Article
Gastroenterology & Hepatology
Runhua Lin, Yanli Qian, Jinhai Zhang, Di Xia, Dongming Guo, Liangli Hong, Bojuan Qing, Muming Xu, Yiteng Huang, Wenting Lin, Guangcan Chen, Shuhui Liu
Summary: This study identifies DNA methylation aberrations in gastric cardia cancer (GCC) and demonstrates that ADHFE1 gene DNA methylation contributes to the risk of GCC. These findings provide novel mechanistic insights into gastric cardia cancer carcinogenesis.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Medicine, General & Internal
Rashidah Baharudin, Muhiddin Ishak, Azliana Muhamad Yusof, Sazuita Saidin, Saiful Effendi Syafruddin, Wan Fahmi Wan Mohamad Nazarie, Learn-Han Lee, Nurul-Syakima Ab Mutalib
Summary: This study profiles the DNA methylation in colorectal cancer (CRC) and identifies several potential important methylated genes, which may serve as novel candidate biomarker genes in CRC. Aberrant DNA methylation is significantly involved in CRC pathogenesis and is associated with gene silencing.
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
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.
Article
Plant Sciences
Andrew Read, Trevor Weiss, Peter A. Crisp, Zhikai Liang, Jaclyn Noshay, Claire C. Menard, Chunfang Wang, Meredith Song, Candice N. Hirsch, Nathan M. Springer, Feng Zhang
Summary: The study revealed the importance of DOMAIN REARRANGED METHYLTRANSFERASEs (DRMs) in RNA-directed DNA methylation (RdDM) in plants. By using CRISPR-based genome editing, loss-of-function alleles for two putative functional DRM genes in S. viridis were created, showing the loss of methylation, altered gene expression, and activation of transposons in drm1ab mutants. These findings highlight the significance of RdDM in gene expression regulation and transposon repression.
Article
Medicine, General & Internal
Luyao Zhao, Muran Li, Shiwu Zhang, Yandi Liu
Summary: This study evaluated the potential performance of plasma SEPT9 methylation as a noninvasive biomarker for the diagnosis of gastric cancer. The results suggest that mSEPT9 may serve as a useful and noninvasive biomarker for the diagnosis of gastric cancer.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Gastroenterology & Hepatology
Xinting Pan, Yunli Wu, Hewei Peng, Xiaoling Cai, Zhijian Hu, Xu Lin, Xian-e Peng
Summary: This study identified potential DNA methylation biomarkers for nonalcoholic fatty liver disease (NAFLD) through genome-wide DNA methylation profiling. The hypomethylation of PRKCE and SEC14L3 promoters was found to be associated with NAFLD, suggesting their potential as attractive biomarkers.
DIGESTIVE AND LIVER DISEASE
(2022)
Article
Veterinary Sciences
Adelaida Hernaiz, Arianne Sanz, Sara Sentre, Beatriz Ranera, Oscar Lopez-Perez, Pilar Zaragoza, Juan J. Badiola, Hicham Filali, Rosa Bolea, Janne M. Toivonen, Inmaculada Martin-Burriel
Summary: This study found DNA methylation alterations in the thalamus of sheep infected with scrapie, a form of transmissible spongiform encephalopathy. Hypomethylated regions were associated with genes involved in transmembrane transport and cell adhesion, while hypermethylated regions were related to genes involved in intracellular signal transduction. Furthermore, differentially expressed genes and genes highly expressed in specific types of CNS cells contained differentially methylated regions.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Physiology
Ainash Childebayeva, Taylor Harman, Julien Weinstein, Trevor Day, Tom D. Brutsaert, Abigail W. Bigham
Summary: The physiological response to high-altitude hypoxia involves genetic and non-genetic factors, including epigenetic modifications. Epigenetic changes in HIF and RAS pathways were significant at high altitudes. The study identified numerous differentially methylated positions and regions associated with altitude ascent, as well as an association between ACE gene polymorphism and oxygen saturation.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Oncology
Yuyan Han, Mutian Zhang, Junfeng Xu, Jia Li, Yifan Xu, Timothy C. Thompson, Christopher J. Logothetis, Deqiang Sun, Jian Gu
Summary: The study identified a CpG methylation signature in leukocyte DNA associated with aggressive clinical features of prostate cancer.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Article
Medicine, Research & Experimental
Xianghai Liao, Peter J. Kennel, Bohao Liu, Trevor R. Nash, Richard Z. Zhuang, Amandine F. Godier-Furnemont, Chenyi Xue, Rong Lu, Paolo C. Colombo, Nir Uriel, Muredach P. Reilly, Steven O. Marx, Gordana Vunjak-Novakovic, Veli K. Topkara
Summary: Heart failure (HF) is characterized by global alterations in myocardial DNA methylation, and this study investigates the epigenetic regulation of the noncoding genome and reversibility of DNA methylation with LVAD therapy. Mapping of myocardial DNA methylation in HF patients at LVAD implantation and explantation, as well as nonfailing donors, identifies differentially methylated positions (DMPs) in ischemic and nonischemic cardiomyopathy. LVAD support results in normalization of a small percentage of HF-associated DMPs, and analysis reveals genes that are hypomethylated and upregulated or hypermethylated and downregulated in HF. Additionally, a cardiac-specific super-enhancer lncRNA is found to be hypermethylated and downregulated in human HF and is an upstream regulator of gene expression related to sarcomere and calcium channels. These findings suggest that HF-associated changes in DNA methylation are minimally reversible with mechanical unloading, and epigenetic reprogramming may be necessary for sustained clinical recovery from heart failure.
Review
Biochemistry & Molecular Biology
Irina V. Bure, Marina V. Nemtsova
Summary: Despite recent progress, gastric cancer remains a common and deadly cancer with aberrant DNA methylation and deregulation of noncoding RNA expression playing a significant role in tumorigenesis. Interactions among these epigenetic regulators form a complex network that has potential implications for diagnosis, prognosis, and treatment of gastric cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Oncology
Ze Qian, Yifan Jiang, Chunhui Shou, Jinghua Yu, Dongdong Huang, Haiyang Xie, Lin Zhou, Diyu Chen, Shusen Zheng
Summary: In this study, it was found that TFF1 and TFF2 genes are regulated by DNA methylation in gastric cancer and they can suppress the pathogenesis of gastric cancer. These findings suggest that TFF1 and TFF2 could be potential biomarkers and therapeutic targets for gastric cancer.
