Analysis of PTCH/SMO/SHH pathway genes in medulloblastoma

Inactivation of the PTCH tumor suppressor gene occurs in a subset of sporad ic medulloblastomas, suggesting that alterations in the PTCH pathway may be important in the development of this tumor. In order to address the freque ncy of genetic alterations affecting genes in this pathway, we used a combi nation of loss of heterozygosity (LOH) analysis, single-stranded conformati onal polymorphism (SSCP) analysis, and direct sequencing of DNA samples fro m sporadic primitive neuroectodermal tumors (PNETs). To identify alteration s in the PTCH gene, we performed LOH analysis on 37 tumor DNA samples. Of t hose with matched constitutional DNA samples, one demonstrated LOH, Of thos e without matched constitutional DNA, six were homozygous with all markers. All exons of the PTCH gene were sequenced in these seven tumors, and three mutations were found. To identify alterations in the SHH and SMO genes, we analyed ail exons of both genes in 24 tumors with SSCP and sequenced any e xons that showed aberrant band patterns. No mutations were round in either SHH or SMO in any tumor. We also identified the following genes as candidat e tumor suppressors based on their roles in controlling hh/ptc signaling in Drosophila: EN-1 and EN-2, deletion of which results in a lack of cerebell ar development in mice; SMAD family members 1-7, and protein kinase A subun its RI alpha, RI beta, RII beta, C alpha, and C beta. Each of these genes w as investigated in a panel of 24 matched constitutional and tumor DNA sampl es. Our search revealed no mutations in any of these genes. Thus, PTCH is t he only gene in this complex pathway that is mutated with notable frequency in PNET. Genes Chromosomes Cancer 27:44-51, 2000. (C) 2000 Wiley-Liss, Inc .