Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097983 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28645723.fastq.gz | Fastqsanger.gz | |||
| SRR28645724.fastq.gz | Fastqsanger.gz | |||
| SRR28645725.fastq.gz | Fastqsanger.gz | |||
| SRR28645726.fastq.gz | Fastqsanger.gz | |||
| SRR28645727.fastq.gz | Fastqsanger.gz |
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Project description:In this work we analyzed the genomic diversity of several Tropheryma whipplei strains by microarray based-comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples recovered from different countries were compared with the T. whipplei Twist strain. For each isolate, the genes were defined as either present or absent/divergent using the GACK analysis software. Genomic changes were then further characterized by PCR and sequencing. Obtained results revealed a limited genetic variation between these T. whipplei isolates with at most 2.24 % of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding for the WiSP family proteins supporting the view of these membrane proteins as key actors of immune evasion. This work also evidenced a 19.2 kb-pair deletion within T. whipplei DIG15 strain. This deletion takes place in the same region as the large genomic rearrangement previously described between Twist and TW08/27 which can thus be considered as a major hot-spot for intra-specific T. whipplei differentiation. Analysis of this deleted region confirmed the role of WND-domains in generating T. whipplei diversity Keywords: Comparative genomic hybridization
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Project description:Metagenomic sequencing Analysis two genome of Tropheryma whipplei from China
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Project description:Background: It has been shown that intracellular pathogens hijack DC functions to evade immune defense mechanisms. In this study, we investigated the responses of human monocyte derived DCs to four intracellular bacteria, Tropheryma whipplei, Coxiella burnetii, Brucella abortus and Orientia tsutsugamushi, responsible for human infectious diseases and known to infect myeloid cells. Methods: Whole genome microarrays were assessed to define common and specific transcriptionnal responses to bacterial pathogen. Bacterial pathogen ability to affect DC maturation was assessed by measuring lymphoproliferation and endocytosis as well as phenotypic maturation markers (CD80, CD83, CD86 and HLA-DR) expression. Results: We found that Coxiella burnetii, Orientia tsutsugamushi and Brucella abortus induced DC maturation assessed through decreased endocytosis ability, triggering lymphoproliferation, surface expression of HLA class II molecules and phenotypic changes, whereas Tropheryma whipplei did not induce DC maturation. As revealed by microarray analysis, the response of DCs to these bacteria consisted of a core associated with the maturation of DCs and signatures specific for each pathogen. The core response represented 10% of genes modulated in response to pathogens and consisted of general cellular processes including nucleotide binding, protein transport, cell fraction, protein kinase, cell cycle, mitochondrial membrane and cytoskeleton. The specific transcriptional signature induced by C. burnetii is associated with the communication between innate and adaptive immune cells and DC maturation. B. abortus signature specifically involved arachidonic acid and lipooxygenase pathways and O. tsutsugamushi signature involved type I and type III IFN responses. Conclusion: This study demonstrates that intracellular bacteria use multifaceted pathways to induce DC maturation which may lead to unadapted immune response. The understanding of these pathways may be useful to improve our knowledge of bacterial recognition by the immune system but also intracellular bacterial diseases. IL4/GM-CSF monocyte-derived dendritic cells were stimulated by T. whipplei, B. abortus, C. burnetii, O. tsutsugamushi and LPS during 6 hours. Common and specific signatures were determined by comparison with uninfected DCs. moDCs (5.10^6) were plated in 6 well plates and stimulated with bacteria or LPS for 6 hours, and total RNA was extracted using the RNeasy minikit (Qiagen, adresse CA) and DNase treatment. The Agilent-014850 4X44k Human Whole Genome microarrays (Agilent Technologies, CA) representing 44,000 probes were used as recently described. Reverse transcription, sample labeling and hybridization were performed according to protocols specified by the manufacturer (One-Color Microarray-Based Gene Expression Analysis). Three samples per experimental condition were included in the analysis.
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