Novel cost-effective screen test can speed up cancer genes' discovery

Washington, November 19 : Scientists at Cold Spring Harbor Laboratory (CSHL) have devised a cost-effective screen test that can speed up the rate of discovering cancer-related genes and validating their function in living animals.

The novel test resulting from a combination of five research groups' expertise has been found to succeed in uncovering 13 new tumour suppressors, genes that inhibit the activity of cancer genes, in a preliminary study.

Given that cancer sufferers, specifically people with liver cancer, usually lack tumour suppressors, these discoveries "are a huge step forward in understanding the genetics of cancer and open up a host of new strategies to improve its diagnosis and treatment," according to the authors.

Dr. Scott Powers, Director of the Human Cancer Genome Center at CSHL, used a highly efficient genome-sequencing technique to scan the genomes of liver cancers from more than 100 patients to compile a list of deletions of chromosomal regions, which were hypothesized to be the location of most of the missing tumor suppressor genes.

Upon comparing that list with the genome sequence of a normal human cell, the researcher could identity approximately 300 genes within the deleted chromosomal segments.

Since chromosomal deletions are not limited to cancer-related genes alone, and may cause any number of unrelated neighbouring genes to be lost, the researchers had to pinpoint the tumour suppressors among the 300 genes.

"Genomic analysis of human tumours is important, but combining it with functional screening in mouse models is a notable step forward," Powers observed.

CSHL Professor Scott W. Lowe bypassed the time-consuming step of mutating a gene in mouse embryos, and then creating lines of mice that can be examined for the mutation's effects. The researcher instead engineered mutations into the genome of adult mouse cells, and then re-injected them into adult mice.

The team used a method honed by Dr. Gregory J. Hannon of introducing stable mutations into mouse cells via RNA interference (RNAi), a technique in which small RNA molecules are introduced into cells to shut off specific genes.

RNA sequences that corresponded to all the 300 or so deleted genes were obtained from an RNAi "library" compiled by the Hannon lab.

Lowe and colleagues introduced the RNAi tools into progenitor cells that develop into mature liver cells, albeit ones engineered to over-produce a cancer gene product called Myc.

The engineered cells that carried a Myc mutation and an shRNA were injected into mice. Dramatically, those that received cells in which a tumour suppressor gene had been "silenced" by an shRNA developed tumours within a month.

The scientists homed in on the identity of the silenced tumour suppressors by simply isolating and analysing the genetic material from the tumours, and their strategy identified 13 new tumour suppressor genes, most of which had not been linked to cancer before.

"The nature of these new genes is not obvious and we wouldn't have guessed their relationship to cancer if we hadn't followed this approach. They may now allow us to make headway into poorly understood areas of cancer," says Lowe.

The researchers say that the newly identified tumour suppressor genes affect a wide array of cellular activities, including maintenance of cell structure, cellular metabolism, cell proliferation, and control of the levels of various tumour growth-enhancing proteins in the cell's nucleus.

In one instance, the team's strategy uncovered an entire network of genes that go awry in liver cancer.

"Given that the cancer puzzle involves multiple genes in various combinations, we need to find all the hits that make the cell tip over the edge," says Lowe, explaining one advantage of his team's broad strategy.

The researchers are of the opinion that some of the genes identified might also lead to new strategies for cancer therapy.

A report on this study has been published in the online edition of the journal Cell.

ANI