Drug Target Analysis And Drug Discovery Of Triple-negative Breast Cancer Via Bioinformatics Methods

Triple negative breast cancer(TNBC)is a highly heterogeneous malignant tumor.Currently,the treatment to TNBC is mostly chemotherapy.No effective target therapy has been developed.It is urgent to find new drug targets and develop new drugs.In this dissertation,we used bioinformatics methods to analyze the existing high-throughput data and clinical information of the transcriptome of the TNBC,and tried to discover new therapeutic targets and therapeutic drugs,in order to provide clues for the treatment of TNBC.We also conducted experimental validation.The results suggest that the gene and the drug are potential drug target and the drug for TNBC treatment.This dissertation is composed of two parts.The first part discusses the target analysis of TNBC using BCIP database.The second part discusses the drug analysis of TNBC by drug repurposing method using CMap database.The first part analyzes the potential target of TNBC using bioinformatics methods.We performed a pan-cancer analysis of the transcriptome data of 13 tumor types of TCGA and screened 92 pan-cancer genes.These 92 genes are over expressed across multiple types of tumors.To explore the importance of the 92 genes in TNBC,we conducted the comprehensive analysis of each gene via BCIP.BCIP is established by us for the purpose of facilitate evaluating the importance of genes in breast cancer.We collected gene expression profiles and clinical information from almost 10000 samples of breast cancer..All the data are subjected to unified and strict quality control.BCIP also provides rich clinical information including survival,drug responses of treatment,ER/RP/HER2 expression and other clinical data.Among the 92 pan-cancer genes,FAM64 A is significantly over expressed in TNBC and is associated with survival,metastasis and drug responses of neoadjuvant chemotherapy.In the subsequent experimental verification,knockdown of FAM64 A significantly inhibited the proliferation of TNBC cell lines.Therefore,FAM64 A may play a key role in the development of TNBC and has the potential to be a new drug target.The second part discovers potential TNBC drugs based on drug repurposing strategy.At present,TNBC lacks effective therapeutic drugs and is subjected to mainly chemotherapy in clinic.The research and development of new anti-tumor drugs against TNBC are quite costly and the failure rate is high.Moreover,the heterogeneity of TNBC is very strong.So far,driver genes are found only in a minor of TNBC patients.For example,the widely known driver genes BRCA1/2 are only found mutated in <10% of TNBCs.There is still a long way to go to find TNBC new drugs from the aspect of genome.This study intends to discover possible therapeutic drugs using the transcriptome as a new breakthrough.CMap is a database of drug response expression profiles designed and developed by the Broad Institute of MIT and Harvard University.It contains gene expression profiles of more than 1,300 small-molecule drugs added to 5 tumor cell lines.Changes in gene expression profiles before and after drug treatment are regarded as drug expression signature.Since its publication,CMap has been widely used and has become one of the most effective tools for drug repositioning.Combining CMap,effective TNBC drug expressionsignature,TNBC expression profiles,and adjacent normal tissue expression profiles reported in previous studies,we search for possible TNBC drugs by drug repurposing method.We first focused on THZ1,a smallmolecule drug that has recently been reported to be effective in both TNBC cell experiments and animal experiments.THZ1 expression signature was calculated from the transcriptome data of THZ1-treated TNBC cells.Drugs with similar expression signature were selected by calculations of THZ1 signature and >1300 drug signatures in CMap.At the same time,we also adopted the idea of reversing the tumor transcriptome to normal transcriptome.We first calculated TNBC expression signature using TNBC tumor and adjacent normal transcriptome data.Then we compared TNBC signature with drug signatures in CMap and selected the drugs with adverse effects.GW8510 ranks the first place in both strategies,which makes it a possible drug for TNBC.To verify this finding,we further conducted cell experiments.In the proliferation and apoptosis experiments of breast cancer cells,GW8510 showed killing effect on TNBC cells.Our study provided a clue for new therapeutic drug for TNBC treatment.Based on the bioinformatics method,we screened the new potential target gene FAM64 A of TNBC and the new potential therapeutic drug GW8510,and we conducted biological experiments to verify our findings preliminarily,which provided clues for TNBC drug research.