Epigenetics of asthma

Biochimica et Biophysica Acta 1810 (2011) 1103–1109

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Biochimica et Biophysica Acta j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / b b a g e n

Review

Epigenetics of asthma☆ Andrew L. Durham ⁎, Coen Wiegman, Ian M. Adcock Airways Disease Section, Guy Scadding Building, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London SW3 6LY, UK

a r t i c l e

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Article history: Received 3 December 2010 Received in revised form 18 February 2011 Accepted 3 March 2011 Available online 11 March 2011 Keywords: Asthma Epigenetics Acetylation Methylation Environmental stress

a b s t r a c t Asthma is caused by both heritable and environmental factors. It has become clear that genetic studies do not adequately explain the heritability and susceptibility to asthma. The study of epigenetics, heritable non-coding changes to DNA may help to explain the heritable component of asthma. Additionally, epigenetic modifications can be influenced by the environment, including pollution and cigarette smoking, which are known asthma risk factors. These environmental trigger-induced epigenetic changes may be involved in skewing the immune system towards a Th2 phenotype following in utero exposure and thereby enhancing the risk of asthma. Alternatively, they may directly or indirectly modulate the immune and inflammatory processes in asthmatics via effects on treatment responsiveness. The study of epigenetics may therefore play an important role in our understanding and possible treatment of asthma and other allergic diseases. This article is part of a Special Issue entitled: Biochemistry of Asthma. © 2011 Elsevier B.V. All rights reserved.

1. Introduction Chronic inflammatory diseases of the lung, including asthma, are the second largest cause of mortality worldwide after cardiac conditions [1]. Asthma and allergy are complex diseases with many influencing risk factors. It has been established that asthma runs in families [2] with between 37 and 80% of the risk of asthma being heritable rather than environmental [3]. However, as with many diseases asthma shows complex and non-Mendelian patterns of inheritance and many gene loci are thought to be involved [2,4]. Candidate gene and genome wide association studies (GWA), looking for single nucleotide polymorphisms (SNPs), have provided valuable insight into the genetic architecture of asthma by providing evidence for the involvement of novel genes such as ORMDL3 and IL-18R in asthma and emphasised the importance of distinct asthma subjects associated with specific genotypes [4]. However, in agreement with data in other complex diseases and other traits including height [5], these SNPs still only account for a small proportion of the identifiable risk of disease [4,6]. In addition to Mendelian inheritance, heritable changes to gene expression can be caused by epigenetic changes. The term epigenetics is used to describe heritable changes in gene expression due to noncoding changes to the DNA [7]. Epigenetic modifications can alter the structure of DNA itself, such as DNA methylation, or alter the structure of chromatin through alterations to scaffolding proteins, such as histones [8]. Once established, these changes in DNA methylation and histone modifications can be maintained through many cell divisions, ☆ This article is part of a Special Issue entitled: Biochemistry of Asthma. ⁎ Corresponding author. Tel.: +44 20 7351 8127; fax: +44 20 7351 8126. E-mail address: [email protected] (A.L. Durham). 0304-4165/$ – see front matter © 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.bbagen.2011.03.006

leading to a state whereby specific gene expression patterns are determined by the epigenetic profile [8]. There is a complex interaction between these various epigenetic marks positioned by various writers that are read by the transcriptional machinery and can be erased by regulatory enzymes [9]. This results in an epigenetic ‘language’ rather than a strict code that interprets external cellular stimuli in a context-dependent manner within the nucleus to provide the correct functional response [9]. Epigenetics was first recognised in cell differentiation but has been shown to play an important role in the regulation of a wide variety of genes, which includes the genes involved in the inflammatory immune response [10]. These epigenetic modifications may help to explain the patterns of inheritance seen in asthma and explain how they interact with environmental factors [11]. This may be particularly valid when accounting for the effects of environmental stressor such as cigarette smoke and air pollution on enhancing the risk of asthma in children exposed in utero [12]. 2. DNA methylation The first epigenetic mechanism recognised was DNA methylation, which is a reversible modification of DNA structure, adding a methyl group to the 5 position of a cytosine residue often as part of a CpG island or cluster, which generally results in gene silencing [8], although there are exceptions to this rule [13]. DNA methylation is most recognised for its role in cell differentiation and gene silencing, in mammals 60–90% of CpG sites are methylated, and most of the remaining unmethylated residues are clustered in CpG islands within functional gene promoters [14]. The methylation of DNA is performed by specific DNA methyltransferases (Dnmt) [8]. During DNA replication the daughter DNA duplex

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becomes hemimethylated, with only one strand being correctly methylated. Dnmt1 methylates hemimethylated DNA and thereby conserves DNA methylation markers through DNA relpication and prevents the genome becoming demethylated over time [8]. This process is termed maintenane methylation [8]. In addition, native DNA can be methylated by de novo methylation which is performed by Dnmt3A and Dnmt3B in response to cellular stressors [8]. Such methylation will subsequently be maintained by the action of Dmnt1 [8].DNA methylation affects the transcription of genes in two ways. The methylation of DNA itself can physically impede the binding of activating or repressive transcription factors to the gene promoter or enhancer, and secondly methylated DNA can be bound by proteins known as methyl-CpG-binding domain proteins (MBDs) [14,15]. MBD proteins then recruit additional proteins to the locus, such as histone deacetylases (HDACs) and other chromatin remodeling proteins that can modify histones, thereby forming compact, inactive chromatin, termed hetero- or silent chromatin. Once thought to be irreversible methylation is a reversible regulatory event, and methyl groups can be removed allowing transcription to occur [14,15]. Although the majority of research into methylation has focussed on CpG islands, it has been shown that other regions up to 2 kb away from the CpG islands, termed CpG shores, play an important role in tissue differentiation [16]. Although these may be distant from gene promoters CpG island shore methylation is strongly related to gene expression [16]. Because DNA methylation can be affected by diet, stress and other environmental factors – including heavy metals, pesticides, diesel exhaust and tobacco smoke – it is one mechanism to explain how many dietary and environmental risk factors contribute to the development and inheritance of allergy [17]. 3. Histone acetylation The other main aspect of epigenetics is alterations to the packaging structures of DNA, which alter the ability of transcription factors and transcriptional regulatory enzymes to interact with specific DNA sequences or each other and elicit the ‘correct’ transcriptional response [8]. The several metres of DNA need to be tightly folded or packaged to fit within the confines of the nucleus which raises issues as to how this then becomes available for binding by activating factors following cell stimulation. Post-translational modifications of DNAassociated proteins induced by transcription factor activation appear to overcome this problem by inducing local DNA unwinding and thereby aid the tightly controlled regulation of gene transcription. These modifications affect the structure of chromatin, and specifically the basic component of chromatin: the nucleosome, which is a 146 base pair (bp) length of DNA wrapped around an octomer of core histone proteins (2 molecules each of H2A, H2B, H4 and H4) [8,15]. The nucleosomes are subsequently compacted together to form 30 nM chromatin fibres which are in turn compacted in the chromosome structure [8]. The structure of chromatin is important for controlling gene expression. Tightly wound DNA is inaccessible to transcription factors and other DNA binding proteins resulting in gene silencing; conversely chromatin loosening enables gene expression. In general, acetylation of histones H3 and H4, by the epigenetic writers histone acetyltransferases (HAT) along with histone H3 lysine (K)4 methylation by specific histone methylases (HMT), results in the formation of tags that allow subsequent recruitment of other transcriptional complexes and chromatin remodelling engines, loosening of the local nucleosomal structure and gene transcription to occur [18]. These changes occur predominantly at the transcriptional start site [19,20] and are closely associated with gene transcription [21] and appear invariant across many cell types in contrast to the greater variability seen in histone modifications in enhancer regions [21]. Less frequently transcribed or silenced genes have repressive marks, remain more tightly packaged

