A comprehensive analysis of the Bencao(herbal)small RNA Atlas reveals novel RNA therapeutics for treating human diseases  

作　　者：Yinghao Cao Yexuan Lin Na Sun Xinyi Du Yixin Dong Song Mei Xingyu Deng Xiaobei Li Shaoting Guo Kegong Tang Jiaqi Liu Xiangyu Qiao Dandan Zhao Yuhao Qin Cong Zhang Tianyi Xin Xiaohu Shi Congzhao Zhou Tao Dong De-an Guo Benedikt MKessler Dong Xu Jingyuan Song Fengming Huang Xiaoyue Wang Chengyu Jiang 

机构地区：[1]State Key Laboratory of Common Mechanism Research for Major Diseases,Department of Biochemistry,Institute of Basic Medical Sciences Chinese Academy of Medical Sciences,School of Basic Medicine Peking Union Medical College,Beijing 100005,China [2]Key Laboratory of Chinese Medicine Resources Conservation,State Administration of Traditional Chinese Medicine of China,Engineering Research Center of Chinese Medicine Resource of Ministry of Education,Institute of Medicinal Plant Development,Chinese Academy of Medical Sciences&Peking Union Medical College,Beijing 100193,China [3]Department of Traditional Chinese Medicine,Peking Union Medical College Hospital,Chinese Academy of Medical Sciences,Beijing 100005,China [4]Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences,University of Science and Technology of China,Hefei 230027,China [5]MRC Human Immunology Unit,MRC Weatherall Institute of Molecular Medicine,Radcliffe Department of Medicine,University of Oxford,Oxford OX37FZ,UK [6]Chinese Academy of Medical Sciences(CAMS),CAMS Oxford Institute(COI),Nuffield Department of Medicine,University of Oxford,Oxford,OX37FZ,UK [7]Shanghai Research Center for Modernization of Traditional Chinese Medicine,National Engineering Laboratory for TCM Standardization Technology,Shanghai Institute of Materia Medica,Chinese Academy of Sciences,Shanghai 201203,China [8]Target Discovery Institute,Centre for Medicines Discovery,Nuffield Department of Medicine,University of Oxford,Oxford,OX37FZ,UK [9]Department of Electrical Engineering and Computer Science,and Christopher S.Bond Life Sciences Center,University of Missouri,Columbia MO 65211,USA

出　　处：《Science China(Life Sciences)》2023年第10期2380-2398,共19页中国科学（生命科学英文版）

基　　金：the National Natural Science Foundation of China(81788101,32100104);the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences(2021-I2M-1022);the CAMS Endowment Fund(2021-CAMS-JZ001);the Overseas Expertise Introduction Center for Discipline Innovation(“111 Center”)(BP0820029)。

摘　　要：Cross-kingdom herbal mi RNA was first reported in 2012.Using a modified herbal extraction protocol,we obtained 73,677,287sequences by RNA-seq from 245 traditional Chinese Medicine(TCM),of which 20,758,257 were unique sequences.We constructed a Bencao(herbal)small RNA(s RNA)Atlas(http://bencao.bmicc.cn),annotated the sequences by sequence-based clustering,and created a nomenclature system for Bencao s RNAs.The profiles of 21,757 mi RNAs in the Atlas were highly consistent with those of plant mi RNAs in mi RBase.Using software tools,our results demonstrated that all human genes might be regulated by s RNAs from the Bencao s RNA Atlas,part of the predicted human target genes were experimentally validated,suggesting that Bencao s RNAs might be one of the main bioactive components of herbal medicines.We established roadmaps for oligonucleotide drugs development and optimization of TCM prescriptions.Moreover,the decoctosome,a lipo-nano particle consisting of 0.5%–2.5%of the decoction,demonstrated potent medical effects.We propose a Bencao(herbal)Index,including small-molecule compounds(SM),protein peptides(P),nucleic acid(N),non-nucleic and non-proteinogenic large-molecule compounds(LM)and elements from Mendeleev's periodic table(E),to quantitatively measure the medical effects of botanic medicine.The Bencao s RNA Atlas is a resource for developing gene-targeting oligonucleotide drugs and optimizing botanical medicine,and may provide potential remedies for the theory and practice of one medicine.

关 键 词：small RNA herbal decoction cross-kingdom regulation traditional Chinese medicine RNA oligonucleotide drug RNA therapeutics Bencao small RNA Atlas 

分 类 号：R285[医药卫生—中药学]