Article
Oncology
Takeshi Hori, Kosuke Yokobori, Rick Moore, Masahiko Negishi, Tatsuya Sueyoshi
Summary: This study found that Gadd45b plays an important regulatory role in the development of mouse HCC, and regulates the expression of the irisin/Fndc5 and Tgfbr2 genes. In addition, the study also found that PB treatment has different effects on growth and gene expression in wild-type mice compared to Gadd45 beta KO mice.
FRONTIERS IN ONCOLOGY
(2023)
Article
Genetics & Heredity
Vincenza Ylenia Cusenza, Luca Braglia, Raffaele Frazzi
Summary: This study analyzed data from the TCGA database and found that colon and liver tumors consistently exhibit methylation heterogeneity, and the downregulation of the SPG20 gene suggests its role in tumor progression control.
Article
Cell Biology
Chuan Zhang, Lu Wang, Chi Jin, Jiahui Zhou, Chaofan Peng, Yong Wang, Ziwei Xu, Dongsheng Zhang, Yuanjian Huang, Yue Zhang, Dongjian Ji, Wen Peng, Kangpeng Jin, Junwei Tang, Yifei Feng, Yueming Sun
Summary: Colorectal cancer is a common cancer worldwide, with liver metastasis being a key factor affecting prognosis. A study revealed that Lnc-LALC can regulate CRC cell metastasis ability by affecting DNA methylation status, highlighting its important role in CRLM.
CELL DEATH & DISEASE
(2021)
Article
Oncology
Xiaoqing Yu, Ling Cen, Y. Ann Chen, Joseph Markowitz, Timothy Shaw, Kenneth Y. Tsai, Jose R. Conejo-Garcia, Xuefeng Wang
Summary: DNA methylation signatures can be used as reliable biomarkers to predict patient prognosis and immune status in tumors. This study introduces the concept of tumor-based expression quantitative trait methylation (eQTM) for the identification of predictive biomarkers. eQTM CpGs and genes represent new and efficient candidate targets for prognosis and immune status monitoring.
Article
Multidisciplinary Sciences
Xinyue Qiu, Cheng Shen, Wenjing Zhao, Xunlei Zhang, Dakun Zhao, Xuming Wu, Lei Yang
Summary: The expression of DYRK2 varies significantly in different cancers, and is associated with the prognosis of cancer patients. Mutations in DYRK2 are closely related to the prognosis of certain tumors. Additionally, phosphorylation and methylation levels of DYRK2 differ between tumor tissues and adjacent normal tissues. In the tumor microenvironment, DYRK2 expression correlates with cancer-associated fibroblast infiltration.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan Celedon, Chris McKennan, Wei Chen, Jiebiao Wang
Summary: This study focuses on using cellular deconvolution methods to extract cell-type-specific signals from tissue-level omics data. However, different methods produce different results under various real data settings. The study proposes EnsDeconv, an ensemble deconvolution method that synthesizes the results from multiple single deconvolution methods to achieve robust and accurate estimation of cellular fractions.
Article
Biology
Hiroshi Hamamoto, Suresh Panthee, Atmika Paudel, Suguru Ohgi, Yutaka Suzuki, Koichi Makimura, Kazuhisa Sekimizu
Summary: In this study, we performed in vivo RNA-sequencing analysis to investigate the gene expression of Staphylococcus aureus during infection in mouse liver. Our results showed that the gene expression of S. aureus was affected by changes in the host environment, such as the upregulation of hypoxia response genes and immune response genes. Genes related to anaerobic respiration and metal transporters exhibited different expression patterns at different time points post-infection.
COMMUNICATIONS BIOLOGY
(2022)
Article
Neurosciences
Anna Welle, Carmen Kasakow, Annemarie M. Jungmann, Davide Gobbo, Laura Stopper, Karl Nordstroem, Abdulrahman Salhab, Gilles Gasparoni, Anja Scheller, Frank Kirchhoff, Joern Walter
Summary: This study reveals significant differences in gene expression and DNA methylation between astrocytes from the cerebral cortex and cerebellum, linked to region-specific transcription factor networks. The epigenetic variations suggest complex combinatorial regulation of regional astrocyte transcriptomes.
