Depletion of Fumarate Hydratase, an Essential TCA Cycle Enzyme, Drives Proliferation in a Two-Step Model

SIMPLE SUMMARY: Fumarate hydratase (FH) is an evolutionary conserved TCA cycle enzyme and has a moonlight function in the DNA damage response (DDR). FH has a contradictory function, as it is pro-survival through its role in the TCA cycle, yet its loss can drive tumorigenesis. Here, we solve this contradiction and show that in both non-cancerous (HEK-293T) and cancerous cell lines (HepG2), the cell response to FH loss is separated into two distinct time frames. During the early stages of FH loss, cell proliferation and DNA damage repair are inhibited. However, over time, cells overcome the FH loss and form proliferative knockout stable clones. Furthermore, we discovered that the impaired DDR induces mutations enriched in central signaling pathways, such as JAK/STAT3, allowing the cells to circumvent FH and TCA cycle loss. ABSTRACT: Fumarate hydratase (FH) is an evolutionary conserved TCA cycle enzyme that reversibly catalyzes the hydration of fumarate to L-malate and has a moonlight function in the DNA damage response (DDR). Interestingly, FH has a contradictory cellular function, as it is pro-survival through its role in the TCA cycle, yet its loss can drive tumorigenesis. Here, we found that in both non-cancerous (HEK-293T) and cancerous cell lines (HepG2), the cell response to FH loss is separated into two distinct time frames based on cell proliferation and DNA damage repair. During the early stages of FH loss, cell proliferation rate and DNA damage repair are inhibited. However, over time the cells overcome the FH loss and form knockout clones, indistinguishable from WT cells with respect to their proliferation rate. Due to the FH loss effect on DNA damage repair, we assumed that the recovered cells bear adaptive mutations. Therefore, we applied whole-exome sequencing to identify such mutated genes systematically. Indeed, we identified recurring mutations in genes belonging to central oncogenic signaling pathways, such as JAK/STAT3, which we validated in impaired FH-KO clones. Intriguingly, we demonstrate that these adaptive mutations are responsible for FH-KO cell proliferation under TCA cycle malfunction.