{"paper_id":"eac55b3e-8e1c-4b7b-8a95-7924b076a58b","body_text":"Bronchial asthma (BA) is a chronic, recurrent disease whose pathogenesis is\nassociated with altered bronchial reactivity caused by both specific\nimmunological and nonspecific mechanisms. The major (essential) clinical sign\nof BA involves choking episodes that result from bronchial spasm, mucus\nhypersecretion, and edema of the bronchial mucosa\n[ 1 ].\nThe WHO considers bronchial asthma to be among the most serious chronic,\nnon-communicable diseases. Most deaths due to BA occur in low- and\nmiddle-income countries, which are characterized by insufficiently efficient\ndiagnosis and treatment capabilities for the disease, as well as the healthcare\nsystem in general [ 2 ]. Up to 350 million\npeople worldwide currently have BA [ 1 ],\nand this figure may increase to 450 million by 2025\n[ 3 ].\nAccording to official statistics, there are 1.3 million patients with BA in\nRussia. This means that the prevalence of this disease in Russia is less than\n1%, while the proportion of people with BA is less than 0.4% of all patients\nwith asthma worldwide. Meanwhile, the European Respiratory Society has\nestimated the incidence of BA in a number of European countries at 5% among\nadults and more than 7% among children. A trend towards growing rates of\ndisability and death due to BA is observed in many countries. Thus, the rate of\nBA deaths in Great Britain has increased sevenfold over the past 20 years, and\ntwo- to threefold, in North America. More than 5,000 people die due to BA in\nthe U.S. each year.\nBA develops due to a number of factors, including the intensity of allergen\nexposure, habitat destruction, overactive immune response, and individual\ngenetic features [ 3 ]. It has been\ndemonstrated that there is a 25% risk that a child whose parent suffers from\nbronchial asthma also develop this disease. If both parents have asthma, the\nrisk increases to 50% [ 4 ]. Furthermore,\nit has been proved that there exists an association between the increasing\nincidence rate of BA and aggravated soil, air, and water contamination\n[ 5 ].\nIn 2018, the direct expenses of the Russian healthcare system for BA treatment\namounted to ~ 8.5 billion rubles; two-thirds of this amount was spent on\nhospital stays. Moreover, substantial funds are needed to cover temporary\ndisability leaves and disability payments\n[ 6 ].\nEarly diagnosis and prevention of BA will make it possible\nboth to reduce these costs and the prevalence of bronchial asthma in Russia.\n\nBuilding the cohorts\nThe manifestation and course of BA is significantly different in men than it is\nin women, which is largely due to the different contributions of reproductive\nhormones to the pathogenesis of BA [ 7 ].\nTherefore, our study participants were divided into cohorts according to such\nfactors as history of BA and sex.\nThe 7,303 study participants were allotted to four cohorts:\n1A – women with a confirmed diagnosis of BA (mean age, 52 ± 10\nyears), n = 218;\n2A – men with a confirmed diagnosis of BA (mean age, 41 ± 12 years),\nn = 70;\n3H – apparently healthy women without a history of BA or other diagnoses\nwith a similar clinical presentation (mean age, 52 ± 8 years), n = 4,015;\n4H – apparently healthy men without a history of BA or other diagnoses\nwith a similar clinical presentation (mean age, 44 ± 6 years), n = 3,000.\nAn inclusion criterion for groups 1A and 2A was a history of bronchial asthma\nin the anamnesis. Groups 3H and 4H contained visibly healthy men and women; the\nexclusion criteria for these cohorts were medical records indicating that a\npatient had a history of diseases whose symptoms were similar to manifestations\nof BA, such as acute bronchitis, pulmonary emphysema, allergic rhinitis,\ngastroesophageal reflux, tracheoesophageal fistula, congenital heart disease,\ntracheomalacia and bronchomalacia, cystic fibrosis, primary ciliary dyskinesia,\nbronchiectasis of other etiologies, tuberculosis, lung cancer, a vascular ring\nanomaly, sarcoidosis, intrathoracic lymphadenopathy, bronchopulmonary\ndysplasia, allergic bronchopulmonary aspergillosis, systemic anaphylaxis,\nprimary immunodeficiency, vocal cord dysfunction, psychogenic cough, and\naffective respiratory paroxysms [ 8 ].