Article
Veterinary Sciences
Zhu Caiye, Shuzhen Song, Minna Li, Xaioyu Huang, Yan Luo, Suli Fang
Summary: The study aimed to analyze genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which have different tail types, and identify the differentially methylated genes (DMGs) affecting tail type. Whole genome bisulfite sequencing (WGBS) was used to detect three individuals from each breed, and the degree of methylation, differentially methylated regions (DMRs) and DMGs were analyzed. Functional analysis revealed several genes involved in fat metabolism, such as NFATC4, LPIN2, MGAT2 and MAT2B. These findings provide new insights into the epigenetic regulation mechanisms of fat deposition in sheep tails and contribute to the study of local sheep.
FRONTIERS IN VETERINARY SCIENCE
(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.
Article
Biology
Jiahui Si, Songchun Yang, Dianjianyi Sun, Canqing Yu, Yu Guo, Yifei Lin, Iona Y. Millwood, Robin G. Walters, Ling Yang, Yiping Chen, Huaidong Du, Yujie Hua, Jingchao Liu, Junshi Chen, Zhengming Chen, Wei Chen, Jun Lv, Liming Liang, Liming Li
Summary: This study conducted the first prospective epigenome-wide analysis of DNA methylation in relation to incident coronary heart disease (CHD) in the Asian population, identifying novel blood methylation alterations associated with CHD and providing evidence of the role of epigenetic regulations in smoking- and blood pressure-related pathways to CHD risk.
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
Oncology
Yujing Xia, Alison Brewer, Jordana T. Bell
Summary: Coronary heart disease (CHD) is a major global cause of mortality. Recent studies have identified DNA methylation signatures associated with CHD development, suggesting their potential use in predicting future CHD events. New mechanisms involved in CHD progression have been uncovered through DNA methylation studies.
CLINICAL EPIGENETICS
(2021)
Article
Obstetrics & Gynecology
Min Yang, Xin Tao, Katherine Scott, Yiping Zhan, Richard T. Scott, Emre Seli
Summary: The study revealed that embryos with different developmental potentials exhibit different DNA methylation profiles at the blastocyst stage, indicating a potential negative correlation between genome-wide methylation level and embryo quality.
HUMAN REPRODUCTION
(2021)
Article
Biochemistry & Molecular Biology
Christopher Riccardi, Iacopo Passeri, Lisa Cangioli, Camilla Fagorzi, Marco Fondi, Alessio Mengoni
Summary: DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Xuan Luo, Yu Peng, Ying-Ying Chen, An-Qi Wang, Chui-Wen Deng, Lin-Yi Peng, Qing-Jun Wu, Yan Zhao, Yun-Yun Fei, Wen Zhang
Summary: The study identified 2819 differentially methylated positions in monocytes from pSS patients compared to healthy controls, affecting 1313 unique genes, with IFN-signaling pathway related genes being hypomethylated. Functional analysis revealed involvement in various pathways and metabolic diseases, with enrichment in signaling pathways correlated with serum IgG levels.
CHINESE MEDICAL JOURNAL
(2021)
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
Christina Signoretti, Sachin A. Gupte
Summary: Recent advances have uncovered the importance of epigenetic modifications in gene regulation and transcriptional activity. This study focuses on the role of glucose-6-phosphate dehydrogenase (G6PD) in the expression and activity of DNA methyltransferases (DNMT) and demethylases (TET) in healthy vascular tissue. The findings highlight the impact of G6PD on DNA methylation, gene expression, and large artery stiffness.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Anna J. Henningsson, Sandra Hellberg, Maria Lerm, Shumaila Sayyab
Summary: In this study, we conducted the first genome-wide analysis of DNA methylation in peripheral blood cells from patients with and without Lyme neuroborreliosis (LNB). The findings suggest that LNB is associated with immune-related DNA methylation changes.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Cardiac & Cardiovascular Systems
Yinan Zheng, Brian Joyce, Shih-Jen Hwang, Jiantao Ma, Lei Liu, Norrina Allen, Amy Krefman, Jun Wang, Tao Gao, Drew Nannini, Haixiang Zhang, David R. Jacobs, Myron Gross, Myriam Fornage, Cora E. Lewis, Pamela J. Schreiner, Stephen Sidney, Dongquan Chen, Philip Greenland, Daniel Levy, Lifang Hou, Donald Lloyd-Jones
Summary: This study found that cardiovascular health from young adulthood is associated with midlife epigenetic programming. The findings demonstrate the role of epigenetic markers in response to cardiovascular health changes and highlight the potential of epigenomic markers for precision cardiovascular disease prevention and earlier detection of subclinical cardiovascular disease.
