Gene expression analysis in long- and short-term tamoxifen/fulvestrant-induced T47D breast cancer cell lines

Both long- and short-term treatments with endocrine agents sensitize ER+ breast cancer cells to ferroptosis inducers, indicating a non-mutational sensitization mechanism. To delve into the molecular underpinnings of ferroptosis sensitization in breast cancer, we performed gene array analyses on the parental T47D cell line and T47D cell lines subjected to long- and short-term tamoxifen/fulvestrant exposure. The differentially expressed genes between T47D cells after 6 days induction with 4-hydroxytamoxifen or fulvestrant and parental cells were identified using the DESeq2 R package. a total of 906 and 1969 DEGs (log FC >1, FDR <0.05) were obtained, which we call gene set 1 and 2, respectively. The AUC metrics of 40 breast cancer cell lines treated with the three most classical GPX4 targeting small-molecules RSL3, ML162 and ML210 were obtained from the CTRP database. Spearman's correlation analysis of these cell-line gene-expression data from the CCLE portal and their corresponding AUC data of the three drugs were calculated. The genes with correlation coefficient < -0.25 were described as gene set 3 and have a total of 1427 genes. Fifty-five genes intersecting among these 3 gene pools were proposed to represent the gene set most relevant to ferroptosis sensitivity in breast cancer. Then, we introduce a 55-gene signature score (FERscore) by single-sample gene-set enrichment analysis algorithm, tailored to assess ferroptosis susceptibility in breast cancer. We also validated the FERscore in our T47D-TamR and T47D-FulvR cell lines.