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Single-cell transcriptomics of chimeric antigen receptor (CAR) T cell infusion products

ABSTRACT: Single-cell transcriptomics of chimeric antigen receptor (CAR) T cell infusion products

PROVIDER: PRJNA858059 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20106893_1.fastq.gz	Fastqsanger.gz
	SRR20106893_2.fastq.gz	Fastqsanger.gz
	SRR20106894_1.fastq.gz	Fastqsanger.gz
	SRR20106894_2.fastq.gz	Fastqsanger.gz
	SRR20106895_1.fastq.gz	Fastqsanger.gz

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Single-cell transcriptomics of chimeric antigen receptor (CAR) T cell infusion products

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CapID sequencing of 40 chimeric antigen receptor T-cell infusion products were reported

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Single-cell transcriptomics of chimeric antigen receptor T-cell infusion products

Project description:Single-cell transcriptomics of chimeric antigen receptor T-cell infusion products

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Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL

Project description:We report 101,326 single cell transcriptomes and surface protein landscape from the Chimeric antigen receptor-modified (CAR) T infusion products of 12 pediatric ALL patients upon CAR antigen-specific stimulation in comparison with TCR-mediated activation and controls.

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Project description:We performed single cell RNA sequencing of remnants from CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma. Libraries were prepared using 10X 5Ã¢Â€Â™ GEX chemistry and sequenced on an Illumina HiSeq 4000 to obtain >50,000 reads per cell.

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Targeted scRNA-seq and AbSeq of human CAR-T cell infusion product from 28 cancer patients

Project description:Immunotherapy using CD19-directed chimeric antigen receptor (CAR)-T cells has shown excellent results for treatment of B-cell leukaemia and lymphoma. To produce CAR-T cells, the patient’s own T cells are isolated from the blood and modified in a laboratory with a genetic vector to express a tumor antigen-directed CAR on its surface. The CAR-T cells are then expanded in numbers and given back to the patient with the aim to eradicate the tumors. However, some patients display primary resistance to CAR-T treatment while others relapse quickly after CAR-T treatment. In this experiment, we seek to understand whether the quality of the individual CAR-T cell product the patients were given can predict outcome to the therapy. We investigate the transcriptional profile of the individual CAR-T infusion products using single-cell RNA sequencing. In this dataset, we identified a T cell subset correlating with response that could be used as an indicator for clinical outcome. Targeted RNA and protein single-cell libraries were obtained using the BD Rhapsody platform (BD Biosciences). In total four separate targeted libraries were produced with 6 patients per library. Sequencing was performed on NovaSeq 6000 S1 sequencer at the SNP&SEQ Technology Platform (Uppsala, Sweden). The raw scRNA-seq data was pre-processed by BD Biosciences using the Rhapsody Analysis pipeline to convert the raw reads into Unique Molecular Identifier (UMI) counts. UMIs are further adjusted within Rhapsody by applying BD’s Recursive Substitution Error Correction (RSEC) and Distribution-Based Error Correction (DBEC) in order to remove false UMIs caused by sequencing or library preparation errors. Pooled samples were deconvoluted using Sample-tag reads. The scRNA-seq and AbSeq counts were loaded, processed and used for clustering and differential gene expression with Seurat v. 4.0.0.

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