Abstract Glioblastoma (GBM) is the most common and aggressive malignant brain tumor in adults and the standard treatment consists of surgical resection of the tumor followed by radiation and chemotherapy with temozolomide. A combination of standard therapy with other biologically-based therapies is necessary to improve the survival of patients with GBM, which currently stands only to 15-17 months. In this sense many studies have been developed in pursuit of expressed membrane proteins in GBM, which are potential targets for immunotherapy. Our laboratory demonstrated increased CD99 mRNA and protein expression in GBM samples. CD99 has a key role in several biological processes, including cell adhesion, migration, apoptosis, differentiation of T cells and thymocytes, diapedesis of lymphocytes to inflamed vascular endothelium, maintenance of cellular morphology and regulation of intracellular membrane protein trafficking. In this study, the transcriptome of two GBM cell lines (U87MG and A172) transfected with siRNA for CD99 were analyzed in relation to the non-target control (NTC). A total of 728 genes (hypoexpressed with fold change ≤-1.5 relative to NTC or hyperexpressed with fold change ≥1.5 relative to NTC) were observed in both cell lines. An enrichment analysis by MetaCoreTM revealed the following processes as the most significant: (1) Cytoskeleton_Regulation of cytoskeleton rearrangement, (2) Cell adhesion_Cell-matrix interactions (3) Development_Blood vessel morphogenesis. Further, both cell lines were silenced for CD99 expression by shRNA (two clones) to perform functional assays, as wound healing (migration assay), adhesion, invasion and apoptosis. The CD99 knockdown reduced migration in both cell lines, with the highest decrease of the migration observed in the highest CD99 knockdown. Adhesion assay was performed using fibronectin as an extracellular matrix substrate. U87MG cells showed greater adhesion to fibronectin than the control (scrambled shRNA). On the other hand, A172 cells knocked down for CD99 presented lower adherence to fibronectin than the control. Apoptosis analysis with shCD99 U87MG cells showed a tendency of cells entering into late apoptosis when treated with temozolamide for 48 hours, but the same was not observed in shCD99 A172 cells. Additionally, CD99 (RPE) and phaloidin (Alexa Fluor 488) colocalized at lamellipodia, suggesting that CD99 is related to cytoskeleton rearrangement in both GBM cell lines. The different phenotypic behavior of migration and apoptosis observed in these two GBM cell lines with different somatic mutation background may be due to distinct signaling activation. Migration/invasion is the major characteristics of GBM which limits the surgical tumor resection, and consequently leads to tumor recurrence. Therefore, further analysis of CD99 activating pathways in the context of cell migration is worthwhile to unveil new therapeutic strategies to halt GBM progression. Citation Format: Lais C. Cardoso, Antonio M. Lerario, Suely K. Marie, Roseli S. Soares, Sueli M. Oba-Shinjo. CD99 plays an important role in glioblastoma cell migration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 899. doi:10.1158/1538-7445.AM2017-899