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      Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk

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          Abstract

          Exposome-Explorer ( http://exposome-explorer.iarc.fr) is a database of dietary and pollutant biomarkers measured in population studies. In its first release, Exposome-Explorer contained comprehensive information on 692 biomarkers of dietary and pollution exposures extracted from the analysis of 480 peer-reviewed publications. Today, Exposome-Explorer has been further expanded and contains a total of 908 biomarkers. Two additional types of information have been collected. First, 185 candidate dietary biomarkers having 403 associations with food intake (as measured by metabolomic studies) have been identified and added. Second, 1356 associations between dietary biomarkers and cancer risk in epidemiological studies, which were collected from 313 publications, have also been added to the database. Classifications for both foods and compounds have been revised, and new classifications for biospecimens, analytical methods and cancers have been implemented. Finally, the web interface has been redesigned to significantly improve the user experience.

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          Advances in metabolite identification.

          David Wishart (2011)
          One of the central challenges to metabolomics is metabolite identification. Regardless of whether one uses so-called 'targeted' or 'untargeted' metabolomics, eventually all paths lead to the requirement of identifying (and quantifying) certain key metabolites. Indeed, without metabolite identification, the results of any metabolomic analysis are biologically and chemically uninterpretable. Given the chemical diversity of most metabolomes and the character of most metabolomic data, metabolite identification is intrinsically difficult. Consequently a great deal of effort in metabolomics over the past decade has been focused on making metabolite identification better, faster and cheaper. This review describes some of the newly emerging techniques or technologies in metabolomics that are making metabolite identification easier and more robust. In particular, it focuses on advances in metabolite identification that have occurred over the past 2 to 3 years concerning the technologies, methodologies and software as applied to NMR, MS and separation science. The strengths and limitations of some of these approaches are discussed along with some of the important trends in metabolite identification.
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            Comparing metabolite profiles of habitual diet in serum and urine.

            Mary C. Playdon, Joshua Sampson, Amanda Cross … (2016)
            Diet plays an important role in chronic disease etiology, but some diet-disease associations remain inconclusive because of methodologic limitations in dietary assessment. Metabolomics is a novel method for identifying objective dietary biomarkers, although it is unclear what dietary information is captured from metabolites found in serum compared with urine.
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              Biomonitoring in the Era of the Exposome

              Kristine K. Dennis, Elizabeth Marder, David Balshaw … (2016)
              Background: The term “exposome” was coined in 2005 to underscore the importance of the environment to human health and to bring research efforts in line with those on the human genome. The ability to characterize environmental exposures through biomonitoring is key to exposome research efforts. Objectives: Our objectives were to describe why traditional and nontraditional (exposomic) biomonitoring are both critical in studies aiming to capture the exposome and to make recommendations on how to transition exposure research toward exposomic approaches. We describe the biomonitoring needs of exposome research and approaches and recommendations that will help fill the gaps in the current science. Discussion: Traditional and exposomic biomonitoring approaches have key advantages and disadvantages for assessing exposure. Exposomic approaches differ from traditional biomonitoring methods in that they can include all exposures of potential health significance, whether from endogenous or exogenous sources. Issues of sample availability and quality, identification of unknown analytes, capture of nonpersistent chemicals, integration of methods, and statistical assessment of increasingly complex data sets remain challenges that must continue to be addressed. Conclusions: To understand the complexity of exposures faced throughout the lifespan, both traditional and nontraditional biomonitoring methods should be used. Through hybrid approaches and the integration of emerging techniques, biomonitoring strategies can be maximized in research to define the exposome. Citation: Dennis KK, Marder E, Balshaw DM, Cui Y, Lynes MA, Patti GJ, Rappaport SM, Shaughnessy DT, Vrijheid M, Barr DB. 2017. Biomonitoring in the era of the exposome. Environ Health Perspect 125:502–510; http://dx.doi.org/10.1289/EHP474
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 08 January 2020
                Publication date (Electronic): 14 November 2019
                Publication date PMC-release: 14 November 2019
                Volume: 48
                Issue: D1
                Pages: D908-D912
                Affiliations
                [1 ] International Agency for Research on Cancer (IARC), Nutrition and Metabolism Section, Biomarkers Group , 150 Cours Albert Thomas, F-69372 Lyon Cedex 08, France
                [2 ] Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8, Canada
                Author notes
                To whom correspondence should be addressed. Tel: +33 4 72 73 80 95; Email: scalberta@ 123456iarc.fr
                Author information
                http://orcid.org/0000-0001-8604-1732
                http://orcid.org/0000-0002-3207-2434
                http://orcid.org/0000-0001-6651-6710
                Article
                Publisher ID: gkz1009
                DOI: 10.1093/nar/gkz1009
                PMC ID: 7145555
                PubMed ID: 31724701
                SO-VID: 34b6f76f-e493-4bf6-9464-1a4653a9a8bf
                Copyright © © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution 3.0 IGO License ( https://creativecommons.org/licenses/by/3.0/igo/) which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 11 November 2019
                Date revision received : 15 October 2019
                Date received : 14 September 2019
                Page count
                Pages: 5
                Funding
                Funded by: EXPOsOMICS FP7-KBBE-2012
                Award ID: 308610
                Funded by: Joint Programming Initiative FOODBALL
                Funded by: International Agency for Research on Cancer 10.13039/100008700
                Funded by: World Health Organization 10.13039/100004423
                Categories
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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