Mapping of candidate region for chordoma development to 1p36.13 by LOH analysis

Various cytogenetic and molecular findings indicate Ip36 loss as a consistent change in sporadic and inherited chordoma, a rare embryogenetic neoplasm arising from notochord remnants. We studied 27 sporadic chordomas by means of loss of heterozygosity (LOH) of 31 microsatellites localized to the 1p36.32-36.11 region, and restricted the minimal LOH interval shared by 85% of the tumours to 1p36.13. We also used RT-PCR analysis to investigate the role of the candidate genes CASP9, EPH2A, PAX7, DAN and DVL1, which were selected on the basis of the physical mapping of the LOH region and their plausible oncosuppressor function. RT-PCR analysis showed the presence of DAN and PAX7 transcript fragments of the expected size in all of 8 chordoma samples, whereas the CASP9-specific fragment was observed in only 3 and EPH2A was absent in one. Smaller than expected DVLI transcripts were found in 4 tumours as well as in their normal counterpart (nucleus pulposus), which also showed a typically sized transcript. Sequencing revealed the skipping of 3 exons in the smallest DVLI fragment, thus leading to a frameshift and predicting a truncated DVLI gene product. Our study of the largest cohort of chordoma patients recruited so far indicates a common molecular lesion at 1p36.13, and suggests that the CASP9, EPH2A and DVLI genes may play an onco-suppressing role and be involved in the development of chordoma. (C) 2003 Wiley-Liss, Inc.