Epigenetics studies mechanisms such as DNA methylation, histone modifications, non-coding RNAs, and alternative polyadenylation that can modify gene activity without changing the underlying DNA nucleotide base-pair structure. Because these changes are reversible, they have potential in developing novel therapeutics. Currently, seven pharmaceutical agents targeting epigenetic changes are FDA approved and commercially available for treatment of certain cancers. However, studies investigating epigenetics in chronic rhinosinusitis (CRS) have not been undertaken previously in the United States.
Objectives
The goal of this study was to investigate sinonasal DNA methylation patterns in CRS versus controls, to discern environmentally-induced epigenetic changes impacting CRS subjects.
Methods and Results
Ethmoidal samples from CRS and inferior turbinate mucosal tissue samples from controls without CRS were studied. DNA methylation was studied by Reduced Representation Bisulfite Sequencing. RADMeth® biostatistical package was used to identify differentially methylated regions (DMRs) between CRS and controls. Ingenuity Pathway analysis of DMRs was performed to identify top upstream regulators and canonical pathways. Ninety-three samples from 64 CRS subjects (36 CRSwNP; 28 CRSsNP) and 29 controls were studied. CRS and control samples differed in 13 662 CpGs sites and 1381 DMRs. Top upstream regulators identified included: 1. CRS versus controls: TGFB1, TNF, TP53, DGCR8, and beta-estradiol. 2. CRSwNP versus controls: TGFB1, CTNNB1, lipopolysaccharide, ID2, and TCF7L2. 3. CRSsNP versus controls: MYOD1, acetone, ID2, ST8SIA4, and LEPR.
Conclusions
Differential patterns of methylation were identified between controls and CRS, CRSwNP, and CRSsNP. Epigenetic, environmentally-induced changes related to novel, inflammatory, immunologic, and remodeling pathways appear to affect epithelial integrity, cell proliferation, homeostasis, vascular permeability, and other yet uncharacterized pathways and genes.
KatoASchleimerRPBleierBS. Mechanisms and pathogenesis of chronic rhinosinusitis. J Allergy Clin Immunol. 2022;149(5):1491-1503.
2.
OrlandiRRKingdomTTSmithTL, et al.International consensus statement on allergy and rhinology: rhinosinusitis 2021. Int Forum Allergy Rhinol. 2021;11(3):213-739.
MartinMJGarcia-SanchezAEstravisM, et al.Genetics and epigenetics of nasal polyposis: a systematic review. J Investig Allergol Clin Immunol. 2021;31(3):196-211.
6.
YaoQChenYZhouX. The roles of microRNAs in epigenetic regulation. Curr Opin Chem Biol [Internet]. 2019;51:11-17. Available from: https://pubmed.ncbi.nlm.nih.gov/30825741/.
7.
XuS-MCurry-HydeASytnykVJanitzM. RNA polyadenylation patterns in the human transcriptome. Gene [Internet]. 2022;816(August 2021):146133. Available from: https://doi.org/10.1016/j.gene.2021.146133.
8.
TammenSAFrisoSChoiS. Molecular aspects of medicine epigenetics: the link between nature and nurture. Mol Aspects Med. 2013;34(4):753-764.
9.
MooreLDLeTFanG. DNA methylation and its basic function. Neuropsychopharmacology [Internet]. 2013;38(1):23-38. Available from: http://dx.doi.org/10.1038/npp.2012.112.
NepaliKLiouJP. Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends [Internet]. Journal of Biomedical Science. BioMed Central. 2021;28:1-58. Available from: https://doi.org/10.1186/s12929-021-00721-x.
CohenNAWidelitzJSChiuAGPalmerJNKennedyDW. Familial aggregation of sinonasal polyps correlates with severity of disease. Otolaryngol Head Neck Surg [Internet]. 2006;134(4):601-604. Available from: https://pubmed.ncbi.nlm.nih.gov/16564380/.
15.
LockeyRFRucknagelDLVanselowNA. Familial occurrence of asthma, nasal polyps and aspirin intolerance. Ann Intern Med [Internet]. 1973;78(1):57-63. Available from: https://pubmed.ncbi.nlm.nih.gov/4682309/.
16.
OakleyGCurtinKOrbQSchaeferCOrlandiRAltJ. Familial risk of chronic rhinosinusitis with and without nasal polyposis: genetics or environment. Int Forum Allergy Rhinol. 2015;5(4):276-282.
