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Dahl C, Hvidtfeldt UA, Tjønneland A, Guldberg P, Raaschou-Nielsen O. Blood Leukocyte AHRR Methylation and Risk of Non-smoking-associated Cancer: A Case-cohort Study of Non-Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1781-1787. [PMID: 37691855 PMCID: PMC10484117 DOI: 10.1158/2767-9764.crc-23-0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/07/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023]
Abstract
Aryl-hydrocarbon receptor repressor (AHRR) hypomethylation in peripheral blood is tightly linked with tobacco smoking and lung cancer. Here, we investigated AHRR methylation in non-Hodgkin lymphoma (NHL), a non-smoking-associated cancer. In a case-cohort study within the population-based Danish Diet, Cancer and Health cohort, we measured AHRR (cg23576855) methylation in prediagnostic blood from 161 participants who developed NHL within 13.4 years of follow-up (median: 8.5 years), with a comparison group of 164 randomly chosen participants. We measured DNA-methylation levels using bisulfite pyrosequencing and estimated incidence rate ratios (IRR) using Cox proportional hazards models with adjustment for baseline age, sex, educational level, smoking status, body mass index, alcohol intake, physical activity, and diet score. Global DNA-methylation levels were assessed by long interspersed nucleotide element 1 (LINE-1) analysis. Overall, the IRR for AHRR hypomethylation (lowest vs. other quartiles) was 2.52 [95% confidence interval (CI), 1.24-5.15]. When stratified according to time between blood draw and diagnosis, low AHRR methylation levels were associated with a future diagnosis of NHL [IRR: 4.50 (95% CI, 1.62-12.50) at 0-<5 years, 7.04 (95% CI, 2.36-21.02) at 5-<10 years, and 0.56 (95% CI, 0.21-1.45) at ≥10 years]. There was no association between global DNA-methylation levels and risk of NHL. Our results show that AHRR hypomethylation in blood leukocytes is associated with a higher risk of NHL in a time-dependent manner, suggesting that it occurs as a response to tumor development. Significance Our population-based study demonstrated that lower AHRR methylation levels in peripheral blood leukocytes were associated with an increased risk of NHL. This association was independent of tobacco smoking, sex, and lifestyle characteristics, but was highly dependent on time to diagnosis. These findings highlight the potential of AHRR methylation as a biomarker for NHL risk, effective up to 10 years after blood draw.
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Affiliation(s)
- Christina Dahl
- Molecular Diagnostics, Danish Cancer Institute, Copenhagen, Denmark
| | - Ulla A. Hvidtfeldt
- Work, Environment and Cancer, Danish Cancer Institute, Copenhagen, Denmark
| | - Anne Tjønneland
- Diet, Cancer and Health, Danish Cancer Institute, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Per Guldberg
- Molecular Diagnostics, Danish Cancer Institute, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Ole Raaschou-Nielsen
- Work, Environment and Cancer, Danish Cancer Institute, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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2
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Nam AR, Heo M, Lee KH, Kim JY, Won SH, Cho JY. The landscape of PBMC methylome in canine mammary tumors reveals the epigenetic regulation of immune marker genes and its potential application in predicting tumor malignancy. BMC Genomics 2023; 24:403. [PMID: 37460953 DOI: 10.1186/s12864-023-09471-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Genome-wide dysregulation of CpG methylation accompanies tumor progression and characteristic states of cancer cells, prompting a rationale for biomarker development. Understanding how the archetypic epigenetic modification determines systemic contributions of immune cell types is the key to further clinical benefits. RESULTS In this study, we characterized the differential DNA methylome landscapes of peripheral blood mononuclear cells (PBMCs) from 76 canines using methylated CpG-binding domain sequencing (MBD-seq). Through gene set enrichment analysis, we discovered that genes involved in the growth and differentiation of T- and B-cells are highly methylated in tumor PBMCs. We also revealed the increased methylation at single CpG resolution and reversed expression in representative marker genes regulating immune cell proliferation (BACH2, SH2D1A, TXK, UHRF1). Furthermore, we utilized the PBMC methylome to effectively differentiate between benign and malignant tumors and the presence of mammary gland tumors through a machine-learning approach. CONCLUSIONS This research contributes to a better knowledge of the comprehensive epigenetic regulation of circulating immune cells responding to tumors and suggests a new framework for identifying benign and malignant cancers using genome-wide methylome.
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Affiliation(s)
- A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Heo
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji-Yoon Kim
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Ho Won
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
- BK21 Plus and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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3
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Rong J, Pu R, Sun H, Liu Y, Tian T, Bi H, Xia T, Zhang L, Zhang Y, Zhao Y, Zhu L. Association between the Methylation of CpG Islands in JAK-STAT Pathway-Related Genes and Colorectal Cancer. Gene 2023; 868:147357. [PMID: 36914143 DOI: 10.1016/j.gene.2023.147357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/21/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND Aberrant promoter methylation of CpG islands plays an important role in carcinogenesis. However, the association between the DNA methylation of JAK-STAT pathway-related genes in peripheral blood leukocytes and colorectal cancer (CRC) susceptibility remains unclear. METHODS We conducted a case-control study of 403 patients with CRC and 419 cancer free controls, and the DNA methylation levels of JAK2, STAT1, STAT3, and SOCS3 in peripheral blood samples from all subjects were assessed using a methylation-sensitive high-resolution melting (MS-HRM) analysis. RESULTS Compared with controls, the methylation of the JAK2, STAT1 and SOCS3 genes increased the CRC risk (ORadjusted=1.96, 95% CI, 1.12-3.41, P=0.01; ORadjusted=5.37, 95% CI, 3.74-7.71, P<0.01; ORadjusted=3.30, 95% CI, 1.58-6.87, P<0.01). In the multiple CpG site methylation (MCSM) analysis, a high MCSM value denoted an increased CRC risk (ORadjusted=4.97, 95% CI, 3.34-7.37, P<0.01). CONCLUSION In peripheral blood, the methylation of JAK2, STAT1, and high levels of MCSM are promising biomarkers for CRC risk.
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Affiliation(s)
- Jiesheng Rong
- Second Department of Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Rui Pu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Tian Tian
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Haoran Bi
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Lei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China.
| | - Lin Zhu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang, People's Republic of China.
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Jia J, Deng J, Jin H, Yang J, Nan D, Yu Z, Yu W, Shen Z, Lu Y, Liu R, Wang Z, Qu X, Qiu D, Yang Z, Huang Y. Effect of Dl-3-n-butylphthalide on mitochondrial Cox7c in models of cerebral ischemia/reperfusion injury. Front Pharmacol 2023; 14:1084564. [PMID: 36909178 PMCID: PMC9992206 DOI: 10.3389/fphar.2023.1084564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Several studies have demonstrated the protective effect of dl-3-n-Butylphthalide (NBP) against cerebral ischemia, which may be related to the attenuation of mitochondrial dysfunction. However, the specific mechanism and targets of NBP in cerebral ischemia/reperfusion remains unclear. In this study, we used a chemical proteomics approach to search for targets of NBP and identified cytochrome C oxidase 7c (Cox7c) as a key interacting target of NBP. Our findings indicated that NBP inhibits mitochondrial apoptosis and reactive oxygen species (ROS) release and increases ATP production through upregulation of Cox7c. Subsequently, mitochondrial respiratory capacity was improved and the HIF-1α/VEGF pathway was upregulated, which contributed to the maintenance of mitochondrial membrane potential and blood brain barrier integrity and promoting angiogenesis. Therefore, our findings provided a novel insight into the mechanisms underlying the neuroprotective effects of NBP, and also proposed for the first time that Cox7c exerts a critical role by protecting mitochondrial function.
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Affiliation(s)
- Jingjing Jia
- Department of Neurology, Peking University First Hospital, Beijing, China.,National Center for Children's Health, Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Haiqiang Jin
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jie Yang
- Leewe Biopharmaceutical Co., Ltd, Xianlin University, Nanjing, China
| | - Ding Nan
- Department of Neurology, Peking University First Hospital, Beijing, China.,Department of Hyperbaric Oxygen, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Zemou Yu
- Department of Neurology, Peking University First Hospital, Beijing, China.,National Center for Children's Health, Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Weiwei Yu
- Department of Neurology, Peking University First Hospital, Beijing, China.,Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhiyuan Shen
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yuxuan Lu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Ran Liu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Xiaozhong Qu
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Dong Qiu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhong Yang
- Institute of Polymer Science and Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yining Huang
- Department of Neurology, Peking University First Hospital, Beijing, China
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A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA in Chrysemys picta Turtles with Temperature-Dependent Sex Determination Reveals Contrasting Patterns of Somatic and Gonadal Methylation, but No Unobtrusive Sex Diagnostic. Animals (Basel) 2022; 13:ani13010117. [PMID: 36611726 PMCID: PMC9817949 DOI: 10.3390/ani13010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Background: The gonads of Chrysemys picta, a turtle with temperature-dependent sex determination (TSD), exhibit differential DNA methylation between males and females, but whether the same is true in somatic tissues remains unknown. Such differential DNA methylation in the soma would provide a non-lethal sex diagnostic for TSD turtle hatchings who lack visually detectable sexual dimorphism when young. Methods: Here, we tested multiple approaches to study DNA methylation in tail clips of Chrysemys picta hatchlings, to identify differentially methylated candidate regions/sites that could serve as molecular sex markers To detect global differential methylation in the tails we used methylation-sensitive ELISA, and to test for differential local methylation we developed a novel hybrid method by sequencing immunoprecipitated and bisulfite converted DNA (MeDIP-BS-seq) followed by PCR validation of candidate regions/sites after digestion with a methylation-sensitive restriction enzyme. Results: We detected no global differences in methylation between males and females via ELISA. While we detected inter-individual variation in DNA methylation in the tails, this variation was not sexually dimorphic, in contrast with hatchling gonads. Conclusions: Results highlight that differential DNA methylation is tissue-specific and plays a key role in gonadal formation (primary sexual development) and maintenance post-hatching, but not in the somatic tail tissue.
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6
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Oh TJ, Lim E, Bang BR, Lee JJ, Na YG, Shin JH, Lim JS, Song KH, An S. Identification and validation of methylated PENK gene for early detection of bladder cancer using urine DNA. BMC Cancer 2022; 22:1195. [PMID: 36403035 PMCID: PMC9675278 DOI: 10.1186/s12885-022-10275-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/02/2022] [Indexed: 11/21/2022] Open
Abstract
Background Early detection of bladder cancer (BCa) offers patients a favorable outcome and avoids the need for cystectomy. Development of an accurate and sensitive noninvasive BCa diagnostic test is imperative. DNA methylation is an early epigenetic event in the development of BCa. Certain specific aberrant methylations could serve as useful biomarkers. The aim of this study was to identify methylation biomarkers for early detection of BCa. Methods CpG methylation microarray analysis was conducted on primary tumors with varying stages (T1—T4) and paired nontumor tissues from nine BCa patients. Bisulfite-pyrosequencing was performed to confirm the methylation status of candidate genes in tissues and urine sediments (n = 51). Among them, PENK was selected as a potential candidate and validated using an independent set of 169 urine sediments (55 BCa, 25 benign urologic diseases, 8 other urologic cancers, and 81 healthy controls) with a quantitative methylation-specific real time PCR (mePENK-qMSP). All statistical analyses were performed using MedCalc software version 9.3.2.0. Results CpG methylation microarray analysis and stepwise validation by bisulfite-pyrosequencing for tissues and urine sediments supported aberrant methylation sites of the PENK gene as potential biomarkers for early detection of BCa. Clinical validation of the mePENK-qMSP test using urine sediment-DNA showed a sensitivity of 86.5% (95% CI: 71.2 – 95.5%), a specificity of 92.5% (95% CI: 85.7 – 96.7%), and an area under ROC of 0.920 (95% CI: 0.863 – 0.959) in detecting Ta high-grade and advanced tumor stages (T1-T4) of BCa patients. Sensitivities for Ta low-grade, Ta high-grade, T1 and T2-T4 were 55.6, 83.3, 88.5, and 100%, respectively. Methylation status of PENK was not correlated with sex, age or stage, while it was associated with the tumor grade of BCa. Conclusions In this study, we analyzed the comprehensive patterns of DNA methylation identified that PENK methylation possesses a high potential as a biomarker for urine-based early detection of BCa. Validation of PENK methylation confirms that it could significantly improve the noninvasive detection of BCa. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10275-2.
