Bioinformatics Analysis On Molecular Mechanisms Of Experimental Models For Prostate Cancer:A Comparison Study

Prostate cancer(PCa)is the most common malignant solid tumor in men.Currently,cell line and/or model organisms(i.e,mus musculus)are widely used for PCa study.However,these models cannot present the whole process of PCa evolution exactly.In this paper,we focused on the differences among specimen model,cell line model and mouse model,aiming at providing the theoretical basis on the selection of experimental models for PCa study,which could help promote the translation from theoretical findings to clinical practice.In this paper,we downloaded the microarray mRNA data of these three models from NCBI GEO database.Then we used three methods,i.e,RMA,gcRMA and MAS5,to normalized the raw data by R program,and selected the better results through Signal intensity distribution and histogram for differentially expressed(DE)gene screening using t-test,empirical Bayes and the analysis of variance(ANOVA)method separately.To reduce false positives,genes simultaneously identified by three methods(p-value?0.05)were thought to be differentially expressed for further bioinformatics analyses.The Gene ontology,Kyoto Encyclopedia of Genes and Genomes and Ingenuity Pathway Analysis pathway results showed that the DE genes of specimen model and transgenic mouse model are involved with the components of tumor microenvironment,i.e,extracellular matrix and immune system.The DE genes of xenograft mouse model are only involved with the non immune related components of the tumor microenvironment such as cellular lipid metabolic process and postsynaptic density,whereas the DE genes of cell line model are mostly linked to intracellular components or activities such as organelles and protein processing in endoplasmic reticulum.After analyzing the differences among different experimental models,we concluded that the specimen model is appropriate for studying the incluences of extracellular matrix,angiogenesis,tumor necrosis factors and Nerve cells to PCa.The mouse model is appropriate for studying the influences of cellular lipid metabolic process,postsynaptic density and immune system to PCa.The cell line model is appropriate for studying the influences of intracellular components or activities such as organelles,protein processing in endoplasmic reticulum and metabolic pathways to PCa.