1.m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues.
Bowen SONG ; Daiyun HUANG ; Yuxin ZHANG ; Zhen WEI ; Jionglong SU ; João PEDRO DE MAGALHÃES ; Daniel J RIGDEN ; Jia MENG ; Kunqi CHEN
Genomics, Proteomics & Bioinformatics 2023;21(4):678-694
As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats.
Humans
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Methylation
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RNA, Messenger/metabolism*
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Neoplasms/genetics*
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Mutation
2.Nano-bio interfaces effect of two-dimensional nanomaterials and their applications in cancer immunotherapy.
Zhongmin TANG ; Yufen XIAO ; Na KONG ; Chuang LIU ; Wei CHEN ; Xiangang HUANG ; Daiyun XU ; Jiang OUYANG ; Chan FENG ; Cong WANG ; Junqing WANG ; Han ZHANG ; Wei TAO
Acta Pharmaceutica Sinica B 2021;11(11):3447-3464
The field of two-dimensional (2D) nanomaterial-based cancer immunotherapy combines research from multiple subdisciplines of material science, nano-chemistry, in particular nano-biological interactions, immunology, and medicinal chemistry. Most importantly, the "biological identity" of nanomaterials governed by bio-molecular corona in terms of bimolecular types, relative abundance, and conformation at the nanomaterial surface is now believed to influence blood circulation time, bio-distribution, immune response, cellular uptake, and intracellular trafficking. A better understanding of nano-bio interactions can improve utilization of 2D nano-architectures for cancer immunotherapy and immunotheranostics, allowing them to be adapted or modified to treat other immune dysregulation syndromes including autoimmune diseases or inflammation, infection, tissue regeneration, and transplantation. The manuscript reviews the biological interactions and immunotherapeutic applications of 2D nanomaterials, including understanding their interactions with biological molecules of the immune system, summarizes and prospects the applications of 2D nanomaterials in cancer immunotherapy.
3.Expressions of BAG-1 and NF-?B P65 in the mononuclearcell of multiple myeloma patients
Laiquan HUANG ; Zhonglin WEI ; Jun ZHANG ; Daiyun ZHANG ; Xinghong WANG
Chinese Journal of Clinical Pharmacology and Therapeutics 2000;0(03):-
AIM:To investigate the expressions of BAG-1 and NF-?B P65 in the multiple myeloma(MM)and approach the effects of BAG-1 and NF-?B P65 in the pathogenesis of MM and their clinical significance,which would be useful to find a theoretical basis for the treatment of MM.METHODS:The patients diagnosed MM in Yijishan hospital of wannan medical college from 2006.10 to 2008.10 as the experimental group,while the bone trauma patients selected as the control group.The mononuclearcells of bone marrow in the patients were extracted and the BAG-1and NF-?B P65 mRNA RT-PCR were detected.RESULTS:The expression of BAG-1 mRNA(71.4%)in the MM patients was higher than that in the control group(P=0.007).The expression of NF-?B P65 mRNA(75.0%)in the MM patients was higher than that in the control group(P=0.004).There was a positive correlation between the BAG-1 and NF-?B P65 mRNA.The tumor load was high in the MM patients with overexpression of BAG-1 and NF-?B P65,which was ralated to a number of clinical parameters indexes.BAG-1 and NF-?B P65 were positive expressed of MM tumor load,relatived with a number of clinical indicators.CONCLUSION:The expressions of BAG-1 and NF-?B P65 in MM are high,there are no difference between the experimental group and control group.BAG-1 and NF-?B P65 were related to a number of clinical indexes.BAG-1 and NF-?B P65 may be involved in the occurrence and the development of disease,and they can be used as one of the prognosis indexes.

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