Syllabus
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1. What is Biomarker? Theory: Definition of proteomic biomarkers, discovery, and validation of biomarkers Practical: Sample preparation and pre-analytical factors Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
2. Biomarker Pipeline-Part I Theory: Methodologies used to identify novel proteomic biomarkers Practical: Protein extraction from cells and tissues Roman Viták, Mgr., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
3. Biomarker Pipeline-Part II Theory: Identification of candidate biomarker, qualification, verification, validation, and clinical assay development Practical: Protein quantification, sample preparation, enzyme digestion Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
4. Harnessing the Power of Multiparameter Flow Cytometry in Biomarker Discovery (Invited Lecture) Practical: Gel-based proteomics, one-dimensional electrophoresis, staining and de-staining Suhail Tahir, Ph.D., Former researcher (Harvard Medical School), Scientist at BD Biosciences, USA. Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
5. Role of Biomarker in Personalised Medicine Theory: Use of biomarkers to improve patient outcomes, application of biomarkers, Plasma proteomics, Affinity-based technologies, future perspectives Practical: Analysis of digestion efficiency by electrophoresis Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
6. Introduction to Mass Spectrometry Theory: History, principles, mass spectral interpretation, electron ionization, detection, and quantitation, data analysis Practical: A raw data file from the proteomics experiment will be used for analysis. Participants will go through MS spectra to identify and quantify peptides thereby obtaining lists of protein identifiers that can be analyzed further using a wide range of resources. Ing. Tůma Zdeněk, Ph.D., Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Czech Republic Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
7. Recent Advancements in Mass Spectrometry What is targeted proteomics? Selected ion monitoring, extracted ion chromatograms, Multiple Reaction Monitoring, Skyline Software Practical: Raw data from a proteomics experiment will be used for analysis to develop MRM assay. Participants will be able to go through MS spectra to identify and quantify peptides (same line as above) Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic Ing. Tůma Zdeněk, Ph.D., Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
8. FDA-approved Proteomic Markers: Issues & Challenges Theory: Proteomic biomarkers in Cancer, Diabetes, Heart, Neurological disease, and other diseases. Practical: Gel electrophoresis, Immunoblotting. Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
9. The cutting-edge Research on Peptides Theory: Basic concepts of chemical biology, peptide synthesis, post-translational modification Practical: Immunoblot data analysis Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic *
10. In Vitro Diagnostics and Peptide Biomarkers (Invited Lecture) Theory: Peptide chemistry, microwave-assisted peptide synthesis, usage of synthetic peptides in diagnostics Elisa Peroni, Ph.D., Director of the Platform PeptLab@CY of the CY Cergy Paris Université-France Shashank Pandey, Ph.D., Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Czech Republic
Annotation
An optional course is designed on “Proteomic Biomarker Discovery”. In this course, students will focus on topics related to Proteomics which is a rapidly growing field and does not fit into basic pharmacology. In this course, students will not only acquire basic theoretical and practical training on routine techniques used in proteomics but also will acquire good knowledge in proteomic biomarker discovery and its use in clinical settings. In order to achieve a better understanding of this field, a special course will be also developed in MOODLE.
Proteomic Biomarker Discovery
A proteomic biomarker usually refers to disease-related proteins that can be used as an indicator of a specific biological state. Biomarkers are not only used in the clinic to diagnose and monitor the disease but also used to guide the molecular target treatment or evaluation of the therapeutic response. The potential use of proteomic biomarkers has been increased in basic and clinical research in last 2-3 decades. During the course, students will have a chance to learn basic routine techniques used in proteomic laboratories.