1
|
Fan C, Ma Q, Wu X, Dai X, Peng Q, Cai H. Detection of DNA Methylation in Gene Loci ASTN1, DLX1, ITGA4, RXFP3, SOX17, and ZNF671 for Diagnosis of Cervical Cancer. Cancer Manag Res 2023; 15:635-644. [PMID: 37457377 PMCID: PMC10349600 DOI: 10.2147/cmar.s417877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Objective To evaluate the diagnostic value of DNA methylation detection of multiple gene loci in cervical cancer. Methods A total of 61 cases requiring cervical biopsy were selected from the outpatient clinic of Maternal and Child Health Hospital of Hubei Province between January 2018 and December 2019. The patients were divided into four groups based on histopathologic diagnosis: cervical cancer (CC) group, high-grade squamous intraepithelial lesion (HSIL) group, low-grade squamous intraepithelial lesion (LSIL) group, and control group. HPV examination, liquid-based cytology examination, and DNA methylation detection at multiple gene sites were performed. The positive rate of DNA methylation, sensitivity, specificity, area under the curve (AUC), and other efficacy indexes were calculated to evaluate the diagnostic value of DNA methylation detection at multiple gene loci in cervical cancer. Results The positive rates of DNA methylation in CC, HSIL, LSIL, and control groups were 100%, 88%, 83% and 17%, respectively. The ZNF671 gene had the highest positive rate among the cervical lesion group, with rates of 57%, 76%, and 100% in LSIL, HSIL, and CC groups respectively. The combination of DNA methylation detection at multiple gene loci showed the highest diagnostic efficacy for HSIL and cervical cancer, with AUC value of 0.850 (95% CI:0.746-0.954), a Youden index of 0.654, and a sensitivity and specificity of 85% and 85.4%, respectively. The diagnostic efficacy of the combined detection was significantly higher than that of HPV examination and liquid-based cytology examination (P < 0.05). Conclusion DNA methylation detection at multiple gene loci is highly effective and diagnostic tool for cervical cancer, and has potential application value in clinical practice.
Collapse
Affiliation(s)
- Chunli Fan
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Quanfu Ma
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Xufeng Wu
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Xuan Dai
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Qiuzi Peng
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| | - Hongning Cai
- Department of Scientific Research and Teaching Management Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
- Department of Cervical Cancer Prevention Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, People’s Republic of China
| |
Collapse
|
2
|
Li X, Lyu C, Luo Z, Zhao J, Wang Z, Yang C, Dai Q, Li H, Zhou Y, Li Z, Chen F, Gao Y. The roles of IGF2 and DNMT methylation and elongase6 related fatty acids in metabolic syndrome. Food Funct 2021; 12:10253-10262. [PMID: 34549217 DOI: 10.1039/d1fo00502b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: The prevalence of metabolic syndrome (MetS) has increased along with rapid socio-economic development in China in recent decades, aggravating the burden of the health care system. Both plasma levels of fatty acids (FAs) and aberrant DNA methylation profiles are associated with MetS risk. However, studies exploring the role of DNA methylation and FAs simultaneously in MetS etiology are sparse. Objective: We aimed to explore the association between the gene methylation levels of insulin-like growth factor II (IGF2), H19, DNA methyltransferases 1 (DNMT1), DNA methyltransferases 3a (DNMT3a), and DNA methyltransferases 3b (DNMT3b) and MetS risk, and the etiological role of elongation of very-long-chain fatty acid elongase 6 (ELOVL6) related fatty acids. Method: Plasma levels of FAs were measured using a Gas Chromatography-Flame Ionization Detector (GC-FID) after organic extraction, and gene methylation was quantified using a real-time Quantitative Polymerase Chain Reaction (Q-PCR) detecting system after bisulfite treatment. The C18/C16 ratio was used as the indicator of ELOVL6 activity. Odds Ratio (OR) and 95% Confidence Interval (CI) were estimated with logistic regression. Results: Methylation levels in IGF2 and DNMT3a were not significantly associated with MetS risk. However, when stratified by C18/C16 ratio (high vs. low), positive associations were observed between the risk of MetS and methylation levels (>median) of IGF2a3 (OR = 3.1, 95% CI = 1.3-7.5) and DNMT3a (OR = 2.5, 95% CI = 1.1-5.8) genes, in individuals with lower C18/C16 ratios, while no significant associations were observed in subjects with high C18/C16 ratios. Conclusion: Methylation levels in IGF2 and DNMT3a genes may affect the risk of MetS in an ELOVL6 activity-dependent way among Chinese adults. Further studies in other populations are needed to validate this finding.
Collapse
Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health-Bloomington, Indiana University, Bloomington, USA
| | - ZhongCheng Luo
- Lunenfeld-Tanenbaum Research Institute, Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Jing Zhao
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zhongli Wang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Jiaxing University, The Second Hospital of Jiaxing, Jiaxing, China
| | - Chun Yang
- School of Public Health, Capital Medical University, Beijing, China
| | - Qi Dai
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Hui Li
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Yunhua Zhou
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Zi Li
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Fuxue Chen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Ying Gao
- CAS Key Laboratory of Nutrition Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
3
|
Hyaluronic Acid-Functionalized Nanomicelles Enhance SAHA Efficacy in 3D Endometrial Cancer Models. Cancers (Basel) 2021; 13:cancers13164032. [PMID: 34439185 PMCID: PMC8394402 DOI: 10.3390/cancers13164032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary One of the major limitations to cancer therapies are the side effects caused by the drug interacting with any tissue in the body. There is often a balance between patient health and effectively treating the disease. To by-pass this balancing act nanoparticles are being used to deliver therapeutics straight to the tumors, acting as “Trojan Horses”. Endometrial cancers are known to have more of the cell surface protein CD44 than healthy tissues. Here, to efficiently target endometrial cancer, hyaluronic acid, which naturally binds to the CD44 protein was attached to the surface of nanoparticles and tested on microtissues or spheroids to better model a tumor and understand drug delivery performance. We show that our hyaluronic acid-nanoparticle formulations improve drug effects and interact with the cancer cells more than without this targeting agent. Abstract Histone Deacetylase (HDAC) enzymes are upregulated in cancer leading to the development of HDAC inhibiting compounds, several of which are currently in clinical trials. Side effects associated with toxicity and non-specific targeting indicate the need for efficient drug delivery approaches and tumor specific targeting to enhance HDAC efficacy in solid tumor cancers. SAHA encapsulation within F127 micelles functionalized with a surface hyaluronic acid moiety, was developed to target endometrial cancer cells expressing elevated levels of CD44. In vitro viability and morphology analyses was conducted in both 2D and 3D models to assess the translational potential of this approach. Encapsulation enhanced SAHA delivery and activity, demonstrating increased cytotoxic efficacy in 2D and 3D endometrial cancer models. High-content imaging showed improved nanoparticle internalization in 2D and CD44 enhanced penetration in 3D models. In addition, the nano-delivery system enhanced spheroid penetration resulting in cell growth suppression, p21 associated cell cycle arrest, as well as overcoming the formation of an EMT associated phenotype observed in free drug treated type II endometrial cancer cells. This study demonstrates that targeted nanoparticle delivery of SAHA could provide the basis for improving its efficacy in endometrial cancer. Using 3D models for endometrial cancer allows the elucidation of nanoparticle performance and CD44 targeting, likely through penetration and retention within the tumor model.
