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Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program.

Kwekel JC, Forgacs AL, Burgoon LD, Williams KJ, Zacharewski TR - BMC Med Genomics (2009)

Bottom Line: Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes.Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA. joshua.kwekel@gmail.com

ABSTRACT

Background: Tamoxifen (TAM) is a well characterized breast cancer drug and selective estrogen receptor modulator (SERM) which also has been associated with a small increase in risk for uterine cancers. TAM's partial agonist activation of estrogen receptor has been characterized for specific gene promoters but not at the genomic level in vivo.Furthermore, reducing uncertainties associated with cross-species extrapolations of pharmaco- and toxicogenomic data remains a formidable challenge.

Results: A comparative ligand and species analysis approach was conducted to systematically assess the physiological, morphological and uterine gene expression alterations elicited across time by TAM and ethynylestradiol (EE) in immature ovariectomized Sprague-Dawley rats and C57BL/6 mice. Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.

Conclusion: Comparative analysis of EE and TAM differentially expressed gene lists suggest TAM regulates no unique uterine genes that are conserved in the rat and mouse. This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes. Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates that systematic comparative genomic assessments can elucidate important conserved and divergent mechanisms in rodent estrogen signalling during uterine proliferation.

No MeSH data available.


Related in: MedlinePlus

Four Way Venn Analysis of Active Genes. Each data set was converted into ortholog space and processed for activity using relaxed criteria prior to analysis using the 4-way Venn Diagram Generator . The Venn set was subsequently filtered for genes which met the initial, high-stringency criteria to ensure robust comparisons. Gene lists for each Venn set are available [see Additional File 7].
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Figure 6: Four Way Venn Analysis of Active Genes. Each data set was converted into ortholog space and processed for activity using relaxed criteria prior to analysis using the 4-way Venn Diagram Generator . The Venn set was subsequently filtered for genes which met the initial, high-stringency criteria to ensure robust comparisons. Gene lists for each Venn set are available [see Additional File 7].

Mentions: Following pair-wise comparisons by chemical and species, an integrated comparison of all four data sets was performed where differentially expressed orthologous genes (NCBI, HomoloGene) for each data set were entered into the 4-way Venn Diagram Generator. The number and identity of unique genes populating the overlaps of each data set was determined for common orthologs (Figure 6). The comparison of all four data sets resulted in 902 genes being commonly regulated at any time point (Venn subset I). Of the 902 overlapping genes, 398 exhibited a similar temporal profile (CAS) across all four data sets, suggesting comparable modes of regulation which we refer to as "orthologous expression". These genes represented functional categories associated with cellular proliferation and differentiation; hallmarks of estrogen induced uterotrophy. Selected conserved examples exhibiting orthologous expression in terms of either fold-change alone (Fos, C3, Igf1, Ca3, Sepp1) or large increase in copy number, regardless of fold change (Cd24a, Slc25a5, Krt13, Dcn, Itm2b) are provided in Table 1.


Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program.

Kwekel JC, Forgacs AL, Burgoon LD, Williams KJ, Zacharewski TR - BMC Med Genomics (2009)

Four Way Venn Analysis of Active Genes. Each data set was converted into ortholog space and processed for activity using relaxed criteria prior to analysis using the 4-way Venn Diagram Generator . The Venn set was subsequently filtered for genes which met the initial, high-stringency criteria to ensure robust comparisons. Gene lists for each Venn set are available [see Additional File 7].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2683873&req=5

Figure 6: Four Way Venn Analysis of Active Genes. Each data set was converted into ortholog space and processed for activity using relaxed criteria prior to analysis using the 4-way Venn Diagram Generator . The Venn set was subsequently filtered for genes which met the initial, high-stringency criteria to ensure robust comparisons. Gene lists for each Venn set are available [see Additional File 7].
Mentions: Following pair-wise comparisons by chemical and species, an integrated comparison of all four data sets was performed where differentially expressed orthologous genes (NCBI, HomoloGene) for each data set were entered into the 4-way Venn Diagram Generator. The number and identity of unique genes populating the overlaps of each data set was determined for common orthologs (Figure 6). The comparison of all four data sets resulted in 902 genes being commonly regulated at any time point (Venn subset I). Of the 902 overlapping genes, 398 exhibited a similar temporal profile (CAS) across all four data sets, suggesting comparable modes of regulation which we refer to as "orthologous expression". These genes represented functional categories associated with cellular proliferation and differentiation; hallmarks of estrogen induced uterotrophy. Selected conserved examples exhibiting orthologous expression in terms of either fold-change alone (Fos, C3, Igf1, Ca3, Sepp1) or large increase in copy number, regardless of fold change (Cd24a, Slc25a5, Krt13, Dcn, Itm2b) are provided in Table 1.

Bottom Line: Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes.Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA. joshua.kwekel@gmail.com

ABSTRACT

Background: Tamoxifen (TAM) is a well characterized breast cancer drug and selective estrogen receptor modulator (SERM) which also has been associated with a small increase in risk for uterine cancers. TAM's partial agonist activation of estrogen receptor has been characterized for specific gene promoters but not at the genomic level in vivo.Furthermore, reducing uncertainties associated with cross-species extrapolations of pharmaco- and toxicogenomic data remains a formidable challenge.

Results: A comparative ligand and species analysis approach was conducted to systematically assess the physiological, morphological and uterine gene expression alterations elicited across time by TAM and ethynylestradiol (EE) in immature ovariectomized Sprague-Dawley rats and C57BL/6 mice. Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns.

Conclusion: Comparative analysis of EE and TAM differentially expressed gene lists suggest TAM regulates no unique uterine genes that are conserved in the rat and mouse. This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes. Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates that systematic comparative genomic assessments can elucidate important conserved and divergent mechanisms in rodent estrogen signalling during uterine proliferation.

No MeSH data available.


Related in: MedlinePlus