TABLE 1.
DNA methylation studies in bronchial epithelial cells
| Study population | Ethnicity‐origin | Age average (range) or: mean ± SD/SEM | Gender (male%) | Hospital‐ or population‐based cohort | Asthma/AR diagnosis | Sampling method | Methylation measurement method | Important findings | Reference |
|---|---|---|---|---|---|---|---|---|---|
| DNA methylation cohort: n = 25 (7 controls, 9 atopic, 4 atopic asthmatics, 5 non‐atopic asthmatics) | N/A | DNA methylation cohort: Control 7.28 (4.6–10.1) Atopic 6.78 (4.5–10.9); Atopic asthmatic 8.4 (3.3–14.6); Non‐atopic asthmatic 5.96 (2.4–10.5) | N/A | Hospital | Asthma: Physician‐diagnosed plus documented wheeze by a physician in the past 12 months. Positive responses to ISAAC and ATS questionnaires. | Bronchial brushings | Illumina GoldenGate methylation cancer Panel I (Illumina) | Asthmatics versus controls: no difference in methylation signature non‐asthmatic atopics versus controls: no difference in methylation signature atopic asthmatics versus non‐atopic asthmatics: no difference in methylation signature | Stefanowicz et al. (2012) 22 |
| Gene expression cohort: n = 44 (15 controls, 14 atopic, 15 atopic asthmatics) | Gene expression cohort: Control 5.07 (1.2–12.9; Atopic 7.86 (2.2–16.5); Atopic asthmatic 7.74 (1.3–14.1) | Atopy: Positive RAST or skin prick tests to common allergens. | Asthmatics versus atopic: 8 CpGs, 8 genes: CRIP1, FGFR1, STAT5A, S100A2, ITGA2, EGR4, ID1, IGSF4C, functions include: Cell adhesion, mitogenesis, differentiation, cell cycle progression, senescence, cell growth and proliferation. Gene expression (asthmatics): ↓: STAT5, ↑: CRIP1 | ||||||
| n = 24 (7 controls, 10 atopic, 7 non‐atopic asthmatics to dust mites) | N/A | Control 50 (22–71), asthmatic atopic 35 (21–60), asthmatic non‐atopic 47 (28–78) | Control: 14.3% asthmatic; atopic: 40% asthmatic; non‐atopic: 14.3% | Hospital | Asthma diagnosis by physicians, met global initiative for asthma (GINA) asthma definition. History of dyspnea and wheezing during last 12 months, and one of: (1) >15% increase in forced expiratory volume in 1 s (FEV1) or >12% increase + 200 ml following inhalation of a short‐acting bronchodilator; (2) <10 mg/ml PC20 methacholine; (3) >20% increase in FEV1 after 2 weeks inhaled/systemic corticosteroid treatment. Atopy: Wheal reaction ≥3 mm diameter of skin prick tests, or ≥ than histamine induced | Human methylation27 Beadchip (Illumina) | Asthmatics versus controls: 1 CpG, 1 gene: LCN6, function: Involved in single fertilization; Atopic versus non‐atopic: 24 CpGs, 53 DMRs, 52 genes (most significant: MAP3K5, CDH1, C11orf47, B3GALT1, PKHD1, LOC63928, AKR1C4, LRTM1, KRTAP17‐1, CASP1, MGC33407), associated with multicellular process, response to organic substance, hormone metabolic process, and growth factor receptor binding. | Kim et al. (2013) 23 | |
| Cultured cells: n = 116 (58 controls, 58 IL‐13‐treated) | Freshly isolated cells: African American = 69; European American = 42; Other = 5 | Cultured cells: donors 45 ± 13 SD | Asthma 29% control 33% | Population | Asthma: doctor's diagnosis, no conflicting pulmonary diagnoses. | Cultured cells: Lung explants | Infinium human methylation 450K Bead Chip (Illumina) | Cultured cells: IL‐13 treated versus controls: 6522 CpG‐sites, 3771 genes: Notably TNXB (associated with multiple CpGs), CHI3L1 (asthma biomarker), POSTN & SERPINB2 (markers of Th2‐high asthma phenotype), overal significantly enriched for genes associated with asthma. Gene expression: ↓:48% ↑:52% | Nicodemus‐Johnson et al. (2016) 24 |
| Freshly isolated cells: n = 118 (41 controls, 77 asthmatic); atopy (%) = 63 controls, 88 asthma | Freshly isolated cells: asthma = 39.25 ± 12.95 SD; control = 37.56 ± 11.35 SD | Freshly isolated cells: Bronchial brushing | Freshly isolated cells: asthmatics versus controls: 2020 CpG‐sites (31% overlap with cultured cell CpGs); 74% methylation effect direction overlap | ||||||
| n = 24 (13 controls, 11 asthmatics) | N/A | 20.7 (8–42) | Asthma 45%; control 46% | Hospital | N/A | Bronchial brushings, pronase digestion | N/A | Asthmatics versus controls: gene expression: 6 genes: ↓: AURKA (kinase), DZIP3 (ligase), EHMT2 and SUV39H1 (methyltransferases), ↑: CREBBP and EP300 (acetyltransferases); protein expression: AURKA ↑ in asthmatics (but only AURKA & CREBBP examined) | Stefanowicz et al. (2017) 25 |