17.
CheongHSParkSMKimMO, et al.Genome-wide methylation profile of nasal polyps: relation to aspirin hypersensitivity in asthmatics. Allergy Eur J Allergy Clin Immunol. 2011;66(5):637-644.
18.
LiJJiaoJWangM, et al.Hypomethylation of the IL8 promoter in nasal epithelial cells of patients with chronic rhinosinusitis with nasal polyps. J Allergy Clin Immunol [Internet]. 2019;144(4):993-1003.e12. Available from: https://doi.org/10.1016/j.jaci.2019.06.042.
19.
ZhangXHZhangYNLiHB, et al.Overexpression of miR-125b, a novel regulator of innate immunity, in eosinophilic chronic rhinosinusitis with nasal polyps. Am J Respir Crit Care Med. 2012;185(2):140-151.
20.
LuoXQShaoJBXieRD, et al.Micro RNA-19a interferes with IL-10 expression in peripheral dendritic cells of patients with nasal polyposis. Oncotarget. 2017;8(30):48915-48921.
21.
ChoJSMoonYMParkIH, et al.Epigenetic regulation of myofibroblast differentiation and extracellular matrix production in nasal polyp-derived fibroblasts. Clin Exp Allergy. 2012;42(6):872-882.
22.
ChoJSMoonYMParkIH, et al.Effects of histone deacetylase inhibitor on extracellular matrix production in human nasal polyp organ cultures. Am J Rhinol Allergy. 2013;27(1):18-23.
23.
KidoguchiMNoguchiENakamuraT, et al.DNA Methylation of proximal PLAT promoter in chronic rhinosinusitis with nasal polyps. Am J Rhinol Allergy. 2018;32(5):374-379.
24.
KimJYChaMJParkYS, et al.Upregulation of FZD5 in eosinophilic chronic rhinosinusitis with nasal polyps by epigenetic modification. Mol Cells. 2019;42(4):345-355.
25.
YuHJuJLiuJLiD. Aberrant expression of miR-663 and transforming growth factor-β1 in nasal polyposis in children. Exp Ther Med.2018;15:4550-4556.
26.
Callejas-DíazBFernandezGFuentesM, et al.Integrated mRNA and microRNA transcriptome profiling during differentiation of human nasal polyp epithelium reveals an altered ciliogenesis. Allergy Eur J Allergy Clin Immunol. 2020;75(10):2548-2561.
27.
LiJJiaoJGaoYZhangYZhangL. Association between methylation in nasal epithelial TSLP gene and chronic rhinosinusitis with nasal polyps. Allergy, Asthma Clin Immunol [Internet]. 2019;15(1):1-8. Available from: https://doi.org/10.1186/s13223-019-0389-3.
28.
TianPSunYLiY, et al.A global analysis of tandem 3′UTRs in eosinophilic chronic rhinosinusitis with nasal polyps. PLoS One. 2012;7(11):e48997.
29.
TianPLiJLiuX, et al.Tandem alternative polyadenylation events of genes in non-eosinophilic nasal polyp tissue identified by high-throughput sequencing analysis. Int J Mol Med. 2014;33(6):1423-1430.
30.
LiuCCXiaMZhangYJ, et al.Micro124-mediated AHR expression regulates the inflammatory response of chronic rhinosinusitis (CRS) with nasal polyps. Biochem Biophys Res Commun. 2018;500(2):145-151.
31.
XuanLLuanGWangY, et al.MicroRNAs regulating mucin type O-glycan biosynthesis and transforming growth factor β signaling pathways in nasal mucosa of patients with chronic rhinosinusitis with nasal polyps in Northern China. Int Forum Allergy Rhinol. 2019;9(1):106-113.
32.
ZhengYBZhaoYYueLY, et al.Pilot study of DNA methylation in the pathogenesis of chronic rhinosinusitis with nasal polyps. Rhinology. 2015;53(4):345-352.
33.
MaZShenYZengQ, et al.MiR-150-5p regulates EGR2 to promote the development of chronic rhinosinusitis via the DC-Th axis. Int Immunopharmacol. 2018;54:188-197.
34.
