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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 25, 2023 |
| Title |
Rapid TCR:Epitope Ranker (RAPTER): A primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Identifying epitopes that T cells respond to is critical to understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity at single cell resolution. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information. We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR: ligand information can directly enable immunogenic antigen selection for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.
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| Overall design |
Human PBMCs were put through the RAPTER assay described in the manuscript then measured via scRNAseq
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| Contributor(s) |
Deering RP, Blumenberg L, Li L, Dhanik A, Jeong S, Pourpe S, Song H, Boucher L, Ragunathan S, Li Y, Zhong M, Kuhnert J, Adler C, Hawins P, Gupta NT, Moore M, Ni M, Hansen J, Wei Y, Thurston G |
| Citation(s) |
37231180 |
| |
| Submission date |
May 08, 2023 |
| Last update date |
Aug 26, 2023 |
| Contact name |
Lili Blumenberg |
| E-mail(s) |
lili.blumenberg@regeneron.com
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| Organization name |
Regeneron Pharmaceuticals
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| Department |
VI Next
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| Street address |
777 Old Saw Mill River Road
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| City |
Tarrytown |
| State/province |
NY |
| ZIP/Postal code |
10591 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (52)
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| GSM7306830 |
Pre-expandedCD8+ Tc Total, scRNA-seq |
| GSM7306831 |
Pre-expanded CD8+ CMVpp65+ Multimer Selection, scRNA-seq |
| GSM7306832 |
Pre-expandedCMVpp65 restim CD8+ 41BB+ Selection, scRNA-seq |
| GSM7306833 |
Pre-expandedCMVpp65 restim CD8+ PD1+ Selection, scRNA-seq |
| GSM7306834 |
Pre-expandedCD8+ MART1+ Multimer Selection, scRNA-seq |
| GSM7306835 |
Pre-expandedMART1 restim CD8+ 41BB+ Selection, scRNA-seq |
| GSM7306836 |
Pre-expandedMART1 restim CD8+ PD1+ Selection, scRNA-seq |
| GSM7306837 |
Day 1 sort CD3+, CD8+, scRNA-seq |
| GSM7306838 |
Day 1 sort CD3+, CD8+ 41BB+, scRNA-seq |
| GSM7306839 |
Day 8 Pre-expanded sort CD3+, CD8+, scRNA-seq |
| GSM7306840 |
Day8 Pre-expandedsort CD3+, CD8+ 41BB+, scRNA-seq |
| GSM7306841 |
Day 7 Pre-expanded sort CD3+ CD8+ , scRNA-seq |
| GSM7306842 |
Day 7 Pre-expanded sort CD3+ CD8+ Dextramer pool+, scRNA-seq |
| GSM7306843 |
Total Pre-expanded CD3+ T cells , scRNA-seq |
| GSM7306844 |
Pre-expanded CEF pool, hashed, 4-1BB sorted, scRNA-seq |
| GSM7306845 |
Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep1, scRNA-seq |
| GSM7306846 |
Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep2, scRNA-seq |
| GSM7306847 |
Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep1, scRNA-seq |
| GSM7306848 |
Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep2, scRNA-seq |
| GSM7306849 |
Pre-Expanded CMVpp65 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 13, 2 HTOs each), scRNA-seq |
| GSM7306850 |
Pre-Expanded MART1 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 12, 2 HTOs each), scRNA-seq |
| GSM7306851 |
Sorted CD3+CD8+, scRNA-seq |
| GSM7306852 |
Sorted CD3+CD8+41BB+, scRNA-seq |
| GSM7306853 |
Full 50 Dextramer Pool Stained, CD3+CD8+ T Cells, TCR Repertoire Control, scRNA-seq |
| GSM7306854 |
Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep1, scRNA-seq |
| GSM7306855 |
Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep2, scRNA-seq |
| GSM7306856 |
Pre-expandedCD8+ Tc Total, scTCR-seq |
| GSM7306857 |
Pre-expanded CD8+ CMVpp65+ Multimer Selection, scTCR-seq |
| GSM7306858 |
Pre-expandedCMVpp65 restim CD8+ 41BB+ Selection, scTCR-seq |
| GSM7306859 |
