1212569_21823227.jpg logo_mu_cerne.gif 1212570_28446780.jpg logo_mu_cerne.gif Luděk Bláha, PřF MU, RECETOX www.recetox.cz BIOMARKERS AND TOXICITY MECHANISMS 13 – BIOMARKERS Omics + final notes OPVK_MU_stred_2 1212569_21823227.jpg logo_mu_cerne.gif Topics covered in the final presentation •Biomarkers at different levels –Omics –... and beyond • •Biomarkers in human medicine and drug development –Strategy and steps in development –Application examples 1212569_21823227.jpg logo_mu_cerne.gif Systems biology/toxicology/medicine = “omics” The overall hypothesis or idea (for future) Linking genetics / environment / health è èEarly and improved diagnostics èPersonalized prevention (elimination of risk factors) è Personalized treatment/medicine 1212569_21823227.jpg logo_mu_cerne.gif „OMICs“ •“Omics” techniques (Systems biology) –Result of rapid technological advances (microarrays, next generation sequencing, HPLC-mass spectrometry techniques etc.) –Simultaneous and „instant“ assessment of thousands of parameters (biological / toxicological responses) at different levels –„Big data“generated è bottleneck is data analysis (bioinformatics, self-learning machines, artifical intelligence? ) • •Genomics –Genes (DNA) - relatively stable •not responding to immediate environmental changes (e.g. Toxicants) •„slow“ changes possible –Epigenetics (e.g. DNA methylation) –Mutations (evolution) à Single Nucleotide Polymorphisms (SNPs) –Used as “biomarkers of susceptibility” (SNPs / personalized medicine) •Other omics •mRNA levels (transcriptomics) •proteins (proteomics) •metabolites (metabolomics), etc.... –Resposive to stress (including toxicants, therapy etc.) 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers at different biological levels – „omics“ approach Výsledek obrázku pro omics OMICs (1) – from genes …. to … functions Související obrázek 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers at different biological levels – „omics“ approach Výsledek obrázku pro omics Current advanced „omics“ technologies 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers at different biological levels – „omics“ approach http://www.genetris.com/images/uploads/images/Biomarker_discovery.gif OMICs (2) – … including PHENOTYPE (phenomics) Linking „outcome“ (health, intoxication, phenotype) with mechanistic changes (i.e. „biomarkers“) 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers develoment using „omics“ approaches •Different approaches towards new biomarkers –Hypothesis driven –Data driven - omics = screening followed by correlations (example figure – „proteome“) • • http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageSer vice/Articleimage/2008/MB/b802534g/b802534g-f1.gif 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers develoment using „omics“ approaches •Steps towards biomarkers 1.„Big omics data“ generated (easy and fast) 2.Correlations (bioinformatics) with health outcomes (bottleneck) àeventual identification of suspected biomarkers –e.g. Toxicant activates genes à higher level(s) of specific mRNAs (or higher protein levels) –E.g. Complex effects at several levels à modulation of profile(s) of certain metabolites 3.Characterization and validation of biomarkers (bottlenec: time and cost demanding) –Experimental - stability of biomarker responses throughout different stress levels (exposure doses, exposure duration, various conditions, males x females …. Etc) 4.Qualification and approval (clinical and epidemiological studies) – –à Despite of decades of omics era, there are only rare (if any) examples of biomarkers derived by omics currently applied in practice • • 1212569_21823227.jpg logo_mu_cerne.gif More detailed view: 5 steps leading to biomarker use in practice http://www.molecularmedicineireland.ie/uploads/BiomarkerImage_210910.jpg DISCOVERY à VALIDATION STEPS à APPROVAL 1212569_21823227.jpg logo_mu_cerne.gif 1.Biomarker development –High numbers of endpoints (e.g. proteins) –Low numbers of samples compared (e.g. 10 controls vs 10 “treatments”) 1. 2.Biomarker characterization and validation –Decreasing number of markers –Increasing numbers of specimens (biological samples) – 3.Biomarker qualification and approval –Individual markers –Analytical methods validated and well established Detailed zoom = example: proteomics http://www.bloodjournal.org/content/bloodjournal/121/4/585/F1.large.jpg?width=800&height=600 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers have potential for different applications ... such as: http://www.ipc.nxgenomics.org/newsletter/images/Biomarkers.jpg 1212569_21823227.jpg logo_mu_cerne.gif Biomarkers have potential for different applications ... such as: •Biomarkers in research –Search of “potential” therapies/drugs •Changes in biochemical responses provide information on efficiency and mechanism of action –Identification of “early markers” of chronic diseases •Early diagnosis (e.g. identification of developing cancer, coronary disease...) • •Biomarkers in medicine –Identification of status of an individual •Healthy vs Disease –Assessment of therapy/treatment •Efficiency – Did treatment improved situation? (improvements in biomarker responses) •Adverse or side effects of therapy • •Biomarkers in toxicology –Identification of status •Intoxicated (exposed) vs Controls •Forensic toxicology (e.g. consumption of drugs of abuse, alcohol etc) –Early warnings of future health consequences •Biochemical changes are detectable before the actual health problems – 1212569_21823227.jpg logo_mu_cerne.gif Biomarker „validation“– example Good characterization and critical assessment needed during validation. Example: Kim-1 protein related to kidney injury by toxicants •Kim-1 levels significantly elevated only at manifested clinical signs = histopathology grades 1-3 („diagnostic“ biomarker = status) •Poor „prognostic“ potential (overlap of Controls and initial toxicity condition (histo-grade 0) 1212569_21823227.jpg logo_mu_cerne.gif Summary and overview Class on toxicity mechanisms (MoA) and biomarkers 1212569_21823227.jpg logo_mu_cerne.gif Class summary and take home message * Molecular effects of toxicants = MoAs (1) * Propagate to higher levels (2), * … where they induce measurable “responses” - biomarkers (3) https://encrypted-tbn3.gstatic.com/images?q=tbn:ANd9GcTJLahZlgjt9hGQWAfTZhHoUTAU1dGT2XlAGT1vzWh0Ze3 _nMUH MoAs * Molecular interactions * Key targets ...: - DNA, RNAs - proteins (and their functions) - membranes * Complex mechanisms - Oxidative stress - Signalling and hormones - Detoxification 1 2 3 1 Biological organization Biomarkers - types - examples - methods 1212569_21823227.jpg logo_mu_cerne.gif Summary on toxicity mechanisms (MoA) and biomarkers •For excellent performance and successful exam student should: • 1.have an overview of different types of MoAs (see also point 2 below) and be able to link MoAs to higher level effects (toxicity) •Example: inhibition of AcCholE enzymes (mechanism) à propagates as neurotoxicity (effect) 2.know some details for selected example MoAs for different toxicant targets = based on your own interest select one example from each of the following categories, learn details, be able to discuss (i.e. know details for 7 example modes of toxic action) 1.nucleic acids 2.proteins 3.membranes (lipids) 4.cellular 5.Complex 1 – detoxification/metabolization 6.Complex 2 – intra- and inter-cellular signalling, hormones 7.Complex 3 – oxidative stress 3.have understanding of biomarker issues •What is a biomarker and what properties it should have (or not to have)? •Why we search for them = how can they be used? •What different types and groups of biomarkers can be recognized? •What are suitable matrices for sampling and further analyses? •What approaches are applied in biomarker discovery („hypothesis“ vs omics)? 4.and know example biomarkers same approach as for point 2 above = based on your own interest select one example biomarker for each of seven categories and know some details) •