" Single-cell gene expression in tissues and tumors "

Adult tissue-specific stem cells are small populations of cells that reside in key locations within each tissue and are responsible for its maintenance and regeneration through carefully controlled proliferation and differentiation. In cancer, where the regeneration mechanism has been distorted, the tumors are maintained and regenerated by a small sub-population of cancer stem cells that are most likely responsible for relapse and metastasis. However, with contemporary technologies, it is challenging to locate and study the stem cells, which are a small minority.

In order to study the cellular composition of colon epithelial tissues and tumors we used a combination of flow cytometry and microfluidic single cell qPCR to measure the expression of up to 96 genes simultaneously in hundreds of individual cells. This provided us with a single cell genomic "dissection" of primary epithelial tissues and tumors from both human and mouse colon.

We find that human colon cancer tissues contain distinct cell populations whose transcriptional identities mirror those of the different cellular lineages of normal colon. However, some populations were consistently absent in colon tumors and xenografts, specifically, the population of differentiated mature enterocytes expressing the gene SLC26a3 (also known as DRA or "Down-Regulated in Adenoma"), which is a membrane protein responsible for Chloride reabsorption in the colon. In the mouse colon we find a novel sub-population of goblet cells in the crypt base that overexpress cKit, Dll1, Dll4 (Notch ligand), and epidermal growth factor (EGF). These crypt-base goblet cells are adjacent to Lgr5+ cells and provide several crucial factors for crypt homeostasis and Lgr5+ stem cell proliferation, similar to Paneth cells in the small intestine. Finally, we show that contrary to tissues and tumors, gene expression heterogeneity in cell lines originates mainly from cell size and cell cycle phase.