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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [RNA-Seq]

ABSTRACT: Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [RNA-Seq]

PROVIDER: PRJNA540585 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8994242.fastq.gz	Fastqsanger.gz
	SRR8994243.fastq.gz	Fastqsanger.gz
	SRR8994244.fastq.gz	Fastqsanger.gz
	SRR8994245.fastq.gz	Fastqsanger.gz
	SRR8994246.fastq.gz	Fastqsanger.gz

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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [ATAC-Seq]

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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [RNA-Seq]

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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion

Project description:Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion

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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [ATAC-Seq]

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TOX2 coordinates with TET2 to positively regulate central memory differentiation in human CAR T cells

Project description:To investigate the effects of TOX and TOX2 on memory T cell differentiation in human CAR T cells, we used shRNA to knock down TOX2 or TOX, or overexpress FLAG-TOX2. We then performed gene expression profiling analysis using RNAseq, plus examined the binding of TOX2 to chromatin using ChIPseq.

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TOX2 regulates human natural killer cell development by controlling T-BET expression

Project description:Thymocyte selection-associated high mobility group box protein family member 2 (TOX2) is a transcription factor belonging to the TOX family that shares a highly conserved high mobility group DNA binding domain with the other TOX members. While TOX1 has been shown to be an essential regulator of T-cell and natural killer (NK) cell differentiation in mice, little is known about the roles of the other TOX family members in lymphocyte development, particularly in humans. In this study, we found that TOX2 was preferentially expressed in mature human NK cells and was upregulated during in vitro differentiation of NK cells from human umbilical cord blood (UCB)M-bM-^@M-^Sderived CD34+ cells. Gene silencing of TOX2 intrinsically hindered the transition between early developmental stages of NK cells, while overexpression of TOX2 enhanced the development of mature NK cells from UCB CD34+ cells. We subsequently found that TOX2 was independent of ETS-1 but could directly upregulate the transcription of TBX21 (encoding T-BET). Overexpression of T-BET rescued the TOX2 knockdown phenotypes. Given the essential function of T-BET in NK cell differentiation, TOX2 therefore plays a crucial role in controlling normal NK cell development by acting upstream of TBX21 transcriptional regulation. survey of NK cells over time

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Project description:Dysfunction in T cells limits the efficacy of cancer immunotherapy. We profiled the epigenome, transcriptome, and enhancer connectome of exhaustion-prone GD2-targeting HA-28z chimeric antigen receptor (CAR) T cells and control CD19-targeting CAR T cells, which present less exhaustion-inducing tonic signaling, at multiple points during their ex vivo expansion. We found widespread, dynamic changes in chromatin accessibility and 3D chromosome conformation preceding changes in gene expression, notably at loci proximal to exhaustion-associated genes such as PDCD1, CTLA4, and HAVCR2, and increased DNA motif access for AP-1 family transcription factors, which are known to promote exhaustion. Although T cell exhaustion has been studied in detail in mouse, we find that the regulatory networks of T cell exhaustion differ between the species and involve distinct loci of accessible chromatin and cis-regulated target genes in human CAR T cell exhaustion. Deletion of exhaustion-specific candidate enhancers of PDCD1 suppress the expression of PD-1 in an in vitro model of T cell dysfunction and in HA-28z CAR T cells, suggesting enhancer editing as a path forward in improving cancer immunotherapy.

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Project description:Thymocyte selection-associated high mobility group box protein family member 2 (TOX2) is a transcription factor belonging to the TOX family that shares a highly conserved high mobility group DNA binding domain with the other TOX members. While TOX1 has been shown to be an essential regulator of T-cell and natural killer (NK) cell differentiation in mice, little is known about the roles of the other TOX family members in lymphocyte development, particularly in humans. In this study, we found that TOX2 was preferentially expressed in mature human NK cells and was upregulated during in vitro differentiation of NK cells from human umbilical cord blood (UCB)–derived CD34+ cells. Gene silencing of TOX2 intrinsically hindered the transition between early developmental stages of NK cells, while overexpression of TOX2 enhanced the development of mature NK cells from UCB CD34+ cells. We subsequently found that TOX2 was independent of ETS-1 but could directly upregulate the transcription of TBX21 (encoding T-BET). Overexpression of T-BET rescued the TOX2 knockdown phenotypes. Given the essential function of T-BET in NK cell differentiation, TOX2 therefore plays a crucial role in controlling normal NK cell development by acting upstream of TBX21 transcriptional regulation.

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Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion

Project description:This SuperSeries is composed of the SubSeries listed below.

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