Epigenome-wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation

Abstract

BackgroundCerebral palsy (CP) is a clinical description for a group of motor disorders that are heterogeneous with respect to causes, symptoms and severity. A diagnosis of CP cannot usually be made at birth and in some cases may be delayed until 2–3 years of age. This limits opportunities for early intervention that could otherwise improve long-term outcomes. CP has been recorded in monozygotic twins discordant for the disorder, indicating a potential role of non-genetic factors such as intrauterine infection, hypoxia-ischaemia, haemorrhage and thrombosis. The aim of this exploratory study was to utilise the discordant monozygotic twin model to understand and measure epigenetic changes associated with the development of CP.MethodsWe performed a genome-wide analysis of DNA methylation using the Illumina Infinium Human Methylation 450 BeadChip array with DNA from newborn blood spots of 15 monozygotic twin pairs who later became discordant for CP. Quality control and data preprocessing were undertaken using the minfi R package. Differential methylation analysis was performed using the remove unwanted variation (RUVm) method, taking twin pairing into account in order to identify CP-specific differentially methylated probes (DMPs), and bumphunter was performed to identify differentially methylated regions (DMRs).ResultsWe identified 33 top-ranked DMPs based on a nominal p value cut-off of p < 1 × 10−4 and two DMRs (p < 1 × 10−3) associated with CP. The top-ranked probes related to 25 genes including HNRNPL, RASSF5, CD3D and KALRN involved in immune signalling pathways, in addition to TBC1D24, FBXO9 and VIPR2 previously linked to epileptic encephalopathy. Gene ontology and pathway analysis of top-ranked DMP-associated genes revealed enrichment of inflammatory signalling pathways, regulation of cytokine secretion and regulation of leukocyte-mediated immunity. We also identified two top-ranked DMRs including one on chromosome 6 within the promoter region of LTA gene encoding tumour necrosis factor-beta (TNF-β), an important regulator of inflammation and brain development. The second was within the transcription start site of the LIME1 gene, which plays a key role in inflammatory pathways such as MAPK signalling. CP-specific differential DNA methylation within one of our two top DMRs was validated using an independent platform, MassArray EpiTyper.ConclusionsOurs is the first epigenome-wide association study of CP in disease-discordant monozygotic twin pairs and suggests a potential role for immune dysfunction in this condition.Electronic supplementary materialThe online version of this article (10.1186/s13148-018-0457-4) contains supplementary material, which is available to authorized users.

Epigenetic Marks at the Ribosomal DNA Promoter in Skeletal Muscle Are Negatively Associated With Degree of Impairment in Cerebral Palsy

“…However, speaking against a general inability to methylate DNA, as suggested by Schoendorfer et al is a series of papers published in recent years that investigate differences in global DNA methylation between CP and TD children, i.e., DNA methylation in white blood cells. Two of these studies are case (CP) vs. control (TD) studies (30,31), and two are studies on monozygotic twins discordant for CP (32,33). All of these studies indicate that distinct epigenetic imprinting is evident in CP and that this is detectable very early on, even before 1 year of age.…”

Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy

“…The conventional multivariate logistic regression supports the ML prediction. The study of Mohandas et al [16] found significant differential methylation in CpG loci of several genes in 15 monochorionic or ‘monozygotic’ twins, discordant for the later development of CP. This is consistent with our findings of significant epigenetic modifications found similar direction of methylation changes in few genes such as PLOD2, C2orf47, AK2 , and C2orf60.…”

“…DNA methylation is a well-recognized mechanism for control of gene transcription. A recent study of newborn blood spots found differential methylation of several CpG loci in monochorionic twins discordant for subsequent CP development [16].…”

Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy

“…Ultimately, gene sequence heterogeneity has limited the effective use of genomic mutations as an early diagnostic of CP. To date, DNA methylation assays have not been broadly applied in the study of CP biomarkers; however, recent studies suggest that differences in the prevalence of CP in monozygotic twins may be associated with alterations in DNA methylation [ 37 , 38 ], and numerous studies have demonstrated that various stress stimuli, such as hypoxia, infection, and inflammation, cause a long-lasting change to DNA methylation patterns [ 22 ]. Utilizing a novel epigenetic biomarker assay, this is the first report demonstrating a retrospective model capable of identifying CP samples based on blood DNA methylation patterns.…”

“…Linking DNA methylation patterns in blood cells to specific health risks or diseases is an area of active research. Recent studies describe blood cell epigenetic markers for: pediatric cardiac risk [ 41 ], immune stress associated with sclerosis [ 42 ], infant cerebral palsy markers in cord blood [ 38 ], regulatory T cell imprinting as a marker for therapeutic efficacy [ 43 ], and immuno-profiling for specific disease / stress states [ 44 ]. These types of studies demonstrate that information about past environmental exposures and health/disease status are present in blood cell methylation patterns and suggest that such alterations are present in the hematopoietic stem cell populations that give rise to circulating myeloid and lymphoid cells.…”