and therefore less accessible to the transcriptional mechanisms of the cell [8,18]. In addition, activating K4 methylation marks are associated with poised transcription whereby RNA polymerase II is located at the transcriptional start site but does not have all the correct activating epigenetic marks to allow transcription to occur but these may respond quicker to additional cell stimuli [19]. The removal of the acetyl groups from the histones is carried out by histone deacetylase (HDAC) enzymes known as epigenetic erasers. The regulation of DNA structure is therefore tightly regulated by the balance of HDAC and HAT activity [15]. There is a differential expression and activity of HATs and HDACs favouring gene induction in bronchial biopsies of asthmatic patients [22]. Peripheral blood cells from both adults [23] and children [24] also show enhanced HAT/HDAC ratios in more severe patients compared to control subjects. In children this difference is enhanced with increasing bronchial hyperresponsiveness [24]. However the simplistic view of HDAC enzymes only acting as gene repressors by targeting acetylated histones in order to modulate gene expression is not totally correct. Studies show that equal numbers of genes are suppressed by non-selective HDAC inhibitors as are enhanced [15] and HDAC enzymes are also associated with actively transcribed genes [13]. An expanding list of nonhistone proteins has been identified as substrates for HDACs including transcription factors and cytoplasmic signalling and structural proteins [15]. Indeed, phylogenetically HDACs existed prior to histones [25]. Consequently, the stability, localization, protein dimerization, and protein–protein interaction of these acetylated non-histone proteins can also be altered by targeting HDAC enzymes. Although in many cases the HATs involved in acetylating these non-histone proteins are known often the specific protein deacetylases that regulate the reverse process remain unclear [15]. Due the large number of non-histone proteins that are regulated by reversible acetylation the use of non-selective drugs to define a role for epigenetic effects in cellular function is not definitive evidence for a role of histone acetylation and additional experiments need to be performed. The need for better tools, both drugs and antibodies, to examine specific histone acetylation and deacetylation events by selective enzymes is essential. 4. MicroRNA Another level of epigenetic control of gene expression is coordinated by microRNAs (miRNA), which are small non-coding, single stranded RNA molecules, of 19–25 nucleotides in length [26]. miRNAs have been identified in many organisms, including plants, Drosophila, rats, mice, and humans, where they have been shown to control major cellular processes, including metabolism, apoptosis, differentiation and development and the immune system. The miRNAs are able to bind to complimentary sequences in the 3′-untranslated region of target gene mRNAs [26]. Once bound to the 3′-UTR the miRNA can prevent the mRNA from interacting with the cells translational mechanisms or target the mRNA for degradation or both. There are many examples of miRNAs that play a role in inflammation and allergy in humans. The role of miRNA in the immune response is being elucidated using micro-array based approaches to identify miRNA genes with altered expression in allergic airways [27]. Additionally miRNAs can target other epigenetic changes [26]. Epigenetic regulation through miRNA is thought to occur by targeting DNA methylation and histone modifications [26]. RNAdirected DNA methylation (RdDM) was first discovered in plants [28], and has been shown to play a role along with histone acetylation and H3K9 methylation [26]. Ongoing asthmatic inflammation of the airways may be driven by alterations in the expression profile of regulatory microRNA genes [29] despite the fact that initial biopsy studies using a limited array of miRNAs failed to demonstrate either disease or treatment-specific differences [30]. This may reflect the fact that different cell types have a highly specific miRNA profile and this may vary in biopsies [30,31] or

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changes may only occur in more severe disease. Recent bioinformatic approaches that differentiate the role of distinct cellular subsets in complex cell mixtures may allow better resolution of differences [32]. Using single cell types Foster and colleagues [33] delineated a key role for miR-126 in murine allergic airways hyper-responsiveness. House dust mite activation of TLR4 leads to an ‘asthma-like’ phenotype in mice involving type 2 T helper (TH2) and eosinophil recruitment to the airways, inflammation, airways hyperresponsiveness and mucus hypersecretion which is blocked by inhibition of miR-126 and subsequently GATA3 expression. GATA3 is important for the Th2mediated human asthmatic response [34]. This data suggests that miR-126 may make a good target for future drug development. In human bronchial ASM IL-13 exposure results in a reduction in miRNA-133a expression which was also seen in a murine model where loss of miR-133a was associated with increased AHR via modulation of Rho-kinase [35]. IL-13 can up-regulate miR-21 expression and in a number of mouse models of allergic airway inflammation miR-21 expression is enhanced and can regulate Th cell polarization by controlling IL-12p35 mRNA expression [27]. In contrast, the mouse microRNA-ome, particularly that of the let-7 family, changed dramatically following allergen challenge and, furthermore, inhibition of let-7 miRNAs in vivo markedly inhibited the production of allergic cytokines and the disease phenotype [36]. Finally, miR-26a has been implicated in ASM hypertrophy induced by stretch via targeting of glycogen synthase kinase-3β (GSK-3β), an anti-hypertrophic protein [37]. 5. Epigenetic regulation of the immune response Allergy, including asthma, is an IgE-mediated type I hypersensitivity reaction [38]. Type 1 hypersensitivity is induced by specific antigens called allergens resulting in B cell maturation, antibody induction and the production of memory B cells [39]. The difference between type 1 hypersensitivity and the normal humoural immune response is the production of IgE (normally produced in response to parasitic infection), as opposed to IgM and IgG, in response to the activation of allergen specific TH2 cells [39,40]. IgE binds with high affinity to the Fc receptors on granulocytes, which become sensitized [41,42]. Subsequent exposure of the allergen to sensitized cells results in the cross-linking of the IgE on the cells surface [42]. This triggers the release of inflammatory mediators and, in the case of asthma bronchoconstrictor agents, such as histamines, leukotrines and prostaglandins into the surrounding tissues [42]. The differentiation of naïve CD4+ T lymphocytes into the TH2 lineage is an important part of the development of asthma [43]. TH2 cells drive a B cell response to antigens, leading to antibody production. Initially when naïve CD4+ T lymphocytes, termed TH0, encounter an allergen they are capable of differentiating into either the TH1 or TH2 lineage, which depends on numerous factors, including the antigen presenting cells, the cytokines and chemokines present and amount of antigen [43]. Part of the differentiation pathway chosen is dependent on the epigenetics of the cell. In naïve CD4+ cells, the CpGs in the promoter regions are methylated in both the IL-4 and IFN-γ genes [44], which are the key cytokines involved in T-cell lineage. Stimulation of CD4+ T lymphocytes by allergen challenge increases demethylation at the IL-4 locus and importantly in sensitized hosts the extent of the loss of methylation correlates with IL-4 expression [44]. Additionally there is evidence that suggests that HDACs maintain pre-established TH1-like and TH2-like immunity in human T-cells [45]. Phytohemagglutinin (PHA) activation selectively stimulates antigendriven CD45RO(+) memory T cells, eliciting recall cytokine responses [45]. The HDAC inhibitor TSA provoked total cell hyperacetylation and led to increased TH2-associated IL-13 and IL-5 cytokine expression and reduced T H 1-associated IFNγ and IP10-associated recall responses. In addition, IL-2 and IL-10 production was also reduced. TSA treatment shifted the TH1:TH2 ratio 3- to 8-fold, skewing the recall responses more towards a TH2 -like phenotype, independent of

