Evolution and heterogeneity of non-hereditary colorectal cancer revealed by single-cell exome sequencing

Abstract

Recently single-cell whole-exome sequencing (scWES) has deeply expanded and sharpened our knowledge of cancer evolution and subclonality. Herein, with scWES and matched bulk whole-exome sequencing (bulk WES) on two colorectal cancer (CRC) patients with normal or adenomatous polyps, we found that both the adenoma and cancer were of monoclonal origin, and both shared partial mutations in the same signaling pathways, but each showed a specific spectrum of heterogeneous somatic mutations. In addition, the adenoma and cancer further developed intratumor heterogeneity with the accumulation of nonrandom somatic mutations specifically in GPCR, PI3K-Akt and FGFR signaling pathways. We identified novel driver mutations that developed during adenoma and cancer evolution, particularly in OR1B1 (GPCR signaling pathway) for adenoma evolution, and LAMA1 (PI3K-Akt signaling pathway) and ADCY3 (FGFR signaling pathway) for CRC evolution. In summary, we demonstrated that both colorectal adenoma and CRC are monoclonal in origin, and the CRCs further diversified into different subclones with heterogeneous mutation profiles accumulating in GPCR, PI3K-Akt and FGFR signaling pathways. ScWES provides evidence for the importance of mutations in certain pathways that would not be as apparent from bulk sequencing of tumors, and can potentially establish whether specific mutations are mutually exclusive or occur sequentially in the same subclone of cells.

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Abbreviations

CRC:

colorectal cancer

CAN:

copy number alteration

GPCR:

G-protein coupled receptors

PCA:

principal components analysis

scWES:

single-cell whole-exome sequencing

bulk WES:

bulk whole-exome sequencing.

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Acknowledgements

We thank Dr Sherman Weissman for his critical comments on the manuscript. We are indebted to all the individuals who consented to participate in this study. ScWES and bulk WES was performed at the Genseeq Company. The sequenced data was analyzed by Yunkang Biotechnology Co. Ltd. This work was supported by Natural Science Foundation of Zhejiang Province (LZ15H220001 and LY14H160005), Zhejiang Medical and Health Ministry Training Program (2015PYA009), The Science and Technology of Hangzhou Medical and Health Project (2012ZD001), National Natural Science Foundation of China (CN; 81402529).

Author contributions

SW and HW conceived the study. QH and HW performed the experiments under the supervision of SW, ZH, B-GJ and HW. YL, SL, HZ, JY and ZJ prepared the reagents and samples. HW analyzed the data. HW prepared the manuscript. SW, B-GJ, XP and X-YZ reviewed the results and the discussion of the manuscript. All the authors read and approved the manuscript.

Author information

Correspondence to X Pan or B-G Ju or S Wu.

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The authors declare no conflict of interest.

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Supplementary Information accompanies this paper on the Oncogene website

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