Environmental maternal exposures and the risk of premature birth and intrauterine growth restriction: The Generation Gemelli study protocol of newborn exposome. by Leonardo Villani, Angelo Maria Pezzullo, Roberta Pastorino, Alessandra Maio, Francesca Stollagli, Chiara Tirone, Marta Barba, Angela Maria Cozzolino, Denise Pires Marafon, Martina Porcelli, Annamaria Sbordone, Maria Letizia Patti, Anthea Bottoni, Angela Paladini, Simona Fattore, Domenico Marco Romeo, Ornella Parolini, Wanda Lattanzi, Guido Rindi, Luca Tamagnone, Marco Marazza, Maurizio Genuardi, Elisabetta Tabolacci, Eugenio Maria Mercuri, Antonio Chiaretti, Tina Pasciuto, Maurizio Sanguinetti, Vincenzo Valentini, Giovanni Scambia, Walter Ricciardi, Giovanni Vento, Antonio Lanzone, Stefania Boccia

“…We will perform laboratory examinations including dosage of heavy metals and essential elements, investigation of placental distress and fetal brain damage of biomarkers, analysis of microbiota and of DNA methylation profile. We will conduct clinical follow-up assessments in both cases and controls at months 12 and 24 and we will collect anthropometric data, feeding types with particular reference to breastfeeding and its duration, pediatric emergency room visits, hospitalizations, medication usage, known allergies, and neuropsychological development.…”
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Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms by E. V. Ignatieva, E. A. Matrosova

“…A triggering event mediating the effect of a pathogenic genetic variant on the level of gene expression can be, for example, a change in the functional activity of transcription factor binding sites (TFBSs) or DNA methylation change, which, in turn, affects the functional activity of promoters or enhancers. …”
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Role of Sex Hormones in the Development and Progression of Hepatitis B Virus-Associated Hepatocellular Carcinoma by Maurizio Montella, Giovanni D’Arena, Anna Crispo, Mario Capunzo, Flavia Nocerino, Maria Grimaldi, Antonio Barbieri, Anna Maria D’Ursi, Mario Felice Tecce, Alfonso Amore, Massimiliano Galdiero, Gennaro Ciliberto, Aldo Giudice

“…Additionally, sex hormones can also affect HBV-related hepatocarcinogenesis by inducing epigenetic changes such as the regulation of mRNA levels by microRNAs (miRNAs), DNA methylation, and histone modification in liver tissue. …”
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Epigenetics of suicidal behavior by R. N. Mustafin, A. V. Kazantseva, R. F. Enikeeva, Yu. D. Davydova, S. B. Malykh, V. V. Viktorov, E. K. Khusnutdinova

“…The analysis of a brain obtained from suicide victims, representing a unique tool for the analysis of modified genomic processes, revealed a wide range of reprogramming patterns of DNA methylation in promoters of the genes of polyamine (OAZ1, OAZ2, AMD1, ARG2, SKA2), serotonergic (SLC6A4) and GABAergic (GABRA1) systems, HPA-axis (GR, NR3C1), tyrosine kinase (TrkB) receptors, brain-derived neurotrophic factor (BDNF). …”
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IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma by Khuloud Bajbouj, Mahmood Y. Hachim, Rakhee K. Ramakrishnan, Huwaida Fazel, Jumana Mustafa, Shahed Alzaghari, Mahmoud Eladl, Jasmin Shafarin, Ronald Olivenstein, Qutayba Hamid

“…Epigenetic alterations, including DNA methylation and histone modifications, have been reported to contribute to asthma pathogenesis. …”
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Differential Regulation of Methylation-Regulating Enzymes by Senescent Stromal Cells Drives Colorectal Cancer Cell Response to DNA-Demethylating Epi-Drugs by Khushboo Agrawal, Viswanath Das, Natálie Táborská, Ján Gurský, Petr Džubák, Marián Hajdúch

“…Our data show that fibroblasts accelerate cell proliferation and differentially regulate the expression of DNA methylation-regulating enzymes, enhancing DAC-induced demethylation in CRC cells. …”
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Genetic variation reveals the therapeutic potential of BRSK2 in idiopathic pulmonary fibrosis by Zhe Chen, Mingyang Tang, Nan Wang, Jiangjiang Liu, Xiaoyan Tan, Haitao Ma, Jing Luo, Kai Xie

