Liver Disease: A Paradigm for Understanding Environment-Epigenome Interaction
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide and is one of the few tumor types whose incidence is increasing in the United States. Unlike many cancers, the predisposing risk factors for most HCC cases are known, with chronic alcoholism, hepatitis B and C viral infection, and more recently metabolic syndrome driven by obesity accounting for most cases worldwide. In addition, HCC has a long clinical course and a well-defined precancerous progression. Many of the changes that occur in hepatocytes during the long preneoplastic phase of liver disease leading to cirrhosis appear to be epigenetic rather than genetic in nature. This observation likely reflects the known role of the epigenome as an interface with the environment. Insults such as alcohol abuse first alter the epigenome, leading to maladaptive changes in gene expression that promote further epigenetic, and eventually, genetic damage. Alterations in immune cell activation and the extracellular milieu in the liver also likely contribute.
Studies in the Epigenetic Etiology of Human Disease Laboratory focus on roles for the DNA epigenetic marks in HCC initiation and progression, as well as how these agents deregulate enhancer function and create aberrant epigenetic states consistent with an elevated risk of cancer formation. Epigenetic marks and expression patterns are interrogated across the entire genome of primary human liver disease samples and cell line models. This data is related to patient clinical-pathological data available and to cell culture model systems using primary and immortalized human hepatocytes.
Our previous results indicate that DNA methylation changes during liver disease progression are robust; some are common to all environmental exposures, while others appear to be unique to one exposure. This suggests that these agents act in distinct ways to promote HCC via the epigenome. To further understand how epigenetic changes drive liver disease and HCC and to be able to distinguish between changes that are drivers and those that are passengers or late-stage events, the laboratory is investigating spatial epigenetic heterogeneity within diseased and neoplastic regions of the liver. To accomplish this, we use whole livers obtained through liver transplant for end-stage liver disease or early HCC, sample throughout the 3D structure of the tissue, and examine DNA methylation and transcriptional heterogeneity. Findings are correlated with clinical data, gene expression and immunostaining and used in phyloepigenetic analyses to define epigenetic changes acting as early driving events. Such analyses are expected to yield novel HCC driver events, new therapeutic targets and potentially early disease biomarkers.
The laboratory is also developing novel cell culture models to understand the long-term ramifications of chronic hepatitis C virus (HCV) infection of the liver, followed by cure with the direct-acting antiviral drugs that became available in 2011. While viral cure is now highly efficient and long-term risk of HCC driven by HCV infection is reduced, it is not eliminated, necessitating long-term screening of patients. Using models of HCV infection and viral clearance in cell culture, we aim to understand how the virus alters the epigenome, the role of innate immune pathways, and how the epigenome and cellular growth phenotypes respond to viral clearance. Our longer-term goal is to identify ways to further reduce cancer risk in individuals cured of chronic HCV infection.
Given the poor prognosis of people with HCC, driven in part by therapy resistance and late stage of diagnosis, long-term project goals include development of noninvasive tests for human liver disease using DNA methylation markers, to permit early detection and treatment. In addition, it is anticipated that elucidating the role of DNA epigenetic marks in HCC will provide new therapeutic targets for this deadly disease.