MEDICINE: Environmental Biology and Human Disease

Diurnal trends of indoor and outdoor fluorescent biological aerosol particles in a tropical urban area

We evaluated diurnal trends of size-resolved indoor and outdoor fluorescent biological airborne particles (FBAPs) and their contributions to particulate matter (PM) within 0.5-20 μm. After a ten-week continuous sampling via two identical wideband integrated bioaerosol sensors, we found that both indoor and outdoor diurnal trends of PM were driven by its bioaerosol component. Outdoors, the median [interquartile range] FBAP mass concentration peaked at 8.2 [5.8-9.9] μg/m³ around sunrise and showed a downtrend from 6:00 to 18:00 during the daytime and an uptrend during the night. The nighttime FBAP level was 1.8 [1.4-2.2] times higher than that during the daytime, and FBAPs accounted for 45 % and 56 % of PM during daytime and nighttime, respectively. Indoors, the rise in concentrations of FBAPs smaller than 1 μm coincided with the starting operation of the heating, ventilation, and air conditioning (HVAC) system at 6:00, and the concentration peaked at 8:00 and dropped to the daily average by noontime. This indicated that the starting operation of the HVAC system dislodged the overnight settled and accumulated fine bioaerosols into the indoor environment. For particles larger than 1 μm, the variation of mass concentration was driven by occupancy. Based on regression modeling, the contributions of indoor PM, non-FBAP, and FBAP sources to indoor mass concentrations were estimated to be 93 %, 67 %, and 97 % during the occupied period.

Geosocial Features and Loss of Biodiversity Underlie Variable Rates of Inflammatory Bowel Disease in a Large Developing Country: A Population-Based Study

BACKGROUND

The epidemiology of inflammatory bowel disease (IBD) in developing countries may uncover etiopathogenic factors. We investigated IBD prevalence in Brazil by investigating its geographic, spatial, and temporal distribution, and attempted to identify factors associated with its recent increase.

METHODS

A drug prescription database was queried longitudinally to identify patients and verify population distribution and density, race, urbanicity, sanitation, and Human Development Index. Prevalence was calculated using the number of IBD patients and the population estimated during the same decade. Data were matched to indices using linear regression analyses.

RESULTS

We identified 162 894 IBD patients, 59% with ulcerative colitis (UC) and 41% with Crohn's disease (CD). The overall prevalence of IBD was 80 per 100 000, with 46 per 100 000 for UC and 36 per 100 000 for CD. Estimated rates adjusted to total population showed that IBD more than triplicated from 2008 to 2017. The distribution of IBD demonstrated a South-to-North gradient that generally followed population apportionment. However, marked regional differences and disease clusters were identified that did not fit with conventionally accepted IBD epidemiological associations, revealing that the rise of IBD was variable. In some areas, loss of biodiversity was associated with high IBD prevalence.

CONCLUSIONS

When distribution is considered in the context of IBD prevalence, marked regional differences become evident. Despite a background of Westernization, hotspots of IBD are recognized that are not explained by population density, urbanicity, sanitation, or other indices but apparently are explained by biodiversity loss. Thus, the rise of IBD in developing countries is not uniform, but rather is one that varies depending on yet unexplored factors like geoecological conditions.

Exposome and Skin: Part 1. Bibliometric Analysis and Review of the Impact of Exposome Approaches on Dermatology

Introduction

Most skin disorders, such as atopic dermatitis, psoriasis, skin cancer or age-related skin issues, are the result of a complex interaction between genetic and environmental factors over time. As an external organ, the skin provides the opportunity to study the link between exposure to the environment and several specific biological responses using an exposome approach. The aim of this review was to identify the state of the art of exposome approaches and elucidate the impact of the new era of exposomics on dermatology.

Methods

Two parallel and independent bibliometric analyses were conducted based on documents extracted from the Core Collection and the Science Citation Index Expanded (SCI-Expanded) databases from the Clarivate Analytics’ Web of Science (WOS) platform by using the following search terms “exposome” and “skin exposome”. In both searches, we used the topic field that includes title, abstract, author keywords and keywords plus terms and the following filters: “English language” and all documents published up to 30 September 2021. We further analysed and interpreted documents extracted in plain text format.

Results

Based on the defined searches, 910 documents were identified as being related to “exposome” and 45 as being related to “skin exposome”. Environmental sciences and toxicology were the most impacted research areas, and aging, cancer and respiratory allergies were the most documented diseases while, surprisingly, dermatology was much less impacted. Krutmann et al. were the pioneers in implementing this new concept in dermatology with publication of “The skin aging exposome” in 2017 (J Dermatol Sci. 2017;85:152–61). After this tipping point, the number of publications in dermatology evaluating the impact of exposome factors in many skin disorders has steadily increased.

Conclusions

Exposome studies are rapidly attracting interest in dermatology. The results of these studies will undoubtedly improve our understanding of why and under which circumstances some individuals develop skin disorders and help design tailored prevention strategies for patients suffering from these disorders.

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.

Profile of exposures and lung function in adults with asthma: An exposome approach in the EGEA study

BACKGROUND

Environmental research on multifactorial health outcomes calls for exposome approaches able to assess the joint effect of multiple exposures.

OBJECTIVE

Our aim was to identify profiles of exposure to lifestyle/environmental factors associated with lung function in adults with asthma using a cluster-based approach.

METHODS

We used data from 599 adults of the Epidemiological study on the Genetics and Environment of Asthma, bronchial hyperresponsiveness and atopy (EGEA) (mean age 39.0 years, 52% men) who ever had asthma. Exposures to 53 lifestyle/environmental factors were assessed by questionnaires or geographic information systems-based models. A two-step approach was developed: 1) exposome dimension reduction by selecting factors showing association with forced expiratory volume in 1 s (FEV₁) (p < 0.20) in an exposome-wide association study (ExWAS), 2) clustering analysis using the supervised Bayesian Profile Regression (sBPR) to group individuals according to FEV₁ level and to their profile of exposure to a reduced set of uncorrelated exposures (each paired correlation<0.70) identified in step 1.

RESULTS

The ExWAS identified 21 factors showing suggestive association with FEV₁ (none significant when controlling for multiple tests). The sBPR conducted on 15 uncorrelated exposures identified in step 1, revealed 3 clusters composed of 30, 115 and 454 individuals with a mean ± SD FEV₁(%pred) of 79% ± 21, 90% ± 19 and 93% ± 16, respectively. Cluster 1 was composed of individuals with heavy smoking, poor diet, higher outdoor humidity and proximity to traffic, while cluster 2 and 3 included individuals with moderate/low levels of exposure to these factors.

