The Molecular Mechanism Of Berberine Towards Multiple Cancer Types Based On Traditional Chinese Medicine System Pharmacology

ObjectiveBased on the literature review of berberine(BBR)broad-spectrum anti-tumor pharmacological characteristics and its mechanism of action(MOA),traditional chinese medicine(TCM)systematic pharmacological and bioinformatics methods are used to predict the significant mutation genes(SMGs)and key signals involved in cancer.Its established a multi-level comprehensive network model of "component-target-disease-function" and predicted the intervention and treatment of BBR on new tumor types.Given the above analysis,the broad-spectrum antitumor mechanism of BBR was explored at the molecular level,providing a certain theoretical basis and support for further clinical research.MethodsThrough precise excavation and screening of the literature and the combined search of multiple databases to predict the targets of drugs and diseases,a systematic and comprehensive study of the broad-spectrum antitumor mechanism of BBR was conducted.1.Literature review of the broad-spectrum antitumor mechanism of BBRThrough the reptile batch download of the chemical constituents of Traditional Chinese Medicine-tumor-related pharmacological literature in 57 journals,we obtained a summary of targets,pathways and mechanisms of BBR through anti-tumor pharmacological literatures.Use the keyword "berberine[title]and cancer" to search in the PubMed database,download and collect all the retrieved documents for reading and sorting.The collated content is divided into two parts:(1)Summarize the molecular mechanism of BBR antitumor.(2)Analyze all the mechanisms,and summarize the pharmacological literatures that have been verified in vivo and in vitro experiments,mainly related to the study of BBR action and tumors’ multiple proteins and pathways,as well as protein and pathway changing trends.These proteins were mapped to the UniProt database to standardize names,remove duplicates,and finally obtain the source of some data for known targets for BBR anti-tumor.The above contents have been organized and summarized by Office 2007.2.Analysis of pharmacology of Chinese medicine system on broad-spectrum antitumor mechanism of BBRIn the systematic pharmacological study of the mechanism of BBR treatment of tumors,we use the advantages of available data and accurate calculation methods of systematic pharmacology to collect comprehensive targets for drugs and diseases.First,the known targets of BBR were collected from five databases:ChEMBL,Binding DB,PubMed,HIT,STITCH.Among them,for the target source of the STITCH database,we only keep the experimental evidence and the score value is greater than 0.7 as the screening criteria.The prediction method of the data model(bSTDNBI)was used to predict the target of BBR,and only the first 20 targets were retained in the prediction result.Then,further literature mining and network database platforms(THE CANCER GENOME ATLAS,TCGA,ICGC Data Portal)were used to construct a database of various tumor-related targets.Morever,"component-target" network was constructed to decipher the core targets of BBR anti-tumor and "target-function" network to explain the biological processes involved in the target respectively.It conducts enrichment analysis of KEGG pathway to obtain the signal pathway of target participation,and then also uses Cytoscape software to build a"component-target-disease" network and discusses the mechanism in combination with pharmacological literatures.A systematic pharmacological approach(Fisher’s exact)was used to predict the indications for BBR treatment of tumors and visual analysis was performed using the bioinformatics tool Circos Plot.Finally,based on the results of the above predictions and analysis,we selected the top three tumor types for BBR anti-tumor indications to construct a "component-target-disease" sub-network diagram to more specifically illustrate the molecules of BBR for treating tumor mechanism.Results1.Literature review results of BBR broad-spectrum antitumor analysis Completed the mining of 6,000 articles in 57 journals and HIT database,from which the more comprehensive content of berberine antitumor was selected.By categorizing the literature(number>3),8 molecular mechanisms related to BBR and