DNA methylome analysis reveals distinct episignatures in bicuspid aortic valve

Background Bicuspid aortic valve (BAV) is the most common congenital heart malformation in the general population, frequently associated with the development of aortic valve diseases and severe aortopathy. There is a great variability in the clinical progression of this anomaly and, thus, an early prognosis of the individual risk could contribute to a better approach to the clinical follow-up of patients. This malformation is partly determined by different genetic loci and no single gene model explains BAV inheritance, suggesting that more factors are involved. In this regard, characteristic epigenetic and immunological profiles have been documented to be involved in several cardiovascular diseases. Among candidate epigenetic mechanisms, DNA methylation is described as having an important role in the aetiology of some heart diseases. Purpose The present study aimed to explore the genome-wide DNA methylation landscape behind the BAV to identify novel disease biomarkers and novel insights into disease mechanisms. Methods We conducted a genome-wide DNA methylation analysis in aortic valve tissue, obtained at the time of replacement surgery, from non-syndromic patients recruited prospectively at the Cardiology Department in our tertiary hospital. The samples were deposited in the biobank after the patients signed an informed consent for their use in research. DNA methylation data were obtained using a methylation array with 930k markers to detect differentially methylated cytosines (CpG). Linear models were used to identify differential methylation probes (DMPs). Enrichment of resulting DMPs in multiple genomic datasets was calculated using Fisher tests. Principal component analysis was used to identify differences between the BAV and tricuspid aortic valve (TAV) groups. Results A total of 1878 hypermethylated and 863 hypomethylated CpG were identified. The putative binding sites of at least 24 transcription factors were associated with hyper (ARID1B, E2F7, FOS, FOSB, FOSL1, FOSL2, FOXO1, MEF2D, NR2F2, PRDM6, TEAD1, TEAD4, and TWIST1) or hypo methylation (BACH2, ETV6, IRF4, LYL1, MECOM, MTA2, POU2F2, RUNX3, SPI1, TBX21, and TCF3) suggesting a potential functional role of DNA methylation in the aetiology of the BAV. Genes with hypermethylated promoters in BAV included NR2F2, a transcription factor of the zinc-finger family, with mutations associated with congenital heart defects but not previously associated with BAV. The methylation patterns obtained for these genes grouped the patients according to their aortic valve morphology, confirming that BAV may present a specific episignature different from the one in TAV. Conclusion Our data revealed a robust episignature for BAV, supporting that individual epigenetic maps may represent a novel tool in clinical practice. Further research is needed to explore the biological roles of these genes in BAV aiming to predict risk of progression and design therapeutic approaches.