Targeted genomic profiling identifies frequent deleterious mutations in FAT4 and TP53 genes in HBV-associated hepatocellular carcinoma

BMC Cancer. 2019 Aug 8;19(1):789. doi: 10.1186/s12885-019-6002-9.

Abstract

Background: Hepatitis B virus (HBV) is the major risk factor for hepatocellular carcinoma (HCC). The molecular mechanisms underlying HBV-associated HCC pathogenesis is still unclear. Genetic alterations in cancer-related genes have been linked to many human cancers. Here, we aimed to explore genetic alterations in selected cancer-related genes in patients with HBV-associated HCC.

Methods: Targeted sequencing was used to analyze six cancer-related genes (PIK3CA, TP53, FAT4, IRF2, HNF4α and ARID1A) in eight pairs of HBV-associated HCC tumors and their adjacent non-tumor tissues. Sanger sequencing, quantitative PCR, Western-blotting and RNAi-mediated gene knockdown were used to further validate findings.

Results: Targeted sequencing revealed thirteen non-synonymous mutations, of which 9 (69%) were found in FAT4 and 4 (31%) were found in TP53 genes. Non-synonymous mutations were not found in PIK3CA, IRF2, HNF4α and ARID1A. Among these 13 non-synonymous mutations, 12 (8 in FAT4 and 4 in TP53) were predicted to have deleterious effect on protein function by in silico analysis. For TP53, Y220S, R249S and P250R non-synonymous mutations were solely identified in tumor tissues. Further expression profiling of FAT4 and TP53 on twenty-eight pairs of HCC tumor and non-tumor tissues confirmed significant downregulation of both genes in HCC tumors compared with their non-tumor counterparts (P < 0.001 and P < 0.01, respectively). Functional analysis using RNAi-mediated knockdown of FAT4 revealed an increased cancer cell growth and proliferation, suggesting the putative tumor suppressor role of FAT4 in HCC.

Conclusions: This study highlights the importance of FAT4 and TP53 in HCC pathogenesis and identifies new genetic variants that may have potentials for development of precise therapy for HCC.

Keywords: Customized therapies; Deleterious mutations; Gene silencing; Hepatocellular carcinoma; Targeted sequencing.

MeSH terms

  • Alleles
  • Biomarkers, Tumor*
  • Cadherins / genetics*
  • Carcinoma, Hepatocellular / etiology*
  • Cell Line, Tumor
  • DNA Mutational Analysis
  • Gene Expression Profiling
  • Gene Frequency
  • Genomics / methods
  • Hepatitis B / complications*
  • Hepatitis B / virology
  • Hepatitis B virus
  • Humans
  • INDEL Mutation
  • Liver Neoplasms / etiology*
  • Mutation*
  • Tumor Suppressor Protein p53 / genetics*
  • Tumor Suppressor Proteins / genetics*

Substances

  • Biomarkers, Tumor
  • Cadherins
  • FAT4 protein, human
  • Tumor Suppressor Protein p53
  • Tumor Suppressor Proteins