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
Oncology
Caroline Reuter, Matthew Preece, Rawinder Banwait, Sabrina Boer, Jack Cuzick, Attila Lorincz, Belinda Nedjai
Summary: Methylation biomarkers show promise for diagnosis and disease prevention, with S5 classifier specifically designed for early detection of CIN to prevent cervical cancer. S5, based on pyrosequencing, performs well in different sample types. Testing on FFPE biopsies with different conversion kits, EZ DNA Methylation kit showed incomplete conversion in FFPE samples, while other kits had high conversion rates similar to cells.
Article
Biotechnology & Applied Microbiology
Dai Shimizu, Kenzui Taniue, Yusuke Matsui, Hiroshi Haeno, Hiromitsu Araki, Fumihito Miura, Mitsuko Fukunaga, Kenji Shiraishi, Yuji Miyamoto, Seiichi Tsukamoto, Aya Komine, Yuta Kobayashi, Akihiro Kitagawa, Yukihiro Yoshikawa, Kuniaki Sato, Tomoko Saito, Shuhei Ito, Takaaki Masuda, Atsushi Niida, Makoto Suzuki, Hideo Baba, Takashi Ito, Nobuyoshi Akimitsu, Yasuhiro Kodera, Koshi Mimori
Summary: The study established the CACO methylation panel for accurate cancer diagnosis and origin classification, showing high diagnostic potential and specificity in identifying cancer cell type based on methylation profile from liquid or tissue biopsy. This panel can be a powerful tool for cancer classification and diagnosis.
CANCER GENE THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Lian Narunsky-Haziza, Gregory D. Sepich-Poore, Ilana Livyatan, Omer Asraf, Cameron Martino, Deborah Nejman, Nancy Gavert, Jason E. Stajich, Guy Amit, Antonio Gonzalez, Stephen Wandro, Gili Perry, Ruthie Ariel, Arnon Meltser, Justin P. Shaffer, Qiyun Zhu, Nora Balint-Lahat, Iris Barshack, Maya Dadiani, Einav N. Gal-Yam, Sandip Pravin Patel, Amir Bashan, Austin D. Swafford, Yitzhak Pilpel, Rob Knight, Ravid Straussman
Summary: This study comprehensively characterizes the cancer mycobiome in cancer patients and finds low abundances of fungi in various human cancers. The composition of fungal communities differs among cancer types and they are frequently associated with cancer cells and macrophages spatially. Comparisons with bacterial and immune communities reveal co-occurring bi-domain ecologies and distinct immune responses. The tissue and plasma mycobiomes show prognostic and diagnostic capabilities even in early stage cancers, and synergistic predictive performance with bacterial communities.
Article
Endocrinology & Metabolism
Zhuoyuan Chen, Huiqin Yang, Yunfeng Ren, Ze Yang, Jiazheng Huang, Cheng Li, Ying Xiong, Bin Yu
Summary: ADIPOR1 and ADIPOR2 genes encode the AdipoR1 and AdipoR2 proteins, which are receptors for adiponectin secreted by adipose tissue. These proteins play important roles in various diseases, including cancers, and exploring their roles in cancer is urgently needed.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Microbiology
Yuhan Zhou, Hongfen Zeng, Kai Liu, Hui Pan, Baohui Wang, Minghua Zhu, Jiawei Wang, Haoyi Wang, Hongwei Chen, Dan Shen, Yue Wang, Zhaonan Yu
Summary: This study investigates the relationship between the lung microbiome and lung cancer in Chinese patients. It finds differences in the composition of oral and lung microbiota, and constructs a microbiota model that can distinguish between cancerous and non-cancerous tissues. These findings enhance understanding of the pathogenesis of lung cancer and identify potential therapeutic targets.
