High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx

Anna-Kaarina Järvinen, Reija Autio, Sami Kilpinen, Matti Saarela, Ilmo Leivo, Reidar Grénman, Antti A. Mäkitie, Outi Monni (Corresponding Author)

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Abstract

Gene amplifications and deletions are frequent in head and neck squamous cell carcinomas (SCC) but the association of these alterations with gene expression is mostly unknown. Here, we characterized genome‐wide copy number and gene expression changes on microarrays for 18 oral tongue SCC (OTSCC) cell lines. We identified a number of altered regions including nine high‐level amplifications such as 6q12‐q14 (CD109, MYO6), 9p24 (JAK2, CD274, SLC1A1, RLN1), 11p12‐p13 (TRAF6, COMMD9, TRIM44, FJX1, CD44, PDHX, APIP), 11q13 (FADD, PPFIA1, CTTN), and 14q24 (ABCD4, HBLD1, LTBP2, ZNF410, COQ6, ACYP1, JDP2) where 9% to 64% of genes showed overexpression. Across the whole genome, 26% of the amplified genes had associated overexpression in OTSCC. Furthermore, our data implicated that OTSCC cell lines harbored similar genomic alterations as laryngeal SCC cell lines we have previously analyzed, suggesting that despite differences in clinicopathological features there are no marked differences in molecular genetic alterations of these two HNSCC sites. To identify genes whose expression was associated with copy number increase in head and neck SCC, a statistical analysis for oral tongue and laryngeal SCC cell line data were performed. We pinpointed 1,192 genes that had a statistically significant association between copy number and gene expression. These results suggest that genomic alterations with associated gene expression changes play an important role in the malignant behavior of head and neck SCC. The identified genes provide a basis for further functional validation and may lead to the identification of novel candidates for targeted therapies.
Original languageEnglish
Pages (from-to)500-509
JournalGenes, Chromosomes and Cancer
Volume47
Issue number6
DOIs
Publication statusPublished - 2008
MoE publication typeA1 Journal article-refereed

Fingerprint

Microarray Analysis
Larynx
Tongue
Gene Expression
Cell Line
Head
Genes
Neck
TNF Receptor-Associated Factor 6
Gene Amplification
Gene Deletion
Molecular Biology
Carcinoma, squamous cell of head and neck
Genome
Carcinoma
Therapeutics

Keywords

  • gene expression
  • microarray
  • squamous cell carcinoma
  • cell lines
  • head and neck cancer

Cite this

Järvinen, Anna-Kaarina ; Autio, Reija ; Kilpinen, Sami ; Saarela, Matti ; Leivo, Ilmo ; Grénman, Reidar ; Mäkitie, Antti A. ; Monni, Outi. / High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx. In: Genes, Chromosomes and Cancer. 2008 ; Vol. 47, No. 6. pp. 500-509.
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abstract = "Gene amplifications and deletions are frequent in head and neck squamous cell carcinomas (SCC) but the association of these alterations with gene expression is mostly unknown. Here, we characterized genome‐wide copy number and gene expression changes on microarrays for 18 oral tongue SCC (OTSCC) cell lines. We identified a number of altered regions including nine high‐level amplifications such as 6q12‐q14 (CD109, MYO6), 9p24 (JAK2, CD274, SLC1A1, RLN1), 11p12‐p13 (TRAF6, COMMD9, TRIM44, FJX1, CD44, PDHX, APIP), 11q13 (FADD, PPFIA1, CTTN), and 14q24 (ABCD4, HBLD1, LTBP2, ZNF410, COQ6, ACYP1, JDP2) where 9{\%} to 64{\%} of genes showed overexpression. Across the whole genome, 26{\%} of the amplified genes had associated overexpression in OTSCC. Furthermore, our data implicated that OTSCC cell lines harbored similar genomic alterations as laryngeal SCC cell lines we have previously analyzed, suggesting that despite differences in clinicopathological features there are no marked differences in molecular genetic alterations of these two HNSCC sites. To identify genes whose expression was associated with copy number increase in head and neck SCC, a statistical analysis for oral tongue and laryngeal SCC cell line data were performed. We pinpointed 1,192 genes that had a statistically significant association between copy number and gene expression. These results suggest that genomic alterations with associated gene expression changes play an important role in the malignant behavior of head and neck SCC. The identified genes provide a basis for further functional validation and may lead to the identification of novel candidates for targeted therapies.",
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Järvinen, A-K, Autio, R, Kilpinen, S, Saarela, M, Leivo, I, Grénman, R, Mäkitie, AA & Monni, O 2008, 'High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx', Genes, Chromosomes and Cancer, vol. 47, no. 6, pp. 500-509. https://doi.org/10.1002/gcc.20551

High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx. / Järvinen, Anna-Kaarina; Autio, Reija; Kilpinen, Sami; Saarela, Matti; Leivo, Ilmo; Grénman, Reidar; Mäkitie, Antti A.; Monni, Outi (Corresponding Author).

