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Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells.

Nagashima T, Suzuki T, Kondo S, Kuroki Y, Takahashi K, Ide K, Yumoto N, Hasegawa A, Toyoda T, Kojima T, Konagaya A, Suzuki H, Hayashizaki Y, Sakaki Y, Hatakeyama M - PLoS ONE (2008)

Bottom Line: MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription.However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups.These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.

View Article: PubMed Central - PubMed

Affiliation: Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

ABSTRACT
Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.

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Related in: MedlinePlus

OmicBrowse display for the BCAS2 gene.Experimental results (tiling arrays and array CGH) together with genome annotation are represented along the genomic coordinate using OmicBrowse, a web-based genome browser. The upper panel shows the copy number (1st lane) and BCAS2 gene locus (2nd lane) in chromosome 1. The lower panel represents a detailed view of this locus with 5 lanes. Each lane represents 1) H3K9 acetylation signals in the control experiment, 2) RNA mapping signal in the control experiment, 3) Ensembl Gene with exon-intron structure, 4) human CAGE tag counts, and 5) a region of BCAS2 derived from the NCBI Entrez Gene database. The height of the vertical bars in the 1st and 2nd lanes corresponds to the strength of the signals. Light green bars in the top 2 lanes represent regions with significant signal intensity. The upper panel shows that BCAS2 is located in amplified regions. In the lower panel, a high level of acetylation around the TSS, significant and higher signal intensity of the RNA map at exons, and a high CAGE tag can be seen for BCAS2. These data support the view that BCAS2 was expressed in the absence of exogenous stimuli.
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pone-0001803-g006: OmicBrowse display for the BCAS2 gene.Experimental results (tiling arrays and array CGH) together with genome annotation are represented along the genomic coordinate using OmicBrowse, a web-based genome browser. The upper panel shows the copy number (1st lane) and BCAS2 gene locus (2nd lane) in chromosome 1. The lower panel represents a detailed view of this locus with 5 lanes. Each lane represents 1) H3K9 acetylation signals in the control experiment, 2) RNA mapping signal in the control experiment, 3) Ensembl Gene with exon-intron structure, 4) human CAGE tag counts, and 5) a region of BCAS2 derived from the NCBI Entrez Gene database. The height of the vertical bars in the 1st and 2nd lanes corresponds to the strength of the signals. Light green bars in the top 2 lanes represent regions with significant signal intensity. The upper panel shows that BCAS2 is located in amplified regions. In the lower panel, a high level of acetylation around the TSS, significant and higher signal intensity of the RNA map at exons, and a high CAGE tag can be seen for BCAS2. These data support the view that BCAS2 was expressed in the absence of exogenous stimuli.

Mentions: Our current results indicated that the majority of HRG-regulated genes were up-regulated (326 of the 333 genes). However, since MCF-7 is a cancer cell line, there was a concern that high genome copy numbers in the cells may result in strong gene expression in the absence of HRG that may potentially obscure any HGR-related effects. Genes such as NCOA3, PPM1D, PSMD6 and BCAS2 were detected with high expression and copy numbers in MCF-7 cells (Figures 5 and 6), and these genes have been associated with breast cancer progression [27]–[30]. However, our analysis revealed that the overall correlation between average copy number and the extent of gene expression was surprisingly weak.


Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells.

Nagashima T, Suzuki T, Kondo S, Kuroki Y, Takahashi K, Ide K, Yumoto N, Hasegawa A, Toyoda T, Kojima T, Konagaya A, Suzuki H, Hayashizaki Y, Sakaki Y, Hatakeyama M - PLoS ONE (2008)

OmicBrowse display for the BCAS2 gene.Experimental results (tiling arrays and array CGH) together with genome annotation are represented along the genomic coordinate using OmicBrowse, a web-based genome browser. The upper panel shows the copy number (1st lane) and BCAS2 gene locus (2nd lane) in chromosome 1. The lower panel represents a detailed view of this locus with 5 lanes. Each lane represents 1) H3K9 acetylation signals in the control experiment, 2) RNA mapping signal in the control experiment, 3) Ensembl Gene with exon-intron structure, 4) human CAGE tag counts, and 5) a region of BCAS2 derived from the NCBI Entrez Gene database. The height of the vertical bars in the 1st and 2nd lanes corresponds to the strength of the signals. Light green bars in the top 2 lanes represent regions with significant signal intensity. The upper panel shows that BCAS2 is located in amplified regions. In the lower panel, a high level of acetylation around the TSS, significant and higher signal intensity of the RNA map at exons, and a high CAGE tag can be seen for BCAS2. These data support the view that BCAS2 was expressed in the absence of exogenous stimuli.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2266794&req=5

pone-0001803-g006: OmicBrowse display for the BCAS2 gene.Experimental results (tiling arrays and array CGH) together with genome annotation are represented along the genomic coordinate using OmicBrowse, a web-based genome browser. The upper panel shows the copy number (1st lane) and BCAS2 gene locus (2nd lane) in chromosome 1. The lower panel represents a detailed view of this locus with 5 lanes. Each lane represents 1) H3K9 acetylation signals in the control experiment, 2) RNA mapping signal in the control experiment, 3) Ensembl Gene with exon-intron structure, 4) human CAGE tag counts, and 5) a region of BCAS2 derived from the NCBI Entrez Gene database. The height of the vertical bars in the 1st and 2nd lanes corresponds to the strength of the signals. Light green bars in the top 2 lanes represent regions with significant signal intensity. The upper panel shows that BCAS2 is located in amplified regions. In the lower panel, a high level of acetylation around the TSS, significant and higher signal intensity of the RNA map at exons, and a high CAGE tag can be seen for BCAS2. These data support the view that BCAS2 was expressed in the absence of exogenous stimuli.
Mentions: Our current results indicated that the majority of HRG-regulated genes were up-regulated (326 of the 333 genes). However, since MCF-7 is a cancer cell line, there was a concern that high genome copy numbers in the cells may result in strong gene expression in the absence of HRG that may potentially obscure any HGR-related effects. Genes such as NCOA3, PPM1D, PSMD6 and BCAS2 were detected with high expression and copy numbers in MCF-7 cells (Figures 5 and 6), and these genes have been associated with breast cancer progression [27]–[30]. However, our analysis revealed that the overall correlation between average copy number and the extent of gene expression was surprisingly weak.

Bottom Line: MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription.However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups.These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.

View Article: PubMed Central - PubMed

Affiliation: Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

ABSTRACT
Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.

Show MeSH
Related in: MedlinePlus