Exposome Journal Club

In the Spring 2021 semester, the Columbia University Department of Environmental Health Sciences Journal Club will focus on the exposome. We will be posting information about the course as the semester progresses. 

January 11, 2021       1. Introduction and the Wild papers

*Wild CP. Complementing the genome with an “exposome”: the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomarkers Prev. 2005 Aug;14(8):1847-50. doi: 10.1158/1055-9965.EPI-05-0456. PMID: 16103423.

Wild CP. The exposome: from concept to utility. Int J Epidemiol. 2012 Feb;41(1):24-32. doi: 10.1093/ije/dyr236. Epub 2012 Jan 31. PMID: 22296988.

In our first session, Dr. Miller gave an overview of the course structure and discussed these two key papers from Dr. Chris Wild. He spent most of the time on the 2005 paper which introduced the term and laid the foundation for the establishment of the field. It is hard to believe that it was published over 15 years ago. 

January 25, 2021  2. The Berkeley Papers. 

Rappaport SM, Smith MT. Epidemiology. Environment and disease risks. Science. 2010 Oct 22;330(6003):460-1. doi: 10.1126/science.1192603. PMID: 20966241; PMCID: PMC4841276.*

*Rappaport SM. Implications of the exposome for exposure science. J Expo Sci Environ Epidemiol. 2011 Jan-Feb;21(1):5-9. doi: 10.1038/jes.2010.50. Epub 2010 Nov 17. PMID: 21081972.

Rappaport SM. Genetic Factors Are Not the Major Causes of Chronic Diseases. PLoS One. 2016 Apr 22;11(4):e0154387. doi: 10.1371/journal.pone.0154387. PMID: 27105432; PMCID: PMC4841510.

In our second meeting, Dr. Miller discussed the 5 year hiatus from the original Wild paper and highlighted the work of Steve Rappaport and Martyn Smith at UC Berkeley who helped advance the exposome concept in the U.S. We discussed the 2010 NAS meeting on the exposome and how 2010 represented a new beginning in the field.

February 1, 2021       3. Nature vs. Nurture,  Exposure vs. Biology

Miller GW, Jones DP. The nature of nurture: refining the definition of the exposome. Toxicol Sci. 2014 Jan;137(1):1-2. doi: 10.1093/toxsci/kft251. Epub 2013 Nov 9. PMID: 24213143; PMCID: PMC3871934.

Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner S, Miller GW. The Importance of the Biological Impact of Exposure to the Concept of the Exposome. Environ Health Perspect. 2016 Oct;124(10):1504-1510. doi: 10.1289/EHP140. Epub 2016 Jun 3. PMID: 27258438; PMCID: PMC5047763.

The group discussed why was it important to expand the definition of the exposome. For example, the exposome had the potential to be more than an issue of exposure science and epidemiology-it could be used as a broader biological construct. The primary differences from the Wild definition, biological response, behavior, and endogenous processes, were outlined. The group went into depth about the meaning of behavior. Specifically, this was intended to include actions initiated by the individual as well as external forces exerted upon the individual, i.e. built environment, social constructs, access to care, etc. 

February 8, 2021. Capturing the external forces

Escher BI et al. From the exposome to mechanistic understanding of chemical-induced adverse effects. Environ Int. 2017 Feb;99:97-106

This article describes the potential of integrating adverse outcome pathway (AOP) and aggregate exposure pathway (AEP) concepts from (exo)toxicology with exposome research strategies. The authors suggest that AOPs can enhance the exposome approach by providing a mechanistic understanding of chemical exposures and adverse outcomes. Exposomal studies may similarly expand AOP concepts by accounting for mixture effects in space and time, non-linear relationships, as well as multiple chemical and non-chemical stressors. To best characterize exposure sources and their mechanisms of action, the authors advocate for synergic methods to be used in the study of stressor-induced adverse health outcomes.

Mueller W, Steinle S, Pärkkä J, Parmes E, Liedes H, Kuijpers E, Pronk A, Sarigiannis D, Karakitsios S, Chapizanis D, Maggos T, Stamatelopoulou A, Wilkinson P, Milner J, Vardoulakis S, Loh M. Urban greenspace and the indoor environment: Pathways to health via indoor particulate matter, noise, and road noise annoyance. Environ Res. 2020 Jan;180:108850.

This study determined the effect of greenspace, defined through Normalized DIfference Vegetation Index (NDVI), tree-cover density, and green land-use, on indoor air pollution (PM2.5), indoor noise levels (dB) and a self-reported noise annoyance measure. Study recruitment and exposure monitoring assessments were performed on 131 households across 4 European cities, under the Health and Environment-wide Association based on Large population Surveys (HEALS) study. Overall, the relationship between greenspace measures pollution/noise measures varied, with only summer-NDVI statistically significantly and inversely associated with PM2.5 levels, and summer-NDVI and winter-NDVI statistically significantly and inversely associated with self-reported noise annoyance.

February 15, 2021. Exposome databases-part 1.

Wishart D, Arndt D, Pon A, Sajed T, Guo AC, Djoumbou Y, Knox C, Wilson M, Liang Y, Grant J, Liu Y, Goldansaz SA, Rappaport SM. T3DB: the toxic exposome database. Nucleic Acids Res. 2015 Jan;43(Database issue):D928-34. doi: 10.1093/nar/gku1004. Epub 2014 Nov 5. PMID: 25378312; PMCID: PMC4383875.

This article describes updates to the Toxin-Toxin-Target Database (T3DB), a resource for looking up information about the toxic exposome. The T3DB was released in 2010 containing data on nearly 2900 common toxic substances along with detailed information on their chemical properties, descriptions, targets, toxic effects, toxicity thresholds, sequences (for both targets and toxins), and mechanisms. This 2015 update improves on the original T3DB in two ways: 1) by adding data on new compounds, and 2) by adding new types of data for each compound. First, the list of indexed compounds has been expanded to include relatively benign, naturally occurring or chronically toxic compounds such as glucose, fructose and cholesterol. This change reflects changes in the fields of molecular epidemiology, metabolomics and exposome science, which are increasingly shifting research interest toward chronic, minimally toxic exposures rather than just acute toxins. These additions also reflect an increasingly expanded definition of the exposome which includes endogenous compounds. Second, new information on each compound has been added. Of note, T3DB now also included gene expression data, normal and abnormal concentration ranges in different biofluids, and an updated taxonomy of chemical compounds. 

February 22, 2021. Exposome databases-part 2.

Neveu V, Nicolas G, Salek RM, Wishart DS, Scalbert A. Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. Nucleic Acids Res. 2020 Jan 8;48(D1):D908-D912. doi: 10.1093/nar/gkz1009. PMID: 31724701; PMCID: PMC7145555.

The Exposome-Explorer database was started in 2012 as a place to compile exposure biomarkers from the scientific literature. This database was published online in 2017. In this article, the authors describe recent updates and improvements to version 2.0 of the database. There were two main updates, increasing the total number of biomarkers in the system from 692 to 908 and focusing on the inclusion of dietary biomarkers. Version 2.0 includes the addition of 185 dietary biomarkers and 1,356 associations between diet and cancer from epidemiological studies. Additionally, in version 2.0 there were database upgrades including interface enhancements, improvements to the hierarchy of classification terms, and new forms and fields to organize information.