E3240 Biomarkers I - Methods and Tools

Přírodovědecká fakulta
podzim 2025
Rozsah
2/1/0. 3 kr. (příf plus uk plus > 4). Ukončení: zk.
Vyučováno kontaktně
Vyučující
Mgr. Ondřej Adamovský, Ph.D. (přednášející)
prof. RNDr. Luděk Bláha, Ph.D. (přednášející)
Mgr. Lucie Bláhová, Ph.D. (přednášející)
RNDr. Luděk Sehnal, Ph.D. (přednášející)
Garance
prof. RNDr. Luděk Bláha, Ph.D.
RECETOX – Přírodovědecká fakulta
Kontaktní osoba: prof. RNDr. Luděk Bláha, Ph.D.
Dodavatelské pracoviště: RECETOX – Přírodovědecká fakulta
Rozvrh
Čt 13:00–15:50 Kontaktujte učitele
Předpoklady
The course does not have any specific pre-requisites. Basic knowledge in (molecular) biology and (analytical) chemistry is advantagoues.
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
Cíle předmětu
The objectives of the course (organized in the Autumn semester, lectured in English) is to introduce and review various types of biomarkers, discuss relevant concepts in science as well as practical use and interpretations in different contexts. Further, the course introduces principles of biomarker development, instrumental analysis or biodetection. The course is primarily concerned with biomarkers related to interactions of SMALL MOLECULES (drugs, toxicants, environmental pollutants etc.) with living systems – humans, experimental organisms and wild biota. Correspondingly, the course focuses on BIOMARKERS OF EXPOSURE, BIOMARKERS OF RESPONSE-EFFECTS and BIOMARKERS OF SUSCEPTIBILITY relevant to interactions with small molecules. The course focuses on methodological aspects at all levels, i.e. designing a study, sampling and sample preparation, biomarker determination, result analysis and interpretation. The topics related to biomarkers in clinical medicine or epidemiology are briefly introduced and interested students are invited to enroll into a sister course E0290 (Interpretace biomarkerů v klinických a epidemiologických studiích), which is offered in synergy and complements the present course.
Výstupy z učení
At the end of the course students will be able to:
- discuss and describe biomarkers of exposure, response (effects), and susceptibility
- know and apply principles of sampling, sample processing, instrumental or (bio)analytical determination and analysis of biomarkers
- propose a plan and design studies with various purposes (aims) that incorporate biomarkers
- use knowledge from practical examples of biomarker applications – namely in pharmacology, toxicology and ecotoxicology
Osnova
The content of the course is planned for 12 weeks of regular semester. The content starts with biomarkers of EFFECTS/RESPONSE, moving to biomarkers of EXPOSURES and concluding with biomarkers of SUSCEPTIBILITY.
1. Introduction, types of biomarkers, concepts in different disciplines, terminology, NIEHS and FDA classifications, alignment. Research vs real life applications. (From genome to phenome). EXAMPLE 1 – occupational exposures.
2. Biomarkers of EFFECTS/RESPONSE in toxicology and ecotoxicology; small molecules and (eco)toxic effects - translation to biomarkers. Systemic biomarkers (in vivo behavioral and clinical; imunohistopathology, chemistry and hematology responses). EXAMPLE 2 – Ecotoxicology study.
3. SEMINAR 1 - Environmental toxicology - case study elaborated in group work, problem solving and discussion
4. Biomarkers in pharmacology - biologically active molecules in living systems, reflections as biomarkers - predictive, pharmacodynamic response, safety. EXAMPLE 3 - Drug safety.
5. Methods for biomarkers in pharmacology - approaches to analyze mode-of-action based biomarkers (from gene trascription through proteins to metabolites; general biomarkers (oxidative damage; hsp)
6. SEMINAR 2 - Biomarkers in human toxicology and pharmacology - - case study elaborated in group work, problem solving and discussion
7. Biomarkers of EXPOSURES - detecting small malecules in biological matrices, target/suspect/non-target assessment; exogenous chemicals vs metabolites vs adducts.
8. Exposome and omics biomarkers - methods, workflows, dataflows; top-down / bottom-up approaches
9. SEMINAR 3 - Interpreting the exposure biomarkers - case study elaborated in group work, problem solving and discussion
10. Biomarkers of SUSCEPTIBILITY - evolutionary and physiological adaptations; ADME, activation of compounds (pro-drugs, pro-carcinogens), examples of CYPs and their role in individual susceptibility.
11. Methods in evaluation of susceptibility and personalized medicine including genomics, metagenomics, transcriptomics and multi-omics approaches
12. SEMINAR 4 – Designing the biomarkers for exposome study - case study elaborated in group work, problem solving and discussion.
Literatura
    doporučená literatura
  • VESPALCOVÁ, Hana. Application of statistical analyses for identification of effect biomarkers from multiomics data. Edited by Ondřej Adamovský. ??? URL info
