Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer(Dataset ID: STDS0000216)

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PMID: 37327339
Summary
Visualization
Data
Analysis results
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Dataset information
Summary:
In this study, we comprehensively charted the cellular landscape of colorectal cancer (CRC) and well-matched liver metastatic CRC using single-cell and spatial transcriptome RNA sequencing. We generated 41892 CD45- non-immune cells and 196473 CD45+ immune cells from 27 samples of 6 CRC patients, and found that CD8_CXCL13 and CD4_CXCL13 subsets increased significantly in liver metastatic samples that exhibited high proliferation ability and tumor-activating characterization, contributing to better prognosis of patients. Distinct fibroblast profiles were observed in primary and liver metastatic tumors. The F3+ fibroblasts enriched in primary tumors contributed to worse overall survival by expressing pro-tumor factors. However, the MCAM+ fibroblasts enriched in liver metastatic tumors might promote generation of CD8_CXCL13 cells through Notch signaling. In summary, we extensively analyzed the transcriptional differences of cell atlas between primary and liver metastatic tumors of CRC by single-cell and spatial transcriptome RNA sequencing, providing different dimensions of the development of liver metastasis in CRC
Overall design:
For single-cell RNA sequencing, 6 CRC patients with liver metastasis were enrolled after written informed consent was obtained. Primary CC, CN (at least 2 cm from matched tumors), LM, LN (at least 2 cm from matched tumors) and PB of the enrolled patients were collected following resection. All the patients received preoperative chemotherapy and/or radiotherapy. For spatial transcriptome sequencing, formalin-fixed paraffin embedded (FFPE) tissues of 6 CRC patients were prepared. Submitter states: Raw data are not included due to patient privacy concerns, which are deposited in the CNGB Nucleotide Sequence Archive (CNSA: https://db.cngb.org/cnsa; accession number: CNP0002540 for single cell RNA sequencing data, and CNP0003321 for spatial transcriptome RNA sequencing data)
Technology:
scRNA,10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Homo sapiens(hg38)
Tissues:
Colon,Liver
Organ parts:
Colorectal tissue,Liver tissue
Submission date: 2023-02-22Update date: 2023-06-16
Sample number: 8
DOI: To be continue
Contributors
Long, Jie,Wang, Fei
Accessions
GEO Series Accessions: GSE225857
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Long, Jie,Wang, Fei. Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer[DS/OL]. STOmicsDB, 2023[2023-02-22]. https://db.cngb.org/stomics/datasets/STDS0000216/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Wang, Fei et al. “Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer.” Science advances vol. 9,24 (2023): eadf5464. doi:10.1126/sciadv.adf5464