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Barrett JE, Jones A, Evans I, Reisel D, Herzog C, Chindera K, Kristiansen M, Leavy OC, Manchanda R, Bjørge L, Zikan M, Cibula D, Widschwendter M. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat Commun 2022; 13:448. [PMID: 35105887 PMCID: PMC8807742 DOI: 10.1038/s41467-021-26615-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/04/2021] [Indexed: 02/03/2023] Open
Abstract
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
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Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Mark Kristiansen
- UCL Genomics, Zayed Centre for Research into Rare Disease in Children, University College London, London, WC1N 1DZ, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Department of Non-communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ranjit Manchanda
- Department of Gynaecological Oncology, Barts Health NHS Trust, Royal London Hospital, London, E1 1BB, UK
- Centre for Prevention, Detection & Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Health Services Research, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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Jareid M, Snapkov I, Holden M, Busund LTR, Lund E, Nøst TH. The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PLoS One 2021; 16:e0256442. [PMID: 34449791 PMCID: PMC8396762 DOI: 10.1371/journal.pone.0256442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/06/2021] [Indexed: 11/22/2022] Open
Abstract
Epithelial ovarian cancer (EOC) has a 5-year relative survival of 50%, partly because markers of early-stage disease are not available in current clinical diagnostics. The aim of the present study was to investigate whether EOC is associated with transcriptional profiles in blood collected up to 7 years before diagnosis. For this, we used RNA-stabilized whole blood, which contains circulating immune cells, from a sample of EOC cases from the population-based Norwegian Women and Cancer (NOWAC) postgenome cohort. We explored case-control differences in gene expression in all EOC (66 case-control pairs), as well as associations between gene expression and metastatic EOC (56 pairs), serous EOC (45 pairs, 44 of which were metastatic), and interval from blood sample collection to diagnosis (≤3 or >3 years; 34 and 31 pairs, respectively). Lastly, we assessed differential expression of genes associated with EOC in published functional genomics studies that used blood samples collected from newly diagnosed women. After adjustment for multiple testing, this nested case-control study revealed no significant case-control differences in gene expression in all EOC (false discovery rate q>0.96). With the exception of a few probes, the log2 fold change values obtained in gene-wise linear models were below ±0.2. P-values were lowest in analyses of metastatic EOC (80% of which were serous EOC). No common transcriptional profile was indicated by interval to diagnosis; when comparing the 100 genes with the lowest p-values in gene-wise tests in samples collected ≤3 and >3 years before EOC diagnosis, no overlap in these genes was observed. Among 86 genes linked to ovarian cancer in previous publications, our data contained expression values for 42, and of these, tests of LIME1, GPR162, STAB1, and SKAP1, resulted in unadjusted p<0.05. Although limited by sample size, our findings indicated less variation in blood gene expression between women with similar tumor characteristics.
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Affiliation(s)
- Mie Jareid
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Igor Snapkov
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | | | - Lill-Tove Rasmussen Busund
- Faculty of Health Sciences, Department of Medical Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Eiliv Lund
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
- Cancer Registry of Norway, Oslo, Norway
| | - Therese Haugdahl Nøst
- Faculty of Health Sciences, Department of Community Medicine, UiT – The Arctic University of Norway, Tromsø, Norway
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3
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Fang R, Yang H, Gao Y, Cao H, Goode EL, Cui Y. Gene-based mediation analysis in epigenetic studies. Brief Bioinform 2021; 22:bbaa113. [PMID: 32608480 PMCID: PMC8660163 DOI: 10.1093/bib/bbaa113] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studies with the goal to identify important DNA methylations that act as mediators between an exposure disease outcome. Specifically, we focus on gene-based high-dimensional mediation analysis implemented with kernel principal component analysis to capture potential nonlinear mediation effect. We first review the current high-dimensional mediation models and then propose two gene-based analytical approaches: gene-based high-dimensional mediation analysis based on linearity assumption between mediators and outcome (gHMA-L) and gene-based high-dimensional mediation analysis based on nonlinearity assumption (gHMA-NL). Since the underlying true mediation relationship is unknown in practice, we further propose an omnibus test of gene-based high-dimensional mediation analysis (gHMA-O) by combing gHMA-L and gHMA-NL. Extensive simulation studies show that gHMA-L performs better under the model linear assumption and gHMA-NL does better under the model nonlinear assumption, while gHMA-O is a more powerful and robust method by combining the two. We apply the proposed methods to two datasets to investigate genes whose methylation levels act as important mediators in the relationship: (1) between alcohol consumption and epithelial ovarian cancer risk using data from the Mayo Clinic Ovarian Cancer Case-Control Study and (2) between childhood maltreatment and comorbid post-traumatic stress disorder and depression in adulthood using data from the Gray Trauma Project.
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Reid BM, Fridley BL. DNA Methylation in Ovarian Cancer Susceptibility. Cancers (Basel) 2020; 13:E108. [PMID: 33396385 PMCID: PMC7795210 DOI: 10.3390/cancers13010108] [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: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations are somatically acquired over the lifetime and during neoplastic transformation but may also be inherited as widespread 'constitutional' alterations in normal tissues that can cause cancer predisposition. Epithelial ovarian cancer (EOC) has an established genetic susceptibility and mounting epidemiological evidence demonstrates that DNA methylation (DNAm) intermediates as well as independently contributes to risk. Targeted studies of known EOC susceptibility genes (CSGs) indicate rare, constitutional BRCA1 promoter methylation increases familial and sporadic EOC risk. Blood-based epigenome-wide association studies (EWAS) for EOC have detected a total of 2846 differentially methylated probes (DMPs) with 71 genes replicated across studies despite significant heterogeneity. While EWAS detect both symptomatic and etiologic DMPs, adjustments and analytic techniques may enrich risk associations, as evidenced by the detection of dysregulated methylation of BNC2-a known CSG identified by genome-wide associations studies (GWAS). Integrative genetic-epigenetic approaches have mapped methylation quantitative trait loci (meQTL) to EOC risk, revealing DNAm variations that are associated with nine GWAS loci and, further, one novel risk locus. Increasing efforts to mapping epigenome variation across populations and cell types will be key to decoding both the genomic and epigenomic causal pathways to EOC.
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Affiliation(s)
- Brett M. Reid
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
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Polymorphisms in JAK2 Gene are Associated with Production Traits and Mastitis Resistance in Dairy Cattle. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The present study was designed to investigate the effects of single nucleotide polymorphisms (SNPs) in the JAK2 gene on the production and mastitis related traits in dairy cattle. Blood and milk samples were collected from 201 lactating dairy cattle of three breeds, i.e. Holstein Friesian (HF), Jersey (J) and Achai (A) and their crosses maintained at well-established dairy farms in Khyber Pakhtunkhwa, Pakistan. Generalized linear model was used to evaluate the association between genotypes and the studied traits. A DNA pool was made from randomly selected 30 samples which revealed three SNPs, i.e. SNP 1 in 5’ upstream region (G>A, rs379754157), SNP 2 in intron 15 (A>G, rs134192265), and SNP 3 in exon 20 (A>G, rs110298451) that were further validated in the population under study using SNaPshot technique. Of the three SNPs, SNP 1 did not obey Hardy-Weinberg equilibrium (P<0.05). SNP 2 and SNP 3 were found to be in strong linkage disequilibrium and allele G was highly prevalent compared to allele A in these SNPs. in SNP 1, the GG genotype was associated with significantly (P<0.01) higher SCC, whereas SNP 2 and SNP 3 were significantly (P<0.01) associated with higher lactose percentage compared to the other geno-types. The haplogroups association analysis revealed that H1H2 (GG GG AG) has significantly lower SCC than H2H2 (GG GG GG). The results infer that JAK2 could be an important candidate gene and the studied SNPs might be useful genetic markers for production and mastitis related traits.