“…Additionally, we conducted a comprehensive evaluation of therapeutic value, pathogenic mechanisms, and safety through phenome-wide association study (PheWAS), mediation analysis, transcriptomic analyses, shared causal variant exploration, DNA methylation MR, and protein interactions. Results Multiple MR results revealed that BRSK2 has a significant pathogenic impact on IPF at both transcriptional and translational levels, with a lung tissue-specific association (OR = 1.596; CI, 1.300–1.961; Pval = 8.290 × 10 − 6). …”
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Association between Genetic Instability and Helicobacter pylori Infection in Gastric Epithelial Dysplasia by Jin Su Kim, Woo Chul Chung, Kang-Moon Lee, Chang Nyol Paik, Kyeong Soo Lee, Hye Ji Kim, Young Wook Kim, Ji Han Jung, Seung June Noh, Yun Kyung Lee

“…In gastric carcinogenesis, changes of DNA methylation appear to be an early molecular event, and the genome-wide methylation state is closely correlated with the level of long interspersed nucleotide element-1 (LINE-1) methylation. …”
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Comprehensive investigation of matrix metalloproteinases in skin cutaneous melanoma: diagnostic, prognostic, and therapeutic insights by Lingxia Wu, Chenxiaoxiao Liu, Weicai Hu

“…Furthermore, our analysis demonstrated a significant (p-value < 0.05) inverse correlation between MMP expression levels and promoter methylation status, suggesting a potential regulatory role of DNA methylation in MMP dysregulation. Notably, MMP7, MMP11, and MMP14 exhibited significant (p-value < 0.05) associations with the overall survival of SKCM patients, emphasizing their prognostic significance. …”
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Identification of HOXA9 methylation as an epigenetic biomarker predicting prognosis and guiding treatment choice in acute myeloid leukemia by Fei Xie, Ting-juan Zhang, Xin-long Zhang, Zi-jun Xu, Liang Qiao, Yun Wang, Yang-jing Zhao, Jun Qian, Jing-dong Zhou

“…However, very few studies determined the DNA methylation-mediated epigenetic regulation of the HOXA cluster genes in AML. …”
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A comprehensive analysis of molecular characteristics of hot and cold tumor of gastric cancer by Chenxi Lv, Tianwei Chen, Jiangtao Li, Yuqiang Shan, Hong Zhou

“…Methods Consensus clustering was utilized to classify GC patients into distinct immune states, followed by an in-depth analysis of differences in mutation profiles, copy number variations, and DNA methylation patterns. Weighted gene co-expression network analysis (WGCNA) and correlation analysis were applied to identify gene modules underlying the classification of immune “hot” and “cold” tumors. …”
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Associations of Serum Cystatin C, DNAm Cystatin C, Renal Function, and Mortality in U.S. Adults by Yu-Wei Fang, Wei-Chung Huang, Chikang Wang, Chien-Yu Lin

“…Serum cystatin C is a well-established marker of renal function and a valuable predictor of health risks and mortality. DNA methylation-predicted cystatin C (DNAmCystatinC), an advanced epigenetic biomarker, serves as a proxy for serum cystatin C levels. …”
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Unleashing the potential of a low CpG Passer transposon for superior CAR-T cell therapy by Jianyao Zeng, Yan Sun, Yan Sun, Yuan Fang, Xiaodie Wang, Qian Huang, Pingjing Zhang, Meiqi Shao, Pei Wang, Jingbo Cheng, Meng Di, Tao Liu, Qijun Qian, Qijun Qian, Qijun Qian

“…Additionally, de novo DNA methylation programs promote T cell exhaustion, which poses a significant limitation for CAR-T cell therapy applications.MethodsHigh-throughput liquid protein chip and CBA analyses were utilized to determine the expression levels of inflammatory factors. …”
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The adaptation of rainbow trout to warmer water: Oxidative damage in the germinal line by Vianel Sevastei, Sonia A. Crichigno, M. Victoria Santos, Andrea Trochine, Julio C. Painefilú, Noemí Zaritzky, Víctor E. Cussac

