Quantitative real-time PCR does not show selective targeting of p14 ARF but concomitant inactivation of both p16 INK4A and p14 ARF in 105 human primary gliomas

In many human cancers, the INK4A locus is frequently mutated by homozygous deletions. By alternative splicing this locus encodes two non-related tumor suppressor genes, p16 INK4A and p14 ARF (p19 ARF in mice), which regulate cell cycle and cell survival in the retinoblastoma protein (pRb) and p53 pathways, respectively. In mice, the role of p16 INK4A as the critical tumor suppressor gene at the INK4A locus was challenged when it was found that p19 ARF only knock-out mice developed tumors, including gliomas. We have analysed the genetic status of the INK4A locus in 105 primary gliomas using both microsatellite mapping (MSM) and quantitative real-time PCR (QRT–PCR). Comparison of the results of the two methods revealed agreement in 67% of the tumors examined. In discordant cases, fluorescence in situ hybridization (FISH) analysis was always found to support QRT–PCR classification. Direct assessment of p14 ARF exon 1β, p16 INK4A exon 1α and exon 2 by QRT–PCR revealed 43 (41%) homozygous and eight (7%) hemizygous deletions at the INK4A locus. In 49 (47%) gliomas, both alleles were retained. In addition, QRT–PCR, but not MSM, detected hyperploidy in five (5%) tumors. Deletion of p14 ARF was always associated with co-deletion of p16 INK4A and increased in frequency upon progression from low to high grade gliomas. Shorter survival was associated with homozygous deletions of INK4A in the subgroup of glioblastoma patients older than 50 years of age ( P =0.025, Anova test single factor, α=0.05).