Collapse
|
4
|
Sohn SH, Sul HJ, Kim B, Kim HS, Kim BJ, Lim H, Kang HS, Soh JS, Kim KC, Cho JW, Seo J, Koh Y, Zang DY. RNF43 and PWWP2B inhibit cancer cell proliferation and are predictive or prognostic biomarker for FDA-approved drugs in patients with advanced gastric cancer. J Cancer 2021; 12:4616-4625. [PMID: 34149925 PMCID: PMC8210561 DOI: 10.7150/jca.56014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Abnormal regulation of genes has been closely related to gastric cancer. The characterization of gastric cancer has necessitated the development of new therapeutics as well as the identification of prognostic markers to predict the response to novel drugs. In our study, we used RNA sequencing analyses to show that on gastric cancer tissues to identification of gastric cancer prognostic markers. We specifically chose to study RNF43 because it inhibits gastric cancer-related Wnt/β-catenin signaling by interacting with Wnt receptors. PWWP2B was chosen because it is a gene which is downregulated in gastric cancer. Methods: Utilizing RNA sequencing analysis, we evaluated the mRNA expression profile in gastric cancer patients. Also, we used HAP1 cells which is a human near-haploid cell line derived from the male chronic myelogenous leukemia cell line KBM-7. These cell line has one copy of each gene, ensuring the edited allele will not be masked by additional alleles. We investigated the screening of 1,449 FDA-approved drugs in HAP1, HAP1 RNF43 KO and HAP1 PWWP2B KO cells. RNA sequencing data reveals that RNF43 and PWWP2B expression were down-regulated in recurrence gastric cancer patients. Next, we investigated the anti-cancer effects of selected drugs in RNF43 and PWWP2B down-regulated MKN45 gastric cancer cells and xenograft model. Results: Among these FDA-approved drugs, three drugs (docetaxel trihydrate, pelitinib and uprosertib) showed strong inhibitory effects in RNF43 KO cells and PWWP2B KO cells. In MKN45 xenograft model, tumor volumes were significantly reduced in the docetaxel trihydrate, uprosertib or pelitinib-treated group. Our data demonstrated that RNF43 and PWWP2B are a biomarker that predict recurrence of gastric cancer. Conclusions: Our findings suggest that docetaxel trihydrate, uprosertib and pelitinib could be used as novel therapeutic agents for the prevention and treatment of gastric cancer with a decrease in RNF43 and PWWP2B expression.
Collapse
Affiliation(s)
- Sung-Hwa Sohn
- Hallym Translational Research Institute, Hallym University Sacred Heart Hospital, Anyang, 14066, Republic of Korea
| | - Hee Jung Sul
- Hallym Translational Research Institute, Hallym University Sacred Heart Hospital, Anyang, 14066, Republic of Korea
| | - Bohyun Kim
- Hallym Translational Research Institute, Hallym University Sacred Heart Hospital, Anyang, 14066, Republic of Korea
| | - Hyeong Su Kim
- Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Bum Jun Kim
- Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Hyun Lim
- Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Ho Suk Kang
- Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Jae Seung Soh
- Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Kab Choong Kim
- Department of Surgery, Hallym University Medical Center, Hallym University Kangnam Sacred Hospital, Singil-ro Yeongdeungpo-gu, Seoul, 07441, Republic of Korea
| | - Ji Woong Cho
- Department of Surgery, Hallym University Medical Center, Hallym University Kangnam Sacred Hospital, Singil-ro Yeongdeungpo-gu, Seoul, 07441, Republic of Korea
| | - Jinwon Seo
- Department of Pathology, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| | - Youngho Koh
- Department of Bio-medical Gerontology, Ilsong Institute of Life Sciences, Hallym University, Anyang, Gyeonggi-do, Republic of Korea
| | - Dae Young Zang
- Hallym Translational Research Institute, Hallym University Sacred Heart Hospital, Anyang, 14066, Republic of Korea.,Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang-si, Gyeonggi-do 14068, Republic of Korea
| |
Collapse
|
5
|
Therapeutic Implications of a Polymethoxylated Flavone, Tangeretin, in the Management of Cancer via Modulation of Different Molecular Pathways. Adv Pharmacol Pharm Sci 2021; 2021:4709818. [PMID: 33748757 PMCID: PMC7954633 DOI: 10.1155/2021/4709818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/25/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Abstract
Chemotherapeutics can induce oxidative stress, inflammation, apoptosis, mitochondrial dysfunction, and abnormalities in neurotransmitter metabolism leading to toxicity. Because there have been no therapeutic strategies developed to target inflammation and oxidative stress, there is a continuing need for new and improved therapy. As a result, there has been increasing interest in complementary and alternative medicine with anticancer potential. Studies have shown that the antioxidant activities and anti-inflammatory effects of citrus fruits are promising natural phytochemicals in the development of new anticancer agents. Tangeretin is a naturally polymethoxylated flavone compound extracted from the citrus peel that has shown significant intestinal absorption and adequate bioavailability, with the added benefit of promoting longevity. In addition, tangeretin is known to exhibit considerable selective toxicity to many types of cancer cell proliferation such as ovarian, brain, blood, and skin cancer. Evidence indicates that tangeretin acts through several mechanisms including growth inhibition, induction of apoptosis, autophagy, antiangiogenesis, and estrogenic-like effects. Furthermore, tangeretin works through mitigating levels of inflammatory mediators in the immune system. Using tangeretin in combination with clinically applied anticancer drugs could be a good strategy for increasing the efficiency of these agents and protecting noncancerous cells from damage caused by chemotherapy. The purpose of this review is to highlight the protective effects of a novel natural product, tangeretin against chemotherapeutic-induced toxicity. The development of chemoprevention strategies can lead to significant health care improvement in cancer survivors. Thus, study outcomes may attract more investigators to conduct tangeretin-related research and find out potentially significant impacts on health care of cancer patients and decreased health problems associated with chemotherapeutics-induced toxicity.
