Article
Clinical Neurology
Emrin Horgusluoglu, Ryan Neff, Won-Min Song, Minghui Wang, Qian Wang, Matthias Arnold, Jan Krumsiek, Beatriz Galindo-Prieto, Chen Ming, Kwangsik Nho, Gabi Kastenmueller, Xianlin Han, Rebecca Baillie, Qi Zeng, Shea Andrews, Haoxiang Cheng, Ke Hao, Alison Goate, David A. Bennett, Andrew J. Saykin, Rima Kaddurah-Daouk, Bin Zhang
Summary: This study aims to identify AD-specific metabolomic changes and their potential upstream genetic and transcriptional regulators through an integrative systems biology framework. The findings suggest that short-chain acylcarnitines/amino acids and medium/long-chain acylcarnitines are most associated with AD clinical outcomes. Integration of gene expression data reveals ABCA1 and CPT1A are involved in regulating acylcarnitines and amino acids in AD.
ALZHEIMERS & DEMENTIA
(2022)
Article
Oncology
Xiaoli Luo, Yi Hu, Junwei Shen, Xinwen Liu, Tao Wang, Li Li, Jue Li
Summary: This study used RNA-seq and MeDIP-seq technologies to observe gene expression and DNA methylation changes in an AMI mouse model. We found a large number of differential methylation positions and differentially expressed genes at different stages of AMI. Especially, the 6-hour stage of AMI showed significant changes in DEGs and enriched functional pathways in KEGG, suggesting it may be the most critical stage of AMI. We also identified genes that showed a negative correlation between mRNA expression and DNA methylation, and confirmed their function through experimental validation.
CLINICAL EPIGENETICS
(2022)
Review
Biochemistry & Molecular Biology
Nan Wang, Ting Ma, Bin Yu
Summary: Drug resistance is a major cause of cancer recurrence and poor prognosis. Epigenetic regulation, which involves heritable changes in gene expression, is independent of changes in nucleotide sequences. Three common mechanisms of epigenetic regulation, DNA methylation, histone modification, and non-coding RNA regulation, have been extensively studied. Aberrant epigenetic regulation has been shown to contribute to tumor resistance, making targeting epigenetic regulators an effective strategy to reverse drug resistance. This review summarizes the roles of epigenetic regulation in tumor resistance and discusses the functions and regulatory mechanisms of histone demethylases, as well as therapeutic strategies for overcoming drug resistance.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Yipeng Song, Rongna Ma
Summary: PBX4 is differentially expressed in 17 types of human cancer and significantly correlated with tumor-related characteristics and prognosis. PBX4 is also associated with mutation status, DNA methylation, immune infiltration, drug sensitivity, and immune checkpoint blockade therapy. From the single-cell perspective, PBX4 is involved in different functional states of multiple cancers.
Article
Environmental Sciences
Meng -Die Cheng, Chang -Lei Li, Xiang -Yu Pei, Yi-Fei Zhang, Dong-Dong Jia, Ying-Bing Zuo, Shang -Lang Cai, Pei-Feng Li, Hui Xin, Yin-Feng Zhang
Summary: Cardiac hypertrophy can lead to heart dysfunction and failure, and bisphenols (BPs) such as BPA and its alternatives BPAF, BPF, and BPS, which are widely used in various products, may pose high cardiovascular risks for humans. This study aimed to investigate the effects of BPs on heart function and cardiomyocyte hypertrophy, as well as their role in DNA methylation and transcription dysregulation. The results showed that BPAF, BPF, and BPS exposure, similar to BPA, deteriorated heart function in mice and induced cardiomyocyte hypertrophy. These BPs also exhibited similar effects on transcription and methylation as BPA. Moreover, the study validated the upregulation of four candidate genes related to cardiomyocyte hypertrophy, Psmc1, Piptnm2, Maz, and Dusp18, which showed DNA hypomethylation. The findings suggest the potential detrimental risks of BPA analogues on heart function through cardiomyocyte hypertrophy and DNA methylation.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Genetics & Heredity
Yifan Chen, Shanwu Ma, Chutong Lin, Zhipeng Zhu, Jie Bai, Zhongnan Yin, Yan Sun, Fengbiao Mao, Lixiang Xue, Shaohua Ma
Summary: This study identified seven novel methylation markers from cfDNA methylation data that are associated with lung adenocarcinoma risk. These markers can be used to classify different prognostic subgroups and are significantly associated with overall survival in lung adenocarcinoma patients. The reliability of these markers was further validated.
