Targeted scRNA-seq and AbSeq of human CAR-T cell infusion product from 24 cancer patients

Backgroud information

The dataset contains single cell targeted RNA sequencing (RNAseq) and targeted antibody-oligonucleotide conjugates sequencing (Abseq) data from chimeric antigen receptor (CAR)-engineered T cells used to treat each individual cancer patients in a clinical study. The starting material was in all cases autologous T cells harvested from peripheral blood of patients. The data is collected from 24 participants of which 23 were adult patients with relapsed or refractory B cell lymphoma and one was a pediatric patient with relapsed B cell acute lymphoblastic leukemia. The data were generated as part of a study by Sarén et. al, Clinical Cancer Research (2023).

Targeted RNA and protein single-cell libraries were generated using the BD Rhapsody™ platform (BD Biosciences). Cells were labeled with sample tags from the BD Human Immune Single-Cell Multiplexing Kit and BD Ab-seq Ab-Oligos and live cells were collected by flow cytometry. CAR-T cells were loaded on BD Rhapsody cartridge and mRNA captured with cell capture beads and used as template for cDNA synthesis. Four separate targeted libraries were produced and pooled for paired-end sequencing on NovaSeq 6000 S1 sequencer (Illumina) at the SNP&SEQ Technology Platform (Uppsala, Sweden).

Terms of access

Sequencing data generated during the current study are not publicly available due to the European General Data Protection Regulation (GDPR) to protect patients’ privacy but are available from the corresponding author on reasonable request (see contact info). The dataset is only to be used for research that is seeking to advance the understanding of CAR-T cell treatment of cancer.

Ancillary datasets and code

Processed RNAseq and AbSeq data, in the form of raw and normalized count matrices, are available on BioStudies (Accession: E-MTAB-12407).

R code used to process the data is available on the study GitHub repository:https://github.com/magnessa/EudraCT_2016-004043-36