Limits...
The evolving transcriptome of head and neck squamous cell carcinoma: a systematic review.

Yu YH, Kuo HK, Chang KW - PLoS ONE (2008)

Bottom Line: In total, 1442 genes were verified, i.e. reported at least twice, with ECM1, EMP1, CXCL10 and POSTN shown to be highly reported across all three stages.Notably, functional estimates derived from topological characteristics of integrin signaling networks identified such important genes as ITGA3 and ITGA5, which were supported by findings of invasiveness in vitro.Moreover, we computed genome-wide probabilities of reporting differential gene activities for the Pre, TvN, and Meta stages, respectively.

View Article: PubMed Central - PubMed

Affiliation: School of Dentistry, National Yang-Ming University, Taipei, Taiwan. yauhuayu@gmail.com

ABSTRACT

Background: Numerous studies were performed to illuminate mechanisms of tumorigenesis and metastases from gene expression profiles of Head and Neck Squamous Cell Carcinoma (HNSCC). The objective of this review is to conduct a network-based meta-analysis to identify the underlying biological signatures of the HNSCC transcriptome.

Methods and findings: We included 63 HNSCC transcriptomic studies into three specific categories of comparisons: Pre, premalignant lesions v.s. normal; TvN, primary tumors v.s. normal; and Meta, metastatic or invasive v.s. primary tumors. Reported genes extracted from the literature were systematically analyzed. Participation of differential gene activities across three progressive stages deciphered the evolving nature of HNSCC. In total, 1442 genes were verified, i.e. reported at least twice, with ECM1, EMP1, CXCL10 and POSTN shown to be highly reported across all three stages. Knowledge-based networks of the HNSCC transcriptome were constructed, demonstrating integrin signaling and antigen presentation pathways as highly enriched. Notably, functional estimates derived from topological characteristics of integrin signaling networks identified such important genes as ITGA3 and ITGA5, which were supported by findings of invasiveness in vitro. Moreover, we computed genome-wide probabilities of reporting differential gene activities for the Pre, TvN, and Meta stages, respectively. Results highlighted chromosomal regions of 6p21, 19p13 and 19q13, where genomic alterations were shown to be correlated with the nodal status of HNSCC.

Conclusions: By means of a systems-biology approach via network-based meta-analyses, we provided a deeper insight into the evolving nature of the HNSCC transcriptome. Enriched canonical signaling pathways, hot-spots of transcriptional profiles across the genome, as well as topologically significant genes derived from network analyses were highlighted for each of the three progressive stages, Pre, TvN, and Meta, respectively.

Show MeSH

Related in: MedlinePlus

QUOROM flow diagram of the systematic reviews and meta-analysis.The diagram summarized the search strategy. In order to be included, studies had to examine the HNSCC tumor samples by means of microarray-based gene expression profiling.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2533097&req=5

pone-0003215-g001: QUOROM flow diagram of the systematic reviews and meta-analysis.The diagram summarized the search strategy. In order to be included, studies had to examine the HNSCC tumor samples by means of microarray-based gene expression profiling.

Mentions: We conducted this meta-analysis in accordance with the standard protocol recommended by the Quality of Reporting of Meta-analyses group [10]. A systematic search in the PubMed database (Jan 1994 to Apr 2008) was performed using a complex query, consisted of keywords “head and neck neoplasm”, “gene expression profiling”, “oligonucleotide array sequence analysis”, “microarray” and “carcinoma, squamous cell”. Details of the complex query were provided in Text S1. A total of 410 potentially relevant articles were identified. First, we excluded studies examining lesions located in thyroid glands (n = 82), salivary glands (n = 16), nasopharynx (n = 23), eyes or elsewhere (n = 5). Studies were further excluded if the primary data reported was not differential gene expression profiling (n = 118), or if the samples used in the experiment were not human tumor tissue (n = 96). Of the remaining 70 studies, six were examining HPV-related or smoking-related transcriptional profiles and one was unavailable. Sixty-three studies of transcriptional profiles of HNSCC were included in the meta-analysis and classified into three specific comparisons: Pre, premalignant lesions v.s. normal (n = 5); TvN, primary tumors v.s. normal (n = 41); and Meta, disseminated (regional lymph node involvement, distant metastases, or local recurrence) v.s. primary localized tumors (n = 26). Figure 1 demonstrated the QUOROM flow diagram of screening microarray-based HNSCC transcriptional profiles.


