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Single-cell RNA-seq analysis of human tumor ascites dendritic cells and macrophages

ABSTRACT: Single-cell RNA-seq analysis of human tumor ascites dendritic cells and macrophages

PROVIDER: PRJNA473508 | ENA |

REPOSITORIES: ENA

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Project description:Purpose: Malignant ascites is an abnormal accumulation of fluid within the peritoneal cavity, caused by metastasis of several cancer types including colorectal cancer. Cancer cells in ascites reflect poor prognosis and can be a source of recurrence. They also represent a good source of specimens for the study of tumor heterogeneity. Single-cell RNA-sequencing (scRNA-seq) has recently emerged as a powerful tool for exploring and characterizing cellular heterogeneity in both normal tissues and cancers. However, molecular profiles of malignant ascites cells in response to treatment are still poorly understood. Materials and Methods: We have performed scRNA-seq of ascites-derived cells from a colorectal cancer patient to profile and characterize the cellular heterogeneity and different expression hallmarks within the cell populations before and after a chemotherapy treatment. The effect of different single cell preparation protocols, namely, manual and enzymatic methods, on cell viability and gene expression were also assessed. Results: Unbiased clustering of 19,653 cells in total reveals 12 sub-clusters with unique transcriptomic patterns from four major cell types: epithelial cells, myeloid cells, fibroblast, and lymphocytes. Interestingly, the percentages of cells recovered from different cell types appeared to be influenced by the preparation protocols; enzymatic and mechanical separations, with more than 90% reduction in myeloid cell number when enzymatic method was used. Subcluster analysis of epithelial cell populations before and after chemotherapy treatment identified distinct cell clusters with unique transcriptomic profiles. Moreover, there were only three out of 11 epithelial subclones with more than 50% reduction in tumor cell number after treatment. This finding indicated that most clones were resistant to the treatment, which reflected the poor treatment outcome observed in our patient. Conclusions: Overall, our study underscores cellular heterogeneity within malignant ascites and uncovers the gene expression profile of colorectal cancer ascites-derived cells in single-cell resolution. Our findings emphasize the potential benefit of using scRNA-Seq to monitor real-time treatment response in cancer patients.

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Single-cell RNA-seq analysis of human tumor ascites dendritic cells and macrophages

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