Article
Biochemistry & Molecular Biology
Renzo J. M. Riemens, Gunter Kenis, Jennifer Nolz, Sonia C. Susano C. Chaves, Diane Duroux, Ehsan Pishva, Diego Mastroeni, Kristel Van Steen, Thomas Haaf, Daniel L. A. van den Hove
Summary: A novel approach combining LCM and LDBSP is developed to quantify and analyze the DNA methylation patterns of individual genes in neuronal cells. The method proves to be efficient and accurate, providing further validity to this approach in neuroepigenomic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Veronika N. Laine, Bernice Sepers, Melanie Lindner, Fleur Gawehns, Suvi Ruuskanen, Kees van Oers
Summary: The field of molecular biology is rapidly advancing and there is a growing interest in studying ecological epigenetics, particularly in wild vertebrates. This review provides a practical guide for researchers studying DNA methylation variation in wild vertebrates, discussing technical aspects, limitations, and data analysis methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Biochemistry & Molecular Biology
Fabio Coppede, Utsa Bhaduri, Andrea Stoccoro, Vanessa Nicoli, Eleonora Di Venere, Giuseppe Merla
Summary: The central objective of combining discovery science with biomedical applications is to benefit patients and reduce the global disease burden. The conversion of DNA methylation (DNAm) from a biological process to a diagnostic tool is a prime example of this transformation, which took nearly a century. In recent years, DNAm studies have been standardized in clinical applications more than ever before, offering great potential for diagnosing various diseases associated with epigenetic alterations. DNAm detection plays a role in noninvasive prenatal testing and indicates prenatal risk factors in very preterm infants. In the field of cancer, liquid biopsy-based DNAm profiling provides valuable epigenetic biomarkers for early-stage diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Antonella Sarnataro, Giulia De Riso, Sergio Cocozza, Antonio Pezone, Barbara Majello, Stefano Amente, Giovanni Scala
Summary: DNA methylation is an important epigenetic modification that influences gene regulation, genomic imprinting, and genome stability. EpiStatProfiler is an R package that allows the analysis of CpG and non-CpG epialleles based on bisulfite sequencing data, with additional features for genomic annotation and analysis. It is the first package to provide functionalities specifically for epiallele composition analysis from any type of bisulfite sequencing experiment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Oncology
Sherif Mohamed Elsharkawi, Dalal Elkaffash, Pacint Moez, Nour El-Etreby, Eman Sheta, Raghda Saad Zaghloul Taleb
Summary: This study compared the methylation status of the PCDH17 gene promoter between females diagnosed with epithelial ovarian cancer and a control group. It found that the methylation levels were significantly higher in ovarian cancer patients compared to the control group.
Review
Physiology
Myriam Hemberger, Wendy Dean
Summary: The placenta is a unique organ system that combines maternal and fetal cell types with distinct lineage origins. It not only supplies nutrients to the fetus but also plays a pivotal role in directing proper organ formation. Understanding placental development and function is essential for pregnancy outcome and lifelong health.
PHYSIOLOGICAL REVIEWS
(2023)
Article
Genetics & Heredity
N. Kuzub, V. Smialkovska, V. Momot, V. Moseiko, O. Lushchak, A. Koliada
Summary: Epigenetic clocks are models that use CpG methylation levels to predict the age of an organism. In this study, two epigenetic clock models based on 4 CpG sites and 2 CpG sites were evaluated, and both showed good age predictive accuracy in the Ukrainian population. The models had small prediction errors for individuals aged 18 to 80.
FRONTIERS IN GENETICS
(2022)
Article
Veterinary Sciences
Caijuan Yue, Jiakang Wang, Yifei Shen, Junli Zhang, Jian Liu, Aiping Xiao, Yisha Liu, Hehua Eer, Qiao-e Zhang
Summary: In this study, whole-genome bisulfite sequencing and bioinformatics analysis were used to compare the DNA methylation patterns between Tan sheep and Hu sheep. It was found that six genes - ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 - showed significant differences in methylation levels between Tan sheep and Hu sheep, and these genes are involved in muscle cell differentiation and development. This study highlights the importance of gene methylation in the formation of muscle-related traits.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson
Summary: ARPEGGIO is a workflow for analyzing epigenetic data in allopolyploids, utilizing the EAGLE-RC read classification algorithm to address sequence similarity challenges among parental genomes. This workflow offers automation and a complete set of analyses starting from raw WGBS data to outputting a list of genes showing differential methylation, ensuring reproducibility with simple set up and interpretation. ARPEGGIO stands out as the only workflow supporting polyploid data, as shown through its performance evaluation and agreement with published results.
