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Open Access Research article

1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1

Pavlo L Kovalenko1, Zhentao Zhang1, Min Cui1, Steve K Clinton2 and James C Fleet1*

Author Affiliations

1 Department of Foods and Nutrition and the Interdepartmental Nutrition Program, Purdue University, West Lafayette, IN 47907-2059 USA

2 Department of Internal Medicine, Division of Hematology and Oncology and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210 USA

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BMC Genomics 2010, 11:26  doi:10.1186/1471-2164-11-26

Published: 13 January 2010

Additional files

Additional file 1:

Significantly differentially expressed transcripts. Significantly changed transcripts at any time point from SAM analyzed microarray data on RWPE1 cells treated 100 nm 1,25(OH)2D vs. vehicle.

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Additional file 2:

GSA currated gene sets c2. GSA curated genesets (c2) significantly enriched in differentially expressed transcripts.

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Additional file 3:

GSA motif genesets c3. GSA motif genesets (c3) significantly enriched in differentially expressed transcripts.

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Additional file 4:

GSA cancer computational genesets (c4). GSA cancer computational genesets (c4) significantly enriched in differentially expressed transcripts.

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Additional file 5:

GenMAPP local map results. Table of GenMAPP analysis of local maps for enrichment (SAM, FDR<5%).

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Additional file 6:

GenMAPP GO group results. GenMAPP Gene Ontology terms significantly changed (Z > 0, Permute P <= 0.1).

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Additional file 7:

Metacore summary. Metacore Maps enriched in significantly changed genes (SAM, <5%FDR).

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Additional file 8:

GeneMAPP SOM groups Local maps results. Table showing GenMAPP analysis on SOM groups using Local maps.

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Additional file 9:

GeneMAPP SOM groups GO group results. Table of GeneMAPP GO map analysis for SOM groups.

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Additional file 10:

Effect of 1,25(OH)2D on Wnt and Notch signaling at 6 h. Figure showing the effect of 1,25(OH)2D (100 nM, 6 h) on transcripts controlling Wnt and Notch signaling in RWPE1 cells. Differentially expressed transcripts (SAM, any time point, FDR<5%) were examined by time point for functional changes using GenMAPP and GSA. The GeneMapp local map for Wnt signaling (Hs_WNT_Signaling) was identified as significantly down regulated at 6 h. In addition, a GSA motif geneset (c3 #162) for genes containing Lef1 domains in their promoters (a Wnt pathway targeted transcription factor) was significantly down-regulated.

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Additional file 11:

Effect of 1,25(OH)2D on c-Myc transcriptional activity at 6 h. Image representing effect of vitamin D induced supression of c-Myc on the mRNA level of c-myc target genes. Significantly differentially expressed transcripts at 6 h (SAM, FDR<5%) were analyzed by using Metacore Network analysis (Transcription factor). Up--regulated genes are marked with red circles; down--regulated with blue circles. Arrows are color coded to reflect the known regulatory action between two proteins. Red arrows between proteins indicates a negative regulatory effect, green arrows indicate a positive regulator effect, gray arrows indicate an unspecified regulatory effect.

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Additional file 12:

Effect of 1,25(OH)2D on antioxidant and DNA protection at 6 h. Figure showing the effect of 1,25(OH)2D (100 nM, 6 h) on transcripts controlling antioxidant and DNA repair systems in RWPE1 cells. Differentially expressed transcripts (SAM, any time point, FDR<5%) were examined by time point for functional changes using GenMAPP and GSA. The GenMAPP local map for antioxidant responses to reactive oxygen (Hs_Oxidative_Stress) was identified as significantly up-regulated at 6 h. While not on this map, the up-regulation of G6PD is also relevant as this enzyme system contributes to glutathione production.

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Additional file 13:

1,25(OH)2D suppresses proinflammatory cytokine signaling. Figure representing regulation of transcripts controlling cytokine signaling in RWPE1 cells by 1,25(OH)2D treatment (100 nM). Differentially expressed transcripts (SAM, any time point, FDR<5%) were examined for functional changes using GenMAPP and GSA. A large number of pathways related to the signaling through cytokine pathways were identified as down-regulated. Most of these pathways utilize a JAK-STAT intracellular signaling pathway. A selection of transcripts affected and their relationship to JAK-STAT signaling are shown.

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Additional file 14:

1,25(OH)2D suppresses STAT1, STAT3 and PU.1 networks at 48 h. Image representing suppression of transcripts regulated by STAT1, STAT3 and PU.1. Significantly differentially expressed transcripts at 48 h (SAM, FDR<5%) were analyzed by using Metacore Network analysis (Transcription factor). Most of these transcripts are regulated by STAT1 or STAT3. Up--regulated transcripts are marked with red circles; down--regulated transcripts are identified by blue circles. Arrows are color coded to reflect the known regulatory action between two proteins. Red arrows between proteins indicates a negative regulatory effect, green arrows indicate a positive regulator effect, gray arrows indicate an unspecified regulatory effect.

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Additional file 15:

VDRE containing genes, comparison with Wang et al, 2005. Comparison of VD regulated transcripts in RWPE1 to those reported for EB1089 by Wang et al. in SCC25 cells.

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Additional file 16:

RT-PCR primers. List of RT-PCR primers used for validation of differential expression identified in 1,25(OH)2D-treated RWPE1 cells.

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Additional file 17:

Genes tested for functional VDRE. Table of genes tested for functional VDRE in promoter regions.

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