DNA methylation biomarkers of future health outcomes in children

Premature infants are known to have an increased risk of later life neurocognitive impairment. Two studies have attempted to identify DNA methylation biomarkers of future cognitive impairment in premature infants. Tilley et al. [35] examined genome-wide methylation, using the 450K array, in a homogenised sample of chorionic placental tissue of 84 extremely premature infants (born at < 28 weeks gestation). At 10 years of age, participants underwent a cognitive assessment using the School-Age Differential Ability Scales–II. Using logistic regression analysis, they identified 17 probe sites, corresponding to 16 genes involved in neuronal development and function, where increased DNA methylation was associated with cognitive impairment at 10 years. Ten of the probes were located in the gene body, 3 in the promoter region, 3 in the 5′UTR, and 1 in the 3′UTR. The effect size was modest with odds ratios (OR) for these associations between 1.04 and 1.09. For each of the genes, a 1% increase in methylation at their respective probe site resulted in a 4–7% increase in the odds of cognitive impairment. There was evidence of a dose-response relationship, with higher levels of methylation being associated with greater impairment. Arpon et al. [36] examined 22 full-term infants and 24 premature infants (< 34 weeks gestation). They performed an EWAS using a 450K array on whole blood samples collected at 12 months of age. Neurodevelopmental outcome at 2–3 years of age was assessed using the Bayley Scale of Infant Development. Correlations were assessed using Pearson or Spearman tests, and linear regression was performed where significant correlations existed. Correction for multiple testing was undertaken using the Benjamini-Hochberg procedure. They found methylation of a single CpG site located in the 5′UTR of SLC6A3 showed the greatest difference between preterm and term infants (increased methylation in preterm) and that increased methylation in both term and preterm infants was associated with significantly poorer motor function (r = − 0.55, p = 0.0001) and mental function (r = − 0.44, p = 0.0028). The sites of differential methylation identified in each of these studies did not overlap, which may reflect differences in sample size, the biospecimen used for methylation analysis, outcome assessment tool, and age at both methylation analysis and outcome assessment.

In a large study examining 65 patients with food allergy, Martino et al. [18] assessed DNA methylation in naive CD₄ T cells at enrolment and then 2–4 years later. Subjects were aged between 11 and 15 months at enrolment and defined as being food allergic based on a positive skin prick test and clinical reactivity. At reassessment, patients were classified as having persistent food allergy (based on oral food challenge) or resolved allergy. The investigators examined whether the change in DNA methylation profiles from baseline to reassessment could predict the likelihood of persistent allergy, and they focused on 26 loci which were demonstrated to be differentially methylated between patients with and without food allergy. They found that in 24 of 26 loci, there was a significant change (adjusted p value < 0.05) in methylation from baseline to follow-up in patients with persistent allergy, whereas methylation was stable in patients whose allergy resolved. In the group with persistent allergy, the maximum change in methylation at an individual locus between baseline and follow-up was 17.2%. Fu et al. [42] studied methylation in the 5′UTR of β2 adrenoreceptor (ADRB2) in 182 children with asthma aged between 5 and 12 years. Blood was collected at enrolment, and patients were followed up for 12 months. Parent-reported symptoms were used to calculate an asthma severity score, which was used to classify patients into mild or severe disease. Multivariate logistic regression (adjusted for age and gender) was used. DNA methylation was classified as ‘low,’ ‘intermediate,’ and ‘high,’ and asthma as ‘mild’ or ‘severe.’ In a dose-dependent manner, increasing methylation of ADRB2 was associated with more severe asthma, with those with intermediate methylation having an OR 4.11 (95% CI 1.58–10.73) for severe asthma and those with high methylation having an OR 7.63 (95% CI 3.02–19.26). The median methylation level in the severe asthma group was 1.14% (range 0.2 to 3.6%) and in the mild asthma group was 0.81% (0 to 2.4%). They also examined nitrous oxide exposure and found that in the highly exposed group, those with ADRB2 hypermethylation had an OR of 4.59 (95% CI 1.03–20.55) of having severe asthma.