FRONTIERS IN GENETICS
(2023)
Article
Oncology
Siddesh Southekal, Sushil Kumar Shakyawar, Prachi Bajpai, Amr Elkholy, Upender Manne, Nitish Kumar Mishra, Chittibabu Guda
Summary: Osteosarcoma is a common bone malignancy in children and adolescents. This study aimed to understand the molecular subtypes of osteosarcoma and identify diagnostic and prognostic biomarkers for effective treatments. DNA methylation, mRNA and miRNA gene expression in patients with osteosarcoma were analyzed, revealing highly mutated mucin family genes and enrichment of molecular pathways such as Wnt signaling and PI3K-Akt signaling. Survival analyses showed that certain genes and non-coding RNAs were associated with the survival of osteosarcoma patients. Molecular subtyping identified two distinct molecular subtypes with different gene expression profiles, providing a basis for better prognostic treatment strategies.
Article
Cell Biology
Raha Weigert, Sara Hetzel, Nina Bailly, Chuck Haggerty, Ibrahim A. Ilik, Philip Yuk Kwong Yung, Carmen Navarro, Adriano Bolondi, Abhishek Sampath Kumar, Chiara Anania, Bjoern Braendl, David Meierhofer, Dario G. Lupianez, Franz-Josef Mueller, Tugce Aktas, Simon J. Elsaesser, Helene Kretzmer, Zachary D. Smith, Alexander Meissner
Summary: Weigert et al. demonstrate that the balance between DNA methyltransferase and Polycomb activity is crucial for maintaining intermediate methylation levels in trophoblast stem cells. The extra-embryonic epigenome exhibits globally intermediate DNA methylation levels, which are maintained through dynamic recruitment of de novo methyltransferase and antagonism by Polycomb. Despite the disordered molecular appearance, a controlled equilibrium between repressors allows for stable maintenance of these methylation levels.
NATURE CELL BIOLOGY
(2023)
Article
Oncology
Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song
Summary: This study characterized the expression profiles of RNA m6A regulators in 13 cancer types using TCGA data, revealing potential regulatory mechanisms of miRNA and DNA methylation in governing m6A regulators' expression. Informative regulatory pairs with potential prognostic values were identified, providing new insights into the molecular mechanisms of m6A modification in human cancers.
FRONTIERS IN ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Maria Teruel, Guillermo Barturen, Manuel Martinez-Bueno, Olivia Castellini-Perez, Miguel Barroso-Gil, Elena Povedano, Martin Kerick, Francesc Catala-Moll, Zuzanna Makowska, Anne Buttgereit, Jacques-Olivier Pers, Concepcion Maranon, Esteban Ballestar, Javier Martin, Elena Carnero-Montoro, Marta E. Alarcon-Riquelme
Summary: The primary Sjogren's syndrome is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The complex etiology of SS involves environmental triggers and genetic factors. Through an integrated multi-omics study, researchers identified a vast coordinated hypomethylation and overexpression in IFN-related genes known as the IFN signature in SS, as well as a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature. Additionally, a novel epigenetic signature characterized by increased DNA methylation levels in genes enriched in pathways such as collagen metabolism and extracellular matrix organization was reported.
SCIENTIFIC REPORTS
(2021)
Article
Reproductive Biology
Hossam El-Sheikh Ali, Pouya Dini, Kirsten Scoggin, Shavahn Loux, Carleigh Fedorka, Yatta Boakari, Jamie Norris, Alejandro Esteller-Vico, Theodore Kalbfleisch, Barry Ball
Summary: This study characterized the transcriptome changes and pathological mechanisms during equine placentitis, involving inflammation and placental insufficiency, providing important insights for the development of future therapeutic methods.
BIOLOGY OF REPRODUCTION
(2021)
Article
Cell Biology
Jingyun Zhang, Xiaoyi Sun, Xueqing Jia, Binggui Sun, Shijun Xu, Weiping Zhang, Zuyun Liu
Summary: This study explores the relationship between aging and Alzheimer's disease (AD) and identifies a gene module, including PBXIP1, that is significantly associated with various neuropathological traits of AD. The study also suggests the potential of using multi-omics data to investigate complex disease mechanisms.
