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Feature Articles : May 1, 2013 (Vol. 33, No. 9)

Exposing the Exposome

  • Richard A. Stein, M.D., Ph.D.

Understanding the interplay between genetic and environmental factors that shape phenotypes has represented, historically, a thought-provoking area for biomedical, medical, and social sciences.

While the biology of the genome has witnessed unprecedented advances in the past three decades, identifying and studying the impact of environmental factors on live organisms remains a challenging endeavor. To address this unmet need, a new concept was defined to include all the environmental exposures that act during an individual’s lifetime, starting with the prenatal period.

“The principle behind the concept of the exposome was to be able to characterize a person’s complete exposure history throughout life, and this includes factors shaped by environment, lifestyle, occupation, socio-economic, and demographic conditions in order to better understand the causes of the diseases they experience,” says Christopher P. Wild, Ph.D., director of the International Agency for Research on Cancer (IARC), and author of the landmark 2005 article that first introduced the concept of the exposome.

Exposome research capitalizes on technological advances that previously provided unprecedented opportunities to mine the human genome and compare genomic regions across individuals and populations. “At this time, we do not have an equivalent set of tools to capture an individual’s exposure history to environmental or lifestyle factors,” says Dr. Wild.

This gap promises to be at least partially addressed by applying genomics and other related technologies such as metabolomics to reveal details about exposures. A key development is in epigenetics, a field that assumes a central position in the study of the exposome.

In addition to the DNA damage model for carcinogenesis, recent years revealed that gene expression and function may also be modulated by mechanisms that do not involve mutagenesis, and several environmental and lifestyle factors were shown to act by these pathways, which became known as epigenetic pathways.

Of these, DNA methylation is at the most advanced stage of understanding. “With methods that can comprehensively measure the DNA methylation status, for example, it has now become possible to explore the correlation between a particular exposure, the underlying mechanism of action, and disease risk,” explains Dr. Wild.

Cancer Research

One of the areas where the exposome promises a paradigm shift is cancer research. While significant advances over the past few decades helped understand the molecular pathways of carcinogenesis, translating the findings into the clinic has been more challenging. “This has to do mostly with the fact that cancer is so heterogeneous at the molecular level, that finding treatments for any single malignant tumor will be a very complex task,” explains Dr. Wild.

Additionally, as it is anticipated that the incidence of cancer will increase in the coming decades, particularly in the poorest countries, as a result of population expansion, an increasing life expectancy, and increased exposure to some cancer risk factors, the development of preventive interventions emerges as a priority in medicine and public health.

“Reducing the cancer burden will not be possible solely through treatment, and this was part of the motivation behind the exposome idea, to better understand the causes of disease and implement preventive strategies,” says Dr. Wild. The focus on the exposome provides the unique opportunity to use emerging knowledge about mechanisms to identify and characterize risk factors that drive molecular changes involved in carcinogenesis.

“I refer to this approach as two-way translational research because in addition to applying concepts from the bench to the bedside, there is also an opportunity to extend information from the bench to the population, and this is the strategy that will help understand mechanisms and lead to disease prevention,” adds Dr. Wild.

Estrogens

“Interest in the study of the exposome is growing,” says Anthony Macherone, Ph.D., senior applications chemist at Agilent Technologies, and visiting scientist at the Johns Hopkins School of Medicine. Studies on the exposome allow data from multiple layers of experimental inquiry to be integrated. Since most complex diseases are determined by genetic and environmental factors, this approach promises to help better understand environmental contributions that shape gene expression and function. Of these two groups of factors, our knowledge about genetic contributions to disease is currently at the most advanced level of understanding.

“The environmental components will need to be further analyzed, and hopefully more long-term studies will be conducted to monitor exposure,” says Dr. Macherone. To provide a framework that illustrates the powerful applications of the emerging field of exposomics, Dr. Macherone and colleagues will present, at the upcoming American Society for Mass Spectrometry meeting, an integrated analysis of the clinical and environmental monitoring of the exposure to estrogens, hormones that are instrumental during reproductive development, participate in the morphogenesis of multiple organs and tissues, and are involved in the pathology of several conditions.

Relying on microarray studies, endogenous measurements of estrogens, and environmental groundwater and wastewater surveys, this approach unveils the multidisciplinarity and interdisciplinarity that define this emerging field.

“Exposomics will require a more open milieu, in which scientists across disciplines will be engaged and integrate their findings in a way that is very different from what many scientists are doing right now,” explains Dr. Macherone.

“In terms of exploring the exposome, our tools are still limited and need to be improved, but several groups are working toward trying to better assess exposures during an individual’s lifespan,” says Francine Einstein, M.D., associate professor of obstetrics and gynecology and Women’s Health at Albert Einstein College of Medicine.

Researchers in Dr. Einstein’s lab recently revealed that methylation changes during development occur in a sex-specific manner, with the most accentuated modification being visualized in growth-restricted male babies and overgrown female babies, indicating that sexual differences play an important and previously unsuspected role in shaping the link between epigenetic changes and phenotypes.

In addition to measuring various types of exposures, an emerging challenge is the need to integrate all the information, to be able to visualize cumulative effects over the lifetime. “A good analogy is with meteorologists, who rely on very precise tools to measure different parameters and use sophisticated techniques to integrate them,” says Dr. Einstein. While complex approaches to integrate multiple layers of scientific data could open the possibility to model future behavior and predict response to therapy, the integration and modeling represent, at this time, some of the main challenges in the emerging field of exposomics.

