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Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.

Carlson MW, Iyer VR, Marcotte EM - BMC Genomics (2007)

Bottom Line: We find a wide variation in the extent to which different cell culture models mimic late-stage invasive cervical cancer biopsies.The lowest agreement was from monolayer HeLa cells, a common cervical cancer model; the highest agreement was from primary epithelial cells, C4-I, and C4-II cell lines.Applying this method to individual pathways, we identified the appropriateness of particular cell lines for studying specific pathways in cervical cancer.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA. mark.carlson@tufts.edu <mark.carlson@tufts.edu>

ABSTRACT

Background: Cell lines have been used to study cancer for decades, but truly quantitative assessment of their performance as models is often lacking. We used gene expression profiling to quantitatively assess the gene expression of nine cell line models of cervical cancer.

Results: We find a wide variation in the extent to which different cell culture models mimic late-stage invasive cervical cancer biopsies. The lowest agreement was from monolayer HeLa cells, a common cervical cancer model; the highest agreement was from primary epithelial cells, C4-I, and C4-II cell lines. In addition, HeLa and SiHa cell lines cultured in an organotypic environment increased their correlation to cervical cancer significantly. We also find wide variation in agreement when we considered how well individual biological pathways model cervical cancer. Cell lines with an anti-correlation to cervical cancer were also identified and should be avoided.

Conclusion: Using gene expression profiling and quantitative analysis, we have characterized nine cell lines with respect to how well they serve as models of cervical cancer. Applying this method to individual pathways, we identified the appropriateness of particular cell lines for studying specific pathways in cervical cancer. This study will allow researchers to choose a cell line with the highest correlation to cervical cancer at a pathway level. This method is applicable to other cancers and could be used to identify the appropriate cell line and growth condition to employ when studying other cancers.

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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.
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Figure 6: 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.

Mentions: HeLa and SiHa cell lines were cultured in a different type of media to assess whether small changes to the environment could have a large impact on the correlation to tissue. The effect of different culture media on the correlation to cervical tissue was assessed at the pathway level using both SiHa and HeLa cell lines. An example of three biologically relevant pathways that changed in correlation between the two media is shown in Figure 6, though the changes were not restricted to metabolic pathways. The correlation to cervical cancer increased by changing the medium to DMEM; the increased correlation to cervical tissue was expected after the transition from a minimal medium (MEM) to a richer medium (DMEM). We hypothesized that the increase in correlation was due to the addition of glucose in DMEM, which is absent from MEM. After ranking the genes based on their impact on the correlation, the third highest gene that lowered the correlation of HeLa cultured in MEM was PDK4. Pyruvate dehydrogenase kinase has been found to increase its expression during starvation [38]. In our experiments, PDK4 was found to have a 4-fold decrease in expression in cervical cancer, a 2-fold increase in expression in HeLa cultured with DMEM, and a 20-fold increase in expression in HeLa cultured with MEM. As the function of PDK4 is the regulation of glucose metabolism, this indicates HeLa cultured in MEM experience starvation-like conditions, whereas HeLa cultured in DMEM have an environment similar to in vivo cancer conditions. This example of PDK4, along with the three metabolic pathways shown in Figure 6, provided examples of how an increase in the correlation to normal cervix was achieved by simply changing the medium. Simple changes to the culturing environment can therefore have a dramatic affect on the relevance of some cell lines as models of cervical cancer.


Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.

Carlson MW, Iyer VR, Marcotte EM - BMC Genomics (2007)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1878486&req=5

Figure 6: 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.
Mentions: HeLa and SiHa cell lines were cultured in a different type of media to assess whether small changes to the environment could have a large impact on the correlation to tissue. The effect of different culture media on the correlation to cervical tissue was assessed at the pathway level using both SiHa and HeLa cell lines. An example of three biologically relevant pathways that changed in correlation between the two media is shown in Figure 6, though the changes were not restricted to metabolic pathways. The correlation to cervical cancer increased by changing the medium to DMEM; the increased correlation to cervical tissue was expected after the transition from a minimal medium (MEM) to a richer medium (DMEM). We hypothesized that the increase in correlation was due to the addition of glucose in DMEM, which is absent from MEM. After ranking the genes based on their impact on the correlation, the third highest gene that lowered the correlation of HeLa cultured in MEM was PDK4. Pyruvate dehydrogenase kinase has been found to increase its expression during starvation [38]. In our experiments, PDK4 was found to have a 4-fold decrease in expression in cervical cancer, a 2-fold increase in expression in HeLa cultured with DMEM, and a 20-fold increase in expression in HeLa cultured with MEM. As the function of PDK4 is the regulation of glucose metabolism, this indicates HeLa cultured in MEM experience starvation-like conditions, whereas HeLa cultured in DMEM have an environment similar to in vivo cancer conditions. This example of PDK4, along with the three metabolic pathways shown in Figure 6, provided examples of how an increase in the correlation to normal cervix was achieved by simply changing the medium. Simple changes to the culturing environment can therefore have a dramatic affect on the relevance of some cell lines as models of cervical cancer.

Bottom Line: We find a wide variation in the extent to which different cell culture models mimic late-stage invasive cervical cancer biopsies.The lowest agreement was from monolayer HeLa cells, a common cervical cancer model; the highest agreement was from primary epithelial cells, C4-I, and C4-II cell lines.Applying this method to individual pathways, we identified the appropriateness of particular cell lines for studying specific pathways in cervical cancer.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA. mark.carlson@tufts.edu <mark.carlson@tufts.edu>

ABSTRACT

Background: Cell lines have been used to study cancer for decades, but truly quantitative assessment of their performance as models is often lacking. We used gene expression profiling to quantitatively assess the gene expression of nine cell line models of cervical cancer.

Results: We find a wide variation in the extent to which different cell culture models mimic late-stage invasive cervical cancer biopsies. The lowest agreement was from monolayer HeLa cells, a common cervical cancer model; the highest agreement was from primary epithelial cells, C4-I, and C4-II cell lines. In addition, HeLa and SiHa cell lines cultured in an organotypic environment increased their correlation to cervical cancer significantly. We also find wide variation in agreement when we considered how well individual biological pathways model cervical cancer. Cell lines with an anti-correlation to cervical cancer were also identified and should be avoided.

Conclusion: Using gene expression profiling and quantitative analysis, we have characterized nine cell lines with respect to how well they serve as models of cervical cancer. Applying this method to individual pathways, we identified the appropriateness of particular cell lines for studying specific pathways in cervical cancer. This study will allow researchers to choose a cell line with the highest correlation to cervical cancer at a pathway level. This method is applicable to other cancers and could be used to identify the appropriate cell line and growth condition to employ when studying other cancers.

Show MeSH
Related in: MedlinePlus