Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAseq analysis of γδ T-APCs generated in the presence of IL-2, IL-15 or IL-21, aiming to define the molecular mechanism underlying selective induction of IL-10 in naïve and memory CD4+ T-cells

ABSTRACT: This experiment involved isolating monocytes and irradiating them before co-culturing with autologous γδ T-cells at a 1:10 ratio. The cell culture experiments were analysed after HMB-PP activation only, or in combination with different interleukins (IL-2, IL-15, or IL-21). After three days, CD3+ Vδ2+ T-cells were selected via FACs (> 99% purity).

INSTRUMENT(S): RNeasy Micro Kit (Qiagen), NA, Illumina Stranded Total RNA Prep, FACSAria II, NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Daniel Griffiths

PROVIDER: E-MTAB-13875 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Abstract: Bovine tuberculosis (bTB), caused by infection with Mycobacterium bovis, continues to cause significant issues for the global agriculture industry as well as for human health. An incomplete understanding of the host immune response contributes to the challenges of control and eradication of this zoonotic disease. In this study, high-throughput bulk RNA sequencing (RNA-seq) was used to characterize differential gene expression in γδ T cells – a subgroup of T cells which bridge innate and adaptive immunity and have specific anti-mycobacterial response mechanisms. γδ T cell subsets are classified on the basis of expression of a pathogen-recognition receptor known as Workshop Cluster 1 (WC1) and we hypothesised that bTB infection may alter the phenotype and function of specific γδ T cell subsets. Peripheral blood was collected from naturally M. bovis-infected (positive for single intradermal comparative tuberculin test (SICTT) and IFN-γ ELISA) and age- and sex-matched, non-infected control Holstein-Friesian cattle. γδ T subsets were isolated using fluorescence activated cell sorting (n = 10-12 per group) and high-quality RNA extracted from each purified lymphocyte subset (WC1.1+, WC1.2+, WC1- and γδ-) was used to generate transcriptomes using bulk RNA-seq (n = 6 per group, representing a total of 48 RNA-seq libraries). Relatively low numbers of differentially expressed genes (DEGs) were observed between most cell subsets; however, 163 genes were significantly differentially expressed in the M. bovis-infected compared to control groups for the WC1.1+ γδ T cell compartment (Log 2 FC ≥ 1.5 and FDR P adj ≤ 0.1). The majority of these DEGs (146) were significantly increased in expression in cells from the bTB+ cattle and included genes encoding transcription factor (TBX21 and EOMES), chemokine receptors (CCR5 and CCR7), granzymes (GZMA, GZMM and GZMH) and multiple killer cell immunoglobulin-like receptors (KIR) indicating cytotoxic functions. Biological pathway overrepresentation analysis revealed enrichment of genes with multiple immune functions including cell activation, proliferation, chemotaxis and cytotoxicity of lymphocytes. In conclusion, WC1.1+ γδ T cells have been proposed as major regulatory cell subset in cattle, and we provide evidence for preferential differential activation of this specific subset in cattle naturally infected with M. bovis. Understanding the role of these critical immune cells during mycobacterial infection contributes to our understanding of host immunity to bTB and identifies multiple novel cytotoxic functions of WC1.1+ γδ T cells.

Dataset Information

RNAseq analysis of γδ T-APCs generated in the presence of IL-2, IL-15 or IL-21, aiming to define the molecular mechanism underlying selective induction of IL-10 in naïve and memory CD4+ T-cells

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