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Characterization and effective expansion of CD4-CD8- TCRab+ T cells from individuals living with type 1 diabetes

ABSTRACT: Characterization and effective expansion of CD4-CD8- TCRab+ T cells from individuals living with type 1 diabetes

PROVIDER: PRJNA1204964 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31864456.fastq.gz	Fastqsanger.gz
	SRR31864457.fastq.gz	Fastqsanger.gz
	SRR31864458.fastq.gz	Fastqsanger.gz
	SRR31864459.fastq.gz	Fastqsanger.gz
	SRR31864460.fastq.gz	Fastqsanger.gz

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Characterization and effective expansion of CD4-CD8- TCRab+ T cells from individuals living with type 1 diabetes

Project description:CD4-CD8- TCRab+ (double-negative [DN]) T cells represent a rare T cell population that promotes immunological tolerance through various cytotoxic mechanisms. In mice, autologous transfer of DN T cells has shown protective effects against autoimmune diabetes and graft-versus-host disease. Here, we characterized humanDNT cells from people living with type 1 diabetes (PWT1D) and healthy controls. We found that while DN T cells and CD8+ T cells share many similarities, DN T cells are a unique T cell population, both at the transcriptomic and protein levels. We also show that by using various cytokine combinations, human DN T cells can be expanded in vitro up to 1,000- fold (mean >250-fold) and remain functional post-expansion. In addition, we report that DN T cells from PWT1D display a phenotype comparable to that of healthy controls, efficiently expand, and are highly functional. As DN T cells are immunoregulatory and can prevent T1D in various mouse models, these observations suggest that autologous DN T cells may be amenable to therapy for the prevention or treatment of T1D.

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Genetic code expansion reveals site-specific lactylation in living cells reshapes protein function

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Global expression profiling of peripheral Qa-1 class Ib-restricted CD8aa+TCRab+ regulatory T Cells reveals innate-like features: implications for immune regulatory repertoire

Project description:To better understand the function of CD8aa Tregs, we have recently characterized several CD8aa+TCRab+ T cell clones and lines that are physiologically primed and are involved in recovery and protection from EAE (REF). In this report, we present a comparison of global gene expression patterns in CD8aa Tregs versus OT-1 CD8aa+TCRab+ T cells. The results of microarray data analysis are confirmed by real-time PCR and flow cytometry for better accuracy and phenotype expression. Our study reveals a unique gene signature in the CD8aa Tregs, including enhanced expression of several inhibitory molecules associated with the maintenance of peripheral T cell homeostasis. The identification of differentially expressed molecules by CD8aa Tregs should facilitate future functional studies in this area. gene expression patterns in CD8aa Tregs versus OT-1 CD8aa+TCRab+ T cells

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Blood RNA sequencing in HIV-negative healthy volunteers and people living with HIV on effective, long-term anti-retroviral therapy

Project description:Immune activation in people living with HIV on anti-retroviral therapy is associated with increased risk of morbidity and mortality, but the underlying mechanisms are poorly understood. To identify whether perturbation of immunological pathways persist at systems level, we compared genome-wide whole blood transcriptomes from 26 people living with HIV on long-term anti-retroviral therapy with 12 HIV-negative healthy controls. All participants were Caucasian male adults recruited from London, UK. People living with HIV were on anti-retroviral therapy for a median of 8.5 years (interquartile range 3-16 years). They had undetectable plasma HIV viral load (<40 copies/ml) and median circulating CD4 counts of 703 cells/µl (interquartile range 491-841 cells/µl).

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Project description:Still in its infancy, the functions of lactylation remain elusive. To address this, we established a comprehensive workflow for lactylation studies that integrates the discovery of lactylation sites with proteomics, the expression of site-specifically lactylated proteins in living cells via genetic code expansion (GCE), and the evaluation of the resulting biological consequences. Specifically, we developed a wet-and-dry-lab combined proteomics strategy, and identified highly conserved lactylation at ALDOA-K147. Driven by its potential biological significance, we site-specifically expressed this lactylated ALDOA in mammalian cells and interrogated the biological changes. We discovered that it not only inhibited enzyme activity but also elicited gain-of-function effects——it dramatically reshaped the functionality of ALDOA by improving stability, enhancing nuclear translocation and affecting gene expression. Further, we demonstrated broad applicability of this workflow to study distinct histone lactylation sites. Together, we anticipate its wide uses in elucidating causative links between site-specific lactylation and target-centric or cell-wide changes.

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Project description:Naive CD4 T cells defined as (TCRab+ CD4+ CD45RA+ CD62L+ CD127+) were further divided by CD25 and CD31 expression with FACS-based flow sorting. Subsequently, gene expression levels of each subset were assessed by using transcription arrays.

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Project description:This experiment exploits the life-cycle of Strongyloides ratti, which is a parasitic nematode of brown rats that exhibits three adult stages within its life-cycle - parasitic females, freeliving females and free-living males. We use a cDNA microarray to examine patterns of (i) gender-biased gene expression by contrasting free-living females against free-living males, and (ii) parasitic-biased expression by contrasting parasitic females against free-living females. Of the 3688 distinct transcripts represented on our array, 20% exhibited male-biased expression 19% exhibit female-biased expression, 11% exhibit parasitic-biased expression and 8% exhibit free-living-biased expression. Among the top responding genes, an orthologue of major sperm protein is upregulated in males, distinct aspartic protease orthologues are upregulated in either parasitic or in free-living females, and orthologues of hsp-17 chaperone are upregulated in parasitic females. Upon a global analysis of gene expression, we find that female-biased expression is associated with genes involved in reproductive processes and larval development, that male-biased expression is associated with genes involved in metabolism, and that free-living biased expression is associated with genes involved in regulation of body fluids and response to external stimulus. The association of gene ontology with parasite-biased expression is less clear. Our results provide an initial gene expression analysis of gender- and parasite-biased expression in S. ratti, may be more generally applicable to other parasitic nematodes, and may help to refine the search for novel drug or vaccine targets against parasitic nematodes.

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Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor

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