Review
Multidisciplinary Sciences
Toshikazu Ushijima, Susan J. Clark, Patrick Tan
Summary: Cancer, driven by genomic and epigenomic derangements, requires multimodal data integration to understand the molecular evolution of malignant cell states across its lifecycle. Driver mutations and epigenetic alterations in normal-appearing tissues prompt a reassessment of cancer initiation, while studying clonal selection, epigenomic adaptation, and persister cells in metastasis and therapy resistance is an emerging field. The importance of tumor ecosystems in cancer development is being unveiled by advancing single-cell and spatial technologies.
Review
Biochemistry & Molecular Biology
Stefano Amente, Giovanni Scala, Barbara Majello, Somaiyeh Azmoun, Helen G. Tempest, Sanjay Premi, Marcus S. Cooke
Summary: Exposure from external and internal environments leads to modifications in genomic DNA, contributing to various diseases. Understanding the impact of damage on cellular function and pathogenesis remains unclear, but mapping DNA adductomics may provide valuable insights.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemical Research Methods
Yuangao Wang, Meng Wang, Yi Zhang
Summary: A new three-step eccDNA purification (3SEP) procedure is proposed to efficiently purify eccDNA with high purity. In addition, a full-length eccDNA sequencing technique is developed, along with an eccDNA caller software, for accurate identification and mapping of eccDNA. These methods will facilitate the study of eccDNA and have potential diagnostic and clinical applications.
Review
Cell Biology
Courtney W. Hanna, Gavin Kelsey
Summary: Genomic imprinting refers to the monoallelic expression of a gene based on parent of origin, which is a result of differential epigenetic marking between male and female germlines. Apart from the canonical DNA methylation-mediated imprinting, there is also non-canonical imprinting caused by maternal H3K27me3-independent of DNA methylation. Conservation of canonical and noncanonical genomic imprinting and the role of endogenous retroviral elements are discussed in this review.
GENES & DEVELOPMENT
(2021)
Article
Biochemical Research Methods
Alli L. Gombolay, Francesca Storici
Summary: Ribonucleotides are commonly found in genomic DNA, but their distribution and signatures in DNA are not well understood. Ribose-Map is a standardized bioinformatics toolkit that allows researchers to analyze the locations and biological signatures of ribonucleotides in DNA. It standardizes the analysis of ribonucleotide sequencing experiments and enables direct comparisons of results.
Review
Oncology
Khay Guan Yeoh, Patrick Tan
Summary: This review discusses the advances in understanding the genomic landscape of gastric cancer, including driver gene alterations, molecular subtypes, transcriptomic changes, and their interactions with environmental influences and tumor microenvironment. Genomic findings will facilitate precision oncology and prevention strategies for gastric cancer.
NATURE REVIEWS CANCER
(2022)
Article
Biochemistry & Molecular Biology
Christopher Riccardi, Iacopo Passeri, Lisa Cangioli, Camilla Fagorzi, Marco Fondi, Alessio Mengoni
Summary: DNA methylation is a commonly observed epigenetic modification found in both eukaryotes and prokaryotes, and it is implicated in various biological phenomena such as gene regulation and adaptation to the environment. Advances in third-generation sequencing technologies have enabled the direct detection of genome-wide methylation profiles, providing opportunities to understand and utilize the epigenomic landscape at the individual and population levels. Here, we introduce a pipeline called MeStudio, which analyzes and combines genome-wide methylation profiles with genomic features, allowing for the identification of DNA methylation in coding and noncoding sequences. We demonstrate the utility and performance of MeStudio using single-molecule real-time sequencing outputs from Sinorhizobium meliloti strains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Sunil Sharma, Owias Iqbal Dar, Kirpal Singh, Sharad Thakur, Anup Kumar Kesavan, Arvinder Kaur
Summary: This study found that Triclosan has significant toxicity to hatchlings of Labeo rohita, inducing alterations in antioxidant/detoxification, metabolic, and neurological genes as well as DNA damage. Principal component analysis identified OTM, TL, TM, TDNA, SOD, and GR as biomarkers for Triclosan toxicity.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Review
Oncology
Arlou Kristina Angeles, Florian Janke, Simone Bauer, Petros Christopoulos, Anja Lisa Riediger, Holger Sueltmann
Summary: Liquid biopsy and cell-free DNA (cfDNA) analysis provide a non-invasive method to diagnose and profile tumors, as well as gain insights into therapy response, resistance mechanisms, and epigenetic modifications. While panel next-generation sequencing (NGS) of driver mutations is commonly used for individualized cancer treatment adjustment, there is growing interest in exploring deeper genomic and epigenomic characterization of tumor cfDNA, including fragmentomics, nucleosome modifications, and methylation patterns, to enhance disease monitoring and early cancer detection. Recent progress in emerging technologies of cfDNA analysis highlights the added clinical value, identifies strengths and limitations compared to conventional targeted NGS analysis, and discusses current challenges and future directions in oncology research.