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the stimulus used and highlighting the role of HDACs in the development and maintenance of TH1:TH2 immunity [45]. The inflammation in general is associated with activation of a number of key signalling pathways particularly that of nuclear factor kappaB (NF-κB) which is activated in all types of asthma particularly in severe asthma [46,47]. As with all inflammatory gene expression, binding of NF-κB to inflammatory gene promoters and induction of inflammatory mediators involves changes in the epigenetic profile which occurs in a regulated temporal manner [48,49]. Most data has focussed on changes in histone acetylation and increases in H3K4 methylation but there has been increasing reports that a loss of the repressive H3K9 methylation mark is important [49,50] and this is likely to be true of other repressive marks such as H3K27Me3. Changes in histone acetylation are important in the induction of numerous pro-inflammatory genes in human lung epithelial and smooth muscle cells [15]. In human airway smooth muscle (HASM) cells TNFα-stimulated eotaxin release is associated with NF-κB binding and histone H4 acetylation of the eotaxin gene promoter region [51]. In contrast, IFNγ is able to markedly inhibit TNFα-induced expression of the NF-κB-sensitive genes IL-6, IL-8, and eotaxin [52]. IFNγ decreased TNFα-induced p65-associated HAT activity and increased total nuclear HDAC activity. Importantly, the HDAC inhibitor TSA prevented the inhibitory effect of IFNγ on TNFαinduced gene expression. Therefore, inhibition of TNFα-induced cytokine and chemokine expression by IFNγ is mediated through HDAC activity and/or expression in HASM cells [52]. Overall, inflammatory stimuli including environmental agents, viral infection, and allergen exposure can lead to enhanced inflammatory gene expression and TH2 skewing as a result of changes in histone acetylation status. Enhanced histone acetylation is in turn associated with inflammation while reduced acetylation is associated with decreased inflammation. 6. Epigenetics and the inheritance of asthma Asthma has an important heritable component which is not simply associated with DNA sequence polymorphisms [2,3]. It is thought that the heritable component of asthma may be, at least partially, explained by epigenetics [53]. Epigenetics changes have been shown to be inherited transgenerationally, especially DNA methylation which is inherited by a process called imprinting [8]. Interestingly imprinting can lead to altered inheritance of gene expression depending on which parent the gene is inherited from, regardless of DNA sequence. Studies have shown that maternal inheritance may be more important for the development of asthma than paternal inheritance [54]. However, an argument could be made for a role of paternal obesity in asthma associated with obesity in offspring since the propensity for being overweight is paternally driven via an epigenetic process [55]. In children less than 5 years of age the risk associated with maternal asthma was more than three times greater than the risk associated with paternal asthma [56]. Childhood atopy was also strongly linked with maternal asthma in a New Zealand cohort and with hayfever in both parents [57]. Studies into the mechanisms of maternal inheritance have revealed several candidate genes. For example polymorphisms in FcεRI-β (the β-chain of the high-affinity receptor for IgE) showed stronger associations with positive skin prick tests and greater allergen specific IgE levels when inherited from the mother [54,58–60]. Another example of maternal inheritance is HLA-G, which is a novel human leukocyte antigen (HLA) gene [61] expressed predominantly at the maternal–neonatal interface and is involved in immuno-modulation, downregulating NK and T cells [61]. HLA-G has been linked to asthma [62] and the HLA-G allele was overexpressed in children with bronchial hyper-responsiveness if the mother was also affected by bronchial hyper-responsiveness [62]. The exact mechanism underlying maternal inheritance in asthma is yet to

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be established; however, it has been suggested that this difference in gene expression from each parent may be due to allelic imprinting or other epigenetic mechanisms. 7. Environmental factors altering the epigenetic profile Epigenetic changes do not alter the underlying genetic code of the person but affect a cell's transcriptional programme in response to environmental challenge and, importantly, are reversible throughout a person's life [63]. This is exemplified by the epigenetic differences reported with age in monozygous twins exposed to different environmental stresses [64,65]. Environmental exposure in utero has been proposed as an important driver of gene programming that determines subsequent physiological changes in adult life [66]. Alteration of this programming due to environment stress, including diet, may lead to greater risk of disease in later life [67]. The variable histories of asthma patients (i.e. development, incidence and remission) may also be the result of epigenetic changes due to environmental exposures [68]. Research has focused on the time when a person is most susceptible to the environmental exposures that trigger asthma and other allergies. These implicate prenatal development, early childhood and adolescence [69,70]. In asthma and other allergic diseases the alteration of the epigenetic profile is potentially very important particularly in utero when it may be associated with predisposition to childhood wheeze and subsequent disease. 8. Effect of diet on epigenetics and allergy There has been an increase in the levels of asthma worldwide especially in the developing world such as India and is associated with the uptake of Western lifestyles. Parts of India have shown a 50% increase in the incidence of asthma, although the more traditional communities have been the least effected [71]. Diet plays an important role in the development and maintenance of epigenetic profiles. To maintain normal DNA methylation patterns, several essential nutrients are required from the diet, including a source of methyl groups (e.g., methionine or choline) and folate. Altered folic acid (vitamin B9) levels in murine maternal diet have been shown to alter the methylation status and expression of genes associated with allergy in mice [72]. Hollingsworth et al. demonstrated that increasing the levels of methyl donors in the diet of female mice increased the levels of allergic airway disease in their offspring [72]. The change in diet altered methylation at specific CpG motifs and thus altered the expression of key genes that regulate the development of an adaptive immune response, increasing TH2 immunity, lung eosinophilia and airway remodelling and enhancing the heritable risk of developing allergic airway disease. The maternal dietary intake of methyl donors enhanced the severity of allergic airway disease in offspring of the mice and that this trait is inherited transgenerationally [72]. In addition, it is becoming evident that perinatal differences extend beyond the basic Th1/Th2 effector paradigm and that there are differences in regulatory and Il-17-associated T-cells [12]. In adults these are controlled at the epigenetic level and this is probably also the case in response to environmental or dietary stimuli [73]. However, the risk/benefits of folic acid in the diet in man require further analysis, although increasing folic acid levels may have a protective effect in counteracting the asthma-risk enhancing effects of air pollution on DNA methylation [74]. 9. Effect of smoking on epigenetics and asthma There is a large body of evidence that prenatal exposure to environmental tobacco smoke (ETS) is associated with impaired respiratory function and increased risk of transient wheeze or asthma [75–77]. Maternal smoking in last trimester is correlated with asthma by

