Fig. 4: A genetic interaction map identifies KRAS synthetic lethal suppressors.

a Overview of approach to generate an epistatic mini-array profile (E-MAP) using combinatorial RNAi to measure 5828 pairwise genetic interactions in MCF10A KRAS G12D cells grown in minimal media. esiRNAs targeting a set of genes are arrayed in a pairwise fashion (in quadruplicate) in tissue culture plates. Reverse transfection is then performed, and the resulting fitness defects are observed using high-content imaging. Raw data are normalized and scored (see Methods). b Overview of genetic interaction map for 30 KRAS synthetic lethal genes and candidate modifiers. Interactions scoring >2 (red) or <−2 (blue) are shown. c Relative proliferation of knockdown of three KRAS synthetic lethals identified or confirmed in this study, CCND1, CDK6 and STK33, in eGFP or KRAS G12D MCF10A cells alone and in combination with their top positive interaction partners. Proliferation normalized to mock. p values based on a two-sided t test, Data are presented as mean values ± s.d. n = 4 biologically independent samples. d Categorical annotations for groups of genes displaying significantly strong genetic interactions with synthetic lethal query genes with p < 0.01 based on two-tailed Student’s t test (see Methods). Edge width is proportional to significance. e Genetic interaction partners involving two KRAS synthetic lethal genes identified in this study, RGL1 and DNMT3A, and associated pathways enriched for genetic interactions. Edge thickness is proportional to interaction score.