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Epigenetics Chromatin. 2019 Feb 1;12(1):10. doi: 10.1186/s13072-019-0255-z.

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

Author information

1
Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA.
2
Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.
3
2nd Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland.
4
Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany.
5
California Pacific Medical Center, San Francisco, CA, USA.
6
Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA.
7
Department of Surgery, University of California Davis, Sacramento, CA, USA.
8
Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA. vmedici@ucdavis.edu.

Abstract

BACKGROUND:

Wilson 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.

RESULTS:

WGBS 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.

CONCLUSIONS:

We identified a disease-mechanism relevant epigenomic signature of WD that reveals new insights into potential biomarkers and treatments for this complex monogenic disease.

KEYWORDS:

Biomarker; Blood; Chromatin; Copper; DNA methylation; Enhancer; Epigenetics; Liver; Whole-genome bisulfite sequencing; Wilson disease

PMID:
30709419
PMCID:
PMC6357467
DOI:
10.1186/s13072-019-0255-z
[Indexed for MEDLINE]
Free PMC Article

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