Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Agency for Science, Technology and Research · Genome Institute of Singapore · +11 more institutions
Abstract
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more…
Citation impact
- FWCI
- 37.65
- Percentile
- 100%
- References
- 74
Authors
53- IJIgnasius JoanitoCorresponding
Agency for Science, Technology and Research, Genome Institute of Singapore
- PWPratyaksha Wirapati
SIB Swiss Institute of Bioinformatics
- NQNancy Q. Zhao
Agency for Science, Technology and Research, Genome Institute of Singapore
- ZNZahid Nawaz
Agency for Science, Technology and Research, Genome Institute of Singapore
- GHGrace Hui Ting Yeo
Agency for Science, Technology and Research, Genome Institute of Singapore
Topics & keywords
- Biology
- Transcriptome
- Microsatellite instability
- Colorectal cancer
- Cancer
- Cancer research
- Gene
- Microsatellite
- Good health and well-being