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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 05, 2022 |
| Title |
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment
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| Contributor(s) |
Barkley D, Yanai I |
| Citation(s) |
35931863 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F30 CA257400 |
Cancer cell state interactions with immune populations of the tumor microenvironment |
NEW YORK UNIVERSITY SCHOOL OF MEDICINE |
Dalia Barkley |
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| Submission date |
May 23, 2022 |
| Last update date |
Dec 11, 2022 |
| Contact name |
Dalia Barkley |
| E-mail(s) |
dalia.barkley@nyulangone.org
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| Organization name |
NYU Langone Health
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| Department |
Institute for Computational Medicine
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| Lab |
Yanai
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| Street address |
435 E 30th st
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (31)
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| Relations |
| BioProject |
PRJNA841591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE203612_RAW.tar |
675.5 Mb |
(http)(custom) |
TAR (of CSV, H5, JPG, JSON, MTX, PNG, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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