Mitochondrial complex IV remodeling in tumor-associated macrophages amplifies interferon signaling and promotes anti-tumor immunity (RNA-Seq)

Tumor-associated macrophages (TAMs) play a critical role in the clinical outcome of solid tumors and the efficacy of immune checkpoint blockade (ICB) therapies. Interferon (IFN)-TAMs are a potent anti-tumor TAM subset recently identified in several human cancers, with higher frequencies strongly predicting improved overall survival and ICB responses. Yet the molecular mechanisms governing IFN-TAM gene expression programs and population dynamics remain largely unknown. Herein, we uncover a mitochondrial process where NDUFA4, a subunit of Complex IV of the electron transport chain, serves as a switch that controls TAM functions and tumor immunity. We demonstrate that in response to interferons (IFNs) within the tumor microenvironment, NDUFA4 is dramatically downregulated in TAMs by the cooperative activity of the NDUFA4 homolog NDUFA4L3 and the microRNA miR-147, both encoded by a single highly conserved bifunctional transcript. Notably, repression of NDUFA4 is necessary for the expansion of IFN-TAMs and subsequent anti-tumor immunity via NK and CD8+ T cell recruitment, whereas constitutive NDUFA4 expression supports pro-tumoral TAMs. Unexpectedly, we find that NDUFA4 minimally contributes to mitochondrial respiration but instead primarily functions as a gatekeeper of mitochondrial DNA (mtDNA) release into the cytoplasm. Consequently, NDUFA4 repression enhances mtDNA-induced stimulator of interferon genes (STING) activation, thereby amplifying anti-tumor IFN-induced transcriptional programs in TAMs. Finally, leveraging the exceptional specificity of miR-147 for Ndufa4 mRNA, we demonstrate that RNA-based therapeutics targeting this functional switch enhance ICB efficacy and inhibit tumor growth. In summary, we uncover that tumor microenvironmental cues control the abundance of IFN-TAMs and subsequent anti-tumor immunity through the regulation of NDUFA4 and that this novel functional switch can be exploited for cancer immunotherapies.