Limits...
Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries.

Silveira NJ, Varuzza L, Machado-Lima A, Lauretto MS, Pinheiro DG, Rodrigues RV, Severino P, Nobrega FG, Head and Neck Genome Project GENCAPOSilva WA, de B Pereira CA, Tajara EH - BMC Med Genomics (2008)

Bottom Line: As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues.Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development.This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, UNIVAP, São José dos Campos, SP, Brazil. nelsonjfs@univap.br

ABSTRACT

Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes.

Methods: Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries.

Results: Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis, quantitative PCR confirmed the upregulation of BST2 and MFAP2 and the downregulation of KRT31 when samples of HNSCC were compared to tumor-free surgical margins. As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues.

Conclusion: To the best of our knowledge, this is the first study reporting SAGE data in head and neck squamous cell tumors. Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development. The differential expression of a subset of genes was confirmed in additional larynx carcinoma samples and in carcinomas from a distinct head and neck subsite. This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

No MeSH data available.


Related in: MedlinePlus

Fluxogram showing the strategy used in SAGE data analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2629771&req=5

Figure 1: Fluxogram showing the strategy used in SAGE data analysis.

Mentions: Tag frequency tables, composed of a "tag" column (10 bp sequences) and a "count" column (number of times that the tag appears in the library) were obtained by the SAGE™ Analysis 2000 Software 4.0, with minimum tag count set to 1 and maximum di-tag length set to 28 bp, whereas other parameters were set on default. A relational MySQL database [13] was developed to store data from SAGE experiments. The datasets contained information on: gene name, accession number, UniGene code, gene symbol, absolute frequency tags in metastatic and non-metastatic tumors and normal tissues. Other tables were generated to store information on metabolic pathways and gene ontology. Scripts developed in Perl [14] integrated with the MySQL database allowed the identification of genes and their respective frequencies in the three libraries which were used as input data in the program that performed statistical analysis. A schematic representation of databases, data analysis, and experimental validation representing our approach is shown in Figure 1.


Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries.

Silveira NJ, Varuzza L, Machado-Lima A, Lauretto MS, Pinheiro DG, Rodrigues RV, Severino P, Nobrega FG, Head and Neck Genome Project GENCAPOSilva WA, de B Pereira CA, Tajara EH - BMC Med Genomics (2008)

Fluxogram showing the strategy used in SAGE data analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2629771&req=5

Figure 1: Fluxogram showing the strategy used in SAGE data analysis.
Mentions: Tag frequency tables, composed of a "tag" column (10 bp sequences) and a "count" column (number of times that the tag appears in the library) were obtained by the SAGE™ Analysis 2000 Software 4.0, with minimum tag count set to 1 and maximum di-tag length set to 28 bp, whereas other parameters were set on default. A relational MySQL database [13] was developed to store data from SAGE experiments. The datasets contained information on: gene name, accession number, UniGene code, gene symbol, absolute frequency tags in metastatic and non-metastatic tumors and normal tissues. Other tables were generated to store information on metabolic pathways and gene ontology. Scripts developed in Perl [14] integrated with the MySQL database allowed the identification of genes and their respective frequencies in the three libraries which were used as input data in the program that performed statistical analysis. A schematic representation of databases, data analysis, and experimental validation representing our approach is shown in Figure 1.

Bottom Line: As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues.Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development.This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, UNIVAP, São José dos Campos, SP, Brazil. nelsonjfs@univap.br

ABSTRACT

Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes.

Methods: Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries.

Results: Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis, quantitative PCR confirmed the upregulation of BST2 and MFAP2 and the downregulation of KRT31 when samples of HNSCC were compared to tumor-free surgical margins. As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues.

Conclusion: To the best of our knowledge, this is the first study reporting SAGE data in head and neck squamous cell tumors. Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development. The differential expression of a subset of genes was confirmed in additional larynx carcinoma samples and in carcinomas from a distinct head and neck subsite. This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

No MeSH data available.


Related in: MedlinePlus