Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line
Abstract Background The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety of tumor types. There are at least four splice variants of the mRNA en...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2944-9 |
| _version_ | 1818848696460115968 |
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| author | Claus Weinholdt Henri Wichmann Johanna Kotrba David H. Ardell Matthias Kappler Alexander W. Eckert Dirk Vordermark Ivo Grosse |
| author_facet | Claus Weinholdt Henri Wichmann Johanna Kotrba David H. Ardell Matthias Kappler Alexander W. Eckert Dirk Vordermark Ivo Grosse |
| author_sort | Claus Weinholdt |
| collection | DOAJ |
| description | Abstract Background The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety of tumor types. There are at least four splice variants of the mRNA encoding four protein isoforms of EGFR in humans, named I through IV. EGFR isoform I is the full-length protein, whereas isoforms II-IV are shorter protein isoforms. Nevertheless, all EGFR isoforms bind the epidermal growth factor (EGF). Although EGFR is an essential target of long-established and successful tumor therapeutics, the exact function and biomarker potential of alternative EGFR isoforms II-IV are unclear, motivating more in-depth analyses. Hence, we analyzed transcriptome data from glioblastoma cell line SF767 to predict target genes regulated by EGFR isoforms II-IV, but not by EGFR isoform I nor other receptors such as HER2, HER3, or HER4. Results We analyzed the differential expression of potential target genes in a glioblastoma cell line in two nested RNAi experimental conditions and one negative control, contrasting expression with EGF stimulation against expression without EGF stimulation. In one RNAi experiment, we selectively knocked down EGFR splice variant I, while in the other we knocked down all four EGFR splice variants, so the associated effects of EGFR II-IV knock-down can only be inferred indirectly. For this type of nested experimental design, we developed a two-step bioinformatics approach based on the Bayesian Information Criterion for predicting putative target genes of EGFR isoforms II-IV. Finally, we experimentally validated a set of six putative target genes, and we found that qPCR validations confirmed the predictions in all cases. Conclusions By performing RNAi experiments for three poorly investigated EGFR isoforms, we were able to successfully predict 1140 putative target genes specifically regulated by EGFR isoforms II-IV using the developed Bayesian Gene Selection Criterion (BGSC) approach. This approach is easily utilizable for the analysis of data of other nested experimental designs, and we provide an implementation in R that is easily adaptable to similar data or experimental designs together with all raw datasets used in this study in the BGSC repository, https://github.com/GrosseLab/BGSC. |
| first_indexed | 2024-12-19T06:21:27Z |
| format | Article |
| id | doaj.art-e5c24fd2acd4455a8e1ee9813754ae8d |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T06:21:27Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
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| series | BMC Bioinformatics |
| spelling | doaj.art-e5c24fd2acd4455a8e1ee9813754ae8d2022-12-21T20:32:42ZengBMCBMC Bioinformatics1471-21052019-08-0120111410.1186/s12859-019-2944-9Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell lineClaus Weinholdt0Henri Wichmann1Johanna Kotrba2David H. Ardell3Matthias Kappler4Alexander W. Eckert5Dirk Vordermark6Ivo Grosse7Institute of Computer Science, Martin Luther University Halle–WittenbergDepartment of Oral and Maxillofacial Plastic Surgery, Martin Luther University Halle–WittenbergDepartment of Oral and Maxillofacial Plastic Surgery, Martin Luther University Halle–WittenbergMolecular Cell Biology, School of Natural Sciences, University of CaliforniaDepartment of Oral and Maxillofacial Plastic Surgery, Martin Luther University Halle–WittenbergDepartment of Oral and Maxillofacial Plastic Surgery, Martin Luther University Halle–WittenbergDepartment of Radiotherapy, Martin Luther University Halle–WittenbergInstitute of Computer Science, Martin Luther University Halle–WittenbergAbstract Background The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety of tumor types. There are at least four splice variants of the mRNA encoding four protein isoforms of EGFR in humans, named I through IV. EGFR isoform I is the full-length protein, whereas isoforms II-IV are shorter protein isoforms. Nevertheless, all EGFR isoforms bind the epidermal growth factor (EGF). Although EGFR is an essential target of long-established and successful tumor therapeutics, the exact function and biomarker potential of alternative EGFR isoforms II-IV are unclear, motivating more in-depth analyses. Hence, we analyzed transcriptome data from glioblastoma cell line SF767 to predict target genes regulated by EGFR isoforms II-IV, but not by EGFR isoform I nor other receptors such as HER2, HER3, or HER4. Results We analyzed the differential expression of potential target genes in a glioblastoma cell line in two nested RNAi experimental conditions and one negative control, contrasting expression with EGF stimulation against expression without EGF stimulation. In one RNAi experiment, we selectively knocked down EGFR splice variant I, while in the other we knocked down all four EGFR splice variants, so the associated effects of EGFR II-IV knock-down can only be inferred indirectly. For this type of nested experimental design, we developed a two-step bioinformatics approach based on the Bayesian Information Criterion for predicting putative target genes of EGFR isoforms II-IV. Finally, we experimentally validated a set of six putative target genes, and we found that qPCR validations confirmed the predictions in all cases. Conclusions By performing RNAi experiments for three poorly investigated EGFR isoforms, we were able to successfully predict 1140 putative target genes specifically regulated by EGFR isoforms II-IV using the developed Bayesian Gene Selection Criterion (BGSC) approach. This approach is easily utilizable for the analysis of data of other nested experimental designs, and we provide an implementation in R that is easily adaptable to similar data or experimental designs together with all raw datasets used in this study in the BGSC repository, https://github.com/GrosseLab/BGSC.http://link.springer.com/article/10.1186/s12859-019-2944-9EGFRSplice variantsRNAiBayesian Information CriterionBayesian Gene Selection Criterion |
| spellingShingle | Claus Weinholdt Henri Wichmann Johanna Kotrba David H. Ardell Matthias Kappler Alexander W. Eckert Dirk Vordermark Ivo Grosse Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line BMC Bioinformatics EGFR Splice variants RNAi Bayesian Information Criterion Bayesian Gene Selection Criterion |
| title | Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| title_full | Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| title_fullStr | Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| title_full_unstemmed | Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| title_short | Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| title_sort | prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line |
| topic | EGFR Splice variants RNAi Bayesian Information Criterion Bayesian Gene Selection Criterion |
| url | http://link.springer.com/article/10.1186/s12859-019-2944-9 |
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