Homozygous deletion of CDKN2A (p16(INK4a)/p14(ARF)) but not within 1p36 orat other tumor suppressor loci in neuroblastoma

Loss of heterozygosity of several specific genomic regions is frequently ob served in neuroblastoma tumors and cell lines, but homozygous deletion (HD) is rare, and no neuroblastoma tumor suppressor gene (TSG) has yet been ide ntified. We performed a systematic search for HD, indicative of a disrupted TSG, in a panel of 46 neuroblastoma cell lines. An initial search focused on a well-characterized consensus region of hemizygous deletion at 1p36.3, which occurs in 35% of primary neuroblastomas. Each cell line was screened with 162 1p36 markers, for a resolution of 13 kb within the consensus 1p36. 3 deletion region and 350 kb throughout the remainder of 1p36. No HDs were detected. This approach was expanded to survey 21 known TSGs, specifically targeting intragenic regions frequently inactivated in other malignancies. HD was detected only at the CDKN2A (p16(INK4a)/p14(ARF)) gene at 9p21 and w as observed in 4 of 46 cell lines. The observed region of HD included all e xons of both CDKN2A and the closely linked CDKN2B (p15(INK4b)) gene for cel l lines LA-N-6 and CHLA-174, all exons of CDKN2A but none of CDKN2B for CHL A-179, and only 104 bp within CDKN2A exon 2 for CHLA-101. All four deletion s are predicted to inactivate the coding regions of both p16(INK4a) and p14 (ARF). HD was observed in corresponding primary tumor samples fur CHLA-101 and CHLA-174 but was not present in constitutional samples. These results s uggest that for neuroblastoma, large HDs do not occur within 1p36, most kno wn TSGs are not homozygously deleted, and biallelic inactivation of CDKN2A may contribute to tumorigenicity in a subset of cases.