Using Metabolomics to Characterize Exposure

Transcription

1 Using Metabolomics to Characterize Exposure David Wishart, University of Alberta Metabolomics as a Tool for Characterizing the Exposome National Academy of Sciences Washington DC, May 28-29, 2015

2 Exposures & Human Disease Lifetime Risk (12 most common diseases in North America) Common cold/influenza 100% (viruses) Tooth decay 92% (sugars, bacteria) Hypertension 90% (salt, lipids, tobacco) Heart disease/atherosclerosis 58% (lipids, TMAO, tobacco) Cancer 41% (toxins, mutagens, lipids, tobacco) Obesity 38% (sugars, lipids) Diabetes 37% (sugars, lipids, BCAAs, amino adipic acid) Acid reflux disease 17% (spices, lipids, sugars) Stroke 15% (lipids, sugars, tobacco) Migraine 10% (sugars, polyphenols, dyes) Allergies/Asthma 9% (various chemicals) Alzheimer s disease 6%

3 Exposure & Mortality (USA)

4 Key Points Most common and most complex/chronic diseases have an environmental (chemical or infectious) origin >90% of deaths and disease in the US and other developed countries are due to some kind of environmental exposure (excess or deficiency) How can we measure environmental exposures and their consequences?

5 The Answer: Metabolomics Physiological Influence Environmental Influence Metabolome Proteome Metabolomics Proteomics Genomics Genome

6 The complete collection of small molecules found in a given biosample including endogenous and exogenous compounds The Metabolome

7 Measuring Exposures Epidemiologist s view: ask a person about their location, diet, behavior, lifestyle Indirect, categorical, surrogate predictors Molecular epidemiologist s view: measure a biomarker inside a person Relates to internal dose Exposure scientist s view: measure what is found outside a person External levels from air or water or dermal contact

8 Measuring the Metabolome Biological or Tissue Samples Extraction Biofluids or Extracts ppm Data Analysis Chemical Analysis

9 Measuring the Exposome Exposures Metabolism Biofluids ppm Data Analysis Chemical Analysis

10 Measuring the Environment ppm Data Analysis Chemical Analysis

11 Measurement Technologies UPLC, HPLC CE/microfluidics LC-MS FT-MS QqQ-MS ICP-MS (metals) NMR spectroscopy GC-MS FTIR

12 Technology & Sensitivity # Metabolites detected (Log 10 ) Known unknowns NMR GC-MS TOF GC-MS Quad M mm µm nm pm fm Sensitivity or LDL Unknown unknowns LC-MS or DI-MS

13 2 Routes to Metabolomics ppm Quantitative (Targeted) Methods Chemometric (Profiling) Methods TMAO hippurate allantoin creatinine taurine hippurate urea water fumarate ppm creatinine citrate 2-oxoglutarate succinate PC ANIT Control PAP PC

14 Metabolomics The Problem With Metabolomics Genomics Gene IDs + Transcript Abundance Protein IDs + Concentrations Proteomics? Metabolite IDs + Concentrations

15 The Human Metabolome Project $7.5 million Genome Canada Project launched in Jan Based at the University of Alberta, Canada Key objective was to create a comprehensive database of all human metabolites that included compound data, source data, concentration data and a wide range (NMR, GC-MS, MS/MS) of spectral data Special focus on metabolites in biofluids such as urine, CSF and blood as well as tissues using HT experiments and text analysis Associate metabolite concentrations to ~600 diseases or conditions Make all data freely and electronically accessible

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17 Human Metabolomes (2015) 3670 (T3DB) Toxins/Env. Chemicals 1240 (DrugBank) Drug metabolites (FooDB) Food additives/phytochemicals 1550 (DrugBank) Drugs (HMDB) Endogenous metabolites M mm µm nm pm fm

18 Meet the Metabolomes

19 The Human Metabolome Database (HMDB) A web-accessible resource containing detailed information on 41,993 quantified, detected and expected metabolites Normal/abnormal concentrations 600+ disease links 10,000+ reference spectra Supports sequence, spectral, structure and text searches as well as compound browsing Full data downloads

