ABSTRACT: In human colon cancer, the malignant component of tumor tissues often contains multiple sub-types of cancer cells, whose transcriptional profiles and surface marker phenotypes correspond to those of the epithelial lineages that are found in normal colonic crypts (e.g., goblet cells, enterocytes, LGR5+ columnar basal cells). Among those various sub-types of malignant cells, those characterized by a surface marker phenotype that is characteristic of epithelial stem/progenitor cells residing at the bottom of colonic crypts (EpCAM+, CD44+, CD166+) are enriched in cells with "cancer stem cell" (CSC) properties, such as self-renewal (i.e., the capacity to sustain the formation of new tumors upon serial xeno-transplantation in immune-deficient animals) and multi-lineage differentiation (i.e., the capacity to sustain the formation of other cell-types, thus reconstituting the heterogeneous population of the parent tumors from which they have been isolated). Cell populations with "cancer stem cell" (CSC) properties are known to be preferentially resistant to several cytotoxic agents used in conventional chemotherapy, but the molecular mechanisms underpinning this property remain poorly understood. In this dataset, we report the analysis by gene-expression microarrays of the transcriptional profile of two sub-populations of human colon cancer cells: 1) cells with a "bottom-of-the-crypt" phenotype (EpCAM+, CD44+, CD166+), which are known to be enriched in "cancer stem cells" (CSCs); and 2) cells with a "top-of-the-crypt" phenotype (EpCAM+, CD44neg, CD166neg), which are known to be non-tumorigenic upon xeno-transplantation in immune-deficient mice. The two populations were purified in parallel by fluorescence activated cell sorting (FACS), starting from solid tumors established by sub-cutaneous (s.c.) engraftment in immune-deficient mice of a patient-derived xenograft (PDX) line representative of a moderately differentiated (G2) primary colon carcinoma. To identify genes whose expression is modulated by in vivo exposure to chemotherapy (and thus potentially involved in the mechanistic regulation of chemo-resistance), we compared the transcriptional profile of cells purified from tumors that were exposed to 4 weeks of in vivo treatment with either irinotecan (CPT-11) or a placebo control (saline solution).
