Article
Agriculture, Dairy & Animal Science
Xinhua Hou, Ligang Wang, Fuping Zhao, Xin Liu, Hongmei Gao, Lijun Shi, Hua Yan, Lixian Wang, Longchao Zhang
Summary: In this study, RNA-seq technology was used to characterize the transcriptome profiles of skeletal muscle between Beijing Black and Yorkshire pigs, revealing the role of differentially expressed mRNAs, lncRNAs, and circRNAs in skeletal muscle development and fatty acid metabolism relevant to muscle-related traits. The findings provide valuable candidate genes responsible for muscle phenotypic variation in pigs.
Article
Medicine, Research & Experimental
Dezhi Yue, Ruipeng Yang, Chengliang Xiong, Ruifeng Yang
Summary: Oligoasthenospermia (OAZ), the most common cause of male infertility, is still poorly understood. This study investigated the composition and role of exosomal circular RNAs (circRNAs) in OAZ. RNA sequencing of exosomes from 12 OAZ patients and 12 controls revealed differentially expressed circRNAs associated with OAZ. Functional enrichment analysis indicated their involvement in protein binding, intracellular organelles, and cellular metabolism. Pathway analysis revealed enrichment in pathways related to spermatogenesis, such as ubiquitin-mediated proteolysis, endocytosis, and RNA transport. Multiple circRNAs were predicted and validated as putative upstream targets, and a circRNA-microRNA-mRNA network was constructed to predict their functions. These findings lay a preliminary foundation for the potential diagnostic value of critical exosomal circRNAs in OAZ.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Yi Liu, Hejing Liu, Bo Sheng, Shuya Pan, Zhi-wei Wang, Xueqiong Zhu
Summary: This review describes the incidence and development of HPV-negative cervical cancer, pointing out the differences in diagnosis, age, stage, and prognosis between HPV-negative and HPV-positive cervical cancer. Furthermore, the significant role and functions of lncRNAs in HPV-negative cervical cancer are clarified.
Article
Biotechnology & Applied Microbiology
Xinran Yang, Xinhao Ma, Chugang Mei, Linsen Zan
Summary: This study provides insights into the differential expression patterns of different types of RNA in intramuscular preadipocyte differentiation. It identifies key genes and networks related to intramuscular adipogenesis, providing data support for studying the molecular mechanisms of IMF deposition and potential markers for beef cattle breeding.
Article
Agriculture, Dairy & Animal Science
Jingya Xing, Xingzhen Qi, Guiqin Liu, Xinyu Li, Xing Gao, Gerelchimeg Bou, Dongyi Bai, Yiping Zhao, Ming Du, Manglai Dugarjaviin, Xinzhuang Zhang
Summary: The Mongolian horse, a unique breed in China, has excellent endurance quality but is prone to muscle damage during exercise. This study investigates the mechanism of L-leucine promoting the proliferation of equine skeletal muscle satellite cells, aiming to improve equine performance and reduce muscle injuries.
Article
Virology
Yingjie Li, Cankun Wang, Anjun Ma, Abdul Qawee Rani, Mingjue Luo, Jenny Li, Xuefeng Liu, Qin Ma
Summary: In this study, single-cell transcriptome analysis was used to investigate the heterogeneity of viral gene and host cell differentiation in HPV-positive cervical cancer tissue. The results showed differential gene expression in HPV-positive cells compared to normal cells, indicating functional heterogeneity and altered epithelial structuring in cancer tissues.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Siew-Woh Choo, Yu Zhong, Edward Sendler, Anton -Scott Goustin, Juan Cai, Donghong Ju, Mary Ann Kosir, Roberta Giordo, Leonard Lipovich
Summary: This study investigates the impact of estrogen on transcription and translation in breast cancer cells. Through integrated analysis of RNA-Seq and Ribo-seq, it reveals distinct gene-specific responses to estrogen at the transcriptional and translational levels. The findings also indicate that most lncRNAs are not associated with ribosomes and are not affected by estrogen, while pseudogenes exhibit transcriptional and translational responses to estrogen.
