Article
Biochemistry & Molecular Biology
Bo Yan, Duan Wang, Romualdas Vaisvila, Zhiyi Sun, Laurence Ettwiller
Summary: Covalent modifications of genomic DNA are essential for the survival of organisms. Methyl-SNP-seq is a novel technology that can extract methylation and original sequence information using the complementarity of the double helix. It allows detection of the methylation status of any DNA, even without a reference genome.
Article
Dentistry, Oral Surgery & Medicine
Oscar Rapado-Gonzalez, Nicolas Costa-Fraga, Aida Bao-Caamano, Jose Luis Lopez-Cedrun, Roberto Alvarez-Rodriguez, Ana Belen Crujeiras, Laura Muinelo-Romay, Rafael Lopez-Lopez, Angel Diaz-Lagares, Maria Mercedes Suarez-Cunqueiro
Summary: This is the first large-scale genome-wide DNA methylation study on OTSCC, identifying a group of novel tumor-specific DNA methylation markers with diagnostic potential in saliva.
Article
Oncology
Nitin Patil, Mohammed L. Abba, Chan Zhou, Shujian Chang, Timo Gaiser, Joerg H. Leupold, Heike Allgayer
Summary: Changes in methylation patterns can significantly impact the expression of miRs involved in cancer progression and metastasis, highlighting alternative mechanisms of gene regulation. Genome-wide methylation analysis in colorectal cancer revealed differential methylation of several miR genes, with implications for important cancer-related pathways. These findings suggest the importance of considering epigenetic changes in addition to genetic and transcriptional regulation of miRs in cancer.
Article
Genetics & Heredity
Majid Nikpay
Summary: This study integrated GWAS data and used Mendelian randomization to identify 107 methylation sites associated with 84 metabolites. The majority of associations were with lipids, which was significantly higher than expected. The study also identified 82 genes that mediate the impact of methylation sites on metabolites and cardiometabolic traits.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Alberto Magi, Gianluca Mattei, Alessandra Mingrino, Chiara Caprioli, Chiara Ronchini, GianMaria Frige, Roberto Semeraro, Davide Bolognini, Alessandro Rambaldi, Anna Candoni, Emanuela Colombo, Luca Mazzarella, Pier Giuseppe Pelicci
Summary: DNA methylation patterns in sparse CpG regions drive chemoresistance in Acute Myeloid Leukemia patients.
COMMUNICATIONS BIOLOGY
(2023)
Article
Clinical Neurology
Bo Hao, Bu Fang Fan, Can-Can Cao, Lu Liu, Shou-Min Xuan, Li Wang, Zhen-Jie Gao, Yan-Wei Shi, Xiao-Guang Wang, Hu Zhao
Summary: Fear memory is critical for individual survival, but maladaptive fear response is a hallmark of fear-related disorders. This study reveals the role of nucleus accumbens (NAc) and DNA methylation in fear discrimination. Inhibition of DNA methyltransferase 3a gene (DNMT3a) in NAc leads to a maladaptive fear response, while whole-genome bisulfite sequencing (WGBS) identifies differentially methylated sites and genes related to synaptic function and cGMP-PKG signaling pathway.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2023)
Article
Immunology
Ling Guo, Hongxing Cheng, Shulin Fu, Jun Liu, Yunfei Zhang, Yinsheng Qiu, Hongbo Chen
Summary: This study analyzed the changes in DNA methylome and transcriptome of porcine brain infected with G. parasuis using deep sequencing, and integrated the data to identify key differential methylation regions/sites involved in the regulation of the inflammatory response. The findings showed that the genes inversely correlated with DNA methylation were mainly associated with cell adhesion molecules, bacterial invasion, RIG-1-like receptor signaling pathways, and hematopoietic cell lineage signaling pathways.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Jihoon E. Joo, Khalid Mahmood, Romy Walker, Peter Georgeson, Ida Candiloro, Mark Clendenning, Julia Como, Sharelle Joseland, Susan Preston, Lise Graversen, Mathilda Wilding, Michael Field, Michelle Lemon, Janette Wakeling, Helen Marfan, Rachel Susman, Joanne Isbister, Emma Edwards, Michelle Bowman, Judy Kirk, Emilia Ip, Lynne McKay, Yoland Antill, John L. Hopper, Alex Boussioutas, Finlay A. Macrae, Alexander Dobrovic, Mark A. Jenkins, Christophe Rosty, Ingrid M. Winship, Daniel D. Buchanan
Summary: MLH1 epimutation can cause colorectal cancer, and it can be classified into germline MLH1 promoter variants and MLH1 methylated early-onset CRCs based on tumour molecular profiles. Genome-wide DNA methylation and somatic mutational profiles were compared between different types of MLH1 epimutation CRCs and reference CRCs. Mosaic MLH1 methylation can be detected in blood, normal mucosa, and buccal DNA using methylation-sensitive ddPCR.