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Affiliation(s)
- Tae Jeong Oh
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea
| | - Eunkyung Lim
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea
| | - Bo-Ram Bang
- Promis Diagnostics Inc., 1 Post, Irvine, CA 92618 USA
| | | | - Yong Gil Na
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Ju Hyun Shin
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Jae Sung Lim
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Ki Hak Song
- grid.254230.20000 0001 0722 6377Department of Urology, Chungnam National University College of Medicine, 266 Munhwa-Ro Jung-Gu, Daejeon, 35015 Republic of Korea
| | - Sungwhan An
- Genomictree, Inc., 44-6 Techno 10-Ro Yuseong-Gu, Daejeon, 34027 Republic of Korea ,Promis Diagnostics Inc., 1 Post, Irvine, CA 92618 USA
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7
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Kim S, White SM, Radke EG, Dean JL. Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment. ENVIRONMENT INTERNATIONAL 2022; 164:107278. [PMID: 35537365 DOI: 10.1016/j.envint.2022.107278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response to some chemical exposures. Characterization of these methylation events is critical to understand the molecular consequences of chemical exposures. In this context, a novel workflow was developed to interrogate publicly available epidemiological transcriptomic and methylomic data to identify relevant pathway level changes in response to chemical exposure, using inorganic arsenic as a case study. Gene Set Enrichment Analysis (GSEA) was used to identify causal methylation events that result in concomitant downstream transcriptional deregulation. This analysis demonstrated an unequal distribution of differentially methylated regions across the human genome. After mapping these events to known genes, significant enrichment of a subset of these pathways suggested that arsenic-mediated methylation may be both specific and non-specific. Parallel GSEA performed on matched transcriptomic samples determined that a substantially reduced subset of these pathways are enriched and that not all chemically-induced methylation results in a downstream alteration in gene expression. The resulting pathways were found to be representative of well-established molecular events known to occur in response to arsenic exposure. The harmonization of enriched transcriptional patterns with those identified from the methylomic platform promoted the characterization of plausibly causal molecular signaling events. The workflow described here enables significant gene and methylation-specific pathways to be identified from whole blood samples of individuals exposed to environmentally relevant chemical levels. As future efforts solidify specific causal relationships between these molecular events and relevant apical endpoints, this novel workflow could aid risk assessments by identifying molecular targets serving as biomarkers of hazard, informing mechanistic understanding, and characterizing dose ranges that promote relevant molecular/epigenetic signaling events occuring in response to chemical exposures.
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Affiliation(s)
- Stephanie Kim
- Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USA.
| | - Shana M White
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
| | - Elizabeth G Radke
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C., USA.
| | - Jeffry L Dean
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
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Lin S, Gu S, Qian S, Liu Y, Sheng J, Li Q, Yang J, Ying X, Li Z, Tang M, Wang J, Chen K, Jin M. Genome-Wide Methylation Profiling of lncRNAs Reveals a Novel Progression-Related and Prognostic Marker for Colorectal Cancer. Front Oncol 2022; 11:782077. [PMID: 35127488 PMCID: PMC8811200 DOI: 10.3389/fonc.2021.782077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Sporadic colorectal cancer (CRC) develops principally through the adenoma-carcinoma sequence. Previous studies revealed that DNA methylation alterations play a significant role in colorectal neoplastic transformation. On the other hand, long noncoding RNAs (lncRNAs) have been identified to be associated with some critical tumorigenic processes of CRC. Accumulating evidence indicates more intricate regulatory relationships between DNA methylation and lncRNAs in CRC. Nevertheless, the methylation alterations of lncRNAs at different stages of colorectal carcinogenesis based on a genome-wide scale remain elusive. Therefore, in this study, we first used an Illumina MethylationEPIC BeadChip (850K array) to identify the methylation status of lncRNAs in 12 pairs of colorectal cancerous and adjacent normal tissues from cohort I, followed by cross-validation with The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Then, the abnormal hypermethylation of candidate genes in colorectal lesions was successfully confirmed by MassARRAY EpiTYPER in cohort II including 48 CRC patients, and cohort III including 286 CRC patients, 81 advanced adenoma (AA) patients and 81 nonadvanced adenoma (NAA) patients. DLX6-AS1 hypermethylation was detected at all stages of colorectal neoplasms and occurred as early as the NAA stage during colorectal neoplastic progression. The methylation levels were significantly higher in the comparisons of CRC vs. NAA (P < 0.001) and AA vs. NAA (P = 0.004). Moreover, the hypermethylation of DLX6-AS1 promoter was also found in cell-free DNA samples collected from CRC patients as compared to healthy controls (Padj = 0.003). Multivariate Cox proportional hazards regression analysis revealed DLX6-AS1 promoter hypermethylation was independently associated with poorer disease-specific survival (HR = 2.52, 95% CI: 1.35-4.69, P = 0.004) and overall survival (HR = 1.64, 95% CI: 1.02-2.64, P = 0.042) in CRC patients. Finally, a nomogram was constructed and verified by a calibration curve to predict the survival probability of individual CRC patients (C-index: 0.789). Our findings indicate DLX6-AS1 hypermethylation might be an early event during colorectal carcinogenesis and has the potential to be a novel biomarker for CRC progression and prognosis.
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Affiliation(s)
- Shujuan Lin
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Simeng Gu
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Environmental Health, Institute of Endemic Diseases, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Sangni Qian
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qilong Li
- Department of Screening, Jiashan Institute of Cancer Prevention and Treatment, Jiashan, China
| | - Jinhua Yang
- Department of Screening, Jiashan Institute of Cancer Prevention and Treatment, Jiashan, China
| | - Xiaojiang Ying
- Department of Anorectal Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Zhenjun Li
- Department of Anorectal Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Mengling Tang
- Department of Epidemiology and Biostatistics at School Public Health and the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianbing Wang
- Department of Epidemiology and Biostatistics at School of Public Health and National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Chen
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Mingjuan Jin, ; Kun Chen,
| | - Mingjuan Jin
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Mingjuan Jin, ; Kun Chen,
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9
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Li L, Li S, Qin S, Gao Y, Wang C, Du J, Zhang N, Chen Y, Han Z, Yu Y, Wang F, Zhao Y. Diet, Sports, and Psychological Stress as Modulators of Breast Cancer Risk: Focus on OPRM1 Methylation. Front Nutr 2022; 8:747964. [PMID: 35024367 PMCID: PMC8744450 DOI: 10.3389/fnut.2021.747964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
Background: DNA methylation is influenced by environmental factors and contributes to adverse modification of cancer risk and clinicopathological features. Methods: A case-control study (402 newly diagnosed cases, 470 controls) was conducted to evaluate the effect of environmental factors and OPRM1 methylation in peripheral blood leukocyte (PBL) DNA on the risk of breast cancer. A case-only study (373 cases) was designed to evaluate the effects of environmental factors on OPRM1 methylation in tumor tissue and the relationship of methylation with clinicopathological features. Results: We found a significant association between hypermethylation of OPRM1 and the risk of breast cancer (OR = 1.914, 95%CI = 1.357–2.777). OPRM1 hypermethylation in PBL DNA combined with low intake of vegetable, garlic, soybean, poultry, and milk; high pork intake; less regular sports and a high psychological stress index significantly increased the risk of breast cancer. Soybean intake (OR = 0.425, 95%CI: 0.231–0.781) and regular sports (OR = 0.624, 95%CI: 0.399–0.976) were associated with OPRM1 hypermethylation in tumor DNA. OPRM1 hypermethylation in tumor tissue was correlated with estrogen receptor (ER) (OR = 1.945, 95%CI: 1.262–2.996) and progesterone receptor (PR) (OR = 1.611, 95%CI: 1.069–2.427) negative status; in addition, OPRM1 hypermethylation in PBL DNA was associated with human epidermal growth factor receptor 2 (HER-2) negative status (OR = 3.673, 95%CI: 1.411–9.564). Conclusion: A healthy diet, psychosocial adaptability, and regular sports are very beneficial for breast cancer prevention and progress, especially for OPRM1 hypermethylation carriers. Personalized treatment considering the correlation between OPRM1 hypermethylation and ER and PR status may provide a novel benefit for breast cancer patients.
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Affiliation(s)
- Liangliang Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Shuo Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Shidong Qin
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Gao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Chao Wang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinghang Du
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Nannan Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Yanbo Chen
- The Third Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhen Han
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Yue Yu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
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10
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Yu C, Jordahl KM, Bassett JK, Joo JE, Wong EM, Brinkman MT, Schmidt DF, Bolton DM, Makalic E, Brasky TM, Shadyab AH, Tinker LF, Longano A, Hopper JL, English DR, Milne RL, Bhatti P, Southey MC, Giles GG, Dugué PA. Smoking Methylation Marks for Prediction of Urothelial Cancer Risk. Cancer Epidemiol Biomarkers Prev 2021; 30:2197-2206. [PMID: 34526299 DOI: 10.1158/1055-9965.epi-21-0313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/22/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Self-reported information may not accurately capture smoking exposure. We aimed to evaluate whether smoking-associated DNA methylation markers improve urothelial cell carcinoma (UCC) risk prediction. METHODS Conditional logistic regression was used to assess associations between blood-based methylation and UCC risk using two matched case-control samples: 404 pairs from the Melbourne Collaborative Cohort Study (MCCS) and 440 pairs from the Women's Health Initiative (WHI) cohort. Results were pooled using fixed-effects meta-analysis. We developed methylation-based predictors of UCC and evaluated their prediction accuracy on two replication data sets using the area under the curve (AUC). RESULTS The meta-analysis identified associations (P < 4.7 × 10-5) for 29 of 1,061 smoking-associated methylation sites, but these were substantially attenuated after adjustment for self-reported smoking. Nominally significant associations (P < 0.05) were found for 387 (36%) and 86 (8%) of smoking-associated markers without/with adjustment for self-reported smoking, respectively, with same direction of association as with smoking for 387 (100%) and 79 (92%) markers. A Lasso-based predictor was associated with UCC risk in one replication data set in MCCS [N = 134; odds ratio per SD (OR) = 1.37; 95% CI, 1.00-1.90] after confounder adjustment; AUC = 0.66, compared with AUC = 0.64 without methylation information. Limited evidence of replication was found in the second testing data set in WHI (N = 440; OR = 1.09; 95% CI, 0.91-1.30). CONCLUSIONS Combination of smoking-associated methylation marks may provide some improvement to UCC risk prediction. Our findings need further evaluation using larger data sets. IMPACT DNA methylation may be associated with UCC risk beyond traditional smoking assessment and could contribute to some improvements in stratification of UCC risk in the general population.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Kristina M Jordahl
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Julie K Bassett
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Jihoon Eric Joo
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Maree T Brinkman
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia.,Department of Data Science & AI, Faculty of IT, Monash University, Clayton, Victoria, Australia
| | - Damien M Bolton
- Department of Surgery, University of Melbourne and Olivia Newton-John Cancer Centre, Austin Hospital, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Theodore M Brasky
- Division of Medical Oncology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, California
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anthony Longano
- Department of Anatomical Pathology, Eastern Health, Box Hill Hospital, Box Hill, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia. .,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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11
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Evaluation of Methylation Profiles of An Epidermal Growth Factor Receptor Gene in a Head and Neck Squamous Cell Carcinoma Patient Group. Balkan J Med Genet 2021; 23:65-72. [PMID: 33816074 PMCID: PMC8009575 DOI: 10.2478/bjmg-2020-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey, and 48 unrelated healthy volunteers from different geographic regions of Turkey, were included in this study. Methylation status of the promoter region of the EGFR gene was detected by methylation-specific-polymerase chain reaction (MS-PCR). The correlation between EGFR gene promoter methylation profiles and clinical characteristics were examined using the χ2 test. Methylation was observed in 79.0% of HNSCC patients, whereas this ratio was 90.0% in healthy individuals. The results show that promoter region methylation of the EGFR gene was not associated with HNSCC development in the studied Turkish patient group. In addition, the methylation status of the EGFR gene promoter was not found to be related to age, gender or tumor stage.
