Article
Biochemistry & Molecular Biology
James Ord, Toni Gossmann, Irene Adrian-Kalchhauser
Summary: In this study, the relationship between DNA methylation variation and nucleotide diversity in marine and freshwater stickleback populations was analyzed. It was found that differentially methylated sites between populations have higher genetic diversity, with higher diversity observed among sites that gained methylation in freshwater. Surprisingly, although nucleotide diversity is generally lower in the freshwater population, sites that lost methylation have elevated nucleotide diversity in the freshwater population. Furthermore, sites with ancestrally variable methylation have higher nucleotide diversity and positively correlate with the sensitivity to environmentally induced methylation change. These findings suggest that increased epigenetic variance precedes genetic diversification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Immunology
Shivanthan Shanthikumar, Melanie R. Neeland, Richard Saffery, Sarath C. Ranganathan, Alicia Oshlack, Jovana Maksimovic
Summary: In this study, bronchoalveolar lavage samples were used to define DNA methylation profiles for common cell types in the lungs, facilitating reference-based cell type composition estimation. These profiles were then successfully utilized in conjunction with an established methylation deconvolution method to estimate cell type composition in different tissue types, enabling further study of DNA methylation's role in lung health and disease.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Toshitsugu Fujita, Shoko Nagata, Hodaka Fujii
Summary: This study explores the use of blocking RPA method to detect gene mutations and examine DNA epigenetic status through nucleic acid blockers and CRISPR ribonucleoproteins. Moreover, it demonstrates that Methyl-CpG binding proteins can inhibit DNA polymerase elongation on CpG-methylated template DNA, enabling the detection of methylated CpG islands in RPA reactions at low temperatures.
COMMUNICATIONS BIOLOGY
(2021)
Review
Oncology
Hannah O'Neill, Heather Lee, Ishaan Gupta, Euan J. Rodger, Aniruddha Chatterjee
Summary: Cancer is a complex disease composed of diverse cell populations/subpopulations with varying genetic and epigenetic states. Aberrant DNA methylation, an epigenetic modification, has been implicated in oncogenesis. Traditional sequencing methods provide averaged methylation profiles of thousands of cells, but with single-cell sequencing technologies, the methylome of individual cells can now be acquired. This technology has important implications for cancer biology research, biomarker discovery, and less invasive diagnostic tests.
Article
Medicine, General & Internal
Biyuan Luo, Fang Ma, Hao Liu, Jixiong Hu, Le Rao, Chun Liu, Yongfang Jiang, Shuyu Kuangzeng, Xuan Lin, Chenyang Wang, Yiyu Lei, Zhongzhou Si, Guangshun Chen, Ning Zhou, Chengbai Liang, Fangqing Jiang, Fenge Liu, Weidong Dai, Wei Liu, Yawen Gao, Zhihong Li, Xi Li, Guangyu Zhou, Bingsi Li, Zhihong Zhang, Weiqi Nian, Lihua Luo, Xianling Liu
Summary: This study developed a sensitive blood-based non-invasive screening model for hepatocellular carcinoma (HCC) that can effectively distinguish early-stage HCC patients from high-risk population, and it demonstrated superior performance in an independent validation cohort.
Article
Environmental Sciences
Arce Domingo-Relloso, Anne Bozack, Samara Kiihl, Zulema Rodriguez-Hernandez, Pilar Rentero-Garrido, J. Antonio Casasnovas, Montserrat Leon-Latre, Tamara Garcia-Barrera, J. Luis Gomez-Ariza, Belen Moreno, Ana Cenarro, Griselda de Marco, Faruque Parvez, Abu B. Siddique, Hasan Shahriar, Mohammad N. Uddin, Tariqul Islam, Ana Navas-Acien, Mary Gamble, Maria Tellez-Plaza
Summary: The study identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, but differences in As-related epigenetic sites across the study populations may also reflect low and high As-specific associations. This work contributes to a deeper understanding of potential epigenetic dysregulations of As, with further research needed to confirm biological consequences associated with DIP2C epigenetic regulation and investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.
ENVIRONMENTAL RESEARCH
(2022)
Article
Neurosciences
Maren Stolp Andersen, Ingvild Sorum Leikfoss, Ina Skaara Brorson, Chiara Cappelletti, Conceicao Bettencourt, Mathias Toft, Lasse Pihlstrom
Summary: Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is important for potential therapeutic implications. This study investigated epigenome-wide DNA methylation in different peripheral immune cell types and identified differential methylation patterns in CD14+ monocytes and CD8+ T cells. Methylation changes upstream of RAB32, a gene linked to LRRK2, were found in monocytes and correlated negatively with mRNA expression.
