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Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines

BACKGROUND: Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer c...

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Autores principales: Junnila, Siina, Kokkola, Arto, Karjalainen-Lindsberg, Marja-Liisa, Puolakkainen, Pauli, Monni, Outi
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837868/
https://www.ncbi.nlm.nih.gov/pubmed/20187983
http://dx.doi.org/10.1186/1471-2407-10-73
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author Junnila, Siina
Kokkola, Arto
Karjalainen-Lindsberg, Marja-Liisa
Puolakkainen, Pauli
Monni, Outi
author_facet Junnila, Siina
Kokkola, Arto
Karjalainen-Lindsberg, Marja-Liisa
Puolakkainen, Pauli
Monni, Outi
author_sort Junnila, Siina
collection PubMed
description BACKGROUND: Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes. METHODS: To highlight genes of potential biological and clinical relevance in gastric cancer, we carried out a systematic array-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines and validated the results using an affinity capture based transcript analysis (TRAC assay) and real-time qRT-PCR. RESULTS: Integrated microarray analysis revealed altogether 256 genes that were located in recurrent regions of gains or losses and had at least a 2-fold copy number- associated change in their gene expression. The expression levels of 13 of these genes, ALPK2, ASAP1, CEACAM5, CYP3A4, ENAH, ERBB2, HHIPL2, LTB4R, MMP9, PERLD1, PNMT, PTPRA, and OSMR, were validated in a total of 118 gastric samples using either the qRT-PCR or TRAC assay. All of these 13 genes were differentially expressed between cancerous samples and nonmalignant tissues (p < 0.05) and the association between copy number and gene expression changes was validated for nine (69.2%) of these genes (p < 0.05). CONCLUSION: In conclusion, integrated gene expression and copy number microarray analysis highlighted genes that may be critically important for gastric carcinogenesis. TRAC and qRT-PCR analyses validated the microarray results and therefore the role of these genes as potential biomarkers for gastric cancer.
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spelling pubmed-28378682010-03-14 Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines Junnila, Siina Kokkola, Arto Karjalainen-Lindsberg, Marja-Liisa Puolakkainen, Pauli Monni, Outi BMC Cancer Research Article BACKGROUND: Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes. METHODS: To highlight genes of potential biological and clinical relevance in gastric cancer, we carried out a systematic array-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines and validated the results using an affinity capture based transcript analysis (TRAC assay) and real-time qRT-PCR. RESULTS: Integrated microarray analysis revealed altogether 256 genes that were located in recurrent regions of gains or losses and had at least a 2-fold copy number- associated change in their gene expression. The expression levels of 13 of these genes, ALPK2, ASAP1, CEACAM5, CYP3A4, ENAH, ERBB2, HHIPL2, LTB4R, MMP9, PERLD1, PNMT, PTPRA, and OSMR, were validated in a total of 118 gastric samples using either the qRT-PCR or TRAC assay. All of these 13 genes were differentially expressed between cancerous samples and nonmalignant tissues (p < 0.05) and the association between copy number and gene expression changes was validated for nine (69.2%) of these genes (p < 0.05). CONCLUSION: In conclusion, integrated gene expression and copy number microarray analysis highlighted genes that may be critically important for gastric carcinogenesis. TRAC and qRT-PCR analyses validated the microarray results and therefore the role of these genes as potential biomarkers for gastric cancer. BioMed Central 2010-03-01 /pmc/articles/PMC2837868/ /pubmed/20187983 http://dx.doi.org/10.1186/1471-2407-10-73 Text en Copyright ©2010 Junnila et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Junnila, Siina
Kokkola, Arto
Karjalainen-Lindsberg, Marja-Liisa
Puolakkainen, Pauli
Monni, Outi
Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title_full Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title_fullStr Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title_full_unstemmed Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title_short Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
title_sort genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837868/
https://www.ncbi.nlm.nih.gov/pubmed/20187983
http://dx.doi.org/10.1186/1471-2407-10-73
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