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Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity

ABSTRACT: Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity

PROVIDER: PRJNA773118 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16506789.fastq.gz	Fastqsanger.gz
	SRR16506790.fastq.gz	Fastqsanger.gz
	SRR16506791.fastq.gz	Fastqsanger.gz
	SRR16506792.fastq.gz	Fastqsanger.gz

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Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity

Project description:Robust expansion of adoptively transferred T cells is a prerequisite for effective cancer immunotherapy, but how many genes in the genome modulate T cell expansion remains unknown. Here, we performed in vivo and in vitro CRISPR screens to systematically identify genes influencing CD8 T cell expansion. In the mouse genome, ~ 2,600 and ~ 1,500 genes were required for optimal CD8 T cell expansion in vivo and in vitro, respectively. In vivo-specific CD8 T cell essential genes were enriched in metabolic pathways including mitochondrial metabolism. The strongest repressor of CD8 T cell expansion was Roquin, ablation of which drastically boosted T cell proliferation by enhancing cell cycle progression and upregulation of IRF4. Roquin-deficiency or IRF4 overexpression potently enhanced anti-tumor immunity. These data provide a functional catalog of CD8 T cell fitness genes, and suggest targeting Roquin-IRF4 axis is an effective strategy to enhance efficacy of adoptive transfer therapy for cancer.

2021-10-27 | GSE186284 | GEO

Analysis of Roquin targetome during HCMV infection

Project description:To investigate how Roquin regulates cellular transcripts during Human cytomegalovirus (HCMV) infection, we examined the levels of cellular transcripts in cells treated control or Roquin-targeting siRNA during HCMV replication. Also, we performed Roquin crosslinking and immunoprecipitation followed by high-throughput sequencing (Roquin CLIP-seq) in HCMV-infected cells to identify which transcripts are directly bound by Roquin.

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Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Project description:The degradation of TNFM-NM-1 mRNA is critical for restricting TNFM-NM-1 synthesis and involves a constitutive decay element (CDE) in the 3M-bM-^@M-^Y untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale. Expression profiles of LPS treated Raw264.7 cells (input), after Roquin IP or control IP were generated by deep sequencing, in three biological replicates, using Illumina HiSeq 2000.

2013-05-15 | E-GEOD-44775 | biostudies-arrayexpress

Fitness trade-offs lead to suppressor tolerance in yeast

Project description:Fitness trade-offs lead to suppressor tolerance in yeast

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Roquin suppresses PI3K-mTOR signaling to control T cell differentiation and Treg effector function

Project description:Roquin proteins are required to preclude spontaneous T cell activation and aberrant T follicular helper (Tfh) or T helper 17 (Th17) differentiation. Here, we show that deletion of Roquin encoding alleles in regulatory T cells (Tregs) also caused the activation of conventional T cells. These Tregs exhibited a follicular Treg phenotype, CD25 downregulation and could not protect from colitis. Mechanistically, Roquin was required for full expression and activity of Pten and Foxo1, two essential signaling molecules in Tregs and effector T cells. Roquin upregulated Pten by interfering with miR-17~92 binding to an overlapping cis-element in the Pten 3' UTR and downregulated the Foxo1-specific E3 ubiquitin ligase Itch. Loss of Roquin enhanced mTOR signaling and global protein synthesis, while inhibition of PI3K or mTOR in Roquin-deficient CD4+ T cells corrected increased Tfh and Th17 differentiation. Thereby, the control of PI3K-mTOR signaling by Roquin prevents autoimmunity through T cell-intrinsic and Treg-mediated regulation.

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Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Project description:The degradation of TNFα mRNA is critical for restricting TNFα synthesis and involves a constitutive decay element (CDE) in the 3’ untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale.

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MiRNAs sequence of macrophages derived exosoms in WT group and Roquin-1 san:san group.

Project description:We reported the function of Roquin-1 in the miRNA-sorting of macrophages derived exosomes. At first, we used the supernatant of 929 cells to culture the bone marrow derived macrophages (BMDM) from bone marrow cells of WT and Roquin-1 san:san mice. Then, we isolated the macrophages derived exosomes by ultracentrifugation. At last, we performed Next-generation sequencing to detect the differences of miRNA-sorting between WT and Roquin-1 macrophages derived exosomes.

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RNA-binding preference of the Roquin-1 CCCH-type zinc finger

Project description:Zinc finger (ZnF) domains are widespread RNA-binding domains, recognizing single stranded and double stranded RNAs. Together with other RNA-binding domains, ZnFs enhance the affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing RBP Roquin controls mRNA decay by recognizing stem-loop elements in the 3'-UTR of its target mRNAs. Stem-loop elements are bound in a shape-specific manner by the unique ROQ domain with nanomolar affinity. The ZnF was suggested to play an essential role in RNA decay by Roquin. However, its RNA motif preference was not investigated so far. Here, we use RBNS to elucidate the RNA binding preference of the isolated Roquin-1 ZnF domain. We find that the ZnF preferentially recognizes single-stranded AU-rich elements (ARE).

2024-03-21 | GSE253536 | GEO

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