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Yasuhiro Kinugawa, Takeshi Uehara, Kazuyuki Matsuda, Yukihiro Kobayashi, Tomoyuki Nakajima, Hideaki Hamano, Shigeyuki Kawa, Kayoko Higuchi, Noriko Hosaka, Satoshi Shiozawa, Hiroki Ishigame, Toshitsugu Nakamura, Yasuhiro Maruyama, Koh Nakazawa, Masato Nakaguro, Kenji Sano, Hiroyoshi Ota
The relationship between methylation abnormality and autoimmune pancreatitis (AIP)-a representative IgG4-related disease-has not yet been elucidated. We identified SKI might have a significant methylation abnormality in AIP through methylation array analysis using the Illumina Infinium Human Methylation 450K BeadChip array, and investigated the relationship of SKI with AIP clinicopathological features. The methylation rate of SKI was assessed by quantitative SYBR green methylation-specific PCR, and the degree of SKI expression in tissue specimens was assessed by immunohistochemistry in 10 AIP cases, 14 cases of obstructive pancreatitis area in pancreatic ductal adenocarcinoma (PDA) without a history of AIP, and 9 normal pancreas (NP) cases...
March 6, 2018: Pathology, Research and Practice
Ida K Karlsson, Alexander Ploner, Yunzhang Wang, Margaret Gatz, Nancy L Pedersen, Sara Hägg
Background: This study aims to investigate if DNA methylation of the apolipoprotein E (APOE) locus affects the risks of dementia, Alzheimeŕs disease (AD) or cardiovascular disease (CVD). Methods: DNA methylation across the APOE gene has previously been categorized into three distinct regions: a hypermethylated region in the promoter, a hypomethylated region in the first two introns and exons and a hypermethylated region in the 3'exon that also harbours the APOE ε2 and ε4 alleles...
March 2, 2018: International Journal of Epidemiology
Cheng-Jian Xu, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Olena Gruzieva, Ulrike Gehring, Dan Mason, Leda Chatzi, Mikel Basterrechea, Sabrina Llop, Maties Torrent, Francesco Forastiere, Maria Pia Fantini, Karin C Lødrup Carlsen, Tari Haahtela, Andréanne Morin, Marjan Kerkhof, Simon Kebede Merid, Bianca van Rijkom, Soesma A Jankipersadsing, Marc Jan Bonder, Stephane Ballereau, Cornelis J Vermeulen, Raul Aguirre-Gamboa, Johan C de Jongste, Henriette A Smit, Ashish Kumar, Göran Pershagen, Stefano Guerra, Judith Garcia-Aymerich, Dario Greco, Lovisa Reinius, Rosemary R C McEachan, Raf Azad, Vegard Hovland, Petter Mowinckel, Harri Alenius, Nanna Fyhrquist, Nathanaël Lemonnier, Johann Pellet, Charles Auffray, Pieter van der Vlies, Cleo C van Diemen, Yang Li, Cisca Wijmenga, Mihai G Netea, Miriam F Moffatt, William O C M Cookson, Josep M Anto, Jean Bousquet, Tiina Laatikainen, Catherine Laprise, Kai-Håkon Carlsen, Davide Gori, Daniela Porta, Carmen Iñiguez, Jose Ramon Bilbao, Manolis Kogevinas, John Wright, Bert Brunekreef, Juha Kere, Martijn C Nawijn, Isabella Annesi-Maesano, Jordi Sunyer, Erik Melén, Gerard H Koppelman
BACKGROUND: DNA methylation profiles associated with childhood asthma might provide novel insights into disease pathogenesis. We did an epigenome-wide association study to assess methylation profiles associated with childhood asthma. METHODS: We did a large-scale epigenome-wide association study (EWAS) within the Mechanisms of the Development of ALLergy (MeDALL) project. We examined epigenome-wide methylation using Illumina Infinium Human Methylation450 BeadChips (450K) in whole blood in 207 children with asthma and 610 controls at age 4-5 years, and 185 children with asthma and 546 controls at age 8 years using a cross-sectional case-control design...
