Profiling of Breast Cancer Stem Cell Types/States Shows the Role of CD44hi/CD24lo-ALDH1hi as an Independent Prognostic Factor After Neoadjuvant Chemotherapy

Multiple markers exist for breast cancer stem cells (CSCs), which are believed to represent the phenotypes of various CSC types and/or states. The relationship between each CSC subpopulation/state and the primary hallmarks of cancer has not been sufficiently clarified. In this study, six CSC markers (CD44hi/CD24lo, CD24, Ep-CAM, ALDH1, CD10, and BMI1) were assessed in a surgical cohort of 73 breast cancer patients. The expression of a single or multiple CSC markers was correlated with clinicopathological parameters, including markers of immune evasion, proliferation, epithelial–mesenchymal transition (EMT), and survival. All CSC phenotypes, except for CD10, correlated with markers indicative of higher proliferation. The CD44hi/CD24lo phenotype correlated with markers of EMT and PD-L1 expression, unlike ALDH1hi. Both Ep-CAMhi and CD24hi breast cancer were associated with indicators of immune evasion, including PD-L1 expression, and the infiltration of FOXP3+ and PD-1+ tumor-infiltrating lymphocytes (TIL). While the CD44hi/CD24lo, Ep-CAMhi, and ALDH1hi phenotypes correlated with shorter overall survival (OS), CD24hi correlated with reduced disease-free survival (DFS). Interestingly, among all tested CSC markers, the CD44hi/CD24lo-ALDH1hi combination phenotype correlated with the worst DFS (HR 2.8, p = 0.014 in univariate/multivariate analysis) and OS (p < 0.001, HR 6.4 in univariate and 5.4 in multivariate analysis). A side-by-side comparison of multiple CSC markers demonstrated the differential linkage of CSC phenotype/state with distinct features of breast cancer. This comparison demonstrates the advantage of the CD44hi/CD24lo-ALDH1hi combination marker for prognostication, especially after neoadjuvant chemotherapy. In the future, distinct markers of CSCs can hopefully be leveraged to trace/monitor different disease characteristics or treatment outcomes.