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Modrzejewska M, Gawronski M, Gackowski D. Normalization of metabolic data to total thymine content and its application to determination of 2-hydroxyglutarate. Anal Biochem 2021; 618:114129. [PMID: 33556332 DOI: 10.1016/j.ab.2021.114129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Our first objective was to develop an approach useful for reliable normalization of 2-hydroxyglutarate (2-HG) intracellular levels. The second objective was to use our data normalization strategy to verify previously published report on the higher d-2-HG level in tumors of colorectal cancer (CRC) patients than in normal colon fragments. We examined various methods of 2-HG level normalization in cell/tissue extracts (number of cells, mass of tissue, total protein). In order to solve the problems with reliable normalization of the 2-HG levels in colon fragments, we proposed a strategy based on relating the concentrations of 2-HG isomers to total thymine concentrations measured by ultra-performance liquid chromatography (UPLC) with UV detection in acid hydrolysates of the cell/tissue extracts. We used a common method of derivatization with diacetyl-l-tartaric anhydride (DATAN) to separate l- and d-2-HG enantiomers. DATAN-derivatized 2-HG was quantitated by UPLC with tandem mass spectrometry (MS/MS) in the selected reaction monitoring (SRM) mode. We observed a linear dependence of the total amount of thymine released from lymphocytes, HCT 116, K562, and PC-3 by acid hydrolysis on their number of cells. Our results showed a significantly higher level of l- and d-2-HG in cancer-free colon than in tumor.
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Affiliation(s)
- Martyna Modrzejewska
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092, Bydgoszcz, Poland.
| | - Maciej Gawronski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092, Bydgoszcz, Poland.
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-092, Bydgoszcz, Poland.
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2
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Precision Nutrition and Childhood Obesity: A Scoping Review. Metabolites 2020; 10:metabo10060235. [PMID: 32521722 PMCID: PMC7345802 DOI: 10.3390/metabo10060235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/18/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
Environmental exposures such as nutrition during life stages with high developmental plasticity—in particular, the in utero period, infancy, childhood, and puberty—may have long-lasting influences on risk of chronic diseases, including obesity-related conditions that manifest as early as childhood. Yet, specific mechanisms underlying these relationships remain unclear. Here, we consider the study of ‘omics mechanisms, including nutrigenomics, epigenetics/epigenomics, and metabolomics, within a life course epidemiological framework to accomplish three objectives. First, we carried out a scoping review of population-based literature with a focus on studies that include ‘omics analyses during three sensitive periods during early life: in utero, infancy, and childhood. We elected to conduct a scoping review because the application of multi-‘omics and/or precision nutrition in childhood obesity prevention and treatment is relatively recent, and identifying knowledge gaps can expedite future research. Second, concomitant with the literature review, we discuss the relevance and plausibility of biological mechanisms that may underlie early origins of childhood obesity identified by studies to date. Finally, we identify current research limitations and future opportunities for application of multi-‘omics in precision nutrition/health practice.
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Ma B, Allard C, Bouchard L, Perron P, Mittleman MA, Hivert MF, Liang L. Locus-specific DNA methylation prediction in cord blood and placenta. Epigenetics 2019; 14:405-420. [PMID: 30885044 DOI: 10.1080/15592294.2019.1588685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA methylation is known to be responsive to prenatal exposures, which may be a part of the mechanism linking early developmental exposures to future chronic diseases. Many studies use blood to measure DNA methylation, yet we know that DNA methylation is tissue specific. Placenta is central to fetal growth and development, but it is rarely feasible to collect this tissue in large epidemiological studies; on the other hand, cord blood samples are more accessible. In this study, based on paired samples of both placenta and cord blood tissues from 169 individuals, we investigated the methylation concordance between placenta and cord blood. We then employed a machine-learning-based model to predict locus-specific DNA methylation levels in placenta using DNA methylation levels in cord blood. We found that methylation correlation between placenta and cord blood is lower than other tissue pairs, consistent with existing observations that placenta methylation has a distinct pattern. Nonetheless, there are still a number of CpG sites showing robust association between the two tissues. We built prediction models for placenta methylation based on cord blood data and documented a subset of 1,012 CpG sites with high correlation between measured and predicted placenta methylation levels. The resulting list of CpG sites and prediction models could help to reveal the loci where internal or external influences may affect DNA methylation in both placenta and cord blood, and provide a reference data to predict the effects on placenta in future study even when the tissue is not available in an epidemiological study.
