Your browser doesn't support javascript.
loading
The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model.
Faktor, Jakub; Grasso, Giuseppa; Zavadil Kokas, Filip; Kurkowiak, Malgorzata; Mayordomo, Marcos Yébenes; Kote, Sachin; Singh, Ashita; Ruidong, Li; O'Neill, J Robert; Muller, Petr; Goodlett, David; Vojtesek, Borek; Hupp, Ted.
Afiliación
  • Faktor J; Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
  • Grasso G; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK.
  • Zavadil Kokas F; Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
  • Kurkowiak M; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.
  • Mayordomo MY; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.
  • Kote S; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.
  • Singh A; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK.
  • Ruidong L; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK; Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
  • O'Neill JR; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK; University of Cambridge, Cambridge, UK.
  • Muller P; Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
  • Goodlett D; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland; School of Pharmacy, University of Maryland, ICCVS, Baltimore, USA.
  • Vojtesek B; Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic. Electronic address: vojtesek@mou.cz.
  • Hupp T; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK; Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 8
Biochim Biophys Acta Gen Subj ; 1864(12): 129722, 2020 12.
Article en En | MEDLINE | ID: mdl-32866596
BACKGROUND: The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape. METHODS: An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database. RESULTS: Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes. CONCLUSION: Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells. GENERAL SIGNIFICANCE: This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems.
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteína p53 Supresora de Tumor / Proteoma / Silenciador del Gen / Melanoma Límite: Humans Idioma: En Revista: Biochim Biophys Acta Gen Subj Año: 2020 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Países Bajos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteína p53 Supresora de Tumor / Proteoma / Silenciador del Gen / Melanoma Límite: Humans Idioma: En Revista: Biochim Biophys Acta Gen Subj Año: 2020 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Países Bajos