Article
Genetics & Heredity
Qiushi Wang, Libo Wu, Jiaxing Yu, Guanghua Li, Pengfei Zhang, Haozhe Wang, Lin Shao, Jinying Liu, Weixi Shen
Summary: This study analyzed the methylation levels in tumor samples, tumor-adjacent tissues, and tumor-distant normal tissues from non-small cell lung cancer patients, and identified tumor-specific differentially methylated regions and progressively aggravating aberrant methylations during cancer development. The results suggest the essential role of DNA methylation in pre-malignant field defects and provide potential markers for lung cancer screening.
BMC MEDICAL GENOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Adam Nunn, Christian Otto, Mario Fasold, Peter F. Stadler, David Langenberger
Summary: This study presents a computational pre-processing approach to enable downstream analysis on a per-strand basis using conventional variant calling software. The method improves precision and sensitivity compared to specialized tools, and is applicable to both human and model plant variants.
Article
Biotechnology & Applied Microbiology
Dorothea Seiler Vellame, Isabel Castanho, Aisha Dahir, Jonathan Mill, Eilis Hannon
Summary: The combination of sodium bisulfite treatment with highly-parallel sequencing is commonly used to quantify DNA methylation levels. Factors such as read depth, sample size, and DNA methylation differences between groups all influence the power to detect differences. A tool called POWEREDBiSeq has been developed to predict study-specific power for identifying DNA methylation differences, taking into account read depth filtering parameters and sample size requirements.
Review
Plant Sciences
Shilpa, Rajni Kant Thakur, Pramod Prasad, S. C. Bhardwaj, O. P. Gangwar, Subodh Kumar
Summary: The outcome of host-pathogen interactions is influenced by both genetic and epigenetic systems.
Article
Biotechnology & Applied Microbiology
Qian Yan, Ying Tang, Fan He, Jiao Xue, Ruisheng Zhou, Xiaoying Zhang, Huiyan Luo, Daihan Zhou, Xiongwen Wang
Summary: This study investigated alterations in DNA methylation patterns in hepatocellular carcinoma (HCC) using whole-genome bisulfite sequencing technology. The research identified a genome-wide hypomethylation pattern in HCC, with hyper-DMGs mainly involved in metabolism pathways and hypo-DMGs mainly involved in cell adhesion. By constructing a prognostic model based on aberrantly methylated genes, the study provided insights into the epigenetic mechanisms of HCC development.
Article
Biochemical Research Methods
Mengya Liu, Yun Xu
Summary: The novel method EM-MUL proposed in this study can effectively resolve the issue of multireads in BS-reads, with experimental results showing high accuracy and efficiency in aligning multireads.
BMC BIOINFORMATICS
(2021)
Article
Substance Abuse
Jeroen L. A. Pennings, Anne Havermans, Charlotte G. G. M. Pauwels, Erna J. Z. Krusemann, Wouter F. Visser, Reinskje Talhout
Summary: The presence of nicotine salt-containing e-liquids in the Netherlands market has increased significantly in recent years. Nicotine salts, due to their characteristics, make these e-liquids more addictive and attractive, particularly to young and inexperienced users. Policymakers are advised to regulate products containing nicotine salts.
Article
Substance Abuse
Jeroen L. A. Pennings, Geoffrey Ferris Wayne, Walther N. M. Klerx, Charlotte G. G. M. Pauwels, Reinskje Talhout
Summary: This study explores the impact of tobacco blend and design characteristics on the sensory experience of cigarette consumers. The findings suggest that while some variations in design are noticeable to consumers, many products on the market are not discernibly different, indicating that brand diversity may serve non-sensory purposes such as marketing.
Article
Substance Abuse
Ingrid M. E. Bakker-'t Hart, Frank Bakker, Jeroen L. A. Pennings, Naomi Weibolt, Selma Eising, Reinskje Talhout
Summary: This study examines the commonly used flavors and flavorings in waterpipe tobacco and related products, and presents a waterpipe tobacco flavor wheel for experts' reference. The analysis reveals that the majority of waterpipe tobacco products are flavored, with fruit flavors being the most prevalent. Herbal molasses and steam stones contain similar levels of flavorings, with lower levels compared to waterpipe tobacco. The flavorings in waterpipe products are mainly fruity and sweet, often combined with menthol/mint flavorings. Banning flavorings in all waterpipe products could be an effective strategy to reduce waterpipe smoking among youth.
