Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis

Abstract

Hereditary transthyretin (TTR) amyloidosis (hATTR) is a rare life-threatening disorder caused by amyloidogenic coding mutations located in TTR gene. To understand the high phenotypic variability observed among carriers of TTR disease-causing mutations, we conducted an epigenome-wide association study (EWAS) assessing more than 700,000 methylation sites and testing epigenetic difference of TTR coding mutation carriers vs. non-carriers. We observed a significant methylation change at cg09097335 site located in Beta-secretase 2 (BACE2) gene (standardized regression coefficient = -0.60, p = 6.26 × 10^-8). This gene is involved in a protein interaction network enriched for biological processes and molecular pathways related to amyloid-beta metabolism (Gene Ontology: 0050435, q = 0.007), amyloid fiber formation (Reactome HSA-977225, q = 0.008), and Alzheimer's disease (KEGG hsa05010, q = 2.2 × 10^-4). Additionally, TTR and BACE2 share APP (amyloid-beta precursor protein) as a validated protein interactor. Within TTR gene region, we observed that Val30Met disrupts a methylation site, cg13139646, causing a drastic hypomethylation in carriers of this amyloidogenic mutation (standardized regression coefficient = -2.18, p = 3.34 × 10^-11). Cg13139646 showed co-methylation with cg19203115 (Pearson's r² = 0.32), which showed significant epigenetic differences between symptomatic and asymptomatic carriers of amyloidogenic mutations (standardized regression coefficient = -0.56, p = 8.6 × 10^-4). In conclusion, we provide novel insights related to the molecular mechanisms involved in the complex heterogeneity of hATTR, highlighting the role of epigenetic regulation in this rare disorder.

Keywords: Amyloidosis; Epigenetics; Methylation; Modifier gene; Val30Met mutation; hATTR.

Fig. 1

Methylation levels (beta-values) of cg09097335 site in carriers (cases) vs. non-carriers (controls) of amyloidogenic mutations. Regression line is shown in blue. The M values of this comparison are reported in Additional file 1. Standardized regression coefficient and p value reported are derived from the analysis conducted on the M values

Fig. 2

Upper Panel: Co-expression of TTR and BACE2 in liver and in hATTR target organs; Bottom Panel: Co-expression of TTR, DSG2, DSC2, DSC3, and B4GALT6 in hATTR target organs (transcriptomic data from GTEx project, available at https://www.gtexportal.org/)

Fig. 3

BACE2 protein interaction network. Node color of the protein is proportional to the interaction score with BACE2. Connector shade and width are proportional to the interaction confidence, highest, high, and medium