In: Genes, Chromosomes and Cancer, Vol. 47, No. 6, 2008, p. 500-509.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx

AU - Järvinen, Anna-Kaarina

AU - Autio, Reija

AU - Kilpinen, Sami

AU - Saarela, Matti

AU - Leivo, Ilmo

AU - Grénman, Reidar

AU - Mäkitie, Antti A.

AU - Monni, Outi

PY - 2008

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N2 - Gene amplifications and deletions are frequent in head and neck squamous cell carcinomas (SCC) but the association of these alterations with gene expression is mostly unknown. Here, we characterized genome‐wide copy number and gene expression changes on microarrays for 18 oral tongue SCC (OTSCC) cell lines. We identified a number of altered regions including nine high‐level amplifications such as 6q12‐q14 (CD109, MYO6), 9p24 (JAK2, CD274, SLC1A1, RLN1), 11p12‐p13 (TRAF6, COMMD9, TRIM44, FJX1, CD44, PDHX, APIP), 11q13 (FADD, PPFIA1, CTTN), and 14q24 (ABCD4, HBLD1, LTBP2, ZNF410, COQ6, ACYP1, JDP2) where 9% to 64% of genes showed overexpression. Across the whole genome, 26% of the amplified genes had associated overexpression in OTSCC. Furthermore, our data implicated that OTSCC cell lines harbored similar genomic alterations as laryngeal SCC cell lines we have previously analyzed, suggesting that despite differences in clinicopathological features there are no marked differences in molecular genetic alterations of these two HNSCC sites. To identify genes whose expression was associated with copy number increase in head and neck SCC, a statistical analysis for oral tongue and laryngeal SCC cell line data were performed. We pinpointed 1,192 genes that had a statistically significant association between copy number and gene expression. These results suggest that genomic alterations with associated gene expression changes play an important role in the malignant behavior of head and neck SCC. The identified genes provide a basis for further functional validation and may lead to the identification of novel candidates for targeted therapies.

AB - Gene amplifications and deletions are frequent in head and neck squamous cell carcinomas (SCC) but the association of these alterations with gene expression is mostly unknown. Here, we characterized genome‐wide copy number and gene expression changes on microarrays for 18 oral tongue SCC (OTSCC) cell lines. We identified a number of altered regions including nine high‐level amplifications such as 6q12‐q14 (CD109, MYO6), 9p24 (JAK2, CD274, SLC1A1, RLN1), 11p12‐p13 (TRAF6, COMMD9, TRIM44, FJX1, CD44, PDHX, APIP), 11q13 (FADD, PPFIA1, CTTN), and 14q24 (ABCD4, HBLD1, LTBP2, ZNF410, COQ6, ACYP1, JDP2) where 9% to 64% of genes showed overexpression. Across the whole genome, 26% of the amplified genes had associated overexpression in OTSCC. Furthermore, our data implicated that OTSCC cell lines harbored similar genomic alterations as laryngeal SCC cell lines we have previously analyzed, suggesting that despite differences in clinicopathological features there are no marked differences in molecular genetic alterations of these two HNSCC sites. To identify genes whose expression was associated with copy number increase in head and neck SCC, a statistical analysis for oral tongue and laryngeal SCC cell line data were performed. We pinpointed 1,192 genes that had a statistically significant association between copy number and gene expression. These results suggest that genomic alterations with associated gene expression changes play an important role in the malignant behavior of head and neck SCC. The identified genes provide a basis for further functional validation and may lead to the identification of novel candidates for targeted therapies.

KW - gene expression

KW - microarray

KW - squamous cell carcinoma

KW - cell lines

KW - head and neck cancer

U2 - 10.1002/gcc.20551

DO - 10.1002/gcc.20551

M3 - Article

VL - 47

SP - 500

EP - 509

JO - Genes, Chromosomes and Cancer

JF - Genes, Chromosomes and Cancer

SN - 1045-2257

IS - 6

ER -