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Sequencing analysis of CAR T cell products and apheresis cells in DLBCL patients treated with tandemCAR-T cell

ABSTRACT: Sequencing analysis of CAR T cell products and apheresis cells in DLBCL patients treated with tandemCAR-T cell

PROVIDER: PRJNA1017828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26071611_1.fastq.gz	Fastqsanger.gz
	SRR26071611_2.fastq.gz	Fastqsanger.gz
	SRR26071612.fastq.gz	Fastqsanger.gz
	SRR26071613_1.fastq.gz	Fastqsanger.gz
	SRR26071613_2.fastq.gz	Fastqsanger.gz

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Sequencing analysis of CAR T cell products and apheresis cells in DLBCL patients treated with tandemCAR-T cell

Project description:In this study, 58 r/r DLBCL patients treated with tandem CD19/CD20 CAR T cells. Twenty-seven patients had durational responses for more than 24 months, and the median PFS was 21.7 months. But 15 patients still did not have an objective response, and 11 patients relapsed within 1 year. The analysis found that CD8+TSCM cells with higher frequency and stronger activation ability in CART products were the key to achieving clinical sustained objective response. Bulk RNA-Seq and single-cell RNA-Seq then were performed on CAR-T cell products and pre-manufacture T cells of patients with DLBCL. We note that a CD8+ stem cell-like memory T cell population with a higher proportion and stronger activating capacity of the CAR-T cell products was key to achieving durable clinical response. By analyzing autologously-derived, pre-manufacture T cells, our data suggest that heterogeneity in the cellular and molecular features of pre-manufacture T cells contribute to the variation in efficacy after CAR-T cell therapy in DLBCL. The differences in anti-tumour efficacy of CAR-T cells among patients with different clinical outcomes appear to be due to the loss of CCR7 gene expression accompanied by increased expression of activation- and inhibitor-related genes in the CD8+ naïve-T cell populations among the apheresis T cells from patients with a poor molecular response. These findings significantly advance our understanding of the underlying molecular determinants of pre-manufacture T cell function.

2023-11-09 | GSE243325 | GEO

Characteristics of premanufacture CD8+T cells determine CAR-T efficacy in patients with diffuse large B-cell lymphoma

Project description:In this study, 58 r/r DLBCL patients treated with tandem CD19/CD20 CAR T cells. Twenty-seven patients had durational responses for more than 24 months, and the median PFS was 21.7 months. But 15 patients still did not have an objective response, and 11 patients relapsed within 1 year. The analysis found that CD8+TSCM cells with higher frequency and stronger activation ability in CART products were the key to achieving clinical sustained objective response. Bulk-RNA-seq results confirmed that CD8+CART cells in CR group had higher expression of memory-related genes and transcription factors and lower expression of activation/depletion related genes than those in PD patients. Naive CD8 cells also showed similar differential expression in apheresis. The use of Naive cells as the source cell population for CART preparation could partially improve CART function, but could not completely reverse it. It is suggested that the resistance of DLBCL to tandem CD19/CD20 CAR T cell therapy may be caused by the decreased function and the loss of expression of memory genes of the source Naive T cells.

2023-11-09 | GSE223655 | GEO

Gene expression profile of CD22 CAR T-cell products

Project description:Gene expression profile of CD22 CAR T-cell products

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Single Cell Transcriptomic Characterization of CAR T-Cell Products Reveals Subpopulations, Stimulation and Exhaustion Signatures

Project description:Chimeric antigen receptor (CAR) T-cell adoptive therapy is set to transform the treatment of a rapidly expanding range of malignancies. Although the activation process of normal T cells is well characterized, comparatively little is known about the activation of cells via the CAR. Here we have used flow cytometry together with single cell transcriptome profiling to characterize the starting material (peripheral blood mononuclear cells –PBMCs-) and CAR therapeutic products of 3 healthy donors in the presence and absence of antigen specific stimulation. Bioinformatic analysis of the 57,676 single cell transcriptomes showed the CAR products to contain several subpopulations of cells, with the cellular composition reproducible from donor to donor, and all major cellular subsets compatible with CAR expression. Only 50% of CAR-expressing cells displayed transcriptional changes upon CAR-specific antigen exposure. The resulting molecular signature for CAR T-cell activation provides a rich resource for future dissection of the underlying mechanisms. Targeted data interrogation also revealed that a small proportion of antigen-responding CAR-expressing cells displayed an exhaustion signature, with both known markers and genes not previously associated with T-cell exhaustion. Comprehensive single cell transcriptomic analysis thus represents a powerful way to guide the assessment and optimization of clinical-grade CAR-T-cells, and inform future research into the underlying molecular processes.

2021-01-22 | GSE145809 | GEO

Single cell RNA sequencing of CD19 CAR T-cell infusion products

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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Single cell RNA-seq for bone marrow mononuclear cells from CAR-T therapy received DLBCL patient

Project description:To investigate whether metoprolol treatment could affect immune cells population and proinflammatory gene expression in bone marrow mononuclear cells from CAR-T therapy received DLBCL patient

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Project description:DLBCL patients

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

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

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

Project description:Adoptive immunotherapy with T cells expressing chimeric antigen receptors (CARs) for B-cell malignancies serves as a model for identifying subsets with superior clinical activity. We profiled the infusion products (IP) of 9 patients with large B-cell lymphoma (LBCL) using scRNA-sequencing to reveal the therapeutic potential of CD19-specific CAR+ T cells. ScRNA-seq demonstrated that T cells from responders were enriched in pathways related to T-cell killing, migration and actin cytoskeleton, and TCR clustering.

2023-03-12 | GSE208052 | GEO

Generation of clinical grade CD19-specific CAR-modified CD8+ memory stem cells for the treatment of B-cell malignancies

Project description:Long-lived, self-renewing, multipotent T memory stem cells (TSCM) can trigger profound and sustained tumor regression but their rareness poses a major hurdle to their clinical application. Presently, clinically compliant procedures to generate relevant numbers of this T cell population are undefined. Here, we provide a strategy for deriving large numbers of clinical grade tumor-redirected TSCM cells starting from naÃ¯ve precursors. CD8+CD62L+CD45RA+ naÃ¯ve T cells enriched by streptamer-based serial positive selection were activated by CD3/CD28 engagement in the presence of IL-7, IL-21 and the glycogen synthase-3Î² inhibitor TWS119, and genetically engineered to express a CD19-specific chimeric antigen receptor (CD19-CAR). These conditions allowed for the generation of CD19-CAR modified TSCM cells that were phenotypically, functionally and transcriptomically equivalent to their naturally occurring counterpart. Compared with T cell products currently under clinical investigation, CD19-CAR modified TSCM cells exhibit enhanced metabolic fitness, persistence and anti-tumor activity against systemic acute lymphoblastic leukemia xenografts. Based on these findings, we have initiated a phase 1 clinical study to evaluate the activity of CD19-CAR modified TSCM in patients with B-cell malignancies refractory to prior allogeneic hematopoietic stem cell transplantation. Three healthy human blood donors provided lymphocyte-enriched apheresis blood for this study after informed consent. From all samples, total RNA was isolated using an miRNeasy Mini Kit (Qiagen), processed by Ambionâ??s WT expression kit, fragmented and labeled with a WT Terminal Labeling Kit (Affymetrix), hybridized to WT Human Gene 1.0 ST arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), all according to the respective manufacturer's instructions. Samples represent exon-level and gene-level analyses.

2016-06-29 | E-GEOD-68003 | biostudies-arrayexpress

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