Impact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research by Sarah M. Merrill, Chaini Konwar, Fizza Fatima, Kristy Dever, Julia L. MacIsaac, Nicole Letourneau, Gerald F. Giesbrecht, Deborah Dewey, Gillian England-Mason, Candace R. Lewis, Dennis Wang, Ai Ling Teh, Michael J. Meaney, Andrea Gonzalez, Jennie G. Noll, Carolina De Weerth, Nicole R. Bush, Kieran J. O’Donnell, S. Evelyn Stewart, Michael S. Kobor

“…Abstract Cheek swabs, heterogeneous samples consisting primarily of buccal epithelial cells, are widely used in pediatric DNA methylation studies and biomarker creation. However, the decrease in buccal proportion with age in adults remains unexamined in childhood. …”
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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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First Indonesian Nasopharyngeal Cancer Whole Epigenome Sequencing Identify Tumour Suppressor CpG Methylation by Handoko, Adham M, Rachmadi L, Tobing DL, Asmarinah A, Fadilah F, Dai W, Lee AWM, Gondhowiardjo SA

“…While Epstein–Barr virus (EBV) infection is a known risk factor, recent studies highlight the significant role of DNA methylation in NPC pathogenesis. Aberrant methylation, particularly at CpG sites, can silence tumour suppressor genes, promoting uncontrolled cell growth. …”
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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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A two‐phase epigenome‐wide four‐way gene–smoking interaction study of overall survival for early‐stage non‐small cell lung cancer by Leyi Chen, Xiang Wang, Ning Xie, Zhongwen Zhang, Xiaowen Xu, Maojie Xue, Yuqing Yang, Liya Liu, Li Su, Maria Bjaanæs, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, David C. Christiani, Feng Chen, Ruyang Zhang

“…Our previous work has identified a three‐way interaction among pack‐year of smoking (the number of packs of cigarettes smoked per day multiplied by the number of years the person has smoked) and two DNA methylation probes (cg05293407TRIM27 and cg00060500KIAA0226). …”
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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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Disulfidptosis-related gene signatures as prognostic biomarkers and predictors of immunotherapy response in HNSCC by Haotian Qin, Haotian Qin, Juan Xu, Yaohang Yue, Yaohang Yue, Meiling Chen, Zheng Zhang, Panpan Xu, Yan Zheng, Hui Zeng, Jian Weng, Jian Weng, Jun Yang, Fei Yu

“…The study also covers single-cell analysis and DNA methylation analysis of DRGs, and the prediction of potential microRNA and long non-coding RNA target genes. …”
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Stratification system with dual human endogenous retroviruses for predicting immunotherapy efficacy in metastatic clear-cell renal cell carcinoma by Li Xu, Stephane Oudard, Catherine Sautes-Fridman, Xiaoping Su, Gabriel G. Malouf, Virginie Verkarre, Salma Kotti, Fangrong Yan, Yann-Alexandre Vano, Wolf Herve Fridman, Cheng-Ming Sun, Xiaofan Lu, Wenxuan Cheng

“…Notably, this ERV-based classification outperformed traditional transcriptomic signatures in predicting ICI efficacy and showed further improvement when combined with epigenetic DNA methylation markers.Conclusions Our findings introduce a dual ERV-based stratification system that effectively categorizes patient risk and predicts clinical outcomes for ccRCC patients undergoing ICI therapy. …”
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An exceptionally rare case of a diffuse midline glioma with concomitant H3.1 K27M and G34R mutations in the HIST1H3C (H3C3) gene by Zita Reisz, Rita Pereira, Smitha Nevis, Alan Mackay, Leena Bhaw, Yura Grabovska, Ross Laxton, Valeria Molinari, Anna Burford, Barnaby Clark, Cristina Bleil, Bassel Zebian, Erika Pace, Annette Weiser, Fernando Carceller, Lynley Marshall, Andrew King, Istvan Bodi, Safa Al-Sarraj, Chris Jones, Matthew Clarke

“…Histology showed diffusely infiltrating pleomorphic astrocytes, multinucleated cells, and conspicuous mitotic activity; the diagnosis was DMG, H3 K27-altered (immunohistochemistry: H3K27me3 loss, H3K27M positivity). DNA methylation profiling (Illumina EPIC BeadArrays, brain tumour classifier (MNP v12.5 R package)) classified the tumour as ‘DMG, H3 K27-altered’ (calibrated score = 0.99). …”
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