Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer

Abstract

CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.

Cross-species analysis of LZTR1 loss-of-function mutants demonstrates dependency to RIT1 orthologs

“…Interestingly, Sewduth et al, demonstrate that pharmacological inhibition of the RAF/MEK/ERK MAPK or AKT pathway was unable to fully rescue the embryonic lethality and vascular defects of mice with conditional Lztr1 KO in blood vessels ( Sewduth et al, 2020 ). Given that our Lztr1/Rit1 DKO mice did not exhibit cardiovascular abnormalities during embryogenesis, excessive accumulation of Rit1 protein in Lztr1 KO cells likely results in the hyperactivation or dysregulation of additional Rit1 effector pathways that contribute to Lztr1 -/- embryonic lethality ( Cuevas-Navarro et al, 2021 ; Meyer Zum Büschenfelde et al, 2018 ; Vichas et al, 2021 ).…”

Cell Painting predicts impact of lung cancer variants

“…Resolving the impact of variants at high throughput has the potential to accelerate precision oncology ( Suzuki et al. , 2019 ; Vichas et al. , 2021 ).…”

The blended phenotype of a germline RIT1 and a mosaic PIK3CA variant

“…The RIT1 Arg122Leu substitution found in our patient must also be growth-promoting, as evidenced by the birth macrosomia (5178 g in week 35.5) and large placenta (1 kg) and a positive transformation assay of NIH3T3 cells in soft agar ( Berger et al 2014 ). Oncogenic RIT1 variants, like this one, have recently been shown to weaken mitotic assembly checkpoints and accelerate mitosis ( Vichas et al 2021 ). It is unknown if the PIK3CA Asn345Thr substitution also contributes to this, but neither fetal macrosomia nor placentomegaly are known PROS features.…”

“…Of note, placentomegaly is not a recognized feature of a RASopathy either, unlike fetal macrosomia. However, because growth-promoting RIT1 signaling seems independent of KRAS but not PTPN11 and SOS1 ( Vichas et al 2021 ), an effect on placental growth that is not seen in most other RASopathies is conceivable. The reason for this is that other RASopathy genes signal through a cascade involving KRAS, and RIT1 signaling appears KRAS-independent.…”

“…The reason for this is that other RASopathy genes signal through a cascade involving KRAS, and RIT1 signaling appears KRAS-independent. It has also been speculated that RIT1 stimulates receptor tyrosine kinases like GRB2 and IGF1R directly ( Vichas et al 2021 ). Taken together, both the RIT1 and the PIK3CA variants are undoubtedly growth-promoting—the first mainly during fetal development, the second during somatic development.…”