\nBiomaterial sampling and personal data of study participants\nSamples from collections previously created by the Center for Strategic\nPlanning of FMBA of Russia were used in this study. In all cases, the data were\ncollected in full compliance with the procedural requirements: the following\nrespective data were included and verified for each donor: sex, age, region of\nresidence, nationality, past medical history, informed consent (signed by the\ndonor) for biomaterial sampling, handling, transportation, storage and personal\ndata use; proper procedures for sample (venous blood) collection, handling,\ntransportation, and storing was ensured, per the State Standard GOST\n R53079 .4-2008.\nAll the specimens selected for the final study sample were checked to make sure\nthat the donor’s ID code and the information deciphered in that code were\nunique. Furthermore, it was guaranteed that the biomaterial had no signs of\nhemolysis or lipemia. The samples were transported under constant temperature\ncontrol.\nCreating a candidate gene list\nOver 150 genes associated with the development of BA have been reported thus\nfar. The following tentative gene groups are of special interest:\nthe atopy-related genes. These genes include IL4, IL5, IL13, IL4RA, CHI3L1,\nRAD50, etc. and are responsible for the blood level of total and specific IgE,\nas well as the development of allergic responses;\nthe genes related to bronchial hyperreactivity, including ADRB2, TNF, IL5, IL9,\nNOS1, NPSR1, TAC1, TACR2, TACR1, TACR3, ADAM33, ACE, etc., being responsible\nfor bronchial hyperresponsiveness, which is tightly related to the blood IgE\nlevel and inflammation;\nthe inflammation-related genes such as TNF, IL4, IL5, IL13, ORMDL3, SCGB3A2,\nCCL11, IRAK3, CSF2, ALOX5, CYSLTR1, CYSLTR2, LTC4S, STAT3, STAT6, etc., being\nresponsible for the level of inflammatory mediators by their role in regulating\nthe immune response and behavior of inflammatory cells in body fluids [ 8 ].\nA list comprising 167 candidate genes was created according to 107 references\nto search for phenotype– genotype associations. The list of these genes,\nwith a brief description of the functions of the proteins encoded by them, is\nprovided in Discussion.\nDNA isolation, construction of genomic libraries, and sequencing\nDNA was isolated from whole blood samples using a MagAttract HMW DNA Kit\n(Qiagen, Germany). The DNA isolation protocol was automated on the Tecan\nFreedom EVO workstation (Tecan, Switzerland). The concentration and purity of\nthe isolated DNA were measured on a Tecan Infinite® F Nano Plus microplate\nreader (Tecan, Switzerland).\nThe genomic libraries for sequencing were prepared using a Nextera DNA Flex kit\n(Illumina, USA), in accordance with the manufacturer’s recommendations.\nEach sample in the flow cell was labelled using indexes from the IDT-ILMN\nNextera DNA UD kit (Illumina, USA).\nThe concentrations of the genomic libraries were measured using a Tecan\nInfinite® F Nano Plus spectrophotometer. The size of the genomic libraries\nwas determined on an Agilent TapeStation 4200 system using an Agilent DNA 1000\nkit (Agilent, USA). The library pools consisting of 24 samples were combined on\na Tecan Freedom EVO robotic platform.\nGenome-wide sequencing was performed on a NovaSeq 6000 sequencing system and a\nS4 reagent kit (300 cycles) (Illumina, USA) for paired-end reads 2 × 150\nbp.\nBioinformatic analysis of the whole-genome sequencing data\nDemultiplication was performed at the first stage of the analysis of the\nprimary sequencing data. During this procedure, the initial reads of the\nNovaSeq 6000 sequencing system was converted from the BCL format to the FASTQ\nformat using the Illumina bcl2fastq conversion software v2.20 [ 9 ]. The Illumina Sequencing Analysis Viewer\nsoftware v2.4.7 was employed to control the overall sequencing quality of the\nentire cell [ 10 ]. The quality of\nindividual reads was controlled using the FastQC v0.11.9 bioinformatic tool\n[ 11 ].\nThe final sample contained blood specimens that had undergone quality control\nfor such parameters as homogeneity of the nucleotide distribution in the reads\nand GC composition.\nRead alignment against a reference genome was performed at the second stage of\nthe bioinformatic analysis using the DRAGEN platform [ 12 ]. The GRCh38.d1.vd1 sequence was used as the reference\ngenome. Blood samples with average coverage over genome < ×30 were\nexcluded from the study.\nThe CrosscheckFingerprints software (Picard) [ 13 ] was used to check whether the sample contained any\nduplicates. All duplicate specimens were excluded from the study.\nSearch for short genetic variations\nThe Strelka software was used to process VCF files and search for short genetic\nvariations (SNPs, indels up to 50 bp long) [ 14 ].