Two studies have investigated whether DNA methylation markers can predict response to corticosteroids during an acute asthma exacerbation. Xiao et al. [27] studied Vanin-1 (VNN1) methylation in nasal epithelial cells, a surrogate for lower airway epithelium, obtained in 18 children aged 5–18 years at presentation to hospital with an acute asthma exacerbation and again after 12–24 h. VNN1 was identified as a gene of interest via an initial gene expression investigation of > 20,000 genes. Patients were treated with a standardised asthma protocol which included criteria for discharge. Good corticosteroid response was defined as a length of hospital stay ≤ 24 h, whereas poor response was defined as a length of stay > 24 h. Those who had a good response to corticosteroids had an increase in methylation at a single CpG, located in the promoter region of VNN1, whereas those that did not respond to corticosteroids had evidence of decreased methylation, although the raw figures were not reported. When assessed using Fischer’s exact test, the differences were significant (p = 0.003). At the same hospital, Zhang et al. [28] used the same design but assessed genome-wide methylation using the 450K array. Their study involved 33 children presenting with acute asthma exacerbations aged 5–18 years. They used linear regression and surrogate variable analysis to correct for confounders, as well as correcting for multiple testing. They found hypermethylation at 1 site in the promoter of lactate dehydrogenase C (LDHC) at presentation was associated with poor treatment response. The mean (standard error) methylation level was 87.7% (2.1%) in the poor response group, and 78.6% (2.4%) in the good responders (p = 0.007). A major strength of the two studies looking at treatment effect was the use of nasal epithelial cells to assess DNA methylation, which is a better surrogate for bronchial epithelial cells than peripheral blood [43].

Another area which has been widely studied in psychiatric disorders. In a group of 164 patients with 22q11 microdeletion syndrome, who are at an increased risk of psychiatric disorders, Starnawska et al. [38] performed an EWAS using the 450K array on neonatal blood spot samples. The later development of a psychiatric disorder was assessed by examining the Danish national psychiatric registry at a mean age of 14.7 years. Linear regression was used to adjust for confounders such as sex and age. A total of 9 differentially methylated probes were significantly associated with development of a psychiatric disorder (unadjusted p value < 10⁻⁶). The effect size of each individual CpG was not described. The probes were located in the promoter region of associated genes (4/9), intergenic regions (3/9), and the gene body (2/9). A further 9 probes associated with intellectual disability, 3 with schizophrenia, 2 with behavioural disorders, and 8 with development disorders. The individual effect size was not detailed for any of these associations. The most common location of probes associated with intellectual disability was the promoter (4/9), and for development disorders, it was the body (4/9). Several studies have examined whether DNA methylation biomarkers can predict response to treatment of psychiatric conditions. Gasso et al. [29] examined whether methylation at 7 CpG sites in the promoter region of 5-hydroxytryptamine receptor 1B (HTR1B), measured in blood, could predict treatment response to 12 weeks of the selective serotonin reuptake inhibitor medication, fluoxetine. They studied 83 children aged between 10 and 17 years who were treated with fluoxetine due to major depressive disorder, obsessive-compulsive disorder, or generalised anxiety disorder. Subjects completed multiple validated scales which measure disease severity, and the change in these scales across 12 weeks was used to define treatment response. Pearson’s test was used to assess correlation, and a Bonferroni correction for multiple testing was performed. When the methylation level at the 7 CpG sites was averaged, they found a moderately strong inverse relationship with higher methylation level associated with reduced fluoxetine response (r = −0.335; p = 0.004). The methylation level for the two groups was not reported. In a study of 116 children aged 6–13 years with an anxiety disorder, the response to cognitive behaviour therapy (CBT) was assessed [31]. Using buccal swab samples, targeted analysis of methylation of 6 CpG sites in the promoter region of the serotonin transporter (SLC6A4) was performed pre- and post-treatment with CBT. Treatment response was based on whether the anxiety disorder had resolved. Subjects with a sustained CBT response (measured 6 months post-treatment) were more likely to have increased methylation at a single CpG during treatment (+ 3.48%), whereas non-responders were more likely to decrease (− 5.44%), and this relationship was significant when corrected for multiple testing (p = 0.002). In another study also examining buccal swabs from children (n = 98) with anxiety disorders, and their response to cognitive behaviour therapy, DNA methylation of CpG sites in the promoter region of FK506 binding protein 5 (FKBP5) and glucocorticoid receptor (GR) was assessed before and immediately after treatment [30]. The children were aged between 5 and 18 years. Treatment response was defined as a change in primary anxiety disorder severity. No significant effect of FKBP5 or GR methylation was found. In a study of 111 children, mean age 9.25 years, with attention deficit hyperactivity disorder (ADHD) who were treated with methylphenidate, dopamine transporter (DAT1), and dopamine receptor D4 (DRD4), promoter methylation was assessed in blood samples collected pre-treatment to see if this predicted treatment response [32]. The diagnosis of ADHD was based on fulfilling international criteria, and treatment response was based on change in a validated ADHD severity questionnaire across 6 weeks. Spearman’s rank correlation test was used to assess correlations. They found lower mean DAT1 methylation was associated with greater treatment response (rho = − 0.222, p = 0.019) although the mean methylation levels were not reported.

