadherin, and COX-2 and UC-CRC remained significant. In multivariable analysis of the six genes, only RUNX3, MINT1, and COX-2 remained significantly associated with the UC-CRC cases (odds ratio=12.6, 9.0, and 0.2, respectively). The results remained unaffected by the presence of PSC or severity of inflammation. Logistic regression modeling with the three genes showed interactions that increased the odds ratio for each gene. CONCLUSIONS RUNX3, MINT1, and COX-2 are potential biomarkers for detecting the presence of CRC in patients with UC. These genes should be evaluated as biomarkers for colorectal dysplasia.
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Miladi-Abdennadher I, Abdelmaksoud-Damak R, Ayadi L, Khabir A, Frikha F, Kallel L, Amouri A, Frikha M, Sellami-Boudawara T, Gargouri A, Mokdad-Gargouri R. Hypermethylation of RARβ2 correlates with high COX-2 expression and poor prognosis in patients with colorectal carcinoma. Tumour Biol 2010; 31:503-11. [PMID: 20571967 DOI: 10.1007/s13277-010-0063-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/05/2010] [Indexed: 12/20/2022] Open
Abstract
Silencing of gene expression by aberrant methylation at the CpG islands is common in human tumors, including colorectal cancer. This epigenetic alteration affects promoter of genes having crucial cellular functions such as tumor suppressor, DNA repair, apoptosis, cell adhesion, etc. We investigated the methylation status in the promoter regions of the RARβ2, RASSF1A, DAPKinase, and CDH1 genes in 73 colorectal carcinoma and 43 paired normal tissues of Tunisian patients using methylation-specific PCR assays. The association between methylation status and the clinicopathological features was evaluated. To determine whether aberrant methylation affects gene expression, we performed immunohistochemistry analysis for E-cadherin and COX-2, a target gene of RARβ2. The methylation frequencies vary from 80.8% for RARβ2 to 35.6% for RASSF1A while in non-tumor-paired samples; the frequencies of methylation are significantly lower for all the fourth genes tested. The methylation status did not correlate with any of the clinical features considered; however, aberrant methylation of RARβ2 was associated with a shortened overall patients' survival (p log rank = 0.026); nevertheless, it needs to be confirmed on larger sample size. Moreover, a significant inverse association was observed between methylation status of RARβ2 and COX-2 protein expression in tumor specimen (p = 0.014). On the other hand, we found that loss of E-cadherin expression was significantly associated with aberrant methylation of the CDH1 promoter (p = 0.005). Our findings showed that RARβ2 was frequently methylated in colorectal cancer and correlated with a worse prognosis and high expression of COX-2 suggesting a link between these two proteins in colorectal carcinogenesis. We also showed that epigenetic alteration of CDH1 is a major mechanism of the loss of E-cadherin protein expression in primary colorectal tumors.
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