基于转录组学的人参属多药材多组分的药效 和分子机制研究

中药由于其特殊的方剂用法， 使其良好的药效未能得到广泛的应用与推广。
目前从中药中提取出来的化合物数量繁多， 并且在临床使用中也具有明显的效果，
具有药理活性化合物的寻找及其作用机制的研究， 是一个亟待解决的问题。 人参
（Panax ginseng） 是一种用于医疗保健和治疗疾病的中药材， 主要通过其含有的人
参皂苷等生物活性物质发挥其多种治疗功效。 过去对人参的分子药理研究主要在
个别基因和分子通路上分析单一化合物的作用机理， 脱离了中医整体观的指导原
理， 未能阐明中药发挥系统功效的作用机理。
本文利用多种系统生物学手段对人参属四种药典记载药材（人参、 西洋参、
三七和竹节参） 中近 60 种单体和混合活性成份进行系统的功效分析和分子机制研
究。 通过根据化合物引起的基因表达差异建立该化合物的“基因标签”， 与 1309 个
现行药物的基因表达谱比对以分析其功能， 并找寻出化合物作用的靶点和通路等，
把受中药化合物调控的基因和细胞通路、 疾病、 以及药物交叉连接起来， 完成药
物／ 基因／ 病理／ 靶点的系统网络分析， 从而揭示中药化合物可能的疗效和作用
原理。
本文首先建立了四种人参属人参皂苷的结构分类全景图， 并选择出具有结构
代表性的化合物进行研究。 利用 XTT 比色法测定化合物对人乳腺癌细胞的增殖影
响， 并初步探究了人参皂苷发挥毒性作用可能与 6 位碳原子以及 20 位碳原子上基
团的数量和种类有关。 再通过获取约 40 个化合物的近 180 个转录组数据， 进一步
探究化合物潜在的功效关系以及可能的作用机制。 利用连接图谱(connectivity map
profiles)发现 ginsenoside Rg1 和 ginsenoside Rb1 具有雌激素样作用， 20(S) 原人参
二醇和 20(S) 原人参三醇具有细胞毒性样作用。 20(S) 原人参三醇与细胞致死和多
巴胺受体拮抗剂类化合物的表达谱高度相似， 利用 GO 分析和 KEGG 分析， 本文
初步探索了 20(S) 原人参三醇可能的作用机制。 发现其可能通过上调血管生成相
关基因， 下调细胞复制和 ERBB 通路相关基因发挥作用， 这些数据为开发 20(S)
protopanaxatriol 作为抗癌药物或者抗精神病类药物提供了理论依据。
综上， 本文为人参属化合物人参皂苷建立了第一个基于转录组数据的功能网
络平台“MecoTCM”， 并证明了其用于天然化合物功能预测和阐明分子机制的可靠
性， 本文认为这是中药现代化和全球化的关键。
 

Traditional Chinese medicines (TCMs) has not been widely recognized and
promoted because of its special prescription. Encouraged by the good clinic efficacy,
large number of compounds have been extracted from many TCM materials. Therefore,
how to explain the mechanism of action of pharmacologically active compounds in
TCMs is the pivotal problem for globalization of TCM. Panax ginseng is a precious
Chinese herbal medicine that is widely used on health care. The main active
components in ginseng are ginsenosides, which had been suggested to promote the
immune system and treat cardiovascular diseases and cancer. However, these studies
mainly focused on single ginsenoside and investigated normally individual gene and
pathway in one experiment, the concept that contradict the holistic therapeutic principle
of TCM. Rapid progress in systems biology paved the way for understanding both the
effects and mechanism of TCM at global level.
The purpose of the project is to explore the relationship between the structure and
functions of more than 50 ginseng compounds through constructing TCM transcriptome
data analysis platform—MecoTCM, which utilized several systems biology approaches.
On the platform, both the functions and molecular mechanisms of ginseng compounds
can be revealed. After collecting the transcriptome data via RNA-seq, the altered gene
expressions caused by the compounds were regarded as the "gene signature" of each
compound for functional annotation by comparing with the gene expression profiles of
1309 known drugs in connectivity map database. Furthermore, the possible pathways
impacted by compounds could also be discovered via Gene Set Enrichment Analysis
(GO and KEGG). Thus, gene expression levels can be correlated with cellular pathways,
disease, and drugs to complete a systematic network analysis of
drugs/genes/pathology/targets, which can reveal possible therapeutic effects and
mechanisms of action of Chinese herbal ingredients.
The detailed chemical structure classification of ginsenosides was built up in this
research, and then several compounds with structural characteristics were selected to
study molecular mechanism. The effect of the compounds on the proliferation of human
breast cancer cells (MCF7) was determined by XTT colorimetry. The toxic effects of
ginsenosides may be related to the number of carbon atoms and functional groups on
the 6th position and the 20th position of compound. The potential efficacy relationship
and possible mechanism of action of the compounds were further explored by around180 transcriptome profiles generated by around 40 compounds. Additionally, by using
the connectivity map, ginsenoside Rg1 and ginsenoside Rb1 were found to exert
estrogen-like effects, while both 20(S) protopanaxadiol and 20(S) protopanaxatriol
possess cytotoxicity.
The results of connectivity map indicate that expression profile of 20(S)
protopanaxatriol is highly similar to the drugs causing cell death and having functions
of dopamine receptor antagonists. 20(S) protopanaxatriol may perform biological
functions by upregulating the gene expression in angiogenesis pathway, and
downregulating gene expression related to cell replication and ERBB pathway. These
data provide experimental evidence to further development of the compound as an
anticancer or antipsychotic drug.
In summary, we established the 1st transcriptome-based functional network
“MecoTCM” for large number of genus Ginseng compounds and demonstrated the high
reliability in functional prediction and molecular mechanism elucidation of natural
compounds, which we regard as the key for TCM modernization and globalization.
 

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