The transcriptional characterization of different states of cancer stem cells in triple-negative breast cancer

Breast cancer stem cells (BCSCs) are thought to be responsible for tumor initiation, metastasis and relapse. The biomarkers of BCSCs were widely recognized as Aldehyde dehydrogenase positive (ALDH+) and CD24-CD44+. Previous studies showed that tumor populations expressing ALDH+ and CD24-CD44+ represented epithelial-like BCSCs and mesenchymal-like BCSCs, respectively. However, the overlapped population of ALDH+CD24-CD44+, which have greatest tumor-initiating and invasive capacity, is lack of transcriptional characterization. Here we used biomarker combinations ALDH and CD24/CD44 to sort four populations from two triple-negative breast cancer patient-derived xenografts (PDXs), and performed whole-transcriptome sequencing on each population. We systematically compared three states of BCSCs with differentiated tumor cell population, as well as characterization of the ALDH+CD24-CD44+ BCSCs compared with other three populations at the first time. By the pair-comparisons, we identified 90 unique differential expressed genes (DEGs) in ALDH+CD24-CD44+ BCSCs of two PDXs, 32 upregulated and 58 downregulated DEGs. We proposed that P4HA2, PTGR1 and RAB40B were potential prognostic genes in TNBC.