\nFinally, 380,564 short genetic variations were detected in 167 candidate genes\n(7,303 samples); 253,628 of those were found more than once.\nThe procedure for searching for genetic variations whose frequency was\nstatistically significantly different in different cohorts was employed to\nidentify the polymorphisms associated with BA. The Fisher’s exact test\nwas used to determine the significance level of the differences.\nThe case with identical occurrence of the \"zero\" variant in all four cohorts\nwas assumed to be the null hypothesis. The significance level at which the null\nhypothesis was rejected was set equal to 10-4. The calculations were performed\nusing the R programming language.\n\nComparison of male cohorts\nSNPs associated with bronchial asthma in the cohorts of men\nOur analysis revealed four genetic variants in the introns of the TACR3,\nZNF257, FOXP1, and EGFR genes; their frequencies differ statistically\nsignificantly (the p value being no higher than the significance level of\n10 -4 ) in the cohorts of men with a verified diagnosis of BA and in\nthe cohort of apparently healthy men. These genetic variants are found\nsignificantly more frequently in cohort 2A (more than fivefold)\n( Table 1 ) than in cohort 4H.\nThe TACR3 gene that encodes tachykinin receptors and has an indirect effect on\nthe bronchial tone [15, 16] was found to carry the rs1461555098 deletion\n(chr4:g.103629850_103629861del). According to our calculations, the relative\nrisk of developing BA in individuals carrying this deletion stands at 6.9,\nwhile this parameter is normally equal to 1.0. The deletion rs1461555098\n(chr4:g.103629850_103629861del) was detected in cohort 2A twice as frequently\nas in cohort 4H.\nThe ZNF257 gene encoding the transcription factor (a zinc finger\nmotif-containing protein) was found to carry the genetic variant rs1199362453\n(chr19:g.22076863T>C), which was encountered three times in cohort 2A but\nwas absent in cohort 4H.\nThe FOXP1 gene encoding the transcription factor and expressed in the proximal\nairway epithelium [ 18 ] was found to\ncarry the genetic variant rs869106717 (chr3:g.71465326del), which was\nencountered in cohort 2A 33.6 times more frequently than in cohort 4H. The\nrelative risk of developing BA in individuals carrying this mutation is 36.0.\nIn the EGFR gene that encodes the transmembrane receptor binding extracellular\nligands belonging to the epidermal growth factor group [ 19 ], the frequency of the genetic variant rs189649077\n(chr7:g.55168296G>T) in cohort 2A was 143-fold higher compared to that in\ncohort 4H. The relative risk of developing BA in individuals carrying this\nmutation is 34.3.\nComparison of female cohorts\nIt was demonstrated that in the cohort of women with a confirmed diagnosis of\nBA, five genetic variants were six times more frequent compared to the cohort\nof apparently healthy women (the p value is no higher than the significance\nlevel of 10-4). These genetic variants resided in the CYSLTR1, IL5RA, NRG1,\nHDC, and DPP10 genes ( Table 2 ).\nSNPs associated with bronchial asthma in the cohorts of women\nThe CYSLTR1 gene that encodes the protein affecting the secretion of\ninflammatory mediators (leukotrienes) [ 16 ,  20 ] was found to\ncarry the rs1923038536 (chrX:g.78306516G>A) variant, which was detected in\ncohort 1A 45.8 times more frequently compared to cohort 3H. The relative risk\nof developing BA in individuals carrying this mutation is 14.2.\nT h e g e n e t i c va r i a n t r s 1 8 1 0 6 6 1 1 9 (chr3:g.3102851A>G)\nwas found in the IL5RA gene encoding the subunit of the heteromeric receptor of\ninterleukin 5, a cytokine that plays a crucial role in eosinophil\ndifferentiation [ 21 ]; this variant\noccurred in cohort 1A 36.6 times more frequently than in cohort 3H. The\nrelative risk of developing asthma in individuals carrying this mutation is\n13.2.\nT h e g e n e t i c va r i a n t r s 1 4 3 2 4 7 1 7 5 (chr8:g.32692193T>A)\nwas found in the NRG1 gene encoding mucin production by airway goblet cells\n[ 22 ]; like the previous genetic variant,\nit was found in cohort 1A 36.6 times more frequently than in cohort 3H. The\nrelative risk of developing BA in individuals carrying this mutation is also\n13.2.\nThe HDC gene codes for the enzyme catalyzing histamine synthesis from\nL-histidine [ 23 ]. The genetic variant\nrs140597386 (chr15:g.50261726dup) was identified for this gene; it occurred in\ncohort 1A 6.2 times more frequently than in cohort 3H. The relative risk of\ndeveloping BA in individuals carrying this mutation was 5.0.