February 26, 2018: Lancet Respiratory Medicine
Brian Thomas Joyce, Yinan Zheng, Zhou Zhang, Lei Liu, Masha Kocherginsky, Robert Murphy, Chad Achenbach, Jonah Musa, Firas Wehbe, Allan Just, Jincheng Shen, Pantel Vokonas, Joel Schwartz, Andrea Baccarelli, Lifang Hou
BACKGROUND: Dysregulation of microRNA (miRNA) and methylation levels are epigenetic hallmarks of cancer, potentially linked via miRNA processing genes. Studies have found genetic alterations to miRNA processing genes in cancer cells and human population studies. Our objective was to prospectively examine changes in DNA methylation of miRNA processing genes and their associations with cancer risk. METHODS: We examined cohort data from the Department of Veterans' Affairs' Normative Aging Study...
February 23, 2018: Cancer Epidemiology, Biomarkers & Prevention
Jacqueline Alexander, April M Teague, Jing Chen, Christopher E Aston, Yuet-Kin Leung, Steven Chernausek, Rebecca A Simmons, Sara E Pinney
AIMS/HYPOTHESIS: We hypothesized that diabetes during pregnancy (DDP) alters genome-wide DNA methylation in placenta resulting in differentially methylated loci of metabolically relevant genes and downstream changes in RNA and protein expression. METHODS: We mapped genome-wide DNA methylation with the Infinium 450K Human Methylation Bead Chip in term fetal placentae from Native American and Hispanic women with DDP using a nested case-control design (n = 17 pairs)...
2018: PloS One
I V Yang, W Zhang, E J Davidson, T E Fingerlin, K Kechris, D Dabelea
AIMS: To identify gestational diabetes mellitus exposure-associated DNA methylation changes and assess whether such changes are also associated with adiposity-related outcomes. METHODS: We performed an epigenome-wide association analysis, using Illumina 450k methylation arrays, on whole blood collected, on average, at 10.5 years of age from 81 gestational diabetes-exposed and 81 unexposed offspring enrolled in the EPOCH (Exploring Perinatal Outcomes in Children) study, and on the cord blood of 31 gestational diabetes-exposed and 64 unexposed offspring enrolled in our own 'Healthy Start' cohort...
February 20, 2018: Diabetic Medicine: a Journal of the British Diabetic Association
Diana A van der Plaat, Kim de Jong, Maaike de Vries, Cleo C van Diemen, Ivana Nedeljković, Najaf Amin, Hans Kromhout, Roel Vermeulen, Dirkje S Postma, Cornelia M van Duijn, H Marike Boezen, Judith M Vonk
OBJECTIVES: Occupational pesticide exposure is associated with a wide range of diseases, including lung diseases, but it is largely unknown how pesticides influence airway disease pathogenesis. A potential mechanism might be through epigenetic mechanisms, like DNA methylation. Therefore, we assessed associations between occupational exposure to pesticides and genome-wide DNA methylation sites. METHODS: 1561 subjects of LifeLines were included with either no (n=1392), low (n=108) or high (n=61) exposure to any type of pesticides (estimated based on current or last held job)...
February 19, 2018: Occupational and Environmental Medicine
Genevieve Housman, Lorena M Havill, Ellen E Quillen, Anthony G Comuzzie, Anne C Stone
Objective Osteoarthritis (OA) affects humans and several other animals. Thus, the mechanisms underlying this disorder, such as specific skeletal tissue DNA methylation patterns, may be evolutionary conserved. However, associations between methylation and OA have not been readily studied in nonhuman animals. Baboons serve as important models of disease and develop OA at rates similar to those in humans. Therefore, this study investigated the associations between methylation and OA in baboons to advance the evolutionary understanding of OA...
February 1, 2018: Cartilage
George S Krasnov, Nataliya V Melnikova, Valentina A Lakunina, Anastasiya V Snezhkina, Anna V Kudryavtseva, Alexey A Dmitriev
We present MethyMer, a Python-based tool aimed at selecting primers for amplification of complete CpG islands. These regions are difficult in terms of selecting appropriate primers because of their low-complexity, high GC content. Moreover, bisulfite treatment, in fact, leads to the reduction of the 4-letter alphabet (ATGC) to 3-letter one (ATG, except for methylated cytosines), and this also reduces region complexity and increases mispriming potential. MethyMer has a flexible scoring system, which optimizes the balance between various characteristics such as nucleotide composition, thermodynamic features (melting temperature, dimers [Formula: see text]G, etc...
