Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer
Dataset ID: STDS0000216
|
PMID:37327339
Catalog
Dataset information
Contributors
Accessions
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
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
Submission date: 2023-02-22Update date: 2023-06-16
Sample number: 8
Contributors
Long, Jie; Wang, Fei
Accessions
GEO Series Accessions: GSE225857