Article
Biochemistry & Molecular Biology
Manon C. Bouwmeester, Yu Tao, Susana Proenca, Frank G. van Steenbeek, Roos-Anne Samsom, Sandra M. Nijmeijer, Theo Sinnige, Luc J. W. van der Laan, Juliette Legler, Kerstin Schneeberger, Nynke I. Kramer, Bart Spee
Summary: In vitro toxicity testing using hepatocyte-like intrahepatic cholangiocyte organoids (HL-ICOs) allows for the evaluation of drug metabolism gene expression and activity, providing insights into the extent of drug-induced hepatotoxicity.
Article
Reproductive Biology
Laura M. M. Samrani, Jeroen L. A. Pennings, Nina Hallmark, Remi Bars, Helen Tinwell, Marc Pallardy, Aldert H. Piersma
Summary: The study investigates the effect of exposure duration on gene expression changes in the all-trans retinoic acid (ATRA) signaling pathway in zebrafish embryotoxicity test (ZET). It is found that the highest magnitudes of gene expression regulation occur after 2-24 hrs exposure, with the optimal response at 4 hrs. Early assessment of gene expression regulation after exposure onset in ZET could be optimal for predicting developmental toxicity.
REPRODUCTIVE TOXICOLOGY
(2023)
Article
Substance Abuse
Jeroen L. A. Pennings, Anne Havermans, Erna J. Z. Krusemann, Dion Zijtveld, Eva H. W. Huiberts, Peter M. J. Bos, Erna Schenk, Wouter F. Visser, Ingrid M. EBakker-'t Hart, Yvonne C. M. Staal, Reinskje Talhout
Summary: The Dutch government plans to only allow tobacco flavors in e-liquids to discourage e-cigarette use among youth. Researchers have compiled a restrictive list of 16 tobacco flavorings to implement this policy.
Article
Pharmacology & Pharmacy
Susana Proenca, Nick van Sabben, Juliette Legler, Jorke H. Kamstra, Nynke I. Kramer
Summary: This study investigates the effects of hexabromocyclododecane (HBCD) on human liver cells using different cell models. The 3D model exhibited the strongest response to HBCD, but none of the models showed changes in enzyme activity related to thyroid hormone metabolism. This suggests that transcriptome changes may not accurately reflect the adverse effects of HBCD on thyroid hormone.
Review
Chemistry, Medicinal
Christina H. J. Veltman, Jeroen L. A. Pennings, Bob van de Water, Mirjam Luijten
Summary: Nongenotoxic (NGTX) carcinogens induce cancer through mechanisms other than direct DNA damage, primarily involving the induction of oxidative stress leading to regenerative proliferation. However, current carcinogenicity assessment methods mainly focus on genetic toxicity, which may overlook NGTX carcinogens. To improve the predictivity of carcinogenicity assessment, a mechanism-based approach such as the adverse outcome pathway (AOP) network for chemically induced oxidative stress leading to (NGTX) carcinogenesis is proposed. This AOP network considers the role of oxidative stress in cancer development and explores the mechanisms and biological effects of chemical-induced oxidative damage. Developing AOP networks relevant to human carcinogenesis will facilitate a transition to a mechanism-based, human-relevant carcinogenicity assessment with reduced reliance on laboratory animals.
CHEMICAL RESEARCH IN TOXICOLOGY
(2023)
Article
Neurosciences
Faycal Guedj, Elise Kane, Lauren A. Bishop, Jeroen L. A. Pennings, Yann Herault, Diana W. Bianchi
Summary: The effectiveness of the Ts65Dn mouse model in improving neurocognition in Down syndrome has not been successfully translated to humans. The Ts66Yah mouse model, which carries an extra chromosome and identical segmental trisomy as Ts65Dn, was used to investigate the underlying factors.
BIOLOGICAL PSYCHIATRY
(2023)
Article
Substance Abuse
Charlotte G. G. M. Pauwels, Wouter F. Visser, Jeroen L. A. Pennings, Ernesto P. Baloe, Arnout P. T. Hartendorp, Loes van Tiel, Mirjam van Mourik, Wim Vaessen, Sanne Boesveldt, Reinskje Talhout
Summary: This study aimed to determine whether nicotine salts increase sensory appeal at lower concentrations and compared the inhalation intensity of both types of e-liquids. The results showed that nicotine salts did not significantly affect sensory appeal, harshness, and puffing intensity compared to free-based nicotine.
