Synthetic lethality: general principles, utility and detection using genetic screens in human cells

Abstract

Synthetic lethality occurs when the simultaneous perturbation of two genes results in cellular or organismal death. Synthetic lethality also occurs between genes and small molecules, and can be used to elucidate the mechanism of action of drugs. This area has recently attracted attention because of the prospect of a new generation of anti-cancer drugs. Based on studies ranging from yeast to human cells, this review provides an overview of the general principles that underlie synthetic lethality and relates them to its utility for identifying gene function, drug action and cancer therapy. It also identifies the latest strategies for the large-scale mapping of synthetic lethalities in human cells which bring us closer to the generation of comprehensive human genetic interaction maps.

Fig. 1

Schematic representation of synthetic lethality. Two genes are synthetic lethal only when their simultaneous inactivation results in cellular or organismal death. In this example, deletion of either gene A or gene B does not affect viability whereas inactivation of both at the same time is lethal.

Fig. 2

Cartoon of a hypothetical synthetic interaction network. Genes are represented by blue, red and purple circles and their synthetic lethal interactors (buffering connections) indicated by red lines. Two processes (e.g., DNA repair and DNA replication) are buffered such that many single genes within each process are not essential (circles connected by red lines). Some genes are extrinsically buffered across two different processes whereas others are buffered by independent capacitator genes.

Fig. 3

Forward screen approach to identify synthetic lethality. Cell lines (A–H) are grouped based on mutant status of a single gene (X). Essential genes that are common in the mutants but not in the wild type cell lines are potential synthetic lethal (SL) interactions with gene X and are selected for validation in an independent panel of cell lines.

Fig. 4

Overview of a pooled shRNA screen set-up. Cell lines (A and B) are infected with short hairpin RNA libraries targeting thousands of gene products by RNAi. Cells are cultured to allow the depletion of those containing shRNAs that target essential genes. Genomic DNA is isolated and the vectors are quantified using so-called barcode sequences (short stretches of DNA) that are unique for each shRNA vector. By comparing the genes that are required in one cell line but not the other by custom micro-array or deep sequencing, potential synthetic interactions can be identified.

Fig. 5

The synthetic lethality window. In both examples the mutant cells (purple lines) display a genetic interaction with a second gene that is progressively inhibited (x-axis). However, in the upper graph the synthetic lethality window is limited, as the wild type cells are also affected before viability is completely inhibited in the mutant cells (red line). In contrast, the lower graph shows that full inhibition of viability can be achieved in mutant cells without affecting the wild type cells.