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Evaluation of Colorectal Cancer Organoids by Single-Cell RNA-Seq

Written by Charlotte Harrison, Science Writer

Organoids, which are cell-derived 3D culture system, are emerging as a powerful model for studying the molecular mechanisms of cancers. A study in Genome Biology shows that organoids derived from colorectal cancers retain the genomic and epigenomic features of the colorectal tumour. This indicates that colorectal cancer organoids represent an excellent model system.

Organoid sequencing

The authors established organoids from seven patients with colorectal cancer. They then performed single-cell RNA-seq on cells from the organoid, the corresponding tumour, and normal tissues. They also used whole-exome sequencing, whole-genome sequencing, whole-genome bisulfite sequencing, and Sanger sequencing to characterize the genomic and epigenomic features of the cells.

Reassuringly, they found that the tumour-derived organoids maintained the gene expression signatures, gene regulatory networks, DNA methylation levels of the tumour. The same genomic mutations, such as copy number variations and point mutations, were also conserved.

Organoids derived from adjacent normal tissue retained normal genomic features, such as copy-number variations, point mutations, and normal global DNA methylation levels. However, normal-tissue organoids still bore some tumour-like gene expression patterns. This suggests that the culture media had a different impact on gene expression than in vivo culture systems. As such, caution is warranted when using organoids to study the transcriptome of normal colonic cells.

Culture media comparison

The researchers also tested the effect of two types of commonly used culture media on the gene expression patterns in tumour organoids and normal-tissue organoids. These media were a chemically defined medium and a conditioned medium, which is a culture medium that has been exposed to cells and their secretory factors.

Organoids that were grown in both media retained the genomic and epigenetic features of the tumour. However, the conditioned medium was better than the chemically defined one for the long-term culture of tumour-derived organoids. Namely, the conditioned medium better reflected differences in the level of differentiation between tumour cells and normal cells. Therefore, the authors highlighted that if a chemically defined medium is used for long-term culture of organoids, normal cells will likely replace tumour cells.

Overall, this study adds to the weight of evidence indicating that organoids hold great promise as models for the study of cancer and other diseases.

Image Credit: Canva