NR3C1 and asthma

The NR3C1 gene encodes glucocorticoid receptor (GR), which has DNA binding, nuclear localization, ligand binding, and two activation function domains, and has the ability to inhibit the expression of asthma-related cytokines such as IL-5. ^{Reference Panek, Jonakowski and ZioŁo29} IL-5 induces the activity of eosinophils in asthma, after being released from the active macrophages and T lymphocytes. IL-5-induced leukotrienes, therefore, causes asthmatic reactions and symptoms. In a recent bioinformatics study that evaluated ignored genes that might have a function in allergic asthma, NR3C1 was found to be downregulated. ^{Reference Riba, Garcia Manteiga and Bošnjak30} It has also been shown that polymorphisms and mutations in specific sites of this gene has correlation with increase in transforming growth factor (TGF)-β expression in asthma patients, ^{Reference Panek, Pietras and Fabijan31} which is a well-known mediator that leads smooth muscle proliferation and airway remodeling. Regarding the epigenetic regulation of NR3C1, maternal stress during pregnancy, caused increased methylation in the umbilical cord blood mononuclear cells that cause decreased GR expression in the child, which may affect cytokine production and treatment response in the childhood asthma. ^{Reference Al‐Hussainy and Mohammed32}

FKBP5 and asthma

FKBP5 or FK506-binding protein 51, is a member of immunophilin protein family that has peptidyl-prolyl isomerases to catalyze isomeric shape of proline amino acid and thus, act as co-chaperon to assist protein folding in various proteins. Increased levels of protein is found in central and peripheric airway brushings of severe asthma patients comparing to healthy subjects. ^{Reference Singhania, Rupani and Jayasekera33} It also serves as a receptor for steroids and immune suppressive drugs and therefore, mostly studied for the effects of treatment response in asthma. FKBP5 express an inhibitory effect on GR function by binding to glucocorticoid-GR complex and delays nuclear translocation of the signal. ^{Reference Zannas, Wiechmann, Gassen and Binder34} There are also other rules of this protein in different pathways related with asthma pathogenesis. Increased levels of FKBP5 induce T-cell proliferation and function by binding to calcineurin and activating nuclear factor of activated T-cells pathway. ^{Reference Zannas, Wiechmann, Gassen and Binder34} Besides, stress induced decrease in FKBP5 methylation, upregulated the protein levels in blood and immune cells and this increase in FKBP5 promotes NF-kB (nuclear factor kappa-light-chain enhancer of activated B cells) mediated inflammation. ^{Reference Zannas, Jia and Hafner35} Thus, reduced methylation of FKBP5 in the abused children, might play role in the asthma development.

FANK1 and asthma

The relationship of FANK1 (Fibronectin type 3 and ankyrin repeat domains protein 1) with asthma is not well studied. There are studies that suggest the role of FANK1 in inhibition or activation of apoptosis. It is known to be expressed mostly by testis cells, but recently shown to be present also in T cells, alveolar, and epithelial cells of bronchi. ^{Reference Wu, Orozco and Boyer36} In a computational analysis of asthma-related genes, FANK1 has come forward as one of the 10 genes found to be associated with asthma. ^{Reference Tremblay, Lemire and Potvin37} However, the functional relation currently remains unknown.

CHRNA5 and asthma

CHRNA5 (Neuronal acetylcholine receptor subunit alpha-5), is a cholinergic nicotinic receptor gene that acts in opening ion channels on the plasma membrane after acetylcholine binding. Expression of the gene is mostly found in airway myocytes and epithelial cells throughout the lungs. ^{Reference Wilk, Shrine and Loehr38} In a meta-analysis that evaluate chromosome 15q25 region and airflow obstruction, Asp389Asn missense single nucleotide polymorphism in CHRNA5 was associated with airflow obstruction in never smokers. ^{Reference Wilk, Shrine and Loehr38} Silencing this gene in three-dimensional cell culture model, increased thickness of the epithelium, suggesting the lead to airway remodeling. ^{Reference Krais, Hautefeuille and Cros39} Studies show increased dependency to cigarette smoking in men ^{Reference Xie, Kranzler and Zhang40,Reference Zhang, Chen, Mu and Wang41} but there is no data that shows relation with epigenetic regulation of CHRNA5 and asthma but since genetically modification of the gene contributes airflow obstruction, and in vitro knock-down of the gene causes increased thickness in the airway models, it is possible that the increased methylation might contribute to asthma phenotype in the abused child.