“If we look at the approach that is being used for predicting storms, several models are run iteratively, allowing comparisons across them, and scientists can subsequently go back to identify specific areas where the models can be improved, and this strategy could be useful in studying the exposome,” says Dr. Einstein.

“We study how cells lining the respiratory tract respond to environmental toxins that they are exposed to,” says Avrum E. Spira, M.D., professor of medicine, pathology, and bioinformatics at Boston University. Several options are available to examine the response to inhaled toxins, and these may rely on assessing the amount of cigarette smoke that an individual is exposed to, measuring the breakdown products of specific chemicals, or monitoring the response of individual genes in the airway epithelium to exposure.

Researchers in Dr. Spira’s lab showed that genome-wide changes in microRNA and mRNA levels that occur in respiratory epithelial cells in response to smoking can be integrated to assess the biological response to exposure. These modifications were used to establish biomarkers with potential diagnostic relevance, which can predict which subset of smokers have or are at higher risk for lung cancer. “We can measure expression of all 20,000 genes in these cells at one time, and look at how patterns differ and how these differences relate to lung disease,” says Dr. Spira.

“The exposome can provide the opportunity to look at all the exposures that a person had during their lifetime, and this includes not just what they perceive or is associated with environmental exposures but, in addition, endogenous exposures that originate within the organism and are often missed in traditional environmental health,” says Stephen M. Rappaport, Ph.D., professor of environmental sciences at the University of California, Berkeley.

While typically less than 10% of an individual’s risk is associated with the genetic makeup for most cancers, the contribution of nongenetic factors is assuming increasing medical and public health relevance, but also represents the most challenging component to explore. Historically, environmental exposures have been explored by asking individuals about their contact with specific chemicals.

“This works for some exposures, such as cigarette smoke,” explains Dr. Rappaport. However, for many other exposures, individuals might not remember or even be aware of having been exposed, making this approach unreliable and prompting the need for more sophisticated tools. “By looking at the -omics signals in the blood, we can obtain a much more reliable picture of what people have been exposed to than has been possible by traditional methods to assess exposure,” says Dr. Rappaport.

In analyzing small molecules from the blood, one of the challenges is the inability to predict the ones that are meaningful indicators of exposure. “I have proposed the idea of an exposome-wide study to identify from the many chemicals that a person is exposed to throughout life the molecules that one should focus on,” says Dr. Rappaport. This approach involves obtaining biospecimens from individuals with a specific disease and matched control subjects, comparatively investigating the profile of -omics signals, validating the results on additional cohorts, and studying the emergence of the respective modifications over time, prior to disease, as a result of exposure.

“Through a very ordered set of experiments, this would allow us to zero in on probably the very few relatively simple chemicals that can be predictive, and understand what we can do to reduce or mitigate exposures,” explains Dr. Rappaport. Conceptually similar to the strategy employed in genome-wide association studies, exposome-wide studies present a much stronger potential to identify factors that are important in shaping phenotypes.

In making the comparison with genome-wide association studies, it is also important to reminisce about the fact that gene variants associated with disease risk were often not the ones that investigators predicted ahead of time, based on initial candidate gene studies, to be the most important ones. “The best geneticists were not able to predict which genes are playing the most significant roles, and this is a valuable lesson because we do not have any reasons to think that it will be different in the case of the exposome,” says Dr. Rappaport.

While technological advances helped unveil the intricacies of the human genome and shed light on interindividual genetic variation, significant efforts are currently focusing on advancing the ability to survey epigenetic perturbations in a high-throughput fashion. Among epigenetic marks, visualizing 5-hydroxymethylcytosine, an epigenetic modification increasingly described in several tissues and still insufficiently understood functionally, has been challenging from a technological perspective.

“What is interesting is that, to date, bisulfite conversion could not distinguish between 5-methylcytosine and 5-hydroxymethylcytosine, but with some of our newest techniques we can selectively analyze the two modifications,” says Marc E. Van Eden, Ph.D., vp for business development and marketing at Zymo Research.

Investigators at Zymo Research found that, while 5-methylcytosine makes opening of the double-stranded DNA helix more difficult than cytosine, the effect is reversed in the case of 5-hydroxymethylated cytosine. “These modifications act almost like a molecular switch, a DNA code above the one that is made by the four nucleotides,” says Dr. Van Eden.

At this time, Zymo Research is the only provider for genome-wide 5-hydroxymethylcytosine analysis services at the single-nucleotide resolution. “We have three platforms available for genome-wide methylation analyses, which can cover 10%, 30%, or the entire methylome,” says Dr. Van Eden.

The availability of this approach is critical for investigators looking at putative epigenetic biomarkers, and this is an area of science that promises to become increasingly important, as it will become easier to integrate advances in genetics and genomics with those in epigenetics, to dissect the causes of complex diseases. “A few years from now, these approaches will become routine, and these tools will undoubtedly also be embraced by diagnostics and pharmaceutics markets,” says Dr. Van Eden.

As an emerging concept, exposomics is sculpturing a novel framework to integrate genetic factors with environmental contributions, incorporating all the external and internal exposures that an individual encounters throughout life, starting with the intrauterine period.

Advances defining this vibrant multidisciplinary field have become reality thanks to strides in genetics and genomics, the advent of additional -omics sciences, including metabolomics and metabonomics, and the epigenetics revolution that we are currently witnessing. Forecasting an exciting era for the biomedical world, the exposome promises to fill a long-existing gap in preventive medicine and public health, one that historically has been the most challenging to scrutinize and exploit.