Abstract 785: Multi-omics profiling identifies genetic and epigenetic regulation underlying alcohol induced liver fibrosis in a porcine hepatocellular carcinoma model

Abstract

Abstract Background: Cirrhosis is a form of end-stage liver disease which manifests with a host of metabolic and hematologic derangements, and is commonly the result of long-term ethanol exposure. Large animal models of cirrhosis, and of one of its common long-term sequelae, hepatocellular carcinoma (HCC), are needed to study novel and emerging therapeutic interventions. Methods: Liver fibrosis was induced in the Oncopig cancer model, a large animal model of HCC, via intrahepatic, intra-arterial ethanol infusion. Post-mortem liver sections from five fibrosis induction and five age-matched controls were harvested for RNA-seq (mRNA and lncRNA), small RNA-seq (miRNA), and reduced representation bisulfite sequencing (RRBS; DNA methylation). Supervised, multi-omic analysis of the 5,000 genes and methylated regions demonstrating the largest inter-sample variance with non-zero counts along with all sequenced miRNA were analyzed using the DIABLO method within the mixOmics 6.8.5 R library. Results: Single component DIABLO latent variable analysis of mRNAs, lncRNAs, miRNAs, and methylated regions was performed to identify the genetic elements (variables) which most reliably discriminated between experimental arms. Analysis of the top 100 discriminatory variables from each ‘omics data set was performed to provide sufficient data for pathway analysis while maintaining separation of the experimental arms within the latent space. IPA pathway analysis of these genes revealed differential regulation of pathways related to hepatic fibrosis, adipogenesis, ketogenesis as well as several other liver-specific metabolic pathways. Identification of the five most discriminatory variables was also performed. Single component, five variable analysis revealed ELOVL2, LIPK, and LAMA3 most reliably differentiated control and fibrosis groups, along with two lncRNA transcripts, XLOC035153 and XLOC036409 which were predicted to target S1PR1 and UHRF1BP1L, respectively. LAMA3, XLOC036409, and its target UHRF1BP1L were overexpressed in Oncopig fibrotic liver samples. UHRF1, a potential binding target for UHRF1BP1L, has previously been implicated as an oncogene for hepatocellular carcinoma. S1PR1 is involved in vasculogenesis and cancer cell motility via the RAC-CDC42 and ERK pathways. Conclusions The differentially regulated genetic elements identified by the multi-omic analyses were largely concordant with known alterations in human alcoholic liver disease. This agreement lends validity to the Oncopig model as a model organism for human alcoholic liver disease. In addition, novel genes, UHRF1BP1L and S1PR1, were associated with porcine liver fibrosis and further work to characterize their precise mechanistic roles in the natural history of this disease is required. Citation Format: Mark Hieromnimon, Lawrence Schook, Ron Gaba, Kyle Schachtschneider. Multi-omics profiling identifies genetic and epigenetic regulation underlying alcohol induced liver fibrosis in a porcine hepatocellular carcinoma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 785.