| n = 115 (41 controls, 74 asthmatics) | African American = 69; European American = 42; Other = 5 | Asthma = 39.09 ± 12.94 SD; control = 37.56 ± 11.35 SD | Asthma 30%; control 33% | Population | Asthma: doctor's diagnosis, no conflicting pulmonary diagnoses, were using medication (75% inhaled corticosteroids, 41% oral corticosteroids, 4% smokers) | Bronchial brushing | Infinium human methylation 450K Bead Chip (Illumina) | Asthmatics versus controls: 40,892 CpGs, notable genes: CCL26 (chemokine elevated in asthmatic airways), MUC5AC (mucin with roles in airway defence) | Nicodemus‐Johnson et al. (2016b) 26 |
| Gene expression: Modest correlation with nearest gene expression | |||||||||
| N/A | N/A | N/A | N/A | N/A | N/A | N/A | Sodium bisulfite sequencingPyrosequencing: EpiTect bisulfite kit (Qiagen) | Gene expression (17q12‐q21 genes): unaffected: ORMDL3, IKZF3 ↑: GSDMB ↑↑: GSDMA, ZPBP2 | Moussette et al. (2017) 27 |
| Found DNA methylation changes resulted in allelic bias changes of ZPBP2 and ORMDL3 | |||||||||
| n = 33 (pronase digestion: nine controls, eight asthmatics/bronchial brushings: seven controls, nine asthmatics) | N/A | Pronase digestion asthmatic 18.63 ± 3.173 SEM Pronase digestion non‐asthmatic 21 ± 3.27 SEM Bronchial brush asthmatic 31.85 ± 5.0 SEM Bronchial brush Non‐asthmatic 56.22 ± 3.8 SEM | Pronase digestion asthmatic 25%; Pronase digestion non‐asthmatic 78%; Bronchial brush asthmatic 44%; Bronchial brush non‐asthmatic 71% | Hospital | N/A | Bronchial brushings, pronase digestion | Infinium human methylation 450K Bead Chip (Illumina) | DNA methylation profiles alter based on isolation method. | Clifford et al. (2019) 28 |
| Bisulfite PCR‐pyrosequencing | Control pronase versus control bronchial brush: 111 CpGs, 103 genes: Including CHRNE, EDAR, GALNT9, LOC149837, LINC00654, GRIK2, CECR1, OR2I1P, DAXX, HEYL. | ||||||||
| Asthmatics pronase versus controls pronase: 15 DMRs, 1 gene: DUSP22 (asthma‐associated) asthmatics bronchial brush versus controls bronchial brush: 849 DMRs, genes: Notable KALRN and WNT7B (asthma‐associated) | |||||||||
| No DMRs were identified by both pronase and bronchial brushings | |||||||||
| n = 135 (70 controls, 26 persistent asthmatics, 39 remission asthmatics) | N/A | Controls = 39.5 ± 2.03 SEM persistent asthmatics = 48.8 ± 1.85 SEM remission asthmatics = 47.5 ± 2.33 SEM | Persistent asthmatics 58%; remission asthmatics 46%; controls 57% | Population | Asthma: Documented reversibility and/or airway hyperresponsiveness to histamine (PC 20 =< 32 mg/ml). | Bronchial brushings | Infinium human methylation 450K Bead Chip (Illumina) | Asthma versus remission: 4 CpGs, 42 DMRs, genes: Notable KRBOX1, TNXB, LBX1, DGKQ, RPL13 A (role in chronic inflammation amelioration) | Vermeulen et al. (2020) 29 |
| Clinical remission: no asthma attack/wheeze in last 3 years, and no asthma medication. | Gene expression: ↑: ACKR2, DGKQ, RPL13 A. | ||||||||
| Complete remission: no airway hyperresponsiveness to histamine & AMP (>32 mg/ml in 30 s tidal breathing and >320 mg/ml in 2 min tidal breathing), no airflow obstruction signs (FEV 1% predicted >80% pre‐bronchodilator or >90% post bronchodilator). | Remission versus controls: 1163 CpGs, 328 DMRs, genes: Notable PDLIM4, ETV6, GMPR | ||||||||
| Persistent asthma: Divided on the basis of use of inhaled corticosteroids | |||||||||
| n = 13 (5 control, 8 asthmatics) | White | Controls: 37.35 ± 13.26; asthmatics: 44.53 ± 13.55 | Asthma 37.5%; control 40% | Hospital | Asthma diagnosis by pulmonologist/allergologist as per GINA guidelines. 37.5% of asthmatics were atopic | Bronchial brushings | Illumina Infinium EPIC array | Asthmatics versus controls: Methylation Asthmatics: ↑ cytoskeletal remodeling and cell growth: FIGN, PIK3R5, DSC1, TEKT1, PCDHB11, DLC1, TMDO3, TNXB, CAPNSZ, RBM38 ↑ ion transport and metabolism: PDZK1, DDO, HPD, ATP11 B, MANBA, UROS ↑ T‐cell signaling pathway: CMIP ↓ pro‐inflammatory cytokines: IL‐6R, IL1R1, IL1R2, IL36 B, IL17 B, IL17RE, IL4I1 ↑ regulatory genes: IL10RA, TGFBR2 ↑ chemokines: CCL26, CCL24 ↑ bronchial barrier regulation: AMOTL1, CLDN11, CLDN18, MAGI1, TJP2, JAM3 (tight junction family members)/ACTB (actin protein)/TUBA1C, ROCK2, LLGL1 (cytoskeleton components) | Wawrzyniak et al. (2021) 30 |
| Methylation Controls: ↑ transcription coactivation, posttranscription activation, intracellular signaling: GREBBD, SORBS2, PCBR3, TBX2, BRD2, DAXX, ACTB, POLD2, MGAT3 | |||||||||
| Notable: TET1 (epigenetic modifier) methylated, PRMTs (histone methyltransferases) not methylated |