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Affiliation(s)
- Baoshan Ma
- a College of Information Science and Technology , Dalian Maritime University , Dalian , Liaoning Province , China
| | - Catherine Allard
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Luigi Bouchard
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,c Department of Biochemistry, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada.,d ECOGENE-21 Biocluster , CSSS de Chicoutimi , Chicoutimi , Quebec , Canada
| | - Patrice Perron
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,e Department of Medicine, Faculty of Medicine and Life Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Murray A Mittleman
- f Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , MA , USA.,g Cardiovascular Epidemiology Research Unit , Beth Israel Deaconess Medical Center , Boston , MA , USA
| | - Marie-France Hivert
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,e Department of Medicine, Faculty of Medicine and Life Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada.,h Department of Population Medicine , Harvard Pilgrim Health Care Institute, Harvard Medical School , Boston , MA , USA.,i Diabetes Unit , Massachusetts General Hospital , Boston , MA , USA
| | - Liming Liang
- f Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , MA , USA.,j Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
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4
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Elbere I, Silamikelis I, Ustinova M, Kalnina I, Zaharenko L, Peculis R, Konrade I, Ciuculete DM, Zhukovsky C, Gudra D, Radovica-Spalvina I, Fridmanis D, Pirags V, Schiöth HB, Klovins J. Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals. Clin Epigenetics 2018; 10:156. [PMID: 30545422 PMCID: PMC6293577 DOI: 10.1186/s13148-018-0593-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/29/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Metformin is a widely prescribed antihyperglycemic agent that has been also associated with multiple therapeutic effects in various diseases, including several types of malignancies. There is growing evidence regarding the contribution of the epigenetic mechanisms in reaching metformin's therapeutic goals; however, the effect of metformin on human cells in vivo is not comprehensively studied. The aim of our study was to examine metformin-induced alterations of DNA methylation profiles in white blood cells of healthy volunteers, employing a longitudinal study design. RESULTS Twelve healthy metformin-naïve individuals where enrolled in the study. Genome-wide DNA methylation pattern was estimated at baseline, 10 h and 7 days after the start of metformin administration. The whole-genome DNA methylation analysis in total revealed 125 differentially methylated CpGs, of which 11 CpGs and their associated genes with the most consistent changes in the DNA methylation profile were selected: POFUT2, CAMKK1, EML3, KIAA1614, UPF1, MUC4, LOC727982, SIX3, ADAM8, SNORD12B, VPS8, and several differentially methylated regions as novel potential epigenetic targets of metformin. The main functions of the majority of top-ranked differentially methylated loci and their representative cell signaling pathways were linked to the well-known metformin therapy targets: regulatory processes of energy homeostasis, inflammatory responses, tumorigenesis, and neurodegenerative diseases. CONCLUSIONS Here we demonstrate for the first time the immediate effect of short-term metformin administration at therapeutic doses on epigenetic regulation in human white blood cells. These findings suggest the DNA methylation process as one of the mechanisms involved in the action of metformin, thereby revealing novel targets and directions of the molecular mechanisms underlying the various beneficial effects of metformin. TRIAL REGISTRATION EU Clinical Trials Register, 2016-001092-74. Registered 23 March 2017, https://www.clinicaltrialsregister.eu/ctr-search/trial/2016-001092-74/LV .
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Affiliation(s)
- Ilze Elbere
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Linda Zaharenko
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ilze Konrade
- Riga East Clinical University Hospital, 2 Hipokrata Street, Riga, LV-1038, Latvia
| | - Diana Maria Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Christina Zhukovsky
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Dita Gudra
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Ilze Radovica-Spalvina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga, LV-1067, Latvia.
