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

• Published in: BMC cancer Vol. 19; no. 1; p. 789
• Main Authors: Huang, Fung-Yu, Wong, Danny Ka-Ho, Tsui, Vivien Wai-Man, Seto, Wai-Kay, Mak, Lung-Yi, Cheung, Tan-To, Lai, Keane K-Y, Yuen, Man-Fung
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 08.08.2019; BioMed Central; BMC
• Subjects: Alleles; Biomarkers, Tumor; Cadherins - genetics; Cancer; Cancer genetics; Cancer patients; Carcinoma; Carcinoma, Hepatocellular - etiology; Causes of; Cell Line, Tumor; Complications and side effects; Criminal investigation; Customized therapies; Deleterious mutations; DNA Mutational Analysis; DNA sequencing; Gene Expression Profiling; Gene Frequency; Gene mutation; Gene silencing; Genes; Genetic aspects; Genetic research; Genomics - methods; Hepatitis B; Hepatitis B - complications; Hepatitis B - virology; Hepatitis B virus; Hepatocellular carcinoma; Humans; INDEL Mutation; Liver Neoplasms - etiology; Mutation; Physiological aspects; Polymerase chain reaction; RNA interference; Targeted sequencing; Tumor proteins; Tumor Suppressor Protein p53 - genetics; Tumor Suppressor Proteins - genetics; Tumors; Hong Kong; Gene silencing; Hepatocellular carcinoma; Targeted sequencing; Deleterious mutations; Customized therapies
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-019-6002-9

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. 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. 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. 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.