Biomarkers intersect with the exposome

The exposome concept promotes use of omic tools for discovering biomarkers of exposure and biomarkers of disease in studies of diseased and healthy populations. A two-stage scheme is presented for profiling omic features in serum to discover molecular biomarkers and then for applying these biomarkers in follow-up studies. The initial component, referred to as an exposome-wide-association study (EWAS), employs metabolomics and proteomics to interrogate the serum exposome and, ultimately, to identify, validate and differentiate biomarkers of exposure and biomarkers of disease. Follow-up studies employ knowledge-driven designs to explore disease causality, prevention, diagnosis, prognosis and treatment.

[1]  Christophe Junot,et al.  Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review. , 2011, Clinical biochemistry.

[2]  Alan D. Lopez,et al.  Global and regional burden of disease and risk factors, 2001: systematic analysis of population health data , 2006, The Lancet.

[3]  Pauline M. Rudd,et al.  Glycomic and glycoproteomic analysis of serum from patients with stomach cancer reveals potential markers arising from host defense response mechanisms. , 2011, Journal of proteome research.

[4]  Ian J. Brown,et al.  Human metabolic phenotype diversity and its association with diet and blood pressure , 2008, Nature.

[5]  C. Hansch,et al.  IARC carcinogens reported in cigarette mainstream smoke and their calculated log P values. , 2003, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[6]  Rachel B. Brem,et al.  Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation , 2012, PLoS biology.

[7]  R. Lewensohn,et al.  Metabolomics: Moving to the Clinic , 2010, Journal of Neuroimmune Pharmacology.

[8]  C. Wild Complementing the Genome with an “Exposome”: The Outstanding Challenge of Environmental Exposure Measurement in Molecular Epidemiology , 2005, Cancer Epidemiology Biomarkers & Prevention.

[9]  S. Rappaport Implications of the exposome for exposure science , 2011, Journal of Exposure Science and Environmental Epidemiology.

[10]  Daniel C Liebler,et al.  Protein damage by reactive electrophiles: targets and consequences. , 2008, Chemical research in toxicology.

[11]  He Li,et al.  Profiling Cys34 Adducts of Human Serum Albumin by Fixed-Step Selected Reaction Monitoring* , 2010, Molecular & Cellular Proteomics.

[12]  G. Gibson The environmental contribution to gene expression profiles , 2008, Nature Reviews Genetics.

[13]  Claude Villard,et al.  Advances in top-down proteomics for disease biomarker discovery. , 2011, Journal of proteomics.

[14]  Christoph Hiemke,et al.  Clinical utility of drug measurement and pharmacokinetics – therapeutic drug monitoring in psychiatry , 2008, European Journal of Clinical Pharmacology.

[15]  A. B. Hill The Environment and Disease: Association or Causation? , 1965, Proceedings of the Royal Society of Medicine.

[16]  J. Castle,et al.  An integrative genomics approach to infer causal associations between gene expression and disease , 2005, Nature Genetics.

[17]  Abraham P. Fong,et al.  Genome-wide transcription factor binding: beyond direct target regulation. , 2011, Trends in genetics : TIG.

[18]  Joshua LaBaer,et al.  So, you want to look for biomarkers (introduction to the special biomarkers issue). , 2005, Journal of proteome research.

[19]  Kevin F Krenitsky,et al.  Reduction of novel circulating long-chain fatty acids in colorectal cancer patients is independent of tumor burden and correlates with age , 2010, BMC gastroenterology.

[20]  S. Hanash,et al.  Mining the plasma proteome for cancer biomarkers , 2008, Nature.

[21]  J. Candell‐Riera,et al.  Nuclear magnetic resonance‐based metabolomics predicts exercise‐induced ischemia in patients with suspected coronary artery disease , 2008, Magnetic resonance in medicine.

[22]  D. Goldstein Common genetic variation and human traits. , 2009, The New England journal of medicine.

[23]  D. Thomas,et al.  Gene–environment-wide association studies: emerging approaches , 2010, Nature Reviews Genetics.

[24]  Frank Dieterle,et al.  New technologies around biomarkers and their interplay with drug development , 2008, Analytical and bioanalytical chemistry.

[25]  Frank H. Wilhelm,et al.  Cell aging in relation to stress arousal and cardiovascular disease risk factors , 2006, Psychoneuroendocrinology.

[26]  Philip J. Landrigan,et al.  Biological markers in environmental health research , 1987 .

[27]  D. Goodenowe,et al.  Human serum-derived hydroxy long-chain fatty acids exhibit anti-inflammatory and anti-proliferative activity , 2011, Journal of experimental & clinical cancer research : CR.

[28]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[29]  Hans-Peter Deigner,et al.  Targeted Metabolomics for Biomarker Discovery , 2010 .

[30]  Christian Baumgartner,et al.  Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. , 2008, The Journal of clinical investigation.

[31]  N. Kitteringham,et al.  Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics. , 2009, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[32]  Frederick P Roth,et al.  Metabolomic Identification of Novel Biomarkers of Myocardial Ischemia , 2005, Circulation.