Article
Computer Science, Information Systems
Ankita Pandey, Arun Kumar
Summary: This proposed breast cancer classification work aims to develop an automated and reliable system for early detection of breast cancer. Three transfer learning-based classifiers, Binary, Benign, and Malignant, are constructed to classify breast cancer into different categories. These classifiers are trained individually and then integrated into a combined system, resulting in improved accuracy in classifying cancer. The performance of these classifiers and the combined system is evaluated using various metrics and compared with state-of-the-art methods.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Multidisciplinary Sciences
Divya Gopinath, Rohit Kunnath Menon, Chong Chun Wie, Moinak Banerjee, Swagatika Panda, Deviprasad Mandal, Paresh Kumar Behera, Susanta Roychoudhury, Supriya Kheur, Michael George Botelho, Newell W. Johnson
Summary: Microbial dysbiosis is implicated in the pathogenesis of oral cancer, with significant differences in microbial composition and metabolic profiles between tumor surfaces and deep tissues. Saliva from oral cancer patients also exhibited distinct microbial communities compared to tumor tissue, indicating potential implications for oncogenic properties.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Paula Stancl, Rosa Karlic
Summary: Despite improvements in cancer diagnostics, there are still cancers of unknown primary (CUP) where the tissue-of-origin cannot be determined. Machine learning methods have been introduced to predict the primary site of cancer patients based on genomic data. This review assesses the reproducibility, interpretability, and robustness of recent studies using machine learning for prediction, and identifies potential issues with the datasets used.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Multidisciplinary Sciences
Ziyao Wang, Kang Lin, Hai Xiao
Summary: This study revealed that FAT1 is highly expressed in various tumors and is significantly correlated with prognosis. The association of FAT1 with tumors was analyzed from multiple perspectives, providing a comprehensive understanding of its oncogenic role in tumors.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Zhiyong Ding, Nan Wang, Ning Ji, Zhe-Sheng Chen
Summary: The complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies have hindered the development of proteomics. However, novel protein technologies are urgently needed for biomarker discovery in cancer liquid biopsies. Traditional and innovative proteomic technologies are being rapidly developed and have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution.
Article
Materials Science, Multidisciplinary
Mohamed S. Abdo, Ashraf Maher, Ahmed Fouly, Saud M. Almotairy, Muhammad A. Shar, Hany S. Abdo
Summary: This study investigates the performance of different shapes of antennas in microwave ablation (MWA) for the treatment of hepatocellular carcinoma (HC). A numerical model was established to examine specific absorption rate (SAR), temperature distribution, and coefficient of reflection. The findings of the study can aid in determining the optimal parameters for the highest effectiveness of MWA in the treatment of early-stage HC with minimal invasiveness and collateral harm.
Article
Oncology
Mayur Divate, Aayush Tyagi, Derek J. Richard, Prathosh A. Prasad, Harsha Gowda, Shivashankar H. Nagaraj
Summary: This study developed a deep learning neural network model using pan-cancer gene expression data to accurately identify cancer tissue-of-origin specific gene expression signatures. Specific gene signatures that significantly contributed to cancer-type classification were identified using Shapley additive explanations. These findings have important implications for the diagnosis and treatment of cancer.
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)
Article
Oncology
Yize Li, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P. Calinawan, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieslik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J. Domagalski, Francois Aguet, David Fenyo, Myvizhi Esai Selvan, Steven M. Foltz, Alicia Francis, Tania Gonzalez-Robles, Zeynep H. Euromueuros, David Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J. Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A. Ketchum, Robert J. Klein, Jonathan T. Lei, Wen-Wei Liang, Yuxing Liao, Caleb M. Lindgren, Weiping Ma, Lei Ma, Michael J. Maccoss, Fernanda Martins Rodrigues, Wilson Mckerrow, Ngoc Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul Rudnick, Kelly V. Ruggles, Dmitry Rykunov, Sara R. Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V. Terekhanova, Ratna R. Thangudu, Mathangi Thiagarajan, Liang-Bo Wang, Joshua M. Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A. Wyczalkowski, Yi Xin, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I. Nesvizhskii, Pei Wang, Ana I. Robles, Bing Zhang, Samuel H. Payne, Clin Proteomic Tumor Anal Consortium
Summary: The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. We have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to facilitate pan-cancer investigations and aid scientific discovery. Challenges of integrating nucleotide sequencing and mass spectrometry proteomics data are also discussed.
