Genes, the environment and personalized medicine: We need to harness both environmental and genetic data to maximize personal and population health

The Roadmap toward Personalized Medicine: Challenges and Opportunities

In 2019, the International Consortium for Personalised Medicine (ICPerMed) developed a vision on how the use of personalized medicine (PM) approaches will promote "next-generation" medicine in 2030 more firmly centered on the individual's personal characteristics, leading to improved health outcomes within sustainable healthcare systems through research, development, innovation, and implementation for the benefit of patients, citizens, and society. Nevertheless, there are significant hurdles that healthcare professionals, researchers, policy makers, and patients must overcome to implement PM. The ICPerMed aims to provide recommendations to increase stakeholders' awareness on actionable measures to be implemented for the realization of PM. Starting with best practice examples of PM together with consultation of experts and stakeholders, a careful analysis that underlined hurdles, opportunities, recommendations, and information, aiming at developing knowledge on the requirements for PM implementation in healthcare practices, has been provided. A pragmatic roadmap has been defined for PM integration into healthcare systems, suggesting actions to overcome existing barriers and harness the potential of PM for improved health outcomes. In fact, to facilitate the adoption of PM by diverse stakeholders, it is mandatory to have a comprehensive set of resources tailored to stakeholder needs in critical areas of PM. These include engagement strategies, collaboration frameworks, infrastructure development, education and training programs, ethical considerations, resource allocation guidelines, regulatory compliance, and data management and privacy.

In Silico Clinical Trials: Is It Possible?

Modeling and simulation (M&S), including in silico (clinical) trials, helps accelerate drug research and development and reduce costs and have coined the term "model-informed drug development (MIDD)." Data-driven, inferential approaches are now becoming increasingly complemented by emerging complex physiologically and knowledge-based disease (and drug) models, but differ in setup, bottlenecks, data requirements, and applications (also reminiscent of the different scientific communities they arose from). At the same time, and within the MIDD landscape, regulators and drug developers start to embrace in silico trials as a potential tool to refine, reduce, and ultimately replace clinical trials. Effectively, silos between the historically distinct modeling approaches start to break down. Widespread adoption of in silico trials still needs more collaboration between different stakeholders and established precedence use cases in key applications, which is currently impeded by a shattered collection of tools and practices. In order to address these key challenges, efforts to establish best practice workflows need to be undertaken and new collaborative M&S tools devised, and an attempt to provide a coherent set of solutions is provided in this chapter. First, a dedicated workflow for in silico clinical trial (development) life cycle is provided, which takes up general ideas from the systems biology and quantitative systems pharmacology space and which implements specific steps toward regulatory qualification. Then, key characteristics of an in silico trial software platform implementation are given on the example of jinkō.ai (nova's end-to-end in silico clinical trial platform). Considering these enabling scientific and technological advances, future applications of in silico trials to refine, reduce, and replace clinical research are indicated, ranging from synthetic control strategies and digital twins, which overall shows promise to begin a new era of more efficient drug development.

Flourishing tumor organoids: History, emerging technology, and application

Malignant tumors are one of the leading causes of death which impose an increasingly heavy burden on all countries. Therefore, the establishment of research models that closely resemble original tumor characteristics is crucial to further understanding the mechanisms of malignant tumor development, developing safer and more effective drugs, and formulating personalized treatment plans. Recently, organoids have been widely used in tumor research owing to their advantages including preserving the structure, heterogeneity, and cellular functions of the original tumor, together with the ease of manipulation. This review describes the history and characteristics of tumor organoids and the synergistic combination of three-dimensional (3D) culture approaches for tumor organoids with emerging technologies, including tissue-engineered cell scaffolds, microfluidic devices, 3D bioprinting, rotating wall vessels, and clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). Additionally, the progress in research and the applications in basic and clinical research of tumor organoid models are summarized. This includes studies of the mechanism of tumor development, drug development and screening, precision medicine, immunotherapy, and simulation of the tumor microenvironment. Finally, the existing shortcomings of tumor organoids and possible future directions are discussed.