DISCUSSION

This exposome study identified a specific profile of joint lifestyle and environmental factors, associated with a low FEV₁ in adults with asthma. None of the exposures revealed significant association when considered independently.

Redox Systems Biology of Nutrition and Oxidative Stress

Diet and nutrition contribute to both beneficial and harmful aspects of oxidative processes. The harmful processes, termed oxidative stress, occur with many human diseases. Major advances in understanding oxidative stress and nutrition have occurred with broad characterization of dietary oxidants and antioxidants, and with mechanistic studies showing antioxidant efficacy. However, randomized controlled trials in humans with free-radical-scavenging antioxidants and the glutathione precursor N-acetylcysteine have provided limited or inconsistent evidence for health benefits. This, combined with emerging redox theory, indicates that holistic models are needed to understand the interplay of nutrition and oxidative stress. The purpose of this article is to highlight how recent advances in redox theory and the development of new omics tools and data-driven approaches provide a framework for future nutrition and oxidative stress research. Here we describe why a holistic approach is needed to understand the impact of nutrition on oxidative stress and how recent advances in omics and data analysis methods are viable tools for systems nutrition approaches. Based on the extensive research on glutathione and related thiol antioxidant systems, we summarize the advancing framework for diet and oxidative stress in which antioxidant systems are a component of a larger redox network that serves as a responsive interface between the environment and an individual. The feasibility for redox network analysis has been established by experimental models in which dietary factors are systematically varied and oxidative stress markers are linked through integrated omics (metabolome, transcriptome, proteome). With this framework, integrated redox network models will support optimization of diet to protect against oxidative stress and disease.

Biomarkers of exposure in environment-wide association studies - Opportunities to decode the exposome using human biomonitoring data

BACKGROUND

The European Union's 7th Framework Programme (EU's FP7) project HEALS - Health and Environment-wide Associations based on Large Population Surveys - aims a refinement of the methodology to elucidate the human exposome. Human biomonitoring (HBM) provides a valuable tool for understanding the magnitude of human exposure from all pathways and sources. However, availability of specific biomarkers of exposure (BoE) is limited.

OBJECTIVES

The objective was to summarize the availability of BoEs for a broad range of environmental stressors and exposure determinants and corresponding reference and exposure limit values and biomonitoring equivalents useful for unraveling the exposome using the framework of environment-wide association studies (EWAS).

METHODS

In a face-to-face group discussion, scope, content, and structure of the HEALS deliverable "Guidelines for appropriate BoE selection for EWAS studies" were determined. An expert-driven, distributed, narrative review process involving around 30 individuals of the HEALS consortium made it possible to include extensive information targeted towards the specific characteristics of various environmental stressors and exposure determinants. From the resulting 265 page report, targeted information about BoE, corresponding reference values (e.g., 95th percentile or measures of central tendency), exposure limit values (e.g., the German HBM I and II values) and biomonitoring equivalents (BEs) were summarized and updated.

RESULTS

64 individual biological, chemical, physical, psychological and social environmental stressors or exposure determinants were included to fulfil the requirements of EWAS. The list of available BoEs is extensive with a number of 135; however, 12 of the stressors and exposure determinants considered do not leave any measurable specific substance in accessible body specimens. Opportunities to estimate the internal exposure stressors not (yet) detectable in human specimens were discussed.

CONCLUSIONS

Data about internal exposures are useful to decode the exposome. The paper provides extensive information for EWAS. Information included serves as a guideline - snapshot in time without any claim to comprehensiveness - to interpret HBM data and offers opportunities to collect information about the internal exposure of stressors if no specific BoE is available.

T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders

We performed integrative analysis of genes associated with type 2 Diabetes Mellitus (T2DM) associated complications by automated text mining with manual curation and also gene expression analysis from Gene Expression Omnibus. They were analysed for pathogenic or protective role, trends, interaction with risk factors, Gene Ontology enrichment and tissue wise differential expression. The database T2DiACoD houses 650 genes, and 34 microRNAs associated with T2DM complications. Seven genes AGER, TNFRSF11B, CRK, PON1, ADIPOQ, CRP and NOS3 are associated with all 5 complications. Several genes are studied in multiple years in all complications with high proportion in cardiovascular (75.8%) and atherosclerosis (51.3%). T2DM Patients' skeletal muscle tissues showed high fold change in differentially expressed genes. Among the differentially expressed genes, VEGFA is associated with several complications of T2DM. A few genes ACE2, ADCYAP1, HDAC4, NCF1, NFE2L2, OSM, SMAD1, TGFB1, BDNF, SYVN1, TXNIP, CD36, CYP2J2, NLRP3 with details of protective role are catalogued. Obesity is clearly a dominant risk factor interacting with the genes of T2DM complications followed by inflammation, diet and stress to variable extents. This information emerging from the integrative approach used in this work could benefit further therapeutic approaches. The T2DiACoD is available at www.http://t2diacod.igib.res.in/ .

Idiopathic Pulmonary Fibrosis: Diagnosis and Clinical Manifestations

Idiopathic pulmonary fibrosis (IPF) is a parenchymal lung disease characterized by progressive interstitial fibrosis. The clinical course of IPF can be unpredictable and may be punctuated by acute exacerbations. Although much progress is being made in unraveling the mechanisms underlying IPF, effective therapy for improving survival remains elusive. Longitudinal disease profiling, especially in terms of clinical manifestations in a large cohort of patients, should lead to proper management of the patients and development of new treatments for IPF. Appropriate multidisciplinary assessment in ongoing registries is required to achieve this. This review summarizes the current status of the diagnosis and clinical manifestations of IPF.

The Exposome: Embracing the Complexity for Discovery in Environmental Health

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.

