Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

Abstract

BackgroundWilson disease (WD) is an autosomal recessive disease caused by mutations in ATP7B encoding a copper transporter. Consequent copper accumulation results in a variable WD clinical phenotype involving hepatic, neurologic, and psychiatric symptoms, without clear genotype–phenotype correlations. The goal of this study was to analyze alterations in DNA methylation at the whole-genome level in liver and blood from patients with WD to investigate epigenomic alterations associated with WD diagnosis and phenotype. We used whole-genome bisulfite sequencing (WGBS) to examine distinct cohorts of WD subjects to determine whether DNA methylation could differentiate patients from healthy subjects and subjects with other liver diseases and distinguish between different WD phenotypes.ResultsWGBS analyses in liver identified 969 hypermethylated and 871 hypomethylated differentially methylated regions (DMRs) specifically identifying patients with WD, including 18 regions with genome-wide significance. WD-specific liver DMRs were associated with genes enriched for functions in folate and lipid metabolism and acute inflammatory response and could differentiate early from advanced fibrosis in WD patients. Functional annotation revealed that WD-hypermethylated liver DMRs were enriched in liver-specific enhancers, flanking active liver promoters, and binding sites of liver developmental transcription factors, including Hepatocyte Nuclear Factor 4 alpha (HNF4A), Retinoid X Receptor alpha (RXRA), Forkhead Box A1 (FOXA1), and FOXA2. DMRs associated with WD progression were also identified, including 15 with genome-wide significance. However, WD DMRs in liver were not related to large-scale changes in proportions of liver cell types. DMRs detected in blood differentiated WD patients from healthy and disease control subjects, and distinguished between patients with hepatic and neurologic WD manifestations. WD phenotype DMRs corresponded to genes enriched for functions in mental deterioration, abnormal B cell physiology, and as members of the polycomb repressive complex 1 (PRC1). 44 DMRs associated with WD phenotype tested in a small validation cohort had a predictive value of 0.9.ConclusionsWe identified a disease-mechanism relevant epigenomic signature of WD that reveals new insights into potential biomarkers and treatments for this complex monogenic disease.Electronic supplementary materialThe online version of this article (10.1186/s13072-019-0255-z) contains supplementary material, which is available to authorized users.

mtDNA depletion‐like syndrome in Wilson disease

“…Thirty-seven healthy controls and 61 patients with a diagnosis of WD according to Leipzig criteria were previously described in detail [25][26][27] and included in the metabolomic study; of these, 47 WD were included in the mtDNA study ( Figure S3; Table S3). Informed written consent was obtained from all subjects and patients, and the study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in a priori approval by the Institutional Review Board at the University of California, Davis.…”

“…36,37 Based on our previous work and to determine if differentially methylated nuclear genes were associated with mtDNA replication/ translation, we re-analysed existing genome-wide methylome data from the same WD subjects. 25 Pathway analysis revealed 114 WD differentially methylated genes with essential roles in one-carbon metabolism, mitochondrial network organization, and mitochondrial protein synthesis as well as mtDNA transcription, replication, and stability (Table S1). From this subset of nuclear-encoded genes with F I G U R E 3 Hepatic mtDNA and mitochondrial bioenergetic outcomes in tx-j mice.…”

Metabolic dysregulation in theAtp7b−/−Wilson’s disease mouse model

“…Additional results in humans [PPARα (9, 10)] and mice [FXR (7, 8), LXR (5)] link metabolic and nuclear receptor dysfunction to Wilson's disease. Wholegenome sequencing revealed differentially methylated regions for genes involved in lipid metabolism, including HNF4α and RXR α targets, in Wilson's disease patients (11).…”

Oxylipin Profiles in Plasma of Patients with Wilson’s Disease

“…The influence of epigenetics, environment, age, and sex-related factors on the WD phenotype further complicates diagnosis [3,7,10]. The clear-phenotype correlations for WD are still unclear, although recent epigenetic whole genome screening data may shed light on in-depth pathogenic mechanisms [11]. Obtained from liver and blood samples from patients with WD, the data have shown specific sets of modified genes, enriched for functions in lipid metabolism and inflammatory responses [11].…”

“…The clear-phenotype correlations for WD are still unclear, although recent epigenetic whole genome screening data may shed light on in-depth pathogenic mechanisms [11]. Obtained from liver and blood samples from patients with WD, the data have shown specific sets of modified genes, enriched for functions in lipid metabolism and inflammatory responses [11]. Such changes can manifest themselves on the level of the organism as a whole in a variety of ways and be the cause of the observed differences in manifestations of the disease.…”