QingXZhangYPengYHeGLiuALiuH. Mir-142-3p regulates inflammatory response by contributing to increased TNF-α in chronic rhinosinusitis with nasal polyposis. Ear, Nose Throat J. 2021;100(1):NP50-NP56.
35.
SeiberlingKAChurchCAHerringJLSowersLC. Epigenetics of chronic rhinosinusitis and the role of the eosinophil. Int Forum Allergy Rhinol. 2012;2(1):80-84.
36.
MahdaviniaMSuhLACarterRG, et al.Increased noneosinophilic nasal polyps in chronic rhinosinusitis in US second-generation Asians suggest genetic regulation of eosinophilia. J Allergy Clin Immunol [Internet]. 2015;135(2):576-579. Available from: https://pubmed.ncbi.nlm.nih.gov/25312761/.
37.
RosenfeldRMPiccirilloJFChandrasekharSS, et al.Clinical practice guideline (update): adult sinusitis. Otolaryngol Head Neck Surg. 2015;152(2 suppl):S1-39.
38.
HopkinsCGillettSSlackRLundVJBrowneJP. Psychometric validity of the 22-item Sinonasal Outcome Test. Clin Otolaryngol [Internet]. 2009;34(5):447-454. Available from: https://pubmed.ncbi.nlm.nih.gov/19793277/.
39.
LundVJKennedyDW. Quantification for staging sinusitis. The staging and therapy group. Ann Otol Rhinol Laryngol Suppl. 1995;167:17-21.
40.
SunZBahetiSMiddhaS, et al.SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics [Internet]. 2012;28(16):2180-2181. Available from: https://pubmed.ncbi.nlm.nih.gov/22689387/.
LiHHandsakerBWysokerA, et al.The sequence alignment/map format and SAMtools. Bioinformatics [Internet]. 2009;25(16):2078-2079. Available from: https://pubmed.ncbi.nlm.nih.gov/19505943/.
43.
DolzhenkoESmithAD. Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. BMC Bioinformatics [Internet]. 2014;15(1):215. Available from: https://pubmed.ncbi.nlm.nih.gov/24962134/.
44.
AnkamSRoviniABahetiS, et al.DNA Methylation patterns in human iPSC-derived sensory neuronal differentiation. Epigenetics [Internet]. 2019;14(9):927-937. Available from: https://pubmed.ncbi.nlm.nih.gov/31148524/.
45.
BahetiSSinghPZhangY, et al.Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation. Epigenomics [Internet]. 2017;9(11):1423-1435. Available from: https://pubmed.ncbi.nlm.nih.gov/28967791/.
46.
LiuTSunYBaiW. The role of epigenetics in the chronic sinusitis with nasal polyp. Curr Allergy Asthma Rep. 2021;21(1):1.
47.
KimJYKimDKYuMSChaMJYuSLKangJ. Role of epigenetics in the pathogenesis of chronic rhinosinusitis with nasal polyps. Mol Med Rep. 2018;17(1):1219-1227.
48.
WangQPEscudierERoudot-ThoravalFAbd Al SamadIPeynègreRCosteA. Myofibroblast accumulation induced by transforming growth factor-beta is involved in the pathogenesis of nasal polyps. Laryngoscope [Internet]. 1997;107(7):926-931. Available from: https://pubmed.ncbi.nlm.nih.gov/9217133/.
49.
SaitoAHorieMNagaseT. TGF-β signaling in lung health and disease. Int J Mol Sci [Internet]. 2018;19(8):2460. Available from: https://pubmed.ncbi.nlm.nih.gov/30127261/.
50.
KimS-HParkH-SHollowayJWShinH-DParkC-S. Association between a TGFbeta1 promoter polymorphism and rhinosinusitis in aspirin-intolerant asthmatic patients. Respir Med. 2007;101(3):490-495.
51.
HenmyrVVandeplasGHalldénC, et al.Replication study of genetic variants associated with chronic rhinosinusitis and nasal polyposis. J Allergy Clin Immunol [Internet]. 2014;133(1):273-275. Available from: https://pubmed.ncbi.nlm.nih.gov/24074519/.
52.
HoltmannMNeurathM. Differential TNF-signaling in chronic inflammatory disorders. Curr Mol Med [Internet]. 2004;4(4):439-444. Available from: https://pubmed.ncbi.nlm.nih.gov/15354874/.
53.