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Zhao Q, Zhang C, Li D, Huang X, Ren B, Yue L, Du B, Godfrey O, Zhang W. CBS gene polymorphism and promoter methylation‐mediating effects on the efficacy of folate therapy in patients with hyperhomocysteinemia. J Gene Med 2020; 22:e3156. [DOI: 10.1002/jgm.3156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 12/01/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Qinglin Zhao
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Chengda Zhang
- Department of International Medicine, Beaumont Health System Royal Oak MI USA
| | - Dankang Li
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Xiaowen Huang
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Bingnan Ren
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Limin Yue
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Binghui Du
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Opolot Godfrey
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
| | - Weidong Zhang
- Department of Epidemiology, School of Public HealthZhengzhou University Zhengzhou Henan People's Republic of China
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Souza AMD, Lopes OS, Liberato ADL, Oliveira PJRD, Herrero SST, Nascimento ALD, Longui CA, Carvalho Filho IRD, Soares LF, Silva RBD, Burbano RR, Delatorre P, Lima EM. Association between SNPs and Loss of Methylation Site on the CpG island of the Promoter Region of the Smoothened Gene, Potential Molecular Markers for Susceptibility to the Development of Basal Cell Carcinoma in the Brazilian Population. Asian Pac J Cancer Prev 2020; 21:25-29. [PMID: 31983159 PMCID: PMC7294008 DOI: 10.31557/apjcp.2020.21.1.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Objective: Perform genotyping of SNPs in the promoter region of the SMO gene in BCC samples from patients from northeastern Brazil, and to determine if there is an association of these SNPs of the gene in question with the susceptibility to the development of the BCC. Methods: 100 samples of paraffined tissue from patients with histopathological diagnosis of BCC and 100 control samples were analyzed for each polymorphism by a newly developed genotyping method, the Dideoxy Single Allele Specific – PCR. The software Bioestat - version 5.3 and Haploview 4.2 were used for the statistical analysis. For all tests a P-value <0.05 was considered significant. Results: The SNP rs538312246 is the Hardy-Weinberg equilibrium, therefore, it did not present significant association with the BCC (X² =2.343 and P<0.158). However, the CpG-SNPs rs375350898 and rs75827493 were significantly associated to the BCC in the analyzed samples (X2 = 27,740/21,500 and P <0001), the SNP rs75827493 showed a significant association with the BCC of the nodular subtype (P <0.0069). Therefore, our results suggest that SNPs rs375350898 and rs75827493 are potential molecular markers for susceptibility to BCC. Conclusion: The ability to detect SNP in a population, especially in promoter regions, has profoundly changed human genetic studies. This study allowed the understanding of the relationship between the presence of SNPs in CpG islands of the promoter region of the SMO gene can modify the methylation pattern and provide susceptibility to BCC in the population.
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Affiliation(s)
- Augusto Monteiro de Souza
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Otávio Sérgio Lopes
- Department of Dermatology, Dermatological Clinic Santa Catarina, João Pessoa - PB - Brazil.,Postgraduate Program in Health Sciences; Santa Casa School of Medical Sciences of São Paulo; Sao Paulo - SP, Brazil
| | - Andressa de Lima Liberato
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Paulo Junior Ribeiro de Oliveira
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Sylvia Satomi Takeno Herrero
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Agnaldo Luiz do Nascimento
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil
| | - Carlos Alberto Longui
- Postgraduate Program in Health Sciences; Santa Casa School of Medical Sciences of São Paulo; Sao Paulo - SP, Brazil
| | | | | | - Renally Barbosa da Silva
- Postgraduate Program in Natural Sciences and Biotechnology, Federal University of Campina Grande - UFCG, Campus de Cuité - PB, Brazil
| | | | - Plínio Delatorre
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil.,Molecular Biology Department; Federal University of Paraiba; João Pessoa - PB, Brazil
| | - Eleonidas Moura Lima
- Laboratory of Structural Molecular Biology and Oncogenetics - LBMEO, Federal University of Paraiba, João Pessoa - PB, Brazil.,Postgraduate Program in Cellular and Molecular Biology, Federal University of Paraiba, João Pessoa - PB, Brazil.,Molecular Biology Department; Federal University of Paraiba; João Pessoa - PB, Brazil
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Gao Y, Yang H, Fang R, Zhang Y, Goode EL, Cui Y. Testing Mediation Effects in High-Dimensional Epigenetic Studies. Front Genet 2019; 10:1195. [PMID: 31824577 PMCID: PMC6883258 DOI: 10.3389/fgene.2019.01195] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 10/29/2019] [Indexed: 12/24/2022] Open
Abstract
Mediation analysis has been a powerful tool to identify factors mediating the association between exposure variables and outcomes. It has been applied to various genomic applications with the hope to gain novel insights into the underlying mechanism of various diseases. Given the high-dimensional nature of epigenetic data, recent effort on epigenetic mediation analysis is to first reduce the data dimension by applying high-dimensional variable selection techniques, then conducting testing in a low dimensional setup. In this paper, we propose to assess the mediation effect by adopting a high-dimensional testing procedure which can produce unbiased estimates of the regression coefficients and can properly handle correlations between variables. When the data dimension is ultra-high, we first reduce the data dimension from ultra-high to high by adopting a sure independence screening (SIS) method. We apply the method to two high-dimensional epigenetic studies: one is to assess how DNA methylations mediate the association between alcohol consumption and epithelial ovarian cancer (EOC) status; the other one is to assess how methylation signatures mediate the association between childhood maltreatment and post-traumatic stress disorder (PTSD) in adulthood. We compare the performance of the method with its counterpart via simulation studies. Our method can be applied to other high-dimensional mediation studies where high-dimensional mediation variables are collected.
