Expression of DNA-dependent protein kinase and DNA topoisomerase I in human hepatocellular carcinoma and adjacent normal liver tissues

Abstract

OBJECTIVE: To investigate the gene expression of DNA-dependent protein kinase (DNA-PK) and DNA topoisomerase I (DNA TOPO I) in hepatocellular carcinoma (HCC) by use of Atlas Human Cancer cDNA Expression Array membranes, semiquantitative reverse transcription polymerase chain reaction and northern blotting. METHODS: Hybridization of the cDNA array membrane was performed with α-32P-labeled cDNA probes synthesized from RNA isolated from HCC and adjacent non-cirrhotic normal liver. Reverse trans­cription polymerase chain reaction of 24 pairs of specimens and northern blotting of four pairs of specimens were used to confirm the expression patterns of DNA-PK and DNA TOPO I identified by Atlas array hybridization. RESULTS: Among 588 genes spotted on the membrane, 33 genes were related to DNA damage response/ repair/recombination. DNA-dependent protein kinase and DNA TOPO I were upregulated in HCC. There were no genes downregulated in HCC. Reverse transcription polymerase chain reaction gave results consistent with Atlas Human Cancer cDNA Array findings in DNA-PK 16/24 and DNA TOPO I 18/24. Northern blot analysis of DNA TOPO I of four paired specimens all showed upregulation in HCC compared with that in normal liver tissues. CONCLUSION: The result obtained from the Atlas microarray provides for the first time a liver cancer-specific expression profile, which identifies gene expression comprehensively and systematically. In addition, the finding about genes related to DNA damage response/repair/recombination may lead to clues about the mechanism of multiple drug resistance. The quick method of profiling gene expression by cDNA array provides an overview of key factors that may be involved in HCC. The precise relationship between the altered genes and HCC needs further investigation.