ErbekSSYurtcuEErbekSAtacFBSahinFICakmakO. Proinflammatory cytokine single nucleotide polymorphisms in nasal polyposis. Arch Otolaryngol Head Neck Surg [Internet]. 2007;133(7):705-709. Available from: https://pubmed.ncbi.nlm.nih.gov/17638785/.
54.
BernsteinJMAnonJBRontalMConroyJWangCSuchestonL. Genetic polymorphisms in chronic hyperplastic sinusitis with nasal polyposis. Laryngoscope. 2009;119(7):1258-1264.
55.
BatikhanHGokcanMKBederEAkarNOzturkAGercekerM. Association of the tumor necrosis factor-alpha −308 G/A polymorphism with nasal polyposis. Eur Arch Otorhinolaryngol. 2010;267(6):903-908.
56.
WangCSHoneybrookAChapurinNKeswaniAJangDW. Sinusitis in patients on tumor necrosis factor alpha inhibitors. Int Forum Allergy Rhinol [Internet]. 2017;7(4):380-384. Available from: https://pubmed.ncbi.nlm.nih.gov/27958666/.
57.
WeeJHKoYKKhalmuratovaRShinHWKimDWRheeCS. Effect of lipopolysaccharide and polyinosinic: polycytidylic acid in a murine model of nasal polyp. Sci Rep [Internet]. 2021;11(1):1021. Available from: https://pubmed.ncbi.nlm.nih.gov/33441902/.
58.
WangXZhangNBoM, et al.Diversity of TH cytokine profiles in patients with chronic rhinosinusitis: a multicenter study in Europe, Asia, and Oceania. J Allergy Clin Immunol [Internet]. 2021;144(10):993-1003.e12. Available from: http://dx.doi.org/10.1038/s41588-018-0314-6.
59.
CaoPPLiHBWangBF, et al.Distinct immunopathologic characteristics of various types of chronic rhinosinusitis in adult Chinese. J Allergy Clin Immunol [Internet]. 2009;124(3):478-84. Available from: https://pubmed.ncbi.nlm.nih.gov/19541359/.
60.
Van BruaeneNPérez-NovoCABasinskiTM, et al.T-cell regulation in chronic paranasal sinus disease. J Allergy Clin Immunol. 2008;121(6):1435-1441.e3.
61.
KajiIKaunitzJD. Chemosensing in the colon. Physiol Gastrointest Tract Sixth Ed. 2018;1–2:671-682.
62.
LiXLongJHeTBelshawRScottJ. Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer’s disease. Sci Reports[Internet]. 2015;5(1):1-12. Available from: https://www.nature.com/articles/srep12393.
63.
Fernández-BertolínLMullolJFuentes-PradoM, et al.Effect of lipopolysaccharide on glucocorticoid receptor function in control nasal mucosa fibroblasts and in fibroblasts from patients with chronic rhinosinusitis with nasal polyps and asthma. PLoS One [Internet]. 2015;10(5):e0125443. Available from: https://pubmed.ncbi.nlm.nih.gov/25943109/.
64.
HolmilaRBornholdtJHeikkiläP, et al.Mutations in TP53 tumor suppressor gene in wood dust-related sinonasal cancer. Int J Cancer [Internet]. 2010;127(3):578-588. Available from: https://pubmed.ncbi.nlm.nih.gov/19950227/.
PytelMWójtowiczTMercikK, et al.17 beta-estradiol modulates GABAergic synaptic transmission and tonic currents during development in vitro. Neuropharmacology [Internet]. 2007;52(6):1342-1353. Available from: https://pubmed.ncbi.nlm.nih.gov/17418284/.
67.
AudesirkTCabellLKernMAudesirkG. beta-estradiol influences differentiation of hippocampal neurons in vitro through an estrogen receptor-mediated process. Neuroscience [Internet]. 2003;121(4):927-934. Available from: https://pubmed.ncbi.nlm.nih.gov/14580943/.
68.
SciosciaGCarpagnanoGELacedoniaD, et al.The role of airways 17β-estradiol as a biomarker of severity in postmenopausal asthma: a pilot study. J Clin Med [Internet]. 2020;9(7):1-10. Available from: https://pubmed.ncbi.nlm.nih.gov/32610544/.
69.
