modifications and their role in of atopy and allergic diseases

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Citation Alaskhar Alhamwe, B., R. Khalaila, J. Wolf, V. von Bülow, H. Harb, F. Alhamdan, C. S. Hii, et al. 2018. “Histone modifications and their role in epigenetics of atopy and allergic diseases.” Allergy, Asthma, and Clinical Immunology : Official Journal of the Canadian Society of Allergy and Clinical Immunology 14 (1): 39. doi:10.1186/ s13223-018-0259-4. http://dx.doi.org/10.1186/s13223-018-0259-4.

Published Version doi:10.1186/s13223-018-0259-4

Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:37160091

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REVIEW Open Access Histone modifcations and their role in epigenetics of atopy and allergic diseases Bilal Alaskhar Alhamwe1,2†, Razi Khalaila1†, Johanna Wolf1†, Verena von Bülow1, Hani Harb1,2,6,8, Fahd Alhamdan1, Charles S. Hii3,4, Susan L. Prescott2,5, Antonio Ferrante2,3,4, Harald Renz1,2,6‡, Holger Garn1,6‡ and Daniel P. Potaczek1,2,6,7*‡

Abstract This review covers basic aspects of histone modifcation and the role of posttranslational histone modifcations in the development of allergic diseases, including the immune mechanisms underlying this development. Together with DNA , histone modifcations (including histone , methylation, , ubiquitina- tion, etc.) represent the classical epigenetic mechanisms. However, much less attention has been given to histone modifcations than to DNA methylation in the context of allergy. A systematic review of the literature was undertaken to provide an unbiased and comprehensive update on the involvement of histone modifcations in allergy and the mechanisms underlying this development. In addition to covering the growing interest in the contribution of histone modifcations in regulating the development of allergic diseases, this review summarizes some of the evidence sup- porting this contribution. There are at least two levels at which the role of histone modifcations is manifested. One is the regulation of cells that contribute to the allergic infammation (T cells and macrophages) and those that partici- pate in airway remodeling [(myo-) fbroblasts]. The other is the direct association between histone modifcations and allergic phenotypes. Inhibitors of histone-modifying may potentially be used as anti-allergic drugs. Further- more, epigenetic patterns may provide novel tools in the diagnosis of allergic disorders. Keywords: Allergy, Asthma, Atopy, Epigenetic (-s), Histone acetylation, Histone methylation, Histone modifcation (-s), Histone phosphorylation, Infammation, Immunity

Background phenomenon [5–9]. While DNA methylation has been In the last few decades, there has been a substantial extensively studied as the epigenetic mechanism involved increase in the prevalence of allergic diseases in the in the etiopathogenesis of allergic disorders, posttrans- industrialized countries [1–3]. Since this change could lational histone modifcations, another important clas- not be explained by a rather stable population genetic sical epigenetic mechanism, have not been as widely profle [2–4], increased exposure to harmful and reduced investigated and discussed because it is not considered exposure to protective epigenetically-mediated envi- as important as DNA methylation [5–7, 10]. Te review ronmental factors have been considered, at least in frstly describes the (bio-) chemical basics of epigenetic part, as a possible explanation for this epidemiological histone modifcations. Tis is followed by an assessment of recent evidence that supports a role for histone modif- cations in the epigenetic regulation of the pathogenesis of *Correspondence: [email protected]‑marburg.de allergy and related disorders, together with a description †Bilal Alaskhar Alhamwe, Razi Khalaila and Johanna Wolf contributed equally to this work as frst authors of the underlying cellular and molecular mechanisms. ‡Harald Renz, Holger Garn and Daniel P. Potaczek contributed equally to this work as senior authors Main text 1 Institute of Laboratory Medicine and Pathobiochemistry, Molecular Histone modifcations: the basics Diagnostics, Philipps University Marburg, Hans‑Meerwein‑Straße 3, 35043 Marburg, Germany Similarly to DNA methylation, posttranslational histone Full list of author information is available at the end of the article modifcations do not afect DNA nucleotide sequence but

© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat​iveco​mmons​.org/ publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Alaskhar Alhamwe et al. Allergy Asthma Clin Immunol (2018) 14:39 Page 2 of 16

can modify its availability to the transcriptional machin- summarizes the various forms of histone modifcations ery. Although histone modifcations play also other roles, appearing in this review along with their efects on gene such as histone phosphorylation, best known for its transcriptional activity. contribution to DNA repair in response to cell damage, this review deals primarily with general mechanisms of histone modifcations in the context of their role in epi- Histone acetylation genetic modulation of gene expression. Several types of Histone acetylation status is regulated by two groups of histone modifcations are known, amongst which acety- enzymes exerting opposite efects, histone acetyltrans- lation, methylation, phosphorylation, and ubiquitination ferases (HATs) and histone deacetylases (HDACs). HATs are the best studied and most important in terms of the catalyze the transfer of an from acetyl-CoA regulation of structure and (transcriptional) to an amino acid group of the target residues in activity [11–15]. In general, histone modifcations are the histone tails, which leads to the removal of a posi- catalyzed by specifc enzymes that act, predominantly, tive charge on the , weakening the interaction but not exclusively (e.g. some types of histone phospho- between histones and (negatively charged phosphate rylation), at the histone N-terminal tails involving amino groups of) DNA. Tis in turn typically makes the chro- acids such as lysine or arginine as well as serine, threo- matin less compact and thus more accessible to the tran- nine, tyrosine, etc. Histone acetylation usually leads to scriptional machinery. HDACs remove acetyl groups higher gene expression. Tis may not always be the case from histone tail lysine residues and thereby work as for histone H4 [16–18]. Histone methylation in turn has repressors of gene expression [5, 14, 21–24]. either transcriptionally permissive or repressive charac- HATs are classifed into fve (or sometimes six) fami- ter, depending on the location of targeted amino acid res- lies. Te GCN5-related N-acetyltransferase (GNAT) idues in the histone tail and/or the number of modifying family comprises KAT2A and KAT2B enzymes. Tey (e.g. methyl) groups added [5, 6, 14, 15, 19, 20]. Table 1 are involved in acetylation of histones and transcription

Table 1 List of histone modifcations appearing in this review along with their efects on the transcriptional activity Modifcation and site Abbreviation Efect on transcription­ a

