Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis

• DOI: 10.1186/s13059-022-02673-3
• Publication Date: 2022-04-28T09:03:24Z
• Authors: Rui Wang; Yunuo Mao; Wendong Wang; Xin Zhou; Wei Wang; Shuai Gao; Jingyun Li; Lu Wen; Wei Fu; Fuchou Tang
• Keywords: Organoid; 0301 basic medicine; Cancer Research; Cell biology; QH301-705.5; Biomedical Engineering; Cancer cell; Cancer research; QH426-470; FOS: Medical engineering; Gene; Computational biology; 03 medical and health sciences; Engineering; Cancer Genomics; Biochemistry, Genetics and Molecular Biology; Health Sciences; Genetics; Humans; Biology (General); Biology; Cancer; DNA methylation; 3D Bioprinting Technology; Sequence Analysis, RNA; Organoid Models; Research; Organ-on-a-Chip; Life Sciences; DNA Methylation; Colorectal cancer; Genomic Landscape of Cancer and Mutational Signatures; 3. Good health; Organoids; Oncology; Cancer Stem Cells and Tumor Metastasis; FOS: Biological sciences; Physical Sciences; Medicine; Gene expression; Colorectal Neoplasms; Transcriptome

AbstractBackgroundPatient-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.ResultsHere, 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.ConclusionsOur work gives a thorough evaluation of both the cultural conditions and the biological features of organoids of CRC patients.