1 year of age [57] and this is associated with changes in global and gene specific DNA methylation patterns [78]. However, as with many studies in this area a true cause and effect has not been defined. Furthermore, ETS has also been linked to the development of adult asthma [79]. Smoking is thought to alter DNA methylation oxidative stress [80] which can cause lesions in the DNA (formation of 8-OH-dG for example) that interfere with the binding of DNA methyltransferases, preventing their binding to and methylating DNA resulting in hypomethylation [80]. Recent evidence has emerged indicating that prolonged chronic exposure of airway epithelial cells to cigarette smoke media induced a concentration- and time-dependent modification of a number of epigenetic tags including reduction in H4K16Ac and H4K20Me3 and increasing H3K27Me3. There was also an alteration in the methylation status of a number of repetitive DNA sequences and specific gene promoters which was linked to changes in Dnmt1 and Dnmt3b expression [81]. Pre-natal cigarette smoking may also affect subsequent responsiveness to steroid therapy in asthmatics [82]. Thus, in data from the Childhood Asthma Management Programme (CAMP), asthmatic children who were exposed to cigarette smoke in utero had a 26% less improvement in airway hyper-responsiveness to budesonide compared to unexposed subjects [82]. Cigarette smoke reduces the expression and activity of a key glucocorticoid receptor (GR) co-repressor HDAC2 both at the protein and mRNA level and it is tempting to speculate that in utero exposure to smoke may affect the epigenetic profile of the HDAC2 promoter and/or that of other GR-co-factors such as Suv39H1 or other methylases [83], thereby repressing their endogenous expression which may account for the altered HAT/HDAC ratio seen in adult asthmatics [84] and children with asthma [24]. Other mechanisms for a lack of GR action may include repression of HDAC2 activity via a PI3K-mediated phosphorylation [85] or nitration event [86] or competition for the GR-associated HAT GR-interacting protein GRIP with inflammatory, particularly IFNγ-stimulated, responses in macrophages [87]. Some specific gene and tobacco smoke interactions underlying asthma have been identified. Specific short nucleotide polymorphisms (SNP) in the CD14 gene combined with ETS result in significantly altered levels of IgE production [88]. Furthermore, children lacking the glutathione S-transferase M1 (GSTM1) enzyme (involved in the detoxification of tobacco smoke and reactive oxygen species [ROS]) were more susceptible to the effects of environmental tobacco smoke exposure in utero [89,90], a pattern which has also been shown with glutathione S-transferase T1 (GSTT1) [90]. Importantly the same group has recently demonstrated that the methylation status of the DNA repetitive element LINE1 was observed in in utero tobacco smoke exposed children with the common GSTM1 null genotype. In addition, the associations with maternal smoking varied by a common GSTP1 haplotype, thus indicating that variants in detoxification genes may modulate the effects of in utero exposure through epigenetic mechanisms. In contrast, other epidemiological studies have not reported a direct effect of smoking on global DNA methylation, although the association between global methylation patterns in fathers and their offspring was lost if the offspring ever smoked [91]. Importantly, these alterations to the epigenetic profile are heritable and may even cross to the F2 generation in both animal models [72] and in man [78]. Indeed, a child whose grandmother smoked has double the chance of developing asthma than one whose grandmother did not [92] and this risk is further increased by maternal smoking during pregnancy [92]. 10. Effect of air pollution on epigenetics of asthma Exposure to air pollution has long been associated with asthma and other lung diseases [93,94]. Air pollution, such as from traffic or industry, consists of both gaseous, such as benzene, and particulate matter, including diesel exhaust particulate matter (DEP), which due to their small size can be inhaled deeply into the airways. The effects of traffic pollution on public health have been extensively studied and

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ambient level of black carbon particles, used as a tracer for traffic pollution, has been consistently associated with a variety of adverse health outcomes [95]. The role of air pollution in respiratory diseases is of great interest, and although the role of pollutants in causing asthma exacerbations has been demonstrated, the role air pollution plays in the cause of asthma is less well defined [96,97]. Pollutants such as ozone have been shown to directly damage the airways [98]. In addition to causing direct damage to the airways, air pollution has been linked to epigenetic changes in the lung. For example, as with smoking, air pollution can result in oxidative stress, leading to DNA lesions and hypomethylation [80,99]. Furthermore, pollution decreases methylation across the genome which was associated with oxidative stress [95]. Benzene, toluene, xylene and other volatile organic compounds (VOC) are associated with an increased asthma risk [100]. Childhood exposure to benzene is associated with an eight-fold increase in asthma risk [100]. In addition, exposure to benzene has been associated with altered DNA methylation [101,102]. Small particulate matter (b10 μm) can be inhaled deeply into the lungs. In utero exposure to particulate pollutants such as polycyclic aromatic hydrocarbons (PAHs) was linked to asthma status in a New York city cohort [103]. Particulate matter has been shown to alter the DNA methylation in both in vitro [104] and in vivo models [105]. Pollutants such as DEP can increase levels of ROS, which can in turn lead to increase pro-inflammatory cytokines, through redox sensitive transcription factors such as NF-κB and MAP kinase pathways [106]. Particulate matter from the steel industry exposure was associated with demethylation of nitric oxide synthetase (NOS)2 promoter DNA and increased NOS2 gene transcription [107]. Importantly, exhaled NO is raised in asthma particularly in more severe disease and has been considered a marker of airway inflammation in asthma and even to play a role in asthma pathogenesis [108]. DEP induces pulmonary inflammation and exacerbates asthma in vivo and is a potent inducer of inflammatory responses in human airway epithelial cells [109]. DEP induces the expression of cyclooxygenase-2 (COX-2) in BEAS-2B cells at both the transcriptional and protein levels. The induction of COX-2 gene expression is associated with p300-mediated induction of histone H4 acetylation at the native COX-2 promoter start site. DEP also caused the degradation of HDAC1 and selective knockdown of HDAC1 using siRNA and overexpression of HDAC1 confirmed a role for HDAC1 in regulating DEP-induced COX2 transcription [109]. Changes in CpG methylation in mice have been associated with TH2 polarization. When the mice were exposed to a combination of DEP and the fungus Aspergillus fumigatus the combination altered the DNA methylation status of the IL-4 and IFNγ promoters. The IL-4 promoter was hypomethylated and the IFNγ promoter was hypermethylated and these changes corresponded to increased IgE production [110]. Air pollution can therefore alter the epigenetic state of the genome and may play an important role in the regulation of asthma associated genes.

11. Conclusion There are a diverse number of epigenetic mechanisms which are involved in the regulation of gene expression, generally silencing gene expression by preventing interactions of DNA binding proteins with the DNA sequence. Although these do not alter the DNA sequence the changes in DNA structure can be inherited across generations. Epigenetic mechanisms help to explain many of the characteristics of asthma development and inheritance including maternal inheritance and how environmental impacts can alter the immune response, leading to inappropriate signalling and allergy. However, the proof that these epigenetic changes are causal of disease in man is still awaited. The need to examine potentially reversible changes in

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individual cell types in a temporal manner where there is cross-talk between the epigenetic marks makes this a highly challenging task. It is hoped that the combination of in vitro, in vivo animal model and cohort driven human environmental, epidemiological and interventional studies will be able to further our understanding of epigenetics as an underlying cause or driver of asthma. The various roles of airborne pollutants such as diesel particles and tobacco smoke as well as the role of parental and grand-parental diet along with genetic predisposition all need to be elucidated.

Acknowledgements Work in our labs is supported by the MRC (UK), the Wellcome Trust, European Union Innovative Medicines Initiative (IMI) and the Royal Brompton Hospital Biomedical Research Unit. I.M.A. is a member of the MRC/Asthma UK Centre in Allergic Mechanisms in Asthma and Allergy and the Wellcome Trust Centre for Respiratory Infections (CRI).

