Synthetic lethality

Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death, whereas a mutation in only one of these genes does not, and by itself is said to be viable. In a synthetic lethal genetic screen, it is necessary to begin with a mutation that does not kill the cell, although may confer a phenotype (for example, slow growth), and then systematically test other mutations at additional loci to determine which confer lethality. Synthetic lethality indicates functional relationships between genes {refs?}.

Background

File:Synthetic lethality.jpg

Schematic of basic synthetic lethality. Simultaneous mutations in gene pair confer lethality while any other combination of mutations is viable.

The phenomenon of synthetic lethality was first described by Calvin Bridges in 1922, who noticed that some combinations of mutations in the model organism Drosophila melanogaster confer lethality. Theodore Dobzhansky coined the term “synthetic lethality” in 1946 to describe the same type of genetic interaction in wildtype populations of Drosophila. If the combination of genetic events results in a non-lethal reduction in fitness, the interaction is called synthetic sickness. Although in classical genetics the term synthetic lethality refers to the interaction between two genetic perturbations, synthetic lethality can also apply to cases in which the combination of a mutation and the action of a chemical compound causes lethality, whereas the mutation or compound alone are non-lethal.

Synthetic lethality is a consequence of the tendency of organisms to maintain buffering schemes that allow phenotypic stability despite genetic variation, environmental changes and random events such as mutations. This genetic robustness is the result of parallel redundant pathways and “capacitor” proteins that camouflage the effects of mutations so that important cellular processes do not depend on any individual component. Synthetic lethality can help identify these buffering relationships, and what type of disease or malfunction that may occur when these relationships break down, through the identification of gene interactions that function in either the same biochemical process or pathways that appear to be unrelated.

High-throughput screens

Synthetic lethality may be explored in a variety of model organisms, including Drosophila melanogaster and Saccharomyces cerevisiae. Since synthetic lethal mutations are inherently inviable, common approaches are to employ temperature sensitive mutations or put mutations under the control of a regulated promoter to allow exploration of the phenotype without leading to death. Some synthetic lethal pairs are detected while attempting to elucidate molecular mechanisms of fundamental biological processes without the use of high-throughput screens. For instance, the synthetic lethality of Parkin and MTF1 in Drosophila was discovered when examining the relationship between oxidative stress and metal homeostasis in the pathogenesis of Parkinson’s disease.

However, high-throughput synthetic lethal screens may help illuminate questions about how cellular processes work without previous knowledge of gene function or interaction. Screening strategy must take into account the organism used for screening, the mode of genetic perturbation, and whether the screen is forward or reverse. Many of the first synthetic lethal screens were performed in S. cerevisiae. Budding yeast has many experimental advantages in screens, including a small genome, fast doubling time, both haploid and diploid states, and ease of genetic manipulation. Gene ablation can be performed using a PCR-based strategy and complete libraries of knockout collections for all annotated yeast genes are publicly available. Synthetic genetic array (SGA), synthetic lethality by microarray (SLAM), and genetic interaction mapping (GIM) are three high-throughput methods for analyzing synthetic lethality in yeast. A genome scale genetic interaction map was created by SGA analysis in S. cerevisiae that comprises about 75% of all yeast genes. By examining 5.4 million gene-gene pairs for synthetic lethality, an unbiased network of functional connections between genetic interactions was constructed.

High-throughput synthetic lethality screens are also performed in metazoans, but a major challenge is efficient gene perturbation. In the nematode C. elegans, RNA-interference can be combined with a query strain loss-of-function mutation. While RNA-interference is more experimentally demanding in Drosophila, living cell microarrays allow knockdown of two genes simultaneously. RNA-interference is also feasible in mammalian cells, and chemical screens in mammalian cell lines is important for identifying pharmacological targets of drugs.

Synthetic lethality in chemotherapeutics

A synthetic lethal approach to cancer therapy is currently being explored as a means of developing therapies that reduce off-target effects of chemotherapies and chemopreventative drugs. Cancer cells are marked by genetic instability, errors in DNA repair, and uncontrolled transcription, which create new synthetic lethal partners in cancer cells. Because a drug effect targeting a specific gene product resembles the phenotype caused by a mutation in that gene, a cancer-related mutation can sensitize cancer cells to chemotherapeutics that target its synthetic lethal partner. Consequently, drugs that target synthetic lethal partners of mutations in cancer cells may not be toxic to normal cells, which could avoid off-target side effects of chemotherapeutics.

Synthetic lethal analysis can be used to elucidate mechanisms of known chemotherapeutic drugs by identifying genes whose function is necessary for drug function. For example, BRCA1 and BRCA2 are important for repairing double-strand breaks in DNA, and mutations in these genes predispose individuals to breast cancer and ovarian cancer. The enzyme PARP1 is involved in repairing single-strand breaks, and the inhibition of PARP1 in a BRCA mutant background is selectively lethal to tumors because cancer cells accumulate DNA lesions that they cannot repair. Synthetic lethality is also useful for screening libraries of molecules to detect drugs that selectively inhibit cancer cells. In a recent chemical-genetic screen, one compound of 3200 screened molecules was a synthetic lethal inhibitor of pancreatic cancer KRAS gain-of-function cells, which suggests a potential treatment for this cancer type.

See also

• Synthetic genetic array
• Synthetic rescue

External links

• Data Repository of Yeast Genetic INteractions
• Saccharomyces Genome Deletion Project
• Syn-Lethality Database