Review
Oncology
Shanshan Wang, Wei Lv, Tao Li, Shubing Zhang, Huihui Wang, Xuemei Li, Lianzi Wang, Dongyue Ma, Yan Zang, Jilong Shen, Yuanhong Xu, Wei Wei
Summary: N-6-Methyladenosine (m6A) is the most abundant internal modification associated with eukaryotic mRNAs, and it plays a dynamic regulatory role in gene expression by affecting various steps of mRNA metabolism. This review discusses the general role of m6A, focusing on the three major types of enzymes that determine the level of m6A modification and the regulatory mechanism by which m6A influences RNA metabolism. Understanding the role of m6A in physiological and pathophysiological processes, especially in tumorigenesis, is of great importance.
CANCER CELL INTERNATIONAL
(2022)
Article
Multidisciplinary Sciences
Jiangbo Wei, Xianbin Yu, Lei Yang, Xuelian Liu, Boyang Gao, Boxian Huang, Xiaoyang Dou, Jun Liu, Zhongyu Zou, Xiao-Long Cui, Li-Sheng Zhang, Xingsen Zhao, Qinzhe Liu, P. Cody He, Caraline Sepich-Poore, Nicole Zhong, Wenqiang Liu, Yanhe Li, Xiaochen Kou, Yanhong Zhao, You Wu, Xuejun Cheng, Chuan Chen, Yiming An, Xueyang Dong, Huanyu Wang, Qiang Shu, Ziyang Hao, Tao Duan, Yu-Ying He, Xuekun Li, Shaorong Gao, Yawei Gao, Chuan He
Summary: This study reveals that FTO mediates m(6)A demethylation of LINE1 RNA in mouse embryonic stem cells, regulating LINE1 RNA abundance and the local chromatin state. It also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development.
Article
Biochemistry & Molecular Biology
Leiming Jiang, Shijia Hao, Lirui Lin, Xuefei Gao, Jianzhen Xu
Summary: fRNC is a systems biology tool that uncovers the dynamic spectrum of RBP-ncRNA circuits by integrating transcriptomics, interactomics, and proteomics data. Compared to existing tools, fRNC can detect more accurate and robust sub-networks with scalability. It enables users to analyze the collective behaviors between RBPs and interacting ncRNAs and provides novel insights into disease-associated processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiaoyu Liang, Canyon Calovich-Benne, Adam Norris
Summary: The function and identity of a cell is influenced by transcription factors and RNA binding proteins. By analyzing the cell lineage of Caenorhabditis elegans, the limitations of analyzing sparse single-cell post-transcriptional data can be overcome. In terms of touch-neuron splicing, a small MEC-8-regulated network has been identified. MEC-8 establishes specific transcript isoforms in touch neurons, while non-specific isoforms are present in other neurons.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Shanshan Li, Qing Yang, Rui Jiao, Pengfei Xu, Yazhou Sun, Xin Li
Summary: In this study, different m6A topologies were identified among protein-coding genes, and the dynamic changes of m6A topologies were found to play important roles in tissue development. Genes with m6A loss in 5' UTRs were associated with developmental stage-specific genes, while genes with m6A gain around stop codons were associated with tissue-specific functions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Teng Zhang, Shao-Wu Zhang, Song-Yao Zhang, Qian-qian Ma
Summary: N-6-methyladenosine (m(6)A) is the most abundant form of mRNA modification that plays an important role in regulating gene expression. This study proposed a novel method (m(6)Aexpress-Reader) to predict m(6)A-regulated gene expression in specific contexts, integrating m(6)A sites and reader binding information. The findings reveal the complex characteristic of m(6)A on gene expression regulation and the distinct regulated pattern of m(6)A-regulated genes with different reader binding, especially in cancer.
