Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells

The RB1 tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions with RB1 could lead to new approaches to treating cancers with inactivated RB1. We identified 95 SL partners of RB1 based on a Drosophila screen for genetic modifiers of the eye phenotype caused by defects in the RB1 ortholog, Rbf1. We validated 38 mammalian orthologs of Rbf1 modifiers as RB1 SL partners in human cancer cell lines with defective RB1 alleles. We further show that for many of the RB1 SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels of RB1 was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novel Drosophila cancer model with co-occurring Rbf1, Pten and Ras mutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets for RB1-deficient cells that may be further adapted for the treatment of human cancer.
Author summary RB1 is a tumor suppressor gene that is inactivated in a significant proportion of all cancer cases. A therapeutic approach that specifically targets defects associated with this tumor suppressor is currently not available. A synthetic lethal (SL) interaction occurs between two genes when the inactivation of either gene alone is viable but the inactivation of both genes simultaneously results in the loss of viability. Screening for SL interactions in model organisms can identify candidate genes/pathways that can be targeted to specifically kill tumor cells with a specific mutation. Here we used a cross-species approach to identify evolutionarily conserved SL targets for RB1-deficient cells. We demonstrated that drugs targeting the identified targets, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol, can selectively kill human RB1-deficient cancer cells. Because cancer cells are characterized by the accumulation of mutations in multiple oncogenic pathways, we further confirmed that these interactions are preserved in the presence of additional strong oncogenic alterations. Moreover, low activity of the identified SL genes in human tumors, when combined with low levels of RB1, was associated with improved patient survival. Altogether, we identified several novel targets of RB1-deficient cells that may be further adapted for the treatment of human tumors.