A personalized pharmaco-epistatic network model of precision medicine

Precision medicine, the utilization of targeted treatments to address an individual's disease, relies on knowledge about the genetic cause of that individual's drug response. Here, we present a functional graph (FunGraph) theory to chart comprehensive pharmacogenetic architecture for each and every patient. FunGraph is the combination of functional mapping - a dynamic model for genetic mapping and evolutionary game theory guiding interactive strategies. It coalesces all pharmacogenetic factors into multilayer and multiplex networks that fully capture bidirectional, signed and weighted epistasis. It can visualize and interrogate how epistasis moves in the cell and how this movement leads to patient- and context-specific genetic architecture in response to organismic physiology. We discuss the future implementation of FunGraph to achieve precision medicine. Teaser: We present a functional graph (FunGraph) theory to draw a complete picture of pharmacogenetic architecture underlying interindividual variability in drug response. FunGraph can characterize how each gene acts and interacts with every other gene to mediate therapeutic response.

Molecular mechanisms of environmental exposures and human disease

A substantial proportion of disease risk for common complex disorders is attributable to environmental exposures and pollutants. An appreciation of how environmental pollutants act on our cells to produce deleterious health effects has led to advances in our understanding of the molecular mechanisms underlying the pathogenesis of chronic diseases, including cancer and cardiovascular, neurodegenerative and respiratory diseases. Here, we discuss emerging research on the interplay of environmental pollutants with the human genome and epigenome. We review evidence showing the environmental impact on gene expression through epigenetic modifications, including DNA methylation, histone modification and non-coding RNAs. We also highlight recent studies that evaluate recently discovered molecular processes through which the environment can exert its effects, including extracellular vesicles, the epitranscriptome and the mitochondrial genome. Finally, we discuss current challenges when studying the exposome - the cumulative measure of environmental influences over the lifespan - and its integration into future environmental health research.

3D Printed Pharmaceutical Systems for Personalized Treatment in Metabolic Syndrome

The current healthcare system is widely based on the concept of “one size fit for all”, which emphasizes treating a disease by prescribing the same drug to all patients with equivalent doses and dosing frequency. This medical treatment scenario has shown varied responses with either no or weak pharmacological effects and exaggerated adverse reactions preceded by more patient complications. The hitches to the concept of “one size fits all” have devoted the attention of many researchers to unlocking the concept of personalized medicine (PM). PM delivers customized therapy with the highest safety margin for an individual patient’s needs. PM has the potential to revolutionize the current healthcare system and pave the way to alter drug choices and doses according to a patient’s clinical responses, providing physicians with the best treatment outcomes. The 3D printing techniques is a solid-form fabrication method whereby successive layers of materials based on computer-aided designs were deposited to form 3D structures. The 3D printed formulation achieves PM goals by delivering the desired dose according to patient needs and drug release profile to achieve a patient’s personal therapeutic and nutritional needs. This pre-designed drug release profile attains optimum absorption and distribution, exhibiting maximum efficacy and safety profiles. This review aims to focus on the role of the 3D printing technique as a promising tool to design PM in metabolic syndrome (MS).

Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders

The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.

Urinary Eicosanoid Levels Reflect Allergen and Diesel Exhaust Coexposure and Are Linked to Impaired Lung Function

Eicosanoids are potent regulators of homeostasis and inflammation. Co-exposure to allergen and diesel exhaust (DE) have been shown to lead to eosinophilic inflammation, impaired airflow, and increased airway responsiveness. It is not clear whether eicosanoids mediate the mechanism by which these exposures impair lung function. We conducted a randomized, double-blinded, and four-arm crossover study. Fourteen allergen-sensitized participants were exposed to four conditions: negative control; allergen-alone exposure; DE and allergen coexposure; coexposure with particle-reducing technology applied. Quantitative metabolic profiling of urinary eicosanoids was performed using LC-MS/MS. As expected, allergen inhalation increased eicosanoids. The prostacyclin metabolite 2,3-dinor-6-keto-PGF_1α (PGF_1α, prostaglandin F_1α) increased with coexposure, but particle depletion suppressed this pathway. Individuals with a high genetic risk score demonstrated a greater increase in isoprostane metabolites following coexposure. Causal mediation analyses showed that allergen induced airflow impairment was mediated via leukotriene E₄ and tetranor-prostaglandin D metabolite. Overall, DE exposure did not augment the allergen's effect on urinary eicosanoids, except insofar as variant genotypes conferred susceptibility to the addition of DE in terms of isoprostane metabolites. These findings will add to the body of previous controlled human exposure studies and provide greater insight into how complex environmental exposures in urban air may influence individuals with sensitivity to aeroallergens.

