Limits...
Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation.

Strath J, Georgopoulos LJ, Kellam P, Blair GE - BMC Genomics (2009)

Bottom Line: Analysis of microarray data revealed that a total of 232 genes were differentially expressed in Ad12 E1- or Ad5 E1-transformed BRK cells compared to untransformed baby rat kidney (BRK) cells.Up-regulation of RelA and significant dysregulation of collagen type I mRNA transcripts and proteins were found in Ad-transformed cells.These results suggest that a complex web of cellular pathways become altered in Ad-transformed cells and that Ad E1A is sufficient for the observed dysregulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK. janet_strath@hotmail.com

ABSTRACT

Background: Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulates host cell gene expression, a key factor in both cellular transformation and oncogenesis. To reveal differences in gene expression between cells transformed with oncogenic and non-oncogenic adenoviruses we have performed comparative analysis of transcript profiles with the aim of identifying candidate genes involved in the process of neoplastic transformation.

Results: Analysis of microarray data revealed that a total of 232 genes were differentially expressed in Ad12 E1- or Ad5 E1-transformed BRK cells compared to untransformed baby rat kidney (BRK) cells. Gene information was available for 193 transcripts and using gene ontology (GO) classifications and literature searches it was possible to assign known or suggested functions to 166 of these identified genes. A subset of differentially-expressed genes from the microarray was further examined by real-time PCR and Western blotting using BRK cells immortalised by Ad12 E1A or Ad5 E1A in addition to Ad12 E1- or Ad5 E1-transformed BRK cells. Up-regulation of RelA and significant dysregulation of collagen type I mRNA transcripts and proteins were found in Ad-transformed cells.

Conclusion: These results suggest that a complex web of cellular pathways become altered in Ad-transformed cells and that Ad E1A is sufficient for the observed dysregulation. Further work will focus on investigating which splice variant of Ad E1A is responsible for the observed dysregulation at the pathway level, and the mechanisms of E1A-mediated transcriptional regulation.

Show MeSH

Related in: MedlinePlus

Ingenuity comparative analysis of dysregulated targets by biofunction. Biofunctional analysis of significant dysregulation associated with (a) disease and disorders, (b) molecular and cellular functions and (c) physiological system development and function. The significance value associated with each category is a measure of the likelihood that the association between dysregulated transcripts and a given process or pathway is due to random chance. The y-axis of each graph shows the significance, expressed as the negative exponent of the p-value calculation for each category, increasing with bar height.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651901&req=5

Figure 3: Ingenuity comparative analysis of dysregulated targets by biofunction. Biofunctional analysis of significant dysregulation associated with (a) disease and disorders, (b) molecular and cellular functions and (c) physiological system development and function. The significance value associated with each category is a measure of the likelihood that the association between dysregulated transcripts and a given process or pathway is due to random chance. The y-axis of each graph shows the significance, expressed as the negative exponent of the p-value calculation for each category, increasing with bar height.

Mentions: To identify signalling pathways involved in adenovirus transformation, data sets comprised of gene expression ratios were analysed by Ingenuity. The Ingenuity Pathways Analysis (IPA) is a system that transforms large data sets into a group of relevant networks containing direct and indirect relationships between genes based on known interactions in the literature. It was possible to map 111 out of the 232 dysregulated targets with certainty to the IPA knowledge base: 66 of the mapped genes were eligible for network analysis and 51 were eligible for functions and pathways analysis. Genetic networks were created by the IPA network generation algorithm from lists of fold-change expression in Ad5 E1-TC compared to untransformed BRK cells, Ad12 E1-TC compared to untransformed BRK cells and Ad12 E1-TC compared to Ad5 E1-TC. Comparative analysis across all results was also performed and results were analysed in terms of biofunction (Figure 3) and canonical pathway (Figure 4).


Identification of genes differentially expressed as result of adenovirus type 5- and adenovirus type 12-transformation.

Strath J, Georgopoulos LJ, Kellam P, Blair GE - BMC Genomics (2009)

Ingenuity comparative analysis of dysregulated targets by biofunction. Biofunctional analysis of significant dysregulation associated with (a) disease and disorders, (b) molecular and cellular functions and (c) physiological system development and function. The significance value associated with each category is a measure of the likelihood that the association between dysregulated transcripts and a given process or pathway is due to random chance. The y-axis of each graph shows the significance, expressed as the negative exponent of the p-value calculation for each category, increasing with bar height.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651901&req=5

Figure 3: Ingenuity comparative analysis of dysregulated targets by biofunction. Biofunctional analysis of significant dysregulation associated with (a) disease and disorders, (b) molecular and cellular functions and (c) physiological system development and function. The significance value associated with each category is a measure of the likelihood that the association between dysregulated transcripts and a given process or pathway is due to random chance. The y-axis of each graph shows the significance, expressed as the negative exponent of the p-value calculation for each category, increasing with bar height.
Mentions: To identify signalling pathways involved in adenovirus transformation, data sets comprised of gene expression ratios were analysed by Ingenuity. The Ingenuity Pathways Analysis (IPA) is a system that transforms large data sets into a group of relevant networks containing direct and indirect relationships between genes based on known interactions in the literature. It was possible to map 111 out of the 232 dysregulated targets with certainty to the IPA knowledge base: 66 of the mapped genes were eligible for network analysis and 51 were eligible for functions and pathways analysis. Genetic networks were created by the IPA network generation algorithm from lists of fold-change expression in Ad5 E1-TC compared to untransformed BRK cells, Ad12 E1-TC compared to untransformed BRK cells and Ad12 E1-TC compared to Ad5 E1-TC. Comparative analysis across all results was also performed and results were analysed in terms of biofunction (Figure 3) and canonical pathway (Figure 4).

Bottom Line: Analysis of microarray data revealed that a total of 232 genes were differentially expressed in Ad12 E1- or Ad5 E1-transformed BRK cells compared to untransformed baby rat kidney (BRK) cells.Up-regulation of RelA and significant dysregulation of collagen type I mRNA transcripts and proteins were found in Ad-transformed cells.These results suggest that a complex web of cellular pathways become altered in Ad-transformed cells and that Ad E1A is sufficient for the observed dysregulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK. janet_strath@hotmail.com

ABSTRACT

Background: Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulates host cell gene expression, a key factor in both cellular transformation and oncogenesis. To reveal differences in gene expression between cells transformed with oncogenic and non-oncogenic adenoviruses we have performed comparative analysis of transcript profiles with the aim of identifying candidate genes involved in the process of neoplastic transformation.

Results: Analysis of microarray data revealed that a total of 232 genes were differentially expressed in Ad12 E1- or Ad5 E1-transformed BRK cells compared to untransformed baby rat kidney (BRK) cells. Gene information was available for 193 transcripts and using gene ontology (GO) classifications and literature searches it was possible to assign known or suggested functions to 166 of these identified genes. A subset of differentially-expressed genes from the microarray was further examined by real-time PCR and Western blotting using BRK cells immortalised by Ad12 E1A or Ad5 E1A in addition to Ad12 E1- or Ad5 E1-transformed BRK cells. Up-regulation of RelA and significant dysregulation of collagen type I mRNA transcripts and proteins were found in Ad-transformed cells.

Conclusion: These results suggest that a complex web of cellular pathways become altered in Ad-transformed cells and that Ad E1A is sufficient for the observed dysregulation. Further work will focus on investigating which splice variant of Ad E1A is responsible for the observed dysregulation at the pathway level, and the mechanisms of E1A-mediated transcriptional regulation.

Show MeSH
Related in: MedlinePlus