Collapse
|
6
|
Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, Shields AE, Kelsey KT, Michaud DS. Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array. Epigenetics 2018; 13:1056-1071. [PMID: 30270718 PMCID: PMC6342169 DOI: 10.1080/15592294.2018.1530008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/02/2018] [Accepted: 09/22/2018] [Indexed: 12/29/2022] Open
Abstract
Assessing DNA methylation profiles in human blood has become a major focus of epidemiologic inquiry. Understanding variability in CpG-specific DNA methylation over moderate periods of time is a critical first step in identifying CpG sites that are candidates for DNA methylation-based etiologic, diagnostic and prognostic predictors of pathogenesis. Using the Illumina MethylationEPIC [850K] BeadArray, DNA methylation was profiled in paired whole blood samples collected approximately 1 year apart from 35 healthy women enrolled in the Nurses Study II cohort. The median intraclass correlation coefficient (ICC) across all CpG loci was 0.19 [Interquartile Range (IQR) 0.00-0.50]; 74.8% of ICCs were in the low range (0-0.5), 16.9% in the mid-range of ICCs (0.5-0.8), and 8.3% in the high-range of ICCs (0.8-1). ICCs were similar for CpG probes on the 450K Illumina array (median 0.17) and the new probes added to the 850K array (median 0.21). ICCs for CpG loci on the sex chromosomes and known metastable epialleles were high (median 0.71, 0.97, respectively), and ICCs among methylation quantitative trait loci (mQTL) CpGs were significantly higher as compared to non-mQTL CpGs (median 0.73, 0.16, respectively, P < 2 × 10-16). We observed wide variation in DNA methylation stability over a 1-year period. Probes considered non-stable, due to substantial variation over a moderate period of time and with minimal variability across individuals could be removed in large epidemiological studies. Moreover, adjusting for technical variation that arises from using high-dimensional arrays is critical.
Collapse
Affiliation(s)
- Ina Zaimi
- a Department of Public Health & Community Medicine, Tufts University School of Medicine , Tufts University , Boston , USA
| | - Dong Pei
- b Department of Biostatistics , University of Kansas Medical Center , Kansas City , USA
- c University of Kansas Cancer Center , The University of Kansas Medical Center , Kansas City , USA
| | - Devin C Koestler
- b Department of Biostatistics , University of Kansas Medical Center , Kansas City , USA
- c University of Kansas Cancer Center , The University of Kansas Medical Center , Kansas City , USA
| | - Carmen J Marsit
- d Department of Environmental Health and Department of Epidemiology, Rollins School of Public Health , Emory University , Atlanta , USA
| | - Immaculata De Vivo
- e Channing Division of Network Medicine, Department of Medicine , Brigham and Women's Hospital and Harvard Medical School , Boston , USA
| | - Shelley S Tworoger
- f Department of Cancer Epidemiology , Moffitt Cancer Center , Tampa , USA
- g Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , USA
| | - Alexandra E Shields
- h Department of Medicine , Harvard Medical School , Boston , MA , USA
- k Harvard/MGH Center on Genomics, Vulnerable Populations, and Health Disparities , Massachusetts General Hospital , Boston , MA , USA
| | - Karl T Kelsey
- i Department of Epidemiology , Brown University , Providence , USA
- j Department of Pathology and Laboratory Medicine , Brown University , Providence , USA
| | - Dominique S Michaud
- a Department of Public Health & Community Medicine, Tufts University School of Medicine , Tufts University , Boston , USA
- i Department of Epidemiology , Brown University , Providence , USA
| |
Collapse
|
7
|
Zhou J, Wang Z, Zhang L, Gu Y, Ma Y, Li X. Association of five genetic variations in DNMT1 and DNMT3A with gastric cancer in a Chinese population. Future Oncol 2018; 14:1731-1739. [PMID: 29956566 DOI: 10.2217/fon-2017-0707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM To determine whether genetic variations in DNMT1 and DNMT3A could be associated with gastric cancer risk. MATERIALS & METHODS A total of 466 patients and 452 healthy controls were enrolled in this study. Genotypes were examined by using the Sequenom MassARRAY platform. RESULTS No significant differences in the distribution frequencies were observed between the groups. However, subgroup analysis revealed that, in the group aged ≤60 years, DNMT3A rs13420827 was associated with reduced gastric cancer risk, and that carrier of GC/GG genotype was associated with reduced risk of gastric cancer with low differentiation or at the T3-T4 stage. CONCLUSION This study suggests that five genetic variations of interest in DNMT1 and DNMT3A are not associated with the presence of gastric cancer, but that rs13420827 may contribute to the gastric cancer risk for those younger individuals, the risk of which may be influenced by the characteristics of tumor.
Collapse
Affiliation(s)
- Jin Zhou
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Zhibing Wang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Lei Zhang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Yuanyuan Gu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Yong Ma
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Xiangcheng Li
- Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China
| |
Collapse
|
8
|
Feng X, Wang J, Gu X, Zhang J, Li X, Tao Z, Chen J, Chen B. Association of DNMT3B -283T>C polymorphism with risk of lung and gastric cancer: a case-control study and a meta-analysis. Int J Biol Markers 2018; 33:195-200. [PMID: 29027179 DOI: 10.5301/ijbm.5000306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE To investigate the association of DNMT3B -283T>C polymorphism with the risk of lung or gastric cancer, which was followed by a meta-analysis. METHODS The genotyping of -283T>C was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and was confirmed by sequencing. RESULTS The results of this case-control study showed that -283T>C was not associated with the risk of lung or gastric cancer, and further stratified analysis according to age, gender, smoking status, and alcohol status confirmed the present finding. However, data from a meta-analysis in the Asian population revealed a significant association between -283T>C and lung cancer risk in the allelic model (C vs. T: odds ratio [OR] = 1.28, 95% confidence interval [CI], 1.06-1.55, p = 0.01) and two genetic models (CC vs. TC: OR = 1.29, 95% CI, 1.04-1.59, p = 0.02; CC vs. TC + TT: OR = 1.30, 95% CI, 1.06-1.60, p = 0.01). CONCLUSIONS These results provided evidence that the DNMT3B -283T>C polymorphism might significantly contribute to the lung cancer risk in the Asian population, but not the gastric cancer risk in the Chinese population.
