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Updated: Mar 22, 2026
High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
Published on: May 21, 2020
Characterization of sphere-forming HCT116 clones by whole RNA sequencing
Eunkyung Chung1, Inkyung Oh2, Kil Yeon Lee2
1R&D Center, L&K Biomed Co. Ltd., Seoul, Korea.
Purpose:
To determine CD133(+) cells defined as cancer stem cells (CSCs) in colon cancer, we examined whether CD133(+) clones in HCT116 demonstrate known features of CSCs like sphere-forming ability, chemodrug-resistance, and metastatic potential.
Methods:
Magnetic cell isolation and cell separation demonstrated that <1% of HCT116 cells expressed CD133, with the remaining cells being CD133(-) clones. In colon cancer cells, radioresistance is also considered a CSC characteristic. We performed clonogenic assay using 0.4 Gy γ-irradiation.
Results:
Interestingly, there were no differences between HCT116 parental and HCT116 CD133(+) clones when the cells comprised 0.5% of the total cells, and CD133(-) clone demonstrated radiosensitive changes compared with parental and CD133(+) clones. Comparing gene expression profiles between sphere-forming and nonforming culture conditions of HCT116 subclones by whole RNA sequencing failed to obtain specific genes expressed in CD133(+) clones.
Conclusion:
Despite no differences of gene expression profiles in monolayer attached culture conditions of each clone, sphere-forming conditions of whole HCT116 subclones, parental, CD133(+), and CD133(-) increased 1,761 coding genes and downregulated 1,384 genes related to CSCs self-renewal and survival. Thus, spheroid cultures of HCT116 cells could be useful to expand colorectal CSCs rather than clonal expansion depending on CD133 expressions.