DRUG AND ALCOHOL DEPENDENCE
(2023)
Article
Substance Abuse
Jeroen L. A. Pennings, Charlotte G. G. M. Pauwels, Erna Schenk, Reinskje Talhout
Summary: Cigarillos have emerged as a substitute for flavored cigarettes, which are prohibited in the European Union, and they are also cheaper. To gain a better understanding of the cigarillo market, we analyzed product data from manufacturers via the EU-CEG system.
TOBACCO INDUCED DISEASES
(2023)
Article
Agriculture, Dairy & Animal Science
Jiayi Yang, Jorke Kamstra, Juliette Legler, Hilde Aardema
Summary: Plastic pollution is a crucial global health concern, with micro- and nanoplastics (MNPs) being taken up by humans and animals through food and water, and having the potential to pass through important barriers. While the reproductive effects of MNPs are not well-studied in mammals, evidence from aquatic species suggests potential impacts. Studies in rodents indicate that MNPs can reach the gonads and impact offspring after maternal exposure during pregnancy, possibly due to the particles themselves or plastic contaminants. Further research is needed on the effects of MNP exposure during the periconception and embryonic period.
ANIMAL REPRODUCTION
(2023)
Article
Toxicology
Albert Braeuning, Patrick Balaguer, William Bourguet, Jordi Carreras-Puigvert, Katreece Feiertag, Jorke H. Kamstra, Dries Knapen, Dajana Lichtenstein, Philip Marx-Stoelting, Jonne Rietdijk, Kristin Schubert, Ola Spjuth, Evelyn Stinckens, Kathrin Thedieck, Rik van den Boom, Lucia Vergauwen, Martin von Bergen, Neele Wewer, Daniel Zalko
Summary: In the past, the focus of analyzing the endocrine disrupting properties of chemicals was mainly on estrogenic or androgenic properties, as well as steroidogenesis and thyroid signaling. However, more recent attention has been given to the disruption of energy metabolism and related signaling pathways by exogenous substances known as metabolism-disrupting chemicals (MDCs). This paper provides an overview of the efforts within the EU-funded Partnership for the Assessment of Risks of Chemicals (PARC) to develop novel in vitro methods for detecting endocrine metabolic disruptors and improving the toxicological toolbox.
FRONTIERS IN TOXICOLOGY
(2023)
Article
Hematology
Umeshkumar Vekariya, Monika Toma, Margaret Nieborowska-Skorska, Bac Viet Le, Marie-Christine Caron, Anna-Mariya Kukuyan, Katherine Sullivan-Reed, Paulina Podszywalow-Bartnicka, Kumaraswamy N. Chitrala, Jessica Atkins, Malgorzata Drzewiecka, Wanjuan Feng, Joe Chan, Srinivas Chatla, Konstantin Golovine, Jaroslav Jelinek, Tomasz Sliwinski, Jayashri Ghosh, Ksenia Matlawska-Wasowska, Gurushankar Chandramouly, Reza Nejati, Mariusz Wasik, Stephen M. Sykes, Katarzyna Piwocka, Emir Hadzijusufovic, Peter Valent, Richard T. Pomerantz, George Morton, Wayne Childers, Huaqing Zhao, Elisabeth M. Paietta, Ross L. Levine, Martin S. Tallman, Hugo F. Fernandez, Mark R. Litzow, Gaorav P. Gupta, Jean-Yves Masson, Tomasz Skorski
Summary: Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. Formaldehyde generated by serine/1-carbon cycle metabolism contributes to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells. Oncogenic tyrosine kinases (OTKs) enhance the expression of DNA polymerase theta (POL theta) to repair DPC-containing DNA double-strand breaks. Inhibition of POL theta can be an effective therapeutic strategy for leukemia.
Article
Biotechnology & Applied Microbiology
Himani Vaidya, Hye Seon Jeong, Kelsey Keith, Shinji Maegawa, Gennaro Calendo, Jozef Madzo, Jaroslav Jelinek, Jean-Pierre J. Issa
Summary: DNA methylation drift and increased entropy with age are primarily caused by and are sensors for, stem cell replication in adult tissues. These findings have implications for tissue-specific functional declines with aging and the development of DNA-methylation-based biological clocks.