References [1] World Health Organization. The world health report 2004 - changing history. http://www.who.int/entity/whr/2004/annex/topic/en/annex_2_en.pdf. 2004. [2] W.O.C. Cookson, M.F. Moffatt, Genetics of asthma and allergic disease, Hum. Mol. Genet. 9 (2000) 2359–2364. [3] L.J. Palmer, P.R. Burton, A.W. Musk, W.O. Cookson, Familial aggregation and heritability of asthma-associated quantitative traits in a population-based sample of nuclear families, Eur. J. Hum. Genet. 8 (2000) 853–860. [4] M.F. Moffatt, I.G. Gut, F. Demenais, D.P. Strachan, E. Bouzigon, S. Heath, E. von Mutius, M. Farrall, M. Lathrop, W.O.C.M. Cookson, A large-scale, consortiumbased genomewide association study of asthma, N. Engl. J. Med. 363 (2010) 1211–1221. [5] H. Lango Allen, K. Estrada, G. Lettre, S.I. Berndt, M.N. Weedon, F. Rivadeneira, C.J. Willer, A.U. Jackson, S. Vedantam, S. Raychaudhuri, T. Ferreira, A.R. Wood, R.J. Weyant, A.V. Segre, E.K. Speliotes, E. Wheeler, N. Soranzo, J.H. Park, J. Yang, D. Gudbjartsson, N.L. Heard-Costa, J.C. Randall, L. Qi, A. Vernon Smith, R. Magi, et al., Hundreds of variants clustered in genomic loci and biological pathways affect human height, Nature 467 (2010) 832–838. [6] D.A. Meyers, Genetics of asthma and allergy: what have we learned? J. Allergy Clin. Immunol. 126 (2010) 439–446. [7] C. Waddington, Canalization of development and the inheritance of acquired characters, Nature 150 (1942) 563–565. [8] B. Lewin. Genes IX. Sudbury MA: (2008). [9] J.S. Lee, E. Smith, A. Shilatifard, The language of histone crosstalk, Cell 142 (2010) 682–685. [10] P.J. Barnes, Targeting the epigenome in the treatment of asthma and chronic obstructive pulmonary disease, Proc. Am. Thorac. Soc. 6 (2009) 693–696. [11] S.O. Shaheen, I.M. Adcock, The developmental origins of asthma: does epigenetics hold the key? Am. J. Respir. Crit. Care Med. 180 (2009) 690–691. [12] S.L. Prescott, V. Clifton, Asthma and pregnancy: emerging evidence of epigenetic interactions in utero, Curr. Opin. Allergy Clin. Immunol. 9 (2009) 417–426. [13] I. Guilleret, P. Yan, F. Grange, R. Braunschweig, F.T. Bosman, J. Benhattar, Hypermethylation of the human telomerase catalytic subunit (hTERT) gene correlates with telomerase activity, Int. J. Cancer 101 (2002) 335–341. [14] S.C. Wu, Y. Zhang, Active DNA demethylation: many roads lead to Rome, Nat. Rev. Mol. Cell Biol. 11 (2010) 607–620. [15] I.M. Adcock, P.A. Ford, K. Ito, P.J. Barnes, Epigenetics and airways disease, Respir. Res. 7 (2006) 21. [16] R.A. Irizarry, C. Ladd-Acosta, B. Wen, Z. Wu, C. Montano, P. Onyango, H. Cui, K. Gabo, M. Rongione, M. Webster, H. Ji, J.B. Potash, S. Sabunciyan, A.P. Feinberg, The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores, Nat. Genet. 41 (2009) 178–186. [17] P. Bhavsar, T. Ahmad, I.M. Adcock, The role of histone deacetylases in asthma and allergic diseases, J. Allergy Clin. Immunol. 121 (2008) 580–584. [18] Z. Wang, C. Zang, J.A. Rosenfeld, D.E. Schones, A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, W. Peng, M.Q. Zhang, K. Zhao, Combinatorial patterns of histone acetylations and methylations in the human genome, Nat. Genet. 40 (2008) 897–903. [19] Z. Wang, C. Zang, K. Cui, D.E. Schones, A. Barski, W. Peng, K. Zhao, Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes, Cell 138 (2009) 1019–1031. [20] T.Y. Roh, S. Cuddapah, K. Cui, K. Zhao, The genomic landscape of histone modifications in human T cells, Proc. Natl Acad. Sci. 103 (2006) 15782–15787. [21] N.D. Heintzman, G.C. Hon, R.D. Hawkins, P. Kheradpour, A. Stark, L.F. Harp, Z. Ye, L.K. Lee, R.K. Stuart, C.W. Ching, K.A. Ching, J.E. Antosiewicz-Bourget, H. Liu, X. Zhang, R.D. Green, V.V. Lobanenkov, R. Stewart, J.A. Thomson, G.E. Crawford, M. Kellis, B. Ren, Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature 459 (2009) 108–112.

