BPS2026 – Structural and functional characterization of SCUBE3 protein—A novel oncogenic ligand for EGFR

Signal-peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is an emerging oncogenic factor, with aberrant overexpression reported across diverse cancer types. SCUBE3 is a secreted glycoprotein that localizes to the extracellular milieu, where it engages key cell-surface receptors, including the epidermal growth factor receptor (EGFR) and transforming growth factor-β receptor (TGFBR). These interactions initiate oncogenic signaling cascades that drive tumor cell proliferation, migration, and invasion. SCUBE3 is widely reported to be a co-receptor; however, once cleaved by matrix-metallo proteases (MMPs), it can also function as ligand to activate oncogenic signaling. However, the molecular and structural basis of SCUBE3-receptor interactions remain unresolved, and its biologically active fragment remains elusive. This gap in knowledge has limited mechanistic insights and hindered the development of therapeutic agents that selectively block SCUBE3 function. Structural insight into SCUBE3 will allow a deeper understanding of how this secretory oncoprotein interacts with EGFR and TGFBR to potentiate downstream signaling. Here, we describe the first successful purification of recombinant, fully active SCUBE3 protein. Further, we have used cryo-EM to characterize its architecture and elucidate interaction interfaces with its receptors EGFR and TGFBR. Additionally, we have defined the active portion of the protein in driving oncogenic signaling. Finally, we have demonstrated robust membrane association of SCUBE3. These findings represent the first steps toward establishing the structural and functional framework of SCUBE3. Furthermore, elucidating its architecture provides a critical platform for rational drug design aimed at disrupting SCUBE3–receptor interactions. Ultimately, these advances could open new avenues for targeted therapeutic strategies in cancers driven by SCUBE3 dysregulation.