Gene Expression Aberrations in Alcohol-Associated Hepatocellular Carcinoma

Abstract

Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer, ranking as the sixth most common cancer worldwide and the fourth leading cause of cancer-related deaths. Most HCC cases originate from cirrhotic livers, typically due to chronic liver diseases, such as hepatitis B (HBV) and hepatitis C (HCV) infections, and alcoholism. HCC cells often harbor numerous somatic mutations that are implicated in HCC development, but epigenetic factors, such as miRNA interference, can also affect HCC initiation and progress. miRNA-221 has been explored as a factor affecting HCC development in HCC of viral etiology, but little is known about its effects on gene expression in alcohol-associated HCC. This study aimed to explore potentially similar gene expression aberrations underlying viral and alcohol-induced HCC. We analyzed available transcriptome data from non-tumor hepatocytes and viral-induced HCC tissues. The most notable differences in gene expression associated with miRNA-221 between non-tumor hepatocytes and viral-induced HCC involved NTF-3 and MYBL1 genes. To assess these data in alcohol-induced HCC, we examined 111 tissue samples: tumor tissue and cirrhotic tissue samples from 37 HCC patients and 37 samples from non-tumor liver tissue using RT-Q PCR. We found no significant difference in NTF-3 expression, but MYBL1 expression was significantly lower in HCC tissue compared to non-tumor hepatocytes and cirrhotic tissue. Our findings highlight the importance of the MYBL1 gene in HCC development and emphasize the need for diverse approaches in evaluating tumor mechanisms.

Keywords: MYBL1; NTF-3; alcohol etiology; hepatocellular carcinoma; miRNA-221.

Figure 1

Differential expression analysis between hepatocellular carcinoma (HCC) tissues and primary hepatocytes. Principal component analysis (PCA) visualizing the overall gene expression variability between publicly available HCC and non-adjacent tumors from GSE105130, primary hepatocytes from EGA, and recurrent, tumor, and normal tissues from TCGA-LIHC cohort (A). PCA for only HCC patients with known etiology (risk factor) (B). MA plots illustrating differentially expressed genes between the HCC from GSE105130 and primary hepatocytes with groups expressed based on an absolute log2 fold change greater than 1 and a p-value less than 0.05, as determined by the Wald test using the DESeq2 package (B). Over-representation analysis of Gene Ontology (GO) terms in genes upregulated and downregulated in HCC from GSE105130 compared to primary hepatocytes (C).

Figure 2

Differentially expressed genes regulated by miRNA-221 in hepatocellular carcinoma (HCC) patients compared to primary hepatocytes. Genes were identified as differentially expressed based on an absolute log2 fold change greater than 1 and a p-value less than 0.05, as determined by the Wald test using the DESeq2 package. ns: p > 0.05 *: p ≤ 0.05, **: p ≤ 0.01, ***: p ≤ 0.001, ****: p ≤ 0.0001. Angiopoietin-like protein 2 (ANGPTL2), bcl-2-binding component 3 (BBC3), bcl2 modifying factor (BMF), matrix metalloproteinase-1 (MMP1), MYB proto-oncogene like 1 (MYBL1), neurotrophin 3 (NTF-3), plexin C1 (PLXNC1), ring finger protein 44 (RNF44), and sad1 and UNC84 domain containing 2 (SUN2).

Figure 3

Difference in the neurotrophin 3 (NTF-3) gene expression levels between non-tumor liver tissue, cirrhotic liver tissue, and hepatocellular carcinoma (HCC) tissue.

Figure 4

The results of this study have shown a significantly downregulated MYB proto-oncogene like 1 (MYBL1) in the hepatocellular carcinoma (HCC) tissue compared to the non-tumor liver tissue, as well as a significantly downregulated MYBL1 gene expression in the HCC tissue compared to cirrhotic liver tissue (* p < 0.05).

Figure 5

Statistically significant difference in the expression level of the MYB proto-oncogene like 1 (MYBL1) between the cirrhotic liver tissue and non-tumor liver tissue was not found.