Nature versus nurture—on the origins of a specious argument

The concept of heritability parses out genetic and environmental causes of diseases and does not fit the underlying biology of complex diseases that arise from interactions among genetics and environment. Exposomics places environment on a similar scale as genomics and allows for more modern research approaches that estimate time-varying genome by exposome interactions. By addressing the biological underpinnings of disease comprehensively, we will find the “missing heritability” which is not solely based on genetic variation but is instead driven by time, life stage, and geographic variability in our exposome as it interacts with our genome.

The evolution of personalized healthcare and the pivotal role of European regions in its implementation

Personalized medicine (PM) moves at the same pace of data and technology and calls for important changes in healthcare. New players are participating, providing impulse to PM. We review the conceptual foundations for PM and personalized healthcare and their evolution through scientific publications where a clear definition and the features of the different formulations are identifiable. We then examined PM policy documents of the International Consortium for Personalised Medicine and related initiatives to understand how PM stakeholders have been changing. Regional authorities and stakeholders have joined the race to deliver personalized care and are driving toward what could be termed as the next personalized healthcare. Their role as a key stakeholder in PM is expected to be pivotal.

The economics of precision health: preventing air pollution-induced exacerbation in asthma

The demonstrable value of precision medicine, in the context of common environmental exposures, has scarcely been explored. This study evaluated the cost effectiveness of a preventive personalised intervention to reduce the adverse effect of air pollution in the context of asthma.

A decision–analytic model was used to conduct a cost-utility analysis of prevention interventions in case of acute exposure to air pollution in mild asthma. Three different strategies, as follows, were compared: no preventive intervention; precision health strategy based on information from genotype testing, followed with treating high-risk patients; and prescribing additional medication to all mild asthmatics as a preventive intervention. The costs and quality-adjusted life years (QALYs) in the base case and alternative scenarios were obtained through probabilistic analysis.

The results showed that the precision prevention intervention (anticipatory intervention for asthmatics, guided by relevant genetic abnormality, in the face of acute air pollution) is a cost-effective strategy compared with no such intervention, with an incremental cost-effectiveness ratio of CAD 49 555 per QALY. Furthermore, this strategy is a dominant strategy compared with an intervention that prescribes medication indiscriminately to all asthmatics.

The incorporation of genomic testing to stratify risk of asthmatics to pollution-driven exacerbations, and then tailoring a preventive intervention accordingly, may be cost effective relative to untailored methods. These results lend plausibility to the use of precision medicine for limiting asthma exacerbation in the context of air pollution and, potentially, other exposures.

Glutathione-S-transferase genotyping to determine the use of preventive asthma medication in the face of air pollution is cost effective in this model. Precision prevention in the setting of common environmental exposures may be used in other contexts.https://bit.ly/35Lab4b

Home environment allergen exposure scale in older adult cohort with asthma

OBJECTIVES

Home environmental exposures are a primary source of asthma exacerbation. There is a gap in decision support models that efficiently aggregate the home exposure assessment scores for focused and tailored interventions. Three development methods of a home environment allergen exposure scale for persons with asthma (weighted by dimension reduction, unweighted, precision biomarker-based) were compared, and racial disparity tested.

METHODS

Baseline measures from a longitudinal cohort of 187 older adults with asthma were analyzed using humidity and particulate matter sensors, allergy testing, and a home environment checklist. Weights for the dimension reduction scale were obtained from factor analysis, applied for loadings > 0.35. Scales were tested in linear regression models with asthma control and asthma quality of life outcomes. Racial disparities were tested using t tests. Scale performance was tested using unadjusted regression analyses with asthma control and asthma quality of life outcomes, separately.

