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Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma
Clear cell Renal Cell Carcinoma (ccRCC) is due to loss of von Hippel–Lindau (VHL) gene and at least one out of three chromatin regulating genes BRCA1-associated protein-1 (BAP1), Polybromo-1 (PBRM1) and Set domain-containing 2 (SETD2). More than 350, 700 and 500 mutations are known respectively for...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Impact Journals LLC
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741666/ https://www.ncbi.nlm.nih.gov/pubmed/26452128 |
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author | Piva, Francesco Giulietti, Matteo Occhipinti, Giulia Santoni, Matteo Massari, Francesco Sotte, Valeria Iacovelli, Roberto Burattini, Luciano Santini, Daniele Montironi, Rodolfo Cascinu, Stefano Principato, Giovanni |
author_facet | Piva, Francesco Giulietti, Matteo Occhipinti, Giulia Santoni, Matteo Massari, Francesco Sotte, Valeria Iacovelli, Roberto Burattini, Luciano Santini, Daniele Montironi, Rodolfo Cascinu, Stefano Principato, Giovanni |
author_sort | Piva, Francesco |
collection | PubMed |
description | Clear cell Renal Cell Carcinoma (ccRCC) is due to loss of von Hippel–Lindau (VHL) gene and at least one out of three chromatin regulating genes BRCA1-associated protein-1 (BAP1), Polybromo-1 (PBRM1) and Set domain-containing 2 (SETD2). More than 350, 700 and 500 mutations are known respectively for BAP1, PBRM1 and SETD2 genes. Each variation damages these genes with different severity levels. Unfortunately for most of these mutations the molecular effect is unknown, so precluding a severity classification. Moreover, the huge number of these gene mutations does not allow to perform experimental assays for each of them. By bioinformatic tools, we performed predictions of the molecular effects of all mutations lying in BAP1, PBRM1 and SETD2 genes. Our results allow to distinguish whether a mutation alters protein function directly or by splicing pattern destruction and how much severely. This classification could be useful to reveal correlation with patients’ outcome, to guide experiments, to select the variations that are worth to be included in translational/association studies, and to direct gene therapies. |
format | Online Article Text |
id | pubmed-4741666 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Impact Journals LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-47416662016-03-03 Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma Piva, Francesco Giulietti, Matteo Occhipinti, Giulia Santoni, Matteo Massari, Francesco Sotte, Valeria Iacovelli, Roberto Burattini, Luciano Santini, Daniele Montironi, Rodolfo Cascinu, Stefano Principato, Giovanni Oncotarget Research Paper Clear cell Renal Cell Carcinoma (ccRCC) is due to loss of von Hippel–Lindau (VHL) gene and at least one out of three chromatin regulating genes BRCA1-associated protein-1 (BAP1), Polybromo-1 (PBRM1) and Set domain-containing 2 (SETD2). More than 350, 700 and 500 mutations are known respectively for BAP1, PBRM1 and SETD2 genes. Each variation damages these genes with different severity levels. Unfortunately for most of these mutations the molecular effect is unknown, so precluding a severity classification. Moreover, the huge number of these gene mutations does not allow to perform experimental assays for each of them. By bioinformatic tools, we performed predictions of the molecular effects of all mutations lying in BAP1, PBRM1 and SETD2 genes. Our results allow to distinguish whether a mutation alters protein function directly or by splicing pattern destruction and how much severely. This classification could be useful to reveal correlation with patients’ outcome, to guide experiments, to select the variations that are worth to be included in translational/association studies, and to direct gene therapies. Impact Journals LLC 2015-10-07 /pmc/articles/PMC4741666/ /pubmed/26452128 Text en Copyright: © 2015 Piva et al. http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Paper Piva, Francesco Giulietti, Matteo Occhipinti, Giulia Santoni, Matteo Massari, Francesco Sotte, Valeria Iacovelli, Roberto Burattini, Luciano Santini, Daniele Montironi, Rodolfo Cascinu, Stefano Principato, Giovanni Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title | Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title_full | Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title_fullStr | Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title_full_unstemmed | Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title_short | Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma |
title_sort | computational analysis of the mutations in bap1, pbrm1 and setd2 genes reveals the impaired molecular processes in renal cell carcinoma |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741666/ https://www.ncbi.nlm.nih.gov/pubmed/26452128 |
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