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Series GSE163633 Query DataSets for GSE163633
Status Public on Feb 15, 2022
Title Identification of human tumor-unique signaling networks between antigen-presenting cells and T cells using multi-omic single cell analysis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Tissue residence and prolonged exposure to inflammation profoundly affect lymphocyte and myeloid cell function. Immune cells derived solid tumors are thought to undergo additional adaptation, and the identification of such tumor-driven unique immune cell alterations might allow for more efficient and precise tumor therapies. We used a multi-omic single-cell analysis approach to define the immune landscape of human oral squamous cell carcinomas (OSCC) and inflamed non-malignant oral tissues to identify tumor-unique immune cell interactions. The immune infiltrate in non-malignant, inflamed tissues showed substantial phenotypic congruence with immune phenotypes that are typically tumor-associated. Yet, computational and machine learning analyses of single-cell data allowed identification of putative tumor-unique subsets and interactions of regulatory T cells (Tregs) and antigen-presenting cells (APCs). Subsequent experimental validation confirmed tumor-unique chemokine and cytokine signaling axes between APCs and Tregs. We identified ICOS and IL-1R1 as uniquely co-expressed biomarkers on tumor Tregs that allow for specific therapeutic targeting.
Overall design Immune cells were isolated from inflamed oral mucosa, oral squamous cell carcinomas, or peripheral blood. These cells were then process for transcriptional profiling using both targeted and whole transcriptome approaches (Rhapsody and 10x, respectivly)
Contributor(s) Prlic M, Erickson JR, Mair F
Citation(s) 35545675
Submission date Dec 21, 2020
Last update date May 17, 2022
Contact name Martin Prlic
Phone 2066672216
Organization name Fred Hutch
Street address 1100 Fairview Ave, Mail stop E5-110
City Seattle
State/province WA
ZIP/Postal code 98108
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (131)
GSM4983128 T cells - Oral Mucosa 10x OM121
GSM4983129 T cells - Oral Mucosa 10x OM122
GSM4983130 T cells - Oral Mucosa 10x OM124
BioProject PRJNA686974
SRA SRP298742

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE163633_211109-P405-3_FilteredNormGeneCounts.csv.gz 5.3 Mb (ftp)(http) CSV
GSE163633_RAW.tar 796.4 Mb (http)(custom) TAR (of CSV, MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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