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Affiliation(s)
- Yuzhao Gao
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Haitao Yang
- Division of Health Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Ruiling Fang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yanbo Zhang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ellen L Goode
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, United States
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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Luo GF, Chen CY, Wang J, Yue HY, Tian Y, Yang P, Li YK, Li Y. FOXD3 may be a new cellular target biomarker as a hypermethylation gene in human ovarian cancer. Cancer Cell Int 2019; 19:44. [PMID: 30858761 PMCID: PMC6394078 DOI: 10.1186/s12935-019-0755-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background FOXD3 is aberrantly regulated in several tumors, but its underlying mechanisms in ovarian cancer (OC) remains largely unknown. The present study aimed to explore the role and associated mechanisms of FOXD3 in OC. Methods Microarray data from GEO was used to analyze differential CpG sites and differentially methylated regions (DMR) in tumor tissues and Illumina 450 genome-wide methylation data was employed. The FOXD3 expression level was determined through qRT-PCR and western blot analysis. Wound healing test, colony formation and flow cytometry assay were utilized to analyze cell migration, proliferation abilities, cell cycle and cell apoptosis, respectively. Finally, the effect of FOXD3 on tumor growth was investigated through in vivo xenograft experiments. Results GEO data analysis showed that FOXD3 was hypermethylated in OC tissues. Also, qRT-PCR revealed that FOXD3 was low expressed and methylation-specific PCR (MSP) confirmed that the methylation level of FOXD3 was hypermethylated. Combined treatment of 5-aza-2′-deoxycytidine (5-Aza-dC) could synergistically restored FOXD3 expression. Finally, in vitro and in vivo experiments showed that demethylated FOXD3 decreased cell proliferation and migration abilities, and increased the cell apoptosis. In vivo experiment detected that demethylated FOXD3 restrained tumor growth. Conclusions FOXD3 could act as a tumor suppressor to inhibit cell proliferation, migration and promote cell apoptosis in OC cells. Electronic supplementary material The online version of this article (10.1186/s12935-019-0755-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gui-Fang Luo
- 1Department of Gynecology, The First Affiliated Hospital of University of South China, Hengyang, 421001 People's Republic of China
| | - Chang-Ye Chen
- 1Department of Gynecology, The First Affiliated Hospital of University of South China, Hengyang, 421001 People's Republic of China
| | - Juan Wang
- 2Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, University of South China, Hengyang, 421001 Hunan People's Republic of China
| | - Hai-Yan Yue
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yong Tian
- 4Department of Obstetrics and Gynecology, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, 445000 Hubei People's Republic of China
| | - Ping Yang
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yu-Kun Li
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yan Li
- 5Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, No. 932 South Lushan Road, Yuelu District, Changsha, 410013 Hunan People's Republic of China.,6Reproductive and Genetic Hospital of Citic-Xiangya, No. 84 Xiangya Road, Changsha, 410078 Hunan People's Republic of China
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Yang Y, Wu L, Shu X, Lu Y, Shu XO, Cai Q, Beeghly-Fadiel A, Li B, Ye F, Berchuck A, Anton-Culver H, Banerjee S, Benitez J, Bjørge L, Brenton JD, Butzow R, Campbell IG, Chang-Claude J, Chen K, Cook LS, Cramer DW, deFazio A, Dennis J, Doherty JA, Dörk T, Eccles DM, Edwards DV, Fasching PA, Fortner RT, Gayther SA, Giles GG, Glasspool RM, Goode EL, Goodman MT, Gronwald J, Harris HR, Heitz F, Hildebrandt MA, Høgdall E, Høgdall CK, Huntsman DG, Kar SP, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Koushik A, Lambrechts D, Le ND, Levine DA, Massuger LF, Matsuo K, May T, McNeish IA, Menon U, Modugno F, Monteiro AN, Moorman PG, Moysich KB, Ness RB, Nevanlinna H, Olsson H, Onland-Moret NC, Park SK, Paul J, Pearce CL, Pejovic T, Phelan CM, Pike MC, Ramus SJ, Riboli E, Rodriguez-Antona C, Romieu I, Sandler DP, Schildkraut JM, Setiawan VW, Shan K, Siddiqui N, Sieh W, Stampfer MJ, Sutphen R, Swerdlow AJ, Szafron LM, Teo SH, Tworoger SS, Tyrer JP, Webb PM, Wentzensen N, White E, Willett WC, Wolk A, Woo YL, Wu AH, Yan L, Yannoukakos D, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long J. Genetic Data from Nearly 63,000 Women of European Descent Predicts DNA Methylation Biomarkers and Epithelial Ovarian Cancer Risk. Cancer Res 2019; 79:505-517. [PMID: 30559148 PMCID: PMC6359948 DOI: 10.1158/0008-5472.can-18-2726] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
DNA methylation is instrumental for gene regulation. Global changes in the epigenetic landscape have been recognized as a hallmark of cancer. However, the role of DNA methylation in epithelial ovarian cancer (EOC) remains unclear. In this study, high-density genetic and DNA methylation data in white blood cells from the Framingham Heart Study (N = 1,595) were used to build genetic models to predict DNA methylation levels. These prediction models were then applied to the summary statistics of a genome-wide association study (GWAS) of ovarian cancer including 22,406 EOC cases and 40,941 controls to investigate genetically predicted DNA methylation levels in association with EOC risk. Among 62,938 CpG sites investigated, genetically predicted methylation levels at 89 CpG were significantly associated with EOC risk at a Bonferroni-corrected threshold of P < 7.94 × 10-7. Of them, 87 were located at GWAS-identified EOC susceptibility regions and two resided in a genomic region not previously reported to be associated with EOC risk. Integrative analyses of genetic, methylation, and gene expression data identified consistent directions of associations across 12 CpG, five genes, and EOC risk, suggesting that methylation at these 12 CpG may influence EOC risk by regulating expression of these five genes, namely MAPT, HOXB3, ABHD8, ARHGAP27, and SKAP1. We identified novel DNA methylation markers associated with EOC risk and propose that methylation at multiple CpG may affect EOC risk via regulation of gene expression. SIGNIFICANCE: Identification of novel DNA methylation markers associated with EOC risk suggests that methylation at multiple CpG may affect EOC risk through regulation of gene expression.
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Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, California
| | - Susana Banerjee
- Gynaecology Unit, Royal Marsden Hospital, London, United Kingdom
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Line Bjørge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Center for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ralf Butzow
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ian G Campbell
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kexin Chen
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Linda S Cook
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico
- Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, Alberta, Canada
| | - Daniel W Cramer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Digna Velez Edwards
- Vanderbilt Epidemiology Center, Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | | | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Holly R Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Michelle A Hildebrandt
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
- OVCARE, Vancouver Coastal Health Research Centre, Vancouver General Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Linda E Kelemen
- Hollings Cancer Center and Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anita Koushik
- CHUM Research Centre (CRCHUM) and Département de Médicine Sociale et Préventive, Université de Montréal, Montréal, Quebec, Canada
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB and Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Gynecologic Oncology, Laura and Isaac Pearlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Leon F Massuger
- Department of Gynaecology, Radboud Institute for Molecular Life sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Iain A McNeish
- Department Surgery & Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, United Kingdom
| | - Francesmary Modugno
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Patricia G Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina
| | - Kirsten B Moysich
- Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Roberta B Ness
- School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Utrecht, UMC Utrecht, Utrecht, the Netherlands
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - James Paul
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales Sydney, Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Elio Riboli
- Imperial College London, London, United Kingdom
| | - Cristina Rodriguez-Antona
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Isabelle Romieu
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Veronica W Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kang Shan
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Meir J Stampfer
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, Florida
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Lukasz M Szafron
- Department of Immunology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
- Research Institute and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily White
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Walter C Willett
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yin Ling Woo
- Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Li Yan
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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12
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Hentze JL, Høgdall CK, Høgdall EV. Methylation and ovarian cancer: Can DNA methylation be of diagnostic use? Mol Clin Oncol 2019; 10:323-330. [PMID: 30847169 DOI: 10.3892/mco.2019.1800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a silent killer and, due to late diagnosis and frequent chemo resistance in patients, the primary cause of fatality amongst the various types of gynecological cancer. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, thereby saving lives. Biomarkers could also improve treatment, by predicting which patients will benefit from specific treatment strategies. DNA methylation is an epigenetic mechanism, and 'methylation imbalance' is characteristic of cancer. Previous research suggests that changes in DNA methylation can be used diagnostically, and that they may predict resistance to treatment. This paper gives an up-to-date overview of research investigating the potential of DNA methylation-based markers for diagnostics, prognostics, screening and prediction of drug resistance for ovarian cancer patients. DNA methylation cancer-biomarkers may be useful for cancer treatment, particularly since they are chemically stable and since cancer-associated changes in methylation typically precedes tumor growth. DNA methylation markers could improve diagnosis and treatment and might even be used for screening in the future. Furthermore, DNA methylation biomarkers could facilitate the development of precision medicine. However, at this point no biomarkers for ovarian cancer have a sufficient combination of sensitivity and specificity in a clinical setting. A reason for this is that most studies have focused on a single or a few methylation sites. More large screenings and genome-wide studies must be performed to increase the chance of identifying a DNA methylation marker which can identify ovarian cancer.
