Article
Immunology
Wei Xia, Honglin Chen, Yiwei Feng, Nan Shi, Zongjian Huang, Qingyuan Feng, Xu Jiang, Guangyao He, Mao Xie, Yongjin Lai, Zhi Wang, Xiang Yi, Anzhou Tang
Summary: The study demonstrates that the tree shrew is a suitable animal model for evaluating the mechanisms of EBV infection and for developing vaccines and therapeutic drugs against EBV. This is due to its close phylogenetic relationship with humans, making it a valuable tool for studying viral infections and human diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Henoke K. Shiferaw, Celine S. Hong, David N. Cooper, Jennifer J. Johnston, Leslie G. NISC, Leslie G. Biesecker
Summary: Polyadenylation is a crucial process for mRNA stabilization and export, with hexamers playing a key role. However, only a few disorders have been associated with hexamer variants, possibly due to lack of defined hexamers in molecular analysis. To address this, the study aimed to define functionally important hexamers genome-wide and identified predominant polyA sites and putative predominant hexamers. Variants in these predominant hexamers showed potential pathogenic impact and could be used for interrogating exome and genome data in human diseases.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Miguel Barquin, Ian U. Kouzel, Beat Ehrmann, Michael Basler, Andreas J. Gruber
Summary: This study presents a single cell-based Terminal Exon Annotation database (scTEA-db), which provides yet unannotated terminal exons and associated transcript isoforms for studying their biological role in cell identity and function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Junliang Wang, Wei Chen, Wenjun Yue, Wenhong Hou, Feng Rao, Hanbing Zhong, Yuanming Qi, Ni Hong, Ting Ni, Wenfei Jin
Summary: This study developed a single-cell polyadenylation sequencing method to investigate the landscape of alternative polyadenylation (APA) at the single-cell level. The results showed that genes with multiple polyA sites in bulk data tend to use only one site in each single cell. Cell cycle genes were found to have high variation in polyA site usages. Furthermore, polyA site usage switch played an important role in cell cycle regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Geriatrics & Gerontology
Arttu Autio, Jalmari Kettunen, Tapio Nevalainen, Bryn Kimura, Mikko Hurme
Summary: As we age, the functioning of the immune system declines, but the correlation between viral infections and age is unclear. Epstein-Barr virus (EBV) is the most frequently expressed virus. Activated cell types are associated with EBV expression. These findings contribute to the understanding of the impact of persistent viral infections on elderly health.
Article
Multidisciplinary Sciences
Yoshimi Enose-Akahata, Limin Wang, Fahad Almsned, Kory R. Johnson, Yair Mina, Joan Ohayon, Xin Wei Wang, Steven Jacobson
Summary: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system (CNS), and the cause of MS remains unknown. This study investigated the antibody responses against various viruses in the cerebrospinal fluid (CSF) and serum of MS patients, and found significant differences compared to healthy volunteers, as well as a pattern of antibody responses against multiple viruses, including Epstein-Barr virus. These findings indicate that virus-specific antibody signatures might reflect the disease-associated inflammatory milieu in the CSF of patients with neuroinflammatory diseases.
Article
Biotechnology & Applied Microbiology
Anamika Thakur, Manoj Kumar
Summary: This study identified differentially expressed miRNAs and mRNAs in EBV-infected cell lines and tissue samples, and predicted potential therapeutic targets and candidate drugs for repurposing against EBV-related tumors.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Microbiology
Lisa Beatrice Caruso, Rui Guo, Kelsey Keith, Jozef Madzo, Davide Maestri, Sarah Boyle, Jason Wasserman, Andrew Kossenkov, Benjamin E. Gewurz, Italo Tempera
Summary: The nuclear lamina plays a crucial role in regulating Epstein-Barr virus (EBV) gene expression during latency, and its interaction with the viral genome contributes to the epigenetic control of viral gene expression. This finding may lead to the identification of new therapeutic targets for EBV-associated malignancies.