Review
Oncology
Fan Zhang, Liying Li, Zhimin Fan
Summary: circRNAs play important roles in breast cancer, regulating cancer cell proliferation, metastasis, and apoptosis resistance through various mechanisms. Many circRNAs are also associated with prognosis and treatment sensitivity in breast cancer patients.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2022)
Article
Biochemical Research Methods
Enrico Gaffo, Alessia Buratin, Anna Dal Molin, Stefania Bortoluzzi
Summary: Circular RNAs (circRNAs) are important functional RNAs involved in biological processes and disease mechanisms. Current computational methods for circRNA identification have limitations, and we developed CirComPara2, which combines multiple detection methods to improve the accuracy and recall rates. Our method outperformed state-of-the-art tools and is a reliable approach for comprehensive transcriptome characterization.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Junliang Li, Jie Cui, Cuihong Dai, Tianjiao Liu, Dayou Cheng, Chengfei Luo
Summary: This study conducted a full transcriptomic analysis of sugar beet under salt stress, revealing a ceRNA network and its regulatory roles under salt stress. The findings suggest potential functions of lncRNAs/circRNAs in salt tolerance mechanisms of sugar beet.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Jianting Wen, Jian Liu, Xin Wang, Jie Wang
Summary: The study investigated the changes in circRNAs related to immunity and inflammation in rheumatoid arthritis (RA) patients, identifying hsa_circ_0003353 as a potential biomarker with significant roles in promoting immunity, inflammation, synovial invasion, and joint destruction. The findings suggest that hsa_circ_0003353 may have clinical significance in RA diagnosis and treatment.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Virology
Yajie Hu, Yanyan Xu, Xiaoli Deng, Ruibing Wang, Rufang Li, Ling You, Jie Song, Yunhui Zhang
Summary: In this study, RNA sequencing was used to characterize the expression of circRNAs during EV-A71 infection, identifying key circRNAs associated with the progression of viral infection.
Article
Cell Biology
Taotao Li, Ruirui Luo, Xia Wang, Huihui Wang, Xingxu Zhao, Yunxia Guo, Haitao Jiang, Youji Ma
Summary: The study revealed the temporal expression patterns of circRNAs in testes of Tibetan sheep at different maturation stages, constructed a core circRNA-miRNA-mRNA interaction network related to testicular function, and validated the interactions between circRNAs, miRNAs, and mRNAs. These findings provide new insights into the diverse functions of circRNAs in cell development and maturation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Qiongzi Qiu, Qing Zhou, Aoran Luo, Xufan Li, Kezhen Li, Wenfeng Li, Mengqian Yu, Md Amanullah, Bingjian Lu, Weiguo Lu, Pengyuan Liu, Yan Lu
Summary: Race may play a role in influencing vulnerability to HPV variants and cervical cancer prevalence. Integrated analysis of virus and host transcriptomes reveals differences in tumor subtypes and immune infiltration between populations, shedding light on racial disparities in HPV-associated cervical cancers.
Article
Genetics & Heredity
Tianjiu Zhang, Xiaolin Hu, Song Yu, Chunyan Wei
Summary: In this study, the expression patterns of lncRNAs, miRNAs, and mRNAs in a rabbit model of Perthes disease were analyzed using transcriptome sequencing. The results indicated that multiple genetic pathways are involved in the development of Perthes disease. Network analysis revealed downregulation of genes associated with angiogenesis and platelet activation, consistent with the characteristics of Perthes disease. Furthermore, a ceRNA network was constructed, including differentially expressed lncRNAs, miRNAs, and mRNAs.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Yang Qiu, Yan-Peng Xu, Miao Wang, Meng Miao, Hui Zhou, Jiuyue Xu, Jing Kong, Da Zheng, Rui-Ting Li, Rong-Rong Zhang, Yan Guo, Xiao-Feng Li, Jie Cui, Cheng-Feng Qin, Xi Zhou
Correction
Biology
Xiang Li, Yuhe Song, Gary Wong, Jie Cui
SCIENCE CHINA-LIFE SCIENCES
(2020)
Article
Virology
Yonghong Zhou, Le Van Tan, Kaiwei Luo, Qiaohong Liao, Lili Wang, Qi Qiu, Gang Zou, Ping Liu, Nguyen To Anh, Nguyen Thi Thu Hong, Min He, Xiaoman Wei, Shuanbao Yu, Tommy Tsan-Yuk Lam, Jie Cui, H. Rogier van Doorn, Hongjie Yu
Summary: A molecular characterization of enteroviruses (EVs) causing hand, foot and mouth disease (HFMD) in China from 2013 to 2016 revealed that 89% of 2836 enrolled HFMD patients were EV positive, with CVA16, CVA6, and EV-A71 being the most frequently detected EVs. Sequence analysis showed amino acid variations in the VP1 region, with a known substitution (D31N) detected in 87.5% of EV-A71 samples, potentially enhancing neurovirulence. Further investigation is needed to understand the emergence and virulence of these mutations.
Editorial Material
Multidisciplinary Sciences
Guangping Huang, Xiaoge Ping, Weihua Xu, Yibo Hu, Jiang Chang, Ronald R. Swaisgood, Jiang Zhou, Xiangjiang Zhan, Zejun Zhang, Yonggang Nie, Jie Cui, Michael Bruford, Zhihe Zhang, Baoguo Li, Li Zhang, Zhi Lv, Fuwen Wei
NATIONAL SCIENCE REVIEW
(2021)
Article
Virology
Yicong Chen, Yu-Yi Zhang, Xiaoman Wei, Jie Cui
Summary: This study revealed 412 FVs from 6 lineages in amphibians, with salamander FVs showing a coevolutionary pattern with hosts dating back to the Paleozoic era. Frog FVs were more likely acquired from cross-species transmission in the Cenozoic era. Three distinct FV lineages integrated into a salamander's genome, and an endogenous FV lineage expressing complete major genes was discovered in caecilians, suggesting potential exogenous FV existence outside of mammals. These findings significantly enhance understanding of the macroevolution of complex retroviruses.
