Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)

Interleukin-9 (IL-9) is the hallmark cytokine in Th9 immunity and is also central to Innate Lymphocyte 2 (ILC2) biology. Furthermore, receptor signaling mediated by IL-9 has been linked to inflammatory and autoimmune diseases, and cancer. Despite its functional pleiotropy, the structure-function landscape of IL-9 had remained enigmatic. Here, we show via a combination of X-ray crystallography and NMR that human IL-9 adopts a helical bundle fold with unprecedented structural features among helical cytokines, including five disulfide bridges. Binding of IL-9 to the interdomain junction of IL-9Rα results in marked structural changes on the opposite face of IL-9 that prime the binary complex for recruiting the common gamma chain (γc) for signaling. Surprisingly, this tripartite cytokine-receptor assembly displays a markedly lower affinity than the IL-9: IL-9Rα complex, which we trace to distinct features of IL-9Rα that might destabilize the ternary complex. Furthermore, we developed monoclonal antibodies that antagonize IL-9 activity by sterically competing for the binding footprint of IL-9Rα. Collectively, we here provide a structural and mechanistic blueprint to facilitate interrogation and modulation of pleiotropic signaling outputs of IL-9 in physiology and disease.