Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma (Digital Spatial Profiling)(Dataset ID: STDS0000167)

0
|
227
|
396
|
PMID: 35986012
Summary
Visualization
Data
Analysis results
Related
Sample
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
To progress, tumors need to invade the surrounding tissues. However, the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insights for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas (BCCs), we define the cellular contributors of the invasive front. In the invasive niche, tumor cells harbor a collective migration phenotype, supported by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts (CAFs) with extracellular matrix-remodeling features, as required to support collective migration. Moreover, while tumor cells specifically express Activin A, we find Activin A-induced gene signature enrichment in adjacent CAFs subpopulations, further supporting their biological crosstalk. Altogether, our data identify the subpopulations and their transcriptional reprogramming contributing to the spatial organization of the BCC invasive niche. They also bring the proof-of-concept for integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop therapeutic targeting.
Overall design:
Total 95 areas of interest from 12 basal cell carcinomas were sequenced using Digital Spatial Profiling (DSP) using GeoMX Nanostring, with the Cancer Transcriptome Altas (1812 genes)
Technology:
GeoMx DSP
Platform:
Cancer Transcriptomic Atlas, Human, 1812 genes, Nanostring GeoMx Digital Spatial Profiling (DSP) Pla
Species:
Homo sapiens(hg38)
Tissues:
Basal cell
Organ parts:
Basal cell carcinoma
Disease:
Basal cell carcinoma
Submission date: 2022-08-05Update date: 2022-08-29
Sample number: 94
DOI: To be continue
Contributors
Yerly L,Tissot S,Kuonen F
Accessions
GEO Series Accessions: GSE210648
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] Yerly L,Tissot S,Kuonen F. Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma (Digital Spatial Profiling)[DS/OL]. STOmicsDB, 2022[2022-08-05]. https://db.cngb.org/stomics/datasets/STDS0000167/. 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: Yerly, Laura et al. “Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma.” Nature communications vol. 13,1 4897. 20 Aug. 2022, doi:10.1038/s41467-022-32670-w