Integration of multiple biological contexts reveals principles of synthetic lethality that affect reproducibility

Angel A Ku,Di Wu,Sameera Kongara,Xin Zhao,Khyati N Shah,Hsien-Ming Hu,Sourav Bandyopadhyay,Frank Mccormick,Allan Balmain

doi:10.1038/s41467-020-16078-y

Abstract

Synthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies. In the case of KRAS, we identify that published synthetic lethal screen hits significantly overlap at the pathway rather than gene level. Analysis of pathways encoded as protein networks could identify synthetic lethal candidates that are more reproducible than those previously reported. Lack of overlap likely stems from biological rather than technical limitations as most synthetic lethal phenotypes are strongly modulated by changes in cellular conditions or genetic context, the latter determined using a pairwise genetic interaction map that identifies numerous interactions that suppress synthetic lethal effects. Accounting for pathway, cellular and genetic context nominates a DNA repair dependency in KRAS-mutant cells, mediated by a network containing BRCA1. We provide evidence for why most reported synthetic lethals are not reproducible which is addressable using a multi-faceted testing framework.

Highlights

Synthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies
Integrating across studies, we show that previously published KRAS synthetic lethal screens contain significant information regarding the pathways required for KRAS mutant cells in a manner that extends beyond the single gene that is often reported
As a basis for comparison we selected the top 250 KRAS synthetic lethal genes reported in each study as hits (KSL genes, Supplementary Data 1), and found that there was marginal overlap between any pair of studies based on a hypergeometric test accounting for total number of tested genes in each study, consistent with previous reports (Fig. 1a)[3,15]

Summary

Introduction

Synthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies. Synthetic lethality is a type of genetic interaction that occurs when the simultaneous perturbation of two non-essential genes results in cell death Such an approach has been used to define new vulnerabilities in cancer cells harboring defined mutations, such as the case of BRCA1− or BRCA2− mutant cells which are sensitive to PARP inhibition[1,2]. Historical screens using RNAi technologies have been widely suggested to suffer from library quality and off target effects that have limited the reproducibility of published synthetic lethal candidates[3,4] and it has been suggested that CRISPR pooled screens may overcome these issues. The plasticity of genetic interactions present in singlecelled organisms likely foreshadows the challenges in the identification of clinically relevant synthetic lethal interactions in a heterogeneous disease such as cancer

Methods

Results

Conclusion