A comprehensive karyotypic analysis on Korean hepatocellular carcinoma cell lines by cross-species color banding and comparative genomic hybridization

Abstract

Chromosomal aberrations were investigated in hepatitis B virus integrated into the hepatocellular carcinoma (HCC) cell lines SNU-368, SNU-449, SNU-398, SNU-182, and SNU-475 using Giemsa-banding, cross species color banding, and comparative genomic hybridization (CGH). The origins of the marker chromosomes were confirmed by fluorescence in situ hybridization with constructed chromosome painting probes. Each cell line had unique modal karyotypic characteristics and showed variable numbers of numerical and structural clonal cytogenetic aberrations. The gains were commonly detected on chromosome 1, and chromosome regions 6p, 7q, 8q, 10p, 17q, and 20; the losses were often found on 4q21∼qter, 13, 18q21∼qter, and Y. In particular, the breakpoints on 1p36, 1p13∼q21, 2p13∼q11, 6q10∼q11, 7q11, 7q22, 14q10, 16q10∼q13, 17q21, 18q21, and 19p11∼q11 were involved frequently at the multiple rearranged lesions. CGH analysis further confirmed the cytogenetic data, and the nonrandom rearrangements data suggested the candidate regions for the genes to be isolated which were related to HCC.

Introduction

Hepatocellular carcinoma (HCC) is the most common primary cancer in the liver. It has been a major malignancy in underdeveloped and developing countries, and recently is increasing also in the developed countries 1, 2, 3, 4. Persistent hepatitis B virus (HBV) infection is one of the major causes for HCC [5]. The role of HBV in hepatic carcinogenesis has been studied by several groups 6, 7, 8. Establishment of HCC cell lines will broaden the scope of investigation; a few HBV integrated cell lines have been used for cancer research 9, 10. Although some chromosome aberrations in HCC have suggested that gene aberrations are involved in tumor progression, the characterization of the complex chromosomal rearrangements was difficult with conventional cytogenetic methods. Chromosomal studies on primary HCC and cell lines by conventional methods have frequently reported on the ploidy status and suggested common alterations involving chromosome 1 11, 12, 13, 14. Recently however, using fluorescence in situ hybridization– (FISH)-based techniques such as comparative genomic hybridization (CGH), spectral karyotyping (SKY), and cross-species color banding (RxFISH), it is now possible to identify the genomic imbalance and the chromosomal derivation of marker chromosomes. RxFISH is a new FISH technique that uses the probes originating from flow-sorted and differentially labeled gibbon chromosomes. The hybridization of these probes onto human chromosomes results in a specific color banding pattern for each human chromosome 15, 16.

HBV DNA fragments integrated into the HCC cell lines were established from Korean HCC patients [17]. We report the application of RxFISH, multiple chromosome painting, and CGH to characterize the chromosomal rearrangements in these HCC cell lines.