ABSTRACT: Juvenile pilocytic astrocytoma (JPA) is one of the most common brain tumors in children. The expression profiles of 21 JPAs, determined using Affymetrix GeneChip U133A, were compared with subjects with normal cerebella. The genes involved in neurogenesis, cell adhesion, synaptic transmission, central nervous system development, potassium ion transport, protein dephosphorylation, and cell differentiation were found to be significantly deregulated in JPA. These 21 JPAs were further clustered into two major groups by unsupervised hierarchical clustering using a set of 848 genes with high covariance (0.5-10). Supervised analysis with Significance Analysis of Microarrays software between these two potential subgroups identified a list of significant differentially expressed genes involved in cell adhesion, regulation of cell growth, cell motility, nerve ensheathment, and angiogenesis. Immunostaining of myelin basic protein on paraffin sections derived from 18 incompletely resected JPAs suggests that JPA without myelin basic protein–positively stained tumor cells may have a higher tendency to progress. Experiment Overall Design: Under an Institutional Review Board–approved protocol, brain tumor tissues were obtained, after informed consent, from patients undergoing tumor resection or other tumor-related neurosurgical procedures at the Texas Children's Hospital, Baylor College of Medicine. Samples of normal cerebellar tissue (n = 2) were isolated from surgically removed tissue adjacent to resected tumor tissue. Portions of the tumors were fixed in 10% formaldehyde and embedded in paraffin for sectioning and pathologic reviews, and the residual tissue samples were snap-frozen in liquid nitrogen and stored at –80°C for RNA extraction. All samples were obtained at initial diagnosis with no prior exposure to chemotherapy or radiation therapy. Normal fetal brain RNA was obtained from Stratagene (La Jolla, CA) and a normal cerebellum RNA was from Ambion, Inc. (Austin, TX). Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) followed by DNase I treatment and clean-up on aRNeasy spin column (Qiagen, Valencia, CA). RNA quality and purity were assessed by agarose gel electrophoresis and absorbance measurement at A260/A280.