1108

A.L. Durham et al. / Biochimica et Biophysica Acta 1810 (2011) 1103–1109

[22] K. Ito, G. Caramori, S. Lim, T. Oates, K.F. Chung, P.J. Barnes, I.M. Adcock, Expression and activity of histone deacetylases in human asthmatic airways, Am. J. Respir. Crit. Care Med. 166 (2002) 392–396. [23] M. Hew, P. Bhavsar, A. Torrego, S. Meah, N. Khorasani, P.J. Barnes, I. Adcock, K.F. Chung, for the National Heart Lung and Blood Institute's Severe Asthma Research Program, Relative corticosteroid insensitivity of peripheral blood mononuclear cells in severe asthma, Am. J. Respir. Crit. Care Med. 174 (2006) 134–141. [24] R.C. Su, A.B. Becker, A.L. Kozyrskyj, K.T. HayGlass, Altered epigenetic regulation and increasing severity of bronchial hyperresponsiveness in atopic asthmatic children, J. Allergy Clin. Immunol. 124 (2009) 1116–1118. [25] W.S. Xu, R.B. Parmigiani, P.A. Marks, Histone deacetylase inhibitors: molecular mechanisms of action, Oncogene 26 (2007) 5541–5552. [26] E.J. Finnegan, M.A. Matzke, The small RNA world, J. Cell Sci. 116 (2003) 4689–4693. [27] T.X. Lu, A. Munitz, M.E. Rothenberg, MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression, J. Immunol. 182 (2009) 4994–5002. [28] M. Wassenegger, S. Heimes, L. Riedel, H.L. Sanger, RNA-directed de novo methylation of genomic sequences in plants, Cell 76 (1994) 567–576. [29] R. Kumar, M. Hitchins, P. Foster, Epigenetic changes in childhood asthma, Dis. Model Mech. 2 (2009) 549–553. [30] A.E. Williams, H. Larner-Svensson, M.M. Perry, G.A. Campbell, S.E. Herrick, I.M. Adcock, J.S. Erjefalt, K.F. Chung, M.A. Lindsay, MicroRNA expression profiling in mild asthmatic human airways and effect of corticosteroid therapy, PLoS ONE 4 (2009) e5889. [31] F. Schembri, S. Sridhar, C. Perdomo, A.M. Gustafson, X. Zhang, A. Ergun, J. Lu, G. Liu, X. Zhang, J. Bowers, C. Vaziri, K. Ott, K. Sensinger, J.J. Collins, J.S. Brody, R. Getts, M.E. Lenburg, A. Spira, MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium, Proc. Natl Acad. Sci. 106 (2009) 2319–2324. [32] S.S. Shen-Orr, R. Tibshirani, P. Khatri, D.L. Bodian, F. Staedtler, N.M. Perry, T. Hastie, M.M. Sarwal, M.M. Davis, A.J. Butte, Cell type-specific gene expression differences in complex tissues, Nat. Meth. 7 (2010) 287–289. [33] J. Mattes, A. Collison, M. Plank, S. Phipps, P.S. Foster, Antagonism of microRNA126 suppresses the effector function of TH2 cells and the development of allergic airways disease, Proc. Natl Acad. Sci. 106 (2009) 18704–18709. [34] G. Caramori, S. Lim, K. Ito, K. Tomita, T. Oates, E. Jazrawi, K.F. Chung, P.J. Barnes, I.M. Adcock, Expression of GATA family of transcription factors in T-cells, monocytes and bronchial biopsies, Eur. Respir. J. 18 (2001) 466–473. [35] Y. Chiba, K. Matsusue, M. Misawa, RhoA, a possible target for treatment of airway hyperresponsiveness in bronchial asthma, J. Pharmacol. Sci. (2010 Oct 8)8 [Epub ahead of print]. [36] S. Polikepahad, J.M. Knight, A.O. Naghavi, T. Oplt, C.J. Creighton, C. Shaw, A.L. Benham, J. Kim, B. Soibam, R.A. Harris, C. Coarfa, A. Zariff, A. Milosavljevic, L.M. Batts, F. Kheradmand, P.H. Gunaratne, D.B. Corry, Proinflammatory role for let-7 microRNAS in experimental asthma, J. Biol. Chem. 285 (2010) 30139–30149. [37] J.S. Mohamed, M.A. Lopez, A.M. Boriek, Mechanical stretch up-regulates microRNA-26a and induces human airway smooth muscle hypertrophy by suppressing glycogen synthase kinase-3β, J. Biol. Chem. 285 (2010) 29336–29347. [38] D. Dombrowicz, A.T. Brini, V. Flamnd, E. Hicks, J.K.N. Snouwaert, Anaphylaxis mediated through a humanized high affinity IgE receptor, J. Immunol. 157 (1996) 1645. [39] M. Akdis, Healthy immune response to allergens: T regulatory cells and more, Curr. Opin. Immunol. 18 (2006) 738–744. [40] H.J. Gould, B.J. Sutton, A.J. Beavil, R.L. Beavil, N. McCloskey, H.A. Coker, D. Fear, L. Smurthwaite, The biology of IgE and the basis of allergic disease, Annu. Rev. Immunol. 21 (2003) 579–628. [41] J.P.D. Cook, A.J. Henry, J.M. McDonnell, R.J. Owens, B.J. Sutton, H.J. Gould, Identification of contact residues in the IgE binding site of human FcepsilonRIalpha, Biochemistry 36 (1997) 15579–15588. [42] D.D. Metcalfe, D. Baram, Y.A. Mekori, Mast cells, Physiol. Rev. 77 (1997) 1033–1079. [43] T.J. Kindt, R.A. Goldsby, B.A. Osborne, Kuby Immunology, 6th edFreeman and Company, New York, NY, 2007. [44] N.H. Kwon, J.S. Kim, J.Y. Lee, M.J. Oh, D.C. Choi, DNA methylation and the expression of IL-4 and IFN-γ promoter genes in patients with bronchial asthma, J. Clin. Immunol. 28 (2008) 139–146. [45] R.C. Su, A.B. Becker, A.L. Kozyrskyj, K.T. HayGlass, Epigenetic regulation of established human type 1 versus type 2 cytokine responses, J. Allergy Clin. Immunol. 121 (2008) 57–63. [46] I.M. Adcock, K.F. Chung, G. Caramori, K. Ito, Kinase inhibitors and airway inflammation, Eur. J. Pharmacol. 533 (2006) 118–132. [47] G. Caramori, T. Oates, A.G. Nicholson, P. Casolari, K. Ito, P.J. Barnes, A. Papi, I.M. Adcock, K.F. Chung, Activation of NF-κB transcription factor in asthma death, Histopathology 54 (2009) 507–509. [48] B. Li, M. Carey, J.L. Workman, The role of chromatin during transcription, Cell 128 (2007) 707–719. [49] K.Y. Lee, K. Ito, R. Hayashi, E.P. Jazrawi, P.J. Barnes, I.M. Adcock, NF-κB and activator protein 1 response elements and the role of histone modifications in IL-1β-induced TGF-β1 gene transcription, J. Immunol. 176 (2006) 603–615. [50] D. van Essen, Y. Zhu, S. Saccani, A feed-forward circuit controlling inducible NF-κB target gene activation by promoter histone demethylation, Mol. Cell 39 (2010) 750–760. [51] M. Nie, A.J. Knox, L. Pang, β2-Adrenoceptor agonists, like glucocorticoids, repress eotaxin gene transcription by selective inhibition of histone H4 acetylation, J. Immunol. 175 (2005) 478–486.

