Integrating single-cell and spatial transcriptomics reveals endoplasmic reticulum stress-related CAF subpopulations associated with chordoma progression
| Title | Integrating single-cell and spatial transcriptomics reveals endoplasmic reticulum stress-related CAF subpopulations associated with chordoma progression |
|---|---|
| Description | The present study depicted the cancer-associated fibroblasts (CAFs) landscape of chordoma using transcriptomic sequencing and QIF approaches. We identified a unique cluster of CAF in recurrent tumors that highly expressed hypoxic genes and was functionally enriched in endoplasmic reticulum stress (ERS). The spatial transcriptomics data confirmed the existence of ERS-CAFs subtype and revealed that this cluster displayed the highest probability of proximity to tumor cells. The bulk RNA-seq and multiplexed quantitative immunofluorescence data indicated the crucial roles of ERS-CAFs in the progression of chordoma. Moreover, the ERS-CAF subpopulation contributed to chordoma progression possibly via direct crosstalk with tumor cells. These data suggested the possibility of targeting ERS-CAF for the treatment of chordoma. |
| Organism | Homo sapiens |
| Data Type | Expression Profiling by NGS |
| Data Accessibility | Controlled-access |
| BioProject | PRJCA017530 |
| Release Date | 2023-09-14 |
| Submitter | Mingxiang Zou (zoumx_spine@usc.edu.cn) |
| Organization | First affiliated hospital of university of South China |
| Submission Date | 2023-06-08 |
The data cannot be downloaded as it has not yet been registered in the Human Genetic Resource Management Platform of MOST.
| File ID | File Title | Number/Samples | File Type | File Size | File Suffix | Download Times | Download |
|---|---|---|---|---|---|---|---|
| OMIX004303-01 | bulk RNA-seq | 126 | Expression Profiling by NGS | 40.4 MB | txt | 0 | Unavailable |
| OMIX004303-02 | singlecell | 9 | Expression Profiling by NGS | 564.4 MB | zip | 0 | Unavailable |
| OMIX004303-03 | Spatial | 2 | Expression Profiling by NGS | 113.0 MB | zip | 0 | Unavailable |
| OMIX004303-04 | Spatial-PSC_1 | 1 | Expression Profiling by NGS | 35.9 MB | zip | 0 | Unavailable |