Cargando…

Pathway-specific differences between tumor cell lines and normal and tumor tissue cells

BACKGROUND: Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. METHODS: This study ut...

Descripción completa

Detalles Bibliográficos
Autores principales: Ertel, Adam, Verghese, Arun, Byers, Stephen W, Ochs, Michael, Tozeren, Aydin
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635729/
https://www.ncbi.nlm.nih.gov/pubmed/17081305
http://dx.doi.org/10.1186/1476-4598-5-55
_version_ 1782130711963107328
author Ertel, Adam
Verghese, Arun
Byers, Stephen W
Ochs, Michael
Tozeren, Aydin
author_facet Ertel, Adam
Verghese, Arun
Byers, Stephen W
Ochs, Michael
Tozeren, Aydin
author_sort Ertel, Adam
collection PubMed
description BACKGROUND: Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. METHODS: This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM). RESULTS: Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways. CONCLUSION: Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines.
format Text
id pubmed-1635729
institution National Center for Biotechnology Information
language English
publishDate 2006
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-16357292006-11-11 Pathway-specific differences between tumor cell lines and normal and tumor tissue cells Ertel, Adam Verghese, Arun Byers, Stephen W Ochs, Michael Tozeren, Aydin Mol Cancer Research BACKGROUND: Cell lines are used in experimental investigation of cancer but their capacity to represent tumor cells has yet to be quantified. The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue. METHODS: This study utilized a pathway-specific enrichment analysis of publicly accessible microarray data and quantified the gene expression differences between cell lines, tumor, and normal tissue cells for six different tissue types. KEGG pathways that are significantly different between cell lines and tumors, cell lines and normal tissues and tumor and normal tissue were identified through enrichment tests on gene lists obtained using Significance Analysis of Microarrays (SAM). RESULTS: Cellular pathways that were significantly upregulated in cell lines compared to tumor cells and normal cells of the same tissue type included ATP synthesis, cell communication, cell cycle, oxidative phosphorylation, purine, pyrimidine and pyruvate metabolism, and proteasome. Results on metabolic pathways suggested an increase in the velocity nucleotide metabolism and RNA production. Pathways that were downregulated in cell lines compared to tumor and normal tissue included cell communication, cell adhesion molecules (CAMs), and ECM-receptor interaction. Only a fraction of the significantly altered genes in tumor-to-normal comparison had similar expressions in cancer cell lines and tumor cells. These genes were tissue-specific and were distributed sparsely among multiple pathways. CONCLUSION: Significantly altered genes in tumors compared to normal tissue were largely tissue specific. Among these genes downregulation was a major trend. In contrast, cell lines contained large sets of significantly upregulated genes that were common to multiple tissue types. Pathway upregulation in cell lines was most pronounced over metabolic pathways including cell nucleotide metabolism and oxidative phosphorylation. Signaling pathways involved in adhesion and communication of cultured cancer cells were downregulated. The three way pathways comparison presented in this study brings light into the differences in the use of cellular pathways by tumor cells and cancer cell lines. BioMed Central 2006-11-02 /pmc/articles/PMC1635729/ /pubmed/17081305 http://dx.doi.org/10.1186/1476-4598-5-55 Text en Copyright © 2006 Ertel 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
Ertel, Adam
Verghese, Arun
Byers, Stephen W
Ochs, Michael
Tozeren, Aydin
Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title_full Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title_fullStr Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title_full_unstemmed Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title_short Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
title_sort pathway-specific differences between tumor cell lines and normal and tumor tissue cells
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635729/
https://www.ncbi.nlm.nih.gov/pubmed/17081305
http://dx.doi.org/10.1186/1476-4598-5-55
work_keys_str_mv AT erteladam pathwayspecificdifferencesbetweentumorcelllinesandnormalandtumortissuecells
AT verghesearun pathwayspecificdifferencesbetweentumorcelllinesandnormalandtumortissuecells
AT byersstephenw pathwayspecificdifferencesbetweentumorcelllinesandnormalandtumortissuecells
AT ochsmichael pathwayspecificdifferencesbetweentumorcelllinesandnormalandtumortissuecells
AT tozerenaydin pathwayspecificdifferencesbetweentumorcelllinesandnormalandtumortissuecells