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RNAseq of S. stercoralis PV001 strain developmental stages

ABSTRACT: RNAseq of S. stercoralis PV001 strain developmental stages

PROVIDER: PRJEB3116 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR146941_1.fastq.gz	Fastqsanger.gz
	ERR146941_2.fastq.gz	Fastqsanger.gz
	ERR146942_1.fastq.gz	Fastqsanger.gz
	ERR146942_2.fastq.gz	Fastqsanger.gz
	ERR146943_1.fastq.gz	Fastqsanger.gz

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Project description:BACKGROUND: Differences between noninfective first-stage (L1) and infective third-stage (L3i) larvae of parasitic nematode Strongyloides stercoralisat the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose. METHODS AND FINDINGS: Oligonucleotide hybridization probes for the array were designed to bind 3571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs) obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation System software. We identified 967 differentially expressed genes (457 L3i-biased; 510 L1-biased) having greater than two-fold expression differences and p < 0.01. Based on functional analysis, L1s have a larger number of genes putatively involved in transcription (p = 0.0158), and L3is have higher expression of stress-related genes (such as putative heat shock proteins dnj-12, daf-21, dnj-10). Genes with products that have been shown to be immunoreactive in S. sterocoralis-infected humans (SsIR and NIE) were additionally found to be L3i biased. Unique and abundant L3i contigs of interest included S. stercoralis orthologs of cytochrome oxidase ucr 2.1, daf-12, and daf-21, which may be potential chemotherapeutic targets. The S. stercoralis ortholog of fatty acid and retinol binding protein-1, successfully used in a vaccine against Ancylostoma ceylanicum, was identified among the top 25 most L3i-biased genes. The sperm-containing glycoprotein domain, utilized in a vaccine against the nematode Cooperia punctata, was exclusively found in the L3i group and may be a valuable S. stercoralis target of interest. Conclusions A new DNA microarray tool for the examination of S. stercoralis biology has been developed and provides new and valuable insights regarding differences between infective and noninfective S. stercoralis larvae. Potential therapeutic and vaccine targets were identified for further study.

Project description:Background - Strongyloidiasis is a neglected tropical disease affecting an estimated 600 million people, particularly in resource-limited settings. The infection can persist lifelong due to Strongyloides stercoralis peculiar auto-infective cycle. The cumbersome diagnosis and the limited knowledge of the mechanisms underpinning this chronic infection are key issues in the disease management. To date, only a few proteomics studies have been conducted to elucidate the molecular mechanisms associated with Strongyloides parasitism or to highlight novel immunological markers and our knowledge of S. stercoralis proteome still limited. Methods - S. stercoralis infective larvae (iL3) we isolated from a faecal sample from an infected subject and analysed by high-throughput tandem mass spectrometry. To achieve a more comprehensive characterisation of iL3 proteome the experimental dataset was analysed through an automatic search strategy combined with manual annotation, which included gene ontology (GO) analysis, InterPro annotation, assessment of the homology with Homo sapiens and other pathogens of clinical importance and B-cell epitope prediction. Results – Our pipeline identified 430 S. stercoralis proteins, 187 (43%) of which corresponded to uncharacterized proteins. Oxidoreductases and peptidases were amongst the most represented protein categories as highlighted by GO analyses (molecular function terms); while membrane and mitochondrial proteins were the most represented cellular component GO categories. In our dataset we also identified a high proportion of proteins bearing CAP, SCP or thioredoxin domain or belonging to cysteine-rich secretory, transthyretin-like or peptidase protein families, confirming previous data on the most represented proteins associated with S. stercoralis parasitism, as inferred from genomic and transcriptomic data. Finally, we also highlighted 9 proteins bearing amino acid sequences with immunogenic properties that might represent novel candidates for serological tests. Conclusions – Here we provide a comprehensive description and annotation of S. stercoralis iL3 proteome and propose some proteins as potentially immunogenic, to be evaluated as novel serological diagnostic markers. In order to highlight novel targets to improve current serodiagnosis and treatment, it is in fact fundamental to expand the molecular understanding derived from ‘omics studies beyond the current state of the art.

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RNAseq of S. stercoralis PV001 strain developmental stages

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