Genome-Wide Analysis of DNA Methylation, Copy Number Variation, and Gene Expression in Monozygotic Twins Discordant for Primary Biliary Cirrhosis

Abstract

Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.

Genetics and epigenetics in the pathogenesis of primary biliary cholangitis

“…How these factors are molecularly involved in PBC onset remains unclear. Elsewhere, it was reported that X-chromosome gene expression instability might also participate in female predominance in the disease [64,65], and that monozygotic twins and sisters discordant for PBC exhibited particular epigenetic differences [66]. These collectively support the notion that epigenetic factors influence the onset of PBC.…”

Epigenetics and Primary Biliary Cirrhosis: a Comprehensive Review and Implications for Autoimmunity

“…More recently performed genome-wide study supports consistent differences in discordant twins and siblings for methylation profiles of 60 gene regions [60]. Among 60 differentially methylated regions, 51 genes located to the X chromosome and 9 genes located to autosomal chromosomes.…”

“…In the affected twin in discordant MZ pairs, the gene expression profile, copy number variants resulting from duplications and rearrangement, and DNA methylation, an important epigenetic modification, all differ markedly from the unaffected twin control [60]. These data from MZ twin studies, despite lacking mechanisms, are sufficient to suggest that PBC not only is influenced by genetic factors, but also by epigenetic influences.…”

“…Among 60 differentially methylated regions, 51 genes located to the X chromosome and 9 genes located to autosomal chromosomes. Importantly, for each of these regions, the affected twin was hypermethylated compared with the nonaffected one [60]. However, methylation does not fully correlate with gene expression in most cases, indicating that mechanisms other than DNA methylation may be responsible for gene transcription regulation.…”

“…Twin research not only estimates heritability by comparing phenotypic concordance rates in monozygotic (MZ) twins versus dizygotic (DZ) twins, but also emphasizes the influence of environmental factors [58], and according to three monozygotic twin studies [59][60][61], the concordance of PBC in identical twins is relatively high [62], which implies strong genetic susceptibility [61]. In the affected twin in discordant MZ pairs, the gene expression profile, copy number variants resulting from duplications and rearrangement, and DNA methylation, an important epigenetic modification, all differ markedly from the unaffected twin control [60].…”