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12
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Cappetta M, Fernandez L, Brignoni L, Artagaveytia N, Bonilla C, López M, Esteller M, Bertoni B, Berdasco M. Discovery of novel DNA methylation biomarkers for non-invasive sporadic breast cancer detection in the Latino population. Mol Oncol 2021; 15:473-486. [PMID: 33145876 PMCID: PMC7858097 DOI: 10.1002/1878-0261.12842] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023] Open
Abstract
Human diversity is one of the main pitfalls in the development of robust worldwide biomarkers in oncology. Epigenetic variability across human populations is associated with different genetic backgrounds, as well as variable lifestyles and environmental exposures, each of which should be investigated. To identify potential non-invasive biomarkers of sporadic breast cancer in the Uruguayan population, we studied genome-wide DNA methylation using Illumina methylation arrays in leukocytes of 22 women with sporadic breast cancer and 10 healthy women in a case-control study. We described a panel of 38 differentially methylated CpG positions that was able to cluster breast cancer patients (BCP) and controls, and that also recapitulated methylation differences in 12 primary breast tumors and their matched normal breast tissue. Moving forward, we simplified the detection method to improve its applicability in a clinical setting and used an independent well-characterized cohort of 80 leukocyte DNA samples from BCP and 80 healthy controls to validate methylation results at specific cancer-related genes. Our investigations identified methylation at CYFIP1 as a novel epigenetic biomarker candidate for sporadic breast cancer in the Uruguayan population. These results provide a proof-of-concept for the design of larger studies aimed at validating biomarker panels for the Latin American population.
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Affiliation(s)
- Mónica Cappetta
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Lucía Fernandez
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Lucía Brignoni
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Nora Artagaveytia
- Departamento Básico de MedicinaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Carolina Bonilla
- Departamento de Medicina PreventivaFacultad de MedicinaUniversidad de São PauloBrazil
- Population Health SciencesBristol Medical SchoolUniversity of BristolUK
| | - Miguel López
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL)BarcelonaSpain
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
- Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of BarcelonaSpain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC)MadridSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Bernardo Bertoni
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL)BarcelonaSpain
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
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13
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Qiao R, Di F, Wang J, Wei Y, Zhang Y, Xu T, Wang Y, Gu W, Han B, Yang R. The Association Between RAPSN Methylation in Peripheral Blood and Early Stage Lung Cancer Detected in Case-Control Cohort. Cancer Manag Res 2020; 12:11063-11075. [PMID: 33173339 PMCID: PMC7646459 DOI: 10.2147/cmar.s275321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background Early detection is essential to improve the survival and life quality of lung cancer (LC) patients. Changes of peripheral blood DNA methylation could be associated with malignancy but were mostly studied in Caucasians. Methods Here, in a Chinese population, we performed mass spectrometry assays to investigate the association between very early stage LC and methylation levels of RAPSN in the peripheral blood by a case–control cohort using of 221 LC patients (93.2% LC at stage I) and 285 unrelated cancer free control individuals. Results The odds ratios (ORs) of all CpG sites were evaluated for their risk to LC using inter-quartile analyses by logistic regression. In general, we observed an association between very early LC and decreased methylation of RAPSN_CpG_1.15 and RAPSN_CpG_3.4 (referring to Q4, OR range from 1.64 to 1.81, p<0.05). Stratified by gender, while hypomethylation of RAPSN_CpG_1.15, RAPSN_CpG_3.4 and RAPSN_CpG_7.14 were associated with LC in males (referring to Q4, ORs range from 1.94 to 2.31, p<0.05), RAPSN_CpG_2 and RAPSN_CpG_5 showed significantly lower methylation in female LC patients comparing to controls (referring to Q4, ORs range from 2.49 to 3.60, p<0.05). The risk of RAPSN hypomethylation to LC was enhanced by aging, and typically for people older than 55 years (referring to Q4, ORs range from 2.17 to 3.61 in six out of all 10 analyzed CpG groups, p<0.05). Conclusion Our study reveals an association between RAPSN hypomethylation in peripheral blood and LC and suggests the occurrence of altered blood-based methylation at the early stage of cancer.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Feifei Di
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Jun Wang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yujie Wei
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yanman Zhang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Rongxi Yang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210000, People's Republic of China
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14
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A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data. Genes (Basel) 2020; 11:genes11080931. [PMID: 32806782 PMCID: PMC7465138 DOI: 10.3390/genes11080931] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
DNA methylation change has been useful for cancer biomarker discovery, classification, and potential treatment development. So far, existing methods use either differentially methylated CpG sites or combined CpG sites, namely differentially methylated regions, that can be mapped to genes. However, such methylation signal mapping has limitations. To address these limitations, in this study, we introduced a combinatorial framework using linear regression, differential expression, deep learning method for accurate biological interpretation of DNA methylation through integrating DNA methylation data and corresponding TCGA gene expression data. We demonstrated it for uterine cervical cancer. First, we pre-filtered outliers from the data set and then determined the predicted gene expression value from the pre-filtered methylation data through linear regression. We identified differentially expressed genes (DEGs) by Empirical Bayes test using Limma. Then we applied a deep learning method, "nnet" to classify the cervical cancer label of those DEGs to determine all classification metrics including accuracy and area under curve (AUC) through 10-fold cross validation. We applied our approach to uterine cervical cancer DNA methylation dataset (NCBI accession ID: GSE30760, 27,578 features covering 63 tumor and 152 matched normal samples). After linear regression and differential expression analysis, we obtained 6287 DEGs with false discovery rate (FDR) <0.001. After performing deep learning analysis, we obtained average classification accuracy 90.69% (±1.97%) of the uterine cervical cancerous labels. This performance is better than that of other peer methods. We performed in-degree and out-degree hub gene network analysis using Cytoscape. We reported five top in-degree genes (PAIP2, GRWD1, VPS4B, CRADD and LLPH) and five top out-degree genes (MRPL35, FAM177A1, STAT4, ASPSCR1 and FABP7). After that, we performed KEGG pathway and Gene Ontology enrichment analysis of DEGs using tool WebGestalt(WEB-based Gene SeT AnaLysis Toolkit). In summary, our proposed framework that integrated linear regression, differential expression, deep learning provides a robust approach to better interpret DNA methylation analysis and gene expression data in disease study.
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15
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Gagliardi A, Dugué PA, Nøst TH, Southey MC, Buchanan DD, Schmidt DF, Makalic E, Hodge AM, English DR, Doo NW, Hopper JL, Severi G, Baglietto L, Naccarati A, Tarallo S, Pace L, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Lund E, Giles GG, Pardini B, Sandanger TM, Milne RL, Vineis P, Polidoro S, Fiorito G. Stochastic Epigenetic Mutations Are Associated with Risk of Breast Cancer, Lung Cancer, and Mature B-cell Neoplasms. Cancer Epidemiol Biomarkers Prev 2020; 29:2026-2037. [PMID: 32788174 DOI: 10.1158/1055-9965.epi-20-0451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Age-related epigenetic dysregulations are associated with several diseases, including cancer. The number of stochastic epigenetic mutations (SEM) has been suggested as a biomarker of life-course accumulation of exposure-related DNA damage; however, the predictive role of SEMs in cancer has seldom been investigated. METHODS A SEM, at a given CpG site, was defined as an extreme outlier of DNA methylation value distribution across individuals. We investigated the association of the total number of SEMs with the risk of eight cancers in 4,497 case-control pairs nested in three prospective cohorts. Furthermore, we investigated whether SEMs were randomly distributed across the genome or enriched in functional genomic regions. RESULTS In the three-study meta-analysis, the estimated ORs per one-unit increase in log(SEM) from logistic regression models adjusted for age and cancer risk factors were 1.25; 95% confidence interval (CI), 1.11-1.41 for breast cancer, and 1.23; 95% CI, 1.07-1.42 for lung cancer. In the Melbourne Collaborative Cohort Study, the OR for mature B-cell neoplasm was 1.46; 95% CI, 1.25-1.71. Enrichment analyses indicated that SEMs frequently occur in silenced genomic regions and in transcription factor binding sites regulated by EZH2 and SUZ12 (P < 0.0001 and P = 0.0005, respectively): two components of the polycomb repressive complex 2 (PCR2). Finally, we showed that PCR2-specific SEMs are generally more stable over time compared with SEMs occurring in the whole genome. CONCLUSIONS The number of SEMs is associated with a higher risk of different cancers in prediagnostic blood samples. IMPACT We identified a candidate biomarker for cancer early detection, and we described a carcinogenesis mechanism involving PCR2 complex proteins worthy of further investigations.
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Affiliation(s)
- Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Department of Clinical Pathology | Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research Level 10, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole W Doo
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Concord Repatriation General Hospital, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Concord Clinical School, University of Sydney, Concord, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Laura Baglietto
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Luigia Pace
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network - ISPRO, Villa delle Rose, Via Cosimo il Vecchio, Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Corso Umberto I, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Department of Cancer Registry and Histopathology, Provincial Health Authority (ASP 7) Ragusa, Piazza Igea, Ragusa, Italy
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- The Cancer Registry of Norway, Oslo, Norway
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Giovanni Fiorito
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Department of Biomedical Sciences, Laboratory of Biostatistics, University of Sassari, Sassari, Italy
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16
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Lian Q, Wang B, Fan L, Sun J, Wang G, Zhang J. DNA methylation data-based molecular subtype classification and prediction in patients with gastric cancer. Cancer Cell Int 2020; 20:349. [PMID: 32742196 PMCID: PMC7388223 DOI: 10.1186/s12935-020-01253-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/10/2020] [Indexed: 01/29/2023] Open
Abstract
Background Genetic and epigenetic alterations have been indicated to be closely correlated with the carcinogenesis, DNA methylation is one of most frequently occurring molecular behavior that take place early during this complicated process in gastric cancer (GC). Methods In this study, 398 samples were collected from the cancer genome atlas (TCGA) database and were analyzed, so as to mine the specific DNA methylation sites that affected the prognosis for GC patients. Moreover, the 23,588 selected CpGs that were markedly correlated with patient prognosis were used for consistent clustering of the samples into 6 subgroups, and samples in each subgroup varied in terms of M, Stage, Grade, and Age. In addition, the levels of methylation sites in each subgroup were calculated, and 347 methylation sites (corresponding to 271 genes) were screened as the intrasubgroup specific methylation sites. Meanwhile, genes in the corresponding promoter regions that the above specific methylation sites were located were performed signaling pathway enrichment analysis. Results The specific genes were enriched to the biological pathways that were reported to be closely correlated with GC; moreover, the subsequent transcription factor enrichment analysis discovered that, these genes were mainly enriched into the cell response to transcription factor B, regulation of MAPK signaling pathways, and regulation of cell proliferation and metastasis. Eventually, the prognosis prediction model for GC patients was constructed using the Random Forest Classifier model, and the training set and test set data were carried out independent verification and test. Conclusions Such specific classification based on specific DNA methylation sites can well reflect the heterogeneity of GC tissues, which contributes to developing the individualized treatment and accurately predicting patient prognosis.
