Spotting DNA repair genes gone awry

Spotting DNA repair genes gone awry

Genome instability suppressing (GIS) genes play an important role in correcting DNA damage involving the improper copying or reshuffling of large sections of chromosomes. Called gross chromosomal rearrangements, or GCRs, these structural errors can disrupt gene order or even result in an abnormal number of chromosomes.

"Mutated GIS genes have long been suspected of playing a role in the development of many types of cancers, but identifying them has been difficult due in large part to a lack of comprehensive GCR tests, or assays, in mammalian systems," said one of the first authors of the study.

In the journal Nature Communications, researchers describe a novel two-pronged approach that combines methods from genetics and bioinformatics to identify GIS genes -- first in yeast and then in humans.

In the first step, the scientists used assays and technologies to screen thousands of mutant yeast strains for genes that suppress GCRs. They identified 182 GIS genes, 98 of which had not been described before. The team also uncovered more than 400 previously unknown cooperating Genome Instability Suppressing genes (cGIS) genes, which only affect genome stability when combined with other mutations. "Before our experiment, only a few dozen cGIS genes were known. Now we know of hundreds," said the author.

To determine how many of the yeast GIS genes had human counterparts implicated in cancers, the researchers searched The Cancer Genome Atlas (TCGA)--a compilation of genomic data from thousands of patients -- for such human gene homologues.

They also supplemented their candidate list with human genes that are not found in yeast but that participate in the same pathways and protein complexes as the yeast GIS genes. "We didn't want to just look for the human equivalent of yeast GIS genes because there are human GIS genes that don't have yeast homologs," author said.

Three cancers in the TCGA were selected for screening: ovarian cancer, colorectal cancer and acute myeloid leukemia. The scientists hypothesized that a greater number of GIS gene defects should be implicated in ovarian cancer and colorectal cancer because these two cancers tend to involve numerous large-scale rearrangements of the genome. Leukemia served as an important control because it is a cancer with little genome instability, and thus should not involve any GIS gene defects.

As expected, the team found that 93% of ovarian cancers and 66% of colorectal cancers had genetic defects affecting one or more of the predicted GIS genes, whereas acute myeloid leukemia did not appear to have defects involving GIS genes.

The researchers are already screening more than a dozen other human cancers in the TCGA for GIS gene defects. "Understanding this process allows us to think more about how carcinogenesis proceeds and it might give us insights into defects that could be therapeutically actionable in the future," said the author.