Homozygous deletions of methylthioadenosine phosphorylase (MTAP) are more frequent than p16^INK4A (CDKN2) homozygous deletions in primary non-small cell lung cancers (NSCLC)

Abstract

Homozygous deletions of the tumor suppressor gene p16^INK4A and deficiency of methylthioadenosine phosphorylase (MTAP), both located on chromosome 9p21, have been independently reported in non-small cell lung cancer (NSCLC). To determine the frequency of co-deletion of these two genes, we investigated 50 samples of primary NSCLC using a quantitative PCR-ELISA. All specimens were fixed in formalin, paraffin embedded and stored until assayed. Histologic subtypes included 25 adenocarcinomas (50%), 21 squamous cell carcinomas (42%) and four large cell carcinomas (8%). Homozygous deletions of MTAP exon 8 could be detected in 19 of 50 NSCLC samples (38%). Adenocarcinoma (11 of 25, 44%) showed a higher deletion frequency than squamous cell carcinoma (six of 21, 29%). In contrast, homozygous p16^INK4A deletions were detected in only nine of 50 (18%) samples using specific primers for p16^INK4A exon 1α. No difference between the histological subtypes and p16^INK4A deletion frequency was observed. We further investigated the ten samples with MTAP deletions but intact p16^INK4A exon 1α with primers specific for p16^INK4A exon 3, the exon nearest to MTAP exon 8. Interestingly, none of the ten samples had deletion of the p16^INK4A exon 3 coding region. Fine mapping analysis performed in ten samples showed a frequent breakpoint between MTAP exon 4 and exon 5. In addition, p16 protein expression could not be detected in five out of six samples with intact p16 but deleted MTAP locus. These data show a high frequency of homozygous MTAP deletions in NSCLC which is associated with detectable co-deletion of p16^INK4A in only half of the cases. This result suggests the existence either of another tumor suppressor gene telomeric of p16^INK4A or of deletions involving 3′-untranslated (3′-UTR) regulatory regions of p16^INK4A that can interfere with its expression or function.