\nT h e g e n e t i c va r i a n t r s 7 6 2 0 4 2 5 8 6 (chr2:g.115490670del)\nwas identified in the DPP10 gene encoding membrane-anchored serine protease\n[ 16 ], which was found in cohort 1A 36.6\ntimes more frequently than in cohort 3H. The relative risk of developing BA in\nindividuals carrying this mutation is 13.2.\nT h e g e n e t i c v a r i a n t s r s 2 2 9 1 6 5 1 ( c h r 3 : g . 1 9 5 7 5\n1 1 4 1 G > C ) a n d r s 1 2 1 9 2 4 4 9 8 6 (chr1:g.155189991T>C) of\nthe MUC1 and MUC4 genes occurred in women with asthma much less frequently than\nin apparently healthy women. This means that the identified genetic variants\ncan be considered protective in individuals with BA [ 24 ]. The MUC1 and MUC4 genes encode mucins. The MUC1 gene is\nresponsible for the anti-inflammatory effect in patients with bronchial and\nlung diseases. MUC4 exhibits a mediated effect on the proliferation of airway\nepithelial cells [ 25 ]. The genetic\nvariant rs2291651 (chr3:g.195751141G>C) of the MUC4 gene in cohort 1A\noccurred somewhat more rarely than in cohort 3H. The relative risk of\ndeveloping BA in individuals carrying this mutation is 0.5, while normally this\nparameter is 1.0. This indicates that the risk of developing bronchial asthma\nis down twofold in women carrying the genetic variant rs2291651. The relative\nrisk of developing BA in females carrying the genetic variant rs1219244986\n(chr1:g.155189991T>C) is 0.2 (i.e., lower than 1), corresponding to the\nfivefold reduction in the risk of developing the disease.\nHowever, allowance should be made for the fact that the identified variants in\nthe MUC1 and MUC4 genes reside in GC-rich regions. This region negatively\naffects sequencing quality and, therefore, the quality of the genetic variant\ndetection.\n\nWe have analyzed the candidate genes potentially associated with BA. Eleven\npolymorphisms whose frequency differs significantly in individuals diagnosed\nwith BA and those not diagnosed with the condition have been identified. Nine\nof the identified genetic variants increase the risk of developing BA, while\ntwo variants reduce it. These nine variants increase the risk of developing BA\nat least fivefold. The identified variants are specific to the population of\nRussia.\nArathimos et al. [ 26 ] reported that up\nto 45% of females with bronchial asthma experience an aggravation of their\ncondition before their menstrual period. In 2020, the polymorphism rs2291651 in\nthe MUC4 gene was described to be an accompanying sign of endometriosis in\nSouth Korean women [ 27 ]. The\nrelationship between the single nucleotide polymorphisms in the MUC1 and MUC4\ngenes and endometriosis risk was analyzed in this study. Screening identified\neight genetic variants of MUC4, including rs2291651, whose presence correlated\nwith the development of endometriosis. Women of childbearing age using oral\ncontraceptive pills tended to experience milder asthma attacks [ 28 ]. A number of studies [ 29 ,  30 ]\nalso demonstrated that variations in the estradiol and progesterone levels\nduring the menstrual cycle affected the severity of bronchial asthma symptoms.\nThat means that when studying the genetic predisposition to a severe BA course\nin women, one should pay particular attention to the genes associated with\nfemale sex hormones.\nIn this study, we have analyzed 167 candidate genes associated with bronchial\nasthma. These genes include HNMT, MS4A2, HRH1, HRH2, HRH3, HRH4, AOC1, and HDC,\nwhich code for the histamine receptors that are involved in the regulation of\nhistamine release [ 16 ,  23 ,  31 ,\n 32 ,  33 ].\nThe HDC gene encodes the enzyme histidine decarboxylase catalyzing histamine\nformation from L-histidine; the HDC mRNA level is elevated in patients with\nasthma [ 23 ];\nthe IL3, IL4, IL4R, IL5, IL9, IL13, IL17, IL21R, IL18, IL18R1, IL2RB, IL1RL1,\nIL5RA, IL33, SCGB3A2, TNF, CCL11, IRAK3, CSF2, and TSLP genes encode the\ncytokines involved in inflammation. Thus, IL5 stimulates eosinophil release\ninto the bloodstream, while IL5RA regulates their activity. Stimulation of the\nairways with allergens increases the local IL5 concentration, which correlates\nwith the severity of airway eosinophilia, while IL4RA codes for the α\nchain of the IL4 receptor, which can bind IL4 and IL13 to regulate the IgE\nproduction [ 4 ,  16 ,  21 ,  23 ,  34 ,\n 35 ,  36 ,  37 ,  