# Extracellular vesicle-based targeted protein degradation platform for multiple extracellular proteins

**Authors:** Bide Tong, Xiaoguang Zhang, Dingchao Zhu, Yulei Wang, Junyu Wei, Zixuan Ou, Huaizhen Liang, Hanpeng Xu, Zhengdong Zhang, Jie Lei, Xingyu Zhou, Di Wu, Yu Song, Kun Wang, Xiaobo Feng, Lei Tan, Zhiwei Liao, Cao Yang

PMC · DOI: 10.1038/s44321-025-00371-8 · EMBO Molecular Medicine · 2026-01-12

## TL;DR

Researchers developed a new platform using extracellular vesicles to degrade harmful proteins outside cells, showing promise for treating inflammatory diseases like intervertebral disc degeneration.

## Contribution

A novel extracellular vesicle-based platform for targeted degradation of multiple extracellular proteins is introduced.

## Key findings

- EVs are degraded via the autophagy-mediated lysosomal pathway through LIR motifs recognized by MAP1LC3B.
- EVTPD selectively degrades extracellular proteins like TNF-α and IL-1β without requiring cell surface receptors.
- Dual-targeting EVTPD reduced inflammation in intervertebral disc degeneration models by inhibiting the NF-κB pathway.

## Abstract

Targeted protein degradation (TPD) is an emerging therapeutic approach that enables the degradation of undruggable targets via intracellular degradation systems. Extracellular vesicles (EVs) have shown potential to act as next-generation TPD platforms. However, the molecular mechanism underlying their degradation remains unknown, which restricts their application in TPD. In this study, we found that the autophagy-mediated lysosomal pathway was the major route by which EVs were degraded. MAP1LC3B recognized the LIR motifs of SQSTM1 and induced the degradation of EVs in the autophagy pathway. Based on the EV degradation mode, we developed an EV-based targeted protein degradation platform (EVTPD) using EVs loaded with the LIR motif of SQSTM1 as a degradation signal. Additionally, target protein-binding domains were integrated into the EVTPD to capture target proteins. EVTPD selectively degraded extracellular proteins without requiring receptors on target cells. Furthermore, dual-targeting EVTPD effectively degraded both TNF-α and IL-1β and exhibited potent anti-inflammatory effects in rat and goat models of intervertebral disc degeneration. This study has established a modular EV-based TPD strategy with multi-targeting potential.

This study reports the development of an EV-based targeted protein degradation platform and its application in intervertebral disc degeneration.

Intracellular MAP1LC3B recognizes the LIR motifs within EV-associated SQSTM1, thereby directing extracellular vesicles to the autophagy pathway for lysosomal degradation.LIR motifs and cytokine-binding domains were co-displayed on the surface of extracellular vesicles to establish an EV-based targeted protein degradation platform (EVTPD).The TNF-α/IL-1β-targeted EVTPD specifically facilitates the degradation of TNF-α and IL-1β, effectively suppressing inflammatory responses in intervertebral disc degeneration through inhibition of the NF-κB signaling pathway.

Intracellular MAP1LC3B recognizes the LIR motifs within EV-associated SQSTM1, thereby directing extracellular vesicles to the autophagy pathway for lysosomal degradation.

LIR motifs and cytokine-binding domains were co-displayed on the surface of extracellular vesicles to establish an EV-based targeted protein degradation platform (EVTPD).

The TNF-α/IL-1β-targeted EVTPD specifically facilitates the degradation of TNF-α and IL-1β, effectively suppressing inflammatory responses in intervertebral disc degeneration through inhibition of the NF-κB signaling pathway.

This study reports the development of an EV-based targeted protein degradation platform and its application in intervertebral disc degeneration.

## Linked entities

- **Genes:** MAP1LC3B (microtubule associated protein 1 light chain 3 beta) [NCBI Gene 81631], SQSTM1 (sequestosome 1) [NCBI Gene 8878]
- **Proteins:** TNF (tumor necrosis factor), IL1B (interleukin 1 beta), NFKB1 (nuclear factor kappa B subunit 1)
- **Diseases:** intervertebral disc degeneration (MONDO:0011385)
- **Species:** Mus musculus (taxon 10090), Capra hircus (taxon 9925)

## Full-text entities

- **Genes:** Tnf (tumor necrosis factor) [NCBI Gene 24835] {aka RATTNF, TNF-alpha, Tnfa}, Map1lc3b (microtubule-associated protein 1 light chain 3 beta) [NCBI Gene 64862] {aka LC3B, Map1lc3, Mpl3, zbs559}, Sqstm1 (sequestosome 1) [NCBI Gene 113894] {aka Osi, ZIP, ZIP3}, Il1b (interleukin 1 beta) [NCBI Gene 24494] {aka IL-1F2}
- **Diseases:** intervertebral disc degeneration (MESH:D055959), inflammatory (MESH:D007249)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116]

## Full text

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## Figures

13 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12905291/full.md

## References

1 references — full list in the complete paper: https://tomesphere.com/paper/PMC12905291/full.md

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Source: https://tomesphere.com/paper/PMC12905291