Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses

A.-K. Järvinen, R. Autio, Saija Haapa-Paananen, Maija Wolf, M. Saarela, R. Grénman, I. Leivo, Olli Kallioniemi, A. A. Mäkitie, O. Monni (Corresponding Author)

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Abstract

Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.
Original languageEnglish
Pages (from-to)6997–7008
Number of pages12
JournalOncogene
Volume25
Issue number52
DOIs
Publication statusPublished - 2006
MoE publication typeA1 Journal article-refereed

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Microarray Analysis
Squamous Cell Carcinoma
Gene Expression
Laryngeal Neoplasms
Genes
Gene Ontology
Comparative Genomic Hybridization
Gene Dosage
Gene Amplification
Oligonucleotide Array Sequence Analysis
Computational Biology
Tumor Cell Line
Genome
RNA
Cell Line
DNA
Therapeutics
Neoplasms

Keywords

  • head and neck cancer
  • cDNA microarrays
  • oligonucleotide microarrays
  • comparative genomic hybridization

Cite this

Järvinen, A-K., Autio, R., Haapa-Paananen, S., Wolf, M., Saarela, M., Grénman, R., ... Monni, O. (2006). Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene, 25(52), 6997–7008. https://doi.org/10.1038/sj.onc.1209690
Järvinen, A.-K. ; Autio, R. ; Haapa-Paananen, Saija ; Wolf, Maija ; Saarela, M. ; Grénman, R. ; Leivo, I. ; Kallioniemi, Olli ; Mäkitie, A. A. ; Monni, O. / Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. In: Oncogene. 2006 ; Vol. 25, No. 52. pp. 6997–7008.
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abstract = "Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.",
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Järvinen, A-K, Autio, R, Haapa-Paananen, S, Wolf, M, Saarela, M, Grénman, R, Leivo, I, Kallioniemi, O, Mäkitie, AA & Monni, O 2006, 'Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses', Oncogene, vol. 25, no. 52, pp. 6997–7008. https://doi.org/10.1038/sj.onc.1209690

Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. / Järvinen, A.-K.; Autio, R.; Haapa-Paananen, Saija; Wolf, Maija; Saarela, M.; Grénman, R.; Leivo, I.; Kallioniemi, Olli; Mäkitie, A. A.; Monni, O. (Corresponding Author).

In: Oncogene, Vol. 25, No. 52, 2006, p. 6997–7008.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses

AU - Järvinen, A.-K.

AU - Autio, R.

AU - Haapa-Paananen, Saija

AU - Wolf, Maija

AU - Saarela, M.

AU - Grénman, R.

AU - Leivo, I.

AU - Kallioniemi, Olli

AU - Mäkitie, A. A.

AU - Monni, O.

PY - 2006

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N2 - Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.

AB - Molecular mechanisms contributing to initiation and progression of head and neck squamous cell carcinoma are still poorly known. Numerous genetic alterations have been described, but molecular consequences of such alterations in most cases remain unclear. Here, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 20 laryngeal cancer cell lines and primary tumors. Our aim was to identify genetic alterations that play a key role in disease pathogenesis and pinpoint genes whose expression is directly impacted by these events. Integration of DNA level data from array-based comparative genomic hybridization with RNA level information from oligonucleotide microarrays was achieved with custom-developed bioinformatic methods. High-level amplifications had a clear impact on gene expression. Across the genome, overexpression of 739 genes could be attributed to gene amplification events in cell lines, with 325 genes showing the same phenomenon in primary tumors including FADD and PPFIA1 at 11q13. The analysis of gene ontology and pathway distributions further pinpointed genes that may identify potential targets of therapeutic intervention. Our data highlight genes that may be critically important to laryngeal cancer progression and offer potential therapeutic targets.

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KW - oligonucleotide microarrays

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JO - Oncogene

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