Scientists uncover an epigenetic mechanism that keeps cancer cells alive

A study conducted in the United States by Brazilian researchers identifies epigenetic modifications that are essential for tumor survival.

By Fábio de Castro

Agência FAPESP – A study conducted in the United States by Brazilian researchers identified epigenetic alterations that are essential for survival of cancer cells. The study shows that tumor cells die when genes that had been “disconnected” by the epigenetic anomaly are reactivated.

Epigenetics is genomic information that is not encoded by the DNA sequence itself. Methylation is a major epigenetic mark, in which a methyl group is transferred onto some cytosine bases. In general, cancer cells present anomalous DNA methylation patterns. The aberrant methylation of cytosine bases could cause changes in gene expression patterns and trigger malignant transformation in cancerous cells.

The study was published in the May 14, 2012 edition of Cancer Cell. The first author of the article, Daniel Diniz de Carvalho, is conducting his post-doctoral work in the Department of Urology, Biochemistry and Molecular Biology at the University of Southern California.

With a bachelor’s degree in veterinary medicine from the Universidade de Brasília (UnB), Carvalho completed his doctorate in immunology at the Universidade de São Paulo’s Biomedical Sciences Institute (ICB-USP) under the guidance of Professor Gustavo Amarante-Mendes and with the support of a FAPESP fellowship.

Carvalho’s previous work had already generated major findings, published in Oncogene (Nature Publishing Group) and PLoS Genetics. The scientist has recently been hired by the University of Toronto, where he will direct his own laboratory at the school’s Ontario Institute of Cancer.

According to Carvalho, the main objective of his research, which will be continued in Canada, is to contribute to the development of a new generation of epigenetic therapies.

“There are epigenetic therapies that are being used clinically, but they change the DNA expression pattern, activating not only genes that impede tumor survival but also several others that should not be activated. Because they are nonspecific, they are high-risk therapies. In this study, we identified important targets that might be used to develop more efficient second-generation epigenetic therapies,” Carvalho said in an interview with Agência FAPESP.

All cells of an organism have the same genetic information. What guarantees their differentiation, allowing the formation of several tissues, is the fact that the expression of certain genes is connected or interconnected. This coordinated gene expression is regulated by epigenetic mechanisms such as DNA methylation and chromatin modifications.

“If this mechanism is disrupted by an epigenetic alteration, several diseases can emerge, particularly cancer. When cells with these alterations become a tumor, even more control of the regulatory mechanism is lost. The cell then begins to accumulate other mutations that are not relevant to the genesis of the tumor,” he explains.

Distinguishing the epigenetic alterations that guarantee the survival of tumor from alterations caused by the development of the tumor is a major problem for scientists.

“With the new sequencing techniques available, we mapped all of the genetic and epigenetic alterations in a set of prostate cancer samples. However, since we only analyzed tumor cells at the end of the cancer development process, we don’t know which alterations were the cause and which were consequences,” says Carvalho.

Fundamental genes

Identifying epigenetic alterations that are essential for tumor survival is fundamental for selecting appropriate therapeutic targets, according to Carvalho.

“A genetic alteration, like a mutation, is permanent. However, epigenetic alterations are reversible, and for this reason they are very interesting candidates for possible therapies,” he said.

To identify essential epigenetic alterations, the scientists analyzed a tumor cell with a large quantity of aberrant methylation in the DNA.

“By reducing the availability of methyl groups, we placed selective pressure on the tumor so the cells that survived would have methylation at the fundamental genomic regions. The cancer cells survived up to a certain point. After a certain level of reduction, the cells no longer survived, and we knew that the last genes that had been methylated were essential for survival of the tumor,” said Carvalho.

Then, the scientists mapped the methylated sites in the genome to discover where these fundamental genes were located. Utilizing tumor samples from the International Cancer Genome Atlas Consortium, the scientists found that these fundamental genes were always methylated and inactive in tumor cells.

“We later reactivated the genes in the cells to verify whether they were truly important. As soon as these genes were reactivated, the tumor cells died. In fact, the survival of the tumor was only possible when these genes are silenced,” he affirmed.

Although inactive, the fundamental genes remained intact in tumor cells. According to Carvalho, the challenge now is discovering how to reverse the methylation of the DNA, reactivating these genes to kill the tumor.

One of the main objectives of Carvalho’s future research will be to search for mechanisms that allow the demethylation of specific genes, creating second-generation epigenetic therapies. Another goal is to improve the results of the current nonspecific epigenetic therapies, which activate many genes in the tumor cells, causing the cells to become immunogenic. “We think we can improve the therapies by combining them with immunotherapy,” he said.

The article DNA Methylation Screening Identifies Driver Epigenetic Events of Cancer Cell Survival (doi:10.1016/j.ccr.2012.03.045), by Daniel Diniz de Carvalho and others, can be read by subscribers of Cancer Cell at www.cell.com/cancer-cell.