ADAMs 10 and 17 and asthma

ADAM (A disintegrin and metalloproteinase domain containing protein) family proteins act as sheddase, with its adhesion and protease function, and shed various membrane proteins at the outer cell membrane that cause the maturation of those proteins and/or releasing them from the membrane. A single ADAM protein can cleave more than one protein as well as different ADAM members may cleave the same substrate. ADAM10 and ADAM17 have the similar active sites that both of them can cleave membrane bound TNF-alpha to its mature dissolvable state. ADAM10 has ability to shed ephrin/eph complexes between the cells, helps releasing soluble forms of IL6 and IL11 by mediating cleavage of IL6R and IL11RA, and also other surface proteins including heparin binding epidermal growth factor. ADAM10 also serves as a receptor for S. aureus, increasing the virulence of the bacteria. ADAM17 also cleaves IL6R, IL1RII, TGF-alpha, growth hormone receptor. ^{Reference Dreymueller, Uhlig and Ludwig42} Obviously, there are other many proteins and pathways effected by these two ADAMs that are not listed here. Thus, ADAM 10 and 17 playing role in endothelial permeability, smooth muscle transactivation, leukocyte recruitment, preventing resolution of inflammation and inducing inflammation, are important proteins in asthma pathogenesis and might be target for the treatment of the disease. Loss of function mutations of ADAM10 and ADAM17 are extremely rare and mice with double knockout of these genes do not survive. ^{Reference Dreymueller, Uhlig and Ludwig42} Overall, epigenetic regulation of these genes might affect asthma development in children.

SLC6A4 (SERT) and asthma

SLC6A4 gene, encodes sodium-dependent serotonin transporter and solute carrier family 6-member 4 (also SERT or 5HT transporter) protein that involves in recycling of serotonin (5-hydroxy tryptamine, 5HT) molecules by transporting them from the synaptic area to the presynaptic membrane. 5HT, besides its functions in the central nervous system, has ability to induce cytokine and chemokine synthesis, cell proliferation and tissue regeneration, ^{Reference Kang, Ha and Bahaie43} therefore, it is well studied in the pathogenesis of asthma. Increased levels of serotonin is found in symptomatic asthmatic patients and negatively correlated with FEV1 levels. ^{Reference Kang, Ha and Bahaie43} 5HT, stimulates PGE2 production by alveolar macrophages, activates eosinophils, and suppresses IL-12 expression. ^{Reference Kang, Ha and Bahaie43} 5HT also act as a platelet-stored vasoconstrictor. Termination of the serotonin signal depends on the levels of SLC6A4 and activation of the receptor helps relief of asthma symptoms to release. ^{Reference Flanagan, Sebastian, Battaglia, Foster, Cormier and Nichols44} There are studies that evaluated the relationship between SLC6A4 gene polymorphisms and asthma but have not found any correlations up to now with the studied ones. ^{Reference Farjadian, Moghtaderi, Fakhraei, Nasiri and Farjam45} SLC6A4 knockout mice show anxiety-like behavior and changes in the methylation of the gene may contribute the levels of 5HT and therefore influence asthma genotype in the maltreated and affected children.

OXTR and asthma

OXTR gene codes for oxytocin receptor, which is a G protein coupled receptor that needs to activate phosphatidylinositol-calcium second messenger molecules. Studies have shown that OXTR is expressed both in human and mice airway smooth muscle cells and its expression is affected by cytokines such as IL-13 and TNF-alpha. ^{Reference Amrani, Syed and Huang46} Oxytocine levels in BAL fluids were also found increased in asthmatic patients comparing to healthy control subjects ^{Reference Amrani, Syed and Huang46} suggesting that OXTR and its epigenetic regulation might have a role in the pathogenesis of asthma.

RPTOR, MTOR, and asthma

RPTOR or raptor (Regulatory-associated protein of mTOR), regulates mammalian target of rapamycin complex 1 (mTORC1) activity which involves in cell growth, survival, and autophagy. It also has role in maintaining the size of the cell. It is mostly expressed in muscle cells including lungs. In a study that evaluate airway smooth muscle tissue with RNA sequencing to compare asthmatic and normal people, RPTOR was found one of the four genes which were associated with airway hyper-responsiveness. ^{Reference Yick, Zwinderman and Kunst47} mTOR (mechanistic target of rapamycin kinase), was also found to involve in airway remodeling models in mouse models as well as regulation of Th17/Treg and Th1/Th2 ratio. ^{Reference Zhang, Jing and Qiao48} Therefore, epigenetic regulation of mTOR and related pathways significantly influence asthma development.

RGS3 and HCK and asthma

RGS3 involves in inflammation and Tcell migration, ^{Reference Williams, Yau and Sethakorn49} and HCK takes plays in MAPK signaling pathway which in turn related with airway smooth muscle proliferation. ^{Reference Sakai, Nishimura and Watanabe50} Labonte et al found these two genes were significantly hypermethylated in the brain tissue of the traumatic children, but currently there is no data that shows the epigenetic change in the blood or other tissues in these two genes.

