Guangyan Li

Chemical structures of compounds used in this study

Sensitivity to any single RAS-targeted inhibitor is restricted to the subset of RAS(MUT)-specific inhibitor-sensitive tumors

A high therapeutic index, defined as potent inhibition of oncogenic signaling in tumor cells with minimal effects on normal cells, is critical for effective cancer therapies. Recent advances have introduced diverse RAS-targeting inhibitors, including mutant-specific inhibitors such as KRAS G12C and KRAS G12D, as well as paralog- and state-selective inhibitors. Non–mutant-specific RAS inhibition can be achieved by: (i) guanine nucleotide exchange–OFF inhibitors that indirectly inactivate RAS by targeting SHP2 or SOS1, (ii) KRAS-OFF inhibitors that spare NRAS and HRAS, and (iii) active-state RAS(ON) inhibitors that directly block binding of effector RAF. However, the signaling inhibition index (SII)—the differential suppression of oncogenic signaling between RAS-mutant and normal cells—remains poorly defined for these approaches. We evaluated the SII for state- and paralog-selective RAS inhibitors across diverse RAS-mutant and RAS–wild-type models. Guanine nucleotide exchange–OFF inhibitors exhibited neutral or negative values, with reduced MAPK suppression in KRAS G12X cells compared with wild-type cells. KRAS G13D models, especially with NF1 loss, showed low sensitivity. SHP2 plus MEK inhibition resulted in low selectivity, and RAS Q61X models were resistant due to MEK inhibitor–induced NRAS reactivation and altered SHP2 conformations. KRAS-OFF inhibitors demonstrated higher selectivity, whereas active- state RAS(ON) inhibitors showed broader activity but narrow selectivity. Sensitivity to mutant-specific inhibitors largely overlapped with sensitivity to state-selective agents, suggesting that most RAS-mutant tumors will respond poorly to any currently available RAS inhibitor.Implications:Determining the SII can inform the design and clinical application of RAS-targeted therapies to improve tumor selectivity and therapeutic outcomes.

KRAS(G12X)-expressing cells exhibit differential sensitivity to panRAS- GEF(OFF)i

KRAS(G13D) cells are insensitive to next generation SHP2i and SOS1i

RAS(Q61R/K) cells are insensitive to combined SHP2i+MEKi treatment due to feedback activation of RAS(Q61R/K) and induction of a SHP2 conformation with reduced binding to SHP2i

A high therapeutic index, defined as potent inhibition of oncogenic signaling in tumor cells with minimal effects on normal cells, is critical for effective cancer therapies. Recent advances have introduced diverse RAS-targeting inhibitors, including mutant-specific inhibitors such as KRAS G12C and KRAS G12D, as well as paralog- and state-selective inhibitors. Non–mutant-specific RAS inhibition can be achieved by: (i) guanine nucleotide exchange–OFF inhibitors that indirectly inactivate RAS by targeting SHP2 or SOS1, (ii) KRAS-OFF inhibitors that spare NRAS and HRAS, and (iii) active-state RAS(ON) inhibitors that directly block binding of effector RAF. However, the signaling inhibition index (SII)—the differential suppression of oncogenic signaling between RAS-mutant and normal cells—remains poorly defined for these approaches. We evaluated the SII for state- and paralog-selective RAS inhibitors across diverse RAS-mutant and RAS–wild-type models. Guanine nucleotide exchange–OFF inhibitors exhibited neutral or negative values, with reduced MAPK suppression in KRAS G12X cells compared with wild-type cells. KRAS G13D models, especially with NF1 loss, showed low sensitivity. SHP2 plus MEK inhibition resulted in low selectivity, and RAS Q61X models were resistant due to MEK inhibitor–induced NRAS reactivation and altered SHP2 conformations. KRAS-OFF inhibitors demonstrated higher selectivity, whereas active- state RAS(ON) inhibitors showed broader activity but narrow selectivity. Sensitivity to mutant-specific inhibitors largely overlapped with sensitivity to state-selective agents, suggesting that most RAS-mutant tumors will respond poorly to any currently available RAS inhibitor. Implications: Determining the SII can inform the design and clinical application of RAS-targeted therapies to improve tumor selectivity and therapeutic outcomes.

Figure S9. Colony formation assays of five cell lines treated with MEK1/2 inhibitor trametinib, PRMT5 inhibitor MRTX1719, or the combination across all drug concentrations are shown.

Figure S5. MTAP copy number and mRNA assessment of Cancer DepMap cell lines.