Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Variation in gene transcription between life stages of Trypanosoma vivax

ABSTRACT: Trypanosoma vivax is a major pathogen of domestic cattle and wildlife across sub-Saharan Africa. For many years, the WTSI has had a research interest in developing a genome sequence for T. vivax, as part of a wider programme concerning African trypanosome parasites of Humans and animals. In 2012 a draft genome sequence for T. vivax Y486 was published by the WTSI and our collaborators in comparison with related species, T. brucei and T. congolense. This study identified numerous putative genes in T. vivax that have no known affinity and are therefore species-specific. A related transcriptomic study confirmed that some of these putative genes are transcribed, but lacked accuracy and was based on a single parasite life stage only. Until recently, it has not been possible to culture different T. vivax life stages in refined media. There is now the opportunity to use new approaches to produce whole cell RNA for both insect and bloodstream parasite stages. We sequence stage-specific cDNA and identify stage-specific genes, and compare these features with similar data already available for T. brucei and T. congolense, which display substantial differences in their developmental cycles. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Trypanosoma vivax

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PROVIDER: E-ERAD-100 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The Interleukin-22 (IL22) pathway plays a key role in maintaining homeostasis at the mucosal surfaces and is frequently dysregulated during infectious and inflammatory diseases. Human genome-wide association studies performed at the WTSI have identified SNPs in and around the human IL-22 gene that are associated with IBD susceptibility. The IL-22 cytokine is produced by cells of the innate and adaptive immune systems within the intestinal mucosa and acts on the IL-22 receptor (IL-22RA1) that is present specifically on intestinal epithelial cells. Studies to date have shown the that IL-22 pathway is linked to proliferative and anti-apoptotic pathways, as well as anti-microbial molecule production that help control bacterial invasion and prevent tissue damage. We are characterizing a novel IL-22RA1 KO mouse and have shown that these mice are highly susceptible to enteric bacterial pathogens, such as Citrobacter rodentium and Clostridium difficile. However, the mechanism of this protective immunity is poorly understood. The aim of this project is to identify novel molecules or pathways downstream of IL-22 signaling that provide the mechanistic link between IL-22RA1 and innate immunity. To maintain mouse colonic epithelial cells in vitro, we used an organoid culture system that faithfully recapitulates the crypt architecture of the gastrointestinal epithelium. Primary colonic epithelial crypts were isolated from age-matched wildtype and IL-22ra1 knock-out mice (n = 4 per genotype), and subsequently cultured in the presence of defined growth factors and Matrigel for 5 days. The resulting mature organoids were then either treated with Control medium (Advanced DMEM/F12) or mouse recombinant IL-22 (50ng/ml) for 16 hours. Total RNA were extracted using the QIAgen RNeasy Micro Kit, including an on-column DNAse digestion step, according to manufacturer's protocol. We are submit total RNA samples of good quality (RIN > 7) and quantity.The culture and stimulation conditions have been optimised to achieve significant and specific induction of known target genes such as the antimicrobial peptides RegIIIb, RegIIIg, S100a8 and S100a9. Two technical replicates will be available for each genotype x condition. We aim to sequence 5GBp per replicate, and 5 replicates per lane on an Illumina platform. Through this dataset, we hope to discover epithelial cell-specific pathways downstream of IL-22 signaling that are ablated in the absence of its receptor.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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Variation in gene transcription between life stages of Trypanosoma vivax

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