20 The Drug Database (DrugBank) Database about drugs, drug targets & mechanisms 1552 small molecule drugs Detailed ADMET, MOA and pharmacokinetic data >1000 drugs with metabolizing enzyme data >1200 drug metabolites >600 drugs with transporters >600 MS+NMR spectra >4200 unique drug targets >14,000 drug-drug interactions Supports sequence, spectral, structure and text searches as well as compound browsing Full data downloads

21 The Toxic Exposome Database (T3DB) Comprehensive data on toxic compounds (drugs, pesticides, herbicides, endocrine disruptors, drugs, solvents, PCBs, furans, carcinogens, etc.) Detailed mechanisms, binding constants, target info >3600 toxic compounds ~2100 toxic targets >15,800 gene-chemical links >1900 reference spectra Full data downloads

22 Metabolomics The Problem With Metabolomics Genomics Gene IDs + Transcript Abundance Protein IDs + Concentrations Proteomics? Metabolite IDs + Concentrations

23 Metabolomics Problem Solved! Gene IDs + Transcript Abundance Genomics Protein IDs + Concentrations Proteomics Metabolite IDs + Concentrations

24 What s Possible ICP-based metallomics (~50 metals identified/quantified, pm sensitivity, 300 ul) NMR-based metabolomics (~150 compounds identified/quantified, um sensitivity, 300 ul) GC-MS based metabolomics (~150 compounds identified/quantified, <um sensitivity, 30 ul) DI-MS based metabolomics (180 compounds identified/quantified, nm sensitivity, 10 ul) LC-MS based metabolomics (~400 compounds identified/quantified, nm sensitivity, 10 ul) Lipidomics (3000 lipids identified and semiquantified, nm sensitivity, 1 ml)

25 Processing & Interpreting Metabolomic Data

26 Emerging Trends in Metabolomics Automated metabolomics Discovering useful disease or exposure biomarkers (lots and lots) Metabolite or tissue imaging Miniaturizing metabolomic devices Adductomics

27 Automated Metabolomics Chenomx Automated NMR Bruker Automated NMR Biocrates Automated MS

28 Biomarkers A measurable substance indicative of some biological phenomenon Diagnostic Do you have a given disease/condition Prognostic How well will you do with this disease/condition Predictive Odds of getting a given disease/condition Markers of Effect Response to drug/food/toxin intake Markers of Exposure Indication of drug/toxin/food consumption

29 Metabolite Biomarkers

30 Metabolite/MS Imaging

31 Miniaturizing Metabolomics $10 million instrument, $200/test $1000 instrument, $2/test

32 Adductomics + Adducts Trypsin digestion HSA HSA, HSA-adducts peptides T3, T3-adducts Anti-T3 Affinity Column (enrichment) Identification & quantification of adducts MS analysis

33 Why Metabolomics Is Relevant to Exposure Science It permits comprehensive, quantitative compound analysis from complex biological or environmental matrices It supports quantitative phenotyping It can identify both causes and physiological consequences of environmental exposures It can be fast, cheap and informative It is rapidly evolving and improving

34 Acknowledgements Liang Li Christoph Borchers James Harynuk Jie Chen Khalid Aziat Felicity Allen Richard Fedorak Rupa Mandal Jennifer Reid Tamara Lim Ray Bahado-Singh Jason Dyck David Rush Tom Blydt-Hansen Siamak Ravanbaksh Beomsoo Han Jeff Xia Philip Baker Allison Pon Craig Knox

35 Persistence Time of Exposures Saliva (0-10 minutes) Blood (1 hr 6 hrs) Urine (4 hrs 18 hrs) Feces (12 hrs 72 hrs) Hair (10 days 180 days) Adipose Tissue (1 day 80 years) DNA/Protein Adducts (1 day 80 years) Epigenetic effects (1 day 2 generations)