Article
Multidisciplinary Sciences
Zhe Li, Francesco Baccianti, Susanne Delecluse, Ming-Han Tsai, Anatoliy Shumilov, Xianliang Cheng, Sicong Ma, Ingrid Hoffmann, Remy Poirey, Henri-Jacques Delecluse
Summary: The viral noncoding RNA EBER2 accelerates B cell growth by potentiating expression of the UCHL1 deubiquitinase, even in Burkitt's lymphoma cells that do not express the virus's known oncogenes. This study identifies a direct cellular target of a viral noncoding RNA that is likely crucial for EBV's oncogenic properties.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Oguzhan Begik, Gregor Diensthuber, Huanle Liu, Anna Delgado-Tejedor, Cassandra Kontur, Adnan Muhammad Niazi, Eivind Valen, Antonio J. Giraldez, Jean-Denis Beaudoin, John S. Mattick, Eva Maria Novoa
Summary: RNA polyadenylation plays a central role in RNA maturation, fate, and stability. Nanopore 3' end-capture sequencing (Nano3P-seq) is a method that uses nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. This method can accurately estimate transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
Article
Pathology
Sudipta Samanta, Muthukaruppan Swaminathan, Jianing Hu, Khai Tuck Lee, Ajitha Sundaresan, Chuan Keng Goh, Chor Hiang Siow, Kwok Seng Loh, Soh Ha Chan, Joshua K. Tay, Ian Cheong
Summary: The use of immunofluorescence assay for detecting serum Epstein-Barr virus antibodies is the gold standard screening test for nasopharyngeal cancer in high-risk populations. This study demonstrates that integrating deep learning with automated fuzzy inference can improve the scalability and accuracy of NPC detection.
AMERICAN JOURNAL OF PATHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Phaedra Winstanley-Zarach, Gregor Rot, Shweta Kuba, Aibek Smagul, Mandy J. J. Peffers, Simon R. R. Tew
Summary: Polyadenylation (polyA) defines the 3' boundary of a transcript's genetic information. Alternative polyadenylation (APA) transcripts can exist for a gene, causing variance in regulatory domains and potential coding sequence changes. This study analyzed the polyA site distribution in healthy and osteoarthritic knee articular chondrocytes and found modest differential use of polyadenylation sites between the two conditions, suggesting potential functional relevance in affected genes. This characterization of polyadenylation landscape contributes to understanding the role of polyA in knee osteoarthritis, distinguishing it from other pathologies such as cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Hannes Vietzen, Philippe L. Furlano, Jan J. Cornelissen, Georg A. Boehmig, Peter Jaksch, Elisabeth Puchhammer-Stoeckl
Summary: This study found that nonclassic human leukocyte antigen E (HLA-E)-restricted immune responses have a significant impact on the development of Epstein-Barr virus (EBV) diseases in the individual host. The highly expressed HLA-E*0103/0103 genotype is protective against infectious mononucleosis (IM) by inducing potent EBV BZLF1-specific HLA-E-restricted CD8(+) T-cell responses. Variations in the inhibitory NKG2A/LMP-1/HLA-E axis are associated with the risk of symptomatic EBV reactivations in both immunocompetent individuals and immunocompromised transplant recipients.
Article
Biochemistry & Molecular Biology
Tian-Liang Xia, Xingyang Li, Xueping Wang, Yun-Jia Zhu, Hua Zhang, Weisheng Cheng, Mei-Ling Chen, Ying Ye, Yan Li, Ao Zhang, Dan-Ling Dai, Qian-Ying Zhu, Li Yuan, Jian Zheng, Huilin Huang, Si-Qi Chen, Zhi-Wen Xiao, Hong-Bo Wang, Gaurab Roy, Qian Zhong, Dongxin Lin, Yi-Xin Zeng, Jinkai Wang, Bo Zhao, Benjamin E. Gewurz, Jianjun Chen, Zhixiang Zuo, Mu-Sheng Zeng
Summary: This study demonstrates that EBV transcripts exhibit differential m(6)A modification in human NPC biopsies and cells at different infection stages, and the m(6)A-modified EBV transcripts are recognized and destabilized by the YTHDF1 protein, leading to suppression of EBV infection and replication. YTHDF1 accelerates viral RNA decapping and mediates RNA decay, thereby downregulating the expression of EBV genes post-transcriptionally.
Article
Biochemistry & Molecular Biology
Xubing Long, Jing Yang, Xiaolin Zhang, Ziwei Yang, Yang Li, Fan Wang, Xiaojuan Li, Ersheng Kuang
Summary: The study reveals that Epstein-Barr virus lytic replication inhibits inflammasome activation through the immediate-early protein BRLF1, leading to altered immune responses in T cells and NK cells.
Article
Oncology
Sameer Mirza, Achyuth Kalluchi, Mohsin Raza, Irfana Saleem, Bhopal Mohapatra, Dhananjaya Pal, Michel M. Ouellette, Fang Qiu, Lulu Yu, Alexei Lobanov, Zhi-Ming Zheng, Ying Zhang, Mansour A. Alsaleem, Emad A. Rakha, Hamid Band, M. Jordan Rowley, Vimla Band
Summary: This study reveals a novel role of ECD in viral and cellular mRNA splicing to support HPV-driven oncogenesis. ECD interacts with high-risk HPV E6 proteins and is overexpressed in cervical and head and neck squamous cell carcinoma. Its overexpression predicts shorter survival in patients and ECD knockdown impairs oncogenic behavior in cervical cancer cells.
