Single cell gene expression profiling of the SW620 colorectal cell line

Intra-tumor heterogeneity, i.e. the presence of diverse cell types and subpopulations within tumors, presents a significant obstacle in cancer treatment due to its negative consequences for resistance to therapy and disease recurrence. However, the mechanisms which underlie intra-tumor heterogeneity and result in the plethora of different cancer cells within a single lesion remain poorly understood. Here, we leverage the SW480 and SW620 cell lines as a model system to investigate the molecular and functional diversity of colon cancer cells. Through a combination of fluorescence activated cell sorting (FACS) analysis and transcriptomic profiling, we identify three distinct subpopulations, namely resident cancer stem cells (rCSCs), migratory CSCs (mCSCs), and high-relapse cells (HRCs). These subpopulations show varying Wnt signaling levels and gene expression profiles mirroring their stem-like properties. Examination of publicly available spatial transcriptomic data confirms the presence of these subpopulations in patient-derived cancers and reveals their distinct spatial distribution relative to the tumor microenvironment. Overall design: Cell lines were cultured in DMEM medium with FCS. After FACS sorting of the bulk, live population, single cell gene expression profiling was performed according to droplet based sequencing (10X Genomics)