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Affiliation(s)
- Julie L Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Claus K Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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13
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Hemani G, Bowden J, Davey Smith G. Evaluating the potential role of pleiotropy in Mendelian randomization studies. Hum Mol Genet 2018; 27:R195-R208. [PMID: 29771313 PMCID: PMC6061876 DOI: 10.1093/hmg/ddy163] [Citation(s) in RCA: 790] [Impact Index Per Article: 131.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 02/06/2023] Open
Abstract
Pleiotropy, the phenomenon of a single genetic variant influencing multiple traits, is likely widespread in the human genome. If pleiotropy arises because the single nucleotide polymorphism (SNP) influences one trait, which in turn influences another ('vertical pleiotropy'), then Mendelian randomization (MR) can be used to estimate the causal influence between the traits. Of prime focus among the many limitations to MR is the unprovable assumption that apparent pleiotropic associations are mediated by the exposure (i.e. reflect vertical pleiotropy), and do not arise due to SNPs influencing the two traits through independent pathways ('horizontal pleiotropy'). The burgeoning treasure trove of genetic associations yielded through genome wide association studies makes for a tantalizing prospect of phenome-wide causal inference. Recent years have seen substantial attention devoted to the problem of horizontal pleiotropy, and in this review we outline how newly developed methods can be used together to improve the reliability of MR.
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Affiliation(s)
- Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol
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14
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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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15
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Wu D, Yang H, Winham SJ, Natanzon Y, Koestler DC, Luo T, Fridley BL, Goode EL, Zhang Y, Cui Y. Mediation analysis of alcohol consumption, DNA methylation, and epithelial ovarian cancer. J Hum Genet 2018; 63:339-348. [PMID: 29321518 DOI: 10.1038/s10038-017-0385-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 01/12/2023]
Abstract
Epigenetic factors and consumption of alcohol, which suppresses DNA methylation, may influence the development and progression of epithelial ovarian cancer (EOC). However, there is a lack of understanding whether these factors interact to affect the EOC risk. In this study, we aimed to gain insight into this relationship by identifying leukocyte-derived DNA methylation markers acting as potential mediators of alcohol-associated EOC. We implemented a causal inference test (CIT) and the VanderWeele and Vansteelandt multiple mediator model to examine CpG sites that mediate the association between alcohol consumption and EOC risk. We modified one step of the CIT by adopting a high-dimensional inference procedure. The data were based on 196 cases and 202 age-matched controls from the Mayo Clinic Ovarian Cancer Case-Control Study. Implementation of the CIT test revealed two CpG sites (cg09358725, cg11016563), which represent potential mediators of the relationship between alcohol consumption and EOC case-control status. Implementation of the VanderWeele and Vansteelandt multiple mediator model further revealed that these two CpGs were the key mediators. Decreased methylation at both CpGs was more common in cases who drank alcohol at the time of enrollment vs. those who did not. cg11016563 resides in TRPC6 which has been previously shown to be overexpressed in EOC. These findings suggest two CpGs may serve as novel biomarkers for EOC susceptibility.
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Affiliation(s)
- Dongyan Wu
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.,Department of Medical Affairs, Yanqing Hospital of Peking University Third Hospital, Beijing, 102100, China
| | - Haitao Yang
- Division of Health Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Stacey J Winham
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yanina Natanzon
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Devin C Koestler
- Department of Biostatistics, The University of Kansas Medical center, Kansas City, KS, 66160, USA
| | - Tiane Luo
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Ellen L Goode
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yanbo Zhang
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Yuehua Cui
- Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China. .,Department of Statistics and Probability, Michigan State University, East Lansing, MI, 48824, USA.
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16
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Hemani G, Tilling K, Davey Smith G. Orienting the causal relationship between imprecisely measured traits using GWAS summary data. PLoS Genet 2017; 13:e1007081. [PMID: 29149188 PMCID: PMC5711033 DOI: 10.1371/journal.pgen.1007081] [Citation(s) in RCA: 1022] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 12/01/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022] Open
Abstract
Inference about the causal structure that induces correlations between two traits can be achieved by combining genetic associations with a mediation-based approach, as is done in the causal inference test (CIT). However, we show that measurement error in the phenotypes can lead to the CIT inferring the wrong causal direction, and that increasing sample sizes has the adverse effect of increasing confidence in the wrong answer. This problem is likely to be general to other mediation-based approaches. Here we introduce an extension to Mendelian randomisation, a method that uses genetic associations in an instrumentation framework, that enables inference of the causal direction between traits, with some advantages. First, it can be performed using only summary level data from genome-wide association studies; second, it is less susceptible to bias in the presence of measurement error or unmeasured confounding. We apply the method to infer the causal direction between DNA methylation and gene expression levels. Our results demonstrate that, in general, DNA methylation is more likely to be the causal factor, but this result is highly susceptible to bias induced by systematic differences in measurement error between the platforms, and by horizontal pleiotropy. We emphasise that, where possible, implementing MR and appropriate sensitivity analyses alongside other approaches such as CIT is important to triangulate reliable conclusions about causality. Understanding the causal relationships between pairs of traits is crucial for unravelling the causes of disease. To this end, results from genome-wide association studies are valuable because if a trait is known to be influenced by a genetic variant then this knowledge can be used to test the trait’s causal influences on other traits and diseases. Here we discuss scenarios where the nature of the genetic association with the causal trait can lead existing causal inference methods to give the wrong direction of causality. We introduce a new method that can be applied to summary level data and is potentially less susceptible to problems such as measurement error, and apply it to evaluate the causal relationships between DNA methylation levels and gene expression. While our results show that DNA methylation is more likely to be the causal factor, we point out that is it crucial to acknowledge that systematic differences in measurement error between the platforms could influence such conclusions.
