A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance

Abstract

Cancer cells make extensive use of the folate cycle to sustain increased anabolic metabolism. Multiple chemotherapeutic drugs interfere with the folate cycle, including methotrexate and 5-fluorouracil that are commonly applied for the treatment of leukemia and colorectal cancer (CRC), respectively. Despite high success rates, therapy-induced resistance causes relapse at later disease stages. Depletion of folylpolyglutamate synthase (FPGS), which normally promotes intracellular accumulation and activity of both natural folates and methotrexate, is linked to methotrexate and 5-fluorouracil resistance and its association with relapse illustrates the need for improved intervention strategies. In this study, we characterize a novel antifolate (C1) that, like methotrexate, potently inhibits dihydrofolate reductase (DHFR) and downstream one-carbon metabolism. Contrary to methotrexate, however, C1 displays optimal efficacy in FPGS-deficient contexts, due to decreased competition with intracellular folate concentrations for interaction with DHFR. Indeed, we show that FPGS-deficient patient-derived CRC organoids display enhanced sensitivity to C1-induced growth inhibition, while FPGS-high CRC organoids are more sensitive to methotrexate. Our results thus argue that polyglutamylation-independent antifolates can be applied to exert selective pressure on FPGS-deficient cells during chemotherapy, employing a vulnerability created by polyglutamylation deficiency.

STPP-UP: An alternative method for drug target identification using protein thermal stability

“…2 , C and D and S5 A ). In line with previously published TPP data ( 3 ), we successfully identify dihydrofolate reductase (DHFR) as the primary target for C1 using STPP-UP. While the target-to-background enrichment is not as strong as in the mouse STPP-UP experiment, and there appear to be more off-targets, these effects can mostly be attributed to correcting for abundance differences ( Fig.…”

“…This again resulted in the identification of DHFR as the most stabilized protein under these conditions ( Fig. S5 C ), together with the secondary (off-)target TYMS, which stabilizes due to downstream effects of DHFR inhibition ( 3 ).…”

“…We further validated STPP-UP in human cells, using the anticancer drug C1 ( 3 ) applied to the LS 174T colorectal cancer cell line ( Figs. 2 , C and D and S5 A ).…”

“…S1 A ). Alternatively, compounds that inhibit a certain protein can induce loss of another protein’s normal targets or substrates, resulting in decreased thermal stability ( 3 ).…”