|
| Status |
Public on Jul 28, 2022 |
| Title |
Single-cell sequencing data for circulating CAR T cells in lymphoma patients |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Purpose: To compare cell states amoung three populations of interest among circulating CAR T cells in patients with lymphoma.
Methods: Nine patients with large B-cell lymphoma (LBCL) were treated with axicabtagene ciloleucel (axi-cel), a commercial CD19-targeted CAR T-cell therapy. On day 7, fresh peripheral blood mononuclear cells were stained with an antibody panel for fluorescence-activated cell sorting (FACS), a panel for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and a viability dye. Single live CAR+ T cells were sorted from each patient, counted, processed for 5' single-cell RNA-sequencing with feature barcoding and TCR clonotype analysis on the 10X Genomics platform, and sequenced by the Stanford Genomics Facility (HighSeq 4000) or Novogene (NovaSeq 6000).
Results: We found that circulating CD4+ and CD8+ CAR T cells that express CD57 and T-bet are clonally expanded and display features of effector T cells. In contrast, CD4+ CD57- CAR T cells that express Helios expand polyclonally and display features of T regulatory cells.
Conclusions: This study provides insights into cell states of circulating CAR T cells on day 7 that associate with clinical response or toxicity in LBCL patients treated with axi-cel.
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| |
|
| Overall design |
CAR T cells were sorted from blood of nine LBCL patients on day 7 following axi-cel infusion. Three populations of interest were identified within each CAR T-cell sample.
|
| Web link |
https://purl.stanford.edu/qb215vz6111
|
| |
|
| Contributor(s) |
Good Z, Mackall CL |
| Citation(s) |
36097223 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P30 CA124435 |
Stanford Cancer Institute |
STANFORD UNIVERSITY |
STEVEN E ARTANDI |
| U54 CA209971 |
Spatial-Genomic Integrative Multi-Species Analysis of Lymph Node Metastasis |
STANFORD UNIVERSITY |
SYLVIA KATINA PLEVRITIS |
| P01 CA049605 |
Bone Marrow Grafting and Cellular Therapy for Leukemia and Lymphoma |
STANFORD UNIVERSITY |
Robert S Negrin |
| S10 OD018220 |
High Throughput DNA Sequencer Upgrade |
STANFORD UNIVERSITY |
John Coller |
|
| |
| Submission date |
Mar 15, 2021 |
| Last update date |
Dec 22, 2022 |
| Contact name |
Zinaida Good |
| E-mail(s) |
zinaida@stanford.edu
|
| Phone |
4152908944
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Stanford Cancer Institute, Department of Biomedical Data Science
|
| Lab |
Crystal L. Mackall, Sylvia K. Plevritis
|
| Street address |
265 Campus Drive, Room G2105
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (18)
|
| GSM6415276 |
CAR T cells in blood of Pt110 on day 7 |
| GSM6415277 |
CAR T cells in blood of Pt110 on day 7: TCR |
| GSM6415278 |
CAR T cells in blood of Pt116 on day 7 |
| GSM6415279 |
CAR T cells in blood of Pt116 on day 7: TCR |
| GSM6415280 |
CAR T cells in blood of Pt125 on day 7 |
| GSM6415281 |
CAR T cells in blood of Pt125 on day 7: TCR |
| GSM6415282 |
CAR T cells in blood of Pt129 on day 7 |
| GSM6415283 |
CAR T cells in blood of Pt129 on day 7: TCR |
| GSM6415284 |
CAR T cells in blood of Pt245 on day 7 |
| GSM6415285 |
CAR T cells in blood of Pt245 on day 7: TCR |
| GSM6415286 |
CAR T cells in blood of Pt253 on day 7 |
| GSM6415287 |
CAR T cells in blood of Pt253 on day 7: TCR |
| GSM6415288 |
CAR T cells in blood of Pt263 on day 7 |
| GSM6415289 |
CAR T cells in blood of Pt263 on day 7: TCR |
| GSM6415290 |
CAR T cells in blood of Pt276 on day 7 |
| GSM6415291 |
CAR T cells in blood of Pt276 on day 7: TCR |
| GSM6415292 |
CAR T cells in blood of Pt282 on day 7 |
| GSM6415293 |
CAR T cells in blood of Pt282 on day 7: TCR |
|
| Relations |
| BioProject |
PRJNA714638 |
| SRA |
SRP310699 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168940_FeatureBarcodes-14Nov2020.csv.gz |
1.2 Kb |
(ftp)(http) |
CSV |
| GSE168940_RAW.tar |
40.4 Mb |
(http)(custom) |
TAR (of CSV, HTML) |
| GSE168940_pt110-day7-car-t-filtered_feature_bc_matrix.h5 |
29.2 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt116-day7-car-t-filtered_feature_bc_matrix.h5 |
14.4 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt125-day7-car-t-filtered_feature_bc_matrix.h5 |
15.2 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt129-day7-car-t-filtered_feature_bc_matrix.h5 |
1.6 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt245-day7-car-t-filtered_feature_bc_matrix.h5 |
72.4 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt253-day7-car-t-filtered_feature_bc_matrix.h5 |
22.0 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt263-day7-car-t-filtered_feature_bc_matrix.h5 |
14.0 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt276-day7-car-t-filtered_feature_bc_matrix.h5 |
37.8 Mb |
(ftp)(http) |
H5 |
| GSE168940_pt282-day7-car-t-filtered_feature_bc_matrix.h5 |
48.9 Mb |
(ftp)(http) |
H5 |
| GSE168940_seurat-day7-car-t.rds.gz |
1.1 Gb |
(ftp)(http) |
RDS |
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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