Advances and Applications in Bioinformatics and Chemistry (Nov 2024)
LAMP5, One of Four Genes Related to Oxidative Stress That Predict Biochemical Recurrence-Free Survival, Promotes Proliferation and Invasion in Prostate Cancer
Abstract
Peiqiang Wu,* Jianlei Zhang,* Li Guo, Bohong Chen, Lingxiao Xiong, Yuefeng Du Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, 710061, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yuefeng Du, Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, 710061, People’s Republic of China, Email [email protected]: Prostate cancer (PCa) development largely depends on increased levels of oxidative stress (OS) and a deficient anti-oxidative system. Identifying genes associated with oxidative stress is critical in order to direct PCa therapy and future research.Methods: The TCGA and GTEx databases provided the bulk RNA-seq data, and the GEO database provided the single-cell data GSE141445. Utilizing reactive oxygen species (ROS) markers, single-cell analysis and cluster identification related to oxidative stress were conducted using the R packages “Seurat” and “AUCell”. The differentially expressed genes (DEGs) in normal and PCa samples were identified with the “limma” R package. LASSO regression analysis was used to build a recurrence score (RS) model. The R packages “maftools” and the CIBERSORT method were employed to explore genetic mutation and the infiltrating immune cell, respectively. LAMP5 was chosen for further investigation after random forest analysis was performed.Results: The RS model for PCa was found to be an independent predictor. The tumor immune microenvironment and the frequency of gene mutations differed significantly between the high- and low-risk score groups. Further investigation revealed that downregulation of LAMP5 in PC-3 and DU145 cell lines suppressed cell proliferation and invasion, as demonstrated by the results of in vitro experiments.Conclusion: We successfully created a robust RS model. The result of the study indicates that LAMP5 could contribute to cell proliferation and invasion in PCa.Keywords: prostate cancer, oxidative stress, single-cell analysis, recurrence score model, LAMP5
