Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment(Dataset ID: STDS0000153)

2,900

5,569

Spots: 25,529

Genes: 41,797

Catalog

Dataset information

Contributors

Accessions

How to cite

Dataset information

Summary:

Transcriptional heterogeneity among malignant cells of a tumor has been studied in individual cancer types and shown to be organized into cancer cell states; however, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of gene modules whose expression defines recurrent cancer cell states including ‘stress’, ‘interferon response’, ‘epithelial-mesenchymal transition’, ‘metal response’, ‘basal’ and ‘ciliated’. Spatial transcriptomic analysis linked the interferon response in cancer cells to T cells and macrophages in the tumor microenvironment. Using mouse models, we further found that induction of the interferon response module varies by tumor location and is diminished upon elimination of lymphocytes. Our work provides a framework for studying how cancer cell states interact with the tumor microenvironment to form organized systems capable of immune evasion, drug resistance, and metastasis.

Overall design:

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

Technology:

10x Visium

Platform:

Illumina NextSeq 500 (Homo sapiens), Illumina NextSeq 500 (Mus musculus), Illumina NextSeq 500 (Homo sapiens; Mus musculus)

Species:

Homo sapiens(hg38)

Mus musculus(mm10)

Tissues:

Stomach

Disease:

Breast carcinoma

Submission date: 2022-05-23Update date: 2022-12-11

Sample number: 17Section number: 12

DOI: To be continue

Contributors

Barkley, Dalia,Yanai, Itai

Accessions

GEO Series Accessions: GSE203612

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] Barkley, Dalia,Yanai, Itai. Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment[DS/OL]. STOmicsDB, 2022[2022-05-23]. https://db.cngb.org/stomics/datasets/STDS0000153/. 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: Barkley, Dalia et al. “Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment.” Nature genetics vol. 54,8 (2022): 1192-1201. doi:10.1038/s41588-022-01141-9