Review
Cell Biology
Hanxiao Sun, Kai Li, Cong Liu, Chengqi Yi
Summary: Nucleobase modifications are widespread in eukaryotic mRNA and play crucial roles in post-transcriptional gene regulation. The most extensively studied modification is N-6-methyladenosine (m(6)A), but other modifications are also being investigated. This Review focuses on the emerging mechanisms and functions of these non-m(6)A modifications.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Romain Desert, Wei Chen, Xiaodong Ge, Roselyne Viel, Hui Han, Dipti Athavale, Sukanta Das, Zhuolun Song, Daniel Lantvit, Luis Cano, Alexandra Naba, Orlando Musso, Natalia Nieto
Summary: A study found that there are extracellular matrix (ECM) deposits in liver cancer tumors with high intratumor fibrosis, which contain components such as collagen and growth factors. These deposits are associated with poor patient outcomes.
Article
Biotechnology & Applied Microbiology
Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin, Frank A. Feltus
Summary: This study constructed condition-specific gene co-expression networks for normal lung, LUAD, and LUSC, and integrated tissue-specific gene regulatory networks to elucidate biomarker systems for normal and cancerous lung tissue. The findings identified co-expressed genes under common regulatory control that are relevant in lung cancer.
Review
Agriculture, Dairy & Animal Science
Siyuan Mi, Yuanjun Shi, Gerile Dari, Ying Yu
Summary: Understanding the m(6)A process in domestic animals has the potential to enhance animal production performance and improve reproduction and disease resistance.
JOURNAL OF ANIMAL SCIENCE
(2022)
Review
Cell Biology
Lorenzo Pavanello, Michael Hall, Gerlof Sebastiaan Winkler
Summary: Accurate and precise regulation of gene expression in eukaryotes involves the coordinated control of transcription, mRNA stability, and translation. Recent progress has been made in understanding the role of sequence elements in the 3' untranslated region in mRNA degradation regulation. The recruitment of the Ccr4-Not complex to target mRNA is a critical step in mRNA decay regulation. This article reviews the role of the human Ccr4-Not complex in cytoplasmic deadenylation of mRNA, focusing on its recruitment mechanisms and general mechanisms involving the poly(A) tail.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shuiping Liu, Lu Chen, Yintao Zhang, Ying Zhou, Ying He, Zhen Chen, Shasha Qi, Jinyu Zhu, Xudong Chen, Hao Zhang, Yongchao Luo, Yunqing Qiu, Lin Tao, Feng Zhu
Summary: As the most prevalent internal modification in eukaryotic RNAs, N-6-methyladenosine (m(6)A) has been discovered to play an essential role in cellular proliferation, metabolic homeostasis, embryonic development, etc. A new database named 'M6AREG' is developed to systematically cover, for the first time, data on the effects of m(6)A-centered regulation on both disease development and drug response, and explicitly describe the molecular mechanism underlying each type of regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Lingfang Wang, Guankai Zhan, Yasen Maimaitiyiming, Yingfeng Su, Shitong Lin, Jinfeng Liu, Kunhui Su, Jiebo Lin, Shizhen Shen, Wentao He, Fenfen Wang, Jiafeng Chen, Siqi Sun, Yite Xue, Jiaxin Gu, Xiaojing Chen, Jian Zhang, Lu Zhang, Qianqian Wang, Kao-Jung Chang, Shih-Hwa Chiou, Mikael Bjorklund, Hua Naranmandura, Xiaodong Cheng, Chih-Hung Hsu
Summary: This study reveals that heat treatment can selectively target the messenger RNA (mRNA) containing the E7 onco-transcript complex of human papillomavirus (HPV). By destabilizing the cellular reader protein IGF2BP1, heat treatment downregulates E7 mRNA and protein expression, effectively reversing HPV-induced carcinogenesis. Mechanistically, heat treatment promotes the aggregation of IGF2BP1 only in the presence of m6A-modified E7 mRNA, which is subsequently resolved by the ubiquitin-proteasome system. These findings provide a novel heat treatment-based therapeutic strategy for HPV-associated malignancies.