Histone acetylation Histone 3 panacetylation H3ac Activating/permissive Histone 4 panacetylation H4ac Activating/permissiveb Histone 3 lysine 4 acetylation H3K4ac Activating/permissive Histone 3 lysine 9 acetylation Activating/permissive Histone 3 lysine 14 acetylation H3K14ac Activating/permissive Histone 3 lysine 18 acetylation H3K18ac Activating/permissive Histone 3 lysine 27 acetylation H3K27ac Activating/permissive Histone 4 lysine 16 acetylation H4K16ac Activating/permissive Histone methylation Histone 3 lysine 4 methylation H3K4me1 Activating/permissive Histone 3 lysine 4 dimethylation H3K4me2 Activating/permissive Histone 3 lysine 4 trimethylation H3K4me3 Activating/permissive Histone 3 lysine 9 dimethylation H3K9me2 Repressive Histone 3 lysine 9 trimethylation H3K9me3 Repressive Histone 3 lysine 27 trimethylation H3K27me3 Repressive Histone 3 lysine 36 trimethylation Activating/permissive Histone 3 lysine 79 methylation H3K79me1 Activating/permissive Histone phosphorylation Histone 3 serine 10 phosphorylation H3S10ph Activating/permissive Histone ubiquitination Histone 2A ubiquitination H2Aub Repressive Histone 2B ubiquitination H2Bub Activating/permissive a According to the cells signaling technology webpage [100] and/or other sources referenced in the “Main text” and/or Tables 2 and 3 of this review b See also “Histone modifcations: the basics” Alaskhar Alhamwe et al. Allergy Asthma Clin Immunol (2018) 14:39 Page 3 of 16 - promoter H3ac and H4ac levels were observed were H3ac and H4ac levels in the high promoter - expres and CXCL8 as IL-6 as well cell proliferation TGF-β-induced + that were constant across samples) and correlated samples) and correlated constant across that were the H3K27ac at PTGER4 trast to (TSA) HDACi After mRNA levels). ( PTGER2 expression with EP2 receptor signifcantly subjects with obtained from in fbroblasts increased mRNA levels PTGER2 treatment, controls healthy but not in those from AERD or aspirin-tolerant controls macrophages from severe asthmatic patients was not reduced by CS. Application by asthmatic patients was not reduced severe from macrophages TPCA-1, resulted inhibitor, SB239063, and IKK-2 inhibitor, of a selective p38α MAPK induction of H3S10ph; this inhibitoryin reduced when stronger was even efect combined with CS TPCA-1 were SB239063 or locus. No identifable STAT5 binding at No identifable STAT5 locus. binding at the CCL17 induced STAT6 with IL-3 locus was observed the CCL17 tein levels in supernatants of anti-CD3/CD28-stimulated PBMCs of allergic asthmatic in supernatants levels of anti-CD3/CD28-stimulatedtein PBMCs of allergic locus were of H3ac at the FOXP3 levels The controls. with healthy compared children controls asthmatics than in healthy higher in allergic when compared to healthy controls. This diference correlated with higher IL-13 pro with higher IL-13 correlated diference This controls. healthy to when compared detected between asthmatic and non-asthmatic subjects. However, signifcantly signifcantly betweendetected However, asthmatic and non-asthmatic subjects. and higher binding of bromodomain- specifcally H3K18ac, higher H3ac levels, observed BET were in asthmatics. reduced inhibitors p300 and PCAF, containing HATs, secretion CXCL8 mRNA levels, and IL-6 and CXCL8 protein release) after treatment after treatment release) protein and CXCL8 and IL-6 mRNA levels, sion ( IL6 and CXCL8 with BET mimics JQ1/SGCBD01 and I-BET762 bromodomain was observed. A higher concentration of both mimics was needed depending on the asthma severity T-cells obtained from newborns of obtained from T-cells observedthe IL13 and TBX21 were in CB CD4 + newborns to with fsh oil during of mothers supplemented compared pregnancy mothers the fsh oil-supplemented infants bornThe from mothers. placebo-treated diseases [ 81 , 82 ] risk allergic of developing at the lower were promoter H4ac levels in high folate arm (and a in high folate H4ac levels higher IL9 promoter Signifcantly group. folate A tendency towards also found. H3ac) were a similar association for tendency towards Statistical analyses H4ac was observed group. IFNG promoter in high folate lower CB serum vitamin D levels included adjustment for Higher the transcription start association of H3K18ac (but not H3K9me3) around sites Non-signifcant in asthmatics. was found EGFR , and STAT6 isoform), of TP63 (ΔNp63 with in AECs treated genes was detected of those three expression in protein increase (TSA)HDACi were variable (in con - were of H3K27ac at PTGER2 the levels Independent of disease state, in alveolar in alveolar , and CXCL8 of the IL6 , CCL2 inductionThe of H3S10ph at promoters locus. IL-4 alone but not in combination IL-4 locus. H3ac at CCL17 increased together and IL-4 IL-3 Higher asthma at the IL13 locus observed H3ac and H4ac levels with allergic in children No diferences in H4ac, H3K9me2/3 and H3K4me2/3 or in DNA methylation levels were were levels H3K9me2/3 and H3K4me2/3 or in DNA methylation in H4ac, No diferences An inhibition of FCS , and lower H3/H4ac levels at H3/H4ac levels at the PRKCZ and IFNG , lower higher H3ac levels Signifcantly Signifcantly higher GATA3Signifcantly Higher global H3K18ac and H3K9me3 levels were observedHigher were global H3K18ac and H3K9me3 levels in asthmatic subjects. Major epigenetic results - = 12) = 9), and 14) and form healthy healthy 14) and form = 7) and non-asthmatic = = 36) 9), non-severe asthmatic (n 9), non-severe 9), and healthy control subjects under control 9), and healthy = = = 8) 5) non-transplantable teenage human lung 5) non-transplantable teenage = 34; fsh oil n = 5) and healthy (n 5) and healthy = 9) subjects] = 18) = 11) maternal serum folate levels estimated during estimated the last trimester levels 11) maternal serum folate = 6) = 18), aspirin-tolerant and