A joint team led by Professor Ho Min Kim of the Department of Biological Sciences at the Korea Advanced Institute of Science and Technology (KAIST) and Dr. Sangkyu Lee of the Institute for Basic Science (IBS) has determined the three-dimensional structure of the VEGF-C–VEGFR-3 complex, the central molecular interaction that triggers lymphangiogenesis, the formation of lymphatic vessels. In doing so, the team identified an unexpected layer of regulation: after the initial binding event, multiple receptor complexes gather side by side along the cell membrane, forming higher-order clusters that dramatically amplify the signal transmitted into the cell. The findings were published online on September 9 in the international journal Advanced Science under the title “Structural Basis of Lymphangiogenic Receptor VEGFR-3 Activation Mediated by Distinctive Clustering of the Ligand–Receptor Complex.”

To understand the significance of the discovery, it helps to consider how lymphangiogenic signaling has traditionally been viewed. Vascular endothelial growth factor C, or VEGF-C, is a protein that circulates through the extracellular environment and binds to VEGFR-3, a receptor embedded in the membrane of lymphatic endothelial cells. When VEGF-C engages VEGFR-3, two receptor molecules are brought together in a dimer, and this dimerization has long been considered the decisive step that switches the receptor on. Once activated, VEGFR-3 initiates intracellular signaling cascades, including the ERK pathway, that instruct the cell to proliferate, migrate, and organize into new lymphatic vessels. What happened after dimerization, however, and how the signal might be boosted beyond that initial pairing, remained poorly understood.

The KAIST and IBS researchers turned to cryogenic electron microscopy, or cryo-EM, a technique that flash-freezes protein samples at extremely low temperatures and images them with electron beams to reveal molecular structures at near-atomic resolution. Using this approach, the team visualized the VEGF-C–VEGFR-3 complex in unprecedented detail and made a striking observation: the complexes did not remain as isolated pairs. Instead, multiple VEGF-C–VEGFR-3 assemblies lined up alongside one another in the plane of the cell membrane, forming two distinct types of higher-order clusters. Cryo-EM observation showed that these assemblies organize laterally, creating an architecture that had never been described for this receptor system before.

Among the clustered arrangements, the researchers succeeded in determining the three-dimensional structure of what they term the cis-cluster, a configuration in which multiple VEGF-C–VEGFR-3 complexes are aligned side by side. The analogy the researchers draw is straightforward: two people first form a team to begin a task, and then multiple teams gather together to increase their collective strength. In molecular terms, the ligand-induced dimer represents the formation of the individual team, while the cis-cluster represents the assembly of teams into a larger, more powerful collective unit capable of generating a stronger signal inside the cell.

Crucially, the team did not stop at structural observation. They designed experiments to test whether this clustering actually matters for signaling output. By mutating VEGFR-3 at the regions where the complexes contact one another, they disrupted the ability of the complexes to form cis-clusters. The result was unambiguous: even when VEGF-C was present and able to bind the receptor, the activation of VEGFR-3 and of the downstream ERK signaling molecule was markedly reduced. The researchers also used light-based approaches to control receptor clustering directly, further confirming that the gathering of multiple complexes plays an essential role in amplifying the lymphangiogenic signal.

This identification of clustering as an amplification mechanism effectively reveals a new control point in the signaling pathway, one that Professor Kim has described as a previously unseen “hidden amplification switch” in lymphangiogenic signaling. According to Kim, the study reveals how two VEGFR-3 receptors first form a ligand-induced pair, after which multiple such complexes cluster together to further amplify the signal for lymphangiogenesis. He added that the work is expected to provide an important foundation for developing new therapeutic strategies for related diseases such as lymphedema and cancer metastasis.

The therapeutic logic cuts in two directions. In diseases such as lymphedema, where lymphatic vessel formation is insufficient, a drug that enhances VEGF-C–VEGFR-3 clustering could potentially strengthen the growth signals and encourage the regeneration of functional drainage vessels. Conversely, in cancer, where excessive lymphatic vessel growth around a tumor creates routes for metastatic spread, a molecule that blocks the contact surfaces required for cis-cluster formation could dampen signaling and starve the tumor of its lymphatic escape routes. The same structural interface that the KAIST team mapped in cryo-EM detail thus represents a potential target for both promoting and suppressing lymphangiogenesis, depending on the clinical context.

The researchers are careful to note the limits of the current work. The study did not demonstrate therapeutic effects for lymphedema or the inhibition of cancer metastasis, and considerable further research will be required before the findings can be translated into actual treatments. Structural biology of this kind provides the blueprint rather than the drug: knowing precisely how the complexes contact one another gives medicinal chemists and biologists a concrete molecular target, but designing molecules that safely modulate that interface in patients remains a long road involving drug discovery, preclinical testing, and clinical trials.

The work was a collaborative effort involving multiple contributors. Dr. Ryeongeun Cho of the KAIST InnoCORE AI-CRED Innovative Drug Research Group and Dr. Jinsook Ahn of the KAIST Department of Biological Sciences participated as co-first authors, while Professor Ho Min Kim and Dr. Sangkyu Lee served as co-corresponding authors. The research was supported by the National Research Foundation of Korea, the InnoCORE program of the Ministry of Science and ICT, the NEXUS and CELINE consortium, the KAIST Convergence Research Institute Operation Program, and the Institute for Basic Science, among others. As the structural details of the VEGF-C–VEGFR-3 cis-cluster circulate through the scientific community, the discovery stands as a vivid reminder that even well-studied signaling pathways can conceal entire layers of regulation, and that the tools of modern cryo-EM are increasingly capable of bringing those hidden mechanisms into focus.

Subject of Research: Structural basis of VEGF-C–VEGFR-3 receptor clustering in lymphangiogenic signaling

Article Title: KAIST identifies a “hidden amplification switch” in lymphangiogenic signaling, with implications for lymphedema and cancer metastasis

Article References: KAIST identifies a “hidden amplification switch” in lymphangiogenic signaling, with implications for lymphedema and cancer metastasis. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: VEGF-C, VEGFR-3, lymphangiogenesis, cryo-EM, lymphedema, cancer metastasis, receptor clustering, signal amplification, KAIST, Institute for Basic Science, Advanced Science, structural biology