Gene expression profiling of human gliomas was performed to define the molecular signatures of these tumors and to identify targets for antibody-based therapeutics. Our analysis of expression profiles determined via Affymetrix U133 chips reveals the presence of 3 distinct molecular subtypes of high grade glioma, which we term proneural (PN), mesenchymal (Mes.) and proliferative (Prolif.). The tumors in the PN class express markers of neurogenesis and exhibit a statistically significant improvement in survival time, relative to the other 2 classes. The Mes. And Prolif. subtypes are distinguished primarily by the expression of extracellular matrix/adhesion/motility and cell proliferation/cell cycle/DNA replication or repair genes, respectively. In identifying cell surface or secreted proteins that are overexpressed in tumor and might be used as targets of antibody-based therapy, we observe that most candidate targets show strong evidence for differential expression between the PN and Mes. subclasses of tumor. The list of candidate targets evaluated by Taqman and in situ hybridization includes Brevican, DLL3, YKL-40 (CHI3L1), CD44, GPNMB, CD163, GP38, and FN14. All of these antigens show overexpression of their respective mRNA relative to normal brain in a significant proportion of a large panel of gliomas. Strong expression of the PN tumor antigens Brevican and DLL3 is mutually exclusive with robust expression of the other candidate antigens. A series of monoclonal antibodies (mAbs) directed against Brevican were generated. To develop a targeted cytotoxic agent, one Brevican mAb was chemically coupled to monomethylauristatin F (MMAF), a microtubule-binding antimitotic agent. Brevican-MMAF drug conjugates afforded selective cytoxicity towards cells expressing the GPI-linked isoform of Brevican. In summary, this study demonstrates that high grade gliomas can be usefully classified into 3 dominant molecular subtypes and identifies a panel of antigens that are significantly elevated in gliomas, relative to normal brain. More importantly, our preliminary in vitro findings with Brevican-MMAF drug conjugates suggest that these agents may prove effective in the development of a targeted therapy for gliomas.

[Proc Amer Assoc Cancer Res, Volume 46, 2005]