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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 10, 2022 |
| Title |
Concurrent delivery of immune checkpoint blockade improves tumor microenvironment for vaccine-generated immunity |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Neoantigen vaccines aiming to induce and amplify tumor-specific T cell responses have received promising anti-tumor effect in early clinical trials. However, the underlying mechanism regarding response or resistance to this treatment remains unclear. Here, we observed that neoantigen vaccine-generated T cells could synergize with immune checkpoint blockade (ICB) for effective tumor control. Specifically, we performed single-cell sequencing on over 100,000 T cells and uncovered that combined therapy induced a novel antigen-specific CD8 T cell population with active chemokine signaling (Cxcr3+/Ccl5+), lower co-inhibitory receptor expression (Lag3-/Havcr2-) and higher cytotoxicity (Fasl+/Gzma+). Furthermore, the generation of antigen specific T cells in the drain lymph node is required for combination treatment mediated therapeutic effect. Signature genes of this unique population is associated with T cell clonal frequency and better survival in human. Our study comprehensively profiled the dynamics of tumor infiltrated T cells during neoantigen vaccine and ICB treatments, and high-dimensionally identified neoantigen-reactive T cell signatures for future development of better therapeutic strategies.
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| Overall design |
MC38 tumors, spleen and tumor draining lymph nodes were harvested at day 10 or day 20 post inoculation. CD45+ cells were isolated with CD45 (TIL) MicroBeads (Miltenyi Biotec). Enriched CD45+ cells were washed and re-suspended in FACS buffer (1x PBS with 2% FBS) and stained for CD3e. CD3+ live cells were sorted by BD FACSMelody™. Spleen and draining lymph node were gently mashed and washed through a 70 μm cell strainer with culture medium. After centrifugation at 500g for 5 minutes, red blood cells in the spleen were removed by ACK lysing buffer. Cell pellets were finally re-suspended in FACS buffer and stained for CD3e. CD3+ live cells were sorted by BD FACSMelody™. Single-cell RNA-seq were performed by the 10x Genomic single cell 5’ VDJ library platform. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 900-1100 cells/μl. Cells were loaded between 10,000 and 17,000 cells/chip position using the Chromium Single cell 5’ VDJ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1 barcoding chemistry). Single-cell gene expression and TCR libraries were generated according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by Nextseq sequencer with 150-bp paired-end reads at a targeted median read depth of 50,000 reads per cell from total gene expression libraries and 5,000 reads per cell for TCR librarie.
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| Contributor(s) |
Liu L, Chen J, Zhang H, Ye J, Lu C, Fu Y, Li B |
| Citation(s) |
35393580, 36350695 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA245318 |
Antigen-independent prediction and biomarker identification of cancer-specific T cells |
UT SOUTHWESTERN MEDICAL CENTER |
Bo Li |
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| Submission date |
Jun 25, 2021 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Bo Li |
| E-mail(s) |
lib3@chop.edu
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| Phone |
7345467574
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| Organization name |
The Children’s Hospital of Philadelphia, University of Pennsylvania
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| Department |
Department of Pathology and Laboratory Medicine
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| Lab |
Bo Li lab
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA741385 |
| SRA |
SRP325556 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE178881_cell_information.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE178881_normalized_exp_matrix.txt.gz |
1.3 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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