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RNA sequencing of AC16 and AC16-CAR cells

ABSTRACT: RNA sequencing of AC16 and AC16-CAR cells

PROVIDER: PRJNA649286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12341036_1.fastq.gz	Fastqsanger.gz
	SRR12341036_2.fastq.gz	Fastqsanger.gz
	SRR12341037_1.fastq.gz	Fastqsanger.gz
	SRR12341037_2.fastq.gz	Fastqsanger.gz
	SRR12341038_1.fastq.gz	Fastqsanger.gz

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RNA sequencing of AC16 and AC16-CAR cells

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polysome-IP profiling experiment : Polysomes of untreated or tunicamycin-treated AC16 cells were immunoprecipitated with anti-MRPS15 antibody, followed by RNA sequencing

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Project description:Purpose: Compared the differences in the transcriptome of T cells versus EpCAM CAR-T cells and EpCAM CAR-T cells versus rapamycin-pretreated EpCAM CAR-T cells.Methods: Next-generation sequencing (NGS) has revolutionized the systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) between T cells and EpCAM CAR-T cells，and between EpCAM CAR-T cells and rapamycin-pretreated EpCAM CAR-T cells. Results: RNA-seq showed that CAR-T cells significantly upregulated the expression of exhaustion markers compared to T cells. Gene Set Enrichment Analysis (GSEA) analysis showed that CAR-T cells cells were enriched for signatures of apoptosis. Compared with T cells, Kyoto Encyclopedia of Genes and Genomessignaling(KEGG) pathway analysis showed that the PI3K/AKT/mTOR signaling pathway was significantly enriched. Likewise, GSEA showed that the mTOR signaling pathway was significantly upregulated in CAR-T cells. Next, we analyzed the RNA-seq data between CAR-T cells and rapamycin-pretreated CAR-T cells. RNA-seq showed that rapamycin-treated CAR T down-regulated the expression of exhaustion markers compared with untreated CAR-T cells. GSEA analysis showed that the apoptosis-related gene set was enriched in untreated CAR-T cells.Conclusions:In vitro culture promotes the terminal differentiation of CAR-T cells.CAR-T cells present a highly activated mTOR phenotype. Rapamycin pretreatment prevents CAR-T cells terminal differentiation.

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Project description:Expression data from human myocardial cells, AC16

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RNA sequencing comparison of B7-H3.TMIGD2 and B7-H3.CD28.4-1BB CAR-T cells in vitro

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