[52] S. Keslacy, O. Tliba, H. Baidouri, Y. Amrani, Inhibition of tumor necrosis factor-αinducible inflammatory genes by interferon-γ is associated with altered nuclear factor-κB transactivation and enhanced histone deacetylase activity, Mol. Pharmacol. 71 (2007) 609–618. [53] J. Bousquet, W. Jacot, H. Yssel, A.M. Vignola, M. Humbert, Epigenetic inheritance of fetal genes in allergic asthma, Allergy 59 (2004) 138–147. [54] W. Cookson, R. Young, A. Sandford, M. Moffatt, T. Shirakawa, P. Sharp, J. Faux, C. Julier, Y. Nakumuura, et al., Maternal inheritance of atopic IgE responsiveness on chromosome 11q, Lancet 340 (1992) 381–384. [55] S.F. Ng, R.C.Y. Lin, D.R. Laybutt, R. Barres, J.A. Owens, M.J. Morris, Chronic high-fat diet in fathers programs [bgr]-cell dysfunction in female rat offspring, Nature 467 (7318) (2010 October 21) 963–966. [56] A.A. Litonjua, V.J. Carey, H.A. Burge, S.T. Weiss, D.R. Gold, Parental history and the risk for childhood asthma. does mother confer more risk than father? Am. J. Respir. Crit. Care Med. 158 (1998) 176–181. [57] M.R. Sears, M.D. Holdaway, E.M. Flannery, G.P. Herbison, P.A. Silva, Parental and neonatal risk factors for atopy, airway hyper-responsiveness, and asthma, Arch. Dis. Child. 75 (1996) 392–398. [58] R.G.G. Ruiz, D.M. Kemeny, J.F. Price, Higher risk of infantile atopic dermatitis from maternal atopy than from paternal atopy, Clin. Exp. Allergy 22 (2009) 762–766. [59] S. Dold, M. Wjst, E. von Mutius, P. Reitmeir, E. Stiepel, Genetic risk for asthma, allergic rhinitis, and atopic dermatitis, Arch. Dis. Child. 67 (1992) 1018–1022. [60] J.A. Traherne, M.R. Hill, P. Hysi, M. D'Amato, J. Broxholme, R. Mott, M.F. Moffatt, W.O.C.M. Cookson, LD mapping of maternally and non-maternally derived alleles and atopy in FcεRI-β, Hum. Mol. Genet. 12 (2003) 2577–2585. [61] H. Lin, T.R. Mosmann, L. Guilbert, S. Tuntipopipat, T.G. Wegmann, Synthesis of T helper 2-type cytokines at the maternal-fetal interface, J. Immunol. 151 (1993) 4562–4573. [62] D. Nicolae, N.J. Cox, L.A. Lester, D. Schneider, Z. Tan, C. Billstrand, S. Kuldanek, J. Donfack, P. Kogut, N.M. Patel, J. Goodenbour, T. Howard, R. Wolf, G.H. Koppelman, S.R. White, R. Parry, D.S. Postma, D. Meyers, E.R. Bleecker, J.S. Hunt, J. Solway, C. Ober, Fine mapping and positional candidate studies identify HLA-G as an asthma susceptibility gene on chromosome 6p21, Am. J. Hum. Genet. 76 (2005) 349–357. [63] V. Bollati, J. Schwartz, R. Wright, A. Litonjua, L. Tarantini, H. Suh, D. Sparrow, P. Vokonas, A. Baccarelli, Decline in genomic DNA methylation through aging in a cohort of elderly subjects, Mech. Ageing Dev. 130 (2009) 234–239. [64] P. Poulsen, M. Esteller, A. Vaag, M. Fraga, The epigenetic basis of twin discordance in age-related diseases, Pediatr. Res. 61 (2007) 38R–42R. [65] B.M. Javierre, A.F. Fernandez, J. Richter, F. Al-Shahrour, J.I. Martin-Subero, J. Rodriguez-Ubreva, M. Berdasco, M.F. Fraga, T.P. O'Hanlon, L.G. Rider, F.V. Jacinto, F.J. Lopez-Longo, J. Dopazo, M. Forn, M.A. Peinado, L. Carreño, A.H. Sawalha, J.B. Harley, R. Siebert, M. Esteller, F.W. Miller, E. Ballestar, Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus, Genome Res. 20 (2010) 170–179. [66] D.J.P. Barker, C.N. Hales, C.H.D. Fall, C. Osmond, K. Phipps, P.M.S. Clark, Type 2 (non-insulin-dependent) diabetes mellitus, hypertension and hyperlipidaemia (syndrome X): relation to reduced fetal growth, Diabetologia 36 (1992) 62–67. [67] C.N. Hales, M. Desai, S.E. Ozannes, The thrifty phenotype hypothesis: how does it look after 5 years? Diabet. Med. 14 (2009) 189–195. [68] J.S. Kuriakose, R.L. Miller, Environmental epigenetics and allergic diseases: recent advances, Clin. Exp. Allergy 40 (2010) 1602–1610. [69] F.D. Gilliland, K. Berhane, Y.F. Li, E.B. Rappaport, J.M. Peters, Effects of early onset asthma and in utero exposure to maternal smoking on childhood lung function, Am. J. Respir. Crit. Care Med. 167 (2003) 917–924. [70] P.J. Mandhane, J.M. Greene, J.O. Cowan, D.R. Taylor, M.R. Sears, Sex differences in factors associated with childhood- and adolescent-onset wheeze, Am. J. Respir. Crit. Care Med. 172 (2005) 45–54. [71] P.K. Vedanthan, P.A. Mahesh, R. Vedanthan, A.D. Holla, A.H. Liu, Effect of animal contact and microbial exposures on the prevalence of atopy and asthma in urban vs rural children in India, Ann. Allergy Asthma Immunol. 96 (2006) 571–578. [72] J.W. Hollingsworth, S. Maruoka, K. Boon, S. Garantziotis, Z. Li, J. Tomfohr, N. Bailey, E.N. Potts, G. Whitehead, D.M. Brass, D.A. Schwartz, In utero supplementation with methyl donors enhances allergic airway disease in mice, J. Clin. Invest. 118 (2009) 3462–3469. [73] K.M. Murphy, B. Stockinger, Effector T cell plasticity: flexibility in the face of changing circumstances, Nat. Immunol. 11 (2010) 674–680. [74] A. Baccarelli, P.A. Cassano, A. Litonjua, S.K. Park, H. Suh, D. Sparrow, P. Vokonas, J. Schwartz, Cardiac autonomic dysfunction: effects from particulate air pollution and protection by dietary methyl nutrients and metabolic polymorphisms, Circulation 117 (2008) 1802–1809. [75] L.L. Magnusson, A.B. Olesen, H. Wennborg, J. Olsen, Wheezing, asthma, hayfever, and atopic eczema in childhood following exposure to tobacco smoke in fetal life, Clin. Exp. Allergy 35 (2005) 1550–1556. [76] Y.-F. Li, F. Gilliland, K. Berhane, R.W. McConnell, J. Gauderman, E.B. Rappaport, J. Peters, Effects of in utero and environmental tobacco smoke exposure on lung function in boys and girls with and without asthma, Am. J. Respir. Crit. Care Med. 162 (2000) 2097–2104. [77] C. Raherison, C. Pénard-Morand, D. Moreau, D. Caillaud, D. Charpin, C. Kopfersmitt, F. Lavaud, A. Taytard, I. Annesi-maesano, In utero and childhood exposure to parental tobacco smoke, and allergies in schoolchildren, Respir. Med. 101 (2007) 107–117. [78] C.V. Breton, H.M. Byun, M. Wenten, F. Pan, A. Yang, F.D. Gilliland, Prenatal tobacco smoke exposure affects global and gene-specific DNA methylation, Am. J. Respir. Crit. Care Med. 180 (2009) 462–467.