Three studies have attempted to identify DNA methylation biomarkers of severity of neonatal abstinence syndrome (NAS). Wachman et al. [20] analysed opioid receptor mu 1 (OPRM1) promoter methylation in the saliva of 58 newborns and the relationship with NAS severity. NAS severity was primarily defined based on the need for pharmacological treatment, which was determined based on a standardised protocol. They used linear and logistic regression models as well as correction for multiple testing using the Benjamini and Hochberg method. The study found infants needing pharmacological treatment for NAS had higher methylation at several CpGs: CpG − 18 (11.4% vs 4.4%, p = .001), CpG − 14 (46.1% vs 24.0%, p = .002), and CpG + 23 (26.3% vs 12.9%, p = .008). The same group of authors conducted another study with the same methods and research questions in a group of 86 infants with NAS. They did not replicate the finding with regard to CpGs − 18, +23, but did find that hypermethylation of CpG − 14 was associated with greater severity of NAS measured by need for 2 medications to control symptoms (adjusted difference = 4.9% (95% CI 1.8–8.1%), p = 0.0030) [19]. In a study of 21 babies, McLaughlin et al. [21] also used early life saliva swabs and analysed methylation in ATP binding cassette subfamily B member 1 (ABCB1) promoter, cytochrome P450 family 2 subfamily D member 6 (CYP2D6) exon 1, and OPRM1 promoter and exon 1. They used a standardised protocol for monitoring NAS severity. Unlike the studies by Wachman et al., they did not find any significant effect. A potential explanation is the smaller sample size of 21, as compared to 58 and 86 in the positive studies.

In a group of 20 premature infants, DNA methylation in the GR promoter was analysed in blood from day 4 of life [22]. The outcome of interest was need for treatment with glucocorticosteroids for treatment of lung disease of prematurity or late-onset circulatory collapse, although criteria for exactly when glucocorticosteroids were prescribed were not detailed. Using a logistic regression model, they found a weak association between methylation at a single CpG site and need for treatment with glucocorticosteroids (likelihood ratio 3.889, p = 0.0486). Dhas et al. [37] investigated 51 newborns with sepsis which was defined as clinical features and presence of biochemical markers. They analysed global DNA methylation in whole blood and using independent samples t tests found those who developed renal failure as a complication of sepsis had slightly higher global methylation levels (2.88% vs. 2.39%, p = 0.02).

Two studies have investigated children with inflammatory bowel disease (IBD). Howell et al. [23] used intestinal biopsy samples from 109 children with IBD and performed an EWAS to identify biomarkers which predicted disease severity over the following 18 months. Disease severity was based on clinical factors such as requirement for treatment with biological agents and time to third treatment escalation following diagnosis. They also evaluated genome-wide gene expression. Differential methylation analysis was performed using limma for DNA methylation data, with a significant false discovery rate [FDR] of < 0.01. They identified a DNA methylation profile that was associated with increased disease severity, as well as demonstrating a gene expression profile that is associated with severe disease with significant overlap in the genes involved. A strength of this study was using samples directly from the tissue of interest. Another study used blood samples collected at diagnosis and the EpicArray to perform an EWAS on 164 children with Chron’s disease [24]. They measured disease severity by considering the time to progress to complicated disease and attempted to identify DMP using linear mixed-effects models and the Bonferroni correction for multiple testing. They were unable to find any CpG sites that were associated with disease severity.