38 ,  39 ,\n 40 ];\nthe IL17F gene encodes the pro-inflammatory cytokine involved in\npathophysiological manifestations of asthma. In vivo and in vitro studies have\nshown that IL17F is involved in the pathogenesis of allergic airway\ninflammation [ 41 ];\nthe ADRB2 gene encodes the β2-adrenoceptors that play a crucial role in\nairway contractility. β2-adrenoceptors act as a target for\nβ2-agonists exhibiting a marked bronchodilator and bronchoprotective\nactivity, which is important for assessing the effectiveness of BA therapy\n[ 16 ];\nthe PLA2G7 gene encodes the platelet-activating factor acetylhydrolase. This\nenzyme catalyzes the cleavage of PAF by hydrolyzing the acetyl group down to\nbiologically inactive products [ 31 ];\nthe ALOX5, CYSLTR1, CYSLTR2, and LTC4S genes encode the proteins that affect\nthe production of inflammatory mediators (leukotrienes), contributing to\nvarious allergic and hypersensitivity reactions. It has been shown that altered\nexpression of some of these genes may cause bronchoconstriction of the airways\nand hyperresponsiveness to bronchoconstricting agents such as histamine,\nincreased vascular permeability, edema, eosinophilia and neutrophilia, smooth\nmuscle cell proliferation, collagen deposition and fibrosis in different tissue\nareas, mucin secretion by goblet cells, metaplasia of goblet cells, and\nhypertrophic changes in the respiratory epithelium [ 16 ,  20 ,  42 ];\nthe PTGER2 and PTGDR genes encode prostaglandin receptors and are involved in\nthe pathogenesis of BA [ 16 ,  43 ];\nthe TBX21 and TBX5 genes encode transcriptional activators; their expression is\ndownregulated in airway-resident T cells in asthma patients [ 16 ,  44 ];\nthe STAT6 gene encodes the STAT family transcription factor; expression of this\ngene is significantly upregulated in patients with severe BA [ 16 ];\nthe STAT3 gene encodes the STAT family transcription factor mediating the\ncellular responses to interleukins and regulates the inflammatory response\n[ 45 ,  46 ];\nthe STAT4 gene encodes the STAT family transcription factor; expression of this\ngene is downregulated in patients with BA [ 47 ];\nthe NPSR1 gene encodes the neuropeptide S receptor; the upregulated expression\nof this gene in airway epithelium leads to the activation of matrix\nmetalloproteinases, which are involved in the pathogenesis of BA [ 16 ,  48 ];\nthe TAC1, TACR2, TACR1, and TACR3 genes encode receptors for tachykinins, which\nare found in sensory nerve endings, are activated by inflammatory mediators\n(histamine, platelet-activating factor, and leukotrienes), and add the axon\nreflex mechanism to the pathogenesis of asthma, thus leading to aggravation and\nspread of the initial inflammation. Tachykinins affect the bronchial tone and\nvascular permeability [ 16 ];\nthe CHI3L1 gene encodes the glycoprotein belonging to the glycoside hydrolase\nfamily and contributes to the development of the Th2-type inflammatory response\n[ 16 ,  49 ];\nthe DENND1B gene encodes the protein interacting with tumor necrosis factor and\nplays a crucial role in suppressing T-cell receptors on Th2 cells [ 50 ,  51 ];\nthe ADAM33 gene codes for metalloprotease. ADAM33 is expressed by various types\nof airway cells. ADAM33 expression is elevated in patients with BA; the\nimpaired function of this metalloprotease can be associated with bronchial\nhyperresponsiveness and airway wall remodeling, thus contributing to early\nmanifestation of bronchial asthma [ 52 ];\nthe ORMDL1, ORMDL2, and ORMDL3 genes encode ORM-like proteins, the key\nregulators of serine palmitoyltransferase, which catalyzes the first step of\nsphingolipid biosynthesis. Sphingolipids play an important role in signal\ntransduction in response to stress and affect the mechanical properties of cell\nmembranes. Dysregulation of sphingolipid biosynthesis is associated with\nseveral diseases, including allergies, inflammation, and asthma [ 53 ,  54 ];\nthe VIP gene encodes the vasoactive intestinal peptide responsible for the\nrelaxation of smooth muscles [ 55 ];\nthe genes belonging to the NOS family encode nitric oxide synthases. Mutations\nin the NOS1 gene reduce the nitric oxide concentration in non-eosinophilic\nphenotype patients, which is a marker of bronchial asthma, and cause bronchial\nhyperresponsiveness [ 56 ,  57 ,  58 ];\nthe ACE gene encodes angiotensin, which converts angiotensin I to the\nvasoactive angiotensin II, and is involved in the pathogenesis of BA as it\ncauses proliferation and increases