Elevated monocyte phosphorylated p38 in nearby employees after a chemical explosion

Personalised health surveillance is infrequent or absent in occupational and environmental medicine. The shortage of functional tests in relevant cells and tissues greatly limits our understanding of environmental exposures and associated disease risk. We evaluated single cell signalling in peripheral blood mononuclear cells from 301 individuals in a cross sectional health survey 18 months after a chemical explosion of sulphorous coker gasoline. The accident created a malodourous environment leading to long-term health complaints. Multiple regression analysis revealed T-cell specific elevated phosphorylation of the stress kinase p-p38 (T180/Y182) among tobacco smokers and monocyte-specific elevated phosphorylation in employees at the explosion site. Other studies of the accident reported reduced tear film stability, and more airway obstruction and subjective health complaints among the employees at the accident site. Elevated monocyte p-p38 in the employee group was independent of such health effects, and could therefore be dependent on the sulphuric malodorous environment. The present study proposes signalling status in leukocytes as a scalable biomarker providing information about environmental exposures.

Riboflavin conjugated temperature variant ZnO nanoparticles with potential medicinal application in jaundice

Significant ameliorative efficiency of riboflavin conjugated ZnO nanoparticles against jaundice stress at molecular and cellular levels.

Chloroacetic acid triggers apoptosis in neuronal cells via a reactive oxygen species-induced endoplasmic reticulum stress signaling pathway

Chloroacetic acid (CA), a chlorinated analog of acetic acid and an environmental toxin that is more toxic than acetic, dichloroacetic, or trichloroacetic acids, is widely used in chemical industries. Furthermore, CA has been found to be the major disinfection by-products (DBPs) of drinking water. CA has been reported to be highly corrosive and to induce severe tissue injuries (including nervous system) that lead to death in mammals. However, the effects and underlying mechanisms of CA-induced neurotoxicity remain unknown. In the present study, we found that CA (0.5-2.0 mM) significantly increased LDH release, decreased the number of viable cells (cytotoxicity) and induced apoptotic events (including: increases in the numbers of apoptotic cells, the membrane externalization of phosphatidylserine (PS), and caspase-3/-7 activity) in Neuro-2a cells. CA (1.5 mM; the approximate to LD50) also triggered ER stress, which was identified by monitoring several key molecules that are involved in the unfolded protein responses (including the increase in the expressions of p-PERK, p-IRE-1, p-eIF2α, ATF-4, ATF-6, CHOP, XBP-1, GRP 78, GRP 94, and caspase-12) and calpain activity. Transfection of GRP 78- and GRP 94-specific si-RNA effectively abrogated CA-induced cytotoxicity, caspase-3/-7 and caspase-12 activity, and GRP 78 and GRP 94 expression in Neuro-2a cells. Additionally, pretreatment with 2.5 mM N-acetylcysteine (NAC; a glutathione (GSH) precursor) dramatically suppressed the increase in lipid peroxidation, cytotoxicity, apoptotic events, calpain and caspase-12 activity, and ER stress-related molecules in CA-exposed cells. Taken together, these results suggest that the higher concentration of CA exerts its cytotoxic effects in neuronal cells by triggering apoptosis via a ROS-induced ER stress signaling pathway.

Investigation of maternal environmental exposures in association with self-reported preterm birth

Identification of maternal environmental factors influencing preterm birth risks is important to understand the reasons for the increase in prematurity since 1990. Here, we utilized a health survey, the US National Health and Nutrition Examination Survey (NHANES) to search for personal environmental factors associated with preterm birth. 201 urine and blood markers of environmental factors, such as allergens, pollutants, and nutrients were assayed in mothers (range of N: 49-724) who answered questions about any children born preterm (delivery <37 weeks). We screened each of the 201 factors for association with any child born preterm adjusting by age, race/ethnicity, education, and household income. We attempted to verify the top finding, urinary bisphenol A, in an independent study of pregnant women attending Lucile Packard Children's Hospital. We conclude that the association between maternal urinary levels of bisphenol A and preterm birth should be evaluated in a larger epidemiological investigation.

Systematic evaluation of environmental and behavioural factors associated with all-cause mortality in the United States national health and nutrition examination survey

BACKGROUND

Environmental and behavioural factors are thought to contribute to all-cause mortality. Here, we develop a method to systematically screen and validate the potential independent contributions to all-cause mortality of 249 environmental and behavioural factors in the National Health and Nutrition Examination Survey (NHANES).

METHODS

We used Cox proportional hazards regression to associate 249 factors with all-cause mortality while adjusting for sociodemographic factors on data in the 1999-2000 and 2001-02 surveys (median 5.5 follow-up years). We controlled for multiple comparisons with the false discovery rate (FDR) and validated significant findings in the 2003-04 survey (median 2.8 follow-up years). We selected 249 factors from a set of all possible factors based on their presence in both the 1999-2002 and 2003-04 surveys and linkage with at least 20 deceased participants. We evaluated the correlation pattern of validated factors and built a multivariable model to identify their independent contribution to mortality.

RESULTS

We identified seven environmental and behavioural factors associated with all-cause mortality, including serum and urinary cadmium, serum lycopene levels, smoking (3-level factor) and physical activity. In a multivariable model, only physical activity, past smoking, smoking in participant's home and lycopene were independently associated with mortality. These three factors explained 2.1% of the variance of all-cause mortality after adjusting for demographic and socio-economic factors.

CONCLUSIONS

Our association study suggests that, of the set of 249 factors in NHANES, physical activity, smoking, serum lycopene and serum/urinary cadmium are associated with all-cause mortality as identified in previous studies and after controlling for multiple hypotheses and validation in an independent survey. Whereas other NHANES factors may be associated with mortality, they may require larger cohorts with longer time of follow-up to detect. It is possible to use a systematic association study to prioritize risk factors for further investigation.

Lack of exercise is a major cause of chronic diseases

Chronic diseases are major killers in the modern era. Physical inactivity is a primary cause of most chronic diseases. The initial third of the article considers: activity and prevention definitions; historical evidence showing physical inactivity is detrimental to health and normal organ functional capacities; cause versus treatment; physical activity and inactivity mechanisms differ; gene-environment interaction (including aerobic training adaptations, personalized medicine, and co-twin physical activity); and specificity of adaptations to type of training. Next, physical activity/exercise is examined as primary prevention against 35 chronic conditions [accelerated biological aging/premature death, low cardiorespiratory fitness (VO2max), sarcopenia, metabolic syndrome, obesity, insulin resistance, prediabetes, type 2 diabetes, nonalcoholic fatty liver disease, coronary heart disease, peripheral artery disease, hypertension, stroke, congestive heart failure, endothelial dysfunction, arterial dyslipidemia, hemostasis, deep vein thrombosis, cognitive dysfunction, depression and anxiety, osteoporosis, osteoarthritis, balance, bone fracture/falls, rheumatoid arthritis, colon cancer, breast cancer, endometrial cancer, gestational diabetes, pre-eclampsia, polycystic ovary syndrome, erectile dysfunction, pain, diverticulitis, constipation, and gallbladder diseases]. The article ends with consideration of deterioration of risk factors in longer-term sedentary groups; clinical consequences of inactive childhood/adolescence; and public policy. In summary, the body rapidly maladapts to insufficient physical activity, and if continued, results in substantial decreases in both total and quality years of life. Taken together, conclusive evidence exists that physical inactivity is one important cause of most chronic diseases. In addition, physical activity primarily prevents, or delays, chronic diseases, implying that chronic disease need not be an inevitable outcome during life.