A.L. Durham et al. / Biochimica et Biophysica Acta 1810 (2011) 1103–1109 [79] R. Piipari, J.J.K. Jaakkola, N. Jaakkola, M.S. Jaakkola, Smoking and asthma in adults, Eur. Respir. J. 24 (2004) 734–739. [80] R. Franco, O. Schoneveld, A.G. Georgakilas, M.I. Panayiotidis, Oxidative stress, DNA methylation and carcinogenesis, Cancer Lett. 266 (2008) 6–11. [81] F. Liu, J.K. Killian, M. Yang, R.L. Walker, J.A. Hong, M. Zhang, S. Davis, Y. Zhang, M. Hussain, S. Xi, M. Rao, P.A. Meltzer, D.S. Schrump, Epigenomic alterations and gene expression profiles in respiratory epithelia exposed to cigarette smoke condensate, Oncogene 29 (2010) 3650–3664. [82] R.T. Cohen, B.A. Raby, K. Van Steen, A.L. Fuhlbrigge, J.C. Celedón, B.A. Rosner, R.C. Strunk, R.S. Zeiger, S.T. Weiss, In utero smoke exposure and impaired response to inhaled corticosteroids in children with asthma, J. Allergy Clin. Immunol. 126 (2010) 491–497. [83] K.N. Islam, C.R. Mendelson, Glucocorticoid/glucocorticoid receptor inhibition of surfactant protein-A (SP-A) gene expression in lung type II cells is mediated by repressive changes in histone modification at the SP-A promoter, Mol. Endocrinol. 22 (2008) 585–596. [84] K. Ito, S. Lim, G. Caramori, K.F. Chung, P.J. Barnes, I.M. Adcock, Cigarette smoking reduces histone deacetylase 2 expression, enhances cytokine expression, and inhibits glucocorticoid actions in alveolar macrophages, FASEB J. 15 (2001) 1110–1112. [85] J.A. Marwick, G. Caramori, C.S. Stevenson, P. Casolari, E. Jazrawi, P.J. Barnes, K. Ito, I.M. Adcock, P.A. Kirkham, A. Papi, Inhibition of PI3Kδ restores glucocorticoid function in smoking-induced airway inflammation in mice, Am. J. Respir. Crit. Care Med. 179 (2009) 542–548. [86] G.O. Osoata, S. Yamamura, M. Ito, C. Vuppusetty, I.M. Adcock, P.J. Barnes, K. Ito, Nitration of distinct tyrosine residues causes inactivation of histone deacetylase 2, Biochem. Biophys. Res. Commun. 384 (2009) 366–371. [87] J.R. Flammer, J. Dobrovolna, M.A. Kennedy, Y. Chinenov, C.K. Glass, L.B. Ivashkiv, I. Rogatsky, The type I interferon signaling pathway is a target for glucocorticoid inhibition, Mol. Cell. Biol. 30 (2010) 4564–4574. [88] S. Choudhry, P.C. Avila, S. Nazario, N. Ung, J. Kho, J.R. Rodriguez-Santana, J. Casal, H.J. Tsai, A. Torres, E. Ziv, M. Toscano, J.S. Sylvia, M. Alioto, M. Salazar, I. Gomez, J.K. Fagan, J. Salas, C. Lilly, H. Matallana, R.A. Castro, M. Selman, S.T. Weiss, J.G. Ford, J.M. Drazen, W. Rodriguez-Cintron, et al., CD14 tobacco gene-environment interaction modifies asthma severity and immunoglobulin E levels in latinos with asthma, Am. J. Respir. Crit. Care Med. 172 (2005) 173–182. [89] F.D. Gilliland, Y.F. Li, L. Dubeau, K. Berhane, E. Avol, R. McConnell, W.J. Gauderman, J.M. Peters, Effects of glutathione S-Transferase M1, maternal smoking during pregnancy, and environmental tobacco smoke on asthma and wheezing in children, Am. J. Respir. Crit. Care Med. 166 (2002) 457–463. [90] M. Kabesch, C. Hoefler, D. Carr, W. Leupold, S.K. Weiland, E. von Mutius, Glutathione S transferase deficiency and passive smoking increase childhood asthma, Thorax 59 (2004) 569–573. [91] T. Hillemacher, H. Frieling, S. Moskau, M.A.N. Muschler, A. Semmler, J. Kornhuber, T. Klockgether, S. Bleich, M. Linnebank, Global DNA methylation is influenced by smoking behaviour, Eur. Neuropsychopharmacol. 18 (2008) 295–298. [92] Y.-F. Li, B. Langholz, M.T. Salam, F.D. Gilliland, Maternal and grandmaternal smoking patterns are associated with early childhood asthma, Chest 127 (2005) 1232–1241. [93] M.I. Gilmour, M.S. Jaakkola, S.J. London, A.E. Nel, C.A. Rogers, How exposure to environmental tobacco smoke, outdoor air pollutants, and increased pollen burdens influences the incidence of asthma, Environ. Health Perspect. 114 (2006) 627–633.

1109

[94] J. McCreanor, P. Cullinan, M.J. Nieuwenhuijsen, J. Stewart-Evans, E. Malliarou, L. Jarup, R. Harrington, M. Svartengren, I.K. Han, P. Ohman-Strickland, K.F. Chung, J. Zhang, Respiratory effects of exposure to diesel traffic in persons with asthma, N. Engl. J. Med. 357 (2007) 2348–2358. [95] A. Baccarelli, R.O. Wright, V. Bollati, L. Tarantini, A.A. Litonjua, H.H. Suh, A. Zanobetti, D. Sparrow, P.S. Vokonas, J. Schwartz, Rapid DNA methylation changes after exposure to traffic particles, Am. J. Respir. Crit. Care Med. 179 (2009) 572–578. [96] S.J. London, Gene-air pollution interactions in asthma, Proc. Am. Thorac. Soc. 4 (2007) 217–220. [97] M.M. Patel, R.L. Miller, Air pollution and childhood asthma: recent advances and future directions, Curr. Opin. Pediatr. 21 (2009) 235–242. [98] Committee of the Environmental and Occupational Health Assembly of the American Thoracic Society, Health effects of outdoor air pollution, Am. J. Respir. Crit. Care Med. 153 (1996) 3–50. [99] V. Valinluck, H.H. Tsai, D.K. Rogstad, A. Burdzy, A. Bird, L.C. Sowers, Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2), Nucl. Acids Res. 32 (2004) 4100–4108. [100] L. Archivist, Archivist Some risk factors for asthma, Arch. Dis. Child Ed. Pract. 89 (2004) 78. [101] V. Bollati, A. Baccarelli, L. Hou, M. Bonzini, S. Fustinoni, D. Cavallo, H.M. Byun, J. Jiang, B. Marinelli, A.C. Pesatori, P.A. Bertazzi, A.S. Yang, Changes in DNA methylation patterns in subjects exposed to low-dose benzene, Cancer Res. 67 (2007) 876–880. [102] C.M. Ross, Epigenetics, traffic and firewood, Schizophr. Res. 109 (2009) 193. [103] F. Perera, W.Y. Tang, J. Herbstman, D. Tang, L. Levin, R. Miller, S.M. Ho, Relation of DNA methylation of 5′-CpG island of ACSL3 to transplacental exposure to airborne polycyclic aromatic hydrocarbons and childhood asthma, PLoS ONE 4 (2009) e4488. [104] M. Takiguchi, W.E. Achanzar, W. Qu, G. Li, M.P. Waalkes, Effects of cadmium on DNA-(Cytosine-5) methyltransferase activity and DNA methylation status during cadmium-induced cellular transformation, Exp. Cell Res. 286 (2003) 355–365. [105] S.A. Belinsky, S.S. Snow, K.J. Nikula, G.L. Finch, C.S. Tellez, W.A. Palmisano, Aberrant CpG island methylation of the p16INK4a and estrogen receptor genes in rat lung tumors induced by particulate carcinogens, Carcinogenesis 23 (2002) 335–339. [106] H. Takizawa, Diesel exhaust particles and their effect on induced cytokine expression in human bronchial epithelial cells, Curr. Opin. Allergy Clin. Immunol. 4 (2004) 355–359. [107] L. Tarantini, M. Bonzini, P. Apostoli, V. Pegoraro, V. Bollati, B. Marinelli, L. Cantone, G. Rizzo, L. Hou, J. Schwartz, P.A. Bertazzi, A. Baccarelli, Effects of particulate matter on genomic DNA methylation content and iNOS promoter methylation, Environ. Health Perspect. 117 (2009) 217–222. [108] S.A. Kharitonov, P.J. Barnes, Exhaled Biomark. Chest 130 (2006) 1541–1546. [109] D. Cao, P.A. Bromberg, J.M. Samet, COX-2 Expression induced by diesel particles involves chromatin modification and degradation of HDAC1, Am. J. Respir. Cell Mol. Biol. 37 (2007) 232–239. [110] J. Liu, M. Ballaney, U. Al-alem, C. Quan, X. Jin, F. Perera, L.C. Chen, R.L. Miller, Combined inhaled diesel exhaust particles and allergen exposure alter methylation of T helper genes and IgE production in vivo, Toxicol. Sci. 102 (2008) 76–81.