Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation by Yueyuan Zheng, Benjamin Ziman, Allen S. Ho, Uttam K. Sinha, Li-Yan Xu, En-Min Li, H Phillip Koeffler, Benjamin P. Berman, De-Chen Lin

“…Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of cell-type-specific PMDs and DMRs identified here in esophageal cancer are actually markers that co-occur in other cancers originating from related cell types. …”
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Genomic and transcriptomic features between primary and paired metastatic fumarate hydratase–deficient renal cell carcinoma by Jiayu Liang, Guangxi Sun, Xiuyi Pan, Mengni Zhang, Pengfei Shen, Sha Zhu, Jinge Zhao, Linmao Zheng, Junjie Zhao, Yuntian Chen, Xiaoxue Yin, Junru Chen, Xu Hu, Yuhao Zeng, Jianhui Chen, Yongquan Wang, Zhihong Liu, Jin Yao, Minggang Su, Rui Huang, Banghua Liao, Qiang Wei, Xiang Li, Qiao Zhou, Jiyan Liu, Yali Shen, Zhenhua Liu, Ni Chen, Hao Zeng, Xingming Zhang

“…Conclusions Overall, our study demonstrated the genomic, epigenomic, and transcriptomic features of metastatic lesions in FH-RCC and revealed their early evolutionary trajectory. …”
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Bibliometric and visual analysis of single-cell sequencing from 2010 to 2022 by Ling Chen, Yantong Wan, Tingting Yang, Qi Zhang, Qi Zhang, Yuting Zeng, Shuqi Zheng, Shuqi Zheng, Zhishan Ling, Zhishan Ling, Yupeng Xiao, Yupeng Xiao, Qingyi Wan, Ruili Liu, Chun Yang, Guozhi Huang, Guozhi Huang, Qing Zeng, Qing Zeng

“…Background: Single-cell sequencing (SCS) is a technique used to analyze the genome, transcriptome, epigenome, and other genetic data at the level of a single cell. …”
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DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells by Tianpeng Gu, Xueqiu Lin, Sean M. Cullen, Min Luo, Mira Jeong, Marcos Estecio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Stanley Qi, Jia-Jia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A. Goodell

“…Conclusions We conclude that DNMT3A and TET1 regulate the epigenome and gene expression at specific targets via their functional interplay.…”
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Identification of novel differentially methylated sites with potential as clinical predictors of impaired respiratory function and COPDResearch in context by Mairead L. Bermingham, Rosie M. Walker, Riccardo E. Marioni, Stewart W. Morris, Konrad Rawlik, Yanni Zeng, Archie Campbell, Paul Redmond, Heather C. Whalley, Mark J. Adams, Caroline Hayward, Ian J. Deary, David J. Porteous, Andrew M. McIntosh, Kathryn L. Evans

“…This is the largest single population, whole-genome epigenetic study to date. Methods: Epigenome-wide association studies (EWASs) of respiratory function and COPD were performed in peripheral blood samples from the Generation Scotland: Scottish Family Health Study (GS:SFHS) cohort (n = 3781; 274 COPD cases and 2919 controls). …”
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Epigenetic Regulator KDM4D Restricts Tumorigenesis via Modulating SYVN1/HMGB1 Ubiquitination Axis in Esophageal Squamous Cell Carcinoma by Wenjian Yao, Jianjun Wang, Li Zhu, Xiangbo Jia, Lei Xu, Xia Tian, Shuai Hu, Sen Wu, Li Wei

“…In vivo tumor xenograft models were used to determine whether the HMGB1 inhibition affected the malignant features of ESCC cells.ResultEpigenome screening and low-throughput validations highlighted that KDM4D is a tumor suppressor in ESCC. …”
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The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo by David Latrasse, Natalia Y. Rodriguez-Granados, Alaguraj Veluchamy, Kiruthiga Gayathri Mariappan, Claudia Bevilacqua, Nicolas Crapart, Celine Camps, Vivien Sommard, Cécile Raynaud, Catherine Dogimont, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane

“…Nevertheless, the nature and role of its epigenome in gene expression regulation and more specifically in sex determination remains largely unknown. …”
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Genome-wide DNA methylation pattern in whole blood of patients with coal-burning arsenic poisoning by Shaofeng Wei, Wenjing Wang, Shiwen Liu, Baofei Sun, Qibing Zeng, Guoze Wang, Peng Luo, Aihua Zhang

“…Illumina 850 K methylation beadchip is the most suitable technology for DNA methylation of epigenome-wide association analysis. This study used 850 K to detect changes in Genome-wide DNA methylation in whole blood samples of 12 patients with coal-burning arsenic poisoning ( Arsenic poisoning group) and four healthy control participants (Healthy control group). …”
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Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins by Yunzhang Wang, Robert Karlsson, Erik Lampa, Qian Zhang, Åsa K. Hedman, Malin Almgren, Catarina Almqvist, Allan F. McRae, Riccardo E. Marioni, Erik Ingelsson, Peter M. Visscher, Ian J. Deary, Lars Lind, Tiffany Morris, Stephan Beck, Nancy L. Pedersen, Sara Hägg

“…We identified 1316 age-associated methylation sites (P<1.3×10−7) using a longitudinal epigenome-wide association study design. We measured how estimated cellular compositions changed with age and how much they confounded the age effect. …”
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Assessing the effect of childbearing on blood DNA methylation through comparison of parous and nulliparous females by Su Chen, Miranda Johs, Wilfried Karmaus, John W. Holloway, Parnian Kheirkhah Rahimabad, Jaclyn M. Goodrich, Karen E. Peterson, Dana C. Dolinoy, S. Hasan Arshad, Susan Ewart

“…Results Blood DNAm was available from 89 women (28 parous; 61 nulliparous) at ages 18 and 26 years in the Isle of Wight birth cohort; no significant differences in the population characteristics were present between the analyzed population and the full cohort. We performed an epigenome-wide association study on 389,355 CpGs and identified 184 CpGs to be significantly differentially methylated between parous and nulliparous women after adjusting for confounders and multiple testing. …”
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ABCA1, TCF7, NFATC1, PRKCZ, and PDGFA DNA methylation as potential epigenetic-sensitive targets in acute coronary syndrome via network analysis by Teresa Infante, Monica Franzese, Antonio Ruocco, Concetta Schiano, Ornella Affinito, Katia Pane, Domenico Memoli, Francesca Rizzo, Alessandro Weisz, Paola Bontempo, Vincenzo Grimaldi, Liberato Berrino, Andrea Soricelli, Ciro Mauro, Claudio Napoli

“…Acute coronary syndrome (ACS) is the most severe clinical manifestation of coronary heart disease. We performed an epigenome-wide analysis of circulating CD4+ and CD8+ T cells isolated from ACS patients and healthy subjects (HS), enrolled in the DIANA clinical trial, by reduced-representation bisulphite sequencing (RRBS). …”
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Associations between post translational histone modifications, myelomeningocele risk, environmental arsenic exposure, and folate deficiency among participants in a case control stu... by Jannah Tauheed, Marco Sanchez-Guerra, Jane J. Lee, Ligi Paul, Md Omar Sharif Ibne Hasan, Quazi Quamruzzaman, Jacob Selhub, Robert O. Wright, David C. Christiani, Brent A. Coull, Andrea A. Baccarelli, Maitreyi Mazumdar

“…Arsenic exposure may contribute to disease risk in humans through alterations in the epigenome. Previous studies reported that arsenic exposure is associated with changes in plasma histone concentrations. …”
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Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases by Marcin Nicoś, PhD, Luuk Harbers, MSc, Enrico Patrucco, PhD, Maximilian Kramer-Drauberg, PhD, Xiaolu Zhang, PhD, Claudia Voena, PhD, Anna Kowalczyk, MD, PhD, Aleksandra Bożyk, PhD, Rafał Pęksa, MD, PhD, Bożena Jarosz, MD, PhD, Justyna Szumiło, MD, Michele Simonetti, PhD, Monika Żuk, PhD, Bartosz Wasąg, MD, Katarzyna Reszka, PhD, Renata Duchnowska, MD, Janusz Milanowski, MD, Roberto Chiarle, MD, Magda Bienko, PhD, Paweł Krawczyk, MD, Jacek Jassem, MD, Chiara Ambrogio, PhD, Nicola Crosetto, MD, PhD