  • PEINADO, Francisco M.; Ainhoa PEREZ-CANTERO; Alicia OLIVAS-MARTINEZ; Lydia ESPIN-MORENO; Tomas DE HARO; Luis D. BOADA; Andrea RODRIGUEZ-CARRILLO; Eva GOVARTS; Susana PEDRAZA-DIAZ; Marta ESTEBAN-LOPEZ; Luděk BLÁHA; Lucie BLÁHOVÁ; Beata JANASIK; Wojciech WASOWICZ; Sanna LIGNELL; Loic RAMBAUD; Margaux RIOU; Clemence FILLOL; Sebastien DENYS; Aline MURAWSKI; Anne Lise BRANTSAETER; Amrit Kaur SAKHI; Nina ISZATT; Greet SCHOETERS; Marike KOLOSSA-GEHRING; Mariana F. FERNANDEZ a Vicente MUSTIELES. Adolescent exposure to benzophenone ultraviolet filters: cross-sectional associations with obesity, cardiometabolic biomarkers, and asthma/allergy in six European biomonitoring studies. Environmental Research. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2025, roč. 280, September 2025, s. 1-12. ISSN 0013-9351. Dostupné z: https://doi.org/10.1016/j.envres.2025.121912. URL info
  • NETO, Geraldo A. Mara; Anna BARTOŠKOVÁ; Anna POSPISILOVA; Luděk BLÁHA; Jana KLÁNOVÁ; Martin BOBÁK a Juan P. GONZALEZ-RIVAS. Associations between Per- and Polyfluoroalkyl Substances (PFAS) and Cardiometabolic Biomarkers in Adults of Czechia: The Kardiovize Study. International Journal of Environmental Research and Public Health. Basel: MDPI, 2022, roč. 19, č. 21, s. 1-10. ISSN 1660-4601. Dostupné z: https://doi.org/10.3390/ijerph192113898. URL info
  • KUCHOVSKÁ, Eliška; Bénédicte MORIN; María del Rocío LÓPEZ CABEZA; Mathilde BARRÉ; Corentin GOUFFIER; Lucie BLÁHOVÁ; Jérôme CACHOT; Luděk BLÁHA a Patrice GONZALEZ. Comparison of imidacloprid, propiconazole, and nanopropiconazole effects on the development, behavior, and gene expression biomarkers of the Pacific oyster (Magallana gigas). Science of the Total Environment. Amsterdam: Elsevier Science, 2021, roč. 764, April 2021, s. 1-11. ISSN 0048-9697. Dostupné z: https://doi.org/10.1016/j.scitotenv.2020.142921. URL info
  • Biomarkers and human biomonitoring. Edited by Lisbeth Ehlert Knudsen - Domenico Franco Merlo. Cambridge: RSC Publishing, 2012, xxvi, 471. ISBN 9781849732413. info
  • PAŠKOVÁ, Veronika. Biomarkers in experimental ecotoxicology. Edited by Klára Hilscherová. 2012, 118 s. URL info
  • Biomarkers : in medicine, drug discovery, and environmental health. Edited by Vishal S. Vaidya - Joseph V. Bonventre. Hoboken, N.J.: Wiley, 2010, xxviii, 60. ISBN 9780470452240. info
    neurčeno
  • JANOŠ, Tomáš; Ilse OTTENBROS; Lucie BLÁHOVÁ; Petr ŠENK; Libor ŠULC; Nina PÁLEŠOVÁ; Jessica SHEARDOVÁ; Jelle VLAANDEREN a Pavel ČUPR. Effects of pesticide exposure on oxidative stress and DNA methylation urinary biomarkers in Czech adults and children from the CELSPAC-SPECIMEn cohort. Environmental Research. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2023, roč. 222, April 2023, s. 1-9. ISSN 0013-9351. Dostupné z: https://doi.org/10.1016/j.envres.2023.115368. URL info
Výukové metody
The course combines (i) lectures, i.e. presentations and face-to-face interactions (2 hours per week on average, attendance non obligatory), (ii) interactive seminars - case studies and problem solving - 4-times during the semester on specific dates, each seminar is 3 hours, i.e. 12h total (attendance is obligatory), (iii) homework preparation for seminars is required (ca 18h total homework time estimated over the semester).
Metody hodnocení
Students are obliged to participate at 4 seminars during the semester, where they develop protocols from the case studies. One out of 4 seminars can be eventually missed (provided that student presents formal apology and serious reasons - such as health issues). The course is finished with an exam - written test (open questions, 80% weight) followed by brief oral discussion over the test responses (20% weight).
Náhradní absolvování
For the theoretical parts, students can be provided with study materials (slides, texts, videorecordings of the lectures). Practical / seminar case studies can be agreed on individual basis.
Vyučovací jazyk
Angličtina
Informace učitele

Details on the schedule of the Autumn 2025 semester + instructions on the final exam are available on this link:
https://is.muni.cz/auth/el/sci/podzim2025/E3240/index.qwarp

Please book 4 Thursdays - 23.10., 13.11., 27.11. and 4.12. - for obligatory seminars. Instructions how to prepare for seminars will be announced by the lecturers in advance.

Other weeks during the semester will include lectures accompanied with practical cases and examples.

No lecture is planned for 18th December, which is reserved as potential date for pre-term of the examination.


ACKNOWLEDGEMENTS: "Tento studijní předmět byl vytvořen za podpory EU, Next Generation, Národního plánu obnovy a Ministerstva školství, mládeže a tělovýchovy v rámci projektu NPO 7.4. – Podpora zelených dovedností a udržitelnosti na MU, reg. č. 0016/NPO74_PZDU_VS".



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