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Global changes in gene expression and splicing in alcoholic liver disease
Harvard Univ, MA 02115 USA.
Univ Miami, FL USA.
Univ Pittsburgh, PA USA.
Univ Miami, FL USA.
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2026 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 16, no 1, article id 23367Article in journal (Refereed) Published
Abstract [en]

Alcohol use disorder is a widespread illness commonly leading to alcoholic liver disease (ALD) and cirrhosis with an increased incidence of hepatocellular carcinoma (HCC), but the mechanisms of alcohol-related oncogenesis in the liver are incompletely understood. We tested the hypothesis that ALD predisposes to HCC via dysregulation of splicing. RNA sequencing was performed on liver biopsies from patients with different stages of ALD: early alcoholic steatohepatitis (eASH), non-severe alcoholic hepatitis (nsAH), and severe alcoholic hepatitis (sAH); furthermore, explants were collected from patients who underwent liver transplantation due to sAH (exAH). We found that alcohol caused widespread changes in transcriptome in all stages of ALD: among similar to 58,000 analyzed genomic features, similar to 4900 were altered in eASH, similar to 9100-in nsAH, 14,100-in sAH, and similar to 14,300-in exAH. We observed thousands of missplicing events in all hepatic conditions, with mutually exclusive exons (MEE) being the most common event and exon skipping (ES)-second most common event. Analysis of similar to 600,000 exons revealed that ALD is associated with a genome-wide effect on exon expression, with similar to 50,000 exons being differentially expressed in eASH, similar to 130,000-in nsAH, similar to 150,000-in sAH, and similar to 120,000-in exAH. To determine whether alcohol directly perturbs splicing, we subjected rats to alcohol vapor for 7 weeks and found that the expression of multiple snRNAs was drastically decreased, while expression of splicing factors was not affected. Screening of oncogenes and tumor suppressors, commonly involved in HCC pathogenesis, revealed that ALD affected the hepatic expression and/or splicing of most of these cancer-related genes. In summary, it appears that alcohol causes profound genome-wide changes in gene expression and splicing in the liver, likely via affecting the spliceosome. This results in altered expression and missplicing of key oncogenes and tumor suppressors involved in HCC, suggesting a novel mechanism of oncogenesis in the liver of patients with ALD.

Place, publisher, year, edition, pages
NATURE PORTFOLIO , 2026. Vol. 16, no 1, article id 23367
Keywords [en]
Alcohol use disorder; Alcoholic liver disease; Splicing; Spliceosome; Long non-coding RNA; Hepatocellular carcinoma
National Category
Medical Genetics and Genomics
Identifiers
URN: urn:nbn:se:liu:diva-226943DOI: 10.1038/s41598-026-52759-2ISI: 001834090400005PubMedID: 42168268Scopus ID: 2-s2.0-105046063057OAI: oai:DiVA.org:liu-226943DiVA, id: diva2:2094745
Note

Funding Agencies|[R01 AA029924]; [K12 DA 043490]

Available from: 2026-08-24 Created: 2026-08-24 Last updated: 2026-08-24

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Center for Social and Affective NeuroscienceFaculty of Medicine and Health SciencesPsykiatriska kliniken i Linköping
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