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Affiliation(s)
- Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, School of Social and Community Medicine, Bristol, United Kingdom
- * E-mail:
| | - Kate Tilling
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, School of Social and Community Medicine, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, School of Social and Community Medicine, Bristol, United Kingdom
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17
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Li L, Zheng H, Huang Y, Huang C, Zhang S, Tian J, Li P, Sood AK, Zhang W, Chen K. DNA methylation signatures and coagulation factors in the peripheral blood leucocytes of epithelial ovarian cancer. Carcinogenesis 2017. [PMID: 28637314 DOI: 10.1093/carcin/bgx057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Solid tumors are increasingly recognized as a systemic disease that is manifested by changes in DNA, RNA, proteins and metabolites in the blood. Whereas many studies have reported gene mutation events in the circulation, few studies have focused on epigenetic DNA methylation markers. To identify DNA methylation biomarkers in peripheral blood for ovarian cancer, we performed a two-stage epigenome-wide association study. In the discovery stage, we measured genome wide DNA methylation for 485 000 CpG sites in peripheral blood in 24 epithelial ovarian cancer (EOC) cases and 24 age-matched healthy controls. We selected 96 significantly differentially methylated CpG sites for validation using Illumina's Custom VeraCode methylation assay in 206 EOC cases and 205 controls and 46 CpG sites validated in the independent replication samples. A set of 6 of these 46 CpG sites was found by the receiver operating characteristic analysis to have a prediction accuracy of 77.3% for all EOC (95% confidence interval: 72.9-81.8%). Pathway analysis of the genes associated with the 46 CpG sites revealed an enrichment of immune system process genes, including LYST (cg16962115, FDR = 1.24E-04), CADM1 (cg21933078, FDR = 1.22E-02) and NFATC1 (cg06784563, FDR = 1.46E-02). Furthermore, DNA methylation status in peripheral blood was correlated with platelet parameters/coagulation factor levels. This study discovered a panel of epigenetic liquid biopsy markers closely associated with overall immunologic conditions and platelet parameters/coagulation systems of the patients for detection of all stages and subtypes of EOC.
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Affiliation(s)
- Lian Li
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yubei Huang
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Caiyun Huang
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shuang Zhang
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Jing Tian
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Pei Li
- Department of Epidemiology and Biostatistics, Department of Urology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Anil K Sood
- Gynecologic Oncology and Reproductive Medicine and Center for RNAi and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157, USA
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18
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Ainsworth HF, Shin SY, Cordell HJ. A comparison of methods for inferring causal relationships between genotype and phenotype using additional biological measurements. Genet Epidemiol 2017; 41:577-586. [PMID: 28691305 PMCID: PMC5655748 DOI: 10.1002/gepi.22061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 11/23/2022]
Abstract
Genome wide association studies (GWAS) have been very successful over the last decade at identifying genetic variants associated with disease phenotypes. However, interpretation of the results obtained can be challenging. Incorporation of further relevant biological measurements (e.g. ‘omics’ data) measured in the same individuals for whom we have genotype and phenotype data may help us to learn more about the mechanism and pathways through which causal genetic variants affect disease. We review various methods for causal inference that can be used for assessing the relationships between genetic variables, other biological measures, and phenotypic outcome, and present a simulation study assessing the performance of the methods under different conditions. In general, the methods we considered did well at inferring the causal structure for data simulated under simple scenarios. However, the presence of an unknown and unmeasured common environmental effect could lead to spurious inferences, with the methods we considered displaying varying degrees of robustness to this confounder. The use of causal inference techniques to integrate omics and GWAS data has the potential to improve biological understanding of the pathways leading to disease. Our study demonstrates the suitability of various methods for performing causal inference under several biologically plausible scenarios.
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Affiliation(s)
- Holly F Ainsworth
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - So-Youn Shin
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, United Kingdom
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
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19
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Zhou F, Shen C, Xu J, Gao J, Zheng X, Ko R, Dou J, Cheng Y, Zhu C, Xu S, Tang X, Zuo X, Yin X, Cui Y, Sun L, Tsoi LC, Hsu YH, Yang S, Zhang X. Epigenome-wide association data implicates DNA methylation-mediated genetic risk in psoriasis. Clin Epigenetics 2016; 8:131. [PMID: 27980695 PMCID: PMC5139011 DOI: 10.1186/s13148-016-0297-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Psoriasis is a chronic inflammatory skin disease characterized by epidermal hyperproliferation and altered keratinocyte differentiation and inflammation and is caused by the interplay of genetic and environmental factors. Previous studies have revealed that DNA methylation (DNAm) and genetic makers are closely associated with psoriasis, and strong evidences have shown that DNAm can be controlled by genetic factors, which attracted us to evaluate the relationship among DNAm, genetic makers, and disease status. METHODS We utilized the genome-wide methylation data of psoriatic skin (PP, N = 114) and unaffected control skin (NN, N = 62) tissue samples in our previous study, and we performed whole-genome genotyping with peripheral blood of the same samples to evaluate the underlying genetic effect on skin DNA methylation. Causal inference test (CIT) was used to assess whether DNAm regulate genetic variation and gain a better understanding of the epigenetic basis of psoriasis susceptibility. RESULTS We identified 129 SNP-CpG pairs achieving the significant association threshold, which constituted 28 unique methylation quantitative trait loci (MethQTL) and 34 unique CpGs. There are 18 SNPs were associated with psoriasis at a Bonferoni-corrected P < 0.05, and these 18 SNPs formed 93 SNP-CpG pairs with 17 unique CpG sites. We found that 11 of 93 SNP-CpG pairs, composed of 5 unique SNPs and 3 CpG sites, presented a methylation-mediated relationship between SNPs and psoriasis. The 3 CpG sites were located on the body of C1orf106, the TSS1500 promoter region of DMBX1 and the body of SIK3. CONCLUSIONS This study revealed that DNAm of some genes can be controlled by genetic factors and also mediate risk variation for psoriasis in Chinese Han population and provided novel molecular insights into the pathogenesis of psoriasis.
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Affiliation(s)
- Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Changbing Shen
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA 02131 USA.,Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115 USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jingkai Xu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Jing Gao
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601 Anhui China
| | - Xiaodong Zheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Randy Ko
- Department of Biochemistry, University of New Mexico, Albuquerque, NM 87131 NM USA
| | - Jinfa Dou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Yuyan Cheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Shuangjun Xu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianfa Tang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianbo Zuo
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xianyong Yin
- Department of Genetics, and Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517 USA
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, 100029 China
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.,Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA 02131 USA.,Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115 USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sen Yang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Meishan Road 81, Hefei, 230032 Anhui Province China.,The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Anhui, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, 230032 Anhui China.,Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University, Hefei, 230601 Anhui China
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20
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Richmond RC, Hemani G, Tilling K, Davey Smith G, Relton CL. Challenges and novel approaches for investigating molecular mediation. Hum Mol Genet 2016; 25:R149-R156. [PMID: 27439390 PMCID: PMC5036871 DOI: 10.1093/hmg/ddw197] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 06/06/2016] [Accepted: 06/20/2016] [Indexed: 11/12/2022] Open
Abstract
Understanding mediation is useful for identifying intermediates lying between an exposure and an outcome which, when intervened upon, will block (some or all of) the causal pathway between the exposure and outcome. Mediation approaches used in conventional epidemiology have been adapted to understanding the role of molecular intermediates in situations of high-dimensional omics data with varying degrees of success. In particular, the limitations of observational epidemiological study including confounding, reverse causation and measurement error can afflict conventional mediation approaches and may lead to incorrect conclusions regarding causal effects. Solutions to analysing mediation which overcome these problems include the use of instrumental variable methods such as Mendelian randomization, which may be applied to evaluate causality in increasingly complex networks of omics data.
