1. Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids
- Author
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Tara Srinivasan, David S. Hsu, Xiling Shen, Steven M. Lipkin, Christopher Lin, Kuei-Ling Tung, Kai-Yuan Chen, and Ziyang Gao
- Subjects
0301 basic medicine ,Colorectal cancer ,Cell Culture Techniques ,Cancer ,medicine.disease ,Article ,Oxaliplatin ,Organoids ,Transcriptome ,03 medical and health sciences ,030104 developmental biology ,Single-cell analysis ,Cell culture ,medicine ,Organoid ,Cancer research ,Humans ,Single-Cell Analysis ,Stem cell ,Colorectal Neoplasms ,medicine.drug - Abstract
Organoids are three-dimensional cell cultures that mimic organ functions and structures. The organoid model has been developed as a versatile in vitro platform for stem cell biology and diseases modeling. Tumor organoids are shown to share ~ 90% of genetic mutations with biopsies from same patients. However, it’s not clear whether tumor organoids recapitulate the cellular heterogeneity observed in patient tumors. Here, we used single-cell RNA-Seq to investigate the transcriptomics of tumor organoids derived from human colorectal tumors, and applied machine learning methods to unbiasedly cluster subtypes in tumor organoids. Computational analysis reveals cancer heterogeneity sustained in tumor organoids, and the subtypes in organoids displayed high diversity. Furthermore, we treated the tumor organoids with a first-line cancer drug, Oxaliplatin, and investigated drug response in single-cell scale. Diversity of tumor cell populations in organoids were significantly perturbed by drug treatment. Single-cell analysis detected the depletion of chemosensitive subgroups and emergence of new drug tolerant subgroups after drug treatment. Our study suggests that the organoid model is capable of recapitulating clinical heterogeneity and its evolution in response to chemotherapy.
- Published
- 2018