RESULTS

The 7-item empirically weighted scale demonstrated best performance with asthma control associations (F = 4.65, p = 0.03, R2 = .02) and quality of life (F = 6.45, p = 0.01, R2 = .03) as follows: evidence of roach/mice, dust, mold, tobacco smoke exposure, properly venting bathroom fan, self-report of roach/mice/rats, and access to a HEPA filter vacuum. Pets indoors loaded on a separate scale. Racial differences were observed (t = - 3.09, p = 0.004).

CONCLUSION

The Home Environment Allergen Exposure Scale scores were associated with racial disparities. Replicating these methods in populations residing in high-risk/low-income housing may generate a clinically meaningful, tailored assessment of asthma triggers. Further consideration for variables that address allergic reactivity and biomarker results is indicated to enhance the potential for a precision prevention score.

An update on immunologic mechanisms in the respiratory mucosa in response to air pollutants

Every day, we breathe in more than 10,000 L of air that contains a variety of air pollutants that can pose negative consequences to lung health. The respiratory mucosa formed by the airway epithelium is the first point of contact for air pollution in the lung, functioning as a mechanical and immunologic barrier. Under normal circumstances, airway epithelial cells connected by tight junctions secrete mucus, airway surface lining fluid, host defense peptides, and antioxidants and express innate immune pattern recognition receptors to respond to inhaled foreign substances and pathogens. Under conditions of air pollution exposure, the defenses of the airway epithelium are compromised by reductions in barrier function, impaired host defense to pathogens, and exaggerated inflammatory responses. Central to the mechanical and immunologic changes induced by air pollution are activation of redox-sensitive pathways and a role for antioxidants in normalizing these negative effects. Genetic variants in genes important in epithelial cell function and phenotype contribute to a diversity of responses to air pollution in the population at the individual and group levels and suggest a need for personalized approaches to attenuate the respiratory mucosal immune responses to air pollution.

Predictive, Personalized, Preventive and Participatory (4P) Medicine Applied to Telemedicine and eHealth in the Literature

The main objective of this work is to provide a review of existing research work into predictive, personalized, preventive and participatory medicine in telemedicine and ehealth. The academic databases used for searches are IEEE Xplore, PubMed, Science Direct, Web of Science and ResearchGate, taking into account publication dates from 2010 up to the present day. These databases cover the greatest amount of information on scientific texts in multidisciplinary fields, from engineering to medicine. Various search criteria were established, such as ("Predictive" OR "Personalized" OR "Preventive" OR "Participatory") AND "Medicine" AND ("eHealth" OR "Telemedicine") selecting the articles of most interest. A total of 184 publications about predictive, personalized, preventive and participatory (4P) medicine in telemedicine and ehealth were found, of which 48 were identified as relevant. Many of the publications found show how the P4 medicine is being developed in the world and the benefits it provides for patients with different illnesses. After the revision that was undertaken, it can be said that P4 medicine is a vital factor for the improvement of medical services. It is hoped that one of the main contributions of this study is to provide an insight into how P4 medicine in telemedicine and ehealth is being applied, as well as proposing outlines for the future that contribute to the improvement of prevention and prediction of illnesses.

Gene-environment interactions in Alzheimer's disease: A potential path to precision medicine

Alzheimer's disease (AD) is the leading cause of dementia in the United States and afflicts >5.7 million Americans in 2018. Therapeutic options remain extremely limited to those that are symptom targeting, while no drugs have been approved for the modification or reversal of the disease itself. Risk factors for AD including aging, the female sex, as well as carrying an APOE4 genotype. These risk factors have been extensively examined in the literature, while less attention has been paid to modifiable risk factors, including lifestyle, and environmental risk factors such as exposures to air pollution and pesticides. This review highlights the most recent data on risk factors in AD and identifies gene by environment interactions that have been investigated. It also provides a suggested framework for a personalized therapeutic approach to AD, by combining genetic, environmental and lifestyle risk factors. Understanding modifiable risk factors and their interaction with non-modifiable factors (age, susceptibility alleles, and sex) is paramount for designing personalized therapeutic interventions.

Genomic Data-Sharing Practices

Making data broadly accessible is essential to creating a medical information commons (MIC). Transparency about data-sharing practices can cultivate trust among prospective and existing MIC participants. We present an analysis of 34 initiatives sharing DNA-derived data based on public information. We describe data-sharing practices captured, including practices related to consent, privacy and security, data access, oversight, and participant engagement. Our results reveal that data-sharing initiatives have some distance to go in achieving transparency.

