Analysis of 1p, 19q, 9p, and 10q as prognostic markers for high-grade astrocytomas using fluorescence in situ hybridization on tissue microarrays from Radiation Therapy Oncology Group trials

Abstract

Survival periods vary considerably for patients with high-grade astrocytomas, and reliable prognostic markers are not currently available. We therefore investigated whether genetic losses from chromosomes 1p, 19q, 9p, or 10q were associated with survival in 89 high-grade astrocytomas using tissue microarrays (TMAs) derived from Radiation Therapy Oncology Group clinical trials. Cases included 15 anaplastic astrocytomas (AAs) and 74 glioblastomas (GBMs) selected on the basis of survival times significantly shorter or longer than the expected median. Genetic analysis was performed by TMA-fluorescence in situ hybridization (FISH) on array sections using 8 DNA probes, including those directed at 1p32, 19q13.4, 9p21 (p16/CDKN2A), and 10q (PTEN and DMBT1). Genetic status for each locus was correlated with patient survival group, and data were analyzed by using Fisher's exact test of association (adjusted P = 0.025). Losses of chromosome 1p, either alone or in combination with 19q, were encountered in only 2 cases, both AAs. This contrasts with oligodendrogliomas, in which combined 1p and 19q losses are frequent and predictive of prolonged survival. Solitary 19q loss was noted in 3/15 AAs and in 7/70 GBMs and was more frequent in the long-term survival group (P = 0.041, AA and GBM combined). Chromosome 9p loss was seen in 5/8 AAs and 39/57 GBMs, whereas chromosome 10q loss was detected in 4/15 AAs and 48/68 GBMs. The 9p and 10q deletions were slightly more frequent in short-term survivors, though none of the comparisons achieved statistical significance. Long-term and short-term survival groups of high-grade astrocytomas appear to have dissimilar frequencies of 19q, 9p, and 10q deletions. TMA-FISH is a rapid and efficient way of evaluating genetic alterations in such tumors.

Fig. 1

Low (left panel) and high (right panel) magnification of H&E-stained tissue microarrays (TMAs) constructed from 106 high-grade astrocytomas from patients enrolled in RTOG clinical trials. Each tissue core on the TMA measures 0.7 mm in diameter.

Fig. 2

Representative FISH hybridizations performed on tissue microarrays. A. GBM with a normal disomic complement of 1p. Most cells have 2 green (1p32) and 2 red (1q42) signals. Some appear to have fewer than 2 copies because of the truncation artifact encountered in thin tissue sections (i.e., incomplete DNA complement in sectioned nuclei). Some signals are out of the plane of focus represented in the photograph. B. Pattern of 19q deletion in GBM showing 2 green (19p13) signals and 1 red (19q13.4) signal in most nuclei. C. Pattern of chromosome 10 deletion in a GBM. Only 1 green (PTEN) signal and 1 red (DMBT1) signal are detected in each nucleus, most likely representing either a large 10q deletion or the loss of an entire chromosome 10. D. Pattern of homozygous deletion of 9p21 (p16/CDKN2A) in a GBM. Only green signals from the centromeric probe are noted in the majority of nuclei. Signals from 9p21 (red) are almost entirely absent.