Nejatbakhsh SamimiLFallahpourMKhoshmirsafaM, et al.The impact of 17β-estradiol and progesterone therapy on peripheral blood mononuclear cells of asthmatic patients. Mol Biol Rep [Internet]. 2021;48(1):297-306. Available from: https://pubmed.ncbi.nlm.nih.gov/33315175/.
70.
FalagasMEMourtzoukouEGVardakasKZ. Sex differences in the incidence and severity of respiratory tract infections. Respir Med [Internet]. 2007;101(9):1845-1863. Available from: https://pubmed.ncbi.nlm.nih.gov/17544265/.
71.
BresciaGControGRuaroA, et al.Sex and age-related differences in chronic rhinosinusitis with nasal polyps electing ESS. Am J Otolaryngol [Internet]. 2022;43(2):103342. Available from: https://pubmed.ncbi.nlm.nih.gov/34971999/.
72.
LalDRoundsABDivekarR. Gender-specific differences in chronic rhinosinusitis patients electing endoscopic sinus surgery. Int Forum Allergy Rhinol [Internet]. 2016;6(3):278-286. Available from: https://pubmed.ncbi.nlm.nih.gov/26574907/.
73.
BrarTBahetiSBhagwateAVKitaHMarinoMJLalD. Genomewide epigenetic study shows significant DNA hypermethylation in chronic rhinosinusitis versus control ethmoidal tissue. Int Forum Allergy Rhinol. 2023 Jun 10. doi: 10.1002/alr.23205. Epub ahead of print. PMID: 37300454. Available from: https://pubmed.ncbi.nlm.nih.gov/37300454.
74.
LalDSongLBrarT, et al.Antibody responses to the host microbiome in chronic rhinosinusitis. Int Forum Allergy Rhinol [Internet]. 2023 Aug;13(8):1503-1510.2023. Available from: https://pubmed.ncbi.nlm.nih.gov/36504343/
75.
Pérez-NovoCAZhangYDenilS, et al.Staphylococcal enterotoxin B influences the DNA methylation pattern in nasal polyp tissue: a preliminary study. Allergy Asthma Clin Immunol [Internet]. 2013;9(1):48. Available from: https://pubmed.ncbi.nlm.nih.gov/24341752/.
76.
CavalliGHeardE. Advances in epigenetics link genetics to the environment and disease. Nature. 2019;571(7766):489-499.
77.
PlattMPSolerZMetsonRStankovicKM. Pathways analysis of molecular markers in chronic sinusitis with polyps. Otolaryngol Head Neck Surg [Internet]. 2011;144(5):802-808. Available from: https://pubmed.ncbi.nlm.nih.gov/21493366/.
78.
SeshadriSRosatiMLinDC, et al.Regional differences in the expression of innate host defense molecules in sinonasal mucosa. J Allergy Clin Immunol [Internet]. 2013;132(5):1227-1230. Available from: https://pubmed.ncbi.nlm.nih.gov/23895899/.
79.
WangHSongJPanL, et al.Regional differences in ACE2 expression in the sinonasal mucosa of adult Chinese patients with chronic rhinosinusitis. Allergy [Internet]. 2021;76(5):1565-1568. Available from: https://pubmed.ncbi.nlm.nih.gov/33037637/.
80.
LiYPanXRobertsML, et al.Stability of global methylation profiles of whole blood and extracted DNA under different storage durations and conditions. Epigenomics [Internet]. 2018;10(6):797-811. Available from: https://pubmed.ncbi.nlm.nih.gov/29683333/.
81.
SaffariASilverMJZavattariP, et al.Estimation of a significance threshold for epigenome-wide association studies. Genet Epidemiol [Internet]. 2018;42(1):20-33. Available from: https://pubmed.ncbi.nlm.nih.gov/29034560/.
82.
BrarTMcCabECMiglaniAMarinoMJLalD. Tissue eosinophilia is effective for studying differential expression of genes by RNA sequencing and may offer superior insights into Chronic Rhinosinusitis than study by polyp status. In: ARS ar COSM 2022. Dallas; 2022.
83.
RakyanVKDownTABaldingDJBeckS. Epigenome-wide association studies for common human diseases. Nat Rev Genet.2011;12:529-541.
84.
MartinoDKesperDAAmarasekeraMHarbHRenzHPrescottS. Epigenetics in immune development and in allergic and autoimmune diseases. J Reprod Immunol. 2014;104–105(C):43-48.
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