Social, behavioral, and genetic linkages from adolescence into adulthood

The influence of genetic factors on health and behavior is conditioned by social, cultural, institutional, and physical environments in which individuals live, work, and play. We encourage studies supporting multilevel integrative approaches to understanding these contributions to health, and describe the Add Health study as an exemplar. Add Health is a large sample of US adolescents in grades 7 to 12 in 1994-1995 followed into adulthood with 4 in-home interviews and biomarker collections, including DNA. In addition to sampling multiple environments and measuring diverse social and health behavior, Add Health features a fully articulated behavioral genetic sample (3000 pairs) and ongoing genotyping of 12,000 archived samples. We illustrate approaches to understanding health through investigation of the interplay among biological, psychosocial, and physical, contextual, or cultural experiences.

Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)

New technologies for systems-level determinants of human exposure to drugs, industrial chemicals, pesticides, and other environmental agents provide an invaluable opportunity to extend the understanding of human health and potential environmental hazards. We report here the development of a new computational-systems toxicology framework, called predictive toxicogenomics-derived models (PTDMs). PTDMs integrate three networks of chemical-gene interactions (CGIs), chemical-disease associations (CDAs) and gene-disease associations (GDAs) to infer chemical hazard profiles, identify exposure data gaps and to incorporate genes and disease networks into chemical safety evaluations. Three comprehensive networks addressing CGI, CDA and GDA extracted from the comparative toxicogenomics database (CTD) were constructed. The areas under the receiver operating characteristics curve ranged from 0.85 to 0.97 and were yielded using our methodology using a 10-fold cross validation by a simulation carried out 100 times. As the illustrated examples show, we predicted new potential target genes and diseases for bisphenol A and aspirin. The molecular hypothesis and experimental evidence from published literature for these predictions were provided. The results demonstrated that our method has potential applications for chemical profiling in human health exposure and environmental hazard assessment.

Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease

Motivation: Complex diseases, such as Type 2 Diabetes Mellitus (T2D), result from the interplay of both environmental and genetic factors. However, most studies investigate either the genetics or the environment and there are a few that study their possible interaction in context of disease. One key challenge in documenting interactions between genes and environment includes choosing which of each to test jointly. Here, we attempt to address this challenge through a data-driven integration of epidemiological and toxicological studies. Specifically, we derive lists of candidate interacting genetic and environmental factors by integrating findings from genome-wide and environment-wide association studies. Next, we search for evidence of toxicological relationships between these genetic and environmental factors that may have an etiological role in the disease. We illustrate our method by selecting candidate interacting factors for T2D.

Contact:abutte@stanford.edu

Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus

Diseases such as type 2 diabetes (T2D) result from environmental and genetic factors, and risk varies considerably in the population. T2D-related genetic loci discovered to date explain only a small portion of the T2D heritability. Some heritability may be due to gene–environment interactions. However, documenting these interactions has been difficult due to low availability of concurrent genetic and environmental measures, selection bias, and challenges in controlling for multiple hypothesis testing. Through genome-wide association studies (GWAS), investigators have identified over 90 single nucleotide polymorphisms (SNPs) associated to T2D. Using a method analogous to GWAS [environment-wide association study (EWAS)], we found five environmental factors associated with the disease. By focusing on risk factors that emerge from GWAS and EWAS, it is possible to overcome difficulties in uncovering gene–environment interactions. Using data from the National Health and Nutrition Examination Survey (NHANES), we screened 18 SNPs and 5 serum-based environmental factors for interaction in association to T2D. We controlled for multiple hypotheses using false discovery rate (FDR) and Bonferroni correction and found four interactions with FDR <20 %. The interaction between rs13266634 (SLC30A8) and trans-β-carotene withstood Bonferroni correction (corrected p = 0.006, FDR <1.5 %). The per-risk-allele effect sizes in subjects with low levels of trans-β-carotene were 40 % greater than the marginal effect size [odds ratio (OR) 1.8, 95 % CI 1.3–2.6]. We hypothesize that impaired function driven by rs13266634 increases T2D risk when combined with serum levels of nutrients. Unbiased consideration of environmental and genetic factors may help identify larger and more relevant effect sizes for disease associations.

The genetic and environmental causes of pulmonary fibrosis

Although substantial progress has been made in understanding the clinical, radiological, and pathological manifestations of fibrosing interstitial lung diseases (ILD), it remains difficult for the clinician to predict the clinical course or the response to therapy for the subtypes of ILD, even from individual to individual with the same diagnosis. This article reviews the genetic and environmental causes of pulmonary fibrosis, specifically focusing on genetic and epigenetic variants of MUC5B and several types of ILD, to discuss why only some individuals with the MUC5B promoter polymorphism develop pulmonary fibrosis. Once we discover how these genetic and epigenetic risks lead to the development of ILD, we and others can apply these discoveries to: (1) identify individuals at risk of developing ILD, (2) diagnose the condition at an earlier stage, (3) identify novel mechanisms that cause ILD, and (4) eventually develop personalized therapeutic strategies for intervention.

