Homozygous Deletion Scanning in Hepatobiliary Tumor Cell Lines Reveals Alternative Pathways for Liver Carcinogenesis

Abstract

Despite high rates of loss of heterozygosity affecting various chromosomes, the number of tumor suppressor genes (TSGs) found to be consistently involved in primary liver cancer is low. In the past decade, characterization of homozygous deletions (HDs) in tumors has become instrumental to identify new TSGs or to reveal the influence of a particular TSG on the development of a specific tumor type. We performed a detailed HD profiling at 238 critical loci on a collection of 57 hepatobiliary tumor cell lines (hepatocellular, cholangiocellular, and bile duct carcinomas, hepatoblastomas, and immortalized hepatocytes). We identified HDs at 9 independent loci, the analysis of which was extended to 17 additional hepatobiliary tumor cell lines. In total, 34 homozygous losses involving 9 distinct genes were detected in the 74 cell lines analyzed. Besides expected deletions at the p16-INK4A/p14-ARF, FHIT, AXIN1, and p53 genes, we detected HDs at the PTEN, NF2, STK11, BAX, and LRPDIT genes that were formerly not known to be implicated in human liver tumorigenesis. In conclusion, our data suggest that these genes may represent novel liver tumor suppressive targets. Additional tumorigenic pathways should be carefully considered in hepatocarcinogenesis. ( H epatocellular carcinoma (HCC), the main histologic form of primary liver cancer, is one of the most prevalent human tumors in the world. 1,2 Chronic infections of the liver by hepatitis B or hepatitis C viruses represent the dominant etiologies of HCC. 3 The historically recent spread of hepatitis C virus in human populations will result in a substantial increase in HCC incidence in developed countries and several epidemiologic surveys already have detected such a trend for the past 20 years in Japan, the United States, and Europe. 4,5 Until recently, chromosomal abnormalities occurring in HCC were defined poorly. We and others have performed allelotyping and comparative genomic hybridization studies to characterize the main chromosome targets in human liver tumorigenesis. 6-8 Only a handful of cancer genes are, however, consistently found mutated in this tumor type. p53 and AXIN1 genes are inactivated by somatic mutations in, respectively, 30% and 5% of cases, whereas p16-INK4A and SOCS1 are silenced through promoter hypermethylation in more than 50% of cases. 9-13 Finally, ␤-catenin, the only proto-oncogene previously found to be mutated in liver cancer, is activated in 20% of the samples. 14 The liver tumor-suppressive function of the product of the mannose-6-phosphate/insulinlike growth factor 2 receptor (IGF2/M6PR) gene is suspected but remains still controversial. 15,16 The past decade has seen the isolation of numerous tumor suppressor genes (TSGs) through the characterization of homozygous deletions (HDs) in primary tumors and cell lines. Although, HDs represent rare events, many of the TSG isolations, including WT1, p16-INK4A, BRCA2, FHIT, PTEN, SMAD4, and SNF5, were at least partly attributable to their detection. [17][18][19][20][21][22] In an attempt to

γ-Secretase-mediated Release of the Low Density Lipoprotein Receptor-related Protein 1B Intracellular Domain Suppresses Anchorage-independent Growth of Neuroglioma Cells

“…mLRP1B4 Suppresses Tumor Cell Anchorage-independent Growth-LRP1B is known to be frequently inactivated by genetic or epigenetic alterations in tumor cells (3)(4)(5)(6). We employed PCR to examined LRP1B transcripts in neuroglioma H4 cells and detected aberrant transcripts with deletions in exon 2 to exon 7 leading to a loss of protein (data not shown), revealing that these LRP1B-deficient cells represent a good model system to explore the potential of LRP1B to alter cellular function.…”

Genetic or epigenetic silencing of low density lipoprotein receptor‐related protein 1B expression in oral squamous cell carcinoma

“…In view of previous reports of homozygous deletions of LRP1B in various types of tumors, (17,(19)(20)(21)(22) we screened a panel of OSCC cell lines for homozygous losses by genomic PCR using primers flanking exons 1, 5, 7 and 10 of LRP1B (GenBank accession number NM_018557 for cDNA sequence and NT_005058 for genomic sequence). All primer sequences used in this study are available on request.…”

Hunting for Tumor Suppressor Genes in Liver Cancer

“…Although isolation of TSGs has traditionally been facilitated through the characterization of homologous deletions (HDs) in primary tumors and cell lines, HD is a very rare event. This is clearly shown in the work of Pineau et al 5 The frequency of HDs for the newly identified TSGs in the 48 HCC cell lines were 2%, 4%, 2%, 2%, and 4% for LRPDIT, PTEN, STK11, BAX, and NF2, respectively. Furthermore, only two cell lines, one from the HCC and the other from the CCC lines (HA22TVGH has HDs for NF2 and p53 genes, and TFK1 has HDs for both FHIT and p16/INK4A, respectively), displayed more the one type of HD.…”

“…In particular, LRPDIT, a member of the low-density lipoprotein receptor family (now referred to as lowdensity lipoprotein receptor-related protein, LRP1B), is frequently inactivated in human non-small cell lung cancer and has been proposed as a candidate TSG. 22,23 In conclusion, the work described by Pineau et al 5 constitutes a valuable contribution to the ongoing attempts to define the molecular pathogenesis of human HCC. In particular, further characterization of the novel TSG candidates and the regulatory pathways governed by these genes should hopefully provide novel therapeutic targets for the treatment of human liver cancer.…”

“…In the current issue of HEPATOLOGY, Pineau et al 5 have made a valiant effort to improve our current understanding of the types of TSG that may be involved in HCC development. The investigators have performed a detailed homozygous deletion profiling at 238 loci on a collection of 74 hepatobiliary cell lines composed of hepatocellular, cholangiocellular, and bile duct carcinomas, hepatoblastoma and immortalized hepatocytes.…”