Collapse
Affiliation(s)
- Xianhong Feng
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Jingdong Wang
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
| | - Xiuli Gu
- 3 Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan - PR China
| | - Jingli Zhang
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
| | - Xiaolin Li
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Zhi Tao
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Jiebing Chen
- 1 Clinical Laboratory, Wuhan Xinzhou District People's Hospital, Wuhan - PR China
| | - Bifeng Chen
- 2 Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan - PR China
| |
Collapse
|
9
|
Chen B, Wang J, Gu X, Zhang J, Zhang J, Feng X. The DNMT3B -579G>T Polymorphism Is Significantly Associated With the Risk of Gastric Cancer but not Lung Cancer in Chinese Population. Technol Cancer Res Treat 2017; 16:1259-1265. [PMID: 29332452 PMCID: PMC5762089 DOI: 10.1177/1533034617740475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/12/2017] [Accepted: 10/09/2017] [Indexed: 01/09/2023] Open
Abstract
The -149C>T and -579G>T, 2 single nucleotide polymorphisms in de novo methyltransferase 3B gene promoter, have been previously reported to potentially alter the promoter activity and to influence cancer risk. However, the results from previous studies remain conflicting rather than conclusive. In view of this, we conducted a case-control study and then a meta-analysis to examine the association between these 2 single-nucleotide polymorphisms with risk of lung and gastric cancer in Chinese population. The genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism and confirmed by sequencing. In this case-control study, no significant association with lung or gastric cancer risk was observed for -149C>T, while -579G>T was significantly correlated with the risk of gastric cancer but not lung cancer. Moreover, haplotype analysis showed that haplotype -149T/-579 T, which carried the risk -579 T allele, significantly increased the susceptibility to gastric cancer. However, none of the haplotypes was associated with the risk of lung cancer. The following meta-analysis involved only Chinese population and further confirmed the significant association of -579G>T with gastric cancer but not lung cancer and suggested no significant association between -149C>T and risk of lung or gastric cancer. Collectively, DNMT3B -579G>T polymorphism is associated with gastric cancer risk in Chinese population, and the -579G>T may be used as a genetic biomarker to predict the risk of gastric cancer in Chinese population.
Collapse
Affiliation(s)
- Bifeng Chen
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, China
| | - Jingdong Wang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, China
| | - Xiuli Gu
- Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Wuhan Tongji Reproductive Medicine Hospital, Wuhan, Hubei, China
| | - Jingli Zhang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, China
| | - Jiankun Zhang
- Department of Biological Science and Technology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, Hubei, China
| | - Xianhong Feng
- Clinical Laboratory, Wuhan Xinzhou District People’s Hospital, Wuhan, China
| |
Collapse
|
10
|
The rs1550117 A>G variant in DNMT3A gene promoter significantly increases non-small cell lung cancer susceptibility in a Han Chinese population. Oncotarget 2017; 8:23470-23478. [PMID: 28423585 PMCID: PMC5410319 DOI: 10.18632/oncotarget.15625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/14/2017] [Indexed: 12/31/2022] Open
Abstract
In this study, we conducted a case-control study to explore the association between rs1550117 A>G variant of DNMT3A gene promoter and non-small cell lung cancer (NSCLC) susceptibility in a Han Chinese population. The genotyping of rs1550117 A>G variant was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. Allele G of rs1550117 was associated with an increased risk of NSCLC. Moreover, individuals carrying the GG genotypes had a higher risk to develop NSCLC than the AA and GA genotype carriers. Further stratified analysis showed that rs1550117 A>G was significantly related to age (> 60 years), male, smoking and drinking. In vivo detection of DNMT3A mRNA levels in NSCLC tissues and in vitro luciferase assays consistently showed that the allele G significantly decreased DNMT3A transcription. Additional functional analysis revealed that the increased binding affinity of transcription repressor SP1, which was associated with allele G of rs1550117, led to the significant decreased expression of DNMT3A. Collectively, our results propose a suppression role of DNMT3A in NSCLC development and emphasize the dual roles of DNMT3A in tumorigenesis.
Collapse
|
11
|
Chu SK, Yang HC. Interethnic DNA methylation difference and its implications in pharmacoepigenetics. Epigenomics 2017; 9:1437-1454. [PMID: 28882057 DOI: 10.2217/epi-2017-0046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AIM This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations. RESULTS Ethnicity-associated CpG sites exhibited similar methylation patterns in the two studied populations, but the patterns differed between tumor tissues and lymphoblastoid cell lines. Ethnicity-associated CpG sites may have triggered gene expression, influenced drug absorption, distribution, metabolism and excretion, and showed tumor-specific patterns of methylation and gene regulation. CONCLUSION Ethnicity should be carefully accounted for in future pharmacoepigenetics research.
Collapse
Affiliation(s)
- Shih-Kai Chu
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan.,Department of Statistics, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Statistics, National Tsing Hua University, Hsinchu 300, Taiwan.,Instutite of Public Health, National Yang-Ming University, Taipei 112, Taiwan.,School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| |
Collapse
|
12
|
Priya ES, Kumar TS, Singh PR, Balakrishnan S, Arunakaran J. Impact of Lactational Exposure to Polychlorinated Biphenyl Causes Epigenetic Modification and Impairs Sertoli Cells Functional Regulators in F1 Progeny. Reprod Sci 2017; 25:818-829. [DOI: 10.1177/1933719117699707] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- E. Sugantha Priya
- Department of Endocrinology, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - T. Sathish Kumar
- Department of Endocrinology, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - P. Raja Singh
- Department of Endocrinology, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - S. Balakrishnan
- Department of Endocrinology, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | - J. Arunakaran
- Department of Endocrinology, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| |
Collapse
|
13
|
Gentilini D, Garagnani P, Pisoni S, Bacalini MG, Calzari L, Mari D, Vitale G, Franceschi C, Di Blasio AM. Stochastic epigenetic mutations (DNA methylation) increase exponentially in human aging and correlate with X chromosome inactivation skewing in females. Aging (Albany NY) 2016; 7:568-78. [PMID: 26342808 PMCID: PMC4586102 DOI: 10.18632/aging.100792] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study we applied a new analytical strategy to investigate the relations between stochastic epigenetic mutations (SEMs) and aging. We analysed methylation levels through the Infinium HumanMethylation27 and HumanMethylation450 BeadChips in a population of 178 subjects ranging from 3 to 106 years. For each CpG probe, epimutated subjects were identified as the extreme outliers with methylation level exceeding three times interquartile ranges the first quartile (Q1-(3 × IQR)) or the third quartile (Q3+(3 × IQR)). We demonstrated that the number of SEMs was low in childhood and increased exponentially during aging. Using the HUMARA method, skewing of X chromosome inactivation (XCI) was evaluated in heterozygotes women. Multivariate analysis indicated a significant correlation between log(SEMs) and degree of XCI skewing after adjustment for age (β = 0.41; confidence interval: 0.14, 0.68; p-value = 0.0053). The PATH analysis tested the complete model containing the variables: skewing of XCI, age, log(SEMs) and overall CpG methylation. After adjusting for the number of epimutations we failed to confirm the well reported correlation between skewing of XCI and aging. This evidence might suggest that the known correlation between XCI skewing and aging could not be a direct association but mediated by the number of SEMs.
