Ikoma, Japan—
Extracellular vesicles (EVs) are tiny membrane-bound particles released by cells to transport proteins and other molecules to neighboring cells. Because of this natural delivery ability, EVs have attracted growing interest as potential vehicles for therapeutic protein and genome-editing enzyme delivery. However, EVs can originate either from intracellular endosomal compartments or directly from specialized protrusions on the cell surface, and until now, it has remained unclear which EV type is more effective at delivering functional protein cargo.
To address this question, researchers in Japan conducted a detailed comparison of these two major EV biogenesis pathways. In a study published in Nature Communications (Volume 16) on December 8, 2025, the team discovered that EVs generated from cell-surface protrusions in an I-BAR protein (MIM)–dependent manner deliver active proteins and genome-editing enzymes far more efficiently than conventional endosome-derived, CD63-associated EVs.
The study was led by Professor Shiro Suetsugu of the Nara Institute of Science and Technology (NAIST). The research team included Associate Professor Tamako Nishimura and then-graduate student Toshifumi Fujioka (NAIST), along with collaborators Professor Takanari Inoue (Johns Hopkins University, USA), Professor Kenichi G. N. Suzuki (Gifu University and National Cancer Center Research Institute, Japan), and Professor Osamu Nureki (The University of Tokyo, Japan).
“In this study, we were able to clearly demonstrate that vesicles generated from cell-surface protrusions function as a highly efficient and natural protein delivery system,” says Suetsugu. “By directly comparing them with endosome-derived vesicles, we gained new insight into how cells achieve efficient cytosolic protein transfer without relying on viral mechanisms and how it can be used in the future.”
To compare the two systems, the researchers cultured human cells and isolated both protrusion-derived EVs and endosome-derived EVs. These vesicles were loaded with defined protein cargo and added to recipient cells. Using advanced live-cell and super-resolution imaging, the team tracked EV uptake via endocytosis, their trafficking through endosomal compartments, and the subsequent release of cargo into the cytoplasm.
One major focus of the study was Rac1, a protein that regulates cell migration. The researchers found that Rac1 delivered by protrusion-derived EVs efficiently escaped from late endosomes into the cytoplasm, where it remained active and stimulated cell movement.
The team also examined whether these EVs could deliver Cas12f, a compact genome-editing enzyme. Protrusion-derived EVs transported Cas12f with dramatically higher functional efficiency—on a per-protein basis—than conventional endosome-derived EVs. Importantly, this high level of genome-editing activity was achieved without the use of viral vectors or viral fusogenic proteins, which are often associated with safety concerns in gene-therapy approaches.
“Our findings show that cells might already possess a remarkably effective, virus-free delivery mechanism,” Suetsugu concludes. “By understanding and harnessing this natural system, we may be able to develop safer and more precise strategies for genome editing, regenerative medicine, and protein-based therapeutics.”
By elucidating how MIM-dependent protrusion-derived EVs protect, transport, and release functional proteins into recipient cells, this study provides a foundation for next-generation delivery technologies that leverage the cell’s own molecular machinery rather than engineered viral components.
Credit: Nara Institute of Science and Technology (NAIST)
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Resource
Title: Efficient cellular transformation via protein delivery through the protrusion-derived extracellular vesicles
Authors: Toshifumi Fujioka, Tamako Nishimura, Koichiro M. Hirosawa, Hiroki Kawana, Renta Yamakawa, Hani Sapili, Kayoko Oono-Yakura, Ryoya Nakagawa, Takanari Inoue, Osamu Nureki, Kenichi G.N. Suzuki, and Shiro Suetsugu
Journal : Nature Communications
DOI: https://doi.org/10.1038/s41467-025-66351-1
Information about the Laboratory of Molecular Medicine and Cell Biology can be found at the following website:
https://bsw3.naist.jp/suetsugu/en/440-2/
About Nara Institute of Science and Technology (NAIST)
Established in 1991, Nara Institute of Science and Technology (NAIST) is a national university located in Kansai Science City, Japan. In 2018, NAIST underwent an organizational transformation to promote and continue interdisciplinary research in the fields of biological sciences, materials science, and information science. Known as one of the most prestigious research institutions in Japan, NAIST lays a strong emphasis on integrated research and collaborative co-creation with diverse stakeholders. NAIST envisions conducting cutting-edge research in frontier areas and training students to become tomorrow's leaders in science and technology.
Nature Communications
Experimental study
Cells
Efficient cellular transformation via protein delivery through the protrusion-derived extracellular vesicles
8-Dec-2025
Toshifumi Fujioka, Tamako Nishimura, Hiroki Kawana, and Shiro Suetsugu have submitted a patent application to the Japan Patent Office pertaining to the dimerization-induced protein delivery by the protrusion-derived EVs aspects of this work (Application Number (2024)218454). The remaining authors declare no competing interests.