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5
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Aref-Eshghi E, Rodenhiser DI, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Hood RL, Bulman DE, Kernohan KD, Boycott KM, Campeau PM, Schwartz C, Sadikovic B, Sadikovic B. Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes. Am J Hum Genet 2018; 102:156-174. [PMID: 29304373 DOI: 10.1016/j.ajhg.2017.12.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023] Open
Abstract
Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A5C1, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
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6
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Adams CD, Jordahl KM, Copeland W, Mirick DK, Song X, Sather CL, Kelsey K, Houseman A, Davis S, Randolph T, Bhatti P. Nightshift work, chronotype, and genome-wide DNA methylation in blood. Epigenetics 2017; 12:833-840. [PMID: 28837395 DOI: 10.1080/15592294.2017.1366407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Molecular mechanisms underlying the negative health effects of shift work are poorly understood, which remains a barrier to developing intervention strategies to protect the long-term health of shift workers. We evaluated genome-wide differences in DNA methylation (measured in blood) between 111 actively employed female nightshift and 86 actively employed female dayshift workers from the Seattle metropolitan area. We also explored the effect of chronotype (i.e., measure of preference for activity earlier or later in the day) on DNA methylation among 110 of the female nightshift workers and an additional group of 131 male nightshift workers. Methylation data were generated using the Illumina Infinium HumanMethylation450 BeadChip (450K) Array. After applying the latest methylation data processing methods, we compared methylation levels at 361,210 CpG loci between the groups using linear regression models adjusted for potential confounders and applied the false-discovery rate (FDR) ≤ 0.05 to account for multiple comparisons. No statistically significant associations at the genome-wide level were observed with shift work or chronotype, though based on raw P values and absolute effect sizes, there were suggestive associations in genes that have been previously linked with cancer (e.g., BACH2, JRK, RPS6KA2) and type-2 diabetes (e.g., KCNQ1). Given that our study was underpowered to detect moderate effects, examining these suggestive results in well-powered independent studies or in pooled data sets may improve our understanding of the pathways underlying the negative health effects of shift work and the influence of personal factors such as chronotype. Such an approach may help identify potential interventions that can be used to protect the long-term health of shift workers.
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Affiliation(s)
- Charleen D Adams
- a MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol , Bristol , UK.,b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Kristina M Jordahl
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Wade Copeland
- c Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Dana K Mirick
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Xiaoling Song
- d Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Cassandra L Sather
- e Genomics Resource, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Karl Kelsey
- f Department of Community Health , Brown University , Providence , RI , USA
| | - Andres Houseman
- g College of Public Health and Human Sciences, Oregon State University , Corvallis , OR , USA
| | - Scott Davis
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Timothy Randolph
- c Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Parveen Bhatti
- b Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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7
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Reszka E, Wieczorek E, Przybek M, Jabłońska E, Kałużny P, Bukowska-Damska A, Zienolddiny S, Pepłońska B. Circadian gene methylation in rotating-shift nurses: a cross-sectional study. Chronobiol Int 2017; 35:111-121. [PMID: 29144171 DOI: 10.1080/07420528.2017.1388252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Investigating the methylation status of the circadian genes may contribute to a better understanding of the shift work-related circadian disruption in individuals exposed to artificial light at night. In the present study, we determined the methylation status of the circadian genes associated with a shift work pattern among nurses and midwives participating in a cross-sectional study in Lodz, Poland. Quantitative methylation polymerase chain reaction assays were used to assess promoter CpG methylation in PER1, PER2, PER3, CRY1, CRY2, BMAL1, CLOCK, and NPAS2 in genomic DNA from whole blood of 347 women having a rotating-shift work schedule and 363 women working days only. The percentage of methylated reference (PMR) was assessed using fluorescent probes for PER1, PER2, PER3, CRY1, and NPAS2, and the percentage of gene methylation, as the methylation index (MI), using two sets of primers for BMAL1, CLOCK, and CRY2. We tested the possible association between current and lifetime rotating night-shift work characteristics and circadian gene methylation by using proportional odds regression model with blood DNA methylation, categorized into tertiles, and adjusted for age, current smoking status, folate intake and blood collection time. The findings indicated that CpG methylation in PER2 promoter was significantly decreased (P < 0.004) among nurses and midwives currently working rotating shifts, as compared with day-working nurses and midwives. The lower percentage of PER2 methylation was associated with a higher monthly frequency of current night duties (2-7 night shifts, and eight or more night shifts per month) (P = 0.012) and was associated at borderline significance (P = 0.092) with the lifetime duration of shift work (>10 ≤ 20 years and >20 ≤ 43 years of rotating-shift work) among nurses and midwives (N = 710). Moreover, women with a longer lifetime duration of shift work presented a lower status of PER1 methylation (P = 0.040) than did the women with up to 10 years of rotating-shift work. Long lifetime duration of shift work (> 10 years) among current rotating night-shift workers (N = 347) was associated with BMAL1 hypomethylation (P = 0.013). Among eight of the investigated circadian genes, only PER1, PER2, and BMAL1 showed differential methylation attributable to the rotating-shift work of nurses and midwives. The findings on blood-based DNA methylation in the circadian genes may provide a better insight into the mechanistic principles underlying the possible health effects of night-shift work but these should be verified in further studies recruiting larger populations of shift workers.
