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Despite extensive evidence showing that exposure to specific chemicals can lead to disease, current Measuring chemicals en masse
research approaches and regulatory policies fail to address the chemical complexity of our world. To Several research efforts have pioneered differ-
safeguard current and future generations from the increasing number of chemicals polluting our ent approaches for the systematic mapping of
environment, a systematic and agnostic approach is needed. The “exposome” concept strives to capture the exposome, taking advantage of develop-
the diversity and range of exposures to synthetic chemicals, dietary constituents, psychosocial ments in mass spectrometry, sensors, wearables,
stressors, and physical factors, as well as their corresponding biological responses. Technological study design, biostatistics, and bioinformatics
advances such as high-resolution mass spectrometry and network science have allowed us to take (6)—advances that now position us to pursue
the first steps toward a comprehensive assessment of the exposome. Given the increased recognition Dr. Wild’s original vision of the exposome (1).
of the dominant role that nongenetic factors play in disease, an effort to characterize the exposome at a A prime example is how high-resolution mass
scale comparable to that of the human genome is warranted. spectrometry (HRMS) has transformed our
ability to measure multitudinous chemical
A
species in a wide range of media, expanding
Social capital
l
1 10 100 1000 10,000 100,000 10 million 1 billion chemicals ... ... ...
significant associations (including persistent the exposome. Network science (23), which offer greater coverage (12, 27, 28). The second
organic pollutants and pesticides) validated has well-developed applications in medicine challenge in developing a framework is that
across independent cohorts (22). However, by and systems biology (24), offers a platform the current statistical toolset assumes that we
focusing on a predetermined list of chemi- with which to achieve an understanding of the are faced with a collection of random variables
cals, these initial EWAS studies likely suffer impact of multiple exposures. Each chemical that are independent, identically distributed,
from the same limitations of candidate gene will exert its effect through interactions with and measured with equal precision. In a net-
searches. Further, current EWAS approaches do various cellular components supplying or work environment, these assumptions are inher-
not test for interactions and/or combinations of perturbing cellular networks. To capture the ently false, as interactions couple the probability
factors (mixtures). Recent efforts have been diversity in these interactions, we must first cat- distribution of most network-based variables.
undertaken to develop statistical methods to alog the sum of all physical interactions as a Furthermore, most of the chemicals we are ex-
screen for interactions and test the effects of multilayer network (25) consisting of several posed to represent communities of exposures,
mixtures or to apply frameworks distinct biological layers (Fig. 3). so the effect of a chemical is rarely observed in
such as aggregated exposure and Although each of these networks isolation. Therefore, identifying meaningful
adverse outcome pathways to study
combinatorial effects (9). “Network will rely on different biological
mechanisms, they are not inde-
associations from high-dimensional exposo-
mic data poses major statistical and compu-
As systematic exposomics moves
forward to elucidate the impact
science…offers pendent; for example, protein
production is governed by the
tational challenges that need to be addressed
in parallel with experimental developments.
of the constellation of chemical a platform...to regulatory network, and the cat- The third challenge is that, beyond cataloging
exposures on our health, increas- alysis of the metabolic reactions interactions, we must also understand the
ingly rich and high-dimensional [understand]... is in turn governed by the enzymes dynamics of the biochemical pathways (29)
data must be captured (Fig. 3). In
addition, defining the appropriate
the impact of and protein complexes of the regu-
latory network (26).
through which different elements of the ex-
posome affect our health. Indeed, the human
frameworks for establishing con-
trols, as well as background and
multiple To fully understand the role of
the exposome, we must similarly
interactome, representing the sum of all physi-
cal interactions within a cell (Fig. 3), is often
negative responses, is essential exposures.” develop a multilayer network– depicted as a static graph but is in reality a
for enabling causal inference. To based framework capable of un- temporal network (30) with nodes and links
aid inference, more insights into veiling the role of chemicals, their that disappear and reemerge depending on
the boundaries of what are “normal” responses combinations, and biological perturbations factors ranging from the cell cycle to variabil-
are required and necessitate definitions of a on our health. However, there are several data ity in environmental exposures across the life
reference exposome. and methodological challenges. The first chal- course. Modeling the fully temporal nature of
lenge is the paucity of systematic data on the these networks remains a challenge, as the
Network science to address various dimensions of exposure, from bio- kinetic constants underlying metabolic processes
exposome complexity availability to protein-binding information of are not known and we currently lack system-
The challenge in understanding the role of the the hundreds of thousands of exposome mol- atic tools with which to identify them (31).