NPJ PARKINSONS DISEASE
(2023)
Article
Cell Biology
Fabio M. D'Orazio, Piotr J. Balwierz, Ada Jimenez Gonzalez, Yixuan Guo, Benjamin Hernandez-Rodriguez, Lucy Wheatley, Aleksandra Jasiulewicz, Yavor Hadzhiev, Juan M. Vaquerizas, Bradley Cairns, Boris Lenhard, Ferenc Mueller
Summary: In zebrafish, primordial germ cells (PGCs) respond to regulatory information from the germ plasm in two distinct phases using two distinct mechanisms, activating zygotic genome and germ-cell-specific genes, which are only stabilized in PGCs by cytoplasmic germ plasm determinants. This results in transcriptional divergence between PGC and somatic blastocysts.
DEVELOPMENTAL CELL
(2021)
Article
Biochemical Research Methods
Gaetan De Waele, Jim Clauwaert, Gerben Menschaert, Willem Waegeman
Summary: The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. By adapting the Transformer neural network architecture and combining axial attention with sliding window self-attention, the CpG Transformer shows state-of-the-art performances on various datasets. The CpG Transformer also demonstrates interpretability and rapid transfer learning properties, making it efficient for practitioners to train models on new datasets with limited computational resources and time constraints.
Article
Biology
Paula Esteller-Cucala, Marc Palmada-Flores, Lukas F. K. Kuderna, Claudia Fontsere, Aitor Serres-Armero, Marc Dabad, Maria Torralvo, Armida Faella, Luis Ferrandez-Peral, Laia Llovera, Oscar Fornas, Eva Julia, Erika Ramirez, Irene Gonzalez, Jochen Hecht, Esther Lizano, David Juan, Tomas Marques-Bonet
Summary: This study generates genome assemblies for seven major haplogroups of the human Y chromosome at a unique resolution that overcomes the structurally complex regions within. These data enable the detection and profiling of epigenetic modifications among the considered haplogroups.
COMMUNICATIONS BIOLOGY
(2023)
Article
Medicine, Research & Experimental
Juan Ramon Tejedor, Clara Bueno, Meritxell Vinyoles, Paolo Petazzi, Antonio Agraz-Doblas, Isabel Cobo, Raul Torres-Ruiz, Gustavo F. Bayon, Raul F. Perez, Sara Lopez-Tamargo, Francisco Gutierrez-Aguera, Pablo Santamarina-Ojeda, Manuel Ramirez-Orellana, Michela Bardini, Giovanni Cazzaniga, Paola Ballerini, Pauline Schneider, Ronald W. Stam, Ignacio Varela, Mario F. Fraga, Agustin F. Fernandez, Pablo Menendez
Summary: B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer, with infant B-ALL (iB-ALL) showing unique DNA mutational landscape and potential epigenetic mechanisms contributing to leukemogenesis. Integrated analysis of methylome and transcriptome data from MLLr and non-MLLr iB-ALL patients revealed chromatin state alterations and identified distinct gene expression patterns, particularly related to the AP-1 complex and RUNX factors in MLLr iB-ALL. Pharmacological inhibition of AP-1 showed promising potential in impairing MLLr-leukemic growth, suggesting a novel therapeutic approach for MLLr-iB-ALL.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Biochemistry & Molecular Biology
Artem Nurislamov, Timofey Lagunov, Maria Gridina, Alla Krasikova, Veniamin Fishman
Summary: DNA methylation is an important epigenetic mechanism involved in various genomic processes. This study investigated DNA methylation patterns in chicken diplotene oocytes and found that they closely resemble the genomic distribution observed in somatic tissues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Loraine Kay D. Cabral, Peter Andrew C. Reyes, Lory S. Croce, Claudio Tiribelli, Caecilia H. C. Sukowati
Summary: The study revealed that SOCS1 methylation is significantly higher in HCC compared to peri-HCC and non-tumoral tissues. Treatment with 5-AZA reduced DNMT1 protein expression in different HCC cell subtypes, with the strongest effect observed in stromal subtype lines. The modulatory effect of 5-AZA on SOCS1 expression varied among cell types, with more efficient restoration in CSC HCC cells compared to sorafenib.
Review
Genetics & Heredity
Waleed Iqbal, Wanding Zhou
Summary: Understanding tissue heterogeneity requires analyzing intercellular epigenetic differences at the single-cell level. Recent advances in single-cell DNA methylome profiling have provided the tools to study this heterogeneity in detail. However, these advances also bring challenges in data analysis and interpretation.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Oncology
Joao Lobo, Vera Constancio, Pedro Leite-Silva, Rita Guimaraes, Mariana Cantante, Isaac Braga, Joaquina Mauricio, Leendert H. J. Looijenga, Rui Henrique, Carmen Jeronimo
Summary: The study revealed that the methylation pattern of TGCT samples is influenced by histology, with clustering of samples showing response to cisplatin. Within a specific subtype (embryonal carcinoma), patients with cisplatin resistance demonstrated a significant increase in net methylation levels compared to those with complete response. Furthermore, differentially methylated promoters among sample groups were mostly not shared, indicating heterogeneity in patient tissue samples.
CLINICAL EPIGENETICS
(2021)