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Affiliation(s)
- Edyta Reszka
- a Department of Molecular Genetics and Epigenetics , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Edyta Wieczorek
- a Department of Molecular Genetics and Epigenetics , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Monika Przybek
- a Department of Molecular Genetics and Epigenetics , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Ewa Jabłońska
- a Department of Molecular Genetics and Epigenetics , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Paweł Kałużny
- b Department of Environmental Epidemiology , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Agnieszka Bukowska-Damska
- b Department of Environmental Epidemiology , Nofer Institute of Occupational Medicine , Lodz , Poland
| | - Shanbeh Zienolddiny
- c Section of Toxicology and Biological Work Environment, Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Beata Pepłońska
- b Department of Environmental Epidemiology , Nofer Institute of Occupational Medicine , Lodz , Poland
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Liu Y, Wang Y, Hu F, Sun H, Zhang Z, Wang X, Luo X, Zhu L, Huang R, Li Y, Li G, Li X, Lin S, Wang F, Liu Y, Rong J, Yuan H, Zhao Y. Multiple gene-specific DNA methylation in blood leukocytes and colorectal cancer risk: a case-control study in China. Oncotarget 2017; 8:61239-61252. [PMID: 28977860 PMCID: PMC5617420 DOI: 10.18632/oncotarget.18054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022] Open
Abstract
The relationship between gene-specific DNA methylation in peripheral blood leukocytes and colorectal cancer (CRC) susceptibility is unclear. In this case-control study, the methylation status of a panel of 10 CRC-related genes in 428 CRC cases and 428 cancer-free controls were detected with methylation-sensitive high-resolution melting analysis. We calculated a weighted methylation risk score (MRS) that comprehensively combined the methylation status of the panel of 10 genes and found that the MRS_10 was significantly associated with CRC risk. Compared with MRS-Low group, MRS-High group and MRS-Medium group exhibited a 6.51-fold (95% CI, 3.77-11.27) and 3.85-fold (95% CI, 2.72-5.45) increased risk of CRC, respectively. Moreover, the CRC risk increased with increasing MRS_10 (Ptrend < 0.0001). Stratified analyses demonstrated that the significant association retained in both men and women, younger and older, and normal weight or underweight and overweight or obese subjects. The area under the receiver operating characteristic curves for the MRS_10 model was 69.04% (95% CI, 65.57-72.66%) and the combined EF and MRS_10 model yielded an AUC of 79.12% (95% CI, 76.22-82.15%). Together, the panel of 10 gene-specific DNA methylation in leukocytes was strongly associated with the risk of CRC and might be a useful marker of susceptibility for CRC.
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Affiliation(s)
- Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yibaina Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Zuoming Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xuan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xiang Luo
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Lin Zhu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Rong Huang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yan Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Guangxiao Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Xia Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Shangqun Lin
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Fan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yanhong Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Jiesheng Rong
- Department of Orthopedics Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Huiping Yuan
- Key Laboratory of Ophthalmology, Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin 150081, Heilongjiang Province, The People's Republic of China
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9
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De Carli MM, Baccarelli AA, Trevisi L, Pantic I, Brennan KJ, Hacker MR, Loudon H, Brunst KJ, Wright RO, Wright RJ, Just AC. Epigenome-wide cross-tissue predictive modeling and comparison of cord blood and placental methylation in a birth cohort. Epigenomics 2017; 9:231-240. [PMID: 28234020 DOI: 10.2217/epi-2016-0109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We compared predictive modeling approaches to estimate placental methylation using cord blood methylation. MATERIALS & METHODS We performed locus-specific methylation prediction using both linear regression and support vector machine models with 174 matched pairs of 450k arrays. RESULTS At most CpG sites, both approaches gave poor predictions in spite of a misleading improvement in array-wide correlation. CpG islands and gene promoters, but not enhancers, were the genomic contexts where the correlation between measured and predicted placental methylation levels achieved higher values. We provide a list of 714 sites where both models achieved an R2 ≥0.75. CONCLUSION The present study indicates the need for caution in interpreting cross-tissue predictions. Few methylation sites can be predicted between cord blood and placenta.