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Affiliation(s)
- R C Richmond
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, UK
| | - G Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, UK
| | - K Tilling
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, UK
| | - G Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, UK
| | - C L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, UK
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21
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Chen X, Chen X, Xu Y, Yang W, Wu N, Ye H, Yang JY, Hong Q, Xin Y, Yang MQ, Deng Y, Duan S. Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease. Hum Genomics 2016; 10 Suppl 2:21. [PMID: 27461004 PMCID: PMC4965732 DOI: 10.1186/s40246-016-0067-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Chronic inflammation has been widely considered to be the major risk factor of coronary heart disease (CHD). The goal of our study was to explore the possible association with CHD for inflammation-related single nucleotide polymorphisms (SNPs) involved in cytosine-phosphate-guanine (CpG) dinucleotides. A total of 784 CHD patients and 739 non-CHD controls were recruited from Zhejiang Province, China. Using the Sequenom MassARRAY platform, we measured the genotypes of six inflammation-related CpG-SNPs, including IL1B rs16944, IL1R2 rs2071008, PLA2G7 rs9395208, FAM5C rs12732361, CD40 rs1800686, and CD36 rs2065666). Allele and genotype frequencies were compared between CHD and non-CHD individuals using the CLUMP22 software with 10,000 Monte Carlo simulations. Results Allelic tests showed that PLA2G7 rs9395208 and CD40 rs1800686 were significantly associated with CHD. Moreover, IL1B rs16944, PLA2G7 rs9395208, and CD40 rs1800686 were shown to be associated with CHD under the dominant model. Further gender-based subgroup tests showed that one SNP (CD40 rs1800686) and two SNPs (FAM5C rs12732361 and CD36 rs2065666) were associated with CHD in females and males, respectively. And the age-based subgroup tests indicated that PLA2G7 rs9395208, IL1B rs16944, and CD40 rs1800686 were associated with CHD among individuals younger than 55, younger than 65, and over 65, respectively. Conclusions In conclusion, all the six inflammation-related CpG-SNPs (rs16944, rs2071008, rs12732361, rs2065666, rs9395208, and rs1800686) were associated with CHD in the combined or subgroup tests, suggesting an important role of inflammation in the risk of CHD.
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Affiliation(s)
- Xiaomin Chen
- Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Xiaoying Chen
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yan Xu
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - William Yang
- Texas Advanced Computing Center, University of Texas at Austin, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Nan Wu
- Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, 315010, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huadan Ye
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jack Y Yang
- MidSouth Bioinformatics Center, Department of Information Science, George Washington Donaghey College of Engineering and Information Science, and Joint Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2881 S. University Ave, Little Rock, AR, 72204, USA
| | - Qingxiao Hong
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yanfei Xin
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310007, China
| | - Mary Qu Yang
- MidSouth Bioinformatics Center, Department of Information Science, George Washington Donaghey College of Engineering and Information Science, and Joint Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2881 S. University Ave, Little Rock, AR, 72204, USA
| | - Youping Deng
- Medical College, Wuhan University of Science and Technology, Wuhan, 430064, China.,Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Shiwei Duan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
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22
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López de Maturana E, Pineda S, Brand A, Van Steen K, Malats N. Toward the integration of Omics data in epidemiological studies: still a "long and winding road". Genet Epidemiol 2016; 40:558-569. [PMID: 27432111 DOI: 10.1002/gepi.21992] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 05/22/2016] [Accepted: 06/05/2016] [Indexed: 12/23/2022]
Abstract
Primary and secondary prevention can highly benefit a personalized medicine approach through the accurate discrimination of individuals at high risk of developing a specific disease from those at moderate and low risk. To this end precise risk prediction models need to be built. This endeavor requires a precise characterization of the individual exposome, genome, and phenome. Massive molecular omics data representing the different layers of the biological processes of the host and the nonhost will enable to build more accurate risk prediction models. Epidemiologists aim to integrate omics data along with important information coming from other sources (questionnaires, candidate markers) that has been proved to be relevant in the discrimination risk assessment of complex diseases. However, the integrative models in large-scale epidemiologic research are still in their infancy and they face numerous challenges, some of them at the analytical stage. So far, there are a small number of studies that have integrated more than two omics data sets, and the inclusion of non-omics data in the same models is still missing in most of studies. In this contribution, we aim at approaching the omics and non-omics data integration from the epidemiology scope by considering the "massive" inclusion of variables in the risk assessment and predictive models. We also provide already available examples of integrative contributions in the field, propose analytical strategies that allow considering both omics and non-omics data in the models, and finally review the challenges imbedding this type of research.
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Affiliation(s)
| | - Sílvia Pineda
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela Brand
- Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
| | - Kristel Van Steen
- Laboratory of Biostatistics, Biomedicine and Bioinformatics, GIGA, University of Liège, Belgium
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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23
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Allele-specific DNA methylation reinforces PEAR1 enhancer activity. Blood 2016; 128:1003-12. [PMID: 27313330 DOI: 10.1182/blood-2015-11-682153] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 06/13/2016] [Indexed: 01/07/2023] Open
Abstract
Genetic variation in the PEAR1 locus is linked to platelet reactivity and cardiovascular disease. The major G allele of rs12041331, an intronic cytosine guanine dinucleotide-single-nucleotide polymorphism (CpG-SNP), is associated with higher PEAR1 expression in platelets and endothelial cells than the minor A allele. The molecular mechanism underlying this difference remains elusive. We have characterized the histone modification profiles of the intronic region surrounding rs12041331 and identified H3K4Me1 enhancer-specific enrichment for the region that covers the CpG-SNP. Interestingly, methylation studies revealed that the CpG site is fully methylated in leukocytes of GG carriers. Nuclear protein extracts from megakaryocytes, endothelial cells, vs control HEK-293 cells show a 3-fold higher affinity for the methylated G allele compared with nonmethylated G or A alleles in a gel electrophoretic mobility shift assay. To understand the positive relationship between methylation and gene expression, we studied DNA methylation at 4 different loci of PEAR1 during in vitro megakaryopoiesis. During differentiation, the CpG-SNP remained fully methylated, while we observed rapid methylation increases at the CpG-island overlapping the first 5'-untranslated region exon, paralleling the increased PEAR1 expression. In the same region, A-allele carriers of rs12041331 showed significantly lower DNA methylation at CGI1 compared with GG homozygote. This CpG-island contains binding sites for the methylation-sensitive transcription factor CTCF, whose binding is known to play a role in enhancer activation and/or repression. In conclusion, we report the molecular characterization of the first platelet function-related CpG-SNP, a genetic predisposition that reinforces PEAR1 enhancer activity through allele-specific DNA methylation.
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Lin X, Hu D, Chen G, Shi Y, Zhang H, Wang X, Guo X, Lu L, Black D, Zheng XW, Luo X. Associations of THBS2 and THBS4 polymorphisms to gastric cancer in a Southeast Chinese population. Cancer Genet 2016; 209:215-22. [PMID: 27160021 DOI: 10.1016/j.cancergen.2016.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 12/28/2022]
Abstract
Thrombospondin-2 (THBS2) and Thrombospondin-4 (THBS4) play an important role in cancer development and progression. However, genetic evidence for their roles in gastric cancer (GC) is lacking. The aim of this study was to explore the association of THBS2/THBS4 polymorphisms with risk and clinicopathological features of GC in a Southeast Chinese population. Eight tagging SNPs in THBS2 and THBS4 were genotyped in 761 GC cases and 739 controls from Chinese case-control sets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. THBS2/THBS4 mRNA expression was studied in 82 human GC tumors and in mouse stomach tissues by real-time PCR. We found that both THBS2 and THBS4 were abundantly expressed in mouse stomach. THBS4 mRNA expression in human stomach was associated with tumor size (P = 0.002) and tumor-node-metastasis (TNM) (P = 0.010), and THBS2 mRNA expression was associated with the TNM (P = 0.010). Patients with the rs77878919^AG genotype were more prone to developing diffuse-type GC. THBS4 SNPs (rs77878919 and rs7736549) had a modest cumulative effect on the risk of poor prognosis (TNM), with that risk in the highest trend for patients carrying both these unfavorable genotypes. In addition, individuals carrying the THBS4 rs10474606 variant homozygous AA had a modest reduced GC risk. We conclude that THBS2/THBS4 may be functional in playing important role in GC, which was supported by the evidence of the mRNA overexpression in GC and the modest associations of THBS2/THBS4 polymorphisms to GC. These findings might be useful for risk assessment and prognosis prediction of GC.
