RNA N6-methyladenosine-binding protein YTHDFs redundantly attenuate cancer immunity by downregulating IFN-γ signaling in gastric cancer [RIP-Seq]

Gastric cancer (GC) is a prominent public health issue, especially in East Asia, and holds the fourth rank in terms of cancer mortality. While immunotherapy holds potential as a treatment avenue for GC, resistance to immune checkpoint inhibitors (ICIs) remains an obstacle. One resistance mechanism involves defects in IFN-γ signaling, where IFN-γ is linked to improved responsiveness to ICIs. In this study, we unveiled the role of N6-methyladenosine (m6A) RNA modifications, in the regulation of IFN-γ signaling and the responsiveness to ICIs. The m6A-binding protein YTHDF1 was overexpressed in GC tissues, correlating with the suppression of cancer immunity and poorer survival rates. Overexpression of YTHDF1 impaired the responsiveness to IFN-γ in GC cells, while knockdown studies indicated the redundant effects of YTHDF2 and YTHDF3 with YTHDF1 on IFN-γ responsiveness. RNA immunoprecipitation-sequencing identified that YTHDFs directly targeted the mRNA of IRF1, which is one of master regulators of IFN-γ signaling, leading to reduced RNA stability and consequent downregulation of IFN-γ signaling. Furthermore, in mouse syngeneic tumor models, the depletion of Ythdf1 in cancer cells resulted in reduced tumor growth and heightened tumor infiltrating lymphocytes, which is attributed to the augmentation of IFN-γ signaling. Collectively, our findings highlight how YTHDFs modulate cancer immunity by influencing IFN-γ signaling through IRF1 regulation, thus proposing their viability as therapeutic targets in the realm of cancer immunotherapy. To investigate the target of YTHDF1 in the regulation of IFN-γ responsiveness, we treated IFN-γ after overexpressing YTHDF1 in SNU638 RNA immunoprecipitation (RIP)-sequencing were performed