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Affiliation(s)
- Margherita M De Carli
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Letizia Trevisi
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Ivan Pantic
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA.,Department of Developmental Neurobiology, National Institute of Perinatology, Mexico City, Mexico
| | - Kasey Jm Brennan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Michele R Hacker
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.,Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Holly Loudon
- Department of Obstetrics & Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly J Brunst
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert O Wright
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rosalind J Wright
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allan C Just
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". Curr Behav Neurosci Rep 2016; 3:264-274. [PMID: 28093577 DOI: 10.1007/s40473-016-0083-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Evidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages. RECENT FINDINGS Brain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important. SUMMARY Epigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Alycia Halladay
- Autism Science Foundation, New York City, New York, USA; Department of Pharmacology and Toxicology, Rutgers University, New Brunswick, New Jersey, USA
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK; Institute for Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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11
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Terry MB, McDonald JA, Wu HC, Eng S, Santella RM. Epigenetic Biomarkers of Breast Cancer Risk: Across the Breast Cancer Prevention Continuum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 882:33-68. [PMID: 26987530 PMCID: PMC5305320 DOI: 10.1007/978-3-319-22909-6_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic biomarkers, such as DNA methylation, can increase cancer risk through altering gene expression. The Cancer Genome Atlas (TCGA) Network has demonstrated breast cancer-specific DNA methylation signatures. DNA methylation signatures measured at the time of diagnosis may prove important for treatment options and in predicting disease-free and overall survival (tertiary prevention). DNA methylation measurement in cell free DNA may also be useful in improving early detection by measuring tumor DNA released into the blood (secondary prevention). Most evidence evaluating the use of DNA methylation markers in tertiary and secondary prevention efforts for breast cancer comes from studies that are cross-sectional or retrospective with limited corresponding epidemiologic data, raising concerns about temporality. Few prospective studies exist that are large enough to address whether DNA methylation markers add to the prediction of tertiary and secondary outcomes over and beyond standard clinical measures. Determining the role of epigenetic biomarkers in primary prevention can help in identifying modifiable pathways for targeting interventions and reducing disease incidence. The potential is great for DNA methylation markers to improve cancer outcomes across the prevention continuum. Large, prospective epidemiological studies will provide essential evidence of the overall utility of adding these markers to primary prevention efforts, screening, and clinical care.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| | - Jasmine A McDonald
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hui Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sybil Eng
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Regina M Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
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12
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Barrow TM, Barault L, Ellsworth RE, Harris HR, Binder AM, Valente AL, Shriver CD, Michels KB. Aberrant methylation of imprinted genes is associated with negative hormone receptor status in invasive breast cancer. Int J Cancer 2015; 137:537-47. [PMID: 25560175 DOI: 10.1002/ijc.29419] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 12/19/2014] [Indexed: 11/07/2022]
Abstract
Epigenetic regulation of imprinted genes enables monoallelic expression according to parental origin, and its disruption is implicated in many cancers and developmental disorders. The expression of hormone receptors is significant in breast cancer because they are indicators of cancer cell growth rate and determine response to endocrine therapies. We investigated the frequency of aberrant events and variation in DNA methylation at nine imprinted sites in invasive breast cancer and examined the association with estrogen and progesterone receptor status. Breast tissue and blood from patients with invasive breast cancer (n = 38) and benign breast disease (n = 30) were compared with those from healthy individuals (n = 36), matched with the cancer patients by age at diagnosis, ethnicity, body mass index, menopausal status and familial history of cancer. DNA methylation and allele-specific expression were analyzed by pyrosequencing. Tumor-specific methylation changes at IGF2 DMR2 were observed in 59% of cancer patients, IGF2 DMR0 in 38%, DIRAS3 DMR in 36%, GRB10 ICR in 23%, PEG3 DMR in 21%, MEST ICR in 19%, H19 ICR in 18%, KvDMR in 8% and SNRPN/SNURF ICR in 4%. Variation in methylation was significantly greater in breast tissue from cancer patients compared with that in healthy individuals and benign breast disease. Aberrant methylation of three or more sites was significantly associated with negative estrogen-alpha (Fisher's exact test, p = 0.02) and progesterone-A (p = 0.02) receptor status. Aberrant events and increased variation in imprinted gene DNA methylation, therefore, seem to be frequent in invasive breast cancer and are associated with negative estrogen and progesterone receptor status, without loss of monoallelic expression.
