Gene copy number analysis of granulin-epithelin precursor (GEP) and ATP-binding cassette subfamily F member 1 (ABCF1) in hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the most lethal cancers in Hong Kong and Southeast Asian countries. Cancer progression is often symptomless, making the early diagnosis difficult, thus leading to a high mortality rate. Treatments against HCC were often found to be less effective than other cancers. Systemic chemotherapy, which is widely used in cancer treatments, has a low response rate in HCC. New treatment regimes, such as targeted therapy, have shown partial responses in clinical trials and therefore continuous effort in searching new drug targets is warranted.

Granulin-epithelin Precursor (GEP) is a pluripotent growth factor, and has been shown to be overexpressed in HCC and various cancers. Our group has demonstrated that GEP promotes tumor growth, and regulates chemoresistance in HCC. It shares a highly similar expression pattern with one of the members of ATP-binding cassette (ABC) transporter family, ABCF1. Blocking GEP, both in vitro and in vivo, showed inhibition on HCC growth. These suggest that GEP is a potential target for HCC treatment. However, there is still little information on how GEP and ABCF1 is overexpressed in HCC. This project aims to investigate the mechanisms involved.

GEP and ABCF1 genes are located on chromosomes 17q and 6p, respectively, which both are frequently amplified in HCC. We used quantitative microsatellite analysis (QuMA) to detect GEP and ABCF1 amplification in HCC samples. Both GEP and ABCF1 showed about 20% of HCC cases having amplification, and their copy numbers correlated to the mRNA expression levels. The copy numbers of GEP were also found to correlate to those of ABCF1 significantly. Clinico-pathological analysis showed that GEP copy numbers correlated with gender, serum AFP levels and HBV status, while ABCF1 did not associate with any of the clinico-pathological features.

Fluorescence in situ hybridization (FISH) was performed to validate the results on DNA copy number by QuMA. The cases with highest DNA copy number on GEP and ABCF1, were examined. The average difference between FISH and QuMA results ranged ± 0.3 copies, indicating QuMA and FISH results were corroborated on DNA copy number. Furthermore, the FISH results indicated that there are different degrees of aneuploidy involved in chromosome 6p and 17q in 5 out of 6 cases investigated. These suggest that the copy number variations in GEP and ABCF1 were partly caused by the abnormal number of chromosomes.

In summary, we observed that GEP and ABCF1 gene copy numbers were increased in subsets of HCC cases, and the increase correlated to their respective transcript expression levels. Furthermore, these copy number variations partly could be explained by aneuploidy as demonstrated by FISH analysis. The current study may help to understand the complex genomic aberrations in HCC and allow better treatment designs in the future.