Article
Cardiac & Cardiovascular Systems
Yuru Han, Baoyu Duan, Jing Wu, Yanjun Zheng, Yinchen Gu, Xiaomeng Cai, Changlian Lu, Xubo Wu, Yanfei Li, Xuefeng Gu
Summary: This study utilized RNA-seq and MeDIP-seq to analyze the genetic and epigenetic features of myocardial infarction (MI) at the early stages, revealing changes in gene expression and methylation regions associated with immune response, apoptosis, and energy metabolism. The study identified potential drug targets in genes related to apoptosis and inflammation, as well as highlighted the importance of methylation changes in genes affecting processes such as cardiac muscle contraction and angiogenesis during MI progression.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Oncology
Xiaoli Luo, Yi Hu, Junwei Shen, Xinwen Liu, Tao Wang, Li Li, Jue Li
Summary: This study used RNA-seq and MeDIP-seq technologies to observe gene expression and DNA methylation changes in an AMI mouse model. We found a large number of differential methylation positions and differentially expressed genes at different stages of AMI. Especially, the 6-hour stage of AMI showed significant changes in DEGs and enriched functional pathways in KEGG, suggesting it may be the most critical stage of AMI. We also identified genes that showed a negative correlation between mRNA expression and DNA methylation, and confirmed their function through experimental validation.
CLINICAL EPIGENETICS
(2022)
Article
Biochemistry & Molecular Biology
Ping Zhang, Yongke Lu, Yanli Li, Kesheng Wang, Huimei An, Yunlong Tan
Summary: This study identified a number of methylated genes and pathways associated with tardive dyskinesia (TD) in schizophrenia patients. These findings may provide potential biomarkers for TD and serve as a resource for replication in other populations.
Article
Biochemistry & Molecular Biology
Nhan Nguyen, Matthias Lienhard, Ralf Herwig, Jos Kleinjans, Danyel Jennen
Summary: In this study, the DNA methylation profile and gene expression changes in response to Epirubicin treatment were analyzed in human cardiac microtissues. The results revealed multiple differentially methylated genes that may be involved in cardiac dysfunction mechanisms. These findings provide valuable insights into the toxic effects of Epirubicin on the heart.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2022)
Article
Genetics & Heredity
Yuezhen Tian, Xuemei Yang, Jianwen Du, Weidan Zeng, Weiwei Wu, Jiang Di, Xixia Huang, Kechuan Tian
Summary: The study utilized MeDIP-seq to obtain a genome-wide methylation map of hair follicle development in Super Merino sheep, identifying 65 genes with both differential methylation and expression. Differential methylation genes were found enriched in signaling pathways related to hair follicle development, and further exploration of WNT2 gene function revealed its promotion of skin and hair follicle growth and development. The results provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
FRONTIERS IN GENETICS
(2021)
Article
Environmental Sciences
Yujian Sang, Jianhui Liu, Xiangyang Li, Guiqing Zhou, Yue Zhang, Leqiang Gao, Yanzhi Zhao, Xianqing Zhou
Summary: This study revealed that SiNPs caused extensive methylation changes in the genome of GC-2 cells, identifying 428 hyper-methylated genes and 398 hypo-methylated genes. Gene Ontology and pathway analysis showed that differential DNA methylation induced by SiNPs was probably involved with abnormal transcription and translation, mitochondrial damage, and cell apoptosis.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Cell Biology
Kamalnath S. Rajagopalan, Sara Kazeminia, Logan M. Glasstetter, Rahele A. Farahani, Xiang-Yang Zhu, Hui Tang, Kyra L. Jordan, Alejandro R. Chade, Amir Lerman, Lilach O. Lerman, Alfonso Eirin
Summary: Autologous mesenchymal stem/stromal cells (MSCs) have therapeutic effects in various diseases. Metabolic syndrome (MetS) can induce epigenetic alterations in mitochondria-related genes in porcine MSCs, but this can be modulated by vitamin C. These findings contribute to the development of strategies to mitigate the detrimental effects of MetS on MSCs.
