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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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Project description:We reports the transcript landscape of PR Domain Containing 1, with ZNF domain (PRDM1) in RKO colon cancer cells. We show that PRDM1 alpha and PRDM1 beta transcript isoforms repress and activate a largely overlapping suite of genes, many of which belong to the embryonic stem cell core transcript program.

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PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cells

Project description:Lentiviral vectors have markedly enhanced gene therapy efficiency in treating congenital diseases, but its long-term safety remains controversial. Most gene therapies for congenital eye diseases need to be carried out at early ages, yet the assessment of related risks to ocular development posed by lentiviral vectors is challenging. Utilizing single-cell transcriptomic profiling on human retinal organoids, this study explored the impact of lentiviral vectors on the retinal development and found that lentiviral vectors can cause retinal precursor cells to shift toward photoreceptor fate through the up-regulation of key fate-determining genes such as PRDM1. Further investigation demonstrated that the intron and intergenic region of PRDM1 was bound by PHLDA1, which was also upregulated by lentiviral vector exposure. Importantly, knockdown of PHLDA1 successfully suppressed the lentivirus-induced differentiation bias of photoreceptor cells. The findings also suggest that while lentiviral vectors may disrupt the fate determination of retinal precursor cells, posing risks in early-stage retinal gene therapy, these risks could potentially be reduced by inhibiting the PHLDA1-PRDM1 signaling axis.

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