NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer (RNA-Seq II).

Macrophages orchestrate various aspects of immunity and tissue homeostasis in health and disease. In cancer, the presence of macrophages is largely associated with poor prognosis, due to their reprogramming into immunosuppressive cells in the tumor microenvironment (TME). In this study, we investigated the effects of hypoxia, a key feature of the TME, on the functional, epigenetic, and transcriptional status of macrophages. Surprisingly, we found that hypoxia boosts the immunogenicity of macrophages in vitro, in a process that is partially regulated by DNA methylation. Specifically, we find a cluster of pro-inflammatory genes that undergo DNA demethylation and transcriptional upregulation during macrophage activation in hypoxia. These genes are regulated by NF-κB, while HIF1α contributes to the transcriptional program through DNA methylation-independent mechanisms. In cancers such as bladder and ovarian carcinomas, the signatures of hypoxic inflammatory macrophages are found in immune-rich tumors, where they correlate with better patient prognoses. The NF-κB-associated DNA hypomethylation is recapitulated in an in vivo-equivalent subset of hypoxic inflammatory macrophages, isolated from ovarian tumors, validating the translation of the in vitro results. Functionally, co-culture assays and putative cell-cell communication analyses suggest that hypoxic-activated macrophages enhance T cell-mediated responses. Our results challenge existing paradigms regarding the effects of hypoxia on macrophages and highlight novel target cells to ameliorate cancer responses.