Integrated Bulk and Single-Cell Transcriptomic Analysis Reveals Xenobiotic Metabolism Genes Drive Progression From Liver Cirrhosis to Hepatocellular Carcinoma

<h4>Background</h4>Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, with liver cirrhosis (LC) recognized as a significant precursor. Xenobiotic metabolism plays a pivotal role in liver diseases, where the liver's primary function as a detoxifying organ directly influences health and tumor development. Therefore, exploring the function of genes associated with xenobiotic metabolism in patients with HCC and LC is crucial for advancing diagnosis and treatment strategies.<h4>Methods</h4>This study integrated bulk transcriptome RNA sequencing and single-cell RNA sequencing data of HCC and LC from the GEO database. Differential expression analysis, GO and DO enrichment analyses, and PPI network construction were performed to identify hub genes. ROC curve analysis was used to assess the diagnostic value of these genes, and potential therapeutic drugs were predicted using drug databases. The expression of the identified hub genes was validated in clinical tissue samples (≥ 10 pairs) by qRT-PCR and Western blot. Functional assays, including wound healing, transwell migration, and invasion assays, were conducted following siRNA-mediated knockdown of selected hub genes in Huh7 hepatoma cells.<h4>Results</h4>We identified five key xenobiotic metabolism-related hub genes: AKR1C3, CYB5A, ADH1C, MAOA, and ALDH2. These genes were significantly overexpressed in HCC and LC tissues compared with normal tissues and were associated with xenobiotic metabolism, substance abuse, alcohol use disorders, and cancer. ROC curve analysis indicated that these hub genes have high diagnostic value in HCC and LC. Potential drug prediction identified six compounds, including retinal, isopropanol, and disulfiram, which may have therapeutic effects. Clinical tissue validation confirmed that all five hub genes were significantly upregulated at both mRNA and protein levels in HCC and LC tissues compared with normal controls (<i>p</i> < 0.05). Functional experiments demonstrated that knockdown of ALDH2 or AKR1C3 significantly impaired the migration and invasion abilities of Huh7 cells, with a reduction of over 50% in transwell assays (<i>p</i> < 0.05).<h4>Conclusion</h4>This study systematically analyzed the expression characteristics and functional significance of xenobiotic metabolism-related genes in HCC and LC by integrating multiple high-throughput sequencing technologies. Experimental validation confirmed the upregulation of these hub genes in clinical tissues and demonstrated that ALDH2 and AKR1C3 promote hepatoma cell migration and invasion, providing experimental evidence for their potential roles in disease progression. Potential drugs targeting these hub genes were preliminarily investigated.