Article
Oncology
Xin Zhang, Tao Li, Qiang Niu, Chang-jiang Qin, Ming Zhang, Guang-ming Wu, Hua-zhong Li, Yan Li, Chen Wang, Wen-fei Du, Chen-yang Wang, Qiang Zhao, Xiao-dong Zhao, Xiao-liang Wang, Jian-bin Zhu
Summary: This study identified potential biomarkers for colorectal cancer using genome-wide plasma cfDNA methylation analysis, and found that four differentially methylated genes could serve as potential biomarkers for clinical application in patients with colorectal cancer.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniel Beck, Millissia Ben Maamar, Michael K. Skinner
Summary: Genome-wide DNA methylation analysis is commonly used for genome characterization and differential DNA methylation assessment, with CpG density playing a crucial role in different molecular techniques. Observations show that most genomes have low CpG density, with MeDIP focusing on <5 CpG/100 bp regions and RRBS identifying higher CpG density areas.
Article
Agriculture, Dairy & Animal Science
X-J Li, L-Q Liu, H. Dong, J-J Yang, W-W Wang, Q. Zhang, C-L Wang, J. Zhou, H-Q Cheng
Summary: The study identified differentially methylated genes associated with fatty acid metabolism, muscle development, and pork quality through DNA methylation analysis of two pig breeds. Integrative analysis revealed a significant negative correlation between DNA methylation levels and gene expression levels. Differential methylation of genes related to fat metabolism, lipid metabolism, and skeletal muscle development may contribute to the growth and phenotypic differences observed among different pig breeds.
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
Biochemistry & Molecular Biology
Carolyn F. McCabe, Jennifer L. LaBarre, Steven E. Domino, Marjorie C. Treadwell, Ana Baylin, Charles F. Burant, Dana C. Dolinoy, Vasantha Padmanabhan, Jaclyn M. Goodrich
Summary: Maternal prenatal status plays a crucial role in offspring health and disease, and alterations in DNA methylation may be a mechanism through which suboptimal prenatal conditions confer disease risk later in life. This study investigated the association between maternal one-carbon metabolites and DNA methylation patterns in newborns. The findings highlight the importance of maternal diet and cellular methylation potential in shaping offspring health.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Genetics & Heredity
Rohini Dhat, Dattatray Mongad, Sivarupa Raji, Silpa Arkat, Nitish R. Mahapatra, Nishant Singhal, Sandhya L. Sitasawad
Summary: This study aims to investigate the role of DNA methylation patterns in the development of diabetic cardiomyopathy (DCM) and the effect of AKG supplementation on DCM progression. Genome-wide DNA (hydroxy)methylation profiles were determined in the hearts of control and STZ-induced diabetic rats, and the therapeutic effect of AKG was evaluated. The results showed that the accumulation of 5mC and 5hmC in diabetic hearts was associated with impaired cardiac function and significantly affected calcium signaling. AKG supplementation reversed aberrant methylation patterns and restored cardiac function.
EPIGENETICS & CHROMATIN
(2023)
Article
Biotechnology & Applied Microbiology
F. Naya-Catala, A. Belenguer, D. Montero, S. Torrecillas, B. Soriano, J. Calduch-Giner, C. Llorens, R. Fontanillas, S. Sarih, M. J. Zamorano, M. Izquierdo, J. Perez-Sanchez
Summary: The study found that the influence of broodstock nutrition on gilthead sea bream with different genetic backgrounds results in distinct hepatic transcriptome and genome-wide DNA methylation patterns, with the magnitude of the impact depending on the genetic background.
