A novel 12-gene prognostic signature in breast cancer based on the tumor microenvironment

The progression of breast cancer (BC) is highly dependent on the tumor microenvironment. Inflammation, stromal cells, and the immune landscape have been identified as significant drivers of BC in multiple preclinical studies. Therefore, this study aimed to clarify the predictive relevance of stromal and immune cell-associated genes in patients suffering from BC.

We employed the estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) algorithm to calculate the stromal and immunological scores, which were then used to evaluate differentially expressed genes (DEGs) in BC samples using The Cancer Genome Atlas (TCGA) database. Univariate analyses were conducted to identify the DEGs linked to survival in BC patients. Next, the prognostic DEGs (with a log-rank P<0.05) were used to create a risk signature, and the least absolute shrinkage and selection operator (LASSO) regression method was used to analyze and optimize the risk signature. The following formula was used to compute the prognostic risk score values: Risk score = Gene 1 * β1 + Gene 2 * β2 +… Gene n * βn. The median prognostic risk score values were used to divide BC patients into the low-risk (LR) and high-risk (HR) groups. The patient samples of the validation cohort were then assessed using this formula. We used principal component analysis (PCA) to determine the expression patterns of the different patient groups. Gene Set Enrichment Analysis (GSEA) was used to determine whether there were significant variations between the groups in the evaluated gene sets.

The present study revealed that DEGs linked with survival were closely associated with immunological responses. A prognostic signature was constructed that consisted of 12 genes (ASCL1, BHLHE22, C1S, CLEC9A, CST7, EEF1A2, FOLR2, KLRB1, MEOX1, PEX5L, PLA2G2D, and PPP1R16B). According to their survival, BC patients were separated into LR and HR groups using the identified 12-gene signature. The immunological status and immune cell infiltration were observed differently in the LR and HR groups.

Our results provide novel insights into several microenvironment-linked genes that influence survival outcomes in patients with BC, which suggests that these genes could be candidate therapeutic targets.