smooth muscle contractility, thus leading to\nlung obstruction [ 59 ];\nprotein RAD50 encoded by the RAD50 gene is involved in double-strand DNA break\nrepair. It was shown in transgenic mice that the fragment of the\n3’-terminus of this gene is the Th2 locus control region (LCR), which\nregulates cytokine gene expression [ 60 ];\nthe PTAFR gene encodes the receptor for the platelet-activating factor, a\nchemotactic phospholipid mediator exhibiting strong inflammatory, contractile,\nand hypotensive activities with respect to smooth muscles. The PAF receptor is\ninvolved in various pathological processes, such as allergies, asthma, septic\nshock, arterial thrombosis, and inflammation [ 16 ];\nthe OPN3 gene encodes the G-protein-coupled receptor. Upregulated OPN3\nexpression was detected in bronchial epithelium and immune cells. Mutations in\nthe OPN3 gene increase the risk of bronchial asthma [ 20 ,  61 ];\nthe GSDMB gene encodes the protein whose overexpression in bronchial epithelial\ncells increases expression of the genes that are crucial for both airway\nremodeling and airway hyperresponsiveness [ 16 ,  62 ];\nthe PKN2 gene encodes serine/threonine-specific protein kinase and regulates\napical junction formation in human bronchial epithelium [ 63 ];\nthe PTK2 gene codes for tyrosine protein kinase and plays a crucial role in\nairway hyperresponsiveness and airway remodeling [ 63 ];\nthe ALPP gene encodes the placental alkaline phosphatase catalyzing the\nhydrolysis of phosphoric acid monoesters; the expression level of this gene is\nassociated with childhood asthma [ 63 ];\nthe PTEN gene encodes phosphatidylinositol-3,4,5- triphosphate-3-phosphatase\n[ 20 ]. A low PTEN expression level is\nconsidered to be among the independent factors of BA development [ 64 ];\nthe PRMT1 gene encodes an important epigenetic regulator, protein arginine\nmethyltransferase-1, which contributes to inflammation and airway remodeling in\npatients with BA [ 65 ];\nthe HSPD1 gene encodes the heat shock protein that can modulate the immune and\ninflammatory responses, be involved in pathogenesis, and/or be a risk factor or\na prognostic marker for several diseases, including BA [ 66 ];\nthe TLR2 and TLR4 genes encode proteins belonging to the Toll-like receptor\nfamily, which are essential for pathogen recognition and activation of the\ninnate immune system. Some polymorphisms in these genes are associated with the\nrisk of developing BA [ 67 ];\nthe ZNF208, ZNF257, ZNF676, ZNF729, ZNF98, ZNF492, ZNF99, ZNF723, ZNF728,\nZNF730, and ZNF91 genes encode zinc finger proteins residing within the region\nof the transcription factor cluster area and are associated with the\npathogenesis of BA [ 17 ];\nthe B4GALT1 gene encodes beta-1,4-galactosyltransferase and is associated with\nthe atopic phenotypes and inflammatory conditions [ 68 ];\nthe IGFBP3 gene codes for a protein binding insulin-like growth factor and\ninhibits the specific physiological effects of asthma in an IGF-independent\nmanner [ 69 ];\ngenes belonging to the MUC family encode mucins. MUC7 codes for salivary mucin;\nthe frequency of the MUC7 allele with five tandem repeats is significantly\nreduced in patients with asthma [ 20 ,\n 70 ]. During the late stages of bacterial\ninfection, MUC1 exhibits an anti-inflammatory activity in the airways, which is\ninitiated and mediated by inhibition of Toll-like receptor signaling [ 24 ]. Mucin MUC4 was identified as a\nligand-activating receptor tyrosine kinase, which modulates the proliferation\nof airway epithelial cells in patients with asthma [ 25 ]; MUC19 is mainly expressed in the cells of submucous\nglands in the trachea and salivary glands; in patients with allergic rhinitis\nand chronic otitis media, this gene is expressed in the epithelium. MUC5AC is\nexpressed in the goblet cells of tracheal and bronchial epithelium. MUC5B is\nalso expressed in the submucosal epithelium and ducts and, to a lesser extent,\nin the goblet cells of both tracheal and bronchiolar epithelium. Many\nindividuals with a confirmed diagnosis of bronchial asthma have elevated levels\nof MUC5AC mRNA but reduced levels of MUC5B mRNA [ 71 ];\nthe NRG1 gene encodes the protein-inducing production of mucins MUC5AC and\nMUC5B by human airway goblet cells, so its inhibition can be regarded as a\nnovel therapeutic approach to reducing mucus hypersecretion in patients with\nrespiratory diseases [ 22 ];\nthe DACT1, DACT2, and DACT3 genes code for the proteins involved in the\npathogenesis