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Affiliation(s)
- Qixin Lian
- Oncology Department, First Affiliated Hospital of Jiamusi University, 154002 Qiqihar, Heilongjiang China
| | - Bo Wang
- Oncology Department, First Affiliated Hospital of Jiamusi University, 154002 Qiqihar, Heilongjiang China
| | - Lijun Fan
- Gastroenterology Department, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
| | - Junqiang Sun
- Radiotherapy and Chemotherapy, The First Hospital of Dandong, Liaoning, 118000 China
| | - Guilai Wang
- General Surgery, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
| | - Jidong Zhang
- Gastroenterology Department, The First Hospital of Qiqihar, The Affiliate Qiqihar Hospital of Southern Medical University, Longsha District, 30 of Park Road, Qiqihar, Heilongjiang 161005 China
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17
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Onwuka JU, Li D, Liu Y, Huang H, Xu J, Liu Y, Zhang Y, Zhao Y. A panel of DNA methylation signature from peripheral blood may predict colorectal cancer susceptibility. BMC Cancer 2020; 20:692. [PMID: 32711505 PMCID: PMC7382833 DOI: 10.1186/s12885-020-07194-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/19/2020] [Indexed: 02/07/2023] Open
Abstract
Background Differential DNA methylation panel derived from peripheral blood could serve as biomarkers of CRC susceptibility. However, most of the previous studies utilized post-diagnostic blood DNA which may be markers of disease rather than susceptibility. In addition, only a few studies have evaluated the predictive potential of differential DNA methylation in CRC in a prospective cohort and on a genome-wide basis. The aim of this study was to identify a potential panel of DNA methylation biomarkers in peripheral blood that is associated with CRC risk and therefore serve as epigenetic biomarkers of disease susceptibility. Methods DNA methylation profile of a nested case-control study with 166 CRC and 424 healthy normal subjects were obtained from the Gene Expression Omnibus (GEO) database. The differentially methylated markers were identified by moderated t-statistics. The DNA methylation panel was constructed by stepwise logistic regression and the least absolute shrinkage and selection operator in the training dataset. A methylation risk score (MRS) model was constructed and the association between MRS and CRC risk assessed. Results We identified 48 differentially methylated CpGs sites, of which 33 were hypomethylated. Of these, sixteen-CpG based MRS that was associated with CRC risk (OR = 2.68, 95% CI: 2.13, 3.38, P < 0.0001) was constructed. This association is confirmed in the testing dataset (OR = 2.02, 95% CI: 1.48, 2.74, P < 0.0001) and persisted in both males and females, younger and older subjects, short and long time-to-diagnosis. The MRS also predicted CRC with AUC 0.82 (95% CI: 0.76, 0.88), indicating high accuracy. Conclusions Our study has identified a novel DNA methylation panel that is associated with CRC and could, if validated be useful for the prediction of CRC risk in the future.
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Affiliation(s)
- Justina Ucheojor Onwuka
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Hao Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Jing Xu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Ying Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150081, Heilongjiang Province, People's Republic of China.
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18
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Wu B, Chen S, Zhuang L, Zeng J. The expression level of COX7C associates with venous thromboembolism in colon cancer patients. Clin Exp Med 2020; 20:527-533. [PMID: 32653968 DOI: 10.1007/s10238-020-00644-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
Venous thromboembolism (VTE) is a common complication of colon cancer. In the present study, we aimed to explore the association of the oncogene COX7C to VTE in colon cancer patients. Samples from 580 patients were examined histologically for VTE and pathological characteristic of cancer. Gene mutation and expression analysis were performed using polymerase chain reaction-based assays to evaluate genes related to VTE, including COX7C. Univariate analysis between clinical pathological factors and VTE was conducted. Logistic regression analysis was performed for the prediction of VTE by pathological factors and gene expressions. Among patients investigated, a total of 56 patients had VTE. COX7C had a significant correlation with VTE (p < 0.001). Despite a correlation between tumor size, invasion depth of tumor, lymph node metastasis, lymph node metastasis, distant metastasis, lymphovascular invasion, histologic type and pathology type, Ki-67, and some other genes, to VTE (p > 0.05), only COX7C expression demonstrated significance in its ability to predict VTE. Here, we show that COX7C upregulation strongly correlates with VTE in colon cancer, which implicates its role as a biomarker and therapeutic target of VTE in colon cancer.
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Affiliation(s)
- Biyu Wu
- Department of Nursing, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Shurong Chen
- Department of Geriatric, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Lihong Zhuang
- Second Department of Gastrointestinal Surgery, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China
| | - Jingyang Zeng
- Department of Anesthesiology, Quanzhou First Hospital Affiliated To Fujian Medical University, No.250 East Street, Licheng District, Quanzhou, 362000, Fujian, China.
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19
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Wang Y, Franks JM, Whitfield ML, Cheng C. BioMethyl: an R package for biological interpretation of DNA methylation data. Bioinformatics 2020; 35:3635-3641. [PMID: 30799505 PMCID: PMC6761945 DOI: 10.1093/bioinformatics/btz137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/25/2019] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Motivation The accumulation of publicly available DNA methylation datasets has resulted in the need for tools to interpret the specific cellular phenotypes in bulk tissue data. Current approaches use either single differentially methylated CpG sites or differentially methylated regions that map to genes. However, these approaches may introduce biases in downstream analyses of biological interpretation, because of the variability in gene length. There is a lack of approaches to interpret DNA methylation effectively. Therefore, we have developed computational models to provide biological interpretation of relevant gene sets using DNA methylation data in the context of The Cancer Genome Atlas. Results We illustrate that Biological interpretation of DNA Methylation (BioMethyl) utilizes the complete DNA methylation data for a given cancer type to reflect corresponding gene expression profiles and performs pathway enrichment analyses, providing unique biological insight. Using breast cancer as an example, BioMethyl shows high consistency in the identification of enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data. We find that 12 out of 14 pathways identified by BioMethyl are shared with those by using RNA-seq data, with a Jaccard score 0.8 for estrogen receptor (ER) positive samples. For ER negative samples, three pathways are shared in the two enrichments with a slight lower similarity (Jaccard score = 0.6). Using BioMethyl, we can successfully identify those hidden biological pathways in DNA methylation data when gene expression profile is lacking. Availability and implementation BioMethyl R package is freely available in the GitHub repository (https://github.com/yuewangpanda/BioMethyl). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yue Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jennifer M Franks
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Norris Cotton Cancer Center, Lebanon, NH, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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20
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Wojtczyk-Miaskowska A, Schlichtholz B. Tobacco carcinogens and the methionine metabolism in human bladder cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2019; 782:108281. [PMID: 31843138 DOI: 10.1016/j.mrrev.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/29/2019] [Accepted: 06/03/2019] [Indexed: 01/08/2023]
Abstract
Cigarette smoking is a strong risk factor for bladder cancer. It has been shown that the duration of smoking is associated with a poor prognosis and a higher risk of recurrence. This is due to tobacco carcinogens forming adducts with DNA and proteins that participate in the DNA repair mechanisms. Additionally, polymorphisms of genes responsible for methyl group transfer in the methionine cycle and dosages of vitamins (from diet and supplements) can cause an increased risk of bladder cancer. Upregulated DNA methyltransferase 1 expression and activity results in a high level of methylated products of metabolism, as well as hypermethylation of tumor suppressor genes. The development of a market that provides new inhibitors of DNA methyltransferase or alternatives for current smokers is essential not only for patients but also for people who are under the danger of secondhand smoking and can experience its long-term exposure consequences.
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Affiliation(s)
- A Wojtczyk-Miaskowska
- Department of Biochemistry, Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland.
| | - B Schlichtholz
- Department of Biochemistry, Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland
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21
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Jordahl KM, Phipps AI, Randolph TW, Tindle HA, Liu S, Tinker LF, Kelsey KT, White E, Bhatti P. Differential DNA methylation in blood as a mediator of the association between cigarette smoking and bladder cancer risk among postmenopausal women. Epigenetics 2019; 14:1065-1073. [PMID: 31232174 DOI: 10.1080/15592294.2019.1631112] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Smoking accounts for approximately 52% of bladder cancer incidence among postmenopausal women, but the underlying mechanism is poorly understood. Our study investigates whether changes in DNA methylation, as measured in blood, mediate the impact of smoking on bladder cancer risk among postmenopausal women. We conducted analyses among 206 cases and 251 controls that were current or never smokers at baseline from a previous case-control study of bladder cancer and genome-wide DNA methylation nested within the Women's Health Initiative. Separate mediation analyses were conducted for three CpG sites demonstrating robust associations with smoking in prior methylome-wide association studies: cg05575921 (AhRR), cg03636183 (F2RL3), and cg19859270 (GPR15). We estimated causal effects using the regression-based, four-way decomposition approach, which addresses the interaction between smoking and each CpG site. The overall proportion of the excess relative risk mediated by cg05575921 was 92% (p-value = 0.004) and by cg19859270 was 79% (p-value = 0.02). The largest component of the excess relative risk of bladder cancer due to 30 pack-years of smoking history in current smokers was the mediated interaction for both cg05575921 (72%, p = 0.02) and cg19859270 (72%, p-value = 0.04), where the mediated interaction is the effect of smoking on bladder cancer that both acts through differential methylation and depends on smoking history. There was little evidence that smoking was mediated through cg03636183. Our results suggest that differential methylation of cg05575921 and cg19859270 mediate the effects of smoking on bladder cancer, potentially revealing downstream effects of smoking relevant for carcinogenesis.
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Affiliation(s)
- Kristina M Jordahl
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Amanda I Phipps
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Timothy W Randolph
- Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University Medical Center , Nashville , TN , USA
| | - Simin Liu
- Departments of Epidemiology, Medicine, and Surgery, Brown University , Providence , RI , USA
| | - Lesley F Tinker
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Karl T Kelsey
- Departments of Epidemiology and Pathology and Laboratory Medicine, Brown University , Providence , RI , USA
| | - Emily White
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Parveen Bhatti
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,Cancer Control Research, BC Cancer , Vancouver , BC , Canada
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22
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Sun H, Huang H, Li D, Zhang L, Zhang Y, Xu J, Liu Y, Liu Y, Zhao Y. PBX3 hypermethylation in peripheral blood leukocytes predicts better prognosis in colorectal cancer: A propensity score analysis. Cancer Med 2019; 8:4001-4011. [PMID: 31140752 PMCID: PMC6639175 DOI: 10.1002/cam4.2321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/15/2019] [Accepted: 05/16/2019] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE The significance of gene methylation in peripheral blood leukocytes (PBLs) for assessing cancer prognosis is poorly understood. Our purpose is to assess the association between PBX3 methylation in PBLs and colorectal cancer (CRC) prognosis. METHODS A total of 369 CRC patients were followed up for up to 10 years in this cohort study. PBL PBX3 methylation levels were determined by methylation-sensitive high-resolution melting. Cox regression models and Log-rank tests were used to analyze the associations between PBX3 methylation status and CRC prognosis with a propensity score (PS) method to control confounding biases. RESULTS In this study, we found that CRC patients with PBL PBX3 hypermethylation status had a better overall survival (OS) (hazard ratio [HRPS-adjusted ], 0.72 [95% CI, 0.52-1.00]; P = 0.049). Subgroup analyses showed that the beneficial effect of PBX3 hypermethylation status on CRC 10-years OS remained significant among UICC stage III patients ([HRPS-adjusted ], 0.60 [95% CI, 0.38 to 0.95]; P = 0.029) and colon cancer patients ([HRPS-adjusted ], 0.49 [95% CI, 0.26 to 0.92]; P = 0.027). CONCLUSION PBL PBX3 hypermethylation is positively associated with better prognosis of CRC, especially for the UICC stage III CRC patients and colon cancer patients.