Collapse
Affiliation(s)
- Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Serena Pisoni
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Luciano Calzari
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy
| | - Daniela Mari
- Geriatric Unit, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Giovanni Vitale
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095 Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum- University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | | |
Collapse
|
14
|
Lechner M, Fenton TR. The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease. ADVANCES IN GENETICS 2016; 93:1-56. [PMID: 26915269 DOI: 10.1016/bs.adgen.2015.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis.
Collapse
Affiliation(s)
- M Lechner
- Head and Neck Centre, University College London Hospital, London, UK; UCL Cancer Institute, University College London, London, United Kingdom
| | - T R Fenton
- UCL Cancer Institute, University College London, London, United Kingdom
| |
Collapse
|
15
|
DNA methylation analysis of cancer-related genes in oral epithelial cells of healthy smokers. Arch Oral Biol 2015; 60:825-33. [PMID: 25791328 DOI: 10.1016/j.archoralbio.2015.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/18/2014] [Accepted: 02/24/2015] [Indexed: 12/22/2022]
Abstract
AIM The aim of this study was to investigate the smoking habit influence on DNA methylation status in the promoters of the cancer related-genes MLH1, hTERT and TP53 in oral epithelial cells of healthy subjects. MATERIALS AND METHODS DNA methylation analysis was performed using methylation-sensitive restriction enzymes (MSRE) in oral epithelial cells from non-smokers, smokers and ex-smokers. RESULTS The investigated CpG dinucleotides located at HhaI and HpaII sites in the MLH1 gene promoter were observed to be fully methylated in the majority of DNA samples from the smoker group and statistical differences were found between non-smokers and smokers and between smokers and ex-smokers (p<0.05). The same was observed in the hTERT gene promoter at HhaI sites (p<0.05) and for HpaII sites the unmethylated condition was more frequent in smokers in comparison to non-smokers (p<0.05). For TP53, no differences were found among groups (p>0.05), with the fully methylated condition found to be a common event in healthy oral epithelial cells. CONCLUSION We conclude that smoking may induce changes in DNA methylation status in cancer-related genes of oral epithelial cells and that the cessation of smoking is capable of reversing this process. Based on our data, we suggest that DNA methylation status of the hTERT and MLH1 gene promoters are promising markers for screening a set of smoking-related alterations in oral cells.
Collapse
|
16
|
Abstract
Epigenome-wide association studies (EWAS) face many of the same challenges as genome-wide association studies (GWAS), but have an added challenge in that the epigenome can vary dramatically across cell types. When cell-type composition differs between cases and controls, this leads to spurious associations that may obscure true associations. We have developed a computational method, FaST-LMM-EWASher, which automatically corrects for cell-type composition without needing explicit knowledge of it. In this chapter, we provide a tutorial on using FaST-LMM-EWASher for DNA methylation data and discuss data analysis strategies.
Collapse
Affiliation(s)
- James Y Zou
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
17
|
A miR-199a/miR-214 self-regulatory network via PSMD10, TP53 and DNMT1 in testicular germ cell tumor. Sci Rep 2014; 4:6413. [PMID: 25231260 PMCID: PMC4166711 DOI: 10.1038/srep06413] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/01/2014] [Indexed: 12/16/2022] Open
Abstract
It was previously demonstrated that microRNA-199a (miR-199a) was down-regulated in testicular germ cell tumor (TGCT) partially caused by hypermethylation of its promoter. miR-199a is encoded by two loci in the human genome, miR-199a-1 on chromosome (Chr) 19 and miR-199a-2 on Chr 1. Both loci encode the same miR-199a. Another microRNA, microRNA-214 (miR-214), also locates on Chr 1. Previous study revealed that it is co-transcribed with miR-199a-2. However, the biological significance of the co-expression of miR-199a and miR-214 remains largely unknown. In this study, we determined that miR-199a and miR-214 were concordantly expressed in NT2 cells and TGCT patient tissues. After 5-aza treatment, miR-199-3p/5p and miR-214 expression was significantly increased. Silencing of DNMT1with siRNA restored the expression of miR-199a and miR-214, accompanied by de-methylation of the promoters of miR-199a-1/2. TP53 down-regulated the expression of DNMT1 in NT2 cells and overexpression of TP53 restored the expression of miR-199-3p/5p and miR-214. In addition, silencing of PSMD10 up-regulated the expression of TP53, while miR-214 over-expression resulted in PSMD10 down-regulation and TP53 up-regulation. Collectively, our findings highlighted a miR-199a/miR-214/PSMD10/TP53/DNMT1 self-regulatory network, which might be a potential therapeutic target in the treatment of TGCT.
