Review
Biochemical Research Methods
Xiaoqing Peng, Hong-Dong Li, Fang-Xiang Wu, Jianxin Wang
Summary: This study reviews the development of noninvasive diagnostic methods based on cell-free DNAs, focusing on mutation, methylation, and DNA fragmentation patterns to identify tissues-of-origin. The challenges and future directions in this field are also discussed, providing insights for bioinformatics researchers to improve the identification of tissues-of-origin for cfDNAs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medical Laboratory Technology
Ze Zhou, Suk Hang Cheng, Spencer C. Ding, Macy M. S. Heung, Tingting Xie, Timothy H. T. Cheng, W. K. Jacky Lam, Wenlei Peng, Jeremy Y. C. Teoh, Peter K. F. Chiu, Chi-Fai Ng, Peiyong Jiang, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo
Summary: The study reveals that urinary cfDNA has jagged ends, with a higher index compared to plasma DNA, particularly in patients with bladder cancer showing lower jagged end indexes. This suggests that jagged ends of urinary DNA could potentially serve as a new biomarker for bladder cancer detection.
CLINICAL CHEMISTRY
(2021)
Article
Biology
Wanxia Gai, Ze Zhou, Sean Agbor-Enoh, Xiaodan Fan, Sheng Lian, Peiyong Jiang, Suk Hang Cheng, John Wong, Stephen L. Chan, Moon Kyoo Jang, Yanqin Yang, Raymond H. S. Liang, Wai Kong Chan, Edmond S. K. Ma, Tak Y. Leung, Rossa W. K. Chiu, Hannah Valantine, K. C. Allen Chan, Y. M. Dennis Lo
Summary: The GETMap technique was developed to determine the tissue origin of plasma DNA carrying genetic variants by comparing methylation profiles, showing different contributions from various tissues. Studies in pregnant women, lung transplant recipients, and hepatocellular cancer patients demonstrated the potential applications in noninvasive prenatal testing, transplantation monitoring, and cancer screening, providing valuable insights into the origin of circulating DNA.
Article
Microbiology
Daniel Goncalves-Carneiro, Matthew A. Takata, Heley Ong, Amanda Shilton, Paul D. Bieniasz
Summary: ZAP protein recognizes RNA by binding to CpG dinucleotides, showing specific antiviral activity against non-self viral RNA and evolving in tetrapods. The antiviral activity of ZAP protein exhibits species-specific traits due to the co-evolution with TRIM25 cofactor.
Article
Obstetrics & Gynecology
Weijian Zhu, Lei Jiang, Chengshuang Pan, Junhui Sun, Xuefeng Huang, Wuhua Ni
Summary: The study evaluated DNA methylation patterns in sperm from men with differential levels of sperm DNA fragmentation index (DFI). The results showed that high DFI in male sperm was associated with significantly altered methylation in specific CpG fragments corresponding to nine genes. This suggests that sperm DNA damage may influence DNA methylation patterns in human sperm.
FERTILITY AND STERILITY
(2021)
Article
Cell Biology
Karan K. Budhraja, Bradon R. McDonald, Michelle D. Stephens, Tania Contente-Cuomo, Havell Markus, Maria Farooq, Patricia F. Favaro, Sydney Connor, Sara A. Byron, Jan B. Egan, Brenda Ernst, Timothy K. McDaniel, Aleksandar Sekulic, Nhan L. Tran, Michael D. Prados, Mitesh J. Borad, Michael E. Berens, Barbara A. Pockaj, Patricia M. LoRusso, Alan Bryce, Jeffrey M. Trent, Muhammed Murtaza
Summary: The fragmentation patterns of cell-free DNA (cfDNA) in plasma are influenced by cellular origin and can be used to detect tumor-derived DNA. Researchers developed a metric called iwFAF, which is based on fragment positioning and correlates with tumor fraction. They also used machine learning to differentiate healthy individuals from cancer patients based on iwFAF and nucleotide frequencies.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Medicine, General & Internal
Yanni Zeng, Carmen Amador, Chenhao Gao, Rosie M. Walker, Stewart W. Morris, Archie Campbell, Azra Frkatovic, Rebecca A. Madden, Mark J. Adams, Shuai He, Andrew D. Bretherick, Caroline Hayward, David J. Porteous, James F. Wilson, Kathryn L. Evans, Andrew M. McIntosh, Pau Navarro, Chris S. Haley
Summary: This study identified a set of vulnerable/modifiable parent-of-origin effects (POE)-regulated CpGs, and found several factors that significantly modified the POE on these CpGs. Additionally, plasma proteins and health-related phenotypes associated with the methylation level of one of the identified CpGs were also identified.
