Global Changes in Gene Expression and Splicing in Alcoholic Liver Disease

Area of Science:

• Hepatology
• Molecular Biology
• Oncology

Background:

• Alcohol use disorder is a leading cause of liver disease, including cirrhosis and hepatocellular carcinoma (HCC).
• The precise molecular mechanisms linking alcoholic liver disease (ALD) to liver cancer remain incompletely understood.
• Dysregulation of gene splicing is a potential, yet understudied, factor in alcohol-related hepatocarcinogenesis.

Purpose of the Study:

• To investigate the hypothesis that alcoholic liver disease (ALD) promotes hepatocellular carcinoma (HCC) through aberrant gene splicing.
• To comprehensively analyze genome-wide changes in gene expression and splicing patterns in the liver across different stages of ALD.
• To identify specific cancer-related genes affected by alcohol-induced alterations in hepatic gene expression and splicing.

Main Methods:

• RNA sequencing was performed on human liver biopsies from patients with early alcoholic steatohepatitis (eASH), non-severe alcoholic hepatitis (nsAH), severe alcoholic hepatitis (sAH), and explants from sAH patients (exAH).
• Gene expression and splicing events, including mutually exclusive exons (MEE) and exon skipping (ES), were analyzed across all ALD stages.
• Rats were exposed to alcohol vapor to assess direct effects on splicing machinery, and expression/splicing of key oncogenes and tumor suppressors were screened.

Main Results:

• Alcohol consumption induced widespread transcriptome alterations in all stages of ALD, affecting thousands of genomic features.
• Thousands of missplicing events were observed, with MEE and ES being the most prevalent.
• ALD was associated with genome-wide changes in exon expression, impacting tens to hundreds of thousands of exons depending on disease severity.
• Alcohol exposure in rats decreased snRNA expression, suggesting spliceosome perturbation, and affected expression/splicing of numerous HCC-related genes.

Conclusions:

• Alcohol causes profound, genome-wide changes in gene expression and splicing within the liver, likely by impacting the spliceosome.
• These alcohol-induced alterations lead to altered expression and missplicing of critical oncogenes and tumor suppressors.
• This suggests a novel mechanism for liver oncogenesis in patients with alcoholic liver disease, mediated by splicing dysregulation.