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
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
Immunology
Sergey Yu. Tereshchenko, Marina V. V. Smolnikova, Maxim B. B. Freidin
Summary: This study provides new insights on the prevalence of FCN3 rs532781899 and MASP2 rs72550870 variants among the newborns of aboriginal Siberian Arctic populations and Russians. The genetic data of other proteins in the lectin pathway were also analyzed. A total of 926 dried blood spot specimens were genotyped.
SCANDINAVIAN JOURNAL OF IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Elena Yu. Bragina, Densema E. Gomboeva, Olga V. Saik, Vladimir A. Ivanisenko, Maxim B. Freidin, Maria S. Nazarenko, Valery P. Puzyrev
Summary: Cancer and neurodegenerative disorders pose significant challenges in healthcare worldwide. A study suggests that genes associated with apoptosis and Huntington's disease (HD) might also play a role in carcinogenesis, leading to a decrease in cancer rates among patients with neurodegenerative disorders. By reconstructing gene networks and analyzing genomic data, several high-priority candidate genes, including APOE, PSEN1, and IL6, were identified for further investigation of the molecular relationship between cancer and HD. Functional analysis and expression profiling of these genes were performed using publicly available datasets, revealing their potential roles in disease-specific tissues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Maria S. Nazarenko, Aleksei A. Sleptcov, Aleksei A. Zarubin, Ramil R. Salakhov, Alexander I. Shevchenko, Narek A. Tmoyan, Eugeny A. Elisaphenko, Ekaterina S. Zubkova, Nina V. Zheltysheva, Marat V. Ezhov, Valery V. Kukharchuk, Yelena V. Parfyonova, Suren M. Zakian, Irina S. Zakharova
Summary: This study developed a method for nearly complete sequencing of the LDLR gene using long-read Oxford Nanopore sequencing technology (ONT) and successfully detected variants associated with Mendelian familial hypercholesterolemia (FH). This method provides an efficient and cost-effective tool for diagnosing FH and has important implications for research on the LDLR gene.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Ksenia A. Kobzeva, Maria O. Soldatova, Tatiana A. Stetskaya, Vladislav O. Soldatov, Alexey V. Deykin, Maxim B. Freidin, Marina A. Bykanova, Mikhail I. Churnosov, Alexey V. Polonikov, Olga Y. Bushueva
Summary: This pilot study examined the relationship between HSPA8 SNPs and the risk of ischemic stroke. The results showed that SNPs rs10892958 and rs1136141 in the HSPA8 gene were associated with an increased risk of stroke, especially in smokers and patients with low fruit and vegetable intake.
Article
Health Care Sciences & Services
Yakov A. Tsepilov, Elizaveta E. Elgaeva, Arina V. Nostaeva, Roger Compte, Ivan A. Kuznetsov, Lennart C. Karssen, Maxim B. Freidin, Pradeep Suri, Frances M. K. Williams, Yurii S. Aulchenko
Summary: Chronic back pain (CBP) is a complex heritable trait and a major cause of disability worldwide. We developed and validated a genome-wide polygenic risk score (PRS) for CBP using a large-scale GWAS based on UK Biobank participants of European ancestry (N = 265,000). The PRS showed poor overall predictive ability (AUC = 0.56 and OR = 1.24 per SD, 95% CI: 1.22-1.26), but individuals from the 99th percentile of PRS distribution had a nearly two-fold increased risk of CBP (OR = 1.82, 95% CI: 1.60-2.06). We validated the PRS on an independent TwinsUK sample, obtaining a similar magnitude of effect. The PRS was significantly associated with various ICD-10 and OPCS-4 diagnostic codes, including chronic ischemic heart disease (OR = 1.1, p-value = 4.8 x 10(-15)), obesity, metabolism-related traits, spine disorders, disc degeneration, and arthritis-related disorders. PRS and environment interaction analysis with twelve known CBP risk factors revealed no significant results, suggesting that the magnitude of G x E interactions with studied factors is small. The limited predictive ability of the PRS that we developed is likely explained by the complexity, heterogeneity, and polygenicity of CBP, for which sample sizes of a few hundred thousand are insufficient to estimate small genetic effects robustly.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Review
Agriculture, Multidisciplinary
E. Yu. Bragina, V. P. Puzyrev