Article
Multidisciplinary Sciences
Katie Leap, Iveta Yotova, Steve Horvath, Julian A. Martinez-Agosto
Summary: Endometriosis is a common disease with various presentations. The use of DNA methylation age can help distinguish the origin of ectopic lesions, contributing to clinical classification.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Jennifer Kerkhof, Gabriella Maria Squeo, Haley McConkey, Michael A. Levy, Maria Rosaria Piemontese, Marco Castori, Maria Accadia, Elisa Biamino, Matteo Della Monica, Marilena Carmela Di Giacomo, Cristina Gervasini, Silvia Maitz, Daniela Melis, Donatella Milani, Maria Piccione, Paolo Prontera, Angelo Selicorni, Bekim Sadikovic, Giuseppe Merla
Summary: This study analyzed the methylation profiles of individuals with chromatinopathies and identified unique genome-wide DNA methylation profiles, which were matched and confirmed with known episignatures. Additionally, uncertain variants were reclassified as likely pathogenic, and specific chromatinopathy disorders were identified in some sequencing negative cases. Therefore, DNA methylation analysis plays an important role in diagnosing chromatinopathies.
GENETICS IN MEDICINE
(2022)
Article
Biology
Junying Wang, Wen Zhang, Xiaoqin Liu, Minjee Kim, Ke Zhang, Robert Y. L. Tsai
Summary: This study identified differentially methylated genomic regions (DMRs) in mouse livers that are co-regulated by aging and regeneration using whole-genome bisulfite sequencing (WGBS). The DMRs showed opposite methylation direction changes between 2 and 8 months and 8 and 16 months. Inverse-regulated DMRs by aging and regeneration were found in the promoter/gene regions of 12 genes. These findings provide insights into the epigenomic changes underlying the biology of aging on liver regeneration.
Article
Obstetrics & Gynecology
Weijian Zhu, Lei Jiang, Yan Li, Junhui Sun, Chunchun Lin, Xuefeng Huang, Wuhua Ni
Summary: This study identified a cluster of comethylated patterns associated with sperm DNA fragmentation (SDF) and found that BRCA1 may be the hub gene involved in sperm DNA damage.
FERTILITY AND STERILITY
(2022)
Article
Genetics & Heredity
Pengfei Liu
Summary: This study reveals the mechanisms of DNA methylation in tumors and identifies epigenetic driver genes involved in tumorigenesis through integrative analysis of multi-omics data and molecular regulatory networks. A classifier based on the aberrant methylation status in these driver genes is established to accurately predict the primary sites of metastatic cancer with high accuracy and stability.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Haiyan Liu, Chun Qiu, Bo Wang, Pingping Bing, Geng Tian, Xueliang Zhang, Jun Ma, Bingsheng He, Jialiang Yang
Summary: Carcinoma of unknown primary (CUP) is a metastatic cancer with unidentified primary tumor site, affecting 5% of cancer cases in the US. Recent studies propose integrating machine learning techniques with diverse biomarkers to predict TOO, as traditional methods are limited in accurately identifying tissue-of-origin in CUP patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Geriatrics & Gerontology
Haihua Tian, Zhenyu Hu, Chuang Wang
Summary: Aging is a complex health problem associated with a high risk of chronic diseases, with age-related turnover in adipose tissue being a major contributor to metabolic syndromes and shortened lifespan. DNA methylation regulates cellular senescence, metabolic function and inflammation in adipose tissue, suggesting potential for epigenetic therapeutic strategies against aging-related diseases in clinical settings.
Review
Geriatrics & Gerontology
Hao Xie, Xin Liu, Qing Zhou, Teng Huang, Lu Zhang, Jia Gao, Yuhan Wang, Yanjun Liu, Tong Yan, Shu Zhang, Cong-Yi Wang
Summary: Aging is a complex health problem associated with various chronic diseases. In adipose tissue, age-related changes result in metabolic dysfunction, inflammation, and cellular senescence. DNA methylation plays a role in regulating metabolic function and the beiging process in adipocytes. Understanding the impact of DNAm on adipose aging is important for developing epigenetic therapeutic strategies in clinical settings.
