Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status

Abstract

Paget's Disease of Bone (PDB) is characterized by focal increases in disorganized bone remodeling. This study aims to characterize PDB associated changes in DNA methylation profiles in patients' blood. Meta-analysis of data from the discovery and cross-validation set, each comprising of 116 PDB cases and 130 controls, revealed significant differences in DNA methylation at 14 CpG sites, 4 CpG islands, and 6 gene-body regions. These loci, including two characterized as functional through expression quantitative trait-methylation (eQTM) analysis, were associated with functions related to osteoclast differentiation, mechanical loading, immune function, and viral infection. A multivariate classifier based on discovery samples was found to discriminate PDB cases and controls from the cross-validation with a sensitivity of 0.84, specificity of 0.81, and an area under curve of 92.8%. In conclusion, this study has shown for the first time that epigenetic factors contribute to the pathogenesis of PDB and may offer diagnostic markers for prediction of the disease.

Epigenetic DNA Methylation Signatures Associated With the Severity of Paget’s Disease of Bone

“…Raw methylation data were analyzed using the R RnBeads package ( Müller et al, 2019 ). Details of data pre-processing steps have been described previously ( Diboun et al, 2021 ). Briefly, Samples with low methylated or unmethylated median intensity (<11.0) were excluded ( n = 35) and CpG sites that were cross reactive, containing single nucleotide polymorphisms (SNPs), located on sex chromosome or those associated with epigenetic effects of smoking were removed, leaving 232 samples with 429,156 CpG sites for downstream analyses.…”

“…Effectively, the p -value indicates the improvement in the fit brought about by the inclusion of the sites in the model, whilst normalizing for their number. The two-step Generalized Linear Model has been described in ( Diboun et al, 2021 ) and is here summarized as: (step1) Severity ∼ confounder (step2) Severity ∼ confounder + site 1 +site 2 … ….+site n …”

“…Given the evidence that PDB has both environmental and genetic components, investigating DNA methylation patterns in PDB patients is of great interest. In a previous study, the epigenetic profiles from PDB patients were compared to matched healthy controls, which led to the identification of a number of differentially methylated loci ( Diboun et al, 2021 ). The identified loci highlighted several key mechanisms including pathways of bone remodeling, mechanical loading as well as immune response to viral infection.…”

“…The identified loci highlighted several key mechanisms including pathways of bone remodeling, mechanical loading as well as immune response to viral infection. Moreover, a trained multivariate classifier was able to discriminate PDB patients from healthy controls in a cross-validation cohort with high efficiency ( Diboun et al, 2021 ).…”

Severity of Idiopathic Scoliosis Is Associated with Differential Methylation: An Epigenome-Wide Association Study of Monozygotic Twins with Idiopathic Scoliosis

“…Previous epigenome-wide association studies have provided evidence supporting the role of DNA methylation in numerous complex musculoskeletal diseases including osteoarthritis [70], osteoporosis [70], cerebral palsy [71], and Paget's disease of bone [72]. The role of DNA methylation in IS has not been well studied.…”