Single Cell Analyses of Cancer Cells Identified Two Regulatorily and Functionally Distinct Categories in Differentially Expressed Genes among Tumor Subclones

Colorectal cancer (CRC) accounts for the second most common cancer in females and third in males worldwide. Due to cell heterogeneity prevailing in most tumor, traditional clinical or CMS classification methods may not be efficient in discovering the differences at transcriptomic and genomic level between cancer cells. To explore the feature of cancer cells and tumor subclones in CRC, we analyzed 101,065 single-cell transcriptomes from 12 colorectal cancer (CRC) patients and 92 single-cell genomes from one of those patients. We found that cancer cells, endothelial cells and stromal cells in the tumor tissue expressed significantly more genes and exhibited stronger cell-cell interactions than their counterparts in the normal tissue. We identified copy number variations (CNVs) in each cancer cell and found a correlation between gene copy number and expression level in cancer cells at single-cell resolution. Analysis of tumor subclones inferred by CNVs showed an accumulation of mutations in each tumor subclone along lineage trajectories. We found that differentially expressed genes (DEGs) between tumor subclones had two populations: DEG_CNV and DEG_reg. DEG_CNV showed a high CNV-expression correlation. Its expression differences depended on the variation of CNV level, enriched in housekeeping genes and cell adhesion associated genes. DEG_reg exhited a low CNV-expression correlation and mainly in low CNV variation regions and regions without CNVs, enriched in cytokine signaling genes. Furthermore, cell-cell communication analyses showed that DEG_CNV tends to involve in cell-cell contact, while DEG_reg tends to involve in secreted signaling, which further supports the notion that DEG_CNV and DEG_reg are two regulatorily and functionally distinct categories.

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