[33]  J. Nicholson Global systems biology, personalized medicine and molecular epidemiology , 2006, Molecular systems biology.

[34]  S. Rozen,et al.  Metabolomic analysis and signatures in motor neuron disease , 2005, Metabolomics.

[35]  F. Perera,et al.  Molecular Epidemiology and Biomarkers in Etiologic Cancer Research: The New in Light of the Old , 2008 .

[36]  P. Gao,et al.  Silent myocardial ischemia is associated with altered plasma phospholipids , 2009, Journal of clinical laboratory analysis.

[37]  Justin Lamb,et al.  The Connectivity Map: a new tool for biomedical research , 2007, Nature Reviews Cancer.

[38]  Markus R. Wenk,et al.  The emerging field of lipidomics , 2005 .

[39]  I. Wilson,et al.  Gut microorganisms, mammalian metabolism and personalized health care , 2005, Nature Reviews Microbiology.

[40]  P. Mortensen EPIDEMIOLOGY , 2012, Schizophrenia Research.

[41]  M. Roizen General and Abdominal Adiposity and Risk of Death in Europe , 2009 .

[42]  Steven A Carr,et al.  Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics. , 2011, Circulation research.

[43]  Bernhard Pfeifer,et al.  A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry , 2008, Bioinform..

[44]  V. Mootha,et al.  Metabolite profiles and the risk of developing diabetes , 2011, Nature Network Boston.

[45]  Francis S. Collins,et al.  The case for a US prospective cohort study of genes and environment , 2004, Nature.

[46]  Monya Baker,et al.  In biomarkers we trust? , 2005, Nature Biotechnology.

[47]  Albert Koulman,et al.  From differentiating metabolites to biomarkers , 2009, Analytical and bioanalytical chemistry.

[48]  D. DeMets,et al.  Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework , 2001, Clinical pharmacology and therapeutics.

[49]  Stephen M Rappaport,et al.  Environment and Disease Risks , 2010, Science.

[50]  Atul J. Butte,et al.  An Environment-Wide Association Study (EWAS) on Type 2 Diabetes Mellitus , 2010, PloS one.

[51]  Kevin F Krenitsky,et al.  Reduced levels of hydroxylated, polyunsaturated ultra long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection , 2010, BMC medicine.

[52]  David Broadhurst,et al.  Huntington disease patients and transgenic mice have similar pro-catabolic serum metabolite profiles. , 2006, Brain : a journal of neurology.

[53]  L. Tenori,et al.  The metabonomic signature of celiac disease. , 2009, Journal of proteome research.

[54]  G. Lyon "Epidemiology, epigenetics and the ‘Gloomy Prospect’: embracing randomness in population health research and practice" , 2013 .

[55]  Tim Sprosen,et al.  UK Biobank: from concept to reality. , 2005, Pharmacogenomics.

[56]  Thomas J. Wang,et al.  The search for new cardiovascular biomarkers , 2008, Nature.

[57]  S. Sturla DNA adduct profiles: chemical approaches to addressing the biological impact of DNA damage from small molecules. , 2007, Current opinion in chemical biology.

[58]  Brian J. Bennett,et al.  Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease , 2011, Nature.

[59]  Luigi Atzori,et al.  Metabolomics as a tool for cardiac research , 2011, Nature Reviews Cardiology.

[60]  W. Matson,et al.  Metabolomic profiling to develop blood biomarkers for Parkinson's disease. , 2008, Brain : a journal of neurology.

[61]  Laura K. Schnackenberg,et al.  Metabonomic models of human pancreatic cancer using 1D proton NMR spectra of lipids in plasma , 2006, Metabolomics.

[62]  M. Graeber Biomarkers for Parkinson's disease , 2009, Experimental Neurology.

[63]  Paolo Vineis,et al.  A self-fulfilling prophecy: are we underestimating the role of the environment in gene-environment interaction research? , 2004, International journal of epidemiology.

[64]  Yiran Huang,et al.  Metabonomic profiling of renal cell carcinoma: high-resolution proton nuclear magnetic resonance spectroscopy of human serum with multivariate data analysis. , 2008, Analytica chimica acta.

[65]  R. Chung,et al.  Viral hepatocarcinogenesis , 2010, Oncogene.

[66]  Gregory P Tochtrop,et al.  Metabolomics, Pathway Regulation, and Pathway Discovery* , 2011, The Journal of Biological Chemistry.

[67]  S. Rappaport,et al.  Selected Reaction Monitoring , 2020, Definitions.

[68]  C. Wild,et al.  The exposome: from concept to utility. , 2012, International journal of epidemiology.

[69]  S. Hanash,et al.  Emerging molecular biomarkers—blood-based strategies to detect and monitor cancer , 2011, Nature Reviews Clinical Oncology.

[70]  Ian D. Wilson,et al.  Metabolic Phenotyping in Health and Disease , 2008, Cell.