“…Finally, we identified putative pathogenic alterations in multiple cancer genes, including genes involved in epigenome editing and 3D genome organization, such as EP300, CTCF, and STAG2, which we validated by targeted sequencing of an independent cohort of 115 BM samples. …”
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Genome-wide DNA methylation and gene expression analyses in monozygotic twins identify potential biomarkers of depression by Weijing Wang, Weilong Li, Yili Wu, Xiaocao Tian, Haiping Duan, Shuxia Li, Qihua Tan, Dongfeng Zhang

“…Abstract Depression is currently the leading cause of disability around the world. We conducted an epigenome-wide association study (EWAS) in a sample of 58 depression score-discordant monozygotic twin pairs, aiming to detect specific epigenetic variants potentially related to depression and further integrate with gene expression profile data. …”
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Dopamine Receptor D1 Contributes to Cocaine Epigenetic Reprogramming of Histone Modifications in Male Germ Cells by Betina González, Samanta N. Gancedo, Sahira A. Janeir Garazatua, Eduardo Roldán, Alfredo D. Vitullo, Candela R. González

“…However, the mechanism by which cocaine alters the male germ cells epigenome is almost unexplored. Here, we report that cocaine-treated male mice showed alterations on specific histone post-translational modifications (PTMs) including increased silent chromatin marks H3K9me3 and H3K27me3 and decreased active enhancer and promoter marks H3K27ac and H3K4me3 in isolated germ cells. …”
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Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations by Lingzhao Fang, Shuli Liu, Mei Liu, Xiaolong Kang, Shudai Lin, Bingjie Li, Erin E. Connor, Ransom L. Baldwin, Albert Tenesa, Li Ma, George E. Liu, Cong-jun Li

“…Using butyrate to induce the dynamics of the epigenomic landscape, we were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.…”
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Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis by Emmanuel Karouzakis, Janine Hähnlein, Janine Hähnlein, Cristoforo Grasso, Cristoforo Grasso, Johanna F. Semmelink, Johanna F. Semmelink, Paul P. Tak, Paul P. Tak, Paul P. Tak, Paul P. Tak, Danielle M. Gerlag, Danielle M. Gerlag, Steffen Gay, Caroline Ospelt, Lisa G. M. van Baarsen, Lisa G. M. van Baarsen

“…Here we performed the first epigenomic characterization of LNSCs during health and early RA, by analyzing their transcriptome and DNA methylome in LNSCs isolated from lymph node needle biopsies obtained from healthy controls (HC), autoantibody positive RA-risk individuals and patients with established RA. …”
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Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness by David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan

“…The transcriptome was examined using RNA-seq, and the epigenome was examined using reduced representation bisulfite sequencing and H3K27ac ChIP-seq. …”
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Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice by Veronica S. Gil, Govind Bhagat, Louise Howell, Jiyuan Zhang, Chae H. Kim, Sven Stengel, Francisco Vega, Arthur Zelent, Kevin Petrie

“…Epigenetic modifications play an important role in the germinal center response, and deregulation of the B-cell epigenome as a consequence of mutations and other genomic aberrations are being increasingly recognized as important steps in the pathogenesis of a variety of B-cell lymphomas. …”
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Prospective Epigenetic Actions of Organo-Sulfur Compounds against Cancer: Perspectives and Molecular Mechanisms by Shoaib Shoaib, Mohammad Azam Ansari, Mohammed Ghazwani, Umme Hani, Yahya F. Jamous, Zahraa Alali, Shadma Wahab, Wasim Ahmad, Sydney A. Weir, Mohammad N. Alomary, Nabiha Yusuf, Najmul Islam

“…Notably, the cancer epigenome possesses various HDACs and DNMTs, which participate in the histone modifications and DNA methylation. …”
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