Deep transcriptional profiling of the two cancer stem cell populations present in the SW480 cell line as presented in "Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments"  [bulk RNA-seq]
Tumor heterogeneity derives from diverse populations of cancer cells that contribute unique properties to the microenvironment and tumor progression. While multiple classification systems have been developed to define tumor subtypes in colorectal cancer (CRC), the lack of single cell resolution has prohibited a better understanding of how these distinct cancer cell subtypes influence the overall tumor phenotype. Here were report that two cancer stem cell subtypes that are oncogenic versions of the intestinal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations, are commonly co-present in human CRC. We develop subtype-specific xenograft models utilizing a heterogeneous patient cell line (SW480) that contains CBCs and RSCs, and we define their tumor microenvironments at high resolution via single cell RNA sequencing. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, immune-suppressive, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization. Overall design: Two subtype populations from the human colorectal cancer cell line SW480 (SW480-CBC and SW480-RSC) were isolated by Fluorescence-activated cell sorting (FACS) using the cell surface receptor ROBO1 (clone: MAB7118). Five replicates each of ROBO1pos (SW480-CBC) and ROBO1neg (SW480-RSC) cells were obtained and directly submitted for bulk RNA-sequencing. We then performed DESeq2 analysis to compare gene expression in each subtype.