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BMC Cancer
Published in: BMC Cancer 1/2018

Open Access 01-12-2018 | Research article

In vitro and in silico validation of CA3 and FHL1 downregulation in oral cancer

Authors: Cláudia Maria Pereira, Ana Carolina de Carvalho, Felipe Rodrigues da Silva, Matias Eliseo Melendez, Roberta Cardim Lessa, Valéria Cristina C. Andrade, Luiz Paulo Kowalski, André L. Vettore, André Lopes Carvalho

Published in: BMC Cancer | Issue 1/2018

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Abstract

Background

Aberrant methylation is a frequent event in oral cancer.

Methods

In order to better characterize these alterations, a search for genes downregulated by aberrant methylation in oral squamous cell carcinoma (OSCC) was conducted through the mining of ORESTES dataset. Findings were further validated in OSCC cell lines and patients’ samples and confirmed using TCGA data. Differentially expressed genes were identified in ORESTES libraries and validated in vitro using RT-PCR in HNSCC cell-lines and OSCC tumor samples. Further confirmation of these results was performed using mRNA expression and methylation data from The Cancer Genome Atlas (TCGA) data.

Results

From the set of genes selected for validation, CA3 and FHL1 were downregulated in 60% (12/20) and 75% (15/20) of OSCC samples, respectively, and in HNSCC cell lines. The treatment of cell lines JHU-13 and FaDu with the demethylating agent 5'-aza-dC was efficient in restoring CA3 and FHL1 expression. TCGA expression and methylation data on OSCC confirms the downregulation of these genes in OSCC samples and also suggests that expression of CA3 and FHL1 is probably regulated by methylation. The downregulation of CA3 and FHL1 observed in silico was validated in HNSCC cell lines and OSCC samples, showing the feasibility of integrating different datasets to select differentially expressed genes in silico.

Conclusions

These results showed that the downregulation of CA3 and FHL1 data observed in the ORESTES libraries was validated in HNSCC cell lines and OSCC samples and in a large cohort of samples from the TCGA database. Moreover, it suggests that expression of CA3 and FHL1 could probably be regulated by methylation having an important role the oral carcinogenesis.
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Metadata
Title
In vitro and in silico validation of CA3 and FHL1 downregulation in oral cancer
Authors
Cláudia Maria Pereira
Ana Carolina de Carvalho
Felipe Rodrigues da Silva
Matias Eliseo Melendez
Roberta Cardim Lessa
Valéria Cristina C. Andrade
Luiz Paulo Kowalski
André L. Vettore
André Lopes Carvalho
Publication date
01-12-2018
Publisher
BioMed Central
Published in
BMC Cancer / Issue 1/2018
Electronic ISSN: 1471-2407
DOI
https://doi.org/10.1186/s12885-018-4077-3

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