Article
Gastroenterology & Hepatology
Man Hsin Hung, Ching Wen Chang, Kathy Cheng Wang, Jittiporn Chaisaingmongkol, Mathuros Ruchirawat, Tim F. Greten, Xin Wei Wang
Summary: In this study, the researchers analyzed the purine metabolism pathways in tumor and non-tumor liver tissues of patients with hepatocellular carcinoma (HCC), one of the most lethal cancers globally. The findings showed that purine synthesis genes are upregulated and purine degradation genes are inhibited in HCC tumors. High purine anabolism is associated with specific somatic mutational signatures and leads to dysregulation of DNA damage repairing machinery. Furthermore, high purine anabolism determines the sensitivity of HCC to DDR-targeting agents and correlates with clinical outcomes.
Review
Medicine, Research & Experimental
Yufei Lan, Boyang Liu, Hongbo Guo
Summary: The article summarizes the important role of N-6-methyladenosine (m(6)A) modification in the regulation and function of tumor-related long non-coding RNAs (lncRNAs), and discusses potential applications and future directions in the field.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Virology
Hu Zhang, Douglas K. Fischer, Masahiro Shuda, Patrick S. Moore, Shou-Jiang Gao, Zandrea Ambrose, Haitao Guo
Summary: Two SARS-CoV-2 minigenome replicon systems, IVT-CoV2-Rep and BAC-CoV2-Rep, have been developed for research on SARS-CoV-2 virology and antiviral discovery. IVT-CoV2-Rep demonstrates rapid and transient replication in various cell lines, which can be inhibited by known SARS-CoV-2 replication inhibitors. BAC-CoV2-Rep exhibits a stronger and longer replicon signal, and a portion of the signal shows resistance to antiviral treatment.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Md Azahar Ali, Chunshan Hu, Fei Zhang, Sanjida Jahan, Bin Yuan, Mohammad S. Saleh, Shou-Jiang Gao, Rahul Panat
Summary: Rapid detection of SARS-CoV-2 antibodies is crucial for COVID-19 diagnosis and vaccine evaluation. A 3D biosensor fabricated using aerosol jet 3D printing enables quantification of antibodies in seconds with high sensitivity and regenerability.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Editorial Material
Virology
Shou-Jiang Gao, Haitao Guo, Guangxiang Luo
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiaoyu Qi, Qin Yan, Yuancui Shang, Runran Zhao, Xiangya Ding, Shou-Jiang Gao, Wan Li, Chun Lu
Summary: This study reveals a novel role of viral interferon regulatory factor 1 (vIRF1) in Kaposi's sarcoma-associated herpesvirus (KSHV) metabolic reprogramming. vIRF1 increases glucose uptake and ATP production by downregulating hnRNP Q1, which destabilizes the mRNA of GDPD1 and induces aerobic glycolysis. These findings provide a potential therapeutic target for KSHV infection and KSHV-induced cancers.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Cell Biology
Jian Feng, Teng Zhang, Oceane Sorel, Wen Meng, Xinquan Zhang, Zhao Lai, Weiming Yuan, Yidong Chen, Yufei Huang, Shou-Jiang Gao
Summary: This study reveals the important role of N-6-methyladenosine (m(6)A) in regulating innate immunity against bacterial and viral infections. By examining cellular m(6)A epitranscriptomes, the study shows that many innate immune response genes undergo m(6)A modifications. The findings provide valuable resources for the scientific community.
CELL DEATH & DISEASE
(2022)
Article
Virology
George Fei Zhang, Wen Meng, Luping Chen, Ling Ding, Shenyu Sun, Xian Wang, Yufei Huang, Haitao Guo, Shou-Jiang Gao
Summary: Since the first COVID-19 case in 2019, various SARS-CoV-2 variants of concern (VOCs) with different infectivity and pathology have emerged. Researchers conducted infection analysis on human cells from different organs using VOC pseudoviruses and found that many VOCs had significantly higher infectivity compared to the wild type. Recombinant ACE2 protein was found to be more effective in inhibiting the infection of VOCs such as Delta and Omicron. The study also revealed the role of ACE2 expression levels in different cell types in the infection inhibition by recombinant S1, RBD, Kim-1, and NRP-1 proteins.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Jian Feng, Wen Meng, Luping Chen, Xinquan Zhang, Ashley Markazi, Weiming Yuan, Yufei Huang, Shou-Jiang Gao
Summary: The study reveals that viral and bacterial infections enhance the degradation of DUSP1 transcript, activate p38 and JNK pathways, and promote the expression of innate immune response genes. This is achieved through the rapid increase of DUSP1 transcript and its N-6-methyladenosine (m(6)A) levels, as well as the involvement of the reader protein YTHDF2.
