BMC Genomics 2007, 8:117 http://www.biomedcentral.com/1471-2164/8/117 SFHiimegLupalreceem6lleldiniae'cshcaonrgreeslattoiocnutltource rcvoicnadlitciaonncseirncrease the Simple media changes to culture conditions increase the HeLa cell line's correlation to cervical cancer. Three pathways provided examples of how the correlation to normal cervix increased when HeLa cells were cultured in rich DMEM media versus ATCC recommended MEM media as monolayers. DMEM media contained glucose, and the expression of PDK4 indicated HeLa cells cultured in DMEM experience a nutrient-rich environment, similar to in vivo conditions. ing the overall shift in pathway correlations for different environments, plotted as a histogram in Figure 7A. Since organotypic cultures had a high correlation to tissue, we expected to see an increase in the overall number of path- ways that had a higher correlation to tissue by the organ- otypic culture. This was observed by a shift of the histogram to higher correlation and confirmed statisti- cally (p < 0.004, t-test). Although significance was not reached when compared to normal cervical tissue, likely due to low sample numbers, an increase in the number of pathways with a higher correlation was still evident. The individual gene expression changes between monol- ayer and organotypic environments was studied to shed light on how expression changes of a relatively few genes can affect their correlation to cervical cancer. For example, in the case of SiHa cells cultured as monolayer versus organotypic, we observed specific induction of membrane proteins. Cadherin, a cell adhesion gene, had a 3.6 fold increase in expression in the 3-dimensional culture over the monolayer, arguing for cadherin's role in stimulating cell stacking in the organotypic model. Interestingly, the cell adhesion gene CYR61 had a dramatic decrease (7 fold) in expression. There was an increase in expression in many genes whose function was integral to the plasma membrane, including SLC7A11, SLC04A1, CLDND1, cFHeiegrLutahroaenr7gHaneoLtaypmiconcoultauyreerscaurlteubrestter models of cervical can- HeLa organotypic cultures are better models of cer- vical cancer than HeLa monolayer cultures. A: Histo- gram of the number of pathways at each specific correlation for HeLa cells cultured as monolayer (black) and in an organ- otypic environment (white). There were more pathways with a higher correlation to cervical cancer in the organotypic cul- ture than in monolayer (p < 0.004, t-test). Therefore, organ- otypic cultures were better models of cervical cancer than simple monolayer cultures. B: In the ''Cell-Cell Signaling'' pathway (GO:7267), HeLa cells cultured in an organotypic culture had a higher correlation to both normal cervix and cervical cancer than either monolayer or organotypic control cultures. IER3, HOMER1, and AOC3. Many of these genes play a role in metabolic signaling or plasma membrane trans- port and were possibly up-regulated due to the increased communication between cells in this 3-dimensional cul- ture. Many of the gene changes that allowed a cell line to grow in 3-dimensions were involved in cell-cell signaling pathways (Figure 7B), further highlighting the importance of this pathway in tumorigenesis. As cell-cell attachments and signaling play an important role in differentiation of the epithelium, the pathway "Cell-Cell Signaling" (GO:7267) was analyzed as to whether 3-dimensional culture conditions can improve Page 9 of 13 (page number not for citation purposes)