JOURNAL OF VIROLOGY
(2021)
Review
Virology
Yuhe Song, Xiang Li, Xiaoman Wei, Jie Cui
Summary: HERVs, formed through ancient integration of exogenous retroviruses into the human genome, are considered viral fossils. Although most HERVs have lost coding capability, they still function in regulating host gene expression. Activation of HERVs plays important roles in response to viral infections and diseases, and they have the potential to be used as biomedical markers for early disease diagnosis.
Article
Immunology
Yuan Fang, Zezhong Liu, Yang Qiu, Jing Kong, Yuhong Fu, Yujie Liu, Chong Wang, Jia Quan, Qian Wang, Wei Xu, Lei Yin, Jie Cui, Yi Xu, Stephen Curry, Shibo Jiang, Lu Lu, Xi Zhou
Summary: Targeting peptides against the viral suppressor of RNAi (VSR) in Enterovirus A71 can reduce viral replication in infected cells, protect mice from lethal EV-A71 challenge, and generate detectable vsiRNAs.
Article
Biology
Yu-Yi Zhang, Yicong Chen, Xiaoman Wei, Jie Cui
Summary: This study utilized a meta-transcriptomic approach to characterize the viromes of marine invertebrates, identifying 315 newly discovered RNA viruses in nine viral families or orders. The research revealed a hidden diversity of marine invertebrate RNA viruses, including evidence for possible host sharing and switch events during virus evolution.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Virology
Yicong Chen, Xiaojing Wang, Meng-En Liao, Yuhe Song, Yu-Yi Zhang, Jie Cui
Summary: By analyzing over 30,000 copies of ERV lineages with gamma-type Env (GTE) in anamniotes, several important evolutionary features were identified. First, GTE was found to be widely distributed among different amphibians and fish. Second, nine types of GTE were discovered and defined, revealing their great genetic diversity. Third, the incongruence between the Env and Pol phylogenies suggested that frequent recombination shaped the early evolution of anamniote retroviruses. Fourth, an ancient horizontal gene transfer event was discovered from anamniotes to ERVs with GTE. These findings reveal a complex evolution pattern for retroviral Env in anamniotes.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Yian Li, Guojie Zhang, Jie Cui
Summary: This study provides comprehensive data on the deep origination and distribution of modern HERVs in pan-primates based on in silico genomic mining of 49 primate genomes. The results show that most contemporary HERVs originated from nonhuman sources and are widely spread in different supergroups. Vertical transmission of HERVs within Catarrhini and the tracing of a HERV in 17 species indicate their ancient nature. Additionally, the study reveals that certain HERVs are likely involved in genomic rearrangement and some may function as noncoding RNAs (ncRNAs) in humans.
Article
Medicine, General & Internal
Jinghan Wang, Meng Ren, Jundan Yu, Mingtai Hu, Xiaojing Wang, Wencong Ma, Xiaoqing Jiang, Jie Cui
Summary: This study investigates the role of human endogenous retroviruses in gallbladder cancer, aiming to find new diagnostic and therapeutic approaches.
Article
Virology
Xiaojing Wang, Yicong Chen, Jie Cui
Summary: A novel endogenous foamy virus (CFEFV) was discovered in the genomes of sharks and rays, filling a major gap in the taxonomic investigation of Spumaretrovirinae. These findings reveal the aquatic origin of foamy viruses found in terrestrial vertebrates.
JOURNAL OF VIROLOGY
(2023)
Article
Microbiology
Xiaojing Wang, Jie Cui
Summary: A novel endogenous foamy virus, named TraEFV, was discovered in the genomes of two even-toed ungulate chevrotains. Phylogenetic analysis showed that TraEFV is more closely related to exogenous foamy viruses from feline rather than those from cow and horse. Additionally, TraEFV could be divided into two lineages, indicating multiple ancient invasions of the host species. This study enriches the host taxonomy of spumaretroviruses.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Xiang Li, Hongliang Yan, Gary Wong, Wanli Ouyang, Jie Cui
Summary: This study developed a computational methodology to investigate indel mutations related to viral fitness in SARS-CoV-2 genomes. They identified 65 indel types associated with Pango lineages and proposed the concept of featured indels. The results showed that indels, like substitution mutations, play a key role in SARS-CoV-2 evolution and are important for assessing viral fitness.
MICROBIOLOGY SPECTRUM
(2023)
Article
Immunology
Guimei He, Le Ming, Xiang Li, Yuhe Song, Ling Tang, Min Ma, Jie Cui, Tianhou Wang
Summary: In late 2020, 32 highly pathogenic avian influenza A(H5N8) viruses were detected in migratory ducks in Shanghai, China. Phylogenetic analysis revealed 2 sublineages of clade 2.3.4.4b, each forming separate clusters with isolates from East Asia and Europe.
EMERGING INFECTIOUS DISEASES
(2021)