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Affiliation(s)
- Xiandong Lin
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China; Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian 350014, China
| | - Don Hu
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Gang Chen
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Yi Shi
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Hejun Zhang
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Xiaojiang Wang
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Xiaoyun Guo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Lu Lu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong 226001, China; Department of Genetics, Genomics, Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Dennis Black
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xiong-Wei Zheng
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China; Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian 350014, China.
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
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Koestler DC, Jones MJ, Usset J, Christensen BC, Butler RA, Kobor MS, Wiencke JK, Kelsey KT. Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformatics 2016; 17:120. [PMID: 26956433 PMCID: PMC4782368 DOI: 10.1186/s12859-016-0943-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/09/2016] [Indexed: 12/16/2022] Open
Abstract
Background Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogenous biospecimens offer a promising solution, however the performance of such methods depends entirely on the library of methylation markers being used for deconvolution. Here, we introduce a novel algorithm for Identifying Optimal Libraries (IDOL) that dynamically scans a candidate set of cell-specific methylation markers to find libraries that optimize the accuracy of cell fraction estimates obtained from cell mixture deconvolution. Results Application of IDOL to training set consisting of samples with both whole-blood DNA methylation data (Illumina HumanMethylation450 BeadArray (HM450)) and flow cytometry measurements of cell composition revealed an optimized library comprised of 300 CpG sites. When compared existing libraries, the library identified by IDOL demonstrated significantly better overall discrimination of the entire immune cell landscape (p = 0.038), and resulted in improved discrimination of 14 out of the 15 pairs of leukocyte subtypes. Estimates of cell composition across the samples in the training set using the IDOL library were highly correlated with their respective flow cytometry measurements, with all cell-specific R2>0.99 and root mean square errors (RMSEs) ranging from [0.97 % to 1.33 %] across leukocyte subtypes. Independent validation of the optimized IDOL library using two additional HM450 data sets showed similarly strong prediction performance, with all cell-specific R2>0.90 and RMSE<4.00 %. In simulation studies, adjustments for cell composition using the IDOL library resulted in uniformly lower false positive rates compared to competing libraries, while also demonstrating an improved capacity to explain epigenome-wide variation in DNA methylation within two large publicly available HM450 data sets. Conclusions Despite consisting of half as many CpGs compared to existing libraries for whole blood mixture deconvolution, the optimized IDOL library identified herein resulted in outstanding prediction performance across all considered data sets and demonstrated potential to improve the operating characteristics of EWAS involving adjustments for cell distribution. In addition to providing the EWAS community with an optimized library for whole blood mixture deconvolution, our work establishes a systematic and generalizable framework for the assembly of libraries that improve the accuracy of cell mixture deconvolution. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0943-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - Joseph Usset
- Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, 66160, KS, USA.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA. .,Department of Pharmacology and Toxicology, Dartmouth College, 1 Rope Ferry Rd., Hanover, 03755, NH, USA. .,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr., Lebanon, 03756, NH, USA.
| | - Rondi A Butler
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA.
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, The University of British Columbia, 950 West 28th Ave., Vancouver, V5Z 4H4, BC, Canada.
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, 505 Parnassus Ave., San Francisco, 94143, CA, USA.
| | - Karl T Kelsey
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St., Providence, 02912, RI, USA. .,Department of Epidemiology, Brown University, 121 South Main St., Providence, 02912, RI, USA.
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Shiwa Y, Hachiya T, Furukawa R, Ohmomo H, Ono K, Kudo H, Hata J, Hozawa A, Iwasaki M, Matsuda K, Minegishi N, Satoh M, Tanno K, Yamaji T, Wakai K, Hitomi J, Kiyohara Y, Kubo M, Tanaka H, Tsugane S, Yamamoto M, Sobue K, Shimizu A. Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols. PLoS One 2016; 11:e0147519. [PMID: 26799745 PMCID: PMC4723336 DOI: 10.1371/journal.pone.0147519] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022] Open
Abstract
Differences in DNA collection protocols may be a potential confounder in epigenome-wide association studies (EWAS) using a large number of blood specimens from multiple biobanks and/or cohorts. Here we show that pre-analytical procedures involved in DNA collection can induce systematic bias in the DNA methylation profiles of blood cells that can be adjusted by cell-type composition variables. In Experiment 1, whole blood from 16 volunteers was collected to examine the effect of a 24 h storage period at 4°C on DNA methylation profiles as measured using the Infinium HumanMethylation450 BeadChip array. Our statistical analysis showed that the P-value distribution of more than 450,000 CpG sites was similar to the theoretical distribution (in quantile-quantile plot, λ = 1.03) when comparing two control replicates, which was remarkably deviated from the theoretical distribution (λ = 1.50) when comparing control and storage conditions. We then considered cell-type composition as a possible cause of the observed bias in DNA methylation profiles and found that the bias associated with the cold storage condition was largely decreased (λadjusted = 1.14) by taking into account a cell-type composition variable. As such, we compared four respective sample collection protocols used in large-scale Japanese biobanks or cohorts as well as two control replicates. Systematic biases in DNA methylation profiles were observed between control and three of four protocols without adjustment of cell-type composition (λ = 1.12–1.45) and no remarkable biases were seen after adjusting for cell-type composition in all four protocols (λadjusted = 1.00–1.17). These results revealed important implications for comparing DNA methylation profiles between blood specimens from different sources and may lead to discovery of disease-associated DNA methylation markers and the development of DNA methylation profile-based predictive risk models.
