FBXO44 Silences Repetitive Elements during DNA Replication in Cancer

Transcriptional silencing of repetitive elements (RE) in the genome prevents accumulation of double-stranded RNA and DNA, which may otherwise trigger antipathogen immune responses, trigger MAVS- and cGAS-mediated IFN signaling, and cause DNA replication stress. Recent evidence suggests that antitumor therapies may be augmented by inducing RE transcription, and epigenetic modifications including trimethylation of histone 3 at lysine residue 9 (H3K9me3) contribute to RE silencing. To further elucidate this mechanism, Shen, Qiu, and colleagues performed an RNAi screen in human cancer cell lines to identify regulators of H3K9me3. The screen identified F-box only protein 44 (FBXO44) as a top hit, as knockdown of FBXO44 significantly decreased H3K9me3 and increased pRPA32T21, a readout of replication stress. Chromatin immunoprecipitation and qRT-PCR experiments revealed that FBXO44 colocalized with H3K9me3 at REs and that FBXO44 knockdown activated expression of these REs. Proteomic analysis of FBXO44 interactors followed by immunoprecipitation experiments uncovered that FBXO44 recruited SUV39H1, CRL4, and components of Mi-2/NuRD to the replication fork and that this complex cooperated to silence REs. Inhibiting complex members phenocopied FBXO44 knockdown and activated MAVS- and cGAS-mediated IFN signaling. In vitro, FBXO44 knockdown decreased cancer cell proliferation, migration, and invasion, reduced cell-cycle progression through S phase, and increased apoptosis. Notably, neither genetic inhibition of FBXO44 nor pharmacologic inhibition of SUV39H1 had a significant effect on normal cells, suggesting a potential therapeutic window. In vivo, inhibition of FBXO44 or SUV39H1 slowed mammary tumor growth in mice and increased tumor infiltration of CD8+ T and natural killer cells. Consistent with this increased antitumor immunity phenotype, Fbxo44 or Suv39h1 knockdown sensitized mice to immune checkpoint blockade using anti–PD-1. Patient data revealed that high FBXO44 expression correlated with poor clinical outcome across many cancers and that FBXO44 expression inversely correlated with IFN signaling, antigen processing and presentation, and DNA replication stress. In summary, these findings uncover a mechanism by which cancer cells silence REs and implicate the FBXO44 complex as a therapeutic target that may be important across different cancer types.

Shen JZ, Qiu Z, Wu Q, Finlay D, Garcia G, Sun D, et al. FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells. Cell 2020;184:352–69.E23.

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