Epigenetic effects of environmental chemicals bisphenol A and phthalates

The epigenetic effects on DNA methylation, histone modification, and expression of non-coding RNAs (including microRNAs) of environmental chemicals such as bisphenol A (BPA) and phthalates have expanded our understanding of the etiology of human complex diseases such as cancers and diabetes. Multiple lines of evidence from in vitro and in vivo models have established that epigenetic modifications caused by in utero exposure to environmental toxicants can induce alterations in gene expression that may persist throughout life. Epigenetics is an important mechanism in the ability of environmental chemicals to influence health and disease, and BPA and phthalates are epigenetically toxic. The epigenetic effect of BPA was clearly demonstrated in viable yellow mice by decreasing CpG methylation upstream of the Agouti gene, and the hypomethylating effect of BPA was prevented by maternal dietary supplementation with a methyl donor like folic acid or the phytoestrogen genistein. Histone H3 was found to be trimethylated at lysine 27 by BPA effect on EZH2 in a human breast cancer cell line and mice. BPA exposure of human placental cell lines has been shown to alter microRNA expression levels, and specifically, miR-146a was strongly induced by BPA treatment. In human breast cancer MCF7 cells, treatment with the phthalate BBP led to demethylation of estrogen receptor (ESR1) promoter-associated CpG islands, indicating that altered ESR1 mRNA expression by BBP is due to aberrant DNA methylation. Maternal exposure to phthalate DEHP was also shown to increase DNA methylation and expression levels of DNA methyltransferases in mouse testis. Further, some epigenetic effects of BPA and phthalates in female rats were found to be transgenerational. Finally, the available new technologies for global analysis of epigenetic alterations will provide insight into the extent and patterns of alterations between human normal and diseased tissues. In vitro models such as human embryonic stem cells may be extremely useful in bettering the understanding of epigenetic effects on human development, health and disease, because the formation of embryoid bodies in vitro is very similar to the early stage of embryogenesis.

Genetic variability in molecular responses to chemical exposure

Individuals differ in their response to environmental exposures. In the following, we describe examples and paradigms of studying heritable differences in response to exposure-commonly known as "gene-environment interaction" or "ecogenetics"-and their relation to disease etiology and susceptibility. Our discussion is framed in three parts. In the first, we describe replicated examples of studies that have typified the field, single genetic variant, and exposure associations to disease. Second, we describe how studies have scaled up search for interaction using genome-wide measurement modalities, bioinformatics, and model organisms. Finally, we discuss a more comprehensive representation of chemical exposures as the "envirome" and how we may use the envirome to examine interplay between genetics and the environment.

Developmental basis of disease: environmental impacts

Exposure to environmental chemicals and other environmental stressors have health impacts on the fetus that may not be apparent until later in life. The concept of developmental origins of disease should be expanded to include these early life exposures in addition to the effects of nutrition and maternal factors. This paper will describe the toxicological, biological and epidemiological issues that are pertinent to conducting research on environmental exposures early in life and their health consequences over the life span.

The future: genes, physical activity and health

The assigned title for the Lindhard presentation was to examine the future of genes, physical activity and health. The current review is a summary of this presentation. Caution is expressed that technology is improving so rapidly that a future view is limited to a few years as opposed to the 100 years passing since Lindhard's achievements. The near futuristic opportunities and challenges for four major topic topics are reviewed here. Concerns are expressed over current usage of the terms 'control' group and 'non-responders' in exercise research. Our view is that 'control' needs to be differentiated between its usage for treatments of exercise to restore natural functions in individuals with less than healthy levels of physical activity and the inherited genome's expectation for physical activity levels to maintain normal function. For the second discussed topic, it is proposed that the term 'non-responders' should be replaced by the term 'low sensitivity' as there may be no such human who is a non-responder to every exercise adaptation. The third futuristic topic is exercise prescription as envisioned for individualized medicine. However, numerous limitations and challenges exist to truly optimal exercise medicine at the level of one individual. Finally, preventative physical activity medicine is discussed. Physical activity as a therapy now exists to prevent most of the chronic diseases. The future needs to understand the molecular basis for how the body becomes dysfunctional when its level of physical activity does not match the norm of physical activity that selected our inherited genome.

An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus

Background

Type 2 Diabetes (T2D) and other chronic diseases are caused by a complex combination of many genetic and environmental factors. Few methods are available to comprehensively associate specific physical environmental factors with disease. We conducted a pilot Environmental-Wide Association Study (EWAS), in which epidemiological data are comprehensively and systematically interpreted in a manner analogous to a Genome Wide Association Study (GWAS).

Methods and Findings

We performed multiple cross-sectional analyses associating 266 unique environmental factors with clinical status for T2D defined by fasting blood sugar (FBG) concentration ≥126 mg/dL. We utilized available Centers for Disease Control (CDC) National Health and Nutrition Examination Survey (NHANES) cohorts from years 1999 to 2006. Within cohort sample numbers ranged from 503 to 3,318. Logistic regression models were adjusted for age, sex, body mass index (BMI), ethnicity, and an estimate of socioeconomic status (SES). As in GWAS, multiple comparisons were controlled and significant findings were validated with other cohorts. We discovered significant associations for the pesticide-derivative heptachlor epoxide (adjusted OR in three combined cohorts of 1.7 for a 1 SD change in exposure amount; p<0.001), and the vitamin γ-tocopherol (adjusted OR 1.5; p<0.001). Higher concentrations of polychlorinated biphenyls (PCBs) such as PCB170 (adjusted OR 2.2; p<0.001) were also found. Protective factors associated with T2D included β-carotenes (adjusted OR 0.6; p<0.001).

Conclusions and Significance

Despite difficulty in ascertaining causality, the potential for novel factors of large effect associated with T2D justify the use of EWAS to create hypotheses regarding the broad contribution of the environment to disease. Even in this study based on prior collected epidemiological measures, environmental factors can be found with effect sizes comparable to the best loci yet found by GWAS.

Predicting environmental chemical factors associated with disease-related gene expression data

BACKGROUND

Many common diseases arise from an interaction between environmental and genetic factors. Our knowledge regarding environment and gene interactions is growing, but frameworks to build an association between gene-environment interactions and disease using preexisting, publicly available data has been lacking. Integrating freely-available environment-gene interaction and disease phenotype data would allow hypothesis generation for potential environmental associations to disease.

METHODS

We integrated publicly available disease-specific gene expression microarray data and curated chemical-gene interaction data to systematically predict environmental chemicals associated with disease. We derived chemical-gene signatures for 1,338 chemical/environmental chemicals from the Comparative Toxicogenomics Database (CTD). We associated these chemical-gene signatures with differentially expressed genes from datasets found in the Gene Expression Omnibus (GEO) through an enrichment test.