Collapse
|
18
|
Hansel A, Steinbach D, Greinke C, Schmitz M, Eiselt J, Scheungraber C, Gajda M, Hoyer H, Runnebaum IB, Dürst M. A promising DNA methylation signature for the triage of high-risk human papillomavirus DNA-positive women. PLoS One 2014; 9:e91905. [PMID: 24647315 PMCID: PMC3960142 DOI: 10.1371/journal.pone.0091905] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 02/18/2014] [Indexed: 12/19/2022] Open
Abstract
High-risk human papillomavirus (hrHPV)-DNA testing is frequently performed parallel to cytology for the detection of high-grade dysplasia and cervical cancer particularly in women above 30 years of age. Although highly sensitive, hrHPV testing cannot distinguish between HPV-positive women with or without clinically relevant lesions. However, in principle discrimination is possible on the basis of DNA methylation markers. In order to identify novel DNA regions which allow an effective triage of hrHPV-positive cases, hypermethylated DNA enriched from cervical cancers was compared with that from cervical scrapes of HPV16-positive cases with no evidence for disease by CpG island microarray hybridization. The most promising marker regions were validated by quantitative methylation-specific PCR (qMSP) using DNA from archived cervical tissues and cervical scrapes. The performance of these markers was then determined in an independent set of 217 hrHPV-positive cervical scrapes from outpatients with histopathological verification. A methylation signature comprising the 5′ regions of the genes DLX1, ITGA4, RXFP3, SOX17 and ZNF671 specific for CIN3 and cervical cancer (termed CIN3+) was identified and validated. A high detection rate of CIN3+ was obtained if at least 2 of the 5 markers were methylated. In the subsequent cross-sectional study all cervical carcinomas (n = 19) and 56% (13/23) of CIN3 were identified by this algorithm. Only 10% (11/105) of hrHPV-positive women without histological evidence of cervical disease were scored positive by the methylation assay. Of note is that the detection rate of CIN3 differed between age groups. Eight of nine CIN3 were detected among women ≥30 years of age but only five of fourteen among <30 year old group (p = 0.03). The specificity for CIN3+ in the older age group was 76.6% (95% CI 65.6–85.5%). Clinical validation studies are required to determine the usefulness of these novel markers for triage after primary hrHPV testing in a cervical cancer screening setting.
Collapse
Affiliation(s)
- Alfred Hansel
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Daniel Steinbach
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | | | - Martina Schmitz
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Juliane Eiselt
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | | | | | - Heike Hoyer
- IMSID, Jena University Hospital, Jena, Germany
| | | | - Matthias Dürst
- Department of Gynaecology, Jena University Hospital, Jena, Germany
- * E-mail:
| |
Collapse
|
19
|
Chen BF, Chan WY. The de novo DNA methyltransferase DNMT3A in development and cancer. Epigenetics 2014; 9:669-77. [PMID: 24589714 DOI: 10.4161/epi.28324] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation, one of the best-characterized epigenetic modifications, plays essential roles in development, aging and diseases. The de novo DNA methyltransferase DNMT3A is responsible for the establishment of de novo genomic DNA methylation patterns and, as such, involved in normal development as well as in many diseases including cancer. In recent years, our understanding of this important protein has made significant progress, which was facilitated by stunning development in the analysis of the DNA methylome of multiple organs and cell types. In this review, recent developments in the characterization of DNMT3A were discussed with special emphasis on the roles of DNMT3A in development and cancer.
Collapse
Affiliation(s)
- Bi-Feng Chen
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
| | - Wai-Yee Chan
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
| |
Collapse
|
20
|
Teperino R, Lempradl A, Pospisilik JA. Bridging epigenomics and complex disease: the basics. Cell Mol Life Sci 2013; 70:1609-21. [PMID: 23463237 PMCID: PMC11113658 DOI: 10.1007/s00018-013-1299-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/20/2022]
Abstract
The DNA sequence largely defines gene expression and phenotype. However, it is becoming increasingly clear that an additional chromatin-based regulatory network imparts both stability and plasticity to genome output, modifying phenotype independently of the genetic blueprint. Indeed, alterations in this "epigenetic" control layer underlie, at least in part, the reason for monozygotic twins being discordant for disease. Functionally, this regulatory layer comprises post-translational modifications of DNA and histones, as well as small and large noncoding RNAs. Together these regulate gene expression by changing chromatin organization and DNA accessibility. Successive technological advances over the past decade have enabled researchers to map the chromatin state with increasing accuracy and comprehensiveness, catapulting genetic research into a genome-wide era. Here, aiming particularly at the genomics/epigenomics newcomer, we review the epigenetic basis that has helped drive the technological shift and how this progress is shaping our understanding of complex disease.
Collapse
Affiliation(s)
- Raffaele Teperino
- Max-Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Adelheid Lempradl
- Max-Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - J. Andrew Pospisilik
- Max-Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| |
Collapse
|
21
|
Martin FL. Epigenetic influences in the aetiology of cancers arising from breast and prostate: a hypothesised transgenerational evolution in chromatin accessibility. ISRN ONCOLOGY 2013; 2013:624794. [PMID: 23431470 PMCID: PMC3574745 DOI: 10.1155/2013/624794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 12/26/2012] [Indexed: 01/12/2023]
Abstract
Epidemiological studies have consistently supported the notion that environmental and/or dietary factors play a central role in the aetiology of cancers of the breast and prostate. However, for more than five decades investigators have failed to identify a single cause-and-effect factor, which could be implicated; identification of a causative entity would allow the implementation of an intervention strategy in at-risk populations. This suggests a more complex pathoaetiology for these cancer sites, compared to others. When one examines the increases or decreases in incidence of specific cancers amongst migrant populations, it is notable that disease arising in colon or stomach requires one or at most two generations to exhibit a change in incidence to match that of high-incidence regions, whereas for breast or prostate cancer, at least three generations are required. This generational threshold could suggest a requirement for nonmutation-driven epigenetic alterations in the F0/F1 generations (parental/offspring adopting a more westernized lifestyle), which then predisposes the inherited genome of subsequent generations to mutagenic/genotoxic alterations leading to the development of sporadic cancer in these target sites. As such, individual susceptibility to carcinogen insult would not be based per se on polymorphisms in activating/detoxifying/repair enzymes, but on elevated accessibility of crucial target genes (e.g., oncogenes, tumour suppressor genes) or hotspots therein to mutation events. This could be termed a genomic susceptibility organizational structure (SOS). Several exposures including alcohol and heavy metals are epigens (i.e., modifiers of the epigenome), whereas others are mutagenic/genotoxic, for example, heterocyclic aromatic amines; humans are continuously and variously exposed to mixtures of these agents. Within such a transgenerational multistage model of cancer development, determining the interaction between epigenetic modification to generate a genomic SOS and genotoxic insult will facilitate a new level of understanding in the aetiology of cancer.