Article
Virology
Koushul Ramjattun, Xiaojun Ma, Shou-Jiang Gao, Harinder Singh, Hatice Ulku Osmanbeyoglu
Summary: In order to combat COVID-19, it is crucial to understand the host cell types, cell states, and regulators associated with infection and pathogenesis. SPaRTAN, an integrated tool for analyzing single-cell proteomic and transcriptomic data, has been developed to identify the associations between cell surface proteins and transcription factors in host immune cells. To provide a user-friendly platform for data analysis and visualization, the COVID-19db web server has been established, which includes cell surface protein expression, SPaRTAN-inferred TF activities, and their associations with major host immune cell types.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Long Gao, Yufeng Gao, Kexing Han, Zining Wang, Fang Meng, Jiaying Liu, Xin Zhao, Yun Shao, Jiapei Shen, Weijie Sun, Yanyan Liu, Honghai Xu, Xiaohong Du, Jiabin Li, Frank Xiao-Feng Qin
Summary: This study identified FBXO11 as a crucial regulator of IFN-I signaling and antiviral processes against various RNA/DNA viruses. It was found to enhance IFN-I signaling by promoting the phosphorylation of TBK1 and IRF3, and its expression was positively correlated with disease progression in viral infections. This makes FBXO11 a potential therapeutic target for different viral diseases.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Tingting Li, Shou-Jiang Gao
Summary: Reactive oxygen species (ROS) play a role in controlling cellular behaviors, and cancer cells often have excessive ROS due to oncogenic stress. In this study, we found that KSHV virus upregulates antioxidant genes by activating FoxO1 to maintain intracellular ROS level, which is essential for KSHV-induced cellular proliferation and transformation.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Junxia Feng, Xiaohu Cui, Bing Du, Hanqing Zhao, Yanling Feng, Jinghua Cui, Chao Yan, Lin Gan, Zheng Fan, Tongtong Fu, Ziying Xu, Zihui Yu, Rui Zhang, Shuheng Du, Ziyan Tian, Qun Zhang, Guanhua Xue, Jing Yuan
Summary: This study developed a rapid and sensitive ddPCR assay for detecting Klebsiella pneumoniae in fecal samples. The ddPCR assay showed higher sensitivity, specificity, and lower inhibition compared to real-time PCR and microbial culture. The findings suggest that ddPCR could be an effective tool for detecting K. pneumoniae in fecal samples and guiding treatment decisions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Cell Biology
Xinquan Zhang, Wen Meng, Jian Feng, Xinghong Gao, Chao Qin, Pinghui Feng, Yufei Huang, Shou-Jiang Gao
Summary: This study identifies the suppressive role of RNA methyltransferase METTL16 in KSHV lytic replication. METTL16 regulates the SAM cycle to maintain intracellular SAM level and redox homeostasis, thereby inhibiting KSHV lytic replication.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Qin Yan, Jing Zhou, Ziyu Wang, Xiangya Ding, Xinyue Ma, Wan Li, Xuemei Jia, Shou-Jiang Gao, Chun Lu
Summary: NAT10 is an enzyme that catalyzes RNA acetylation at the cytidine N-4 position, increasing the stability of HIV-1 transcripts and triggering viral reactivation from latency. It also plays a role in KSHV replication and antiviral immunity by modifying PAN RNA and recruiting IFI16 mRNA for inflammasome activation.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Luping Chen, Ling Ding, Xian Wang, Yufei Huang, Shou-Jiang Gao
Summary: This study reveals an important role of the IL-1 pathway in KSHV-induced inflammation and oncogenesis, which can be inhibited by dexamethasone-activated GR signaling.