January 30, 2018: Journal of Bioinformatics and Computational Biology
Marie Forest, Kieran J O'Donnell, Greg Voisin, Helene Gaudreau, Julia L MacIsaac, Lisa M McEwen, Patricia P Silveira, Meir Steiner, Michael S Kobor, Michael J Meaney, Celia M T Greenwood
Epigenome-wide association studies (EWAS) have focused primarily on DNA methylation as a chemically stable and functional epigenetic modification. However, the stability and accuracy of the measurement of methylation in different tissues and extraction types is still being actively studied, and the longitudinal stability of DNA methylation in commonly studied peripheral tissues is of great interest. Here, we used data from two studies, three tissue types, and multiple time points to assess the stability of DNA methylation measured with the Illumina Infinium HumanMethylation450 BeadChip array...
January 30, 2018: Epigenetics: Official Journal of the DNA Methylation Society
Yonghong Zhang, Sophie Petropoulos, Jinhua Liu, David Cheishvili, Rudy Zhou, Sergiy Dymov, Kang Li, Ning Li, Moshe Szyf
Background: The idea that changes to the host immune system are critical for cancer progression was proposed a century ago and recently regained experimental support. Results: Herein, the hypothesis that hepatocellular carcinoma (HCC) leaves a molecular signature in the host peripheral immune system was tested by profiling DNA methylation in peripheral blood mononuclear cells (PBMC) and T cells from a discovery cohort (n = 69) of healthy controls, chronic hepatitis, and HCC using Illumina 450K platform and was validated in two validation sets (n = 80 and n = 48) using pyrosequencing...
2018: Clinical Epigenetics
Izabela M Krzyzewska, Judith B M Ensink, Laura Nawijn, Adri N Mul, Saskia B Koch, Andrea Venema, Vinod Shankar, Jessie L Frijling, Dirk J Veltman, Ramon J L Lindauer, Miranda Olff, Marcel M A M Mannens, Mirjam van Zuiden, Peter Henneman
Posttraumatic stress disorder (PTSD) is a debilitating psychiatric disorder that may develop after a traumatic event. Here we aimed to identify epigenetic and genetic loci associated with PTSD. We included 73 traumatized police officers with extreme phenotypes regarding symptom severity despite similar trauma history: n = 34 had PTSD and n = 39 had minimal PTSD symptoms. Epigenetic and genetic profiles were based on the Illumina HumanMethylation450 BeadChip. We searched for differentially methylated probes (DMPs) and differentially methylated regions (DMRs)...
January 23, 2018: European Journal of Human Genetics: EJHG
Y Alkhaled, M Laqqan, S Tierling, C Lo Porto, H Amor, M E Hammadeh
DNA methylation is an epigenetic modification of the genome. The purpose of this study was to determine the influence of cigarette-smoking on sperm DNA methylation from a genomewide survey of sperm samples and to ascertain its effect on sperm parameters. Twenty-eight sperm DNA samples (from 14 fertile smokers as a case study and 14 proven fertile nonsmokers as controls) were subjected to Infinium 450K BeadChip arrays to identify the changes in the DNA methylation level between the two groups. Then, deep bisulphite sequencing was used to validate five CpGs on 78 samples...
January 9, 2018: Andrologia
Zoya Marinova, Andreas Maercker, Edna Grünblatt, Tomasz K Wojdacz, Susanne Walitza
OBJECTIVE: Complex posttraumatic stress disorder (CPTSD) is a newly proposed diagnosis in the International Classification of Diseases-version 11, which is currently intensively investigated. Childhood trauma is regarded as main source of CPTSD symptoms, even in later life. Induction of DNA methylation changes by childhood trauma may contribute to its long-lasting adverse health consequences. The current study analyzed the correlation of genome-wide DNA methylation profiles with complex posttraumatic sequelae in buccal epithelial cells from 31 elderly former indentured child laborers (Verdingkinder) using the Infinium Illumina 450k Human DNA methylation chip...