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Affiliation(s)
- Timothy M Barrow
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Ludovic Barault
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rachel E Ellsworth
- Clinical Breast Care Project, Henry M. Jackson Foundation for the Advancement of Military Medicine, Windber, PA
| | - Holly R Harris
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alexandra M Binder
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Allyson L Valente
- Clinical Breast Care Project, Windber Research Institute, Windber, PA
| | - Craig D Shriver
- Clinical Breast Care Project, Walter Reed National Military Medical Center, Bethesda, MD
| | - Karin B Michels
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany.,Department of Epidemiology, Harvard School of Public Health, Boston, MA
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13
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Mandaviya PR, Stolk L, Heil SG. Homocysteine and DNA methylation: a review of animal and human literature. Mol Genet Metab 2014; 113:243-52. [PMID: 25456744 DOI: 10.1016/j.ymgme.2014.10.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/04/2014] [Accepted: 10/04/2014] [Indexed: 11/28/2022]
Abstract
Homocysteine (Hcy) is a sulfur-containing non-protein forming amino acid, which is synthesized from methionine as an important intermediate in the one-carbon pathway. High concentrations of Hcy in a condition called hyperhomocysteinemia (HHcy) are an independent risk factor for several disorders including cardiovascular diseases and osteoporotic fractures. Since Hcy is produced as a byproduct of the methyltransferase reaction, alteration in DNA methylation is studied as one of the underlying mechanisms of HHcy-associated disorders. In animal models, elevated Hcy concentrations are induced either by diet (high methionine, low B-vitamins, or both), gene knockouts (Mthfr, Cbs, Mtrr or Mtr) or combination of both to investigate their effects on DNA methylation or its markers. In humans, most of the literature involves case-control studies concerning patients. The focus of this review is to study existing literature on HHcy and its role in relation to DNA methylation. Apart from this, a few studies investigated the effect of Hcy-lowering trials on restoring DNA methylation patterns, by giving a folic acid or B-vitamin supplemented diet. These studies which were conducted in animal models as well as humans were included in this review.
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Affiliation(s)
- Pooja R Mandaviya
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Sandra G Heil
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.
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Barrow TM, Michels KB. Epigenetic epidemiology of cancer. Biochem Biophys Res Commun 2014; 455:70-83. [PMID: 25124661 DOI: 10.1016/j.bbrc.2014.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/15/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.
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Affiliation(s)
- Timothy M Barrow
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Karin B Michels
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
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15
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Izzi B, Binder AM, Michels KB. Pyrosequencing Evaluation of Widely Available Bisulfite Conversion Methods: Considerations for Application. ACTA ACUST UNITED AC 2014; 2:28-36. [PMID: 24944560 PMCID: PMC4058339 DOI: 10.1159/000358882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Introduction Bisulfite treatment of DNA introduces methylation-dependent sequence changes through selective chemical conversion of nonmethylated cytosine to uracil and serves as pretreatment step for the majority of DNA methylation analysis methods. Methods We have evaluated the conversion performance of five of the most commonly used bisulfite treatment kits [MethylDetector (Active Motif), Epitect+ (Qiagen), Zymo Methylation, Zymo Gold and Zymo Lightning (all from Zymo Research)] by pyrosequencing four different regions with variable methylation levels, including: a repetitive element (ALUSX), a gene with low levels of methylation (IL6ST), an imprinted gene expected to be approximately 50% methylated (IGF2), and a fully methylated gene (ST3GAL2). In addition, we have studied the influence of duration (3 vs. 16 h) and type (fixed temperature vs. cycling program) of incubation protocol on the conversion efficiency of each evaluated kit. Results All kits produced similar conversion rates of ALUSX, IGF2 and ST3GAL2, while the conversion of the low methylated IL6ST gene was variable between kits. The Zymo kits were highly consistent in their performance even when different protocols of incubation were applied, generating full conversion at the low methylated gene IL6; this was not true for the MethylDetector and Epitect+ kits. However, long-cycling incubation could produce similar conversion rates for the same locus in combination with Active Motif and Qiagen kits. Conclusions The selection of a long-cycling protocol during conversion permits standardization of protocols, improving the reproducibility of methylation estimates across laboratories for gene-specific, genome-wide and bisulfite-based sequencing analyses.
