Department of Biochemistry

Proteomics

Research team

  • Assoc. Prof. Pavel Bouchal, e-mail: , phone: +420-549493251, fax: +420-549492690, University campus Brno-Bohunice, building A5, room 208, lab 212
  • Ph.D. students: Mgr. Petr Lapčík, Mgr. Lucia Janáčová, Mgr. Josef Maryáš, Mgr. Jakub Faktor
  • Specialists: Mgr. Pavla Bouchalová, Ph.D., Mgr. Karolína Zoufalová
  • Master students:  Bc. Petra Martinková, Bc. Petr Šulc, Bc. Jindřich Beránek, Bc. Juraj Polaček
  • Bachelor students: Jan Novák
  • Alumni-Ph.D. students: Mgr. Monika Dvořáková, Ph.D. 
  • Alumni-master students:  Mgr. Lucia Janáčová, Mgr. Iveta Bačová, Mgr. Petr Lapčík, Mgr. Karolína Zoufalová, Mgr. Petra Kovaříková, Mgr. Josef Maryáš, Mgr. Vendula Pernikářová, Mgr. Jakub Faktor, Mgr. Pavlína Holešínská, Mgr. Dominika Váňová, Mgr. Monika Mudrochová, Mgr. Iva Struhárová, Mgr. Jarmila Sobotková, Mgr. Karin Pěluchová, Mgr. Tereza Vyhlídalová, Mgr. Petra Přecechtělová

Project summary

Proteomics aims at large-scale monitoring of proteins in the analysis, their identification, quantification, comparison of protein expression under different conditions, identification, verification and validation of biomarkers of various physiological and pathological conditions, and making conclusions  on molecular mechanisms of biological processes from high-throughput data. Laboratory of proteomics was established at Department of Biochemistry in 2001. Since 2004 we have been collaborating on cancer research projects, and we have expanded our research program to the field of molecular and cellular cancer biology.

Our studies are currently focused mainly on:

  • Study of molecular mechanisms of metastasis of solid tumors (breast cancer, renal cell carcinoma, endomerial cancer and others) to identify novel therapeutic and diagnostic targets
  • Functional characterization of selected pro-metastatic proteins and their involvement in signalling pathways
  • Proteotyping of cancer tissues using next-generation proteomics - mass spectrometry in data independent acquisition mode 
  • Integration of proteomics and other high-throughput approaches (RNA-Seq, metabolomics)
  • Analysis of interactome in relationship to cancer development and metastasis
  • Development of application of targeted proteomics methods for a routine quuantification of selected proteins based on selected reaction monitoring (SRM)

In collaboration we realize a proteomics parts of other projects, e.g. in the field of biotechnology for studying the molecular mechanisms of adaptation in denitrigying and sulfur oxidizing bacteria on environmental changes, including interactome analysis.

The Laboratory runs its own tissue culture lab and laboratories of proteomics, biochemistry, and molecular biology. Proteomics analyses are based on 1D, 2D and 3D liquid chromatography and high resolution mass spectrometry techniques. Infrastructure for mass spectrometry data processing, gel image analysis and an older two-dimensional gel electrophoresis technique is also available. Pharos FX Pro scanner allows detecting of florescence staining on the presence of phosphoproteins and glycoproteins.

Five most important publications

  • BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Zbyněk BORTLÍČEKIvana IHNATOVÁIva PROCHÁZKOVÁ, JTC HO, Josef MARYÁŠHana IMRICHOVÁEva BUDINSKÁRostislav VYZULA, SD GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Combined Proteomics and Transcriptomics Identifies Carboxypeptidase B1 and Nuclear Factor kappa B (NF-kappa B) Associated Proteins as Putative Biomarkers of Metastasis in Low Grade Breast Cancer. MOLECULAR & CELLULAR PROTEOMICS, BETHESDA: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2015, vol. 14, No 7, p. 1814-1830. ISSN 1535-9476. doi:10.1074/mcp.M114.041335.
  • BOUCHAL, Pavel, Theodoros ROUMELIOTIS, Roman HRSTKARudolf NENUTILBořivoj VOJTĚŠEK and Spiros D. GARBIS. Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography-tandem mass spectrometry (iTRAQ-2DLC-MS/MS) based quantitative proteomic analysis. Journal of Proteome Research, Washington, USA: ACS, 2009, vol. 8, No 1, p. 362-373. ISSN 1535-3893. doi:10.1021/pr800622b.
  • DVOŘÁKOVÁ, Monika, Rudolf NENUTIL and Pavel BOUCHAL. Transgelins, cytoskeletal proteins implicated in different aspects of cancer development. Expert Review of Proteomics, 2014, vol. 11, No 2, p. 149-165. ISSN 1478-9450. doi:10.1586/14789450.2014.860358.
  • PROCHÁZKOVÁ, Iva, Juraj LENČO, Alena FUČÍKOVÁ, Jiří DRESLER, Lenka ČÁPKOVÁRoman HRSTKARudolf NENUTIL and Pavel BOUCHAL. Targeted proteomics driven verification of biomarker candidates associated with breast cancer aggressiveness. Biochimica et Biophysica Acta - Proteins and Proteomics, AMSTERDAM: Elsevier Science, 2017, vol. 1865, No 5, p. 488-498. ISSN 1570-9639. doi:10.1016/j.bbapap.2017.02.012.
  • FAKTOR, Jakub, Rita SUCHÁ, Vendula PÁRALOVÁ, Yansheng LIU and Pavel BOUCHAL. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics, HOBOKEN, USA: Wiley, 2017, vol. 17, No 5, p. nestránkováno. ISSN 1615-9853. doi:10.1002/pmic.201600323.

Collaboration

  • Masaryk Memorial Cancer Institute, Brno, CZ
  • ETH Zurich, Switzerland
  • University of British Columbia, Vancouver, Canada
  • University of Southampton, UK

Financial support

  • Czech Science Foundation 
  • Grant Agency of Masaryk University
  • Ministry of Health of the Czech Republic
  • Ministry of Education, Youth and Sports of the Czech Republic

 


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