asthma-free control subjects with chronic rhinosinusitis subjects with chronic control 18), aspirin-tolerant and asthma-free = induced H3S10ph at promoters of infammatoryinduced H3S10ph at promoters genes on the anti-infammatory of corticosteroidsefect (CS) locus, encoding CCL17, a marker activation encoding CCL17, of the alternative of locus, H3ac at the CCL17 human monocytes T-cells obtained from children with allergic asthma (n with allergic children obtained from T-cells CD4 + control children (n children control subjects (n promoter between asthmatic (n promoter at the CXCL8 tion levels severe asthmatic (n severe cytokine (n healthy in ASMCs [from release going sinus surgery concha bullosa (n for selected form a larger cohort based on conventional extremes of exposure design cohort extremes a larger of exposure selected form based on conventional or low (n or low T-cells obtained from neonates with either high (n neonates obtained from T-cells cells between CB CD4 + tone acetylation and methylation status in alveolar epithelial cells (AECs) obtained epithelial cells (AECs) acetylation status in alveolar tone and methylation asthmatic (n from donors fbroblasts obtained from aspirin-exacerbated obtained from fbroblasts respiratory patients disease (AERD) (n n and polyposis (aspirin-tolerant controls; and several other of PRKCZ and several at promoters H3ac and H4ac levels T-cell and CB CD4 + genes (placebo n T-cell important Analysis of oxidant-associated infammation (such as observed asthma)- Analysis of oxidant-associated in severe Analysis of the efect of IL-3 and IL-4 on STAT5 and STAT6 (respectively) binding and (respectively) and STAT6 on STAT5 and IL-4 of IL-3 Analysis of the efect Comparison of H3ac and H4ac levels at Th1, Th2 and Treg-cell-related genes in isolated genes in isolated Treg-cell-related and Th2 Th1, at Comparison of H3ac and H4ac levels - H3K9me2/3, H3K4me2/3, and DNA methyla Comparison of ASMCs H3ac and H4ac, Analysis of the efect of BET bromodomains on the TGF-β-induced proliferation and proliferation TGF-β-induced of BETAnalysis of the efect on the bromodomains Comparison of H3ac and H4ac levels at gene promoters of Th1, Th2, Th17, and Treg Treg and Th17, Th2, Th1, of at gene promoters Comparison of H3ac and H4ac levels ] his - Comparison of global and gene-specifc EGFR , and STAT6 isoform), [ TP63 (ΔNp63 promoter on EP2-expression in polyp promoter H3K27ac at the PTGER2 Analysis of the efect Major epigenetic aims Analysis of the association between prenatal fsh oil exposure (maternal fsh oil intake) fsh oil exposure Analysis of the association between prenatal Studies on the role of histone modifcations in allergic diseases meeting the primary in allergic modifcations of histone selection on the role Studies criterion Marwick [ 69 ] et al. Borriello68 ] [ et al. 72 ] [ Harb et al. al. [ 54 ] et al. Cliford 55 ] [ Perry et al. al. [ 83 ] Harb et al. al. [ 66 ] et al. Stefanowicz al. [ 62 ] et al. Cahill 2 Table Study al. [ 84 ] Harb et al. Alaskhar Alhamwe et al. Allergy Asthma Clin Immunol (2018) 14:39 Page 4 of 16 - exposed group. Higher of phosphorylation levels of the passive exposed group. of Akt1 in AMs inhibi - Signifcant activity. smoking-exposed with HDAC2 negatively correlated group subjects not exposed from in AMs production TNF-α-induced CXCL8 tion (40%) of the smoking passive to with dexamethasone was observed. after treatment In contrast, smoking-exposed passive from in AMs inhibition was detected no signifcant subjects tion after treatment with TSA was observedTSA and collagen type fbronectin, (α-SMA, with tion after treatment was This diminished). were levels at both RNA transcript and protein I expression four histone and increased and HDAC4 of both HDAC2 expression decreased due to acetylation identifed between Nevertheless, asthmatic and non-asthmatic subjects. slightly but higher H3K4me3 (a mark with transcriptionconsistently associated activation) levels levels H3K9me3 (a mark with transcription associated repression) and much lower H3K9me3 was low The asthmatic subjects. in ASMCs obtained from detected were an aftermath treatment After of abortive of G9a in asthmatic ASMCs. recruitment VEGF expression (HMT) methyltransferase a histone with BIX-01294, G9a inhibitor, near asthmatic levels non-asthmatics to in cells obtained from increased - myof TGF-β1-induced on the efect In its suppressive nasal polyp tissues. addition to and collagen type I expression (α-SMA and ECM production diferentiation broblast morpho TGF-β1-induced also reversed TSA treatment), TSA was diminished after logical changes in nasal polyp-derivedlogical (NPDFs). Inhibition fbroblasts of the HDAC2 application aftermath.TSA also a H3ac and H4ac were and increased expression efect suppressive TSA This TSA. to with siRNA had a similar efect Inhibiting HDAC2 phosphorylationTGF-β1-induced and translocation inhibiting the by was produced with no cytotoxic blockedTSA NPDFs proliferation nucleus). Moreover, of Smad2/3 (to efects cell types 163 of 200 asthma- non-asthmatic subjects. when comparing asthmatic vs. for and 84 of them contained binding sites Th2-specifc enhancers were associated TBX21 and RUNX3) GATA3, (e.g. diferentiation T-cell in transcription factors involved locus (encoding for MKP-1) occurred after treatment of the monocytes after treatment occurred MKP-1) for locus (encoding of the DUSP1 with cal - Preincubation both SS and SR patients with dexamethasone. obtained from enhancement in the dexamethasone-mediated in a signifcant citriol H4ac. resulted Higher H4ac was observed in SS patients than SR were detected. Moreover, no diferences in histone acetylation were observed acetylation in histone were after no diferences Moreover, detected. were in found were levels protein Higher COX-2