Personalized medicine: motivation, challenges, and progress

There is a great deal of hype surrounding the concept of personalized medicine. Personalized medicine is rooted in the belief that since individuals possess nuanced and unique characteristics at the molecular, physiological, environmental exposure, and behavioral levels, they may need to have interventions provided to them for diseases they possess that are tailored to these nuanced and unique characteristics. This belief has been verified to some degree through the application of emerging technologies such as DNA sequencing, proteomics, imaging protocols, and wireless health monitoring devices, which have revealed great inter-individual variation in disease processes. In this review, we consider the motivation for personalized medicine, its historical precedents, the emerging technologies that are enabling it, some recent experiences including successes and setbacks, ways of vetting and deploying personalized medicines, and future directions, including potential ways of treating individuals with fertility and sterility issues. We also consider current limitations of personalized medicine. We ultimately argue that since aspects of personalized medicine are rooted in biological realities, personalized medicine practices in certain contexts are likely to be inevitable, especially as relevant assays and deployment strategies become more efficient and cost-effective.

Synergistic Environmental Exposures and the Airways Capturing Complexity in Humans: An Underappreciated World of Complex Exposures

Paradoxically, the vast majority of research models intended to understand the relationship between exogenous exposures and lung disease are reduced to a single inhalant. This approach is understandable given the practical challenges of investigation, but it is problematic in terms of translation to the real-world human condition. Furthermore, use of data from such models can lead to underestimation of effect, which may adversely influence regulatory imperatives to protect public health based on the most robust information. Efforts to incrementally introduce layers of complexity to observational and experimental systems have revealed pathophysiology previously "hidden" within simplified models. Capturing the effects of co-exposure to traffic-related air pollution and allergens is a paradigmatic example and illustrates the influence of co-exposures across a plethora of clinical and subclinical end points within the respiratory tract. From DNA methylation in the epithelium, to inflammatory mediators and allergen-specific antibodies in the airway, to airflow limitation and symptoms, the addition of a common second exposure induces profound changes. In addition, genetic variation significantly alters the product of these relationships, and capturing multidimensional interactions may reveal susceptible populations who are particularly affected by these exposures and may merit focused measures for protection. Collectively, better modeling, and ultimately deeper knowledge, of these complex relationships has important implications for personalized health and prevention, development and refinement of pharmacologic agents, and public health responses to climate change and the staggering burden of pollution-driven disease worldwide.

Personalised nutrition and health

Jose Ordovas and colleagues consider that nutrition interventions tailored to individual characteristics and behaviours have promise but more work is needed before they can deliver

The Canadian Urban Environmental Health Research Consortium - a protocol for building a national environmental exposure data platform for integrated analyses of urban form and health

BACKGROUND

Multiple external environmental exposures related to residential location and urban form including, air pollutants, noise, greenness, and walkability have been linked to health impacts or benefits. The Canadian Urban Environmental Health Research Consortium (CANUE) was established to facilitate the linkage of extensive geospatial exposure data to existing Canadian cohorts and administrative health data holdings. We hypothesize that this linkage will enable investigators to test a variety of their own hypotheses related to the interdependent associations of built environment features with diverse health outcomes encompassed by the cohorts and administrative data.

METHODS

We developed a protocol for compiling measures of built environment features that quantify exposure; vary spatially on the urban and suburban scale; and can be modified through changes in policy or individual behaviour to benefit health. These measures fall into six domains: air quality, noise, greenness, weather/climate, and transportation and neighbourhood factors; and will be indexed to six-digit postal codes to facilitate merging with health databases. Initial efforts focus on existing data and include estimates of air pollutants, greenness, temperature extremes, and neighbourhood walkability and socioeconomic characteristics. Key gaps will be addressed for noise exposure, with a new national model being developed, and for transportation-related exposures, with detailed estimates of truck volumes and diesel emissions now underway in selected cities. Improvements to existing exposure estimates are planned, primarily by increasing temporal and/or spatial resolution given new satellite-based sensors and more detailed national air quality modelling. Novel metrics are also planned for walkability and food environments, green space access and function and life-long climate-related exposures based on local climate zones. Critical challenges exist, for example, the quantity and quality of input data to many of the models and metrics has changed over time, making it difficult to develop and validate historical exposures.

