Copy Number Variation and Transcription Regulation of Genes and Immune Microenvironment of Tumor Affect the Stemness of Prostate Cancer Cell

Abstract

Background: Prostate cancer stem cells (pCSC) play an important role in tumor metastasis through multiple pathways. From gene, protein to microenvironment, there are many factors affecting the cell stemness of prostate cancer (PCa). However, the effective factors affecting the stemness of prostate cancer cells are still unclear.Methods: Based on the transcription data of prostate cancer in the TCGA database, WGCNA (Weighted Gene Co-expression Network Analysis) and stemness scores were used to find important stemness gene module. According to ATAC-seq and genomic data, analyze their relationship with stemness. The interaction of stemness genes was analyzed with STRING (functional protein association networks) database. Furthermore, based on the immune microenvironment score, the relationship between immune and stemness was analyzed.Results: The most important stemness gene module in prostate cancer was obtained with WGCNA method; then a positive correlation between the gene CNVs (Copy Number Variants) of the most important stemness gene module and PCa stemness was found, as well as a positive correlation between the gene CNVs and Gleason score of PCa was also drug out. Further, the key transcriptional regulators of the most important stemness genes in PCa were obtained. In addition, it's found that immune cells, especially CD8+T cells and M1 macrophages, suppressed the stemness of PCa cells. Finally, by analyzing the protein interactions and the relationship between genes and immune cells, we found that interaction of the proteins of the most important stemness genes module and the relationship between these genes and immune cells of microenvironment of PCa were all important in affecting the stemness of PCa cells.Conclusions: By analyzing multi-omics data of clinical specimen, we got the most important stemness genes and their important transcriptional regulators in PCa; and further mining analysis showed that the stemness of PCa cells is positive regulated by the CNVs and the interaction of the proteins of the most important stemness genes, and negatively regulated by the immune cells of the microenvironment of prostate cancer.