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Series GSE203612 Query DataSets for GSE203612
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
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
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
Submission date May 23, 2022
Last update date Dec 11, 2022
Contact name Dalia Barkley
Organization name NYU Langone Health
Department Institute for Computational Medicine
Lab Yanai
Street address 435 E 30th st
City New York
State/province NY
ZIP/Postal code 10016
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (31)
GSM6177599 NYU_BRCA0_Vis 10x Genomics Visium
GSM6177600 NYU_BRCA1 inDrop
GSM6177601 NYU_BRCA1_Vis 10x Genomics Visium
BioProject PRJNA841591

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Supplementary file Size Download File type/resource
GSE203612_RAW.tar 675.5 Mb (http)(custom) TAR (of CSV, H5, JPG, JSON, MTX, PNG, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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