Background: Triple negative breast cancer (TNBC) carry poor prognosis in all ethnicities, and patients of African ancestry have a higher incidence of TNBC. We hypothesize that there are distinct signaling pathways active in the mesenchymal (CD44+CD24-) and epithelial-like (ALDH+) cancer stem cells in TNBCs that confer especially aggressive metastatic phenotypes to promote motility and migratory behavior versus self-renewal and proliferative expansion in response to tissue signals, respectively. Here we set out to understand the molecular differences between these cell populations in a multi-ethnic cohort of TNBC using RNA-sequencing technologies.

Methods: Xenografts were grown in NSG2 mice from TNBCs of 2 Ghanaian, 3 African American, and 3 Caucasian patients. Cell populations were Fluorescence-activated cell sorting FACS sorted to subselect and collect ALDH+EpCAM+ (ALDH+) cells and CD24-CD44+EpCAM+ALDH- (CD44+) cells. We extracted RNA from sorted cell populations and performed RNA-sequencing using the Illumina Next Generation Sequencing platform. Differential gene expression was performed using DESeq comparing bulk tumor versus either the FACS sorted ALDH+ or CD44+ fractions, and amongst the stem cell compartment, we compared CD44+ versus ALDH+ cells.

Results: For each comparison pair, genes were clustered into the 10 most up- and down-regulated pathways by GeneGo (unsupervised). Across ethnicities, common themes of affected pathways emerge from binary comparisons. Preliminary analyses demonstrated that expression in bulk tumor versus ALDH+ stem cells indicate upregulation of genes primarily involved in modulation of immune responses, cell adhesion, and androgen receptor expression, among others, whereas pathways involved in regulation of cell protrusions and migration are downregulated. In comparison, CD44+ cells exhibit upregulation of pathways involved in cytoskeletal regulation, Akt, and Notch and downregulation of adhesions through Ephrin signaling, gap junctions, and degradation of beta catenin, among others.

Conclusion: This study delineates patterns of gene expression consistent with a migratory phenotype for CD44+ stem cells that resembles neuronal stem cells and a phenotype of ALDH+ stem cells that is consistent with making epithelial junctions and downregulating RhoGTPases and other gene pathways involved in mesenchymal migration.

Citation Format: Evelyn M. Jiagge, Shukmei Wong, Tahra Luthur, Sean McDermott, Shawn Clouthier, Ahmet Kurdoglu, Jessica Aldrich, Sofia Merajver, David Craig, Jeffery Trent, Lisa Newman, Pat LoRusso, Max Wicha, John Carpten. Distinct pathways differentiate the CD44+ mesenchymal-like from the ALDH+ epithelial-like phenotype of triple negative breast cancer stem cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-59. doi:10.1158/1538-7445.AM2014-LB-59