Studies using cultured tumor cells are frequently used to generate large scale data. However, the discrepancy between culture media conditions and host microenvironment factors prevent adequate translation to the clinical reality. Since culturing tumor cells in atmospheric oxygen pressure (20% O2) significantly differs from oxygen pressure within different organs (5-7% O2). We investigated whether the transcriptome of glioma cells cultured under oxygen concentration that is similar to the lesion in the brain (0.5-2% O2) can simulate the transcriptome of tumors growing in vivo.

Materials and Methods

Human glioma, LN229, cells were cultured in MEM supplemented with 10% FBS under 20%, 6% and 1% oxygen pressure. Glioma growing in the brain was established by stereotactic injection of 1×105 LN229 cells into the brain of nude mice, subcutaneous tumors were established by injection of 1×105 cells. Gene microarray was performed using Illumina Human HT-12_v4_BeadChip microarray and data were collected by using an Illumina bead Array Reader

confocal scanner (BeadStation 500GXDW; Illumina). Array data processing and analysis were performed using Illumina BeadStudio software. All statistical analysis was performed using BRB Arraytools Version 4.4.1 under the R language environment. Cluster analysis was performed and Heat Map was generated by Tree view.


Brain and subcutaneous tumors were harvested 3 weeks post injection. RNA was extracted and processed for gene microarray that identified 2187 genes as brain specific transcriptome. Determination of common genes (same direction) between the transcriptome of glioma growing in the brain and cells growing in culture under 20%, 6%, and 1% O2 identified 23, 5, and 174 specific genes, respectively. Ingenuity pathway analysis and gene set enrichment analysis of the 174 common genes (from cells growing in 1% O2) revealed cluster of genes related to cancer and neurologic diseases, cell death/survival, cell-to-cell signaling. Up-regulation of genes associated with survival and resistance such as AKT, MAPK, NFêB1A, VEGF, and GSTA5 were also commonly identified in glioma growing in the brain and LN229 cells cultured under 1% oxygen.


Culturing glioma cells under different oxygen pressures induces different transcriptomes and cells cultured under 1% O2 express transcriptome most similar to cells growing in the brain. These data demonstrate that, to simulate clinical relevance, the oxygen tension of cultures should approximate those found in organs.

Citation Format: Ho Jeong Lee, Hyun Kyung Yu, Seung Wook Kim, Sung Il Choi, Junqin He, Isaiah J. Fidler, Sun Jin Kim. Transcriptome of glioma growing in the brain is simulated by tumor cells cultured under low oxygen pressure. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 737.