Summary: Studying the patterns of disease development and their familial relationships has gained attention. By investigating disease combinations and genetic components, essential genes controlling disease formation can be identified. Existing terminology for disease combinations includes multimorbidity, polypathies, comorbidity, and conglomerates.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2023)
Article
Agriculture, Multidisciplinary
T. V. Nikitina, E. A. Sazhenova, E. N. Tolmacheva, N. N. Sukhanova, S. A. Vasilyev, I. N. Lebedev
Summary: Miscarriage is a significant issue in human reproduction, occurring in 10-15% of clinically recognized pregnancies. This study aimed to compare the frequency of chromosomal abnormalities in extraembryonic tissues between missed abortion (MA) and anembryonic pregnancy (AP). A retrospective analysis of 1551 spontaneous abortions was conducted, revealing a total frequency of chromosomal abnormalities of 53.6%. There was no significant difference in abnormal karyotypes between the AP and MA groups, suggesting the importance of exploring other genomic factors in the development of AP.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2023)
Article
Agriculture, Multidisciplinary
I. A. Goncharova, A. A. Zarubin, N. P. Babushkina, I. A. Koroleva, M. S. Nazarenko
Summary: This study compared the methylation levels of CpG sites between tumor and surrounding liver tissues in HCV-induced hepatocellular carcinoma (HCC) patients and between tumor and normal tissue in non-viral HCC patients. The results showed that there were fewer differentially methylated sites between non-viral HCC and normal liver tissue, as well as between HCC and fibrosis, compared to HCC and cirrhosis. The ratio of hyper-/hypomethylated sites in the tumor decreased as the pathological changes in the surrounding tissue progressed.
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2023)
Editorial Material
Agriculture, Multidisciplinary
V. A. Stepanov, I. N. Lebedev
VAVILOVSKII ZHURNAL GENETIKI I SELEKTSII
(2023)
Article
Cardiac & Cardiovascular Systems
N. Popova, V. A. Popov, A. Sh Revishvili
Summary: This review discusses disputed issues of myocardial revascularization in chronic forms of ischemic heart disease, highlighting the major differences between percutaneous coronary intervention and coronary artery bypass grafting in terms of long-term prognosis and the reliance on the clinical profile of the disease. The review of current publications demonstrates the advantages of open surgery in long-term survival and prevention of adverse outcomes in target groups of patients.
Article
Genetics & Heredity
Irina V. Zorkoltseva, Elizaveta E. Elgaeva, Nadezhda M. Belonogova, Anatoliy V. Kirichenko, Gulnara R. Svishcheva, Maxim B. Freidin, Frances M. K. Williams, Pradeep Suri, Yakov A. Tsepilov, Tatiana I. Axenovich
Summary: This study utilized exome sequencing data to analyze the genetics of back pain and identified the SLC13A1 and FSCN3 genes as contributors to chronic back pain. These findings offer new insights into the genetic mechanisms of back pain and potential drug targets.
Article
Biochemistry & Molecular Biology
Rick Essers, Igor N. Lebedev, Ants Kurg, Elizaveta A. Fonova, Servi J. C. Stevens, Rebekka M. Koeck, Ulrike von Rango, Lloyd Brandts, Spyridon Panagiotis Deligiannis, Tatyana V. Nikitina, Elena A. Sazhenova, Ekaterina N. Tolmacheva, Anna A. Kashevarova, Dmitry A. Fedotov, Viktoria V. Demeneva, Daria I. Zhigalina, Gleb V. Drozdov, Salwan Al-Nasiry, Merryn V. E. Macville, Arthur van den Wijngaard, Jos Dreesen, Aimee Paulussen, Alexander Hoischen, Han G. Brunner, Andres Salumets, Masoud Zamani Esteki
Summary: This study analyzed 1,745 spontaneous pregnancy losses and found that approximately 50.4% of the products of conception (POCs) had chromosomal abnormalities. Parental age was identified as an independent factor contributing to the increased rate of genomic aberrations. By using genome haplarithmisis, the researchers discovered previously undetected chromosomal aberrations in 35.1% of the pregnancy losses. They also found a higher degree of mosaic chromosomal imbalances in the extra-embryonic mesoderm compared to the chorionic villi.
Meeting Abstract
Biochemistry & Molecular Biology
Viktoriia Demeneva, Ekaterina Tolmacheva, Tatyana Nikitina, Elena Sazhenova, Sergey Yuriev, Alisher Makhmutkhodzhaev, Andrew Zuev, Svetlana Filatova, Alexey Dmitriev, Yana Darkova, Igor Lebedev, Stanislav Vasilyev
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Gleb Drozdov, Igor Lebedev, Tatyana Nikitina, Anna Kashevarova, Elizaveta Fonova, Ekaterina Tolmacheva, Elena Sazhenova
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