Article
Multidisciplinary Sciences
Dongxue Wu, Yuhong Li, Qi Ren, Shengfei Pei, Lin Wang, Luming Yang, Yingzhi Chong, Shufeng Sun, Jinqi Hao, Fumin Feng
Summary: Genomic methylation patterns differ between ADLI and non-ADLI patients, with specific CpG sites in the TANC1 gene identified as potential biomarkers for ADLI diagnosis. These findings suggest a promising approach for distinguishing patients with ADLI based on DNA methylation profiles.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Richard Epstein, Frank P. Y. Lin, Robert Brink, James Blackburn
Summary: This study demonstrates that synonymous germline modifications of exonic CpG sites affect murine development, fertility, longevity, and cancer incidence. Additionally, variant-CpG Trp53 sequences in mice are associated with dental anomalies. The study suggests that CpG sites may exert non-coding phenotypic effects through interactions with methyl-binding proteins, which regulate mRNA transcript initiation, expression, or splicing.
Article
Biochemistry & Molecular Biology
Muhammad Azhar, Caoling Xu, Xue Jiang, Wenqing Li, Yuzhu Cao, Xiaoli Zhu, Xuemei Xing, Limin Wu, Jiaqi Zou, Lan Meng, Yu Cheng, Wenjie Han, Jianqiang Bao
Summary: This study reveals the crucial role of Prmt1 in the establishment and maintenance of spermatogonia, and its regulation of transcriptional homeostasis. The enrichment of Prmt1-deposited H4R3me2a mark in mouse spermatogonia has a significant impact on the transcriptomic landscape and alternative splicing pattern.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xu Pan, Xin Li, Jie Sun, Zhiying Xiong, Haoyu Hu, Shangwei Ning, Hui Zhi
Summary: This study reveals that DNA methylation can drive tissue-specific enhancer basal transcription and target gene expression in human cancers. By integrating methylome, transcriptome, and 3D genomic data, enhancer methylation triplets were identified and regulatory patterns within them were dissected. Cancer-specific core TFs regulated by enhancers were observed to shape enhancer methylation forming enhancer methylation-driven CRCs (emCRCs).
Article
Cell Biology
Tao Wei, Jin Li, Jian Zhang, Qi Zhang, Xiaoyu Liu, Qi Chen, Liang Wen, Ke Ma, Wen Chen, Jianhui Zhao, Cheng Zhang, Jinyan Huang, Yali Xie, Hao Qin, Danfeng Qian, Tingbo Liang
Summary: While Mettl3 has been shown to have oncogenic roles in hepatocellular carcinoma (HCC), its function in early HCC tumorigenesis is unclear. Mettl3 loss leads to hepatocyte homeostasis disruption and liver damage, accelerating liver tumorigenesis. Depletion of Mettl3 enhances liver tumor development, while overexpression of Mettl3 inhibits hepatocarcinogenesis. These findings suggest a stage-dependent tumor-suppressive role of Mettl3 in HCC initiation and progression.
Article
Biochemical Research Methods
Isabelle Bichindaritz, Guanghui Liu, Christopher Bartlett
Summary: The study proposes an adaptive multi-task learning method for survival prediction of breast cancer patients using multi-modal learning, achieving more effective results compared to existing approaches. By combining different gene features, reducing dimensions, and introducing auxiliary loss, an ordinal Cox hazards model is built to predict patients' survival risk.
Article
Endocrinology & Metabolism
Mingru Yin, Weina Yu, Wenzhi Li, Qianqian Zhu, Hui Long, Pengcheng Kong, Qifeng Lyu
Summary: The study found that AOA treatment affects the pre- and post-implantation embryo development in mice, resulting in increased expression of the maternal allele-specific gene Igf2r but significantly lower birth weight in newborn mice. However, no other abnormalities were observed in the offspring born following AOA treatment.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2021)
Article
Environmental Sciences
Erin E. Yost, John Stanek, Lyle D. Burgoon
SCIENCE OF THE TOTAL ENVIRONMENT
(2017)
Article
Developmental Biology
Nancy Baker, Alan Boobis, Lyle Burgoon, Edward Carney, Richard Currie, Ellen Fritsche, Thomas Knudsen, Madeleine Laffont, Aldert H. Piersma, Alan Poole, Steffen Schneider, George Daston
BIRTH DEFECTS RESEARCH
(2018)
Article
Genetics & Heredity
Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafstrom, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andon, Chris T. Evelo, Egon L. Willighagen