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Affiliation(s)
- Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Hao Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Lei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Yuanyuan Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Jing Xu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Ying Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, The People's Republic of China
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23
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Lønning PE, Eikesdal HP, Løes IM, Knappskog S. Constitutional Mosaic Epimutations - a hidden cause of cancer? Cell Stress 2019; 3:118-135. [PMID: 31225507 PMCID: PMC6551830 DOI: 10.15698/cst2019.04.183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Silencing of tumor suppressor genes by promoter hypermethylation is a key mechanism to facilitate cancer progression in many malignancies. While promoter hypermethylation can occur at later stages of the carcinogenesis process, constitutional methylation of key tumor suppressors may be an initiating event whereby cancer is started. Constitutional BRCA1 methylation due to cis-acting germline genetic variants is associated with a high risk of breast and ovarian cancer. However, this seems to be a rare event, restricted to a very limited number of families. In contrast, mosaic constitutional BRCA1 methylation is detected in 4-7% of newborn females without germline BRCA1 mutations. While the cause of such methylation is poorly understood, mosaic normal tissue BRCA1 methylation is associated with a 2-3 fold increased risk of high-grade serous ovarian cancer (HGSOC). As such, BRCA1 methylation may be the cause of a significant number of ovarian cancers. Given the molecular similarities between HGSOC and basal-like breast cancer, the findings with respect to HGSOC suggest that constitutional BRCA1 methylation could be a risk factor for basal-like breast cancer as well. Similar to BRCA1, some specific germline variants in MLH1 and MSH2 are associated with promoter methylation and a high risk of colorectal cancers in rare hereditary cases of the disease. However, as many as 15% of all colorectal cancers are of the microsatellite instability (MSI) "high" subtype, in which commonly the tumors harbor MLH1 hypermethylation. Constitutional mosaic methylation of MLH1 in normal tissues has been detected but not formally evaluated as a potential risk factor for incidental colorectal cancers. However, the findings with respect to BRCA1 in breast and ovarian cancer raises the question whether mosaic MLH1 methylation is a risk factor for MSI positive colorectal cancer as well. As for MGMT, a promoter variant is associated with elevated methylation across a panel of solid cancers, and MGMT promoter methylation may contribute to an elevated cancer risk in several of these malignancies. We hypothesize that constitutional mosaic promoter methylation of crucial tumor suppressors may trigger certain types of cancer, similar to germline mutations inactivating the same particular genes. Such constitutional methylation events may be a spark to ignite cancer development, and if associated with a significant cancer risk, screening for such epigenetic alterations could be part of cancer prevention programs to reduce cancer mortality in the future.
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Affiliation(s)
- Per E. Lønning
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Hans P. Eikesdal
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Inger M. Løes
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G.Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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24
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Bermejo JL, Huang G, Manoochehri M, Mesa KG, Schick M, Silos RG, Ko YD, Brüning T, Brauch H, Lo WY, Hoheisel JD, Hamann U. Long intergenic noncoding RNA 299 methylation in peripheral blood is a biomarker for triple-negative breast cancer. Epigenomics 2019; 11:81-93. [DOI: 10.2217/epi-2018-0121] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To identify DNA methylation biomarkers in peripheral blood samples from triple-negative breast cancer (TNBC) patients. Materials & methods: We conducted an epigenome-wide association study (EWAS): the most promising markers were identified in 233 TNBC case–control pairs (discovery set) and subsequently validated in an independent validation set (57 TNBC patients and 124 controls). Results: cg06588802 (LINC00299/ID2) showed a higher methylation in TNBC patients compared with controls (discovery set: 3% increase, p-value = 0.0009; validation set: 2% increase, p-value = 0.01). Consistent results at four neighboring methylation probes and the strong negative correlation (rho = -0.93) with LINC00299 expression add plausibility to this result. Conclusion: Hypermethylation of LINC00299 in peripheral blood may constitute a useful circulating biomarker for TNBC.
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Affiliation(s)
- Justo L Bermejo
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Guanmengqian Huang
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Mehdi Manoochehri
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Karen G Mesa
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Matthias Schick
- Genomics & Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosa G Silos
- Statistical Genetics Group, Institute of Medical Biometry & Informatics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, 53113, Germany
| | - Thomas Brüning
- Institute for Prevention & Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, 44789, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany
- Department of Clinical Pharmacology, University of Tübingen, Tübingen, 70376, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, 70376, Germany
- Department of Clinical Pharmacology, University of Tübingen, Tübingen, 70376, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Ute Hamann
- Department of Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
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25
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Sun H, Zhou H, Zhang Y, Chen J, Han X, Huang D, Ren X, Jia Y, Fan Q, Tian W, Zhao Y. Aberrant methylation of FAT4 and SOX11 in peripheral blood leukocytes and their association with gastric cancer risk. J Cancer 2018; 9:2275-2283. [PMID: 30026822 PMCID: PMC6036714 DOI: 10.7150/jca.24797] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/31/2018] [Indexed: 01/12/2023] Open
Abstract
Background: Aberrant DNA methylation, especially tumor suppressor gene hypermethylation, is a well-recognized biomarker of initial tumorogenesis stages. FAT4 and SOX11 are putative tumor suppressor genes and can be down-regulated by hypermethylation in various cancers tissues. However, in peripheral blood leukocytes, the association between these two genes methylation status, as well as the effects of gene-environment interactions, and gastric cancer (GC) risk remain unclear. Methods: A hospital-based case-control study including 375 cases and 394 controls was conducted. Peripheral blood leukocytes DNA methylation status were detected by methylation-sensitive high-resolution melting (MS-HRM) assay. Logistic regression was adopted to analyze the relationship of FAT4 and SOX11 methylation with GC susceptibility. Results: Positive methylation (Pm) and total positive methylation (Tpm) of FAT4 were significantly increased the risk of GC (OR = 2.204, 95% CI: 1.168-4.159, P = 0.015; OR = 1.583, 95% CI: 1.031-2.430, P = 0.036, respectively). Compared with controls, cases exhibited higher SOX11 Pm frequencies with OR of 2.530 (95% CI: 1.289-4.969, P = 0.007). Nonetheless, no statistically significant association between SOX11 Tpm and GC risk was observed. Additionally, interactions between FAT4 Tpm and increased consumption of freshwater fish (≥1 times/week) displayed an antagonistic effect on GC (OR = 0.328, 95% CI: 0.142-0.762, P = 0.009), and high salt intake interacted with SOX11 Tpm also showed statistically significant (OR = 0.490, 95% CI: 0.242-0.995, P = 0.048). Conclusions:FAT4 aberrant methylation in peripheral blood leukocytes and gene-environment interactions were associated with the risk of GC, while SOX11 was controversial and needed to be more investigated.
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Affiliation(s)
- Hongxu Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Haibo Zhou
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Yan Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Jie Chen
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Xu Han
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Di Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Xiyun Ren
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Yunhe Jia
- Department of Colorectal Cancer Surgery, The third affiliated hospital, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Qing Fan
- Xiangfang Center for Disease Control and Prevention, Harbin 150081, Heilongjiang Province, P. R. China
| | - Wenjing Tian
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
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26
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Jordahl KM, Randolph TW, Song X, Sather CL, Tinker LF, Phipps AI, Kelsey KT, White E, Bhatti P. Genome-Wide DNA Methylation in Prediagnostic Blood and Bladder Cancer Risk in the Women's Health Initiative. Cancer Epidemiol Biomarkers Prev 2018; 27:689-695. [PMID: 29540343 PMCID: PMC5984694 DOI: 10.1158/1055-9965.epi-17-0951] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/31/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Differential DNA methylation as measured in blood is a promising marker of bladder cancer susceptibility. However, previous studies have exclusively used postdiagnostic blood samples, meaning that observed associations may be markers of disease rather than susceptibility.Methods: Genome-wide methylation was measured in prediagnostic blood samples, using the Illumina Infinium HumanMethylation450 Bead Array, among 440 bladder cancer cases with the transitional cell carcinoma (TCC) subtype and 440 matched cancer-free controls from the Women's Health Initiative cohort. After normalization and probe filtering, we used conditional logistic regression models to test for associations between methylation measurements at 361,184 CpG sites and bladder cancer risk.Results: Increased methylation at cg22748573, located in a CpG island within the 5'-UTR/first exon of the CITED4 gene, was associated with an 82% decreased risk of bladder cancer after adjusting for race/ethnicity, smoking status, pack-years of smoking, and leukocyte cell profile and accounting for multiple testing (OR = 0.18, q-value = 0.05). The result was robust to sensitivity analyses accounting for time between enrollment and diagnosis, race, tumor subtype, and secondhand smoke exposure.Conclusions: Although results need to be confirmed in additional prospective studies, differential methylation in CITED4, as measured in blood, is a promising marker of bladder cancer susceptibility.Impact: Identification of biomarkers of bladder cancer susceptibility in easily accessible tissues may allow targeting of screening efforts so as to improve bladder cancer prognosis. This is particularly important among women, who tend to have poorer bladder cancer outcomes than men. Cancer Epidemiol Biomarkers Prev; 27(6); 689-95. ©2018 AACR.
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Affiliation(s)
- Kristina M Jordahl
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Timothy W Randolph
- Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Xiaoling Song
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cassandra L Sather
- Genomics Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lesley F Tinker
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Amanda I Phipps
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Karl T Kelsey
- Department of Community Health, Brown University, Providence, Rhode Island
| | - Emily White
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Parveen Bhatti
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington.
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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27
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Cheng Q, Zhao B, Huang Z, Su Y, Chen B, Yang S, Peng X, Ma Q, Yu X, Zhao B, Ke X. Epigenome-wide study for the offspring exposed to maternal HBV infection during pregnancy, a pilot study. Gene 2018. [PMID: 29526602 DOI: 10.1016/j.gene.2018.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIM Hepatitis B virus (HBV) can be transmitted to infants, and is related to infants' later disease risk. Epigenetic change (such as DNA methylation) may be mechanism underlying the relationship. In this study, we aimed to investigate whether prenatal HBV infection could alter DNA methylation status in newborns. METHOD We selected 12 neonates with intrauterine HBV infection whose mothers were HBsAg-positive during pregnancy, relative to 12 HBV-free neonates with HBsAg-negative mothers. The pattern of genome-wide DNA methylation in the umbilical cord blood was investigated by Illumina Infinium Human Methylation 450K BeadChip. RESULT The average level of global methylation in infected neonates exposed to maternal HBV infection was not significantly different from controls. However, after adjusting for multiple comparisons, we found differential significance in the cases group compared to the controls for 663 CpG sites, associated with 534 genes. Among these sites, 53.85% (357/663) had decreased methylation (ΔM < 0) and 46.15% (306/663) had increased methylation (ΔM > 0). The average percentage change (Δβ) in methylation ranged from -46% to 36%. Validated by pyrosequencing, we identified 4 significantly differentially methylated CpG sites in the KLHL35 gene and additional CpGs for the CPT1B gene. These genes play a role in the development of hepatocellular and colorectal carcinoma and fatty acid oxidation, suggesting the candidature of these genes in HBV related disease. CONCLUSION Prenatal HBV exposure, even without malformation or preterm birth, may alter the epigenome profile in newborns. We identified a set of genes with differentially methylated CpG sites presented in the cord blood of HBV-infected newborns with HBsAg-positive mothers, demonstrating that DNA methylation status at birth can be used as a biomarker of prenatal exposure. These DNA methylation differences suggest a possible role for epigenetic processes in neonatal development in response to prenatal HBV exposure.
