• National Cancer Institute
  • National Human Genome Research Institute

Posted: May 20, 2011

TCGA Glioblastoma Multiforme Data Used in the Discovery of a Gene Pathway Interaction that Affects Tumor Development

Catherine Evans

Cancer genomics researchers are increasingly using The Cancer Genome Atlas's (TCGA) data to develop and test hypotheses about how cancer develops. TCGA’s recently completed glioblastoma multiforme (GBM) dataset of gene changes has informed several recent studies, including one from Harvard and Northwestern researchers in the September 2010 issue of Genes and Development. The group was interested in the TP53 gene signaling pathway, which is involved in GBM, one of the deadliest and most aggressive adult brain cancers. 

The pathway involves the TP53 gene, whose function is disrupted in GBM. When a mutation alters TP53, it cannot turn on tumor-suppressing genes. The investigators suspect that a protein, Bcl2L12, interacts with the p53 protein to limit its activity in some GBM tumors. Bcl2L12 is overexpressed in most GBM tumors, pointing to its relevance to the cancer. They set out to test the p53-Bcl2L12 interaction hypothesis, using TCGA data and cell culture experiments.

Bcl2L12 Interferes with p53 Activities

To start, the group tested whether Bcl2L12 disrupts cell-protective activities carried out by p53.  p53’s actions lead to slowed cell growth or to cell death if DNA is damaged, to ensure that harmful mutations are not passed on to other cells. The investigators expressed Bcl2L12 in cultured cells, and those cells grew much more than untreated cells. In a separate experiment, the researchers added a DNA damaging chemical to cell cultures to induce p53-driven cell death. The presence of Bcl2L12 led to reductions in chemical indicators of cell death. The scientists concluded that Bcl2L12 appears to keep cells from slowing their rates of growth and from dying, activities p53 normally governs.

The researchers then turned to TCGA data to see if p53 and Bcl2L12 are linked in human GBM tumors. If Bcl2L12 does indeed impede p53 tumor suppression, tumors without TP53 mutations might have increased Bcl2L12. They analyzed TCGA data from GBM tumors and found that the more there were alterations leading to increased Bcl2L12, the fewer TP53-damaging alterations there were. On the other hand, in GBM tumors with many TP53-damaging mutations, Bcl2L12 expression levels were reduced. The group suspects that in the cellular environment of a developing cancer, the tumor ensures its own continued growth either via mutations in TP53 (and thus less Bcl2L12 is needed to disrupt p53 activity), or, if TP53 is unaffected, alterations occur to increase Bcl2L12 levels.

Bcl2L12’s Mechanism of Action

The scientists then went back to cell cultures to determine how Bcl2L12 might disrupt p53 activity. They observed that Bcl2L12 and p53 are located near each other in the cell nucleus. Their tests also indicated that the two could chemically bind together. Then they treated cells treated with a DNA-damaging agent to activate p53. Under these conditions, Bcl2L12 and p53 bound together and formed a complex. Thus, Bcl2L12 appeared to be capable of physically interacting with p53 to disrupt its activity.

Next, the researchers wanted to determine how Bcl2L12’s physical interaction with p53 enhances cell growth. In cell cultures, they found that Bcl2L12 prevents the turning on of genes that p53 normally activates. These genes then can’t respond to DNA damage to protect the cell by slowing its growth or killing it. The researchers concluded that Bcl2L12 works by binding to p53, physically holding it back from binding to and activating tumor-suppressor genes. 

In summary, the results from the cell culture experiments and the analyses from the TCGA GBM tumors suggest that future treatments could target Bcl2L12 alone or in combination with chemotherapy in GBM patients whose tumors retain unaltered TP53

Stegh, A.H., Brennan, C., Mahoney, J.A., Forloney, K.L., Jenq, H.T., Luciano, J.P., Protopopov, A., Chin, L. and DePinho, R.A. (2010) Gliomaoncoprotein Bcl2L12 inhibits the p53 tumor suppressor. Genes Dev. 24(19):2194-2204. Read the full article.