An Integrative Analysis of DNA Methylation Pattern in Myotonic Dystrophy Type 1 Samples Reveals a Distinct DNA Methylation Profile between Tissues and a Novel Muscle-Associated Epigenetic Dysregulation

Abstract

Myotonic dystrophy type 1 (DM1) is a progressive, non-treatable, multi-systemic disorder. To investigate the contribution of epigenetics to the complexity of DM1, we compared DNA methylation profiles of four annotated CpG islands (CpGis) in the DMPK locus and neighbouring genes, in distinct DM1 tissues and derived cells, representing six DM1 subtypes, by bisulphite sequencing. In blood, we found no differences in CpGi 74, 43 and 36 in DNA methylation profile. In contrast, a CTCF1 DNA methylation gradient was found with 100% methylation in congenital cases, 50% in childhood cases and 13% in juvenile cases. CTCF1 methylation correlated to disease severity and CTG expansion size. Notably, 50% of CTCF1 methylated cases showed methylation in the CTCF2 regions. Additionally, methylation was associated with maternal transmission. Interestingly, the evaluation of seven families showed that unmethylated mothers passed on an expansion of the CTG repeat, whereas the methylated mothers transmitted a contraction. The analysis of patient-derived cells showed that DNA methylation profiles were highly preserved, validating their use as faithful DM1 cellular models. Importantly, the comparison of DNA methylation levels of distinct DM1 tissues revealed a novel muscle-specific epigenetic signature with methylation of the CTCF1 region accompanied by demethylation of CpGi 43, a region containing an alternative DMPK promoter, which may decrease the canonical promoter activity. Altogether, our results showed a distinct DNA methylation profile across DM1 tissues and uncovered a novel and dual epigenetic signature in DM1 muscle samples, providing novel insights into the epigenetic changes associated with DM1.

Immortalized human myotonic dystrophy type 1 muscle cell lines to address patient heterogeneity

“… 10 , 11 , 12 In addition, our group also demonstrated that the CTCF1 region was methylated in a tissue-specific manner only in DM1 muscle biopsies (and not in skin or blood from the same patients), as well as in primary DM1 muscle cells, whereas tissues from unaffected individuals were completely unmethylated. 12 Importantly, the DM1 immortalized muscle cells showed the previously reported CTCF1 hypermethylation in both myoblasts (muscle progenitor cells) and myotubes (mature muscle cells), indicating that the DNA methylation alterations were conserved. However, we observed a significant difference in the methylation levels between primary and immortalized cell lines.…”

“…Epigenetics may have a role in DM1, as the CTG expansion overlaps with a 3.5 kb CpG island. 10 , 11 , 12 , 13 The DMPK gene is in chromosome 19q surrounded by the DMWD (upstream) and SIX5 (downstream) genes. The DMPK locus contains several CpG islands, including the CTCF1 and CTCF2 regions, which are surrounding the CTG expansion.…”

“…For example, DM1 muscle and muscle derived DM1 cells show CTCF1 hypermethylation compared to controls; while blood samples from congenital cases show CTCF1 hypermethylation compared to controls and adult DM1 cases. 12 , 14 , 15 However, it is not clear how the hypermethylation of this CpG island contributes to the pathogenesis of the disease, although it has been reported that DMPK and the surrounding genes ( DMWD and SIX5 ) are downregulated in DM1. 16 , 17 …”