Our research projects

Background. 2004-2008:

Our project entitled ″Identification of molecular markers for diagnosis and prognosis in cancer using DNA microarrays″, has identified dozens of intronic non-coding anti-sense RNAs (ncRNAs) whose expression levels were correlated to the degree of malignancy of prostate tumors (Reis et al., 2004; PMID: 15221013). This discovery has an impact on the molecular diagnosis of cancer in general, arguing for inclusion of non-coding RNAs, both intra- and inter-genic, into the arsenal of tools used for molecular diagnostics, so far almost exclusively populated by exonic protein-coding RNAs.

In our project we have also identified that:

- the expression profiles of intronic ncRNAs in normal human liver and kidney tissues and in prostate tumors, using customized microarrays with nearly 30 thousand probes for non-coding intronic RNAs. It was observed that the most abundant intronic ncRNAs are transcribed from genomic loci involved with regulation of transcription, in all three tissues studied (Nakaya et al., 2007; PMID: 17386095);

- that the expression of a number of intronic ncRNAs could be modulated by androgen in a prostate cancer cell line, and that androgen modulates both the expression level of certain ncRNAs and the use of alternatively spliced exons of protein-coding genes from the same genomic locus (Louro et al., 2007; PMID: 17263875);

- that a comparative analysis between human and mice intronic ncRNAs revealed a conserved tissue-specific expression profile, suggesting an evolutionarily conserved role of these transcripts among these species, probably involved in the fine tuning of gene expression in mammalian tissues (Louro et al., 2008; PMID: 18495418).

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Current studies:

In August 2008, our group received a new grant from FAPESP for the period 2008-2012. The current thematic project is titled ″Functional characterization of intronic non-coding RNAs expressed in the human genome″, a collaborative project between our group and the research group of Dr. Eduardo M. Reis, an Assistant Professor in our Department. The project aims to investigate the functional implications of intronic ncRNAs in cancer as well as in gene regulation in normal cells, along with their possible use as markers of malignancy in a number of cancers. The present project will permit to consolidate in our group the use of cell biology approaches for the study of ncRNAs, a line of work that has been recently introduced in our laboratory. Currently, our group is studying the effect of over-expression of selected ncRNAs on cell proliferation and cell invasion.

The project is divided into two major parts:

(A) Functional characterization of non-coding RNAs over-expressed in human tumors, and
(B) Identification of novel non-coding RNAs and validation of gene expression profiles as possible tumor markers.

We expect to identify genes that are possible new molecular markers of early diagnosis and prognosis in prostate cancer, as well as to elucidate some of the mechanisms of action of ncRNAs, contributing to broaden the potential targets for therapeutic interventions.

Publications
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Schistosoma mansoni EST genome. Our group has received support from FAPESP to build DNA microarrays on glass-slides containing 4 000 S. mansoni gene fragments. See the project here. These were selected among the 14 000 genes that were identified by the S. mansoni EST Genome Project, coordinated by our group, whose results were published in Nature Genetics on October 1st, 2003 (download PDF; PMID: 12973350).

One of our first goals will be to use microarrays to do large-scale gene expression analysis in adult worms and to study the effect of hormones and cytokines. Gene expression pattern during S. mansoni development and maturation from cercaria to schistosomula will also be studied. Collaboration with other research groups worldwide is envisaged.


Schistosoma mansoni TNF-α receptor. We have recently described (Oliveira et al., 2009; PMID: 19956564) a possible TNF-α receptor (TNFR) homolog gene in S. mansoni (SmTNFR). SmTNFR encodes a complete receptor sequence composed of 599 amino acids, and contains four cysteine-rich domains as described for TNFR members.

Real-time RT-PCR experiments revealed that SmTNFR highest expression level is in cercariae, 3.5 (60.7) times higher than in adult worms. Downstream members of the known human TNF-α pathway were identified by an in silico analysis, revealing a possible TNF-α signaling pathway in the parasite. In order to simulate parasite's exposure to human cytokine during penetration of the skin, schistosomula were exposed to human TNF-α just 3 h after cercariae-to-schistosomula in vitro transformation, and large-scale gene expression measurements were performed with microarrays. A total of 548 genes with significantly altered expression were detected, when compared to control parasites. In addition, treatment of adult worms with TNF-α caused a significantly altered expression of 1857 genes. Interestingly, the set of genes altered in adults is different from that of schistosomula, with 58 genes in common, representing 3% of altered genes in adults and 11% in 3 h-old early schistosomula. The possible molecular elements and targets involved in human TNF-α effect on S. mansoni were described, highlighting the mechanism by which recently transformed schistosomula may sense and respond to this host mediator at the site of cercarial penetration into the skin.

Our present work aims at further characterizing the receptor by its immuno-localization at different organs of the parasite, by searching for possible partner protein ligands with the use of two-hybrid systems, by looking for the possible effect of siRNA of the receptor message on parasite survival in the model host.

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Our group developed competence in bioinformatics to support the large scale transcriptome sequencing and analyses projects of both humans and S. mansoni. Our team of bioinformaticians is composed of technicians with higher degree in computer sciences and graduate students in bioinformatics. They work in the large scale mapping of all human ESTs in the genome, in order to select transcribed genes of interest to be selected as probes for the construction of dedicated microarrays. These are used in our large scale gene expression studies.

Click here to see the Bioinformatics webpage of the group.

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