Meng et al. studied patients with idiopathic scoliosis and the risk of progression of the scoliosis curve beyond 30°, which is a marker of severity. They identified CpG sites of interest in blood, by first investigating two female twin pairs with idiopathic scoliosis who were discordant for curve progression. The top 4 DMP were chosen for replication in a cross-sectional cohort of 92 adolescents who were divided based on the severity of scoliosis at presentation, and only one CpG site (cg01374129) remained a significant DMP. This CpG site is not associated with a gene. They then tested the performance of methylation at this individual CpG in a cohort of 276 adolescent subjects who had mild scoliosis at presentation and then were divided based on whether their scoliosis progressed prior to skeletal maturation. They used the Mann-Whitney U test to compare the mean methylation level and progression status. Mean methylation at cg01374129 was lower in the group that progressed (approximately 10% vs. 16%, p < 0.0001), and when a receiver operator curve was calculated, the area under the curve was 0.827 (95% CI 0.780 to 0.876), with a sensitivity of 76.4% and a specificity of 85.6% at a cutoff level of 15.1%. Two studies have attempted to identify biomarkers of development of chronic pain complications post-scoliosis surgery. In a study of 128 adolescent patients with idiopathic scoliosis undergoing scoliosis surgery, OPRM1 promoter methylation was assessed at 22 CpG sites in blood collected during the operation [40]. Acute and chronic pain outcomes were assessed using internationally validated definitions and were dichotomised for analysis. Linear regression models were used for analysis with significance set at p < 0.05. There was no correction for multiple testing. After adjustment for preoperative pain score and morphine consumption over postoperative days 1 and 2, higher OPRM1 promoter methylation at 3 CpG sites was associated with increased acute postoperative pain. The strength of the association was weak for two CpG sites with a 1% increase in DNA methylation associated with regression coefficients of 0.921 and 1.864; however, one CpG had a regression coefficient of 17.736. When chronic postsurgical pain was assessed, there was significant different methylation at two CpG sites. The OR for these associations were relatively weak: 1.069 (95% confidence interval 1.022–1.119) and 1.037 (1.000–1.075). Once again, adjustment was performed for preoperative pain and postoperative morphine consumption. The two CpG sites did not overlap with those associated with acute postoperative pain. The authors provided further evidence for the role of OPRM1 methylation via using functional genomic analysis from publicly available databases which showed increased methylation would lead to reduced gene expression and reduced response to opioids. In a subsequent study, the same authors assessed 46 adolescents undergoing scoliosis surgery. They performed an EWAS using the EpicArray on peripheral blood samples. For this study, they used medication use and questionnaires to assess pain severity. Surrogate variance analysis was used to control for confounders, and adjusted linear regression models were used to test for DMP. They identified 637 significantly differentially methylated probes associated with chronic postsurgical pain (p < 0.05). The DMPs were most commonly found in the promoter region (23.31%) and gene bodies (36.34%). The 637 DMPs were associated with 310 genes and which are associated with pathways such as GABA receptor signalling, protein kinase C signalling, dopamine receptor, and cyclic adenosine monophosphate-mediated signalling.

A number of other conditions have been investigated by single studies. A single study has investigated 68 children with juvenile idiopathic arthritis [26]. Patients were stratified based on relapsing or sustained remission following cessation of anti-tumour necrosis alpha treatment. The 450K array was performed on CD₄ T cells collected as anti-tumour necrosis alpha treatment was stopped. Weighted gene coexpression network analysis was used to identify differential methylation. This analysis examines correlated CpGs rather than individual CpGs and reports differentially methylated regions (DMR). They identified 5 DMRs between the two groups. The DMRs were associated with genes implicated in T cell activation, and this relationship was confirmed in subsequent gene expression and protein analysis experiments, with elevated markers of T cell activation in those who did not have sustained remission post-therapy cessation. Kuo et al. [33] studied 36 patients with Kawasaki disease and assessed the relationship between Fc fragment of IgG receptor IIa (FCGR2A) promoter methylation and response to treatment with intravenous immunoglobulin (IVIG), based on defervescence within 48 h. The sample source for methylation analysis was not reported. Mean methylation levels between responders and non-responders were compared using the chi-square test. They identified 5 CpG sites where increased methylation was associated with non-response to IVIG. At the 5 CpG sites, the difference in mean methylation level between the two groups ranged from 9.75 to 18.94%, and at all sites, the relationship was strong (p value < 0.0001). Yang et al. [34] studied 20 patients with infantile spasms and whether global DNA methylation in blood collected prior to treatment starting was associated with response to treatment with ACTH (based on change in seizure frequency). Mean methylation between the responders and non-responders was compared using the unpaired Student’s t test. No relationship between mean DNA global methylation level and ACTH treatment effect was identified. In a group of 97 patients with Beckwith-Wiedemann syndrome, Gaston et al. [41] examined the relationship between KCNQ1OT and H19 methylation and risk of tumour development (a known complication of Beckwith-Wiedemann syndrome). They used blood samples, and in some patients, tissue samples from affected organs were also obtained. Using the Kaplan-Meier method, abnormal H19 methylation (defined as a methylation index > 60%) was strongly associated with an increased risk of tumour development (34.6% vs. 4.2%, hazard ratio 10, p < 0.0001).