December 19, 2017: BMC Research Notes
Lars Lind, Erik Ingelsson, Johan Sundström, Agneta Siegbahn, Erik Lampa
BACKGROUND: DNA methylation changes over life at specific sites in the genome, which can be used to estimate "biological age." The aim of this population-based longitudinal cohort study was to investigate the association between estimated biological age and incident cardiovascular disease (CVD). MATERIALS AND METHODS: Based on formulas published by Hannum et al and Horvath et al, "biological age" was calculated using data from the Illumina 450k Bead Methylation chip in 832 participants free from cardiovascular disease in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (50% women, all aged 70 years at the examination)...
February 2018: European Journal of Clinical Investigation
M Laqqan, M E Hammadeh
This study was designed to evaluate the DNA methylation patterns and gene expression in spermatozoa from subfertile males. Thirty samples were subjected to 450K arrays as a screening study to evaluate the variation in sperm DNA methylation levels between cases and controls groups, and then three CpG sites (cg07227024, cg05813498 and cg23081194) have the highest difference in methylation levels and located within ALS2CR12, GAA and UBE2G2 genes respectively; these were selected for further analysis using deep bisulphite sequencing and qPCR in 136 samples (64 proven fertile males "controls" and 72 subfertile males "cases")...
April 2018: Andrologia
Michael C Wu, Pei-Fen Kuan
The Illumina Infinium BeadChips are a powerful array-based platform for genome-wide DNA methylation profiling at approximately 485,000 (450K) and 850,000 (EPIC) CpG sites across the genome. The platform is used in many large-scale population-based epigenetic studies of complex diseases, environmental exposures, or other experimental conditions. This chapter provides an overview of the key steps in analyzing Illumina BeadChip data. We describe key preprocessing steps including data extraction and quality control as well as normalization strategies...
2018: Methods in Molecular Biology
Pierre-Antoine Dugué, Julie K Bassett, JiHoon E Joo, Chol-Hee Jung, Ee Ming Wong, Margarita Moreno-Betancur, Daniel Schmidt, Enes Makalic, Shuai Li, Gianluca Severi, Allison M Hodge, Daniel D Buchanan, Dallas R English, John L Hopper, Melissa C Southey, Graham G Giles, Roger L Milne
The association between aging and cancer is complex. Recent studies have developed measures of biological aging based on DNA methylation and called them "age acceleration." We aimed to assess the associations of age acceleration with risk of and survival from seven common cancers. Seven case-control studies of DNA methylation and colorectal, gastric, kidney, lung, prostate and urothelial cancer and B-cell lymphoma nested in the Melbourne Collaborative Cohort Study were conducted. Cancer cases, vital status and cause of death were ascertained through linkage with cancer and death registries...
April 15, 2018: International Journal of Cancer. Journal International du Cancer
Wen Wang, Zheng Zhao, Fan Wu, Haoyuan Wang, Jiangfei Wang, Qing Lan, Jizong Zhao
Different gene expression and methylation profiles are identified in glioblastoma (GBM). To screen the differentially expressed genes affected by DNA methylation modification and further investigate their prognostic values for GBMs. We included The Cancer Genome Atlas (TCGA) RNA sequencing (676) and DNA methylation (Illumina Human Methylation 450K; 657) databases to detect the gene expression and methylation profiles. Chinese Glioma Genome Atlas (CGGA) RNA sequencing database and TCGA DNA methylation (Illumina Human Methylation 27K; 283) was included for validation...
November 22, 2017: Journal of Neuro-oncology
Eliza Walaszczyk, Mirjam Luijten, Annemieke M W Spijkerman, Marc J Bonder, Helen L Lutgers, Harold Snieder, Bruce H R Wolffenbuttel, Jana V van Vliet-Ostaptchouk
AIMS/HYPOTHESIS: Epigenetic mechanisms may play an important role in the aetiology of type 2 diabetes. Recent epigenome-wide association studies (EWASs) identified several DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels. Here we present a systematic review of these studies and attempt to replicate the CpG sites (CpGs) with the most significant associations from these EWASs in a case-control sample of the Lifelines study. METHODS: We performed a systematic literature search in PubMed and EMBASE for EWASs to test the association between DNA methylation and type 2 diabetes and/or glycaemic traits and reviewed the search results...
November 21, 2017: Diabetologia
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