Collapse
Affiliation(s)
- Francis L. Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| |
Collapse
|
22
|
Towards a "Lyon molecular signature" to individualize the treatment of rectal cancer. Prognostic analysis of a prospective cohort of 94 rectal cancers T1-2-3 Nx MO to be the basis of a molecular signature. Cancer Radiother 2012; 16:688-96. [PMID: 23153504 DOI: 10.1016/j.canrad.2012.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 07/25/2011] [Accepted: 09/30/2012] [Indexed: 02/07/2023]
Abstract
PURPOSE In 1998 a translational research was initiated in Lyon aiming at identifying a prognostic "biomolecular signature" in rectal cancer. This paper presents the clinical outcome of the patients included in this study. PATIENTS AND METHODS A total of 94 patients were included between 1998 and 2001. A staging with rectoscopy and biopsies was performed before treatment. In case of surgery, the operative specimen was analysed to evaluate the pathological response. There were two types of treatment: neoadjuvant radiotherapy (with or without concurrent chemotherapy) followed by surgery (76 cases) and radiotherapy alone with 'contactherapy' often associated with external beam radiotherapy (18 patients). RESULTS The patients had a mean age of 63years. Stage was T1: 4, T2: 24, T3: 65 and T4: 1. The overall survival of the 94 patients was 62% at 8years with a rate of distant metastases of 29%. Rate of local recurrence at 8years was 6% in the neoadjuvant group and 16% in the radiotherapy group with an overall 8years survival in both groups respectively: 64% and 53%. There was a trend towards more metastases in cT3, tumour diameter above 4cm, circumferential extension. There was a significant increase in the risk of metastases for ypT3, ypN1-2 and Dworak score 1-2-3. In multivariate analysis ypT3 was significantly associated with a high rate of metastases (55%; P=0.0003). CONCLUSION The rate of distant metastases is a major prognostic factor. These clinical results will serve as the base line to identify a "biomolecular signature" which could complement the TN(M) classification.
Collapse
|
23
|
Byun HM, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, Apostoli P, Bertazzi PA, Baccarelli A. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS One 2012; 7:e39220. [PMID: 22745719 PMCID: PMC3379987 DOI: 10.1371/journal.pone.0039220] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/21/2012] [Indexed: 01/27/2023] Open
Abstract
Background DNA methylation is an epigenetic mechanism that has been increasingly investigated in observational human studies, particularly on blood leukocyte DNA. Characterizing the degree and determinants of DNA methylation stability can provide critical information for the design and conduction of human epigenetic studies. Methods We measured DNA methylation in 12 gene-promoter regions (APC, p16, p53, RASSF1A, CDH13, eNOS, ET-1, IFNγ, IL-6, TNFα, iNOS, and hTERT) and 2 of non-long terminal repeat elements, i.e., L1 and Alu in blood samples obtained from 63 healthy individuals at baseline (Day 1) and after three days (Day 4). DNA methylation was measured by bisulfite-PCR-Pyrosequencing. We calculated intraclass correlation coefficients (ICCs) to measure the within-individual stability of DNA methylation between Day 1 and 4, subtracted of pyrosequencing error and adjusted for multiple covariates. Results Methylation markers showed different temporal behaviors ranging from high (IL-6, ICC = 0.89) to low stability (APC, ICC = 0.08) between Day 1 and 4. Multiple sequence and marker characteristics were associated with the degree of variation. Density of CpG dinucleotides nearby the sequence analyzed (measured as CpG(o/e) or G+C content within ±200bp) was positively associated with DNA methylation stability. The 3′ proximity to repeat elements and range of DNA methylation on Day 1 were also positively associated with methylation stability. An inverted U-shaped correlation was observed between mean DNA methylation on Day 1 and stability. Conclusions The degree of short-term DNA methylation stability is marker-dependent and associated with sequence characteristics and methylation levels.
Collapse
Affiliation(s)
- Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, Massachusetts, United States of America.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Egger G, Wielscher M, Pulverer W, Kriegner A, Weinhäusel A. DNA methylation testing and marker validation using PCR: diagnostic applications. Expert Rev Mol Diagn 2012; 12:75-92. [PMID: 22133121 DOI: 10.1586/erm.11.90] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA methylation provides a fundamental epigenetic mechanism to establish and promote cell-specific gene-expression patterns, which are inherited by subsequent cell generations. Thus, the epigenome determines the differentiation into a cell lineage but can also program cells to become abnormal or malignant. In humans, different germline and somatic diseases have been linked to faulty DNA methylation. In this article, we will discuss the available PCR-based technologies to assess differences in DNA methylation levels mainly affecting 5-methylcytosine in the CpG dinucleotide context in hereditary syndromal and somatic pathological conditions. We will discuss some of the current diagnostic applications and provide an outlook on how DNA methylation-based biomarkers might provide novel tools for diagnosis, prognosis or patient stratification for diseases such as cancer.
Collapse
Affiliation(s)
- Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
| | | | | | | | | |
Collapse
|
25
|
Peterziel H, Müller J, Danner A, Barbus S, Liu HK, Radlwimmer B, Pietsch T, Lichter P, Schütz G, Hess J, Angel P. Expression of podoplanin in human astrocytic brain tumors is controlled by the PI3K-AKT-AP-1 signaling pathway and promoter methylation. Neuro Oncol 2012; 14:426-39. [PMID: 22394497 DOI: 10.1093/neuonc/nos055] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Recently, we found strong overexpression of the mucin-type glycoprotein podoplanin (PDPN) in human astrocytic brain tumors, specifically in primary glioblastoma multiforme (GB). In the current study, we show an inverse correlation between PDPN expression and PTEN levels in primary human GB and glioma cell lines, and we report elevated PDPN protein levels in the subventricular zone of brain tissue sections of PTEN-deficient mice. In human glioma cells lacking functional PTEN, reintroduction of wild-type PTEN, inhibition of the PTEN downstream target protein kinase B/AKT, or interference with transcription factor AP-1 function resulted in efficient downregulation of PDPN expression. In addition, we observed hypoxia-dependent PDPN transcriptional control and demonstrated that PDPN expression is subject to negative transcriptional regulation by promoter methylation in human GB and in glioma cell lines. Treatment of PTEN-negative glioma cells with demethylating agents induced expression of PDPN. Together, our findings show that increased PDPN expression in human GB is caused by loss of PTEN function and activation of the PI3K-AKT-AP-1 signaling pathway, accompanied by epigenetic regulation of PDPN promoter activity. Silencing of PDPN expression leads to reduced proliferation and migration of glioma cells, suggesting a functional role of PDPN in glioma progression and malignancy. Thus, specific targeting of PDPN expression and/or function could be a promising strategy for the treatment of patients with primary GB.