MOLECULAR CANCER RESEARCH
(2022)
Article
Microbiology
Lulu Yu, Zhi-Ming Zheng
Summary: This article reanalyzes a previous study on HPV16 circular RNA circE7 and finds off-target effects in the research. The experimental results show that the copy number of circE7 in CaSki cells is very low and mainly located in the cytoplasm.
Review
Microbiology
Nishi R. Sharma, Zhi-Ming Zheng
Summary: RNA granules are important for post-transcriptional gene regulation. KSHV, a DNA virus, counteracts RNA granules through the expression of ORF57 protein, allowing it to evade host antiviral immunity and ensure productive infection.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
Summary: Human papillomaviruses (HPV) are a group of viruses that cause cancer, with HPV16 and HPV18 being the most common types responsible for majority of cases. The expression of their genome is regulated by alternative RNA splicing, and epigenetic modifications also play a role in HPV infections and carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Multidisciplinary Sciences
Haibin Liu, Zhi-Ming Zheng
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Letter
Microbiology
Lulu Yu, Alexei Lobanov, Zhi-Ming Zheng
Article
Cell Biology
Ashish Kumar, Yuanzhi Lyu, Yuichi Yanagihashi, Chanikarn Chantarasrivong, Vladimir Majerciak, Michelle Salemi, Kang-Hsin Wang, Tomoki Inagaki, Frank Chuang, Ryan R. Davis, Clifford G. Tepper, Kazushi Nakano, Chie Izumiya, Michiko Shimoda, Ken-ichi Nakajima, Alexander Merleev, Zhi-Ming Zheng, Mel Campbell, Yoshihiro Izumiya
Summary: This study reveals the nuclear microenvironment of Kaposi sarcoma-associated herpesvirus (KSHV) and its role in regulating the latency-lytic replication switch. Viral long non-coding RNAs interact with CHD4 to control KSHV reactivation.
Correction
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Vladimir Majerciak, Beatriz Alvarado-Hernandez, Alexei Lobanov, Maggie Cam, Zhi-Ming Zheng
Summary: In this report, the researchers investigated the role of RNA splicing in the regulation of KSHV gene expression. They found that approximately one-third of viral genes express spliced transcripts, many of which undergo RNA alternative splicing. They identified a subset of viral RNA splicing events that are regulated by the viral RNA-binding protein ORF57, leading to the discovery of its role in the splicing of the bicistronic ORF70-K3 RNA and production of viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3. This regulation allows for the timely expression of these two viral proteins during the KSHV lytic cycle. The study provides new insights into KSHV biology and serves as a blueprint for studying RNA splicing in other pathogens.
Article
Virology
Qiang Xu, Haoru Dong, Zhiyu Wang, Pei Zhang, Andreas E. E. Albers, Andreas M. M. Kaufmann, Zhi-Ming Zheng, Xu Qian
Summary: A new platform was used to genotype HPV DNA in cancer tissues of 361 gastric cancer (GC) and 89 oropharyngeal squamous cell carcinoma (OPSCC). The results showed that 10 GC and 2 OPSCC were infected with HPV16, suggesting a possible involvement of high-risk HPV in gastric carcinoma.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Environmental Sciences
Junjie Niu, Tiequan Zhang, Guang Wen, Zhiming Zheng, Yu Jia, Chin S. Tan, Tom Welackey
Summary: Evaluating the nitrogen use efficiency of animal manure is crucial for optimizing its application in profitable crop production without harming the environment. A four-year field study found that liquid manure achieved comparable corn yields to inorganic fertilizer, while solid and composted manure had minimal agronomical value. Nitrogen use efficiency indices were used to evaluate the different manures, with inorganic fertilizer performing the best followed by liquid manure.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Vladimir Majerciak, Tongqing Zhou, Michael J. Kruhlak, Zhi-Ming Zheng
Summary: In this study, the formation of stress granules (SG) induced by arsenite (ARS) was found to be topologically and mechanically linked to RNA-processing bodies (PB). Two essential PB components, GW182 and DDX6, play direct but distinguishable roles in SG biogenesis under stress. The activity of DDX6 in both PB and SG biogenesis is further modulated by its interaction with CNOT1 and 4E-T.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Lulu Yu, Zhi-Ming Zheng
Summary: The study found that the copy number of circE7 in HPV16-positive cervical cancer cell lines is low, and its function mainly results from off-target effects on E6*I RNA.