Colorectal Cancer Stem Cell States Uncovered by Simultaneous Single-Cell Analysis of Transcriptome and Telomeres

Area of Science:

• Oncology
• Cell Biology
• Genomics

Background:

• Cancer stem cells (CSCs) are implicated in tumor progression and drug resistance.
• Definitive CSC features and their heterogeneity remain incompletely understood.
• Colorectal cancer (CRC) presents a significant challenge due to its complex cellular landscape.

Purpose of the Study:

• To systematically characterize cancer stem cells (CSCs) in primary colorectal cancer (CRC).
• To elucidate the relationship between CSCs, cancer epithelial cells (CEPs), and tumor-initiating cells (TICs).
• To identify molecular features and prognostic markers associated with CSCs.

Main Methods:

• Simultaneous measurement of telomere length and transcriptome in single cells.
• In-depth transcriptome profiling using SMART-seq2.
• Validation via high-throughput single-cell RNA sequencing (scRNA-seq) using 10 × Genomics.
• Analysis of chromosome copy number variation (CNV).

Main Results:

• Rare CSCs identified in a dormant state with plasticity towards cancer epithelial cells (CEPs)/tumor-initiating cells (TICs).
• CSCs and CEPs/TICs share prominent signaling pathways (WNT, TGF-β, HIPPO/YAP).
• CSCs exhibit a distinct CNV pattern from normal stem cells, suggesting a phylogenetic link to CEPs.
• CSCs possess shorter telomeres and minimal telomerase activity, correlating with their nonproliferative state.
• Specific CSC gene signatures (NOTUM, SMOC2, BAMBI, PHLDA1, TNFRSF19) correlate with CRC prognosis.

Conclusions:

• This study provides a detailed characterization of CSC heterogeneity in CRC.
• CSCs are linked to CEPs/TICs, challenging conventional definitions.
• Identified CSC-associated genes serve as potential prognostic biomarkers for colorectal cancer.