The evolving transcriptome of head and neck squamous cell carcinoma: a systematic review.

Yu YH, Kuo HK, Chang KW - PLoS ONE (2008)

QUOROM flow diagram of the systematic reviews and meta-analysis.The diagram summarized the search strategy. In order to be included, studies had to examine the HNSCC tumor samples by means of microarray-based gene expression profiling.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2533097&req=5

pone-0003215-g001: QUOROM flow diagram of the systematic reviews and meta-analysis.The diagram summarized the search strategy. In order to be included, studies had to examine the HNSCC tumor samples by means of microarray-based gene expression profiling.
Mentions: We conducted this meta-analysis in accordance with the standard protocol recommended by the Quality of Reporting of Meta-analyses group [10]. A systematic search in the PubMed database (Jan 1994 to Apr 2008) was performed using a complex query, consisted of keywords “head and neck neoplasm”, “gene expression profiling”, “oligonucleotide array sequence analysis”, “microarray” and “carcinoma, squamous cell”. Details of the complex query were provided in Text S1. A total of 410 potentially relevant articles were identified. First, we excluded studies examining lesions located in thyroid glands (n = 82), salivary glands (n = 16), nasopharynx (n = 23), eyes or elsewhere (n = 5). Studies were further excluded if the primary data reported was not differential gene expression profiling (n = 118), or if the samples used in the experiment were not human tumor tissue (n = 96). Of the remaining 70 studies, six were examining HPV-related or smoking-related transcriptional profiles and one was unavailable. Sixty-three studies of transcriptional profiles of HNSCC were included in the meta-analysis and classified into three specific comparisons: Pre, premalignant lesions v.s. normal (n = 5); TvN, primary tumors v.s. normal (n = 41); and Meta, disseminated (regional lymph node involvement, distant metastases, or local recurrence) v.s. primary localized tumors (n = 26). Figure 1 demonstrated the QUOROM flow diagram of screening microarray-based HNSCC transcriptional profiles.

Bottom Line: In total, 1442 genes were verified, i.e. reported at least twice, with ECM1, EMP1, CXCL10 and POSTN shown to be highly reported across all three stages.Notably, functional estimates derived from topological characteristics of integrin signaling networks identified such important genes as ITGA3 and ITGA5, which were supported by findings of invasiveness in vitro.Moreover, we computed genome-wide probabilities of reporting differential gene activities for the Pre, TvN, and Meta stages, respectively.

View Article: PubMed Central - PubMed

Affiliation: School of Dentistry, National Yang-Ming University, Taipei, Taiwan. yauhuayu@gmail.com

ABSTRACT

Background: Numerous studies were performed to illuminate mechanisms of tumorigenesis and metastases from gene expression profiles of Head and Neck Squamous Cell Carcinoma (HNSCC). The objective of this review is to conduct a network-based meta-analysis to identify the underlying biological signatures of the HNSCC transcriptome.

Methods and findings: We included 63 HNSCC transcriptomic studies into three specific categories of comparisons: Pre, premalignant lesions v.s. normal; TvN, primary tumors v.s. normal; and Meta, metastatic or invasive v.s. primary tumors. Reported genes extracted from the literature were systematically analyzed. Participation of differential gene activities across three progressive stages deciphered the evolving nature of HNSCC. In total, 1442 genes were verified, i.e. reported at least twice, with ECM1, EMP1, CXCL10 and POSTN shown to be highly reported across all three stages. Knowledge-based networks of the HNSCC transcriptome were constructed, demonstrating integrin signaling and antigen presentation pathways as highly enriched. Notably, functional estimates derived from topological characteristics of integrin signaling networks identified such important genes as ITGA3 and ITGA5, which were supported by findings of invasiveness in vitro. Moreover, we computed genome-wide probabilities of reporting differential gene activities for the Pre, TvN, and Meta stages, respectively. Results highlighted chromosomal regions of 6p21, 19p13 and 19q13, where genomic alterations were shown to be correlated with the nodal status of HNSCC.

Conclusions: By means of a systems-biology approach via network-based meta-analyses, we provided a deeper insight into the evolving nature of the HNSCC transcriptome. Enriched canonical signaling pathways, hot-spots of transcriptional profiles across the genome, as well as topologically significant genes derived from network analyses were highlighted for each of the three progressive stages, Pre, TvN, and Meta, respectively.

Show MeSH
Related in: MedlinePlus