of BA. The tissue levels of DACT1, DACT2, and DACT3 mRNA are\nsignificantly elevated in asthma patients [ 72 ];\nthe CYP genes encode the cytochrome proteins involved in the metabolism of many\ndrugs, including nonsteroidal anti-inflammatory drugs, oral anticoagulants and\nangiotensin receptor blockers, as well as in the synthesis of cholesterol,\nsteroids, and other lipids [ 20 ,  70 ,  73 ,\n 74 ,  75 ,  76 ,  77 ];\nthe CHML gene codes for Rab geranylgeranyltransferase regulating the\nintracellular transport of membrane structures. Polymorphisms in this gene are\nassociated with the development of BA [ 61 ];\nthe GSTT2 and GSTP1 genes encode glutathione S-transferase theta 2 and\nglutathione S-transferase P; polymorphisms in these genes may be risk factors\nfor BA [ 78 ];\nthe NAT2 gene codes for N-acetyltransferase 2; polymorphisms in this gene are\nassociated with the development of atopic asthma [ 79 ];\nthe PYHIN1 gene encodes the interferon-inducible HIN-200 protein, which is\ninvolved in the production of proinflammatory cytokines in airway epithelial\ncells [ 80 ];\nthe SMAD3 gene promoter is significantly hypermethylated in patients with BA\n[ 81 ];\nthe PGAP3 gene encodes a glycosylphosphatidylinositol-specific phospholipase\npredominantly residing in the Golgi apparatus. The PGAP3 and ORMDL3 proteins\ncan contribute to the development of BA [ 82 ];\nthe ERBB2 gene encodes the epidermal growth factor receptor tyrosine kinase.\nThe ERBB2 expression level in freshly isolated airway epithelium in asthma\npatients is lower than that in healthy individuals [ 83 ];\nthe COL15A1 gene coding for the alpha chain of collagen type XV, a member of\nthe FACIT collagen family [ 16 ], is\ninvolved in the metabolism of the drugs used to treat lung diseases [ 84 ];\nthe FOXP1 gene encodes the transcription factor belonging to the FOXO family,\nwhich is expressed in the proximal airway epithelium of the lungs;\ndownregulated expression of FOXP1 inhibits early differentiation of secretory\ncells [ 18 ];\nthe ACOT7 gene encodes a protein belonging to the acyl-coenzyme family; an\nepigenome-wide association study revealed an association between the degree of\nmethylation and the development of bronchial asthma [ 85 ];\nthe MTHFR gene codes for the methyltetrahydrofolate reductase. Polymorphisms in\nthe MTHFR gene are associated with predisposition to bronchial asthma and\nglucocorticoid responsiveness in humans [ 86 ];\nthe DICER1 gene encodes RNA helicase involved in cytokine production and signal\ntransduction in patients with BA [ 87 ];\nthe SERPINC1 gene encodes antithrombin III, which inhibits clotting factors;\nvariations in its level may induce thrombosis or pulmonary embolism [ 88 ];\nthe SYNM gene codes for an intermediate filament; there is a hypothesis that\nthe degree of methylation of this gene is associated with the development of BA\n[ 89 ];\nthe GATA3 gene encodes a transcription factor belonging to the GATA family. The\nGATA3 expression level in the airways is significantly increased in patients\nwith asthma. The increased GATA3 expression level correlates with changes in\nIL5 expression and the development of bronchial hyperresponsiveness [ 90 ];\nthe FOXP3 gene encodes an activating transcription factor; the expression level\nof this gene is downregulated in asthma patients [ 91 ];\nthe CCDC80, DAPK3, LOXL1, PROC, FUCA2, SP100, and ITCH genes encode proteins\nassociated with antigen presentation to T lymphocytes. The degree of\nmethylation of these genes was found to be increased in asthma patients [ 76 ];\nthe VDR gene codes for the vitamin D3 receptor. Genetic variants of the VDR\ngene are often found in children with BA; their presence inversely correlates\nwith asthma severity [ 92 ];\nthe DPP10 gene encodes a membrane protein belonging to the serine protease\nfamily. Mutations in this gene increase the risk of BA [ 16 ,  93 ];\nthe genetic variants of the PHF11, SPP1, and PLAUR genes are associated with\nelevated IgE levels [ 94 ];\nthe SLC22A5 gene encodes an organic cation transporter; its expression level in\nthe bronchial epithelium is reduced in asthma patients [ 95 ];\nthe EPHX1 gene codes for microsomal epoxide hydrolase. A high EPHX1 expression\nlevel is associated with an increased risk of developing BA at any time in\none’s life [ 96 ];\nthe CTLA4 gene encodes one of the proteins from the immunoglobulin superfamily.