RESULTS

We were able to verify our analytic method by accurately identifying chemicals applied to samples and cell lines. Furthermore, we were able to predict known and novel environmental associations with prostate, lung, and breast cancers, such as estradiol and bisphenol A.

CONCLUSIONS

We have developed a scalable and statistical method to identify possible environmental associations with disease using publicly available data and have validated some of the associations in the literature.

Recent advances and opportunities in research on lupus: environmental influences and mechanisms of disease

We summarize research on mechanisms through which environmental agents may affect the pathogenesis of lupus, discuss three exposures that have been the focus of research in this area, and propose recommendations for new research initiatives. We examined studies pertaining to key mechanistic events and specific exposures. Apoptosis leading to increased production or decreased clearance of immunogenic intracellular self-antigens and defective apoptosis of autoreactive immune cells both have been implicated in the loss of self-tolerance. The adjuvant or bystander effect is also needed to produce a sustained autoimmune response. Activation of toll-like receptors is one mechanism through which these effects may occur. Abnormal DNA methylation may contribute to the pathogenesis of lupus. Each of the specific exposures has been shown, in humans or in mice, to act upon one or more of these pathogenic steps. Specific recommendations for the continued advancement of our understanding of environmental influences on lupus and other autoimmune diseases include the development and use of mouse models with varying degrees of penetrance and manifestations of disease, identification of molecular or physiologic targets of specific exposures, development and use of improved exposure assessment methodologies, and multisite collaborations designed to examine understudied environmental exposures in humans.

Moderately high altitude habitation modulates lipid profile and alkaline phosphatase activity in aged Khasis of Meghalaya

The indigenous Khasis inhabit different geographical and climatic locations of Meghalaya. In this study, we intended to find out whether habitation in moderately high altitude place has any effect on the lipid and liver profile amongst the aged Khasis. The level of various serum parameters under lipid and liver profile were analyzed and compared from aged (65-70 years) male Khasi residents of moderately high (Shillong city) and low (Byrnihat) altitude places. Results obtained from the lipid profile data show decreased total serum cholesterol (29%), triglyceride (27%) and LDL-cholesterol (42%) level in the old Khasis of Shillong compared to Byrnihat. Furthermore, the alkaline phosphatase activity was significantly raised (47%) in the old Khasis from Shillong as against Byrnihat. The decreased level of total cholesterol, triglyceride and LDL-cholesterol in old Khasis from Shillong may be due to living and acclimatization in high altitude with low annual temperature. Moderately high elevation could have acted as a stressor, thereby reducing the level of serum cholesterol, triglyceride and LDL-cholesterol, which may put them at a lower risk of cardiovascular diseases. In comparison, old residents of Byrnihat with high cholesterol, triglyceride and LDL-cholesterol levels may elevate their risk of coronary complications. The raised alkaline phosphatase activity amongst the old Khasis of Shillong could be due to increased bone and/or intestinal turnover as a result of living in high altitude, which, however, may elevate the risk of osteoporosis. Taken together, we conclude that low cholesterol, triglyceride and LDL-cholesterol levels, accompanied with high alkaline phosphatase activity amongst the old Khasis of Shillong, could be due to the influence of high altitude and mild climatic conditions that prevails.

Advancing exposure characterization for chemical evaluation and risk assessment

A new generation of scientific tools has emerged to rapidly measure signals from cells, tissues, and organisms following exposure to chemicals. High-visibility efforts to apply these tools for efficient toxicity testing raise important research questions in exposure science. As vast quantities of data from high-throughput screening (HTS) in vitro toxicity assays become available, this new toxicity information must be translated to assess potential risks to human health from environmental exposures. Exposure information is required to link information on potential toxicity of environmental contaminants to real-world health outcomes. In the immediate term, tools are required to characterize and classify thousands of environmental chemicals in a rapid and efficient manner to prioritize testing and assess potential for risk to human health. Rapid risk assessment requires prioritization based on both hazard and exposure dimensions of the problem. To address these immediate needs within the context of longer term objectives for chemical evaluation and risk management, a translation framework is presented for incorporating toxicity and exposure information to inform public health decisions at both the individual and population levels. Examples of required exposure science contributions are presented with a focus on early advances in tools for modeling important links across the source-to-outcome paradigm. ExpoCast, a new U.S. Environmental Protection Agency (EPA) program aimed at developing novel approaches and metrics to screen and evaluate chemicals based on the potential for biologically relevant human exposures is introduced. The goal of ExpoCast is to advance characterization of exposure required to translate findings in computational toxicology to information that can be directly used to support exposure and risk assessment for decision making and improved public health.

Challenge assay: A functional biomarker for exposure-induced DNA repair deficiency and for risk of cancer

A variety of biomarkers have been used to monitor exposed populations to determine potential health hazards from their exposure to environmental toxic agents. However, the majority of these biomarkers have been focused onto the identification of biological damage from the exposure. Therefore, there is a need to develop functional biomarkers that can identify exposure-induced functional deficiencies. More importantly, these deficiencies should be positioned along pathways that are responsible for the development of specific diseases. One of such pathways belongs to the extensive and complex DNA-repair machinery. The machinery thus becomes a large target for damage from environmental toxic agents. The hypothesis is that damage to any component of a repair pathway will interfere with the pathway-specific repair activities. Therefore, when cells from exposed populations are challenged with a DNA-damaging agent in vitro, the in vivo exposure-induced repair deficiency will be dramatically amplified and the deficiency will be detectable in a challenge assay as increased chromosome aberrations, micronuclei or un-repaired DNA strand breaks. The challenge assay has been used in different laboratories to show that a variety of exposed populations (with exposure to air pollutants, arsenic, benzene, butadiene, cigarette smoke, incense smoke, lead, mercury, pesticides, uranium or xylene but not to low concentrations of air pollutants or butadiene) expressed abnormal challenge response. The predicted health consequences of some of these studies have also been validated. Therefore, the challenge assay is a useful functional biomarker for population studies. Details of the challenge assay and its application will be presented in this review.

