The contribution of paralog buffering to tumor robustness

Abstract

Tumor cells remain viable in the face of extensive gene loss, suggesting that they are highly robust to genetic perturbations. One potential mechanism of genetic robustness is buffering between paralog pairs – due to originating from an ancestral duplication event, some paralog pairs have redundant functionality that allows them to buffer each other’s loss. Paralog buffering can be observed as synthetic lethality, where individual loss of either gene is well tolerated but concurrent loss results in cell death. In model organisms, particularly Saccharomyces cerevisiae, paralog buffering has been shown to contribute substantially to genetic robustness. The overall aim of this thesis is to characterize the contribution of paralogs to maintaining the robustness of tumor cells. First, through analysis of genome-wide CRISPR screens and molecular profiles of hundreds of cancer cell lines, I show that paralogs are less frequently essential for cellular growth than singletons across a wide range of genetic backgrounds. Furthermore, I provide evidence that variation in gene essentiality can be attributed to paralog buffering relationships in ~13-17% of cases. Finding that certain paralog pairs, such as those that function in protein complexes, are more likely to exhibit buffering relationships, I then develop a classifier to make predictions, accompanied by feature-based explanations, of synthetic lethality between paralog pairs in cancer cell lines. I validate this classifier using results from existing combinatorial CRISPR screens in cancer cell lines, show that it can distinguish between robust and context-specific synthetic lethality, and make predictions for ~36K paralog pairs, which can be used to prioritize pairs for inclusion in future screens. Finally, I investigate the impact of paralog buffering on the evolution of tumor genomes – I show that, across two large patient cohorts, homozygous deletions are more likely to be observed for paralog than singleton non-driver genes and that this difference cannot be explained by other factors known to influence copy number variation. As paralogs essential for growth of cancer cells in vitro are less frequently deleted than non-essential paralogs, I propose that paralogs are more frequently deleted because they are generally more dispensable for tumor cells in vivo. Overall I show that paralog buffering contributes to tumor cell phenotype. Paralog buffering can provide tumor cells with phenotypic stability in the face of genotypic changes, but it can also be exploited, through synthetic lethality, for the development of targeted therapeutics