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Elucidation of the effects of tonic TCR stimulation and tissue environments of the chromatin status of naive CD4 T (TN) cells

ABSTRACT: Elucidation of the effects of tonic TCR stimulation and tissue environments of the chromatin status of naive CD4 T (TN) cells

PROVIDER: PRJNA890598 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21903523_1.fastq.gz	Fastqsanger.gz
	SRR21903523_2.fastq.gz	Fastqsanger.gz
	SRR21903524_1.fastq.gz	Fastqsanger.gz
	SRR21903524_2.fastq.gz	Fastqsanger.gz
	SRR21903525_1.fastq.gz	Fastqsanger.gz

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Elucidation of the effects of tonic TCR stimulation and tissue environments of the chromatin status of naive CD4 T (TN) cells

Project description:Naive CD4 T (TN) cells show some degree of heterogeneity. However, mechanisms that alter TN cells are still largely unknown, and physiological importance in the phenotypic alteration of TN cells is unclear. Thus, to reveal the mechanisms that alter TN cell characteristics, we performed transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) on TN cells from different secondary lymphoid organs with different strength of tonic TCR stimulation.

2024-03-01 | GSE215773 | GEO

Strong basal/tonic TCR signals are associated with chromatin accessibility changes in naive CD4+ T cells

Project description:Naïve T cells constantly experience TCR signals in response to self-peptides presented by MHC (pMHC) in vivo. The intensity of these basal or tonic TCR signals can be indirectly read out by expression of surrogate markers of tonic TCR signaling, including the Nur77-GFP transgene and Ly6c. The strength of tonic TCR signaling varies broadly across the naïve CD4+ T cell population and is correlated with functional heterogeneity.Cells that experience the most basal TCR signaling (Nur77-GFP hi, Ly6c lo) are hyporesponsive to peptide-MHC stimulation. Here we examine whether tonic TCR stimulation is associated with differences in chromatin accessibility.

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Strong basal/tonic TCR signals are associated with gene expression changes in naive CD4+ T cells

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Elucidation of tonic and activated B cell receptor signaling in Burkitt’s lymphoma provides insights into regulation of cell survival

Project description:B-cell receptor (BCR) signaling promotes the survival of malignant B cells, such as Burkitt’s lymphoma (BL) and the activated B-cell-like subtype of diffuse large B cell lymphoma (ABC-DLBCL). In contrast to ABC DLBCL, where malignant cells require chronic activation of the BCR for their survival, BL cells are dependent on tonic BCR signaling that is antigen-independent. Elucidation and systematic comparison of tonic and activated BCR signaling led to the identification of novel signaling effectors, among them ACTN4 and ARFGEF2, which were identified as regulators of BL cell survival. As tonic and activated BCR signaling are relevant for important aspects of B cell biology, our study helps in gaining an understanding of BCR-induced processes not only in malignant but potentially also physiological settings.

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Effects of mTOR inhibition on the phenotypes of spleen naive CD4+ T (TN) cells.

Project description:To analyze the influence of mTOR activity on TN cells, RNA-seq analysis was performed on splenic TN cells from mice treated or not treated with the mTOR inhibitor Rapamycin.

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Project description:Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser and Thr residues, is found on most solid tumors yet rarely detected in adult tissues: featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of the new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn. This exquisite Gal(13C6)-Tn structure is recognized by a human-gut-bacterial enzyme, called OpeRATOR, that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser and Thr residues to yield site-containing glycopeptides. The enzymes C1GalT1 and OpeRATOR could be used concurrently in one-pot. The effectiveness of EXoO-Tn was evaluated by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. Bioinformatic analysis of the identified site-specific Tn-glycoproteins revealed conserved motif, cellular localization, relative position in proteins, and mapped site-specific Tn-glycoproteome in different studies. Given the significance of Tn in cancers, EXoO-Tn is anticipated to have broad utilities in clinical study of cancers.

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Comparison of mRNA expression between naive CD4+ T (TN) cells treated or not treated with IL-1b

Project description:To analyze effects of IL-1b on TN cells, RNA-seq analysis was performed on freshly prepared TN cells (0 h) and TN cells cultured with or without recombinamt IL-1b.

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Effects of IL-1b inhibition on the phenotypes of spleen naive CD4+ T (TN) cells.

Project description:To analyze the influence of IL-1b on TN cells, RNA-seq analysis was performed on spleen TN cells from mice treated or not treated with IL-1b inhibitors.

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Project description:To analyze difference between spleen and mLN TN cells, RNA-seq analysis was performed on TN cells freshly prepared from each organ.

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| PRJNA890594 | ENA