Biologically relevant exposure science for 21st century toxicity testing

High visibility efforts in toxicity testing and computational toxicology including the recent National Research Council of the National Academies (NRC) report, Toxicity Testing in the 21st Century: A Vision and Strategy (NRC, 2007a), raise important research questions and opportunities for the field of exposure science. The authors of the National Academies report (NRC, 2007a) emphasize that population-based data and human exposure information are required at each step of their vision for toxicity testing and that these data will continue to play a critical role in both guiding development and use of the toxicity information. In fact, state-of-the-art exposure science is essential for translation of toxicity data to assess potential for risk to individuals and populations and to inform public health decisions. As we move forward to implement the NRC vision, a transformational change in exposure science is required. Application of a fresh perspective and novel techniques to capture critical determinants at biologically motivated resolution for translation from controlled in vitro systems to the open multifactorial system of real-world human-environment interaction will be critical. Development of an exposure ontology and knowledge base will facilitate extension of network analysis to the individual and population for translating toxicity information and assessing health risk. Such a sea change in exposure science is required to incorporate consideration of lifestage, genetic susceptibility, and interaction of nonchemical stressors for holistic assessment of risk factors associated with complex environmental disease. A new generation of scientific tools has emerged to rapidly measure signals from cells, tissues, and organisms following exposure to chemicals. Investment in 21st century exposure science is now required to fully realize the potential of the NRC vision for toxicity testing.

Biomarkers in population studies: environmental mutagenesis and risk for cancer

Biomarkers of exposure and biological effects have frequently been used to monitor populations for their exposure to toxic substances and for the prediction of disease risk, such as cancer. Current interest is focused on improving the use of biomarkers to better understand biological mechanisms for improved risk assessment. Such improvements involve the understanding of inter-individual variations in response to exposure, integration of genomic and proteomic technologies into biomarker studies, development of functional biomarkers, and the use of high tech procedures like biosensors and lab-on-a-chip approaches. The latter two approaches can provide unique contributions by providing specific and real-time reporting of excessive exposure. Based on the generation of more reliable information regarding exposure-specific effects, biological mechanisms, and health risk, more realistic prevention and intervention protocols have been implemented. The usefulness and application of these biomarkers and technologies will be presented.

Work group II: Using Geographic Information Systems for enhancing research relevant to policy on diet, physical activity, and weight

Geographic Information Systems (GIS) was a theme for one of the four workgroups convened for the Measures of the Food and Built Environment meeting held in Bethesda, Maryland in November 2007. This summary of group discussions frames several critical conceptual, methodologic, and data challenges regarding the use of GIS to enhance research relevant to policy on diet, physical activity, and weight. Broad recommendations are offered in five areas: (1) theoretical and conceptual development in framing place effects on health; (2) contextualizing people and spatial behavior in built environments and improving empirical representations of place; (3) geospatial data availability, quality, and standards; (4) privacy and confidentiality; and, (5) building capacity in GIS personnel and infrastructure. These topics are inter-related. Although our discussion focuses on issues relevant to the role of the built environment in diet and physical activity outcomes, our recommendations also are salient to health and environment research generally.

Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology

BACKGROUND

Despite earlier doubts, a string of recent successes indicates that if sample sizes are large enough, it is possible-both in theory and in practice-to identify and replicate genetic associations with common complex diseases. But human genome epidemiology is expensive and, from a strategic perspective, it is still unclear what 'large enough' really means. This question has critical implications for governments, funding agencies, bioscientists and the tax-paying public. Difficult strategic decisions with imposing price tags and important opportunity costs must be taken.

METHODS

Conventional power calculations for case-control studies disregard many basic elements of analytic complexity-e.g. errors in clinical assessment, and the impact of unmeasured aetiological determinants-and can seriously underestimate true sample size requirements. This article describes, and applies, a rigorous simulation-based approach to power calculation that deals more comprehensively with analytic complexity and has been implemented on the web as ESPRESSO: (www.p3gobservatory.org/powercalculator.htm).

RESULTS

Using this approach, the article explores the realistic power profile of stand-alone and nested case-control studies in a variety of settings and provides a robust quantitative foundation for determining the required sample size both of individual biobanks and of large disease-based consortia. Despite universal acknowledgment of the importance of large sample sizes, our results suggest that contemporary initiatives are still, at best, at the lower end of the range of desirable sample size. Insufficient power remains particularly problematic for studies exploring gene-gene or gene-environment interactions. Discussion Sample size calculation must be both accurate and realistic, and we must continue to strengthen national and international cooperation in the design, conduct, harmonization and integration of studies in human genome epidemiology.

The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study

Background

The etiology of many chronic diseases involves interactions between environmental factors and genes that modulate physiological processes. Understanding interactions between environmental chemicals and genes/proteins may provide insights into the mechanisms of chemical actions, disease susceptibility, toxicity, and therapeutic drug interactions. The Comparative Toxicogenomics Database (CTD; ) provides these insights by curating and integrating data describing relationships between chemicals, genes/proteins, and human diseases. To illustrate the scope and application of CTD, we present an analysis of curated data for the chemical arsenic. Arsenic represents a major global environmental health threat and is associated with many diseases. The mechanisms by which arsenic modulates these diseases are not well understood.

Methods

Curated interactions between arsenic compounds and genes were downloaded using export and batch query tools at CTD. The list of genes was analyzed for molecular interactions, Gene Ontology (GO) terms, KEGG pathway annotations, and inferred disease relationships.

Results

CTD contains curated data from the published literature describing 2,738 molecular interactions between 21 different arsenic compounds and 1,456 genes and proteins. Analysis of these genes and proteins provide insight into the biological functions and molecular networks that are affected by exposure to arsenic, including stress response, apoptosis, cell cycle, and specific protein signaling pathways. Integrating arsenic-gene data with gene-disease data yields a list of diseases that may be associated with arsenic exposure and genes that may explain this association.

Conclusion

CTD data integration and curation strategies yield insight into the actions of environmental chemicals and provide a basis for developing hypotheses about the molecular mechanisms underlying the etiology of environmental diseases. While many reports describe the molecular response to arsenic, CTD integrates these data with additional curated data sets that facilitate construction of chemical-gene-disease networks and provide the groundwork for investigating the molecular basis of arsenic-associated diseases or toxicity. The analysis reported here is extensible to any environmental chemical or therapeutic drug.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks

The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical–gene interactions, chemical–disease relationships and gene–disease relationships from the literature. This strategy allows data to be integrated to construct chemical–gene–disease networks. CTD is unique in numerous respects: curation focuses on environmental chemicals; interactions are manually curated; interactions are constructed using controlled vocabularies and hierarchies; additional gene attributes (such as Gene Ontology, taxonomy and KEGG pathways) are integrated; data can be viewed from the perspective of a chemical, gene or disease; results and batch queries can be downloaded and saved; and most importantly, CTD acts as both a knowledgebase (by reporting data) and a discovery tool (by generating novel inferences). Over 116 000 interactions between 3900 chemicals and 13 300 genes have been curated from 270 species, and 5900 gene–disease and 2500 chemical–disease direct relationships have been captured. By integrating these data, 350 000 gene–disease relationships and 77 000 chemical–disease relationships can be inferred. This wealth of chemical–gene–disease information yields testable hypotheses for understanding the effects of environmental chemicals on human health. CTD is freely available at http://ctd.mdibl.org.