tumors were finally concluded:cell death,cell invasion and metastasis,cell cycle arrest,cell growth,transcription factors,inflammatory factors,angiogenic,chemosensitivity and radio-sensitivity.By further digging the content of the mechanism,28 tumor types were finally obtained:glioblastoma multiforme(GBM),serous ovarian adenocarcinoma(SOC),stomach adenocarcinoma(STAD),colorectal adenocarcinoma(CRAC),breast carcinoma(BRCA),uterine corpus endometrioid(UCEC),medulloblastoma(MBL),acute myeloid leukemia(AML),cutaneous melanoma(CM),lung squamous cell(SQCC),thyroid carcinoma(THCA),lung adenocarcinoma(LUAD),kidney clear cell(CCSK),head and neck squamous(HNSCC),small cell lung(SCLC),lower grade glioma(LGG),bladder carcinoma(BLCA),esophageal carcinoma(EC),prostate adenocarcinoma(PRAD),hepatocarcinoma(HCC),neuroblastoma(NBL),chronic lymphocytic leukemia(CLL),pancreas adenocarcinoma(PAC),multiple myeloma(MM),acute lymphocytic leukemia(ALL),non-small cell lung(NSCLC),diffuse large B-cell lymphoma(DLBCL),and pilocytic astrocytoma(PA)and 238 known targets were acquired.2.Results of systematic pharmacological analysisThrough data mining,a total of 20 predicted targets of BBR and 275 known targets were obtained,and five of the predicted targets were the same as known targets(including CASP3,TP53,CASP9,NFKB1,MAPK1).A total of 289 BBR targets were obtained after deleting duplicates by combining predicted and known targets.A total of 804 significant mutation deletions were collected for tumors:GBM(79),SOC(86),STAD(186),CRAC(116),BRCA(218),UCEC(208),MBL(24),AML(36),CM(250),SQCC(147),THCA(32),LUAD(197),CCSK(118),HNSCC(171),SCLC(61),LGG(50),BLCA(174),EC(102),PRAD(88),HCC(181),NBL(27),CLL(41),PAC(21),MM(24),ALL(12),NSCLC(11),DLBCL(10)and PA(21).After analyzing the "component-target" network,it was concluded that 51 targets are involved in the relevant mechanism of BBR in treating tumors.Functional enrichment results indicate that BBR antitumor is related to eight molecular functions involving 51 targets:cell proliferation,cell death,cell energy metabolism,genetic material replication,immune correlation,gene stability and mutation,angiogenesis,cell invasion and metastasis.Through KEGG pathway enrichment analysis,it was found that these targets were mainly enriched in 56 pathways(P-value<0.05),such as PI3K-Akt(P=2.03E-12),p53(P=2.66E-09),HIF-1(P=3.89E-09),FoxO(P=4.88E-09),VEGF(P=5.72E-07),MAPK(P=2.45E-06),Ras(P=6.42E-06),Jak-STAT(P=9.90E-04),mTOR(P=1.50E-02),AMPK(P=1.88E-02)and NF-kappaB(P=3.97E-02)signal pathway and so on.According to Fisher’ s test,it is concluded that BBR and tumor types HCC(q<1.0 ×10-5;-Log10(q)=19.25),LUAD(q<1.0 × 10-5;-Log10(q)=9.35),BLCA(q<1.0 × 10-5;-Log10(q)=9.31),CM(q<1.0 ×10-5;-Log10(q)=9.29),HNSCC(q<1.0 × 10-5;-Log10(q)=8.52),SQCC(q<1.0 × 10-5;-Log10(q)=6.74),EC(q<1.0 ×10-5;Log10(q)=6.66),UCEC(q<1.0 × 10-5;-Log10(q)=6.52),PRAD(q=1.15 × 10-5;-Log10(q)=6.32),BRCA(q=1.33 × 10-5;-Log10(q)=6.26),CCSK(q=2.30 × 10-5;-Log10(q)=6.02),CLL(q=0.55 × 10-3;-Log10(q)=4.64),STAD(q=1.76 × 10-3;-Log10(q)=4.14),SCLC(q=5.33× 10-3;-Log10(q)=3.65),NBL(q = 1.29 × 10-2;-Log10(q)=3.27),LGG(q=1.67 × 10-2;-Log10(q)=3.16),CRAC(q=3.21 ×10-2;-Log10(q)=2.87),and SOC(q=3.36 × 10-2;-Log10(q)=2.85)are significant and have not been verified by biological experiments,paving the way for future research.ConclusionThis study uses a comprehensive literature review and TCM system pharmacology method to reveal the target,signal pathway,and tumor indications of BBR’s broad-spectrum antitumor effect from the system level.The construction of a multi-level network model goes to a deeper level to illustrate the molecular mechanism of BBR’s antitumor activity.Preliminary clarification of the antitumor mechanism of BBR may be related to its regulation of the co-expression of multiple common mutant genes in tumors.This helps to understand and evaluate the potential advantages of natural drug monomers in the use of "multi-target,multi-function,multi-pathway" in the treatment of complex diseases,and provides clues for the promotion of Chinese medicine system pharmacology in exploring the complex mechanism of anti-cancer of active ingredients of TCM.The ideas can provide data support for the research of drug repositioning,and also make certain theoretical references for clinical research of drugs.