Bioinformatics Analysis On The Mechanisms Of Rheumatoid Arthritis Treatment By Tripterygium Wilfordii In Combination With Methotrexate,Astragalus And Angelica

BackgroundRheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by joint synovitis. The prevalence rate of the disease is0.3-1%worldwide, and the prevalence rate is0.32-0.36%in china according to certain reference, with the appearance in different age groups. If not treated, the disease can induce severe joint deformity, joint dysfunction, which seriously affect the life quality of patients.The goal of rheumatoid arthritis treatment is to improve the patient’s physical, mental and quality of life in society by alleviating the pain caused by arthritis, prevent joint damage and maintain joint function. The core of rheumatoid arthritis treatment is medical treatment, which includes anti-rheumatic drugs, non-steroidal anti-inflammatory drugs and steroidal drugs as to western medicine. Anti-rheumatoid drugs, including immunomodulatory drugs, immunosuppressive drugs and biological agents, control rheumatoid arthritis induced by immune function abnormity. Western medicine treatment is inclined to bring gastrointestinal symptoms and interstitial renal damage, therefore traditional Chinese medicines is often employed in combination with western medicine in clinic. Treatment by traditional Chinese medicines put stress integrity, combating the diseases from multi-level, multi-channel to regulate the body immune function, which exhibits with great potential and advantages. Several clinical studies have also shown that the treatment of RA by some traditional Chinese medicines in combination with western medicines can produce more satisfactory curative effects and reduce more side effects than the treatment by western medicines only.Text mining is an interdisciplinary research field relating to natural language processing, machine learning, data mining, information retrieval etc. It plays an unnegligible role in business, media, education, government, banking, biotechnology, medical and health industry. There is rich knowledge in traditional Chinese medicines and. Abundance of data on traditional Chinese medicines, the majority of which are text data, have been accumulated through the efforts of researchers in the past decade. New knowledge can be discovered from the medical literature by text mining to facilitate the development of traditional Chinese medicines.Bioinformatics is an interdisciplinary science emerging in the late1980s with the launching of human genome project. It covers the storage, retrieval and analysis of bioinformation using computers in life science research. When used in TMC research, it helps to determine the target of drug action. While it is well known that TMC and its compound preparations are effective, TMC has not entered the mainstream international pharmaceutical market, essentially due to the fact that the TMC theories fail to integrate with the internationally accepted modern medical theories. It is likely that screening and isolation of disease-specific pathogenic genes as target for the study of molecular mechanisms of important actions will become one of the main directions of future TMC pharmacology studies. Study of the effects of TMC compound preparations on the cytogene expression profile and protein expression profile by using genetic chip technology and proteome assays promotes the establishment of technology platforms for genetic chips, proteomics and bioinformatics, which allow multi-component, multi-target and multi-path connections between compound TMC preparations and genetic and protein expressions, so as to compare the different expression profiles, determine the gene and protein expression targets for different TMC combinations, allow connections between the organ specificity&level of expression and the TMC theory of "principal,adjuvant,auxiliary and conductant ingredirnts" as well as the dosage, and to determine the relations between different components of compound preparations based on the interactions between gene and protein targets corresponding to different combinations, thus clarifying the material basis for drug action and the combination rules.This methodology will be of practical importance for the research, development and internalization of TMC and its compound preparations.Using the analysis methods of bioinformatics, we intended to generate a network for drug combinations based on existing literature reports and to explore the rules for interactions between Chinese and Western medicines and between different TMC combinations, so as to provide evidence for rational use of integrated Chinese-Western medicine as well as TMC combinations, in an effort to achieve "safe, effective, economic and rational" drug combinations.PurposeTo identify the common Chinese-Western or Chinese-Chinese medicine combinations for RA as the study subject by text mining, and, using Pubchem, identify the corresponding human target proteins, which were to be introduced to Ingenuity Pathways Analysis (IPA) platform to produce the corresponding networks and pathways, etc. for comparison with the networks and pathways obtained when RA differential gene (the gene difference between healthy population and RA patients) was introduced to IPA, so as to explore the structure of biopathway network as well as the mechanism for treatment of RA.Study contentsThe followings were completed for this study:1Mining for the application rules for common Chinese-Western or Chinese-Chinese medicine combinations for RAThe most commonly used Chinese-Western or Chinese-Chinese medicine combinations were identified using text mining.2Establishment of "pharmacology networks of tripterygium wilfordii/methotrexate (MTX) and radix/angelica, and bioinformatics analysis of their therapeutic mechanisms for RA. Specifically, the followings were studied:(1) Human target proteins for tripterygium wilfordii and MTX were identified through Pubchem retrieval and introduced to IPA platform to obtain the corresponding networks and pathways, etc., in exploration of the construction of their biopathway networks; their therapeutic mechanisms for RA were explored by comparing with the biopathway network construction obtained when RA differential gene was introduced to IPA.