“…Our results suggest that the acquired thermal tolerance traits may be part of a wide spectrum of novel characteristics produced as a consequence of an enhanced mutation rate and/or a different DNA methylation pattern, induced by higher temperatures and mediated by ROS.…”
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Melting curve analyses in the quantitative real-time polymerase chain reaction of methylated/non-methylated DNA toward the detection of oral cancer using gargle fluid by Yusaku Noma, Hayate Sawayama, Kouta Yamashiro, Keitaro Nishi, Haruka Yoshinaga, Ryota Takaoka, Tsuyoshi Sugiura, Tomonori Sasahira, Tomofumi Hamada, Yasuo Suda, Tatsuo Okui

“…Our group previously reported a noninvasive test for oral cancer that uses a commercially available methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) method, focusing on the DNA methylation of cells in gargle fluid. However, the conventional MS-MLPA method is complicated, costly, and thus difficult to use for screening and other health examinations. …”
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Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1... by Wangcheng Hu, Hui Luo, Yuekun Yang, Qiong Wang, Ni Hong, Guoping Wang, Aiming Wang, Liping Wang

“…It has high repeat sequence with 9.3% and DNA methylation existence in the genome. The 46.34 Mb genomes contained 14,091 predicted genes, which of 13,135 were annotated. …”
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The multi-omics signatures of telomere length in childhood by Congrong Wang, Dries S. Martens, Mariona Bustamante, Rossella Alfano, Michelle Plusquin, Lea Maitre, John Wright, Rosemary R. C. McEachan, Johanna Lepeule, Remy Slama, Marina Vafeiadi, Leda Chatzi, Regina Grazuleviciene, Kristine B. Gutzkow, Hector Keun, Eva Borràs, Eduard Sabidó, Angel Carracedo, Georgia Escarami, Augusto Anguita-Ruiz, Dolors Pelegrí-Sisó, Juan R. Gonzalez, Martine Vrijheid, Tim S. Nawrot

“…Telomere length was quantified via qPCR in peripheral blood of the children. Blood DNA methylation, gene expression, miRNA expression, plasma proteins and serum and urinary metabolites were measured through microarrays or (semi-) targeted assays. …”
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Deciphering the role of epigenetics in plant pathogen resistance: Strategies for sustainable sugarcane management by Faisal Mehdi, Yuanli Wu, Shuzhen Zhang, Yimei Gan, Zhengying Cao, Shuting Jiang, Limei Zan, Benpeng Yang

“…Epigenetic mechanisms, such as histone modifications and DNA methylation, regulate these gene expressions related to biotic stress responses. …”
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Blood-based epigenome-wide association study and prediction of alcohol consumption by Elena Bernabeu, Aleksandra D. Chybowska, Jacob K. Kresovich, Matthew Suderman, Daniel L. McCartney, Robert F. Hillary, Janie Corley, Maria Del C. Valdés-Hernández, Susana Muñoz Maniega, Mark E. Bastin, Joanna M. Wardlaw, Zongli Xu, Dale P. Sandler, Archie Campbell, Sarah E. Harris, Andrew M. McIntosh, Jack A. Taylor, Paul Yousefi, Simon R. Cox, Kathryn L. Evans, Matthew R. Robinson, Catalina A. Vallejos, Riccardo E. Marioni

“…Instead, molecular data such as blood-based DNA methylation (DNAm) could be used to derive a more objective measure of alcohol consumption by incorporating information from cytosine-phosphate-guanine (CpG) sites known to be linked to the trait. …”
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Health effects of mixed metal exposure on accelerating aging among the elderly population by Chuanli Yang, Jijun Zhang, Haohan Liu, Qin Hong, Yunhe Fan, Jie An, Haijia Zhang, Xiaobing Shen, Xiushan Dong

“…GrimAge acceleration (AgeAccelGrim) was calculated as the residuals from regressing DNA methylation GrimAge on chronological age. Weighted multivariable logistic regression models were applied to analyze the relationship between metal exposure with AgeAccelGrim. …”
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