Evaluation of genes that are differentially expressed in glioblastoma versus normal brain was undertaken using a standard Student t test with BH correction (P < 0.01) and absolute average log2 ratio greater than two. Expression profiling identified 664 over-expressed genes in glioblastoma, including 56 genes over-expressed greater than 30-fold, and 1224 under-expressed genes, including 157 genes under-expressed greater than 30-fold. A list of all of the identified genes is provided in Supporting information File 1. From the top ten of the over-expressed genes, we identified the antiapoptotic gene BIRC5/survivin (Blum et al., 2006) and the transcription factor E2F2 (Okamoto et al., 2007), the activities of which have been already linked to glioblastoma. We also found two highly expressed mitotic kinases, PBK and BUB1, and a potential cell cycle regulator, DLG7/HURP, that have not been previously reported in glioblastoma. Proliferation-related genes were also included among the highly expressed genes. Some of them were previously well described as participating in glioblastoma progression, such as UBE2C (Bredel et al., 2005b), MKI67 (Raghavan et al., 1990), TOP2A (van den Boom et al., 2003), TNC (Sarkar et al., 2006), CHI3L1/YKL-40 (Tanwar et al., 2002), MELK (Liu et al., 2006a,b), and CD44 (Ylagan and Quinn, 1997). The others, NCAPG, KIF20A, CENPA, and RRM2, are novel glioblastoma-associated genes with reported functional roles in cytokinesis and/or cell proliferation (Geiman et al., 2004; Wonsey and Follettie, 2005). Regarding the under-expressed genes, we identified some with known tumor suppressor functions in glioma (CHD5 and LGI1). CHD5 was identified last year as a tumor-suppressor that controls proliferation, apoptosis, and senescence via the p19(Arf)/p53 pathway in glioma (Bagchi et al., 2007). It has been suggested that the leucine-rich, glioma-inactivated gene 1 (LGI1) gene is a candidate tumor suppressor gene involved in progression of glial tumors (Chernova et al., 1998). In addition, four components of the Wnt/β-catenin signaling pathway were highly under-expressed: two Wnt antagonists, WIF1 and SFRP1, and PPP2R2C (PP2A) and WNT10B (Kirikoshi and Katoh, 2002). Such disruptions may result in an improper function of the Wnt/β-signaling pathway leading to aberrant cell proliferation and therefore explaining part of the glioblastoma progression.
Functional annotation of the highly differentially expressed genes (greater or less than 30-fold) underlined distinct biological processes according to groups of over- or under-expression. Highly over-expressed genes were significantly associated with the regulation of the mitotic cell cycle, and more precisely with the following GOTERM_BP_ALL: M phase (P = 5.7e-7), microtubule-based process (P = 3.9e-3), and sister chromatid segregation (P = 0.01). Highly under-expressed genes were significantly associated with cell communication (P = 1.8e-3), cell-cell signaling (P = 3.1e-9), and neurophysiological process (P = 4.9e-5).