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Effect of TET1/3 defiency on iTreg cell differentiation

ABSTRACT: Effect of TET1/3 defiency on iTreg cell differentiation

PROVIDER: PRJNA916488 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22907300_1.fastq.gz	Fastqsanger.gz
	SRR22907300_2.fastq.gz	Fastqsanger.gz
	SRR22907301_1.fastq.gz	Fastqsanger.gz
	SRR22907301_2.fastq.gz	Fastqsanger.gz
	SRR22907302_1.fastq.gz	Fastqsanger.gz

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Effect of TET1/3 defiency on iTreg cell differentiation

Project description:To investigate the how TET1/3 remodels the chromatin landscape during iTreg cell differentiation and the role of autonomous IL-2 in this process, we performed ATAC-Seq on CD4 T cells that had been stimulated for 48hrs in the presence of TGF-b and in the presence or absence of exogenous IL-2.

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Project description:Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first- in-man trials of Treg transfer achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. To gain a comprehensive and unbiased molecular understanding of FOXP3 induction, we performed time-series RNA sequencing (RNA-Seq) and proteomics profiling on the same samples during human iTreg differentiation. To enable the broad analysis of universal FOXP3-inducing pathways, we used five differentiation protocols in parallel. Integrative analysis of the transcriptome and proteome confirmed involvement of specific molecular processes, as well as overlap of a novel iTreg subnetwork with known Treg regulators and autoimmunity-associated genes. Importantly, we propose 37 novel molecules putatively involved in iTreg differentiation. Their relevance was validated by: a targeted shRNA screen confirming a functional role in FOXP3 induction; discriminant analyses classifying iTregs accordingly; and comparable expression in an independent novel iTreg RNA-Seq data set. The data generated by this novel approach facilitate understanding the molecular mechanisms underlying iTreg generation as well as the concomitant changes in the transcriptome and proteome. Our results provide a reference map exploitable for future discovery of markers and drug candidates governing control of Tregs, which has important implications for the treatment of cancer, autoimmune and inflammatory diseases.

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