Project description:Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient.
Project description:This study has two components: (1) Human colon adenoma organoids (n=4 patients) were dissociated into single cells. Cells were incubated with a magnetic bead bound to an LGR5 antibody and run through a magnetic column. Magnet bound cells and flow through negative (FTN) cells were obtained. Magnet bound and FTN cells were incubated with an APC-check reagent (which binds to the magnetic bead on the LGR5 antibody) and DAPI, before being sorted by flow cytometry. 3 populations of live (DAPI-) cells were collected: FTN: Flow through negative. LGR5 negative by magnet and by flow cytometry SortedNeg: Magnet bound cells that were negative for LGR5 by flow cytometry SortedPos: Magnet bound cells that were positive for LGR5 by flow cytometry (2) Human colon organoids, as well as the tissue the organoid was derived from and adjcacent normal tissue (from n=19) were also profiled for known colorectal cancer associated mutations using the Qiagen Qiaseq Colorectal Cancer Panel, which provides targeted sequencing information for 71 genes.
Project description:Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.
Project description:Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient. .
This dataset contains all the data available for this study on 2018-08-13.
Project description:Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient.
Project description:Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serves as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer.To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. We also apply whole-exon sequencing, whole genome sequencing and Sanger sequencing to characterize their genomic features accordingly. We found that tumor-derived organoid in vitro in general faithfully maintained the gene expression signatures, gene regulatory network, tumor-microenvironment cross-talk, as well as mutations such as copy number variants and point mutations of tumor cells in vivo. However adjacent normal tissue-derived organoid, despite remaining normal in genomic levels, changed their gene expression profiles drastically and acquired tumor-like gene expression signatures.
Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations. Analysis of chromosomal stability of colonic tissue or in vitro-cultured organoids via comparison with blood cells derived from the same individual.
Project description:Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serve as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer. To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. We also apply whole-exon sequencing, whole genome sequencing and Sanger sequencing to characterize their genomic features accordingly. We found that tumor-derived organoid in vitro in general faithfully maintained the gene expression signatures, gene regulatory network, tumor-microenvironment cross-talk, as well as mutations such as copy number variants and point mutations of tumor cells in vivo. However adjacent normal tissue-derived organoid, despite remaining normal in genomic levels, changed their gene expression profiles drastically and acquired tumor-like gene expression signatures.