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)
Article
Biochemical Research Methods
Yile Huang, Yulong Qiao, Yu Zhao, Yuying Li, Jie Yuan, Jiajian Zhou, Hao Sun, Huating Wang
Summary: In this study, the researchers utilized eCLIP data and various bioinformatics methods to investigate the roles of RNA-binding proteins (RBPs) in lncRNA nuclear retention. They identified splicing RBPs that bind to nuclear-enriched lincRNAs and found that they may drive lincRNA nuclear retention through distinct binding motifs. Network analyses also uncovered potential co-regulatory RBP clusters.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Xiaona Chen, Jie Yuan, Guang Xue, Silvia Campanario, Di Wang, Wen Wang, Xi Mou, Shiau Wei Liew, Mubarak Ishaq Umar, Joan Isern, Yu Zhao, Liangqiang He, Yuying Li, Christopher J. Mann, Xiaohua Yu, Lei Wang, Eusebio Perdiguero, Wei Chen, Yuanchao Xue, Yoshikuni Nagamine, Chun Kit Kwok, Hao Sun, Pura Munoz-Canoves, Huating Wang
Summary: DHX36 helicase is essential for muscle regeneration by promoting mRNA translation through binding and unwinding rG4 structures during SC activation, thus acting as a crucial post-transcriptional regulator of SC function.
NATURE COMMUNICATIONS
(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
Cell Biology
Xiaona Chen, Guang Xue, Jieyu Zhao, Yuwei Zhang, Suyang Zhang, Wen Wang, Yang Li, Jie Yuan, Liangqiang He, Chun Yin Chan, Yan Liu, Wei Chen, Yu Zhao, Ping Hu, Hao Sun, Chun Kit Kwok, Huating Wang
Summary: This study identifies a lncRNA called Lockd, which is induced in activated muscle stem cells (SCs) upon acute muscle injury. Lockd interacts with RNA helicase DHX36 and stabilizes its interaction with EIF3B proteins, promoting the translation of Anp32e mRNA and ultimately facilitating myoblast proliferation and acute-injury-induced muscle regeneration.
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
Multidisciplinary Sciences
Yu Zhao, Yingzhe Ding, Liangqiang He, Qin Zhou, Xiaona Chen, Yuying Li, Maria Vittoria Alfonsi, Zhenguo Wu, Hao Sun, Huating Wang
Summary: This study comprehensively maps the reorganization of the three-dimensional genome in skeletal muscle stem cells, revealing its importance in cell activation and aging. It also identifies key factors and elements involved in chromatin organization and gene expression.
Article
Multidisciplinary Sciences
Suyang Zhang, Feng Yang, Yile Huang, Liangqiang He, Yuying Li, Yi Ching Esther Wan, Yingzhe Ding, Kui Ming Chan, Ting Xie, Hao Sun, Huating Wang
Summary: This study reveals the role of ATF3 in protecting skeletal muscle stem cells from precocious activation, and demonstrates that ATF3 activates the transcription of Histone 2B genes to achieve this function.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Suyang Zhang, Feng Yang, Yile Huang, Liangqiang He, Yuying Li, Yi Ching Esther Wan, Yingzhe Ding, Kui Ming Chan, Ting Xie, Hao Sun, Huating Wang
NATURE COMMUNICATIONS
(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
Neurosciences
Zijing Zhou, Xiaojie Yu, Biaobin Jiang, Wanying Feng, Ye Tian, Zhiyong Liu, Jiguang Wang, Pingbo Huang
Summary: New splicing isoforms of TMC1, LHFPL5, and TMIE in auditory hair cells have been identified, showing cochlear- and age-specific alternative splicing patterns. These findings contribute to the understanding of the composition and function of the MT complex.
Article
Biology
Yuqing Wang, Tin Hang Chong, Ilona Christy Unarta, Xinzhou Xu, Gianmarco D. Suarez, Jiguang Wang, John T. Lis, Xuhui Huang, Peter Pak-Hang Cheung
Summary: Transcription errors can significantly impact metabolic processes in organisms, with specific Transcription Error-Enriched genomic Loci (TEELs) hypothesized to be linked to cancer, aging, and diseases like Down syndrome and Alzheimer's. However, methodological barriers hinder progress in accurately identifying transcription errors.
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.