DISCUSSION

CANUE represents a unique effort to coordinate and leverage substantial research investments and will enable a more focused effort on filling gaps in exposure information, improving the range of exposures quantified, their precision and mechanistic relevance to health. Epidemiological studies may be better able to explore the common theme of urban form and health in an integrated manner, ultimately contributing new knowledge informing policies that enhance healthy urban living.

PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES

Precision medicine research efforts both in basic science discovery and clinical implementation are well underway and promise to provide individualized preventions and treatments, improving overall health care delivery. To achieve these goals, advances in data capture and analysis are needed spanning different types of 'omic and clinical data. The efforts to enhance precise treatments for all may accentuate healthcare disparities unless specific challenges are identified and addressed. This session of the 2018 Pacific Symposium on Biocomputing presents the latest developments in this transdisciplinary research space of genomics, medicine, and population health.

Decline in Cardiovascular Mortality: Possible Causes and Implications

If the control of infectious diseases was the public health success story of the first half of the 20th century, then the decline in mortality from coronary heart disease and stroke has been the success story of the century's past 4 decades. The early phase of this decline in coronary heart disease and stroke was unexpected and controversial when first reported in the mid-1970s, having followed 60 years of gradual increase as the US population aged. However, in 1978, the participants in a conference convened by the National Heart, Lung, and Blood Institute concluded that a significant recent downtick in coronary heart disease and stroke mortality rates had definitely occurred, at least in the US Since 1978, a sharp decline in mortality rates from coronary heart disease and stroke has become unmistakable throughout the industrialized world, with age-adjusted mortality rates having declined to about one third of their 1960s baseline by 2000. Models have shown that this remarkable decline has been fueled by rapid progress in both prevention and treatment, including precipitous declines in cigarette smoking, improvements in hypertension treatment and control, widespread use of statins to lower circulating cholesterol levels, and the development and timely use of thrombolysis and stents in acute coronary syndrome to limit or prevent infarction. However, despite the huge growth in knowledge and advances in prevention and treatment, there remain many questions about this decline. In fact, there is evidence that the rate of decline may have abated and may even be showing early signs of reversal in some population groups. The National Heart, Lung, and Blood Institute, through a request for information, is soliciting input that could inform a follow-up conference on or near the 40th anniversary of the original landmark conference to further explore these trends in cardiovascular mortality in the context of what has come before and what may lie ahead.

Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation

BACKGROUND

Allergic disease affects 30% to 40% of the world's population, and its development is determined by the interplay between environmental and inherited factors. Air pollution, primarily consisting of diesel exhaust emissions, has increased at a similar rate to allergic disease. Exposure to diesel exhaust may play a role in the development and progression of allergic disease, in particular allergic respiratory disease. One potential mechanism underlying the connection between air pollution and increased allergic disease incidence is DNA methylation, an epigenetic process with the capacity to integrate gene-environment interactions.

OBJECTIVE

We sought to investigate the effect of allergen and diesel exhaust exposure on bronchial epithelial DNA methylation.

METHODS

We performed a randomized crossover-controlled exposure study to allergen and diesel exhaust in humans, and measured single-site (CpG) resolution global DNA methylation in bronchial epithelial cells.

RESULTS

Exposure to allergen alone, diesel exhaust alone, or allergen and diesel exhaust together (coexposure) led to significant changes in 7 CpG sites at 48 hours. However, when the same lung was exposed to allergen and diesel exhaust but separated by approximately 4 weeks, significant changes in more than 500 sites were observed. Furthermore, sites of differential methylation differed depending on which exposure was experienced first. Functional analysis of differentially methylated CpG sites found genes involved in transcription factor activity, protein metabolism, cell adhesion, and vascular development, among others.

CONCLUSIONS

These findings suggest that specific exposures can prime the lung for changes in DNA methylation induced by a subsequent insult.

