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Effect of ablation of PRDM1 on gene expression in human regulatory T cells

ABSTRACT: Effect of ablation of PRDM1 on gene expression in human regulatory T cells

PROVIDER: PRJNA913935 | ENA |

REPOSITORIES: ENA

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Effect of ablation of PRDM1 on gene expression in human regulatory T cells

Project description:To gain an insight into the contribution of BLIMP-1 in human Tregs, we ablated PRDM1 in ex-vivo expaned human Tregs by Crispr/Cas9. Tregs transfected with scramble gRNAs were used as controls. 7 days after transfection, Tregs were rested overnight in media, and were re-stimulated through the TCR and IL2R for 16 hr prior to isolation of RNA for genome-wide RNA-seq. Gene expression profiling analysis was performed using data obtained from RNA-seq of four replicates of PRDM1KO and control cells.

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Project description:PRDM1, encoding a transcription factor (TF), regulates plasma cell and CD8+ T-cell terminal differentiation and Th2 lineage specification, while its role in human NK-cell differentiation and homeostasis is largely unknown. Here, we employed a multi-omics approach to dissect the transcriptional control of PRDM1 on human NK-cells. We also employed the APEX2 proximity-based biotinylation method, which enables efficient biotin-labeling of proteins within ~20 nm radius. NK-cells expressing APEX2-tagged PRDM1 were cultured with feeders for 7 or 28 days for the analysis of proximity-labeled proteins. Of the 30 PRDM1-associated cofactors identified by RIME, 12 (40%) were also detected in the APEX2 assay. Consistent with the RIME assay, RUNX3, RUNX1, and CBF-β were also biotinylated by PRDM1- APEX2. A lot more cofactors were identified in the APEX2 experiment, including HDAC1/2, histone deacetylases present in multiple corepressor complexes, similar to a previous study in mouse plasmablasts.

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The transcriptional repressor Blimp1/Prdm1 regulates post-natal reprogramming of intestinal enterocytes

Project description:Expression profiling of Prdm1 mutant E18.5 small intestine was performed using Illumina whole genome V2 arrays. The hypothesis tested in the present study was that Blimp1 regulates the transcription of key genes involved in enterocyte differentiation and survival. Results identify substantial and premature activation of key components of the adult enterocyte biochemical signature. Villin-Cre and Prdm1BEH/+ animals were intercrossed to generate heterozygous Villin-Cre, Prdm1BEH males that were then mated with homozygous Prdm1 CA/CA females carrying the R26R allele to generate Prdm1+/+ (Prdm1CA/+) or Prdm1-/- (Villin-Cre, Prdm1CA/BEH) offspring. Total RNA obtained from 11 Prdm1+/+ and 10 Prdm1-/- E18.5 small intestine samples was hybridized to Illumina WG6_V2 beadchips.

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Project description:Expression profiling of wild-type and Prdm1 null mouse trophoblast giant cell cultures using Illumina whole genome mouse V2 arrays. The hypothesis tested was that Prdm1/Blimp1 regulates expression of genes required for spiral artery trophoblast giant cell function. Prdm1 null and littermate control wild-type trophoblast stem cell clones were generated from blastocyst outgrowths. Total RNA was obtained from multiple replicates of four wild-type TS cell clones and four Prdm1 null TS cell clones differenitated for zero, two, four and six days by growth factor withdrawal and hybridized to Illumina WG6_V2 arrays

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Project description:Group 1 innate lymphoid cells (ILCs) comprise conventional natural killer (cNK) cells and type 1 innate lymphoid cells (ILC1s). The main functions of liver cNK cells and ILC1s not only include directly killing target cells but also regulating local immune microenvironment of the liver through the secretion of cytokines. Uncovering the intricate mechanisms by which transcriptional factors regulate and influence the functions of liver cNK cells and ILC1s, particularly within the context of liver tumors, presents a significant opportunity to amplify the effectiveness of immunotherapies against liver malignancies. Using Ncr1-drived conditional knockout mouse model, our study reveals the regulatory role of Prdm1 in shaping the composition and maturation of cNK cells. Although Prdm1 did not affect the killing function of cNK cells in an in vivo cytotoxicity model, a significant increase in cancer metastasis was observed in Prdm1 knockout mice. Interferon-gamma (IFN-γ), granzyme B, and perforin secretion decreased significantly in Prdm1 deficient cNK cells and liver ILC1s. scRNA sequencing data also provided evidences that Prdm1 maintains functional subsets of cNK cells and liver ILC1s and facilitates communications between cNK cells, liver ILC1s and macrophages. The present study unveiled a novel regulatory mechanism of Prdm1 in cNK cells and liver ILC1s, showing promising potential for developing innovative immune therapy strategies against liver cancer.

2024-08-12 | GSE271233 | GEO

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