Pre-expandedCMVpp65 restim CD8+ PD1+ Selection, scTCR-seq |
| GSM7306860 |
Pre-expandedCD8+ MART1+ Multimer Selection, scTCR-seq |
| GSM7306861 |
Pre-expandedMART1 restim CD8+ 41BB+ Selection, scTCR-seq |
| GSM7306862 |
Pre-expandedMART1 restim CD8+ PD1+ Selection, scTCR-seq |
| GSM7306863 |
Day 1 sort CD3+, CD8+, scTCR-seq |
| GSM7306864 |
Day 1 sort CD3+, CD8+ 41BB+, scTCR-seq |
| GSM7306865 |
Day 8 Pre-expanded sort CD3+, CD8+, scTCR-seq |
| GSM7306866 |
Day8 Pre-expandedsort CD3+, CD8+ 41BB+, scTCR-seq |
| GSM7306867 |
Day 7 Pre-expanded sort CD3+ CD8+ , scTCR-seq |
| GSM7306868 |
Day 7 Pre-expanded sort CD3+ CD8+ Dextramer pool+, scTCR-seq |
| GSM7306869 |
Total Pre-expanded CD3+ T cells , scTCR-seq |
| GSM7306870 |
Pre-expanded CEF pool, hashed, 4-1BB sorted, scTCR-seq |
| GSM7306871 |
Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep1, scTCR-seq |
| GSM7306872 |
Pre-Expanded CMVpp65 Cells, CD8+ CMVpp65+ Dextramer sorted (TCR repertoire control), rep2, scTCR-seq |
| GSM7306873 |
Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep1, scTCR-seq |
| GSM7306874 |
Pre-Expanded MART1 Cells, CD8+ MART1+ Dextramer sorted (TCR repertoire control), rep2, scTCR-seq |
| GSM7306875 |
Pre-Expanded CMVpp65 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 13, 2 HTOs each), scTCR-seq |
| GSM7306876 |
Pre-Expanded MART1 Cells, overnight re-stimulated CD8+ 41BB+ sorted (pooled n = 12, 2 HTOs each), scTCR-seq |
| GSM7306877 |
Sorted CD3+CD8+, scTCR-seq |
| GSM7306878 |
Sorted CD3+CD8+41BB+, scTCR-seq |
| GSM7306879 |
Full 50 Dextramer Pool Stained, CD3+CD8+ T Cells, TCR Repertoire Control, scTCR-seq |
| GSM7306880 |
Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep1, scTCR-seq |
| GSM7306881 |
Sorted Full 50 Dextramer Pool Stained, CD3+CD8+ Dextramer+ Pool (n = 50 dextramers), rep2, scTCR-seq |
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| Relations |
| BioProject |
PRJNA970348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE231977_RAW.tar |
63.6 Mb |
(http)(custom) |
TAR (of CSV, FASTA) |
| GSE231977_Supplemental_Data.xlsx |
25.4 Kb |
(ftp)(http) |
XLSX |
| GSE231977_dataset1.TPM.csv.gz |
24.1 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset1.metadata.csv.gz |
418.4 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset2.ADT.csv.gz |
199.9 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset2.HTO_norm.csv.gz |
581.7 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset2.TPM.csv.gz |
39.8 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset2.metadata.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset3.TPM.csv.gz |
9.2 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset3.metadata.csv.gz |
223.2 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset4.HTO_norm.csv.gz |
216.8 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset4.TPM.csv.gz |
26.7 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset4.metadata.csv.gz |
571.3 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.41bb.HTO_norm.csv.gz |
62.7 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.41bb.TPM.csv.gz |
3.3 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.41bb.metadata.csv.gz |
99.8 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.HTO_norm.csv.gz |
36.8 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.TPM.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset5.cd8.metadata.csv.gz |
65.1 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8-dex.ADT.csv.gz |
370.3 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8-dex.TPM.csv.gz |
10.4 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8-dex.metadata.csv.gz |
304.1 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8.ADT.csv.gz |
190.6 Kb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8.TPM.csv.gz |
6.1 Mb |
(ftp)(http) |
CSV |
| GSE231977_dataset6.cd3-cd8.metadata.csv.gz |
242.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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