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Affiliation(s)
- Benedetta Izzi
- Institute for Prevention and Cancer Epidemiology, Freiburg Medical Center, University of Freiburg, Freiburg, Germany ; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass., USA
| | - Alexandra M Binder
- Harvard School of Public Health, Department of Epidemiology, Boston, Mass., USA
| | - Karin B Michels
- Institute for Prevention and Cancer Epidemiology, Freiburg Medical Center, University of Freiburg, Freiburg, Germany ; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass., USA ; Harvard School of Public Health, Department of Epidemiology, Boston, Mass., USA
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Ma B, Wilker EH, Willis-Owen SAG, Byun HM, Wong KCC, Motta V, Baccarelli AA, Schwartz J, Cookson WOCM, Khabbaz K, Mittleman MA, Moffatt MF, Liang L. Predicting DNA methylation level across human tissues. Nucleic Acids Res 2014; 42:3515-28. [PMID: 24445802 PMCID: PMC3973306 DOI: 10.1093/nar/gkt1380] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Differences in methylation across tissues are critical to cell differentiation and are key to understanding the role of epigenetics in complex diseases. In this investigation, we found that locus-specific methylation differences between tissues are highly consistent across individuals. We developed a novel statistical model to predict locus-specific methylation in target tissue based on methylation in surrogate tissue. The method was evaluated in publicly available data and in two studies using the latest IlluminaBeadChips: a childhood asthma study with methylation measured in both peripheral blood leukocytes (PBL) and lymphoblastoid cell lines; and a study of postoperative atrial fibrillation with methylation in PBL, atrium and artery. We found that our method can greatly improve accuracy of cross-tissue prediction at CpG sites that are variable in the target tissue [R(2) increases from 0.38 (original R(2) between tissues) to 0.89 for PBL-to-artery prediction; from 0.39 to 0.95 for PBL-to-atrium; and from 0.81 to 0.98 for lymphoblastoid cell line-to-PBL based on cross-validation, and confirmed using cross-study prediction]. An extended model with multiple CpGs further improved performance. Our results suggest that large-scale epidemiology studies using easy-to-access surrogate tissues (e.g. blood) could be recalibrated to improve understanding of epigenetics in hard-to-access tissues (e.g. atrium) and might enable non-invasive disease screening using epigenetic profiles.
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Affiliation(s)
- Baoshan Ma
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA, College of Information Science and Technology, Dalian Maritime University, Dalian, Liaoning Province 116026, China, Cardiovascular Epidemiology Research Unit, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA, National Heart and Lung Institute, Imperial College, London SW3 6LY, UK, Department of Clinical Sciences and Community, University of Milan, Milan 20122, Italy, Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
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Rancourt RC, Harris HR, Barault L, Michels KB. The prevalence of loss of imprinting of H19 and IGF2 at birth. FASEB J 2013; 27:3335-43. [PMID: 23620526 DOI: 10.1096/fj.12-225284] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Imprinted genes are monoallelically expressed according to the parent of origin and are critical for proper placental and embryonic development. Disruption of methylation patterns at imprinted loci resulting in loss of imprinting (LOI) may lead to serious imprinting disorders (e.g., Beckwith-Wiedemann syndrome) and is described in some cancers (e.g., Wilms' tumor). As most research has focused on children with cancer or other abnormal phenotypes, the imprinting status in healthy infants at birth has not been characterized. We examined the prevalence of H19 and IGF2 LOI at birth by allele-specific expression assays analysis on 114 human individuals. Overall expression and methylation analyses were performed on a subset of samples. We found that LOI of H19 was observed for 4% of individuals in cord blood and 3.3% in placenta, and for IGF2 of 22% of individuals in the cord blood and 0% in placenta. Interestingly, LOI status did not correspond to aberrant methylation levels of the imprinted DMRs or with changes in overall gene expression for the majority of individuals. Our observations suggest that LOI is present in phenotypically healthy infants. Determining a "normal" human epigenotype range is important for discovering factors required to maintain a healthy pregnancy and embryonic development.
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Affiliation(s)
- Rebecca C Rancourt
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave., Boston, MA 02115, USA
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