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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2023 |
| Title |
Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted by metastasis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment (TME), recent studies in mice identified responses in lymph nodes (LN) as essential; however, the role of LN in human cancer patients remains unknown. Here, we examined CD8+ T cells in human head and neck squamous cell carcinomas (HNSCC) and regional lymph node (LN) using single-cell genomics. We identified progenitor exhausted CD8+ T cells (TCF7 Exhausted) that were clonally related to terminally exhausted CD8 T cells in the TME. Our results identify an important role for the LN as a reservoir of more functional CD8+ T cells for anti-tumor immune responses in humans.
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| Overall design |
We performed scRNA sequencing to understand how the tissue compartment (lymph node versus tumor) affects T cell phenotype in the context of head and neck squamous cell carcinoma (HNSCC). We used a combination of scRNA-sequencing + scTCR-sequencing and CITE-sequencing, which obtains measurements at both the protein and transcriptome level for a subset of samples, + scTCR-sequencing to obtain TCR sequences to identify and phenotype shared clones in the tissue compartments.
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| Contributor(s) |
Rahim MK, Okholm TH, Jones KB, McCarthy EE, Liu CC, Yee JL, Tamaki SJ, Marquez DM, Tenvooren I, Wai K, Cheung A, Davidson BR, Johri V, Samad B, O'Gorman WE, Krummel MF, Combes AJ, Angelo M, Fong L, Algazi AP, Ha P |
| Citation(s) |
36931243 |
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| Submission date |
Sep 06, 2022 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Matthew Spitzer |
| Organization name |
University of California, San Francicso
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| Street address |
513 Parnassus Ave.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (18)
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| GSM6552596 |
Lymph node, participant 117, mRNA-derived cDNA |
| GSM6552597 |
Tumor, participant 117, mRNA-derived cDNA |
| GSM6552598 |
Lymph node, participant 117, TCR-derived cDNA |
| GSM6552599 |
Tumor, participant 117, TCR-derived cDNA |
| GSM6552600 |
Lymph node, participant 118, mRNA-derived cDNA |
| GSM6552601 |
Tumor, participant 118, mRNA-derived cDNA |
| GSM6552602 |
Lymph node, participant 118, TCR-derived cDNA |
| GSM6552603 |
Tumor, participant 118, TCR-derived cDNA |
| GSM6552604 |
Lymph node, participant 126, mRNA-derived cDNA |
| GSM6552605 |
Tumor, participant 126, mRNA-derived cDNA |
| GSM6552606 |
Lymph node, participant 126, ADT-derived cDNA |
| GSM6552607 |
Tumor, participant 126, ADT-derived cDNA |
| GSM6552608 |
Lymph node, participant 128 and 129, mRNA-derived cDNA |
| GSM6552609 |
Tumor, participant 128 and 129, mRNA-derived cDNA |
| GSM6552610 |
Lymph node, participant 128 and 129, TCR-derived cDNA |
| GSM6552611 |
Tumor, participant 128 and 129, TCR-derived cDNA |
| GSM6552612 |
Lymph node, participant 128 and 129, ADT-derived cDNA |
| GSM6552613 |
Tumor, participant 128 and 129, ADT-derived cDNA |
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| Relations |
| BioProject |
PRJNA877282 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE212797_IPIHNSC117_comb_TCR_filtered_contig_annotations.csv.gz |
285.0 Kb |
(ftp)(http) |
CSV |
| GSE212797_IPIHNSC118_comb_TCR_filtered_contig_annotations.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE212797_IPIPOOL004_IPIPOOL005_comb_TCR_filtered_contig_annotations.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE212797_adata.h5ad.gz |
191.7 Mb |
(ftp)(http) |
H5AD |
| GSE212797_adata_ADT.h5ad.gz |
3.4 Mb |
(ftp)(http) |
H5AD |
| GSE212797_adata_CD8.h5ad.gz |
418.6 Mb |
(ftp)(http) |
H5AD |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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