exposome on our health lies not only in the ecules. The U.S. National Toxicology Program,
large number of chemical exposures in our the EPA, and the European Molecular Biol- Informative exposome study designs
daily lives, but also in the complex ways that ogy Laboratory (EMBL) are developing plat- A systematic and unbiased assessment of the
they interact with cells. A reductionist approach forms to generate, collate, and organize data exposome that does not focus on a selected
might isolate the role of a single variable, but on chemical–biological interactions, but there set of readily measured or priority chemicals
it will inadequately capture the complexity of is a need for high-throughput approaches that requires access to biological samples that
the current chemical and spectral data re- Conclusion 16. E. L. Schymanski et al., Environ. Sci. Technol. 48, 2097–2098
sources needed to identify these signals in A concerted and systematic effort to profile the (2014).
17. C. Ruttkies, E. L. Schymanski, S. Wolf, J. Hollender,
samples; (iii) increase the scale and scope of nongenetic factors associated with disease and S. Neumann, J. Cheminform. 8, 3 (2016).
studies to a level that provides the necessary health outcomes is urgently needed because 18. Y. Djoumbou-Feunang et al., J. Cheminform. 11, 2 (2019).
statistical power to precisely characterize the we lack important insights that might assist 19. D. K. Barupal, O. Fiehn, Environ. Health Perspect. 127, 097008 (2019).
20. J. M. Gauglitz et al., Food Chem. 302, 125290 (2020).
effects of the chemicals and their combina- us in curtailing the ever-growing burden of 21. S. Li et al., Reprod. Toxicol. S0890-6238(18)30603-8 (2019).
tions; (iv) further develop and support chem- chronic disease on society. Emerging exposome 22. C. J. Patel, J. Bhattacharya, A. J. Butte, PLOS ONE 5, e10746 (2010).
informatic and bioinformatic tools, including research frameworks are poised to enable the 23. A.-L. Barabási, Network Science (Cambridge Univ. Press, 2016).
24. J. Loscalzo, A.-L. Barabási, E. K. Silverman, Network Medicine:
network theory and network medicine, to systematic analysis of nongenetic factors in- Complex Systems in Human Disease and Therapeutics.
elucidate the constellation of the chemical volved in disease. Technology has enabled the (Harvard Univ. Press, 2017).
environment and its biological consequences; first generation of studies to evolve into the 25. G. Bianconi, Multilayer Networks: Structure and Function
(Oxford Univ. Press, ed. 1, 2018).
and (v) ensure adequate protection for the comprehensive study of combinatorial chem-
26. A.-L. Barabási, Z. N. Oltvai, Nat. Rev. Genet. 5, 101–113 (2004).
generation of false-positive results by insisting ical exposures. Future efforts must ensure that 27. D. Mendez et al., Nucleic Acids Res. 47 (D1), D930–D940 (2019).
on replication in independent studies and the analytical approaches and study designs are 28. R. R. Tice, C. P. Austin, R. J. Kavlock, J. R. Bucher, Environ.
use of methods to establish causation, such as rigorous and validated. A coordinated and in- Health Perspect. 121, 756–765 (2013).
29. A. Barrat, M. Barthelemy, A. Vespignani, Dynamical Processes
Mendelian randomization, within-sibling com- ternational effort to characterize the exposome, on Complex Networks (Cambridge Univ. Press, 2008).
parisons, and exposure-negative and outcome- akin to the Human Genome Project, would 30. P. Holme, J. Saramäki, “Temporal networks as a modeling
negative controls. provide rigorous data to allow exposome-based framework,” in Understanding Complex Systems (Springer,
2013), pp 1–14.
EWAS to be conducted at the scale of GWAS. 31. M. Santolini, A.-L. Barabási, Proc. Natl. Acad. Sci. U.S.A. 115,
By taking advantage of the nontargeted nature E6375–E6383 (2018).
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