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Affiliation(s)
- Qijun Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Bin Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Zhenxiang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Yanhua Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Biqin Chen
- Women and Children's medical center, Siming District, Xiamen, Fujian, China
| | - Songjing Yang
- Women and Children's medical center, Siming District, Xiamen, Fujian, China
| | - Xueqi Peng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Qilin Ma
- Neurology Department, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Xiaoshan Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China
| | - Benhua Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China.
| | - Xiayi Ke
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Fujian, China.
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28
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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29
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DNA methylation array analysis identifies breast cancer associated RPTOR, MGRN1 and RAPSN hypomethylation in peripheral blood DNA. Oncotarget 2018; 7:64191-64202. [PMID: 27577081 PMCID: PMC5325435 DOI: 10.18632/oncotarget.11640] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/13/2016] [Indexed: 11/30/2022] Open
Abstract
DNA methylation changes in peripheral blood DNA have been shown to be associated with solid tumors. We sought to identify methylation alterations in whole blood DNA that are associated with breast cancer (BC). Epigenome-wide DNA methylation profiling on blood DNA from BC cases and healthy controls was performed by applying Infinium HumanMethylation450K BeadChips. Promising CpG sites were selected and validated in three independent larger sample cohorts via MassARRAY EpiTyper assays. CpG sites located in three genes (cg06418238 in RPTOR, cg00736299 in MGRN1 and cg27466532 in RAPSN), which showed significant hypomethylation in BC patients compared to healthy controls in the discovery cohort (p < 1.00 × 10−6) were selected and successfully validated in three independent cohorts (validation I, n =211; validation II, n=378; validation III, n=520). The observed methylation differences are likely not cell-type specific, as the differences were only seen in whole blood, but not in specific sub cell-types of leucocytes. Moreover, we observed in quartile analysis that women in the lower methylation quartiles of these three loci had higher ORs than women in the higher quartiles. The combined AUC of three loci was 0.79 (95%CI 0.73-0.85) in validation cohort I, and was 0.60 (95%CI 0.54-0.66) and 0.62 (95%CI 0.57-0.67) in validation cohort II and III, respectively. Our study suggests that hypomethylation of CpG sites in RPTOR, MGRN1 and RAPSN in blood is associated with BC and might serve as blood-based marker supplements for BC if these could be verified in prospective studies.
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30
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Angulo JC, López JI, Ropero S. DNA Methylation and Urological Cancer, a Step Towards Personalized Medicine: Current and Future Prospects. Mol Diagn Ther 2017; 20:531-549. [PMID: 27501813 DOI: 10.1007/s40291-016-0231-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Urologic malignancies are some of the commonest tumors often curable when diagnosed at early stage. However, accurate diagnostic markers and faithful predictors of prognosis are needed to avoid over-diagnosis leading to overtreatment. Many promising exploratory studies have identified epigenetic markers in urinary malignancies based on DNA methylation, histone modification and non-coding ribonucleic acid (ncRNA) expression that epigenetically regulate gene expression. We review and discuss the current state of development and the future potential of epigenetic biomarkers for more accurate and less invasive detection of urological cancer, tumor recurrence and progression of disease serving to establish diagnosis and monitor treatment efficacies. The specific clinical implications of such methylation tests on therapeutic decisions and patient outcome and current limitations are also discussed.
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Affiliation(s)
- Javier C Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Departamento Clínico, Facultad de Ciencias Biomédicas, Universidad Europea de Madrid, Laureate Universities, Hospital Universitario de Getafe, Carretera de Toledo Km 12.5, Getafe, 28905, Madrid, Spain.
| | - Jose I López
- Servicio de Anatomía Patológica, Hospital Universitario de Cruces, Instituto BioCruces,Universidad del País Vasco (UPV-EHU), Bilbao, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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31
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Methylation status of IGF2 DMR and LINE1 in leukocyte DNA provides distinct clinicopathological features of gastric cancer patients. Clin Exp Med 2017; 18:215-220. [DOI: 10.1007/s10238-017-0471-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/23/2017] [Indexed: 12/14/2022]
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32
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Schott S, Yang R, Stöcker S, Canzian F, Giese N, Bugert P, Bergmann F, Strobel O, Hackert T, Sohn C, Burwinkel B. HYAL2 methylation in peripheral blood as a potential marker for the detection of pancreatic cancer: a case control study. Oncotarget 2017; 8:67614-67625. [PMID: 28978057 PMCID: PMC5620197 DOI: 10.18632/oncotarget.18757] [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: 10/19/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy which is mostly diagnosed in advanced and inoperable stages though surgery remains the only curable therapeutic approach. Early detection markers are urgently needed to improve diagnosis. Altered hyaluronoglucosaminidase 2 gene (HYAL2) DNA methylation in peripheral blood is known to be associated with malignancy at early stage but has not been evaluated in PDAC patients. This study evaluates the association between blood-based HYAL2 methylation and PDAC by a case-control study with 191 controls and 82 PDAC patients. Decreased methylation of all four investigated HYAL2 methylation sites showed highly significant association with PDAC (odds ratio (ORs) per −10% methylation ranging from 2.03 to 12.74, depending on the specific CpG site, p < 0.0001 for all). HYAL2 methylation sites were also distinguishable between stage I&II PDAC (61 subjects) and controls (ORs per-10% methylation from 3.17 - 23.04, p < 0.0001 for all). Thus, HYAL2 methylation level enabled a very good discrimination of PDAC cases from healthy controls (area under curve (AUC) = 0.92, 95% Confidence interval (C.I.): 0.88 - 0.96), and was also powerful for the detection of PDAC at stage I&II (AUC = 0.93, 95% C.I.: 0.89 - 0.98). Moreover, the blood-based HYAL2 methylation pattern was similar among PDAC patients with differential clinical characteristics, and showed no correlation with the overall survival of PDAC patients. Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and PDAC, and provides a promising blood-based marker for the detection of PDAC.
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Affiliation(s)
- Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), NCT Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rongxi Yang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group (C055), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, 68167 Mannheim, Germany
| | - Frank Bergmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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33
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Liu Y, Wang Y, Hu F, Sun H, Zhang Z, Wang X, Luo X, Zhu L, Huang R, Li Y, Li G, Li X, Lin S, Wang F, Liu Y, Rong J, Yuan H, Zhao Y. Multiple gene-specific DNA methylation in blood leukocytes and colorectal cancer risk: a case-control study in China. Oncotarget 2017; 8:61239-61252. [PMID: 28977860 PMCID: PMC5617420 DOI: 10.18632/oncotarget.18054] [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: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022] Open
Abstract
The relationship between gene-specific DNA methylation in peripheral blood leukocytes and colorectal cancer (CRC) susceptibility is unclear. In this case-control study, the methylation status of a panel of 10 CRC-related genes in 428 CRC cases and 428 cancer-free controls were detected with methylation-sensitive high-resolution melting analysis. We calculated a weighted methylation risk score (MRS) that comprehensively combined the methylation status of the panel of 10 genes and found that the MRS_10 was significantly associated with CRC risk. Compared with MRS-Low group, MRS-High group and MRS-Medium group exhibited a 6.51-fold (95% CI, 3.77-11.27) and 3.85-fold (95% CI, 2.72-5.45) increased risk of CRC, respectively. Moreover, the CRC risk increased with increasing MRS_10 (Ptrend < 0.0001). Stratified analyses demonstrated that the significant association retained in both men and women, younger and older, and normal weight or underweight and overweight or obese subjects. The area under the receiver operating characteristic curves for the MRS_10 model was 69.04% (95% CI, 65.57-72.66%) and the combined EF and MRS_10 model yielded an AUC of 79.12% (95% CI, 76.22-82.15%). Together, the panel of 10 gene-specific DNA methylation in leukocytes was strongly associated with the risk of CRC and might be a useful marker of susceptibility for CRC.
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Affiliation(s)
- Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yibaina Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Zuoming Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xuan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xiang Luo
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Lin Zhu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Rong Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yan Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Guangxiao Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xia Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Shangqun Lin
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Fan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yanhong Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Jiesheng Rong
- Department of Orthopedics Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Huiping Yuan
- Key Laboratory of Ophthalmology, Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
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34
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FitzGerald LM, Naeem H, Makalic E, Schmidt DF, Dowty JG, Joo JE, Jung CH, Bassett JK, Dugue PA, Chung J, Lonie A, Milne RL, Wong EM, Hopper JL, English DR, Severi G, Baglietto L, Pedersen J, Giles GG, Southey MC. Genome-Wide Measures of Peripheral Blood Dna Methylation and Prostate Cancer Risk in a Prospective Nested Case-Control Study. Prostate 2017; 77:471-478. [PMID: 28116812 DOI: 10.1002/pros.23289] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Global measures of peripheral blood DNA methylation have been associated with risk of some malignancies, including breast, bladder, and gastric cancer. Here, we examined genome-wide measures of peripheral blood DNA methylation in prostate cancer and its non-aggressive and aggressive disease forms. METHODS We used a matched, case-control study of 687 incident prostate cancer samples, nested within a larger prospective cohort study. DNA methylation was measured in pre-diagnostic, peripheral blood samples using the Illumina Infinium HM450K BeadChip. Genome-wide measures of DNA methylation were computed as the median M-value of all CpG sites and according to CpG site location and regulatory function. We used conditional logistic regression to test for associations between genome-wide measures of DNA methylation and risk of prostate cancer and its subtypes, and by time between blood draw and diagnosis. RESULTS We observed no associations between the genome-wide measure of DNA methylation based on all CpG sites and risk of prostate cancer or aggressive disease. Risk of non-aggressive disease was associated with higher methylation of CpG islands (OR = 0.80; 95%CI = 0.68-0.94), promoter regions (OR = 0.79; 95%CI = 0.66-0.93), and high density CpG regions (OR = 0.80; 95%CI = 0.68-0.94). Additionally, higher methylation of all CpGs (OR = 0.66; 95%CI = 0.48-0.89), CpG shores (OR = 0.62; 95%CI = 0.45-0.84), and regulatory regions (OR = 0.68; 95% CI = 0.51-0.91) was associated with a reduced risk of overall prostate cancer within 5 years of blood draw but not thereafter. CONCLUSIONS A reduced risk of overall prostate cancer within 5 years of blood draw and non-aggressive prostate cancer was associated with higher genome-wide methylation of peripheral blood DNA. While these data have no immediate clinical utility, with further work they may provide insight into the early events of prostate carcinogenesis. Prostate 77:471-478, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Liesel M FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Cancer, Genetics, and Immunology, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Haroon Naeem
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Jihoon E Joo
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Chol-Hee Jung
- VLSCI Life Sciences Computation Centre, University of Melbourne, Carlton, VIC, Australia
| | - Julie K Bassett
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
| | | | - Jessica Chung
- VLSCI Life Sciences Computation Centre, University of Melbourne, Carlton, VIC, Australia
| | - Andrew Lonie
- VLSCI Life Sciences Computation Centre, University of Melbourne, Carlton, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Dallas R English
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Gianluca Severi
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Université Paris-Saclay, University of Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
- Gustave Roussy, F-94805, Villejuif, France
- HuGeF, Human Genetics Foundation, Torino, Italy
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Université Paris-Saclay, University of Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
| | - John Pedersen
- TissuPath, Mount Waverley, Melbourne, VIC, Australia
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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DUSP1 promoter methylation in peripheral blood leukocyte is associated with triple-negative breast cancer risk. Sci Rep 2017; 7:43011. [PMID: 28220843 PMCID: PMC5318948 DOI: 10.1038/srep43011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is one of the most common epigenetic alterations, providing important information regarding cancer risk and prognosis. A case-control study (423 breast cancer cases, 509 controls) and a case-only study (326 cases) were conducted to evaluate the association of DUSP1 promoter methylation with breast cancer risk and clinicopathological characteristics. No significant association between DUSP1 methylation in peripheral blood leukocyte (PBL) DNA and breast cancer risk was observed. DUSP1 methylation was significantly associated with ER/PR-negative status; in particular, triple-negative breast cancer patients showed the highest frequency of DUSP1 methylation in both tumour DNA and PBL DNA. Soybean intake was significantly correlated with methylated DUSP1 only in ER-negative (OR 2.978; 95% CI 1.245-7.124) and PR negative (OR 2.735; 95% CI 1.315-5.692) patients. Irregular menstruation was significantly associated with methylated DUSP1 only in ER-positive (OR 3.564; 95% CI 1.691-7.511) and PR-positive (OR 3.902, 95% CI 1.656-9.194) patients. Thus, DUSP1 methylation is a cancer-associated hypermethylation event that is closely linked with triple-negative status. Further investigations are warranted to confirm the association of environmental factors, including fruit and soybean intake, irregular menstruation, and ER/PR status, with DUSP1 methylation in breast tumour DNA.