CLINICAL EPIGENETICS
(2023)
Article
Biochemistry & Molecular Biology
Aleksandra Gorska, Maria Urbanowicz, Lukasz Grochowalski, Michal Seweryn, Marta Sobalska-Kwapis, Tomasz Wojdacz, Magdalena Lange, Marta Gruchala-Niedoszytko, Justyna Jarczak, Dominik Strapagiel, Magdalena Gorska-Ponikowska, Iwona Pelikant-Malecka, Leszek Kalinowski, Boguslaw Nedoszytko, Danuta Gutowska-Owsiak, Marek Niedoszytko
Summary: This study aimed to identify the differential methylation profiles and gene expression patterns associated with mastocytosis, a heterogenous disease of the mast cells. Genome-wide DNA methylation analysis was performed on peripheral blood samples from mastocytosis patients and healthy controls. The results showed significant differences in methylation levels of selected regions, including 31 genes located within the regulatory regions. Additionally, three oncogenes-FOXQ1, TWIST1, and ERG-were found to be differentially methylated in mastocytosis patients for the first time. These findings provide insights into the methylation landscape of mastocytosis and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Hongxu Ding, Ioannis Anastopoulos, Andrew D. Bailey, Joshua Stuart, Benedict Paten
Summary: This study introduces a deep learning framework that can predict the characteristic ionic currents of nucleotides to enable novel detection of nucleotide modifications, particularly methylated cytosine and guanine, without the need for controls.
NATURE COMMUNICATIONS
(2021)
Article
Allergy
Loreen Thuermann, Matthias Kloes, Sebastian D. Mackowiak, Matthias Bieg, Tobias Bauer, Naveed Ishaque, Marey Messingschlager, Carl Herrmann, Stefan Roeder, Mario Bauer, Sascha Schaeuble, Erik Faessler, Udo Hahn, Dieter Weichenhan, Oliver Muecke, Christoph Plass, Michael Borte, Erika von Mutius, Gabriele I. Stangl, Roger Lauener, Anne M. Karvonen, Amandine Divaret-Chauveau, Josef Riedler, Joachim Heinrich, Marie Standl, Andrea von Berg, Beate Schaaf, Gunda Herberth, Michael Kabesch, Roland Eils, Saskia Trump, Irina Lehmann
Summary: This study used whole genome bisulfite sequencing to identify dysregulation of enhancer regions as a hallmark of childhood asthma. Abnormal DNA methylation was found in key immune genes and was linked to prenatal influences and genetic susceptibility.
Article
Genetics & Heredity
Bastien Ducreux, Jean Frappier, Celine Bruno, Abiba Doukani, Magali Guilleman, Emmanuel Simon, Aurelie Martinaud, Deborah Bourc'his, Julie Barberet, Patricia Fauque
Summary: This study investigated the DNA methylation profiles of 7-8-year-old children conceived through assisted reproductive technology (ART) or naturally, and found that ART-conceived children displayed limited genome-wide DNA methylation variation compared to naturally conceived children. The mode of conception did not significantly affect DNA methylation differences in childhood.
Article
Sport Sciences
Yuichiro Nishida, Megumi Hara, Hideki Ohmomo, Kanako Ono, Atsushi Shimizu, Mikako Horita, Chisato Shimanoe, Naoto Taguchi, Yasuki Higaki, Keitaro Tanaka
Summary: This study found that higher accelerometer-assessed total PA was associated with increased DNA methylation levels at the cg07030336 (VTI1A/ZDHHC6) site in the general population in Japan. In addition, a divergent relationship was found between methylation levels at the cg07030336 site and several inflammatory biomarkers.
MEDICINE & SCIENCE IN SPORTS & EXERCISE
(2022)
Article
Oncology
Qingxiao Fang, Ziming Yuan, Hanqing Hu, Weiyuan Zhang, Guiyu Wang, Xishan Wang
Summary: Through genome-wide analysis and validation, we identified four CpG sites (cg04486886, cg06712559, cg13539460, and cg27541454) as DNA methylation markers in colorectal cancer tissues. The diagnostic prediction model based on these markers can effectively distinguish colorectal cancer from polyp patients, and the md-score can robustly detect colorectal cancer. The cg27541454 may be a promising candidate noninvasive biomarker for early diagnosis of colorectal cancer.
CLINICAL EPIGENETICS
(2023)
Article
Medicine, General & Internal
Andres Esteban-Cantos, Javier Rodriguez-Centeno, Juan C. Silla, Pilar Barruz, Fatima Sanchez-Cabo, Gabriel Saiz-Medrano, Julian Nevado, Beatriz Mena-Garay, Maria Jimenez-Gonzalez, Rosa de Miguel, Jose I. Bernardino, Roco Montejano, Julen Cadinanos, Cristina Marcelo, Lucia Gutierrez-Garcia, Patricia Martinez-Martin, Cedrick Wallet, Francois Raffi, Berta Rodes, Jose R. Arribas
Summary: This study investigates the effects of antiretroviral therapy (ART) on HIV-induced epigenetic modifications. It found that ART initiation modified DNA methylation levels at 845 CpG positions, with 49.3% of the changes being restored to the uninfected state. Untreated HIV infection was associated with DNA methylation changes in biological processes regulating the immune system and antiviral responses. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio.