Epigenetic Repression of Type I Interferon Signaling by RUNX2 Drives Immune Checkpoint Blockade Resistance in Osteosarcoma

Interferon (IFN) signaling plays a pivotal role in orchestrating antitumor immunity and shaping the response to immune checkpoint blockade (ICB). Although genetic alterations that impair the IFN pathway have been reported, such events are relatively rare, suggesting a potential contribution of epigenetic dysregulation. Here, we identified a RUNX2-mediated epigenetic mechanism that disrupts the type I interferon (IFN-I) signaling pathway in osteosarcoma (OS), thereby limiting the efficacy of ICB. Development of an algorithm to assess the association of 1,425 transcription factors with IFN pathway activation in human OS tumors enabled identification of RUNX2 as a potential negative regulator of IFN signaling. RUNX2 depletion in OS cells activated the IFNB1-driven IFN-I response. Mechanistically, RUNX2 formed a transcriptional repressor complex with NCOR1 and HDAC3 that reduced H3K9 acetylation at the enhancers of key IFN-I genes, leading to their downregulation. Inhibition of the RUNX2-NCOR1-HDAC3 complex enhanced IFN-I signaling, with cGAS, STING, and IFNB1 being required for the induction of interferon-stimulated genes and tumor suppression. Paradoxically, reactivation of IFN-I signaling also upregulated immune checkpoint molecules PD-L1 and PD-L2. Combination treatment with a selective HDAC3 inhibitor and anti-PD-1 antibody led to durable tumor regression in syngeneic OS mouse models, accompanied by increased cytotoxic T cell infiltration. These findings reveal a mechanistic link between RUNX2-driven epigenetic repression and impaired antitumor immunity via the cGAS-STING-IFN-I axis and suggest a rational combinatorial strategy to overcome OS resistance to ICB.