Collapse
Affiliation(s)
- Heike Peterziel
- Divisions of Signal Transduction and Growth Control, DKFZ/ZMBH Alliance, Heidelberg, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Molfese DL. Advancing neuroscience through epigenetics: molecular mechanisms of learning and memory. Dev Neuropsychol 2012; 36:810-27. [PMID: 21978007 DOI: 10.1080/87565641.2011.606395] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Humans share 96% of our 30,000 genes with Chimpanzees. The 1,200 genes that differ appear at first glance insufficient to describe what makes us human and them apes. However, we are now discovering that the mechanisms that regulate how genes are expressed tell a much richer story than our DNA alone. Sections of our DNA are constantly being turned on or off, marked for easy access, or secluded and hidden away, all in response to ongoing cellular activity. In the brain, neurons encode information-in effect memories-at the cellular level. Yet while memories may last a lifetime, neurons are dynamic structures. Every protein in the synapse undergoes some form of turnover, some with half-lives of only hours. How can a memory persist beyond the lifetimes of its constitutive molecular building blocks? Epigenetics-changes in gene expression that do not alter the underlying DNA sequence-may be the answer. In this article, epigenetic mechanisms including DNA methylation and acetylation or methylation of the histone proteins that package DNA are described in the context of animal learning. Through the interaction of these modifications a "histone code" is emerging wherein individual memories leave unique memory traces at the molecular level with distinct time courses. A better understanding of these mechanisms has implications for treatment of memory disorders caused by normal aging or diseases including schizophrenia, Alzheimer's, depression, and drug addiction.
Collapse
Affiliation(s)
- David L Molfese
- Department of Psychology, University of Houston, Houston, Texas 77204-5022, USA.
| |
Collapse
|
27
|
Yang Y, Zhang Q, Xu F, Wu L, He Q, Li X. Tumor suppressor gene BLU is frequently downregulated by promoter hypermethylation in myelodysplastic syndrome. J Cancer Res Clin Oncol 2012; 138:729-37. [DOI: 10.1007/s00432-012-1151-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Accepted: 01/02/2012] [Indexed: 01/16/2023]
|
28
|
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.
Collapse
Affiliation(s)
- Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | | | | |
Collapse
|
29
|
Galeano F, Tomaselli S, Locatelli F, Gallo A. A-to-I RNA editing: the "ADAR" side of human cancer. Semin Cell Dev Biol 2011; 23:244-50. [PMID: 21930228 DOI: 10.1016/j.semcdb.2011.09.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/07/2011] [Accepted: 09/08/2011] [Indexed: 12/14/2022]
Abstract
Carcinogenesis is a complex, multi-stage process depending on both endogenous and exogenous factors. In the past years, DNA mutations provided important clues to the comprehension of the molecular pathways involved in numerous cancers. Recently, post-transcriptional modification events, such as RNA editing, are emerging as new players in several human diseases, including tumours. A-to-I RNA editing changes the nucleotide sequence of target RNAs, introducing A-to-I/G "mutations". Since ADAR enzymes catalyse this nucleotide conversion, their expression/activity is essential and finely regulated in normal cells. This review summarizes the available knowledge on A-to-I RNA editing in the cancer field, giving a new view on how ADARs may play a role in carcinogenesis.
Collapse
Affiliation(s)
- Federica Galeano
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | | | | | | |
Collapse
|
30
|
Junaid MA, Kuizon S, Cardona J, Azher T, Murakami N, Pullarkat RK, Brown WT. Folic acid supplementation dysregulates gene expression in lymphoblastoid cells – Implications in nutrition. Biochem Biophys Res Commun 2011; 412:688-92. [DOI: 10.1016/j.bbrc.2011.08.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 08/08/2011] [Indexed: 12/30/2022]
|
31
|
Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011; 12:529-41. [PMID: 21747404 PMCID: PMC3508712 DOI: 10.1038/nrg3000] [Citation(s) in RCA: 876] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite the success of genome-wide association studies (GWASs) in identifying loci associated with common diseases, a substantial proportion of the causality remains unexplained. Recent advances in genomic technologies have placed us in a position to initiate large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies (EWASs) present novel opportunities but also create new challenges that are not encountered in GWASs. We discuss EWAS design, cohort and sample selections, statistical significance and power, confounding factors and follow-up studies. We also discuss how integration of EWASs with GWASs can help to dissect complex GWAS haplotypes for functional analysis.
Collapse
Affiliation(s)
- Vardhman K Rakyan
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK.
| | | | | | | |
Collapse
|
32
|
Roukos DH. Measurable evidence of miRNAs as regulators of cancer networks and therapeutic targets. Expert Rev Med Devices 2011; 8:123-6. [PMID: 21381902 DOI: 10.1586/erd.11.5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
33
|
Senner CE. The role of DNA methylation in mammalian development. Reprod Biomed Online 2011; 22:529-35. [PMID: 21498123 DOI: 10.1016/j.rbmo.2011.02.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 01/12/2023]
Abstract
DNA methylation is involved in a number of important processes such as maintaining genome stability, silencing of retrotransposons, co-ordinating mono-alleleic expression of parentally imprinted genes and ensuring transcriptional repression of genes on the inactive X chromosome. Further, correct DNA methylation patterns are necessary for normal development and lineage commitment. DNA methylation provides a stable and heritable epigenetic mark. However, it can be removed, either actively or passively, during periods of reprogramming in primordial germ cells and preimplantation embryos. By combining immunofluorescence data with recent insights from genome-wide studies utilizing techniques such as Bisulphite-seq and MeDIP-ChIP, a clearer picture of the dynamic patterns of DNA methylation throughout gametogenesis, preimplantation development and early lineage commitment is beginning to emerge. The continuing use of these next-generation technologies to elucidate genome-wide methylation patterns in a variety of cellular contexts will further understanding of how this epigenetic mark contributes to lineage commitment, differentiation and pluripotency and, ultimately, to human health and disease.
Collapse
Affiliation(s)
- Claire E Senner
- Laboratory of Epigenetics, The Babraham Institute, Babraham Research Campus, Cambridge, UK.
| |
Collapse
|