Article
Biochemistry & Molecular Biology
Yanqun Wang, Jie Li, Lu Zhang, Hai-Xi Sun, Zhaoyong Zhang, Jinjin Xu, Yonghao Xu, Yu Lin, Airu Zhu, Yuxue Luo, Haibo Zhou, Yan Wu, Shanwen Lin, Yuzhe Sun, Fei Xiao, Ruiying Chen, Liyan Wen, Wei Chen, Fang Li, Rijing Ou, Yanjun Zhang, Tingyou Kuo, Yuming Li, Lingguo Li, Jing Sun, Kun Sun, Zhen Zhuang, Haorong Lu, Zhao Chen, Guoqiang Mai, Jianfen Zhuo, Puyi Qian, Jiayu Chen, Huanming Yang, Jian Wang, Xun Xu, Nanshan Zhong, Jingxian Zhao, Junhua Li, Jincun Zhao, Xin Jin
Summary: This study compared cfRNA profiles between COVID-19 patients and healthy donors, and found 380 up-regulated cfRNA molecules in all COVID-19 patients. Several potential biomarkers were identified. Antiviral and neutrophil activation-related genes showed decreased expression levels during treatment, which is consistent with enhanced inflammatory response in COVID-19 patients. Differential expression of noncoding RNAs and changes in tRNA pools related to SARS-CoV-2 replication were also observed. Additionally, pneumonia-related microorganisms were detected in the plasma of COVID-19 patients.
Article
Endocrinology & Metabolism
Susmita Dutta, Soham Tarafdar, Pradip Mukhopadhyay, Nitai P. Bhattacharyya, Sujoy Ghosh
Summary: Measurement of cell-free DNA levels in plasma could be a useful tool for differentiating malignant from benign thyroid nodules, with a high sensitivity and specificity. The established cutoff value of cfDNA showed strong agreement with histopathological classification, indicating its potential clinical utility in the diagnosis of thyroid nodules.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Multidisciplinary Sciences
Yunyun An, Xin Zhao, Ziteng Zhang, Zhaohua Xia, Mengqi Yang, Li Ma, Yu Zhao, Gang Xu, Shunda Du, Xiang'an Wu, Shuowen Zhang, Xin Hong, Xin Jin, Kun Sun
Summary: The authors used orientation-aware fragmentation analysis to identify DNA methylation as a regulator of nuclease function. They found that low-level DNA methylation can increase nucleosome accessibility and alter the cutting activities of nucleases during DNA fragmentation, leading to variation in cutting sites and size distribution of cell-free DNA (cfDNA). They also developed a cfDNA ending preference-based metric for cancer diagnosis, which has been validated by multiple pan-cancer datasets.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Hua Bao, Zheng Wang, Xiaoji Ma, Wei Guo, Xiangyu Zhang, Wanxiangfu Tang, Xin Chen, Xinyu Wang, Yikuan Chen, Shaobo Mo, Naixin Liang, Qianli Ma, Shuyu Wu, Xiuxiu Xu, Shuang Chang, Yulin Wei, Xian Zhang, Hairong Bao, Rui Liu, Shanshan Yang, Ya Jiang, Xue Wu, Yaqi Li, Long Zhang, Fengwei Tan, Qi Xue, Fangqi Liu, Sanjun Cai, Shugeng Gao, Junjie Peng, Jian Zhou, Yang Shao
Summary: This study developed a robust machine learning model for multi-cancer early detection using cell-free DNA fragmentomics. The model showed high accuracy and sensitivity in detecting early-stage and small-size tumors. This research has significant implications for the development of cancer early screening in clinical practice.
Editorial Material
Biotechnology & Applied Microbiology
Peiyong Jiang, Y. M. Dennis Lo
Summary: A new assay for cell-free DNA fragmentation enhances the prediction of gene expression in liquid biopsies.
NATURE BIOTECHNOLOGY
(2022)
Article
Sport Sciences
Christoph C. Kaufmann, Claudia Wegberger, Maximilian Tscharre, Paul M. Haller, Edita Piackova, Irena Vujasin, Mona Kassem, Ioannis Tentzeris, Matthias K. Freynhofer, Bernhard Jaeger, Johann Wojta, Kurt Huber
Summary: This study investigated the impact of marathon and ultra-marathon on inflammation and iron homeostasis, finding that the level of inflammation was higher after ultra-marathon compared to marathon. Additionally, the response patterns of iron homeostasis differed between the two races.
SCANDINAVIAN JOURNAL OF MEDICINE & SCIENCE IN SPORTS
(2021)
Article
Medicine, Research & Experimental
Florent Mouliere, Christopher G. Smith, Katrin Heider, Jing Su, Ymke van der Pol, Mareike Thompson, James Morris, Jonathan C. M. Wan, Dineika Chandrananda, James Hadfield, Marta Grzelak, Irena Hudecova, Dominique-Laurent Couturier, Wendy Cooper, Hui Zhao, Davina Gale, Matthew Eldridge, Colin Watts, Kevin Brindle, Nitzan Rosenfeld, Richard Mair
Summary: The study focused on detecting glioma-derived cell-free DNA (cfDNA) in body fluids and found that tumor-derived DNA could be identified in the majority of CSF, plasma, and urine samples with different tumor fractions. They also discovered a significant difference in cfDNA fragment sizes between glioma patients and individuals with non-malignant brain disorders or healthy individuals, which could potentially aid in non-invasive cancer detection using machine learning models.