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36
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Koestler DC, Usset J, Christensen BC, Marsit CJ, Karagas MR, Kelsey KT, Wiencke JK. DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio: An Epigenetic Tool to Explore Cancer Inflammation and Outcomes. Cancer Epidemiol Biomarkers Prev 2016; 26:328-338. [PMID: 27965295 DOI: 10.1158/1055-9965.epi-16-0461] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/27/2016] [Accepted: 10/19/2016] [Indexed: 01/04/2023] Open
Abstract
Background: The peripheral blood neutrophil-to-lymphocyte ratio (NLR) is a cytologic marker of both inflammation and poor outcomes in patients with cancer. DNA methylation is a key element of the epigenetic program defining different leukocyte subtypes and may provide an alternative to cytology in assessing leukocyte profiles. Our aim was to create a bioinformatic tool to estimate NLR using DNA methylation, and to assess its diagnostic and prognostic performance in human populations.Methods: We developed a DNA methylation-derived NLR (mdNLR) index based on normal isolated leukocyte methylation libraries and established cell-mixture deconvolution algorithms. The method was applied to cancer case-control studies of the bladder, head and neck, ovary, and breast, as well as publicly available data on cancer-free subjects.Results: Across cancer studies, mdNLR scores were either elevated in cases relative to controls, or associated with increased hazard of death. High mdNLR values (>5) were strong indicators of poor survival. In addition, mdNLR scores were elevated in males, in nonHispanic white versus Hispanic ethnicity, and increased with age. We also observed a significant interaction between cigarette smoking history and mdNLR on cancer survival.Conclusions: These results mean that our current understanding of mature leukocyte methylomes is sufficient to allow researchers and clinicians to apply epigenetically based analyses of NLR in clinical and epidemiologic studies of cancer risk and survival.Impact: As cytologic measurements of NLR are not always possible (i.e., archival blood), mdNLR, which is computed from DNA methylation signatures alone, has the potential to expand the scope of epigenome-wide association studies. Cancer Epidemiol Biomarkers Prev; 26(3); 328-38. ©2016 AACR.
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Affiliation(s)
- Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas.
| | - Joseph Usset
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire.,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, New Hampshire.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire
| | - Carmen J Marsit
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire.,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, New Hampshire.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon New Hampshire
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - John K Wiencke
- Department of Neurological Surgery, Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, California
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37
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[Effect of genetics, epigenetics and variations in the transcriptional expression of cadherin-E in breast cancer susceptibility]. BIOMEDICA 2016; 36:593-602. [PMID: 27992986 DOI: 10.7705/biomedica.v36i4.3135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/25/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Cadherin-E (CDH1) is an important regulator of epithelial-mesenchymal transition, invasion and metastasis in many carcinomas. However, germinal epimutations and mutations effect in breast cancer susceptibility is not clear. OBJECTIVE To evaluate rs334558 polymorphism, promoter methylation status and CDH1 expression profile in breast cancer patients. MATERIALS AND METHODS We collected peripheral blood samples from 102 breast cancer patients and 102 healthy subjects. The identification of rs334558 polymorphism was performed using PCR-RFLP, while methylation-specific PCR (MSP) and methylation-sensitive high-resolution melting (MS-HRM) were used to explore CDH1 methylation status; finally, CDH1 transcriptional expression profile was evaluated using RT-qPCR. RESULTS We found no association between rs334558 polymorphism and breast cancer. Aberrant promoter methylation profile was found in breast cancer patients and it was related with early cancer stages. CDH1 down-regulation was significantly associated with metastasis and promoter methylation. CONCLUSION CDH1 alterations were associated with invasion and metastasis in breast cancer. Our results offer further evidence of CDH1 relevance in breast cancer development and progression.
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Johnson KC, Houseman EA, King JE, von Herrmann KM, Fadul CE, Christensen BC. 5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients. Nat Commun 2016; 7:13177. [PMID: 27886174 PMCID: PMC5133638 DOI: 10.1038/ncomms13177] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/09/2016] [Indexed: 12/31/2022] Open
Abstract
Glioblastomas exhibit widespread molecular alterations including a highly distorted epigenome. Here, we resolve genome-wide 5-methylcytosine and 5-hydroxymethylcytosine in glioblastoma through parallel processing of DNA with bisulfite and oxidative bisulfite treatments. We apply a statistical algorithm to estimate 5-methylcytosine, 5-hydroxymethylcytosine and unmethylated proportions from methylation array data. We show that 5-hydroxymethylcytosine is depleted in glioblastoma compared with prefrontal cortex tissue. In addition, the genomic localization of 5-hydroxymethylcytosine in glioblastoma is associated with features of dynamic cell-identity regulation such as tissue-specific transcription and super-enhancers. Annotation of 5-hydroxymethylcytosine genomic distribution reveal significant associations with RNA regulatory processes, immune function, stem cell maintenance and binding sites of transcription factors that drive cellular proliferation. In addition, model-based clustering results indicate that patients with low-5-hydroxymethylcytosine patterns have significantly poorer overall survival. Our results demonstrate that 5-hydroxymethylcytosine patterns are strongly related with transcription, localizes to disease-critical genes and are associated with patient prognosis.
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Affiliation(s)
- Kevin C Johnson
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA.,Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - E Andres Houseman
- Department of Biostatistics, College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jessica E King
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA.,Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - Katharine M von Herrmann
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA.,Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
| | - Camilo E Fadul
- Department of Neurology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Brock C Christensen
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA.,Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756, USA
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Abstract
DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.
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Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
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40
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Zhang L, Liu Y, Li Y, Zhao Y, Wei W, Liu S. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy. Anal Chim Acta 2016; 933:75-81. [DOI: 10.1016/j.aca.2016.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022]
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41
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Kao WY, Yang SH, Liu WJ, Yeh MY, Lin CL, Liu CJ, Huang CJ, Lin SM, Lee SD, Chen PJ, Yu MW. Genome-wide identification of blood DNA methylation patterns associated with early-onset hepatocellular carcinoma development in hepatitis B carriers. Mol Carcinog 2016; 56:425-435. [PMID: 27254796 DOI: 10.1002/mc.22505] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/25/2016] [Accepted: 05/31/2016] [Indexed: 01/26/2023]
Abstract
The etiology of early-onset hepatocellular carcinoma (HCC) among hepatitis B virus (HBV) carriers remains unclear. DNA methylation levels in peripheral leukocytes have been associated with different environmental exposures and immune or inflammatory response. We aimed to identify methylation signatures of peripheral leukocytes that could track hepatitis B progression to HCC, especially for early-onset HCC. We first performed an epigenome-wide association analysis on 48 matched case-control pairs in a nested case-control study within a 22-yr follow-up cohort of HBV carriers. Through this analysis we found that progression to early-onset HCC involved methylation variable positions across the genome, in which a substantial proportion displayed significant variation due to HBV viral load, chronic hepatitis status, and/or leukocyte subtype composition, and these associations were significantly enriched among genes in immune pathways. Methylation at probes cg00300879, cg06872964, and cg07080864, that are located within the proximal promoter of CNKSR1, IFI44L, and PENK, respectively, was validated by bisulfite pyrosequencing and findings were replicated in a case-sibling study of early-onset HCC (134 cases vs. 174 sibling controls). Furthermore, a high methylation score, constructed using the three probes, was predictive for the risk of early-onset HCC in two datasets (adjusted-odds ratios = 0.21-0.32, P ≤ 0.0206). This association was also observed for late-onset HCC (adjusted-odds ratio = 0.42-0.47, P ≤ 0.0194) in a nested case-control study (120 cases vs. 178 controls). In prospective analysis, change in the score was detected 5-9 yr before HCC onset. Blood-based methylation profiling provides new insights into the complexity of virus-host interaction underlying HBV-related HCC, holding promise for the disease risk management. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wei-Yi Kao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Shu-Han Yang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Wen-Jie Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Meng-Yin Yeh
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chih-Lin Lin
- Department of Gastroenterology, Ren-Ai Branch, Taipei City Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chi-Jung Huang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Shi-Ming Lin
- Liver Research Unit, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taipei, Taiwan
| | - Shou-Dong Lee
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Division of Gastroenterology, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Whei Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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42
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Houseman EA, Kim S, Kelsey KT, Wiencke JK. DNA Methylation in Whole Blood: Uses and Challenges. Curr Environ Health Rep 2016; 2:145-54. [PMID: 26231364 DOI: 10.1007/s40572-015-0050-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to its convenience, the blood is commonly used in epigenomic studies, but its heterogeneous nature leads to interpretation difficulties, given the now widely recognized potential for confounding by cell composition effects. Many recent publications have reported significant associations between DNA methylation and a variety of health conditions or exposures. In this review, we summarize many of these recent publications, highlighting the findings in the context of potential cell composition effects, particularly findings that are indicative of immune response or inflammation. While there is substantial evidence for confounding by cell composition, there is nevertheless also evidence for differential DNA methylation suggestive of processes that are not cell mediated. We conclude that important biological insights still may be gained from studying DNA methylation in whole blood, either by investigating the cell composition effects themselves or processes that demonstrate associations even after adjusting for cell composition effects.
