ChemMaps.com v2.0: exploring the environmental chemical universe
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Abstract Access to computationally based visualization tools to navigate chemical space has become more important due to the increasing size and diversity of publicly accessible databases, associated compendiums of high-throughput screening (HTS) results, and other descriptor and effects data. However, application of these techniques requires advanced programming skills that are beyond the capabilities of many stakeholders. Here we report the development of the second version of the ChemMaps.com webserver (https://sandbox.ntp.niehs.nih.gov/chemmaps/) focused on environmental chemical space. The chemical space of ChemMaps.com v2.0, released in 2022, now includes approximately one million environmental chemicals from the EPA Distributed Structure-Searchable Toxicity (DSSTox) inventory. ChemMaps.com v2.0 incorporates mapping of HTS assay data from the U.S. federal Tox21 research collaboration program, which includes results from around 2000 assays tested on up to 10 000 chemicals. As a case example, we showcased chemical space navigation for Perfluorooctanoic Acid (PFOA), part of the Per- and polyfluoroalkyl substances (PFAS) chemical family, which are of significant concern for their potential effects on human health and the environment.Keywords:
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Exposome
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The exposome encompasses the totality of human environmental exposures from conception onwards, complementing the genome. The concept was first proposed in 2005 by Christopher Wild in an article entitled "Complementing the genome with an ‘exposome’: the outstanding challenge of environmental exposure measurement in molecular epidemiology". The idea of the exposome was first proposed during a time of great attention to the genome, and refocused attention on environmental exposure data for casual research. In studying the exposome, there are both technical and ethical challenges. What is the current state of research methods for studying the exposome? What is our level of precision in characterizing the exposome (beneficence – maximize possible benefits and minimize possible harms)? Have these methods been validated? Are there ways to assess whether statistical methods for studying exposure mixtures yield valid results? Do we have sufficient confidence in the methods to communicate the results to the general public (beneficence)? With very complex analytical methods, and considering multiple environmental and lifestyle risk factors simultaneously, how do we communicate risk to the general public (comprehension – present the information at the study subject’s level of understanding)? When returning individual exposure information (from environmental sampling or biomarkers), how many exposures are reasonable to include (respect for autonomy)? Among participants who were minor children at the time the data and biospecimens were collected and are now adults, should they be consented as adults before receiving individual exposure information? What level of responsibility does the environmental epidemiologist have to move research findings into public health action? And how?
Exposome
Environmental epidemiology
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The Exposome Approach in Allergies and Lung Diseases: Is It Time to Define a Preconception Exposome?
Emerging research suggests environmental exposures before conception may adversely affect allergies and lung diseases in future generations. Most studies are limited as they have focused on single exposures, not considering that these diseases have a multifactorial origin in which environmental and lifestyle factors are likely to interact. Traditional exposure assessment methods fail to capture the interactions among environmental exposures and their impact on fundamental biological processes, as well as individual and temporal factors. A valid estimation of exposure preconception is difficult since the human reproductive cycle spans decades and the access to germ cells is limited. The exposome is defined as the cumulative measure of external exposures on an organism (external exposome), and the associated biological responses (endogenous exposome) throughout the lifespan, from conception and onwards. An exposome approach implies a targeted or agnostic analysis of the concurrent and temporal multiple exposures, and may, together with recent technological advances, improve the assessment of the environmental contributors to health and disease. This review describes the current knowledge on preconception environmental exposures as related to respiratory health outcomes in offspring. We discuss the usefulness and feasibility of using an exposome approach in this research, advocating for the preconception exposure window to become included in the exposome concept.
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Environmental epidemiology
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Exposome
Environmental epidemiology
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The attempt to describe complex diseases by solely genetic determination has not been successful. There is increasing recognition that the development of disease is often a consequence of interactions between multiple genetic and environmental factors. To date, much of the research on environmental determinants of disease has focused on single exposures generally measured at a single time point. In order to address this limitation, the concept of the exposome has been introduced as a comprehensive approach, studying the full complement of environmental exposures from conception onwards. However, exposures are vast, dynamic, and diverse, and only a small proportion can be reasonably measured due to limitations in technology and feasibility. In addition, the interplay between genes and exposure as well as between different exposures is complicated and multifaceted, which leads to difficulties in linking disease or health outcomes with exposures. The large numbers of collected samples require well-designed logistics. Furthermore, the immense data sets generated from exposome studies require a significant computational investment for both data analysis and data storage. This report summarizes discussions during an international exposome symposium held at Gunma University in Japan regarding the concept of the exposome, challenges in exposome research, and future perspectives in the field.
