In Computational and mathematical methods in medicine
Background : Breast cancer is a big threat to the women across the world with substantial morbidity and mortality. The pressing matter of our study is to establish a prognostic gene model for breast cancer based on mRNAsi for predicting patient's prognostic survival.
Methods : From The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we downloaded the expression profiles of genes in breast cancer. On the basis of one-class logistic regression (OCLR) machine learning algorithm, mRNAsi of samples was calculated. Kaplan-Meier (K-M) and Kruskal-Wallis (K-W) tests were utilized for the assessment of the connection between mRNAsi and clinicopathological variables of the samples. As for the analysis on the correlation between mRNAsi and immune infiltration, ESTIMATE combined with Spearman test was employed. The weighted gene coexpression network analysis (WGCNA) network was established by utilizing the differentially expressed genes in breast cancer, and the target module with the most significant correlation with mRNAsi was screened. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to figure out the biological functions of the target module. As for the construction of the prognostic model, univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses were performed on genes in the module. The single sample gene set enrichment analysis (ssGSEA) and tumor mutational burden were employed for the analysis on immune infiltration and gene mutations in the high- and low-risk groups. As for the analysis on whether this model had the prognostic value, the nomogram and calibration curves of risk scores and clinical characteristics were drawn.
Results : Nine mRNAsi-related genes (CFB, MAL2, PSME2, MRPL13, HMGB3, DCTPP1, SHCBP1, SLC35A2, and EVA1B) comprised the prognostic model. According to the results of ssGSEA and gene mutation analysis, differences were shown in immune cell infiltration and gene mutation frequency between the high- and low-risk groups.
Conclusion : Nine mRNAsi-related genes screened in our research can be considered as the biomarkers to predict breast cancer patients' prognoses, and this model has a potential relationship with individual somatic gene mutations and immune regulation. This study can offer new insight into the development of diagnostic and clinical treatment strategies for breast cancer.
Zhao Xugui, Lin Jianqing