FRONTIERS IN GENETICS
(2018)
Article
Chemistry, Medicinal
Jaeseong Jeong, Natalia Garcia-Reyero, Lyle Burgoon, Edward Perkins, Taehyun Park, Changheon Kim, Ji-Yeon Roh, Jinhee Choi
CHEMICAL RESEARCH IN TOXICOLOGY
(2019)
Review
Environmental Sciences
Edward J. Perkins, Roman Ashauer, Lyle Burgoon, Rory Conolly, Brigitte Landesmann, Cameron Mackay, Cheryl A. Murphy, Nathan Pollesch, James R. Wheeler, Anze Zupanic, Stefan Scholz
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Kurt A. Gust, Alan J. Kennedy, Jennifer G. Laird, Mitchell S. Wilbanks, Natalie D. Barker, Xin Guan, Nicolas L. Melby, Lyle D. Burgoon, Michael E. Kjelland, Todd M. Swannack
Article
Public, Environmental & Occupational Health
Lyle D. Burgoon, Michelle Angrish, Natalia Garcia-Reyero, Nathan Pollesch, Anze Zupanic, Edward Perkins
Article
Environmental Sciences
Paul S. Price, Annie M. Jarabek, Lyle D. Burgoon
ENVIRONMENT INTERNATIONAL
(2020)
Article
Environmental Sciences
Katherine K. Coady, Lyle Burgoon, Claire Doskey, John W. Davis
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2020)
Article
Environmental Sciences
L. S. McCarty, C. J. Borgert, L. D. Burgoon
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2020)
Article
Environmental Sciences
Anne E. Thessen, Cynthia J. Grondin, Resham D. Kulkarni, Susanne Brander, Lisa Truong, Nicole A. Vasilevsky, Tiffany J. Callahan, Lauren E. Chan, Brian Westra, Mary Willis, Sarah E. Rothenberg, Annie M. Jarabek, Lyle Burgoon, Susan A. Korrick, Melissa A. Haendel
ENVIRONMENTAL HEALTH PERSPECTIVES
(2020)
Article
Toxicology
Lyle D. Burgoon, Claudio Fuentes, Christopher J. Borgert
Summary: This paper introduces a new method for calculating the kinetically derived maximal dose (KMD) based on Bayesian methods and the Kneedle algorithm. The new approach converts toxicokinetic data to the Michaelis-Menten curve using Bayesian methods and uses the Kneedle algorithm to find the point at which the curve begins to taper off. This reshapes the KMD methodology and places it within the Michaelis-Menten framework, leveraging existing biochemical and pharmacological concepts.
ARCHIVES OF TOXICOLOGY
(2022)
Article
Toxicology
C. J. Borgert, C. Fuentes, L. D. Burgoon
Summary: Regulatory toxicology aims to ensure the safe use of chemicals by identifying doses and conditions under which chemical toxicity does not occur, limiting chemical concentrations and exposures. Understanding the kinetic relationship is essential for determining the safe dose range, with the concept of KMD helping to identify the maximum dose at which organisms can efficiently metabolize and eliminate chemicals.
ARCHIVES OF TOXICOLOGY
(2021)
Editorial Material
Medicine, Legal
Joshua A. Harrill, Mark R. Viant, Carole L. Yauk, Magdalini Sachana, Timothy W. Gant, Scott S. Auerbach, Richard D. Beger, Mounir Bouhifd, Jason O'Brien, Lyle Burgoon, Florian Caiment, Donatella Carpi, Tao Chen, Brian N. Chorley, John Colbourne, Raffaella Corvi, Laurent Debrauwer, Claire O'Donovan, Timothy M. D. Ebbels, Drew R. Ekman, Frank Faulhammer, Laura Gribaldo, Gina M. Hilton, Stephanie P. Jones, Aniko Kende, Thomas N. Lawson, Sofia B. Leite, Pim E. G. Leonards, Mirjam Luijten, Alberto Martin, Laura Moussa, Serge Rudaz, Oliver Schmitz, Tomasz Sobanski, Volker Strauss, Monica Vaccari, Vikrant Vijay, Ralf J. M. Weber, Antony J. Williams, Andrew Williams, Russell S. Thomas, Maurice Whelan
Summary: Omics methodologies are widely used in toxicological research, but face challenges in gaining widespread regulatory acceptance due to lack of transparency in data processing methods and standardization in reporting. To foster further regulatory use of Omics data, the OECD's EAGMST launched a project to develop guidance for reporting Omics data.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2021)
Article
Medicine, Research & Experimental
Edward J. Perkins, Kalyan Gayen, Jason E. Shoemaker, Philipp Antczak, Lyle Burgoon, Francesco Falciani, Steve Gutsell, Geoff Hodges, Aude Kienzler, Dries Knapen, Mary McBride, Catherine Willett, Francis J. Doyle, Natalia Garcia-Reyero
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION
(2019)