Associations between dietary methods and biomarkers, and between fruits and vegetables and risk of ischaemic heart disease, in the EPIC Norfolk Cohort Study

BACKGROUND

Methods for assessing diet are prone to measurement error, which may be substantial in large cohort investigations. Biomarkers can be used as objective measures with which to compare estimates of nutritional exposure using different methods

METHODS

Cross sectional comparisons in 12 474 men and women of regression between biomarkers for vitamin C, sodium, potassium, fibre, carbohydrate, fat and phytoestrogens with intakes derived from food diaries and food frequency questionnaires (FFQ), and odds ratios for risk of ischaemic heart disease (IHD) by dietary and plasma vitamin C.

RESULTS

There were strong (P < 0.001) associations between biomarkers and intakes as assessed by food diary. Coefficients were markedly attenuated for data obtained from the FFQ, especially so for vitamin C, potassium and phytoestrogens (Z P < 0.05). Risk of IHD was associated with plasma vitamin C (P < 0.001) and intake of vitamin C and fruit and vegetables assessed by food diary (P quintile trends <0.001, 0.001) but not by the FFQ (P quintile trends 0.923, 0.186).

CONCLUSIONS

Nutritional data that reflect the findings from biomarkers reduce measurement error and will thus improve statistical power in studies of gene nutrient interactions in cohort studies.

Recent advances and opportunities in research on lupus: environmental influences and mechanisms of disease

OBJECTIVES

In this review we summarize research on mechanisms through which environmental agents may affect the pathogenesis of lupus, discuss three exposures that have been the focus of research in this area, and propose recommendations for new research initiatives.

DATA SOURCES AND SYNTHESIS

We examined studies pertaining to key mechanistic events and specific exposures. Apoptosis leading to increased production or decreased clearance of immunogenic intracellular self-antigens and defective apoptosis of autoreactive immune cells both have been implicated in the loss of self-tolerance. The adjuvant or bystander effect is also needed to produce a sustained autoimmune response. Activation of toll-like receptors is one mechanism through which these effects may occur. Abnormal DNA methylation may also contribute to the pathogenesis of lupus. Each of the specific exposures we examined--Epstein-Barr virus, silica, and trichloroethylene--has been shown, in humans or in mice, to act upon one or more of these pathogenic steps. Specific recommendations for the continued advancement of our understanding of environmental influences on lupus and other autoimmune diseases include the development and use of mouse models with varying degrees of penetrance and manifestations of disease, identification of molecular or physiologic targets of specific exposures, development and use of improved exposure assessment methodologies, and multisite collaborations designed to examine understudied environmental exposures in humans.

CONCLUSIONS

The advances made in the past decade concerning our understanding of mechanisms involved in the development of lupus and the influence of environmental agents on this process provide a strong foundation for further developments in this field.

Interpatient variability in rates of asthma progression: can genetics provide an answer?

Asthma is a heterogeneous disorder with a variable natural history. In children 3 patterns of the natural history of asthma have been described: early onset but transient, persistent, and later onset, with only the former leading to persistent asthma later in childhood. In adults a range of different asthma phenotypes differing in their environmental, inflammatory, and prognostic characteristics have also been described. These extend beyond allergic (extrinsic) and nonallergic (intrinsic) asthma to include persistent airflow obstruction and accelerated decrease in lung function over time. Asthma progression can be defined as the change in an individual's phenotype along a continuum ranging from nonasthmatic to asthmatic and subsequent development of severe chronic disease. It is clear that for prevention of asthma progression in patients, there is a need for both better understanding of the pathophysiology of asthma and identification of predictors of progression. Interpatient genetic variability has been shown to affect multiple facets of asthma progression, including increased susceptibility to atopy and subsequent asthma, progression to severe disease, and modification of the response to treatment. Thus genetic testing might provide a means for predicting the likely progression of an individual along the continuum, allowing targeting of preventative treatment. However, the prospect of the use of genetic information in clinical practice raises important social and ethical issues that will need to be addressed before genetic testing can be used to inform the preventative treatment of patients to prevent the development of progression of asthma in individuals.

Review on genetic variants and maternal smoking in the etiology of oral clefts and other birth defects

A spectrum of adverse pregnancy outcomes, including preterm birth, low birth weight, and birth defects has been linked with maternal smoking during pregnancy. This article includes a review of studies investigating interactions between genetic variants and maternal smoking in contributing to birth defects using oral clefting as a model birth defect. The primary gene-smoking studies for other major birth defects are also summarized. Gene-environment interaction studies for birth defects are still at an early stage with several mixed results, but evolving research findings have begun to document clinically and developmentally important interactions. As samples and data become increasingly available, more effort is needed in designing innovative analytical methods to study gene-environment interactions.

The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research

Toxicoproteomics uses the discovery potential of proteomics in toxicology research by applying global protein measurement technologies to biofluids and tissues after host exposure to injurious agents. Toxicoproteomic studies thus far have focused on protein profiling of major organs and biofluids such as liver and blood in preclinical species exposed to model toxicants. The slow pace of discovery for new biomarkers, toxicity signatures and mechanistic insights is partially due to the limited proteome coverage derived from analysis of native organs, tissues and body fluids by traditional proteomic platforms. Improved toxicoproteomic analysis would result by combining higher data density LC-MS/MS platforms with stable isotope labelled peptides and parallel use of complementary platforms. Study designs that remove abundant proteins from biofluids, enrich subcellular structures and include cell specific isolation from heterogeneous tissues would greatly increase differential expression capabilities. By leveraging resources from immunology, cell biology and nutrition research communities, toxicoproteomics could make particular contributions in three inter-related areas to advance mechanistic insights and biomarker development: the plasma proteome and circulating microparticles, the adductome and idiosyncratic toxicity.