Article
Oncology
Peiyong Jiang, Kun Sun, Wenlei Peng, Suk Hang Cheng, Meng Ni, Philip C. Yeung, Macy M. S. Heung, Tingting Xie, Huimin Shang, Ze Zhou, Rebecca W. Y. Chan, John Wong, Vincent W. S. Wong, Liona C. Poon, Tak Yeung Leung, W. K. Jacky Lam, Jason Y. K. Chan, Henry L. Y. Chan, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo
Editorial Material
Oncology
Kun Sun
ANNALS OF TRANSLATIONAL MEDICINE
(2019)
Article
Biochemical Research Methods
Kun Sun
Article
Biochemical Research Methods
Kun Sun, Huating Wang, Hao Sun
Summary: Recent research focuses on novel transcripts and coding potential in plants, presenting a classifier NAMS optimized for plants and demonstrating its high accuracy and performance improvements on a comprehensive dataset from various plant species. The webserver also offers functional annotations to provide informative clues on transcript functions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Gastroenterology & Hepatology
Li-Shi Li, Xiang-Yu Guo, Kun Sun
Summary: Gastrointestinal (GI) cancers are common and early diagnosis is crucial. The article covers recent advances in GI cancer diagnosis, including blood biomarkers and AI technology. In the future, there will be further development in blood and AI technologies for GI cancer diagnosis.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Genetics & Heredity
Xinping Chen, Tao Wu, Lingguo Li, Yu Lin, Zhichao Ma, Jinjin Xu, Hui Li, Fanjun Cheng, Ruoyan Chen, Kun Sun, Yuxue Luo, Chen Zhang, Fang Chen, Jiao Wang, Tingyu Kuo, Xiaojuan Li, Chunyu Geng, Feng Lin, Chaojie Huang, Junjie Hu, Jianhua Yin, Ming Liu, Ye Tao, Jiye Zhang, Rijing Ou, Fang Zheng, Yan Jin, Huanming Yang, Jian Wang, Xun Xu, Shengmiao Fu, Hongyan Jiang, Xin Jin, Haiqiang Zhang
Summary: The study highlights the importance of understanding biological characteristics in severe COVID-19 patients, and demonstrates the potential of cfDNA in assessing disease progression. Upregulated and downregulated genes in the plasma of severe patients are closely related to the affected biological processes and functions. Furthermore, transcriptome analysis reveals viral and antiviral activity in blood cells of severe patients, illustrating the intense viral replication and immune system response.
FRONTIERS IN GENETICS
(2021)
Review
Genetics & Heredity
Yunyun An, Fei Fan, Xiaobing Jiang, Kun Sun
Summary: Brain cancers are a major cause of death worldwide, with varied survival rates depending on tumor type. Liquid biopsy assays using peripheral blood or cerebrospinal fluid have shown favorable characteristics for diagnosis, tumor subtyping, relapse prediction, and prognosis monitoring in brain cancers, making a significant step towards clinical benefits for patients.
FRONTIERS IN GENETICS
(2021)
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
Multidisciplinary Sciences
Qin Peng, Ziliang Huang, Kun Sun, Yahan Liu, Chi Woo Yoon, Reed E. S. Harrison, Danielle L. Schmitt, Linshan Zhu, Yiqian Wu, Ipek Tasan, Huimin Zhao, Jin Zhang, Sheng Zhong, Shu Chien, Yingxiao Wang
Summary: Genome architecture and organization are crucial for cell life, but how they coordinate gene expression and determine cell fate at the single cell level remains unknown. The researchers developed a system called SIMBA which allows for simultaneous imaging and manipulation of genomic loci using biomolecular assemblies. This system can enhance imaging signals and recruit epigenetic modulators to repress transcription at specific genomic loci, making it a valuable tool for visualizing and manipulating gene expression in living cells.
NATURE COMMUNICATIONS
(2022)
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
Clinical Neurology
Yue Cai, Jing Du, Anqi Li, Yalin Zhu, Linsen Xu, Kun Sun, Shaohua Ma, Tengfei Guo
Summary: To better design future clinical trials for Alzheimer's disease (AD) and understand its symptomatology, it is important to clarify the roles of beta-amyloid plaques and tau tangles in longitudinal tau accumulation in the medial temporal lobe (MTL) and how age, sex, APOE-epsilon 4, and KL-VShet modulate these relationships.
ALZHEIMERS RESEARCH & THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Lishi Li, Yunyun An, Li Ma, Mengqi Yang, Pengxiang Yuan, Xiaojian Liu, Xin Jin, Yu Zhao, Songfa Zhang, Xin Hong, Kun Sun
Summary: This article introduces Msuite2, an easy-to-use and high-performance toolkit for DNA methylation data analysis and visualization. Msuite2 is among the fastest tools in read alignment and shows balanced and high performance in mapping efficiency and accuracy. It has great potential to facilitate large-scale DNA methylation analysis in various biomedical studies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Computer Science, Artificial Intelligence
Kun Sun, Lishi Li, Li Ma, Yu Zhao, Lin Deng, Huating Wang, Hao Sun
Article
Biochemistry & Molecular Biology
Fei Fan, Dan Chen, Yu Zhao, Huating Wang, Hao Sun, Kun Sun
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Article
Multidisciplinary Sciences
Kun Sun, Liuqi Gu, Li Ma, Yunfeng Duan
Summary: The study shows that ACE2 is highly conserved in various mammals, with expression in certain human tissues consistent with clinical symptoms of COVID-19 patients. Cats and dogs exhibit exceptionally high ACE2 expression in external body parts, suggesting they may be vulnerable to viral infections.
