Pathways that Prevent Genome Instability: From Model Organisms to Human Cancer

The development of cancer is associated with increased genome instability. To understand the control genome instability, we have developed genetic assays for measuring the rate of accumulating genome rearrangements in Saccharomyces cerevisiae and for characterizing the structure of the genome rearrangements. We have identified more than 100 genes and multiple pathways that prevent the accumulation of genome rearrangements. The rearrangements observed include interstitial deletions, translocations, deletion of an end of a chromosome arm associated with healing by de novo telomere addition and chromosome fusions; many rearranged chromosomes are unstable and undergo secondary rearrangements. The genes identified include those encoding: replication factors, proteins that reassemble or modify chromatin during DNA replication, recombination and repair proteins where the defect leads to aberrant repair, checkpoint proteins that respond to replication errors, proteins that scavenge reactive oxygen species and prevent oxidative damage to DNA, proteins thought to act on damaged replication forks and on aberrant structures generated by recombination between divergent DNA sequences, and proteins that regulate telomerase. Our working hypothesis is that “DNA damage” normally occurs during DNA replication or is the result of other aspects of cellular metabolism such as those that generate reactive oxygen species, possibly in combination with DNA replication. Different pathways that suppress genome rearrangements subsequently act on this damage – S-phase checkpoint functions that suppress mutagenic repair and activate non-mutagenic repair, a pathway that prevents aberrant telomere additions, and homologous recombination. In the absence of one or more of these pathways, different types of mutagenic repair occur. Alternatively, in the absence of telomerase, telomere maintenance is dependent on both recombination and checkpoint functions, and when either the recombination or checkpoint pathways are compromised increased genome instability occurs. Using a bioinformatics approach to analyze the our results combined with various published S. cerevisiae genome-wide systems biology data sets, we have built models of the network of genes that function in the suppression of genome instability and have identified additional genes that prevent genome instability through the study of this network. We are presently using this gene list to examine the genetics of genome instability in cancer.