Transcriptome analysis of Taenia solium cysticerci using Open reading Frame ESTS (ORESTES)

<p>Abstract</p> <p>Background</p> <p>Human infection by the pork tapeworm <it>Taenia solium </it>affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form.</p> <p>Results</p> <p>Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development.</p> <p>Conclusion</p> <p>The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed.</p

Transcriptome analysis of Taenia solium cysticerci using Open Reading Frama ESTs (ORESTES)

Background: Human infection by the pork tapeworm Taenia solium affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form. Results: Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development. Conclusion: The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed

Influence of Genomic Ancestry on the Distribution of SLCO1B1, SLCO1B3 and ABCB1 Gene Polymorphisms among Brazilians

The frequency distribution of SNPs and haplotypes in the ABCB1, SLCO1B1 and SLCO1B3 genes varies largely among continental populations. This variation can lead to biases in pharmacogenetic studies conducted in admixed populations such as those from Brazil and other Latin American countries. The aim of this study was to evaluate the influence of self-reported colour, geographical origin and genomic ancestry on distributions of the ABCB1, SLCO1B1 and SLCO1B3 polymorphisms and derived haplotypes in admixed Brazilian populations. A total of 1039 healthy adults from the north, north-east, south-east and south of Brazil were recruited for this investigation. The c.388A&gt;G (rs2306283), c.463C&gt;A (rs11045819) and c.521T&gt;C (rs4149056) SNPs in the SLCO1B1 gene and c.334T&gt;G (rs4149117) and c.699G&gt;A (rs7311358) SNPs in the SLCO1B3 gene were determined by Taqman 5'-nuclease assays. The ABCB1 c.1236C&gt;T (rs1128503), c.2677G&gt;T/A (rs2032582) and c.3435C&gt;T (rs1045642) polymorphisms were genotyped using a previously described single-base extension/termination method. The results showed that genotype and haplotype distributions are highly variable among populations of the same self-reported colour and geographical region. However, genomic ancestry showed that these associations are better explained by a continuous variable. The influence of ancestry on the distribution of alleles and haplotype frequencies was more evident in variants with large differences in allele frequencies between European and African populations. Design and interpretation of pharmacogenetic studies using these transporter genes should include genomic controls to avoid spurious conclusions based on improper matching of study cohorts from Brazilian populations and other highly admixed populations.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq, Brazil)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), BrazilFinanciadora de Estudos e Projetos (FINEP, Brazil)Financiadora de Estudos e Projetos (FINEP), Brazi

Transcriptome analysis of Taenia solium cysticerci using Open Reading Frama ESTs (ORESTES)

Background: Human infection by the pork tapeworm Taenia solium affects more than 50 million people worldwide, particularly in underdeveloped and developing countries. Cysticercosis which arises from larval encystation can be life threatening and difficult to treat. Here, we investigate for the first time the transcriptome of the clinically relevant cysticerci larval form. Results: Using Expressed Sequence Tags (ESTs) produced by the ORESTES method, a total of 1,520 high quality ESTs were generated from 20 ORESTES cDNA mini-libraries and its analysis revealed fragments of genes with promising applications including 51 ESTs matching antigens previously described in other species, as well as 113 sequences representing proteins with potential extracellular localization, with obvious applications for immune-diagnosis or vaccine development. Conclusion: The set of sequences described here will contribute to deciphering the expression profile of this important parasite and will be informative for the genome assembly and annotation, as well as for studies of intra- and inter-specific sequence variability. Genes of interest for developing new diagnostic and therapeutic tools are described and discussed

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. in addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.Univ São Paulo, Fac Med, Inst Psiquiatria, Neurosci Lab,Dept Psiquiatria, BR-05403010 São Paulo, BrazilUniv São Paulo, Fac Med, Dept Bioquim, BR-05403010 São Paulo, BrazilUniv São Paulo, Fac Med, Lab Bioinformat, Inst Quim, BR-05403010 São Paulo, BrazilUniv São Paulo, Fac Med, Disciplina Oncol, Dept Radiol, BR-05403010 São Paulo, BrazilUniversidade Federal de São Paulo, Mol Endocrinol Lab, Dept Med & Morfol, São Paulo, BrazilHosp Canc AC Camargo, Dept Cirurg Cabeca & Pescoco & Otorrinolaringolog, São Paulo, SP, BrazilUniv Estadual Campinas, Inst Biol, Dept Genet & Evolucao, Lab Biol Mol & Genom Hemoctr, Campinas, SP, BrazilUniv Estadual Campinas, Inst Biol, Dept Genet & Evolucao, Lab Genom & Expressao, Campinas, SP, BrazilUniv Estadual Paulista, Dept Biol, Inst Biociencias, Araraquara, SP, BrazilFac Med Sao Jose Rio Preto, Dept Biol Mol, Sao Jose de Rio Preto, SP, BrazilUniv Estadual Paulista, Escola Farm, Dept Ciencias Biol, Araraquara, SP, BrazilUniversidade Federal de São Paulo, Mol Endocrinol Lab, Dept Med & Morfol, São Paulo, BrazilWeb of Scienc