High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells.
<h4>Background</h4>Transforming growth factor beta 1 (TGFβ1) plays a major role in many lung diseases including lung cancer, pulmonary hypertension, and pulmonary fibrosis. TGFβ1 activates a signal transduction cascade that results in the transcriptional regulation of genes in the nucleu...
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2011
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oai:doaj.org-article:cb04f5dd35134565991379b1fd3d92e82021-11-18T06:53:36ZHigh throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells.1932-620310.1371/journal.pone.0020319https://doaj.org/article/cb04f5dd35134565991379b1fd3d92e82011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21625455/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Transforming growth factor beta 1 (TGFβ1) plays a major role in many lung diseases including lung cancer, pulmonary hypertension, and pulmonary fibrosis. TGFβ1 activates a signal transduction cascade that results in the transcriptional regulation of genes in the nucleus, primarily through the DNA-binding transcription factor SMAD3. The objective of this study is to identify genome-wide scale map of SMAD3 binding targets and the molecular pathways and networks affected by the TGFβ1/SMAD3 signaling in lung epithelial cells.<h4>Methodology</h4>We combined chromatin immunoprecipitation with human promoter region microarrays (ChIP-on-chip) along with gene expression microarrays to study global transcriptional regulation of the TGFβ1/SMAD3 pathway in human A549 alveolar epithelial cells. The molecular pathways and networks associated with TGFβ1/SMAD3 signaling were identified using computational approaches. Validation of selected target gene expression and direct binding of SMAD3 to promoters were performed by quantitative real time RT-PCR and electrophoretic mobility shift assay on A549 and human primary lung epithelial cells.<h4>Results and conclusions</h4>Known TGFβ1 target genes such as SERPINE1, SMAD6, SMAD7, TGFB1 and LTBP3, were found in both ChIP-on-chip and gene expression analyses as well as some previously unrecognized targets such as FOXA2. SMAD3 binding of FOXA2 promoter and changed expression were confirmed. Computational approaches combining ChIP-on-chip and gene expression microarray revealed multiple target molecular pathways affected by the TGFβ1/SMAD3 signaling. Identification of global targets and molecular pathways and networks associated with TGFβ1/SMAD3 signaling allow for a better understanding of the mechanisms that determine epithelial cell phenotypes in fibrogenesis and carcinogenesis as does the discovery of the direct effect of TGFβ1 on FOXA2.Yingze ZhangDaniel HandleyTommy KaplanHaiying YuAbha S BaisThomas RichardsKusum V PanditQilu ZengPanayiotis V BenosNir FriedmanOliver EickelbergNaftali KaminskiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 5, p e20319 (2011) |
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Medicine R Science Q Yingze Zhang Daniel Handley Tommy Kaplan Haiying Yu Abha S Bais Thomas Richards Kusum V Pandit Qilu Zeng Panayiotis V Benos Nir Friedman Oliver Eickelberg Naftali Kaminski High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| description |
<h4>Background</h4>Transforming growth factor beta 1 (TGFβ1) plays a major role in many lung diseases including lung cancer, pulmonary hypertension, and pulmonary fibrosis. TGFβ1 activates a signal transduction cascade that results in the transcriptional regulation of genes in the nucleus, primarily through the DNA-binding transcription factor SMAD3. The objective of this study is to identify genome-wide scale map of SMAD3 binding targets and the molecular pathways and networks affected by the TGFβ1/SMAD3 signaling in lung epithelial cells.<h4>Methodology</h4>We combined chromatin immunoprecipitation with human promoter region microarrays (ChIP-on-chip) along with gene expression microarrays to study global transcriptional regulation of the TGFβ1/SMAD3 pathway in human A549 alveolar epithelial cells. The molecular pathways and networks associated with TGFβ1/SMAD3 signaling were identified using computational approaches. Validation of selected target gene expression and direct binding of SMAD3 to promoters were performed by quantitative real time RT-PCR and electrophoretic mobility shift assay on A549 and human primary lung epithelial cells.<h4>Results and conclusions</h4>Known TGFβ1 target genes such as SERPINE1, SMAD6, SMAD7, TGFB1 and LTBP3, were found in both ChIP-on-chip and gene expression analyses as well as some previously unrecognized targets such as FOXA2. SMAD3 binding of FOXA2 promoter and changed expression were confirmed. Computational approaches combining ChIP-on-chip and gene expression microarray revealed multiple target molecular pathways affected by the TGFβ1/SMAD3 signaling. Identification of global targets and molecular pathways and networks associated with TGFβ1/SMAD3 signaling allow for a better understanding of the mechanisms that determine epithelial cell phenotypes in fibrogenesis and carcinogenesis as does the discovery of the direct effect of TGFβ1 on FOXA2. |
| format |
article |
| author |
Yingze Zhang Daniel Handley Tommy Kaplan Haiying Yu Abha S Bais Thomas Richards Kusum V Pandit Qilu Zeng Panayiotis V Benos Nir Friedman Oliver Eickelberg Naftali Kaminski |
| author_facet |
Yingze Zhang Daniel Handley Tommy Kaplan Haiying Yu Abha S Bais Thomas Richards Kusum V Pandit Qilu Zeng Panayiotis V Benos Nir Friedman Oliver Eickelberg Naftali Kaminski |
| author_sort |
Yingze Zhang |
| title |
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| title_short |
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| title_full |
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| title_fullStr |
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| title_full_unstemmed |
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. |
| title_sort |
high throughput determination of tgfβ1/smad3 targets in a549 lung epithelial cells. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/cb04f5dd35134565991379b1fd3d92e8 |
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