Article
Medicine, General & Internal
Zhiquan Qiu, Jun Ji, Yu Xu, Yan Zhu, Chunfang Gao, Guoqiang Wang, Chengcheng Li, Yuzi Zhang, Jing Zhao, Chenyang Wang, Xiaofang Wen, Zhou Zhang, Bingsi Li, Zhihong Zhang, Shangli Cai, Bin Li, Xiaoqing Jiang
Summary: The study found that DNA methylation is a powerful tool for classifying biliary tract cancer, providing insights into genomic aberrations, survival outcomes, and tumor immune microenvironment.
Article
Microbiology
Sheng Tan, Jie Zhang, Yonglin Peng, Wenfei Du, Jingxuan Yan, Qin Fang
Summary: In this study, transcriptome and DNA methylome analyses were performed to reveal the molecular mechanisms underlying GCRV early infection. The results showed that genes related to defense response and immune response were activated in host cells during early infection. Additionally, alternative polyadenylation may potentially contribute to GCRV early infection.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Wenting Zhang, Lin Lyu, Zhihiong Xu, Jinjing Ni, Danni Wang, Jie Lu, Yu-Feng Yao
Summary: This study reveals the role of DNA methylation in the response of Salmonella enterica serovar Typhimurium (S. Typhimurium) to oxidative stress. The researchers found that there is no significant association between DNA methylation and transcription level in most genes, but there is a coincidence of level change between transcription and m6A GATC in certain regulatory regions. These findings provide new insights into the epigenetic regulatory mechanisms of gene expression in S. Typhimurium in the host microenvironment.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Zhongbo Cao, Wei Du, Gaoyang Li, Huansheng Cao
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemical Research Methods
Wei Du, Gaoyang Li, Nicholas Ho, Landon Jenkins, Drew Hockaday, Jiankang Tan, Huansheng Cao
Summary: CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms in eutrophic waters, summarizing 19 pathways involved in the utilization of nutrients, stress resistance, and more. It provides valuable assistance in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it bridges the gap between genome and ecology.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Ying Li, Qi Zhang, Zhaoqian Liu, Cankun Wang, Siyu Han, Qin Ma, Wei Du
Summary: This paper introduces a novel deep fusion learning framework, GCFM, based on a convolutional neural network and a deep forest algorithm, for accurate clustering of ncRNAs. By classifying alignments of ncRNA sequences, GCFM shows a 6% improvement in F-value compared to existing methods, and outperforms RNAclust, Ensembleclust, and CNNclust in ncRNA family clustering with 20% increased accuracy. Additionally, GCFM is utilized in constructing phylogenetic trees for ncRNAs and predicting RNA interactions, with an accuracy rate of 90.63%.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Ying Li, Hang Sun, Shiyao Feng, Qi Zhang, Siyu Han, Wei Du
Summary: This study presents a novel multichannel capsule network framework, Capsule-LPI, to integrate multimodal features for LPI prediction. Through comprehensive experimental comparisons and evaluations, it is demonstrated that both multimodal features and the architecture of the multichannel capsule network can significantly improve the performance of LPI prediction. The experimental results show that Capsule-LPI outperforms the existing state-of-the-art tools.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Hardware & Architecture
Wei Du, Yu Sun, Hui-Min Bao, Liang Chen, Ying Li, Yan-Chun Liang
Summary: This study introduces a novel deep learning model for accurate identification of blood-secretory proteins using amino acid sequence information. The model combines a binary classification network and a ranking network, applying descriptive loss and compactness loss to improve prediction accuracy. Transfer learning is utilized to train a highly accurate generalized model with limited samples.
JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
(2021)
Article
Genetics & Heredity
Ying Li, Jianing Zhao, Zhaoqian Liu, Cankun Wang, Lizheng Wei, Siyu Han, Wei Du
Summary: In this paper, we propose a novel computational model MEL-MP for predicting moonlighting proteins (MPs) by utilizing specific classifiers for different feature types, resulting in superior prediction performance. Through experiments, it is shown that MEL-MP outperforms the existing machine learning model MPFit, demonstrating its effectiveness in predicting MPs.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
James D. Hocker, Olivier B. Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang E. Li, Yanxiao Zhang, Elie N. Farah, Allen Wang, Andrew D. McCulloch, Kyle J. Gaulton, Bing Ren, Neil C. Chi, Sebastian Preissl
Summary: This study identified cCREs in the human heart and found their associations with cardiac cell types and heart failure. It also discovered that genetic variants associated with cardiovascular diseases are enriched within these cCREs, with some potentially linked to atrial fibrillation.