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It is widely accepted that a relatively small proportion of chronic disease can be explained by genetic factors alone. Although information about environmental exposure is important to comprehensively evaluate chronic diseases, this information is not sufficiently or accurately assessed by comparison with genomic factors. To emphasize the importance of more complete evaluation of environmental exposure, the concept of the exposome, which indicates the entirety of environmental exposure from conception onwards, was introduced in 2005. Since the 2010s several epidemiological studies, such as the Human Early-Life Exposome project, have applied the exposome concept. The exposome consists of three overlapping domains: the general external, the specific external, and the internal environments. General external factors include the broader socioeconomic environment, and specific external factors include lifestyles, occupations, and pollutant exposures. Internal factors include biological effects and responses. Because the exposome covers exposures from conception to death, the birth cohort is an important part of the exposome study. Although there is not yet an established consensus in selecting what, when, and where to measure concerning the exposome, the use of omics analyses, especially analysis of the metabolome, should be considered in order to implement the exposome concept in the birth cohort. The exposome needs to be measured repeatedly in certain important phases of life, such as during pregnancy and infancy. To perform exposome-informed epidemiological studies, untargeted data-driven approaches in conjunction with dimension reduction techniques need to be developed and refined. The exposome concept has the potential to make a breakthrough in overcoming some of the limitations of conventional epidemiology. Concerted national and international efforts are required for future exposome studies. Keywords: Exposome, Omics analysis, Metabolome, Birth cohort, Untargeted data-driven approach
Exposome
Environmental epidemiology
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Summary:Environmental exposures are ubiquitous and play a fundamental role in the development of complex human diseases. The exposome, which is defined as the totality of environmental exposures over the life course, allows for systematic evaluation of the relationship between exposures and associated biological consequences, and represents a powerful approach for discovery in environmental health research. However, implementing the exposome concept is challenged by the ability to accurately assess multiple exposures and the ability to integrate information across the exposure–disease continuum. On 14–15 January 2015, the National Institute of Environmental Health Sciences (NIEHS) held the Exposome Workshop where a group of international and U.S. scientists from different disciplines gathered to review the state of the science in research areas related to the exposome and to provide recommendations for incorporating the exposome concept into each research area. To move the field forward, the NIEHS is establishing a Children's Health Exposure Analysis Resource (CHEAR) to provide infrastructure support for access to laboratory and statistical analyses to children's health studies. It is recognized that incorporating the exposome concept into exposure and environmental health research will be a long journey and will require significant collaborative efforts from different scientific disciplines, nations, and stakeholders.
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Environmental epidemiology
Environmental medicine
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Exposome
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Increasing evidences have revealed a close relationship between various environmental exposures and reproductive health. The real-world complex exposure scenario along with intricate interactions effects of these exposures has high demands of exposome-wide association studies for human risk assessment. With the development of exposomic studies, applying hair exposome to link environmental factors and reproductive health outcomes has obvious potential advantages. However, the reliability of utilizing hair to characterize exposome is always of high concern for researchers. In this review, we briefly summarized studies about the effects of environmental exposures on several typical reproductive health outcomes, described state-of-the-art situation of applying hair exposome for reproductive health risk assessment, elucidated the advantages (e.g., containing abundant exposure factors, low expenses for sampling, and tracing exposure history), and proposed the unsolved issues in this area. We also conducted a comprehensive discussion about the reliability of various hair biomarkers and primarily established the biomarker databases. Finally, a standardized framework on using hair exposome for reproductive health study was proposed to provide fundamental approach for future studies. We concluded that it is promising to apply hair exposome to evaluate the effects of the environmental factors on human reproductive health.
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Environmental epidemiology
Exposure Assessment
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In 2005, Christopher P. Wild introduced the exposome concept, encompassing the biochemical changes in the organism in response to the totality of all environmental exposures throughout the entire lifespan and their association with health outcomes. The exposome concept also aimed at to completing the genome, that describes the genetic predisposition as a determinant of disease and death as well as potential targets of intervention. The exposome can be subdivided into multiple pollutomes related to specific chemical and physical pollutants (or other forms of environmental risks), periods of life (infancy, childhood, adolescence, adulthood, and old age) or geographical locations. While exposome research and, in general, health research of the last decades has predominantly focused on what factors contribute to and initiate morbidity and mortality, little is done on factors that will help to develop, maintain, or even increase human health. We want to contribute to this reorientation by supporting and implementing the beneficial exposome, comprising all environmental exposures with the potential to promote health.
Exposome
Environmental epidemiology
Genetic predisposition
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