Sample information for triple-negative breast cancer in GSE176078

Integration and clustering of scRNA-Seq data from triple-negative breast cancer. (a) t-SNE plot of the 9 major cell clusters. (b) t-SNE plot of the 29 minor cell clusters. (c) t-SNE plot of the 12 major cell clusters. (d) The number of ligand-receptor interactions of different major cell clusters in cell-cell communication network, different colors represent different cell clusters and arrows represent ligand-receptor orientation. (e) Heat map showing the average expression of ferroptosis-related genes in different clinicopathological classifications. (f) Heat map showing the average expression of ferroptosis-related genes in different major cell clusters.

Ferroptosis-related subpopulations of T cells in triple-negative breast cancer. (a) t-SNE plot of the 5 identified clusters of T cells. (b) Heat map showing the expression of ferroptosis-related genes (Top 50) in 3 subpopulations of T cells. (c) Demonstration of the proportion of clusters of T cells in ferroptosis-related subpopulations. (d) Pseudotime trajectories showing the developmental time course of T cells. (e) Pseudotime trajectories of the 5 identified clusters of T cells. (f) Pseudotime trajectories of ferroptosis-related subpopulations of T cells. (g) Heat map showing the average expression of signature genes associated with 8 functions in 15 subpopulations of T-cells. (h) Network diagram of the cell-cell communication between cancer epithelial cells and T cells. (i) Heat map for differential analysis of transcription factors activity.

Ferroptosis-related subpopulations of macrophages in triple-negative breast cancer. (a) t-SNE plot of 2 ferroptosis-related subpopulations of macrophages. (b) Pseudotime trajectories showing the developmental time course of macrophages. (c) Pseudotime trajectories of 2 ferroptosis-related subpopulations of macrophages. (d) Heat map showing the average expression of ferroptosis-related genes in 2 subpopulations of macrophages. (e) t-SNE plot showing the expression patterns of marker genes in M_C2. (f) t-SNE plot showing the expression patterns of marker genes in M_C1. (g) t-SNE plot showing the enrichment score of the TREM2+MAC in each cell. (h) t-SNE plot showing the enrichment score of the FOLR2+MAC in each cell. (i) Bubble plot showing the correlation of enrichment score between TREM2+MAC and FOLR2+MAC. (j) Network diagram of the cell-cell communication between cancer epithelial cells and ferroptosis-related subpopulations of macrophages.

Prognostic differences in triple-negative breast cancer with ferroptosis-related subpopulations. (a) LASSO regression of 23 ferroptosis-related genes. (b) Cross-validation for optimizing the parameter in LASSO regression. (c) Demonstration of regression coefficients corresponding to 23 genes. (d) Graph showing risk scores for all samples. (e) Scatterplot showing recurrence-free survival for all samples. (f) Heat map showing the average expression of 23 genes in the low- and high-risk groups. (g) Kaplan–Meier curves of survival analysis in the low- and high-risk groups. (h) Receiver operating characteristic curves for predicting the recurrence-free survival at 3, 4 and 5 years in training set. (i) Receiver operating characteristic curves for predicting the recurrence-free survival at 3, 4 and 5 years in external validation set.

Analysis of independent prognostic factors for triple-negative breast cancer patients. (a) The forest plot showing the results of univariate and multivariate COX regression analysis of risk score, age, grade, and stage in the GSE25066 database. (b) The forest plot showing the results of univariate and multivariate COX regression analysis of risk score, grade, and stage in the GSE86166 database.

Analysis of immune microenvironment in low- and high-risk groups. (a-d) Correlation of the risk score with the ImmuneScore, StromalScore, ESTIMATEScore, and TumorPurity. (e) Difference of ImmuneScore, StromalScore, and ESTIMATEScore in low- and high-risk groups. (f) Difference of TumorPurity in low- and high-risk groups. (g) Difference of immune infiltration score between low- and high-risk groups calculated by CIBERSORT. * P < 0.05, ** P < 0.01, ns: p>0.05.

Analysis of immune microenvironment in low- and high-risk groups. (a) Box plot showing differences of IC50 for drugs negatively associated with risk scores in different groups. (b) Box plot showing differences of IC50 for drugs positively associated with risk scores in different groups. (c) Box plot showing differences of TIDE scores in different groups. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, ns: p>0.05.