Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS
Abstract RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here, we used a reverse‐engineering approach in an ovarian cancer model to reconstruct KRAS oncogene‐dependen...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2012-07-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2012.32 |
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| _version_ | 1849738839168385024 |
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| author | Iwona Stelniec‐Klotz Stefan Legewie Oleg Tchernitsa Franziska Witzel Bertram Klinger Christine Sers Hanspeter Herzel Nils Blüthgen Reinhold Schäfer |
| author_facet | Iwona Stelniec‐Klotz Stefan Legewie Oleg Tchernitsa Franziska Witzel Bertram Klinger Christine Sers Hanspeter Herzel Nils Blüthgen Reinhold Schäfer |
| author_sort | Iwona Stelniec‐Klotz |
| collection | DOAJ |
| description | Abstract RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here, we used a reverse‐engineering approach in an ovarian cancer model to reconstruct KRAS oncogene‐dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT–PCR and western blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions, we analysed growth parameters and transcriptional deregulation in the KRAS‐transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype. |
| format | Article |
| id | doaj-art-b8b3d98fcfa64c36ad62bff3b1aa72aa |
| institution | DOAJ |
| issn | 1744-4292 |
| language | English |
| publishDate | 2012-07-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-b8b3d98fcfa64c36ad62bff3b1aa72aa2025-08-20T03:06:27ZengSpringer NatureMolecular Systems Biology1744-42922012-07-018111610.1038/msb.2012.32Reverse engineering a hierarchical regulatory network downstream of oncogenic KRASIwona Stelniec‐Klotz0Stefan Legewie1Oleg Tchernitsa2Franziska Witzel3Bertram Klinger4Christine Sers5Hanspeter Herzel6Nils Blüthgen7Reinhold Schäfer8Laboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinInstitute for Molecular BiologyLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinInstitute for Theoretical Biology, Humboldt UniversityLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinLaboratory of Molecular Tumour Pathology, Institute of Pathology, Charité Universitätsmedizin BerlinAbstract RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here, we used a reverse‐engineering approach in an ovarian cancer model to reconstruct KRAS oncogene‐dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT–PCR and western blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions, we analysed growth parameters and transcriptional deregulation in the KRAS‐transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype.https://doi.org/10.1038/msb.2012.32cancer systems biologymodular response analysisoncogenesovarian carcinoma modelsignal transduction |
| spellingShingle | Iwona Stelniec‐Klotz Stefan Legewie Oleg Tchernitsa Franziska Witzel Bertram Klinger Christine Sers Hanspeter Herzel Nils Blüthgen Reinhold Schäfer Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS Molecular Systems Biology cancer systems biology modular response analysis oncogenes ovarian carcinoma model signal transduction |
| title | Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS |
| title_full | Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS |
| title_fullStr | Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS |
| title_full_unstemmed | Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS |
| title_short | Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS |
| title_sort | reverse engineering a hierarchical regulatory network downstream of oncogenic kras |
| topic | cancer systems biology modular response analysis oncogenes ovarian carcinoma model signal transduction |
| url | https://doi.org/10.1038/msb.2012.32 |
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