Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins
Abstract Background RASopathies are a group of syndromes showing clinical overlap caused by mutations in genes affecting the RAS-MAPK pathway. Consequent disruption on cellular signaling leads and is driven by phosphoproteome remodeling. However, we still lack a comprehensive picture of the differen...
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| Format: | Article |
| Language: | English |
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BMC
2021-07-01
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| Series: | Orphanet Journal of Rare Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13023-021-01934-x |
| _version_ | 1818888643540942848 |
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| author | Javier-Fernando Montero-Bullón Óscar González-Velasco María Isidoro-García Jesus Lacal |
| author_facet | Javier-Fernando Montero-Bullón Óscar González-Velasco María Isidoro-García Jesus Lacal |
| author_sort | Javier-Fernando Montero-Bullón |
| collection | DOAJ |
| description | Abstract Background RASopathies are a group of syndromes showing clinical overlap caused by mutations in genes affecting the RAS-MAPK pathway. Consequent disruption on cellular signaling leads and is driven by phosphoproteome remodeling. However, we still lack a comprehensive picture of the different key players and altered downstream effectors. Methods An in silico interactome of RASopathy proteins was generated using pathway enrichment analysis/STRING tool, including identification of main hub proteins. We also integrated phosphoproteomic and immunoblotting studies using previous published information on RASopathy proteins and their neighbors in the context of RASopathy syndromes. Data from Phosphosite database ( www.phosphosite.org ) was collected in order to obtain the potential phosphosites subjected to regulation in the 27 causative RASopathy proteins. We compiled a dataset of dysregulated phosphosites in RASopathies, searched for commonalities between syndromes in harmonized data, and analyzed the role of phosphorylation in the syndromes by the identification of key players between the causative RASopathy proteins and the associated interactome. Results In this study, we provide a curated data set of 27 causative RASopathy genes, identify up to 511 protein–protein associations using pathway enrichment analysis/STRING tool, and identify 12 nodes as main hub proteins. We found that a large group of proteins contain tyrosine residues and their biological processes include but are not limited to the nervous system. Harmonizing published RASopathy phosphoproteomic and immunoblotting studies we identified a total of 147 phosphosites with increased phosphorylation, whereas 47 have reduced phosphorylation. The PKB signaling pathway is the most represented among the dysregulated phosphoproteins within the RASopathy proteins and their neighbors, followed by phosphoproteins implicated in the regulation of cell proliferation and the MAPK pathway. Conclusions This work illustrates the complex network underlying the RASopathies and the potential of phosphoproteomics for dissecting the molecular mechanisms in these syndromes. A combined study of associated genes, their interactome and phosphorylation events in RASopathies, elucidates key players and mechanisms to direct future research, diagnosis and therapeutic windows. |
| first_indexed | 2024-12-19T16:56:23Z |
| format | Article |
| id | doaj.art-c12e4fcf2bed471a8c101c44342df7bf |
| institution | Directory Open Access Journal |
| issn | 1750-1172 |
| language | English |
| last_indexed | 2024-12-19T16:56:23Z |
| publishDate | 2021-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Orphanet Journal of Rare Diseases |
| spelling | doaj.art-c12e4fcf2bed471a8c101c44342df7bf2022-12-21T20:13:24ZengBMCOrphanet Journal of Rare Diseases1750-11722021-07-0116111710.1186/s13023-021-01934-xIntegrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteinsJavier-Fernando Montero-Bullón0Óscar González-Velasco1María Isidoro-García2Jesus Lacal3Metabolic Engineering Group, Department of Microbiology and Genetics, Faculty of Biology, University of SalamancaBioinformatics and Functional Genomics Group, IBMCC Cancer Research CenterInstitute for Biomedical Research of Salamanca (IBSAL)Institute for Biomedical Research of Salamanca (IBSAL)Abstract Background RASopathies are a group of syndromes showing clinical overlap caused by mutations in genes affecting the RAS-MAPK pathway. Consequent disruption on cellular signaling leads and is driven by phosphoproteome remodeling. However, we still lack a comprehensive picture of the different key players and altered downstream effectors. Methods An in silico interactome of RASopathy proteins was generated using pathway enrichment analysis/STRING tool, including identification of main hub proteins. We also integrated phosphoproteomic and immunoblotting studies using previous published information on RASopathy proteins and their neighbors in the context of RASopathy syndromes. Data from Phosphosite database ( www.phosphosite.org ) was collected in order to obtain the potential phosphosites subjected to regulation in the 27 causative RASopathy proteins. We compiled a dataset of dysregulated phosphosites in RASopathies, searched for commonalities between syndromes in harmonized data, and analyzed the role of phosphorylation in the syndromes by the identification of key players between the causative RASopathy proteins and the associated interactome. Results In this study, we provide a curated data set of 27 causative RASopathy genes, identify up to 511 protein–protein associations using pathway enrichment analysis/STRING tool, and identify 12 nodes as main hub proteins. We found that a large group of proteins contain tyrosine residues and their biological processes include but are not limited to the nervous system. Harmonizing published RASopathy phosphoproteomic and immunoblotting studies we identified a total of 147 phosphosites with increased phosphorylation, whereas 47 have reduced phosphorylation. The PKB signaling pathway is the most represented among the dysregulated phosphoproteins within the RASopathy proteins and their neighbors, followed by phosphoproteins implicated in the regulation of cell proliferation and the MAPK pathway. Conclusions This work illustrates the complex network underlying the RASopathies and the potential of phosphoproteomics for dissecting the molecular mechanisms in these syndromes. A combined study of associated genes, their interactome and phosphorylation events in RASopathies, elucidates key players and mechanisms to direct future research, diagnosis and therapeutic windows.https://doi.org/10.1186/s13023-021-01934-xPhosphoproteomicsInteractomicsRASopathiesNeurofibromatosisNoonan syndromeMass spectrometry |
| spellingShingle | Javier-Fernando Montero-Bullón Óscar González-Velasco María Isidoro-García Jesus Lacal Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins Orphanet Journal of Rare Diseases Phosphoproteomics Interactomics RASopathies Neurofibromatosis Noonan syndrome Mass spectrometry |
| title | Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins |
| title_full | Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins |
| title_fullStr | Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins |
| title_full_unstemmed | Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins |
| title_short | Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins |
| title_sort | integrated in silico ms based phosphoproteomics and network enrichment analysis of rasopathy proteins |
| topic | Phosphoproteomics Interactomics RASopathies Neurofibromatosis Noonan syndrome Mass spectrometry |
| url | https://doi.org/10.1186/s13023-021-01934-x |
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