EMBO MOLECULAR MEDICINE
(2021)
Article
Medicine, General & Internal
Binrong Ding, Xuewei Zhang, Zhengqing Wan, Feng Tian, Jie Ling, Jieqiong Tan, Xiaoqing Peng
Summary: The methylation patterns of mitochondrial DNA (mtDNA) in plasma cell-free DNA (cfDNA) differ between Alzheimer's disease (AD) patients and control subjects, with predominantly hypomethylated mtDNA in AD patients. Specifically, the hypomethylation of the D-Loop region in plasma cfDNA is consistent with previous studies and may contribute to the pathogenesis of AD.
Article
Oncology
Shuxin Zhang, Jun Zhang, Xinlei Hu, Senlin Yin, Yunbo Yuan, Lin Xia, Feng Cao, Xiaoqin Yan, Ziyue Yan, Qing Mao, Dan Xie, Yanhui Liu
Summary: A liquid biopsy method based on sequencing of plasma cfDNA fragments carrying 5hmC has been developed, which can detect brain gliomas and predict the aggressiveness of the tumors.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Oncology
Raquel Carrasco, Mercedes Ingelmo-Torres, Josep Oriola, Fiorella L. Roldan, Leonardo Rodriguez-Carunchio, Sandra Herranz, Begona Mellado, Antonio Alcaraz, Laura Izquierdo, Lourdes Mengual
Summary: BC patients show genetic heterogeneity, yet mutations in TERT, ATM, RB1, and FGFR3 were found in primary tumors and metastases of all patients. These mutations were also detected in cfDNA at various follow-up time points, allowing us to track tumor evolution in response to treatment. The analysis of BC mutations in plasma cfDNA could serve as a valuable tool for monitoring tumor evolution and improving clinical management.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biology
Shanwen Chen, Yunfan Jin, Siqi Wang, Shaozhen Xing, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu, Zhi John Lu, Pengyuan Wang
Summary: The utility of cell-free nucleic acids in monitoring cancer has been recognized. By profiling cfRNAs in plasma samples, human and microbe-derived plasma cfRNAs were found to have diagnostic value for cancer detection. Adding microbial features improved the accuracy of tumor classification.
Article
Biochemistry & Molecular Biology
Ray O. O. Bahado-Singh, Sangeetha Vishweswaraiah, Onur Turkoglu, Stewart F. F. Graham, Uppala Radhakrishna
Summary: Precision neurology combines high-throughput technologies and statistical modeling to identify novel disease pathways and predictive biomarkers in Alzheimer's disease (AD). Brain cytochrome P450 (CYP) genes are major regulators of cholesterol, sex hormone, and xenobiotic metabolism, and they could play important roles in neurodegenerative disorders. Epigenetic factors contribute to AD development. We evaluated cytosine ('CpG')-based DNA methylation changes in AD using circulating cell-free DNA (cfDNA) and identified differentially methylated CpG sites within the CYP genes. CYP biomarkers achieved high accuracy in predicting AD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Sara Bonlokke, Magnus Stougaard, Boe Sandahl Sorensen, Berit Bargum Booth, Estrid Hogdall, Gitte-Bettina Nyvang, Jacob Christian Lindegaard, Jan Blaakaer, Jesper Bertelsen, Katrine Fuglsang, Mikael Lenz Strube, Suzan Lenz, Torben Steiniche
Summary: Circulating cell-free HPV DNA (ccfHPV DNA) can serve as a marker for cervical cancer. This study used digital droplet PCR (ddPCR) to detect and quantify ccfHPV DNA in plasma from patients with HPV16- or HPV18-associated cervical cancer. The results showed that ccfHPV DNA may not be useful for early detection of cervical cancer, but it can be a promising tool for establishing tumor burden and monitoring the disease in advanced stage cervical cancer patients.
Article
Biology
Osamu Hisano, Takashi Ito, Fumihito Miura
Summary: This study identified short single-stranded cfDNA fragments approximately 50 nucleotides in length in human plasma, at concentrations comparable to nucleosome-sized fragments. These fragments are derived from open chromatin regions and enriched in transcription factor-binding sites, potentially forming non-canonical DNA structures.
Article
Medicine, General & Internal
Eleni Polatoglou, Zsuzsanna Mayer, Vida Ungerer, Abel J. Bronkhorst, Stefan Holdenrieder
Summary: Plasma cell-free DNA (cfDNA) can be extracted from various tissues and cell types and used for non-invasive diagnosis, treatment, and monitoring of cancer and other diseases. This study compared the performance of six commercial cfDNA extraction kits and found significant differences in DNA yield, with the manual QIAamp Circulating Nucleic Acid Kit and automated MagNA Pure Total NA Isolation Kit performing the best. These results highlight the importance of standardizing preanalytical conditions based on downstream applications.
