Abstract 4878: Modification of gene expression in tumor cells by the culture microenvironment

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Purpose: Since cell culture techniques were developed in 1950s, in vitro assays using monolayer cell cultures have played a major role in cancer research. Despite the absence of cross-talk between tumor cells and their respective host organ-microenvironment, data produced by in vitro assays have often been used to address challenge. However, the potential discrepancy between in vitro and in vivo mircoenvironments should not be overlooked. We have investigated the influence of culture conditions of the biology of tumor cells by comparing the genetic profiles of tumor cells growing in different culture conditions, such as culture media, sera, concentration of sera, and cell confluence. Materials and Methods: We profiled the gene expression of human breast cancer tumor cells (MDA-MB-231) that were cultured for 48 hours under various culture conditions; in different media (MEM, DMEM, RPMI-1640), different sera (FBS, horse serum), different concentrations of FBS (10%, 0.1%), and different cell confluence (90%, 50%) using microarray analysis of total cellular RNA using an Illumina platform (human HT-12v12 expression beadchip) Results: Upon analysis, 2,234 genes were differentially expressed among cultures with varied cell confluence, 2,981 genes differentially expressed in cultures with various FBS concentrations, 422 genes were differentially expressed in cells cultured with different sera, and 8,925 genes were differentially expressed in cells cultured with different media. Of 8,925 genes, 10 (ARHGEF6, CAPN3, COPG, DAMM2, GSTK1, PGM1, QPCT, QPRT, SLC1A4, and VAT1) were identified as commonly upregulated in confluent cultures, regardless of the media, as compared with sub-confluent cultures. In addition, 5 genes (IL7R, MPP4, NOP56, G3BP1 and IFP38) were identified as commonly downregulated in confluent cultures. Collectively, these data indicate that the gene expression profiles varied significantly across different cultures conditions. Conclusion:These results demonstrated that even under commonly “simplified” culture conditions, gene expression profiles can significantly vary across cells exposed to different culture conditions. Some of these conditions parallel those found in vivo, i.e., sub-confluent versus confluent cultures, where cell division is more active in the former than the latter condition. The significant differences in gene expression by cells exposed to fetal bovine serum as compared to horse serum are likely caused by different levels of growth factors within the sera. Likewise, the different gene expressions in tumor cells growing in different media can be attributed to different levels of glucose and salts present. Collectively, our data indicate that any change in culture conditions can lead to significant changes in the gene expression of tumor cells. Hence, to obtain reproducible data, one must strictly adhere to specified experimental details. Citation Format: Seung Wook Kim, Sun Jin Kim, Ho-jeong Lee, Junqin He, Qiuyu Wu, Erica J. Lawson, Isaiah J. Fidler. Modification of gene expression in tumor cells by the culture microenvironment. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4878. doi:10.1158/1538-7445.AM2014-4878