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Affiliation(s)
- Yuh Shiwa
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Tsuyoshi Hachiya
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Ryohei Furukawa
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Kanako Ono
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Hisaaki Kudo
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Jun Hata
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
| | - Atsushi Hozawa
- Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Minegishi
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
| | - Mamoru Satoh
- Division of Biobank and Data Management, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Community Medical Supports and Health Record Informatics, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Science, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Kozo Tanno
- Department of Hygiene and Preventive Medicine, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466–8550, Japan
| | - Jiro Hitomi
- Deputy Executive Director, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Department of Anatomy, School of Medicine, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Yutaka Kiyohara
- Department of Environmental Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812–8582, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Genomic Medicine, RIKEN, Yokohama, Japan
| | - Hideo Tanaka
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Research Center for Cancer Prevention and Screening, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104–0045, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai 980–8573, Japan
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2–1, Aoba-ku, Sendai 980–8575, Japan
| | - Kenji Sobue
- Executive Director, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- Department of Neuroscience, Institute for Biomedical Science, Iwate Medical University, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University Disaster Reconstruction Center, 2-1-1 Nishitokuda, Yahaba-cho, Shiwa-gun, Iwate 028–3694, Japan
- * E-mail:
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Ye H, Zhou A, Hong Q, Chen X, Xin Y, Tang L, Dai D, Ji H, Xu M, Wang DW, Duan S. Association of seven thrombotic pathway gene CpG-SNPs with coronary heart disease. Biomed Pharmacother 2015; 72:98-102. [PMID: 26054681 DOI: 10.1016/j.biopha.2015.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 04/03/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Coronary heart disease (CHD) has been considered a thromboembolic arterial diseases. The aim of this case-control study was to explore whether the CpG-SNPs of the thrombotic pathway genes contributed to the risk of CHD. METHODS AND MATERIALS A total of 784 CHD patients and 738 healthy controls were recruited in the current association study, which evaluated 7 CpG-SNPs of the thrombotic pathway genes. The CpG-SNPs included THBS4 rs17878919, CYP2C19 rs12773342, P2RY12 rs1491974, ITGA2 rs26680, FGB rs2227389, F7 rs510317 and F5 rs2269648. SNP genotyping was performed with a Sequenom Mass Spectrometry Genetic Analyzer. RESULTS Our results demonstrated that CYP2C19 rs12773342 polymorphism was significantly associated with CHD in the recessive model (χ(2)=5.41, df=1, P=0.020, OR=1.455, 95% CI=1.060-1.996). A breakdown analysis by age showed that the association of CYP2C19 rs12773342 with CHD was mainly found in individuals aged 55-65 (genotype: χ(2)=7.93, df=2, P=0.019; allele: χ(2)=4.45, df=1, P=0.035). In addition, we also observed a significant association between F7 rs510317 polymorphism and CHD in males (genotype: χ(2)=7.24, df=2, P=0.027). There was no significant association with CHD for the remaining CpG-SNPs. CONCLUSION Our results supported that the CYP2C19 rs12773342 and F7 rs510317 polymorphisms were associated with CHD in the Han Chinese population.
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Affiliation(s)
- Huadan Ye
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Annan Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiaoying Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yanfei Xin
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongjun Dai
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Huihui Ji
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dao Wen Wang
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
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Xu L, Chen X, Ye H, Hong Q, Xu M, Duan S. Association of four CpG-SNPs in the vascular-related genes with coronary heart disease. Biomed Pharmacother 2015; 70:80-3. [DOI: 10.1016/j.biopha.2015.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/04/2015] [Indexed: 01/04/2023] Open
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Huen K, Yousefi P, Street K, Eskenazi B, Holland N. PON1 as a model for integration of genetic, epigenetic, and expression data on candidate susceptibility genes. ENVIRONMENTAL EPIGENETICS 2015; 1:dvv003. [PMID: 26913202 PMCID: PMC4762373 DOI: 10.1093/eep/dvv003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/30/2015] [Accepted: 07/14/2015] [Indexed: 05/27/2023]
Abstract
Recent genome- and epigenome-wide studies demonstrate that the DNA methylation is controlled in part by genetics, highlighting the importance of integrating genetic and epigenetic data. To better understand molecular mechanisms affecting gene expression, we used the candidate susceptibility gene paraoxonase 1 (PON1) as a model to assess associations of PON1 genetic polymorphisms with DNA methylation and arylesterase activity, a marker of PON1 expression. PON1 has been associated with susceptibility to obesity, cardiovascular disease, and pesticide exposure. In this study, we assessed DNA methylation in 18 CpG sites located along PON1 shores, shelves, and its CpG island in blood specimens collected from newborns and 9-year-old children participating (n = 449) in the CHAMACOS birth cohort study. The promoter polymorphism, PON1-108 , was strongly associated with methylation, particularly for CpG sites located near the CpG island (P << 0.0005). Among newborns, these relationships were even more pronounced after adjusting for blood cell composition. We also observed significant decreases in arylesterase activity with increased methylation at the same nine CpG sites at both ages. Using causal mediation analysis, we found statistically significant indirect effects of methylation (β(95% confidence interval): 6.9(1.5, 12.4)) providing evidence that DNA methylation mediates the relationship between PON1-108 genotype and PON1 expression. Our findings show that integration of genetic, epigenetic, and expression data can shed light on the functional mechanisms involving genetic and epigenetic regulation of candidate susceptibility genes like PON1.
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Affiliation(s)
- Karen Huen
- School of Public Health, University of California, Berkeley, 50 University Hall #7360, Berkeley, CA 94720-7360, USA
| | - Paul Yousefi
- School of Public Health, University of California, Berkeley, 50 University Hall #7360, Berkeley, CA 94720-7360, USA
| | - Kelly Street
- School of Public Health, University of California, Berkeley, 50 University Hall #7360, Berkeley, CA 94720-7360, USA
| | - Brenda Eskenazi
- School of Public Health, University of California, Berkeley, 50 University Hall #7360, Berkeley, CA 94720-7360, USA
| | - Nina Holland
- School of Public Health, University of California, Berkeley, 50 University Hall #7360, Berkeley, CA 94720-7360, USA
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CDH13 promoter SNPs with pleiotropic effect on cardiometabolic parameters represent methylation QTLs. Hum Genet 2014; 134:291-303. [PMID: 25543204 PMCID: PMC4318987 DOI: 10.1007/s00439-014-1521-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022]
Abstract
CDH13 encodes T-cadherin, a receptor for high molecular weight (HMW) adiponectin and low-density lipoprotein, promoting proliferation and migration of endothelial cells. Genome-wide association studies have mapped multiple variants in CDH13 associated with cardiometabolic traits (CMT) with variable effects across studies. We hypothesized that this heterogeneity might reflect interplay with DNA methylation within the region. Resequencing and EpiTYPER™ assay were applied for the HYPertension in ESTonia/Coronary Artery Disease in Czech (HYPEST/CADCZ; n = 358) samples to identify CDH13 promoter SNPs acting as methylation Quantitative Trait Loci (meQTLs) and to investigate their associations with CMT. In silico data were extracted from genome-wide DNA methylation and genotype datasets of the population-based sample Estonian Genome Center of the University of Tartu (EGCUT; n = 165). HYPEST–CADCZ meta-analysis identified a rare variant rs113460564 as highly significant meQTL for a 134-bp distant CpG site (P = 5.90 × 10−6; β = 3.19 %). Four common SNPs (rs12443878, rs12444338, rs62040565, rs8060301) exhibited effect on methylation level of up to 3 neighboring CpG sites in both datasets. The strongest association was detected in EGCUT between rs8060301 and cg09415485 (false discovery rate corrected P value = 1.89 × 10−30). Simultaneously, rs8060301 showed association with diastolic blood pressure, serum high-density lipoprotein and HMW adiponectin (P < 0.005). Novel strong associations were identified between rare CDH13 promoter meQTLs (minor allele frequency <5 %) and HMW adiponectin: rs2239857 (P = 5.50 × 10−5, β = −1,841.9 ng/mL) and rs77068073 (P = 2.67 × 10−4, β = −2,484.4 ng/mL). Our study shows conclusively that CDH13 promoter harbors meQTLs associated with CMTs. It paves the way to deeper understanding of the interplay between DNA variation and methylation in susceptibility to common diseases.
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