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Affiliation(s)
- E Andres Houseman
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA,
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43
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Roos L, van Dongen J, Bell CG, Burri A, Deloukas P, Boomsma DI, Spector TD, Bell JT. Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs. Clin Epigenetics 2016; 8:7. [PMID: 26798410 PMCID: PMC4721070 DOI: 10.1186/s13148-016-0172-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in blood, yet no general cancer biomarker has been identified to date. Here, we explore the potential of blood DNA methylation as a biomarker of pan-cancer (cancer of multiple different origins) in 41 female cancer discordant monozygotic (MZ) twin-pairs sampled before or after diagnosis using the Illumina HumanMethylation450 BeadChip. Results We analysed epigenome-wide DNA methylation profiles in 41 cancer discordant MZ twin-pairs with affected individuals diagnosed with tumours at different single primary sites: the breast, cervix, colon, endometrium, thyroid gland, skin (melanoma), ovary, and pancreas. No significant global differences in whole blood DNA methylation profiles were observed. Epigenome-wide analyses identified one novel pan-cancer differentially methylated position at false discovery rate (FDR) threshold of 10 % (cg02444695, P = 1.8 × 10−7) in an intergenic region 70 kb upstream of the SASH1 tumour suppressor gene, and three suggestive signals in COL11A2, AXL, and LINC00340. Replication of the four top-ranked signals in an independent sample of nine cancer-discordant MZ twin-pairs showed a similar direction of association at COL11A2, AXL, and LINC00340, and significantly greater methylation discordance at AXL compared to 480 healthy concordant MZ twin-pairs. The effects at cg02444695 (near SASH1), COL11A2, and LINC00340 were the most promising in biomarker potential because the DNA methylation differences were found to pre-exist in samples obtained prior to diagnosis and were limited to a 5-year period before diagnosis. Gene expression follow-up at the top-ranked signals in 283 healthy individuals showed correlation between blood methylation and gene expression in lymphoblastoid cell lines at PRL, and in the skin tissue at AXL. A significant enrichment of differential DNA methylation was observed in enhancer regions (P = 0.03). Conclusions We identified DNA methylation signatures in blood associated with pan-cancer, at or near SASH1, COL11A2, AXL, and LINC00340. Three of these signals were present up to 5 years prior to cancer diagnosis, highlighting the potential clinical utility of whole blood DNA methylation analysis in cancer surveillance. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0172-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonie Roos
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jenny van Dongen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Christopher G Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK ; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK ; Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK ; Epigenomic Medicine, Centre for Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
| | - Andrea Burri
- Department of Psychology, University of Zurich, Zurich, Switzerland
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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44
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Gossai A, Waterboer T, Nelson HH, Michel A, Willhauck-Fleckenstein M, Farzan SF, Hoen AG, Christensen BC, Kelsey KT, Marsit CJ, Pawlita M, Karagas MR. Seroepidemiology of Human Polyomaviruses in a US Population. Am J Epidemiol 2016; 183:61-9. [PMID: 26667254 PMCID: PMC5006224 DOI: 10.1093/aje/kwv155] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 06/09/2015] [Indexed: 12/13/2022] Open
Abstract
Polyomaviruses (PyV) are potentially tumorigenic in humans. However, limited data exist on the population seroprevalence of PyVs and individual characteristics that relate to seropositivity. Using multiplex serology, we determined the seroprevalence of 10 human PyVs (BK, JC, KI, WU, MCV, HPyV6, HPyV7, TSV, HPyV9, and HPyV10) among controls from a population-based skin cancer case-control study (n = 460) conducted in New Hampshire between 1993 and 1995. On a subset of participants (n = 194), methylation at CpG dinucleotides across the genome was measured in peripheral blood using the Illumina Infinium HumanMethylation27 BeadChip array (Illumina Inc., San Diego, California), from which lymphocyte subtype proportions were inferred. All participants were seropositive for at least 1 PyV, with seroprevalences ranging from 17.6% (HPyV9) to 99.1% (HPyV10). Seropositivity to JC, MCV, and HPyV7 increased with age. JC and TSV seropositivity were more common among men than among women. Smokers were more likely to be HPyV9-seropositive but MCV-seronegative, and HPyV7 seropositivity was associated with prolonged glucocorticoid use. Based on DNA methylation profiles, differences were observed in CD8-positive T- and B-cell proportions by BK, JC, and HPyV9 seropositivity. Our findings suggest that PyV seropositivity is common in the United States and varies by sociodemographic and biological characteristics, including those related to immune function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Margaret R. Karagas
- Correspondence to Dr. Margaret R. Karagas, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756 (e-mail: )
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45
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Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods. MICROARRAYS 2015; 4:647-70. [PMID: 27600245 PMCID: PMC4996413 DOI: 10.3390/microarrays4040647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/09/2015] [Accepted: 11/18/2015] [Indexed: 11/16/2022]
Abstract
DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies.
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46
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Pignot G, le Goux C, Bieche I. [Recent advances in bladder urothelial carcinogenesis]. Bull Cancer 2015; 102:1020-35. [PMID: 26617115 DOI: 10.1016/j.bulcan.2015.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/13/2015] [Accepted: 10/08/2015] [Indexed: 02/07/2023]
Abstract
Bladder cancer is the sixth cause of cancer mortality in France and prognosis of muscle-invasive tumors remains poor due to lack of effective treatments. Recent advances in molecular biology applied to tumors and results of recent genome-wide studies have brought a important impact on the understanding of bladder carcinogenesis. Main molecular alterations concern FGFR3, TP53 and HER2, and it is now possible to distinguish three subgroups of tumors according to molecular profile. This paper proposes a review of different genetic and epigenetic alterations in bladder cancer, their potential role as theranostic markers in clinical oncology and new targeted therapies according to the concept of personalized medicine.
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Affiliation(s)
- Géraldine Pignot
- Institut Paoli-Calmettes, service de chirurgie urologique, 13009 Marseille, France.
| | - Constance le Goux
- Université Paris Descartes, institut Curie, service de génétique, unité de pharmacogénomique, 75005 Paris, France
| | - Ivan Bieche
- Université Paris Descartes, institut Curie, service de génétique, unité de pharmacogénomique, 75005 Paris, France
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47
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Jiang W, Liu N, Chen XZ, Sun Y, Li B, Ren XY, Qin WF, Jiang N, Xu YF, Li YQ, Ren J, Cho WCS, Yun JP, Zeng J, Liu LZ, Li L, Guo Y, Mai HQ, Zeng MS, Kang TB, Jia WH, Shao JY, Ma J. Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma. Mol Cancer Ther 2015; 14:2864-73. [PMID: 26443805 DOI: 10.1158/1535-7163.mct-15-0260] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/21/2015] [Indexed: 11/16/2022]
Abstract
DNA methylation, the best known epigenetic marker, can be used as a prognostic biomarker in many cancers. We examined DNA methylation status and survival in nasopharyngeal carcinoma (NPC) patients. Aberrant DNA-methylated genes in 24 NPC tissues and 24 noncancer nasopharyngitis biopsy tissues (NCNBT) were identified using Illumina 450K BeadChip. Correlations between DNA methylation and clinical outcomes were evaluated using bisulfite pyrosequencing in 454 NPC patients. Genome-wide methylation analysis demonstrated that NPC tissues had distinct DNA methylation patterns compared with NCNBT. Among all significant CpG sites, 2,173 CpG sites with β change ≥ 0.2 (1,880 hypermethylated, 293 hypomethylated) were identified (P < 0.05). A methylation gene panel comprising six hypermethylated genes was constructed with the average Z-score method. Patients in the training cohort with high methylation had poorer disease-free survival [DFS, HR, 2.26; 95% confidence interval (CI), 1.28-4.01; P, 0.005] and overall survival (OS, HR, 2.47; 95% CI, 1.30-4.71; P, 0.006) than those with low methylation. There were similar results in the validation (DFS, HR, 2.07; 95% CI, 1.17-3.67; P, 0.013; OS, HR, 1.83; 95% CI, 1.01-3.31; P, 0.046) and independent cohorts (DFS, HR, 1.94; 95% CI, 1.08-3.47; P, 0.026; OS, HR, 2.09; 95% CI, 1.10-3.98; P, 0.022). Analysis indicated that the methylation gene panel was an independent prognostic factor. Furthermore, patients with low methylation had a favorable response to concurrent chemotherapy with an improved DFS (P = 0.045) and OS (P = 0.031), whereas patients with high methylation did not benefit from concurrent chemotherapy. The six-hypermethylated gene panel was associated with poor survival in patients with NPC, demonstrating its potential usefulness as a prognostic biomarker to clinicians in NPC management.
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Affiliation(s)
- Wei Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Xiao-Zhong Chen
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Ying Sun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Bin Li
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Xian-Yue Ren
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Wei-Feng Qin
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, People's Republic of China
| | - Ning Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ya-Fei Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jian Ren
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - William C S Cho
- Department of Radiation Oncology, Queen Elizabeth Hospital, Hong Kong, People's Republic of China
| | - Jing-Ping Yun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jing Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Li-Zhi Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Li Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Ying Guo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Hai-Qiang Mai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Mu-Sheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Tie-Bang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jian-Yong Shao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China.
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48
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Abstract
DNA methylation plays a significant role in gastric carcinogenesis. The CpG island methylator phenotype (CIMP) characterizes distinct subtypes of gastric cancer (GC) and the relationship between specific methylation patterns and clinicopathological features has been evaluated. Altered DNA methylation is also observed in Helicobacter pylori-infected gastric mucosa, and its potential utility for GC risk estimation has been suggested. The ability to detect small amounts of methylated DNA among tissues allows us to use DNA methylation as a molecular biomarker in GC in a variety of samples, including serum, plasma and gastric washes. The DNA methylation status of nontargeted tissue, particularly blood, has been associated with predisposition to GC. We focus on the recent development of DNA methylation-based biomarkers in GC.
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Affiliation(s)
- Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, 1-98 Dengakugakubo Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Tomiyasu Arisawa
- Department of Gastroenterology, Kanazawa Medical University, Ishikawa, Japan
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49
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Reis IM, Ramachandran K, Speer C, Gordian E, Singal R. Serum GADD45a methylation is a useful biomarker to distinguish benign vs malignant prostate disease. Br J Cancer 2015; 113:460-8. [PMID: 26171936 PMCID: PMC4522641 DOI: 10.1038/bjc.2015.240] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/22/2015] [Accepted: 06/09/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Prostate-specific antigen (PSA) screening for prostate cancer results in a large number of unnecessary prostate biopsies. There is a need for specific molecular markers that can be used in combination with PSA to improve the specificity of PSA screening. We examined GADD45a methylation in blood DNA as a molecular marker for prostate cancer diagnosis. METHODS The study included 82 men, with PSA levels >4 ng ml(-1) and/or abnormal digital rectal exam, who underwent prostate biopsy. We compared GADD45a methylation in DNA from serum and buffy coat in 44 patients (22 prostate cancer and 22 benign). GADD45a methylation in serum DNA was examined in 82 patients (34 cancer and 48 benign). RESULTS There was no significant difference in buffy coat GADD45a methylation between cancer and benign patients. Serum GADD45a methylation was significantly higher in cancer than in benign patients. Classification and regression tree predictive model for prostate cancer including risk groups defined by PSA, free circulating DNA (fcDNA) level and GADD45a methylation yielded specificity of 87.5%, sensitivity of 94.1% and receiver operator characteristic curve area of 0.937. CONCLUSIONS Serum GADD45a methylation in combination with PSA and fcDNA level was useful in distinguishing benign from prostate cancer patients.
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Affiliation(s)
- I M Reis
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K Ramachandran
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - C Speer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - E Gordian
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - R Singal
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Hematology/Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
- Miami VA Medical Center, Miami, FL, USA
- E-mail:
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50
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DNA methylation as a promising landscape: A simple blood test for breast cancer prediction. Tumour Biol 2015; 36:4905-12. [PMID: 26076810 DOI: 10.1007/s13277-015-3567-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/13/2015] [Indexed: 01/27/2023] Open
Abstract
Breast cancer is the most common malignancy among women worldwide. Risk assessment is one of the main services delivered by cancer clinics. Biomarker analysis on different tissues including the peripheral blood can provide crucial information. One of the potential epigenetic biomarkers (epimarkers) is introduced as the peripheral blood DNA methylation pattern. This study was conducted to evaluate the potential value of peripheral blood epimarkers as an accessible tool to predict the risk of breast cancer development. WBC's DNA was the focus of several case-control studies at both genome wide and candidate gene levels to reveal epigenetic changes accounting for predisposition to breast cancer, leading to suggest that ATM, TITF1, SFRP1, NUP155, NEUROD1, ZNF217, DBC2, DOK7 and ESR1 genes and the LINE1, Alu and Sat2 DNA elements could be considered as the potential epimarkers. To address that by which mechanisms WBC's DNA methylation patterns could be linked to the propensity to breast cancer, several contemplations have been offered. Constitutional epimutation during embryonic life, and methylation changes secondary to either environmental exposures or tumor-mediated immune response, are the two main mechanisms. One can deduce that epimarkers based on their potential properties or regulatory impacts on cancer-related genes may be employed for risk prediction, prognosis, and survival inferences that are highly required for breast cancer management toward personalized medicine.
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