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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: Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected.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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Distribution of signal differences dA and dR between HRG-treated and untreated cells.Upper and lower panel shows the distribution of acetylation and RNA map signal differences, dA ( = Ahrg–Acontrol) and dR ( = Rhrg–Rcontrol) (A and B), respectively. Larger dA (or dR) values represent a higher level of acetylation (or RNA map) in HRG-treated cells compared with untreated cells. Red and green dashed lines show the distribution of these values in the expression array and represent up- and down-regulated genes, respectively. Colored dotted lines depicted along the vertical axis represent average values of each distribution.
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pone-0001803-g002: Distribution of signal differences dA and dR between HRG-treated and untreated cells.Upper and lower panel shows the distribution of acetylation and RNA map signal differences, dA ( = Ahrg–Acontrol) and dR ( = Rhrg–Rcontrol) (A and B), respectively. Larger dA (or dR) values represent a higher level of acetylation (or RNA map) in HRG-treated cells compared with untreated cells. Red and green dashed lines show the distribution of these values in the expression array and represent up- and down-regulated genes, respectively. Colored dotted lines depicted along the vertical axis represent average values of each distribution.

Mentions: HRG-induced up- and down-regulation of genes was assessed by identifying signal differences between HRG-treated and untreated cells. The difference in acetylation signal dA and that of the RNA map dR were calculated as follows: dA = Ahrg–Acontrol and dR = Rhrg–Rcontrol, where Ahrg and Rhrg represent acetylation and RNA map signals in HRG-treated cells, respectively, and Acontrol and Rcontrol represent acetylation and RNA map signals in untreated cells, respectively. If dA or dR was greater than 0, the gene was regarded as being up-regulated. Figure 2 shows the distribution of these values. The average value of dA (2.7, black dotted line in Figure 2A) and dR (0.67, black dotted line in Figure 2B) and the distribution peak were greater than 0, which implies that HRG treatment induced up-regulation of histone acetylation and RNA mapping. If gene expression changes (up- or down-regulation) can be identified by examining acetylation (or RNA map) signals, it is anticipated that this would be reflected in the form of a distinct spread of dA (or dR) values relating to up- and down-regulated genes. However, when independently comparing the signal distribution pertaining to the acetylation (or RNA map) data with the expression array results, no clear difference was observed (red and green dashed lines were not distinct in Figure 2). Thus, our analysis revealed that independent tiling array analysis may have failed to identify the complete range of transcripts associated with HRG-induced gene regulation.


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)

Distribution of signal differences dA and dR between HRG-treated and untreated cells.Upper and lower panel shows the distribution of acetylation and RNA map signal differences, dA ( = Ahrg–Acontrol) and dR ( = Rhrg–Rcontrol) (A and B), respectively. Larger dA (or dR) values represent a higher level of acetylation (or RNA map) in HRG-treated cells compared with untreated cells. Red and green dashed lines show the distribution of these values in the expression array and represent up- and down-regulated genes, respectively. Colored dotted lines depicted along the vertical axis represent average values of each distribution.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001803-g002: Distribution of signal differences dA and dR between HRG-treated and untreated cells.Upper and lower panel shows the distribution of acetylation and RNA map signal differences, dA ( = Ahrg–Acontrol) and dR ( = Rhrg–Rcontrol) (A and B), respectively. Larger dA (or dR) values represent a higher level of acetylation (or RNA map) in HRG-treated cells compared with untreated cells. Red and green dashed lines show the distribution of these values in the expression array and represent up- and down-regulated genes, respectively. Colored dotted lines depicted along the vertical axis represent average values of each distribution.
Mentions: HRG-induced up- and down-regulation of genes was assessed by identifying signal differences between HRG-treated and untreated cells. The difference in acetylation signal dA and that of the RNA map dR were calculated as follows: dA = Ahrg–Acontrol and dR = Rhrg–Rcontrol, where Ahrg and Rhrg represent acetylation and RNA map signals in HRG-treated cells, respectively, and Acontrol and Rcontrol represent acetylation and RNA map signals in untreated cells, respectively. If dA or dR was greater than 0, the gene was regarded as being up-regulated. Figure 2 shows the distribution of these values. The average value of dA (2.7, black dotted line in Figure 2A) and dR (0.67, black dotted line in Figure 2B) and the distribution peak were greater than 0, which implies that HRG treatment induced up-regulation of histone acetylation and RNA mapping. If gene expression changes (up- or down-regulation) can be identified by examining acetylation (or RNA map) signals, it is anticipated that this would be reflected in the form of a distinct spread of dA (or dR) values relating to up- and down-regulated genes. However, when independently comparing the signal distribution pertaining to the acetylation (or RNA map) data with the expression array results, no clear difference was observed (red and green dashed lines were not distinct in Figure 2). Thus, our analysis revealed that independent tiling array analysis may have failed to identify the complete range of transcripts associated with HRG-induced gene regulation.

Bottom Line: Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected.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