\nAccording to the meta-analysis data, some polymorphisms in this gene are risk\nfactors for developing BA [ 16 ,  97 ];\nthe MMP9 gene encodes a matrix metalloprotease involved in local proteolysis of\nthe extracellular matrix, leukocyte migration, and airway remodeling [ 98 ];\nthe SOCS5 gene codes for a protein belonging to the family of cytokine\nsignaling inhibitors. The single-nucleotide polymorphisms identified in this\ngene are associated with the development of BA [ 99 ];\nthe polymorphisms in the FCER2 gene encoding CD23 are associated with atopy,\nhigher risk of exacerbation in patients with asthma, and a high serum IgE level\n[ 100 ];\nthe VEGFA gene encodes the heparin binding protein, one of the PDGF/VEGF growth\nfactors. An elevated expression level of this gene is detected in patients with\nBA [ 101 ];\nthe ASB3 gene codes for the protein involved in smooth muscle cell\nproliferation and muscle cell development. A genome-wide association study\nrevealed an association between polymorphisms in this gene and the development\nof BA [ 102 ];\nthe CRISPLD2 gene encodes the secretory protein LCCL, which increases\nglucocorticoid sensitivity and regulates the immune response [ 103 ];\naccording to a genome-wide association study, polymorphisms in the APOBEC3B,\nAPOBEC3C, and EDDM3B genes are associated with asthma exacerbations [ 104 ];\na whole-genome association study revealed an association between polymorphisms\nin the BBS9 gene and the effectiveness of asthma treatment in children [ 105 ];\nthe PRKG1 gene encodes cGMP-dependent protein kinase, a key mediator of the\nnitric oxide (NO)/cGMP signaling pathway, and contributes to smooth muscle\nrelaxation [ 16 ];\nthe DNAH5 gene codes for the dynein protein. The DNAH5 expression level in the\nbronchial epithelium is reduced in asthma patients compared to that in the\ncontrol group [ 106 ];\nthe JAK1 and JAK2 genes encode the tyrosine kinases involved in the\ninflammatory cytokine signaling pathways associated with a higher frequency of\nasthma exacerbation and increased susceptibility to allergic sensitization and\nenvironmental antigens [ 107 ,  108 ];\nthe CHRNA1 and CHRNA3 genes code for nicotinic acetylcholine receptors.\nPolymorphisms in these genes are considered to be genetic risk factors for\nbronchial obstruction [ 109 ];\nthe TGF- β  gene encodes a secreted ligand belonging to the\nTGF-β protein superfamily. TGF-β isoforms play a role in the\nregulation of airway inflammation and remodeling [ 110 ];\nvariants in the HHIP gene are associated with chronic obstructive pulmonary\ndisease [ 111 ];\nthe SOD3 gene encodes superoxide dismutase. The SOD3 expression level is\nelevated in patients with BA, and some genetic variants of this gene affect the\ndistribution of extracellular superoxide dismutase in the lungs and reduce the\nrisk of manifesting BA symptoms [ 112 ];\nthe EGFR gene encodes a transmembrane receptor binding extracellular ligands\nbelonging to the epidermal growth factor group. Biopsy specimens from asthma\npatients often contain regions of epithelial damage that are immunostained with\nEGFR; an elevated EGFR expression level is also observed in the morphologically\nintact epithelium of asthma patients [ 19 ];\nthe SLC11A1 gene codes for the divalent metal transporter protein carrying iron\nand manganese. A number of studies have revealed an association between\npolymorphisms in this gene and the development of lung diseases [ 113 ]; and\nthe ZPBP2 gene encodes a protein expressed in the bronchial glandular\nepithelium. The degrees of methylation of this gene are different in healthy\nindividuals than they are in patients with BA [ 114 ].\n\nThe genetic variants of a number of genes identified in this study, which\nincrease and reduce the relative risk of developing BA, may facilitate early\ndiagnosis of bronchial asthma and accurate diagnosis-making in case of\nambiguity. In the long run, analysis of the samples collected from residents of\ndifferent regions will help assess the geographic distribution of the\nrisk-editing genetic variants and not only perform mapping of BA prevalence,\nbut also adequately allocate financial and material resources, as well as\nqualified medical staff, across regions. Timely, including prenatal, detection\nof individuals genetically predisposed to BA and accurate diagnosis-making will\nimprove the quality of medical care, reduce the rates of disability and death\ndue to bronchopulmonary events, and decrease the direct and indirect cost of\ncombatting bronchial asthma.","source_license":"CC-BY-4.0","license_restricted":false}