CXCL10 and asthma

C-X-C motif chemokine ligand 10 (IFN-gamma-induced protein 10 (IP-10) or small inducible cytokine B10) is a small protein coded by CXCL10 gene. It is expressed in monocytes, endothelial cells, and fibroblasts and has a variety of role in the inflammation. Therefore, the effects on the asthma pathogenesis is well studied. mRNA levels of CXCL10 were found increased in bronchoalveolar fluid of asthmatic patients and data suggest that it has role in corticosteroid therapy-induced persistent type I inflammation. ^{Reference Gauthier, Chakraborty and Oriss51} Kaufman et al., evaluated epigenetic influences on the obesity in adverse childhood experienced children and found decreased methylation of the promoter region of CXCL10. Therefore, inducing obesity or involving inflammation, epigenetic regulation of the gene may contribute to asthma development in the abused children.

STAT and asthma

STAT family of proteins (signal transducer and activator of transcription) act as transcription factors after extracellular cytokine or growth factor binding in the cell and lead to the expression of proliferation, differentiation, and apoptosis-related genes. STAT1 was reported one of the asthma-ignorome gene together with NR3C1 ^{Reference Riba, Garcia Manteiga and Bošnjak30} and variants of STAT6 found related with risk for asthma in a meta-analysis study. ^{Reference Qian, Gao, Ye and Lu52} Epigenetic regulation of Jak-STAT pathway in childhood asthma has been recently reported. ^{Reference Zhang, Chen, Mu and Wang41}

CREB and asthma

CREB (cAMP response element-binding protein) is another transcription factor that regulate expression or suppression of multiple genes after getting activated by upstream signaling pathways those use cAMP as secondary messenger. Therefore, it involves multiple pathways in Asthma signaling including therapy response. ^{Reference Kim, Cho, Woo and Liggett53}

NFKB, IKappaBR, and asthma

NF-KB (nuclear factor kappa-light-chain enhancer of activated B cells), consists of protein to regulate transcription, cytokine production, and survival when the cell is under stress. Together with MAPK pathway, epigenetic regulation of NF-KB signaling was found significantly affected in adult-onset asthma. ^{Reference Jeong, Imboden and Ghantous54} Researchers have been interested in targeting NF-KB for asthma treatment for the last years. IKappaBR (IKBR) or TONSL gene codes for Tonsoku like DNA Repair protein that negatively regulate NFKB mediated transcription. Therefore, increased methylation of IKBR and demethylation of NFKB would worsen asthma phenotype in the maltreated children.

ALDH2 and asthma

ALDH2 (acetaldehyde dehydrogenase 2) is a member of ALDH family of proteins that acts as an antioxidant and its increased expression inhibits the harmful effects of oxidative stress. Polymorphisms of the gene may cause premature lung aging ^{Reference Kuroda, Hegab and Jingtao55} and ALDH2-deficient mice had alcohol-induced asthma in an animal model study. ^{Reference Shimoda, Obase, Matsuse, Asai and Iwanaga56} These and several other studies indicate that increased methylation of ALDH2 may have role in the asthma pathogenesis.

MAPK pathway, NPY − FOXP4, and asthma

MAPK pathway is a series of signaling cascade pathways that induce distinct pathways in the cell regarding differentiation, proliferation, and cell survival. Its role in asthma pathogenesis has been shown and reviewed in the literature. ^{Reference Chung57}

NPY (Neuropeptid Y) involves in multiple signaling pathways including MAPK pathway, and it also regulates intracellular calcium levels. The expression levels of NPY on antigen presenting cells in allergic asthma has been shown, and its role on cytokine expression is not yet clear. ^{Reference Makinde, Steininger and Agrawal58} In a study, the loss of FOXP4 (Forkhead box protein 4) together with FOXP1, which are transcription factors located in airway cells, led to increased NYP expression resulting in airway hyperreactivity through activation of smooth muscle myosin light-chain phosphorylation. ^{Reference Li, Koziol-White and Jude59}

ATP2A3 and asthma

ATP2A3 (Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 3), involving intracellular calcium levels, influence a variety of signaling pathways. the expression was shown to vary among different childhood asthma phenotypes. ^{Reference Boeck, Landgraf-Rauf and Vogelsang60}

Other relevant genes and gene ontology and pathway analysis

The rest of the genes listed in Table 1 are usually found in the literature that assessed obesity asthma relationship or that took place in the gene expression pathways in immune system.

After reviewing these genes in the literature, we further ran a GO analysis using two different online tools ^{Reference Pomaznoy, Ha and Peters14,Reference Fabregat, Sidiropoulos and Viteri61} and visualized the pathways related with the evaluated genes (Fig. 2 and Fig. S1 and Table S3).

Fig. 2.

Gene enrichment and pathway analysis of the affected genes. Differentially methylated genes in the adults who had childhood adversity, that have relationship with asthma are shown in orange color and significantly related pathways are in green. Dark green shows strongest relation. The full list of the pathways and corresponding full image are given in supplementary material.