GENOMIC DIFFERENCE ANALYSIS BY 2-DIMENSIONAL DNA-FINGERPRINTING REVEALS TYPICAL CHANGES IN HUMAN LOW-GRADE GLIOMAS

Cytogenetic and molecular analyses such as allelotyping studies have r evealed several genetic changes typical for human glial neoplasms. How ever, most studies to date have involved malignant gliomas and thus ar e likely to reflect late events of tumor progression. To elucidate the initial events of glial tumor growth, we performed a genome-wide sear ch for genetic alterations in the DNA of 43 low-grade gliomas as compa red to the constitutional DNA of the patients' peripheral blood leucoc ytes using the two-dimensional (2D) DNA fingerprint approach. Reliable results were obtained for 28 blood/tumor sample pairs (13 astrocytoma s, 9 pilocytic astrocytomas, 1 oligodendroglioma, 3 oligoastrocytomas, and 2 ependymomas). DNA was digested with the restriction enzyme HaeI II and the resulting fragments were separated on 2D gels according to size and sequence in the first and second dimensions, respectively. Pa tterns of hundreds of spots were generated by hybridization with four different mini-and microsatellite core probes. A total of 655 to 1,122 spots could be visualized per sample. Comparison of blood and tumor s pot patterns revealed two to 11 reproducible changes per patient. Most of the differences were spot losses (77.1%), while the others appeare d to be gains or amplifications. Exactly the same changes were found i n tumor recurrences which lacked histological signs of progression. Wh en comparing different patients, many of the affected spots tended to cluster in particular areas of the gel as revealed by computer-aided c omparison of all spot patterns. Eleven different spot clusters were id entified which may correspond to several major deletion targets. This study provides the basis for the future molecular cloning of the candi date tumor suppressor genes affected by the common spot losses and wil l allow new insights into the genetic mechanisms of glial tumorigenesi s. (C) 1998 Wiley-Liss, Inc.