Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis
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发表刊物：Genome Biology
摘要：Background
Patient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types of 3D culture methods for colonic cells, but the similarities and differences between gene expression patterns in different culture media remain largely unexplored.
Results
Here, we establish patient-derived organoids from colorectal cancer patients and perform single-cell RNA-Seq for pairwise samples from seven patients for both organoids and their corresponding tumor and normal tissues in vivo. We find that organoids derived from tumor tissues faithfully recapitulate the main gene expression signatures of cancer cells in vivo. On the other hand, organoids derived from normal tissues exhibited some tumor-like features at the whole transcriptome level but retained normal genomic features, such as CNVs, point mutations, and normal global DNA methylation levels, for both cultural media. More importantly, we show that conditioned medium outperforms chemical-defined medium in long-term culture of tumor epithelial cells. Finally, we mutually exchange the culture medium for the organoids and find that after interchanging the medium, the organoid cells basically maintain the transcriptome characteristics of the original medium.
Conclusions
Our work gives a thorough evaluation of both the cultural conditions and the biological features of organoids of CRC patients.
全部作者：Shuai Gao,Jingyun Li,Lu Wen
第一作者：Rui Wang,Yunuo Mao,Wendong Wang,Xin Zhou,Wei Wang
通讯作者：Wei Fu,Fuchou Tang
是否译文：否