Article
Biochemistry & Molecular Biology
Wei Du, Xuan Zhao, Yu Sun, Lei Zheng, Ying Li, Yu Zhang
Summary: This study introduces a novel deep learning model, SecProCT, which predicts secretory proteins using only amino acid sequences with higher accuracy compared to traditional machine learning and other deep learning approaches. The model's innovation lies in its reliance solely on amino acid sequences, overcoming the dependency on annotated protein features in existing methods, and accurately predicting secretory proteins and cancer protein biomarkers in blood and saliva.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, Olivier B. Poirion, Yunjiang Qiu, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren
Summary: This study utilized single-cell chromatin accessibility assays to analyze gene regulatory elements in diverse cell types and tissues in the human body, integrating data from adult and fetal tissue to reveal the specificity of cCREs in 222 distinct cell types. The findings provide a foundation for understanding gene regulatory programs across tissues, life stages, and organ systems in humans.
Article
Mathematical & Computational Biology
Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui
Summary: The study highlights the importance of human body fluid proteome as a source for disease biomarker discovery and the lack of a centralized database for published body fluid proteins. The newly developed Human Body Fluid Proteome (HBFP) database provides a valuable resource for research in clinical proteomics and biomarker discovery.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biochemical Research Methods
Ying Li, Lizheng Wei, Cankun Wang, Jianing Zhao, Siyu Han, Yu Zhang, Wei Du
Summary: LncRNA plays important roles in biological processes, and extracting LPIs from biomedical literature is challenging. LPInsider is the first webserver for extracting LPIs from literature, utilizing multiple text features and logistic regression. LPInsider helps researchers enhance their comprehension of lncRNAs through text mining and saves time.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Information Systems
Ying Li, Hang Sun, Wensi Fang, Qin Ma, Siyu Han, Rui Wang-Sattler, Wei Du, Qiong Yu
Summary: For classification tasks in the bioinformatics field with limited negative samples, the researchers propose a novel deep reinforcement learning-based model called SURE, which can screen reliable negative samples from unlabeled samples. SURE consists of a sample selector and a sample inspector, which are trained together to optimize the screening strategies. Experimental results show that SURE has a robust negative sample screening capability and outperforms other methods in the task of NPI prediction. Additionally, 5 NPI datasets refined by SURE are provided through a web server.
INFORMATION SCIENCES
(2023)
Article
Computer Science, Information Systems
Ying Li, Wensi Fang, Hang Sun, Xiangyu Liu, Wei Du, Yijun Liu, Qianqian Li
Summary: In this paper, a novel deep reinforcement learning method named PecidRL is proposed for the correction and identification of petition expectation. A dataset containing 237,042 petitions from the largest official petition platform in China is collected. The results show that the proposed method significantly improves the performance of petition expectation identification models.
INFORMATION PROCESSING & MANAGEMENT
(2023)
Article
Multidisciplinary Sciences
Ramya Raviram, Anugraha Raman, Sebastian Preissl, Jiangfang Ning, Shaoping Wu, Tomoyuki Koga, Kai Zhang, Cameron W. Brennan, Chenxu Zhu, Jens Luebeck, Kinsey Van Deynze, Jee Yun Han, Xiaomeng Hou, Zhen Ye, Anna K. Mischel, Yang Eric Li, Rongxin Fang, Tomas Baback, Joshua Mugford, Claudia Z. Han, Christopher K. Glass, Cathy L. Barr, Paul S. Mischel, Vineet Bafna, Laure Escoubet, Bing Ren, Clark C. Chen
Summary: In 2021, glioblastoma, the most common form of adult brain cancer, was reclassified by the World Health Organization into two subtypes based on genetic characteristics. The study analyzed the chromatin accessibility and transcription profiles of clinical samples from both types of tumors, revealing intratumoral heterogeneity and shared chromatin structure among tumor cells. Silencing specific transcription factors suppressed tumor growth, suggesting a potential therapeutic target for addressing the challenges associated with intratumoral heterogeneity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Gaoyang Li, Li Liu, Wei Du, Huansheng Cao
Summary: The authors develop a method called Decrem, which integrates locally coupled reactions and global transcriptional regulation of metabolism, to reconstruct genome-scale metabolic networks. Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology.
NATURE COMMUNICATIONS
(2023)