Genome-wide loss of heterozygosity analysis of chemically induced rat hepatocellular carcinomas reveals elevated frequency of allelic imbalances on chromosomes 1, 6, 8, 11, 15, 17, and 20

Neoplastic development is a multistep process that involves the stochastic accumulation of heritable genetic alterations in proto-oncogenes. DNA repai r genes, and tumor suppressor genes. Loss of heterozygosity (LOH) analysis has been used successfully to identify the genetic determinants of neoplast ic development, including tumor suppressor genes, in several species and or gans but not in the rat liver. We report the results of a sensitive genome- wide LOH analysis of rat hepatocellular carcinomas (HCCs). Heterozygous rat s (Wistar-Furth x Fisher 344) were subjected to an Initiation-Promotion-Pro gression (IPP) protocol of hepatocarcinogenesis. Two weeks after initiation (by partial hepatectomy, 10 mg/kg diethylnitrosamine), the rats were place d on a diet containing 0.05% phenobarbital (PB). After 24 wk of PB promotio n, the rats received either 100 or 150 mg/kg ethylnitrosourea. Hepatocellul ar tumors were resected after a total of 76 wk of PB promotion. LOH analysi s was completed on 26 HCCs by using 60 microsatellite markers covering all 20 rat autosomes and chromosome X. While 85% of the HCCs had one or more al lelic imbalances, the average HCC had 3.3 allelic imbalances (range 0-9). A conditional hypothesis-testing method called the Hot-Cold model was used t o determine the location of statistically significant elevations in the fre quency of allelic imbalances. Elevated allelic imbalances were observed on chromosomes 1q, 6, 8, 11, 15, 17, and 20p. Together, these allelic imbalanc es suggest that the retinoblastoma and insulin-like growth factor genes as well as the resistance to chemical carcinogenesis (rcc) locus may be involv ed in HCC development in the rat but that LOH of the p53 gene is not. The e levated rate of allelic imbalances on chromosomes 8,11, and 17 may indicate the location of undiscovered tumor suppressor genes important to neoplasti c development in rat liver. Microdissection-based LOH analysis of HCC revea led that contamination of non-neoplastic and nonhepatocellular tissue was n ot masking LOH in the whole-tumor analysis. There were no statistically sig nificant differences in the frequency of allelic imbalances between HCC of any differentiation state (histological grade). To the degree that it does not reflect differences in etiological factors, the absence of allelic imba lances in chromosomal regions containing the p53 and mamose-6-phosphate/ins ulin-like growth factor II receptor tumor suppressor genes and the generall y low frequency of allelic imbalances in these rumors, suggests that LOH an d allelic imbalances play a less significant role in the molecular pathogen esis of HCC in rats than humans. Mel. Carcinog. 28:51-61, 2000. (C) 2000 Wi ley-Liss. Inc.