The Autoimmune Ecology

Autoimmune diseases (ADs) represent a heterogeneous group of disorders that affect specific target organs or multiple organ systems. These conditions share common immunopathogenic mechanisms (i.e., the autoimmune tautology), which explain the clinical similarities they have among them as well as their familial clustering (i.e., coaggregation). As part of the autoimmune tautology, the influence of environmental exposure on the risk of developing ADs is paramount (i.e., the autoimmune ecology). In fact, environment, more than genetics, shapes immune system. Autoimmune ecology is akin to exposome, that is all the exposures - internal and external - across the lifespan, interacting with hereditary factors (both genetics and epigenetics) to favor or protect against autoimmunity and its outcomes. Herein, we provide an overview of the autoimmune ecology, focusing on the immune response to environmental agents in general, and microbiota, cigarette smoking, alcohol and coffee consumption, socioeconomic status (SES), gender and sex hormones, vitamin D, organic solvents, and vaccines in particular. Inclusion of the autoimmune ecology in disease etiology and health will improve the way personalized medicine is currently conceived and applied.

Controlled diesel exhaust and allergen coexposure modulates microRNA and gene expression in humans: Effects on inflammatory lung markers

BACKGROUND

Air pollution's association with asthma may be due to its augmentation of allergenic effects, but the role of microRNA (miRNA) and gene expression in this synergy is unknown.

OBJECTIVE

We sought to determine whether exposure to allergen, exposure to diesel exhaust (DE), or coexposures modulate miRNA, gene expression, or inflammatory pathways and whether these measurements are correlated.

METHODS

Fifteen participants with atopy completed this controlled study of 2 hours of filtered air or DE (300 μg PM_2.5/m³) exposure, followed by saline-controlled segmental bronchial allergen challenge. Gene and miRNA expression in bronchial brushings and lung inflammatory markers were measured 48 hours later, in study arms separated by approximately 4 weeks. Expression of miRNAs, messenger RNAs, and inflammatory markers and their interrelationships were determined using regression.

RESULTS

Robust linear models indicated that DE plus saline and DE plus allergen significantly modulated the highest number of miRNAs and messenger RNAs, respectively, relative to control (filtered air plus saline). In mixed models, allergen exposure modulated (q ≤ 0.2) miRNAs including miR-183-5p, miR-324-5p, and miR-132-3p and genes including NFKBIZ and CDKN1A, but DE did not significantly modify this allergenic effect. Repression of CDKN1A by allergen-induced miR-132-3p may contribute to shedding of bronchial epithelial cells.

CONCLUSIONS

Expression of specific miRNAs and genes associated with bronchial immune responses were significantly modulated by DE or allergen. However, DE did not augment the effect of allergen at 48 hours, suggesting that adjuvancy may be transient or require higher or prolonged exposure. In silico analysis suggested a possible mechanism contributing to epithelial wall damage following allergen exposure.

Iranian-Islamic traditional medicine: An ancient comprehensive personalized medicine

Personalized medicine (PM) is a novel term used for a medical model in which all diagnostic, prognostic, and therapeutic aspects of a disease are individualized for a patient using specific molecular testing. In Iranian-Islamic traditional medicine (IITM) an ancient paradigm for PM has been described which has been introduced in this paper. We reviewed the ancient resources of IITM and many valid recent studies on personalized medicine and described an ancient feature of personalized medicine in comparison with new ones. According to IITM scholars, every person has an individual temperament which is concluded of four basic humors combination. The individual temper is influenced by internal and external factors such as age, gender, ethnicity, season, and environment. This variability leads to different physical and mental behaviors toward a particular condition; so if we could identify the patient's temper, we would predict his/her health-related behaviors rather than predisposition and prognosis to different diseases, and select the best treatment. This holistic viewpoint of IITM to the human health and disease justifies the variable phenotypes among similar illnesses; the fact around which more advanced high-tech researches are being developed to explore all specific molecular pathways. IITM offers an ancient comprehensive PM (APM) which is more available and inexpensive compared to the modern PM (MPM). Moreover, APM focuses more on fitness than illness in comparison to MPM. It seems more attention to APM introduced by IITM could help us to promote health community. Design studies using high-tech MPM techniques would likely lead to clarification of most molecular aspects of APM.