(2) Human target proteins for angelica and radix were identified through Pubchem retrieval and introduced to IPA platform to obtain the corresponding networks and pathways, etc., in exploration of the construction of their biopathway networks; their therapeutic mechanisms for RA were explored by comparing with the biopathway network construction obtained when RA differential gene was introduced to IPA.Results 1Mining for application rules for common Chinese-Western or Chinese-Chinese medicine combinations for RAAmong the common Chinese-Western medicine combinations, the combination of tripterygium wilfordii polyglycoside tablet and MTX was predominant. There has been large number of clinical reports on ripterygium wilfordii polyglycoside tablet, which leads the TMC preparations. Search into the literatures found that most literatures reported synergic action with clinical combinations, which were superior over single agent. Large number of literatures support that Chinese-Western combinations have definite therapeutic effect.It was observed through mining that the TMCs ramulus cinnamomi, paeonia, anemarrhenae, radix and angelica were the most frequent to be subject to combinations, which included Paeoniae and Anemarrhenae Decoction and Angelicae Sinensis Decoction for Supplementing Blood. Search into the literatures found that addition to or subtraction from the combinations were possible for each symptomatic type of RA, which warrants further investigation.2Establishment of pharmacology networks of tripterygium wilfordii/methotrexate (MTX) and radix/angelica, and bioinformatics analysis of their therapeutic mechanisms for RA2.1Protein ubiquitinoylation pathway is closely related to RA, an immunologic disease. Bioanalyses indicated that tripterygium wilfordii alone, MTX alone, tripterygium wilfordii/MTX combination, radix alone and radix/angelica combination have therapeutic effect for RA through protein ubiquitinoylation pathways. It was therefore presumed that protein ubiquitinoylation pathway is one of the courses of action for tripterygium wilfordii alone, MTX alone, tripterygium wilfordii/MTX combination, radix alone or radix/angelica combination to treat RA. Further analysis identified a target protein for protein ubiquitinoylation pathway common for these treatments, i.e., E3RING target.E3RING is one of the two major families of ubiquitin protein ligase (E3), and has been reported to be a likely new treatment option for RA.2.2The combination of tripterygium wilfordii and MTX not only acts on the protein ubiquitinoylation pathways, but also allows more extensive biopathways as compared to MTX alone. Bioanalyses indicated that the combination of tripterygium wilfordii and MTX may provide more effective and more comprehensive treatment for RA patients by affecting the granulocyte-macrophage colony stimulating factor(GM-CSF) pathway, the docosahexaenoic acid (DHA) signal pathway, the tyrosine protein kinase (TPK)1and3cytokine signal pathway.etc.2.3Heat shock protein (HSP) is one of the targets for protein ubiquitinoylation pathway common for radix/angelica combination and the differential gene for RA.Bioinformactics results indicate that radix/angelica combination affects the protein ubiquitinoylation pathway through E3RING and HSP, which serves as one of its important mechanisms for treating RA. In addition, bioanalyses identified several biopathway targets common for radix and RA differential gene, including protein ubiquitinoylation pathway, apoptosis signals, and glucocorticoid receptor signals, etc. When radix and angelica were combined, the weighing of their common target pathways was increased in treating RA, while no common biopathway targets were identified for angelica and the RA differential gene.Conclusions1Most of the TMC preparations were used in combination with MTX. Among them, tripterygium wilfordii polyglycoside tablet was the most frequent to be combined with MTX. The TMCs ramulus cinnamomi, paeonia, anemarrhenae, radix and angelica were the mostly used for combinations, including two classic TMC compound preparations, Paeoniae and Anemarrhenae Decoction and Angelicae Sinensis Decoction for Supplementing Blood (radix ad angelica)2One of the mechanisms for tripterygium wilfordii in combination with MTX or radix to treat RA was through affecting the following signal conduction pathway:E3RING→E3ubiquitin protein ligase→protein ubiquitinoylation→NF-κB/TGF-β.3Compared to MTX alone, the combination of tripterygium wilfordii and MTX may provide more comprehensive and more effective treatment for RA patients by affecting the GM-CSF pathway, the DHA signal pathway, the TPK-1and-3cytokine signal pathway, and the apoptosis signal pathway, etc.4Aside from acting on the E3RING→E3ubiquitin protein ligase target and thus the protein ubiquitinoylation pathway, the combination of radix and angelica provides therapeutic effect for RA also through affecting the HSP pathway. In addition, bioinformatics analysis indicated that when Angelicae Sinensis Decoction for Supplementing Blood is used for RA, radix is the principal agent while angelica is the adjuvant agent, contributing to their "mutual enhancing" relationship.