Article
Microbiology
Meiqin Zheng, Yutong Kang, Yangyang Shen, Yi Xu, Fangyi Xu, Yanjiong Chen
Summary: In this study, a highly virulent ocular pathogen was isolated using metagenomic sequencing and bioinformatics analysis, providing important insights into the composition and genome characteristics of pathogens in endophthalmitis patients.
CURRENT MICROBIOLOGY
(2023)
Article
Biology
Zixuan Wang, Meiqin Gong, Yuhang Liu, Shuwen Xiong, Maocheng Wang, Jiliu Zhou, Yongqing Zhang
Summary: This paper provides a comprehensive compendium to better understand TF-DNA binding from genomic features. It summarizes commonly used datasets and data processing methods, and classifies and analyzes current deep learning methods in TFBS prediction. It also illustrates the characterization of functional consequences of TF-DNA binding and discusses the challenges and opportunities of deep learning in TF-DNA binding prediction.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Genetics & Heredity
Jun Liu, Zhuxiang Zhao, Shuquan Wei, Binkai Li, Ziwen Zhao
Summary: This study investigated the genomic features of Chinese small cell lung cancer (SCLC) patients. The results showed that TP53 and RB1 were the most prevalent gene alterations, with most genetic alterations enriched in the cell cycle signaling pathway. Additionally, a significant association was found between high tumor mutation burden and mutations in certain genes. Approximately one-third of patients had actionable alterations, which could guide targeted therapy for Chinese SCLC patients.
BMC MEDICAL GENOMICS
(2022)
Article
Urology & Nephrology
Matthew Mossanen, Filipe L. F. Carvalho, Vinayak Muralidhar, Mark A. Preston, Brendan Reardon, Jake R. Conway, Catherine Curran, Dory Freeman, Sybil Sha, Guru Sonpavde, Michelle Hirsch, Adam S. Kibel, Eliezer M. Van Allen, Kent W. Mouw
Summary: Researchers have identified unique mutational properties in radiation-associated muscle-invasive bladder cancer (RA-MIBC) that contribute to its distinct biological and clinical features compared to non-radiation-associated MIBC.
Article
Multidisciplinary Sciences
Biaobin Jiang, Quanhua Mu, Fufang Qiu, Xuefeng Li, Weiqi Xu, Jun Yu, Weilun Fu, Yong Cao, Jiguang Wang
Summary: The authors have developed a MetaNet framework that integrates clinical and sequencing data to assess the risk of metastasis in primary tumors. The framework achieves high accuracy in distinguishing between metastasis and primary cases in breast and prostate cancers. The study identifies primary tumors with genetic features enriched in metastasis (MFP) and shows their higher risk of metastasis and shorter disease-free survival.
NATURE COMMUNICATIONS
(2021)
Review
Chemistry, Medicinal
Felix Javier Jimenez-Jimenez, Hortensia Alonso-Navarro, Elena Garcia-Martin, Ignacio Alvarez, Pau Pastor, Jose A. G. Agundez
Summary: Research on genetic factors related to ET includes family linkage studies, genome-wide association studies, and candidate gene association studies, but no specific genes have been definitively linked to the risk of ET. Ongoing efforts are still being made to identify responsible genes for ET.
Article
Agriculture, Dairy & Animal Science
Adrian Lopez-Catalina, Valentin Costes, Ramon Peiro-Pastor, Helene Kiefer, Oscar Gonzalez-Recio
Summary: Epigenetic marks can explain part of the phenotypic variance in animal breeding models. Nanopore sequencing shows high correlation with bisulphite sequencing in identifying DNA methylation marks. Different sequencing methods highlight differentially methylated genes and positions of economic interest in animal breeding.