C7189 Introduction to molecular medicine

Faculty of Science
Autumn 2024
Extent and Intensity
0/0/3. 3 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).
In-person direct teaching
Teacher(s)
doc. Mgr. Jiří Šána, Ph.D. (lecturer)
prof. RNDr. Ondřej Slabý, Ph.D. (lecturer)
Mgr. Marek Večeřa (seminar tutor)
Ing. Mgr. Michaela Ručková (seminar tutor)
Mgr. Dagmar Al Tukmachi (seminar tutor)
Mgr. František Siegl (seminar tutor)
Mgr. Matej Jasík (seminar tutor)
Mgr. et Mgr. Marie Boudná (seminar tutor)
Mgr. Jana Orlíčková (seminar tutor)
Mgr. Petra Pokorná (seminar tutor)
Mgr. Tereza Deissová (seminar tutor)
Guaranteed by
prof. RNDr. Ondřej Slabý, Ph.D.
Department of Biochemistry – Chemistry Section – Faculty of Science
Contact Person: doc. Mgr. Jiří Šána, Ph.D.
Supplier department: Department of Biochemistry – Chemistry Section – Faculty of Science
Timetable
Thu 10:00–12:50 C15/211
Prerequisites (in Czech)
C7188 Introduction to molecular medicine ||NOW( C7188 Introduction to molecular medicine )
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 8/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24
fields of study / plans the course is directly associated with
Course objectives
The objective is to introduce students into the methodological principles of molecular medicine with special view on the use of molecular biological methods in cancer diagnosis and therapy individualization. Students will be introduced into design of the study, experimental techniques, statistical analysis, and implementation to the clinical practice.
Learning outcomes
After completing this course, students will be able to: • explain the principle and specifics of biomarker study design • calculate the sample size estimate and financial costs of a simple three-phase biomarker study • explain the principle of high-throughput analyses (PCR arrays, microarrays, next-generation sequencing) • perform modern techniques used in basic and applied research (nucleic acid isolation, reverse transcription, real-time PCR, cell culture, growth curve construction, nucleic acid transfection, analysis of cell viability, proliferation, migration) • explain the principle of cell cycle analysis and apoptosis • process and statistically evaluate the obtained data (PCR data modification, Mann-Whitney U test, ROC analysis, Kaplan-Meier survival analysis) • correctly and concisely present the obtained results of the model biomarker study.
Syllabus
  • 1. Introduction to the basic methodological approaches in molecular medicine, general principles of work in the molecular biological laboratory, demonstration of instruments, inspection of laboratories and facilities used in molecular medical research. 2. Introduction to the principles of study design in molecular medicine, examples of model studies, identification of diagnostic, prognostic, and predictive biomarkers, estimation of sample size required to achieve statistical significance, selection of suitable experimental approaches, availability of biological material, high-throughput analysis=screening and validation, control systems, time schedule, budget calculation. Detailed study design according to the lecturer instruction. 3. Types of biological material, the basic principles of work with biological material in molecular medicine (storage, tissue homogenization, cell separation, selection of the optimal procedure for the isolation of nucleic acids). Tissue homogenization, isolation of nucleic acids (DNA, RNA) and purity (ThermoScientific NanoDrop) and integrity control (LOC technology - Agilent Bioanalyzer, gel electrophoresis). 4. High-throughput analyses - advantages and disadvantages of individual approaches, a global analysis of gene expression (Affymetrix platform) and microRNA expression profiles (qRT-PCR arrays - TaqMan Low-Density Arrays), introduction to the evaluation of experimental data, identification of potential biomarkers, real experimental data analysis. 5. Validation I - the use of individual qRT-PCR assays on large independent sets of patients in accordance with the design of the study. Examples of experimental design Real-Time PCR, multiple-level control systems. Reverse transcription. 6. Validation II - the use of individual qRT-PCR assays on large independent sets of patients in accordance with the design of the study. Real-Time PCR. 7. Statistical analysis of data obtained from the validation. Introduction to the biostatistic methods (Mann-Whitney test, Wilcoxon test, multivariate analysis (Cox regression model), the ROC analysis - sensitivity, specificity, Kaplan-Meier survival analysis, ...). 8. Functional validation of biomarkers. In vitro experiments, general principles of work in the cell culture laboratory, and design of experiments with cell models. 9. Cell cultures cultivation, cell growth curves analyses and cytotoxicity tests (IC50). 10. Cell transfection with synthetic oligonucleotides to suppress selected genes and miRNAs on transcription levels. Evaluation of transfection efficiency (qRT-PCR, western blot). 11. Effect of transfection on cell viability, apoptosis and cell cycle (MTT assay, flow cytometry - Annexin V and propidium iodide). 12. Overall assessment of the study, final protocol and recommendations for possible implementation of tested biomarker into clinical practice.
Literature
    recommended literature
  • SLABÝ, ET AL., Ondřej. Molekulární medicína. 2015. ISBN 978-80-7492-121-6. info
Teaching methods
The course will be taught in person in the form of 1 short introductory meeting, 3 lectures (study design, high-throughput analyses, statistical data processing and evaluation) and 6 laboratory exercises (see syllabus), a consultation and a final presentation of results.
Assessment methods
The condition for granting the credit is the participation in seminars and lectures and the presentation of the obtained results at the end of the course. Before each practical exercise, a short written test verifies the preparation of students for the task. During the course, students must submit two assignments, which the teacher will evaluate; shortcomings must be corrected by students.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.
  • Enrolment Statistics (recent)
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