Article
Biochemistry & Molecular Biology
Laura Moody, Guanying Bianca Xu, Hong Chen, Yuan-Xiang Pan
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2019)
Article
Biochemistry & Molecular Biology
Laura Moody, Daniel Kougias, Paul M. Jung, Isabel Digan, Aaron Hong, Aleksandra Gorski, Hong Chen, Janice Juraska, Yuan-Xiang Pan
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2019)
Article
Nutrition & Dietetics
Laura Moody, Justin Shao, Hong Chen, Yuan-Xiang Pan
Article
Endocrinology & Metabolism
Huan Wang, Guanying Bianca Xu, Diego Hernandez-Saavedra, Hong Chen, Yuan-Xiang Pan
AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM
(2020)
Article
Physiology
Tiffany Y. Yang, Jennie C. Gardner, Zijun Gao, Yuan-Xiang Pan, Nu-Chu Liang
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
(2020)
Article
Genetics & Heredity
Laura Moody, Hong Chen, Yuan-Xiang Pan
BMC MEDICAL GENOMICS
(2020)
Article
Oncology
Laura Moody, Sylvia L. Crowder, Andrew D. Fruge, Julie L. Locher, Wendy Demark-Wahnefried, Laura Q. Rogers, Ashley Delk-Licata, William R. Carroll, Sharon A. Spencer, Molly Black, John W. Erdman, Hong Chen, Yuan-Xiang Pan, Anna E. Arthur
CLINICAL EPIGENETICS
(2020)
Article
Gastroenterology & Hepatology
Huan Wang, Guanying Bianca Xu, Hong Chen, Yuan-Xiang Pan
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Diego Hernandez-Saavedra, Laura Moody, Xinyu Tang, Zachary J. Goldberg, Alex P. Wang, Hong Chen, Yuan-Xiang Pan
Summary: Chronic caloric restriction (CR) was found to significantly reduce muscle inflammation and TNF levels, while affecting cells' methylation status and regulating transcriptional and post-transcriptional regulation. This suggests that chronic CR can regulate muscle inflammation through multiple pathways.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2021)
Article
Nutrition & Dietetics
Mingzhu Cai, Jie Zhang, Hong Chen, Yuan-Xiang Pan
Summary: This study reveals that maternal protein restriction can transcriptionally program hepatic autophagy-related gene expression specifically in female rat offspring through the activation of the eIF2 alpha/ATF4 pathway and intricate regulation by transcription factors such as ATF4 and CHOP.
BRITISH JOURNAL OF NUTRITION
(2022)
Article
Biochemical Research Methods
Laura Moody, Guanying Bianca Xu, Yuan-Xiang Pan, Hong Chen
Summary: This study utilizes a novel mixture modeling approach to identify bimodal miRNA in cancer and demonstrates their importance in predicting overall survival and drug response. The results reveal that high levels of bimodal miRNA expression are characteristic of cancer, and certain miRNA consistently account for tumor heterogeneity and may be involved in oncogenic processes. Bimodal miRNA can be used as biomarkers for prognosis and personalized treatment strategies in certain types of cancer.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Guanying Bianca Xu, Mingzhu Cai, Fatma Zehra Kadayifci, Juncen Dong, Shasha Zheng, Wenyan Mei, Wen Zhao, Yuan-Xiang Pan, Hong Chen
Summary: This study found that a diet with increased nutrient density relieved the inflammation induced by knockout of Hnrnp I, partially due to the reduced expression of inflammatory and immune-modulating cytokines in the mouse distal colon.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Guanying (Bianca) Xu, Yuan-Xiang Pan, Wenyan Mei, Hong Chen
Summary: This study reveals the critical cellular function of colonic tuft cells in promoting type-2 immune responses by communicating with ILC2s via the L1CAM-integrins interaction. This communication leads to increased secretion of inflammatory cytokines in ILC2s.
Article
Agriculture, Dairy & Animal Science
Qianming Jiang, Danielle N. Sherlock, Huimin Zhang, Jessie Guyader, Yuan-Xiang Pan, Juan J. Loor
Summary: Physiological and environmental stresses can lead to gastrointestinal tract dysfunction. One-carbon metabolism contributes to anti-oxidant capacity and the synthesis of various compounds. A study on dairy cows revealed unique differences in one-carbon metabolism and related pathways across sections of the gastrointestinal tract. The findings suggest that targeting these pathways during stressful periods is important.
JOURNAL OF ANIMAL SCIENCE
(2023)