Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain

Chen, P.; Chai, J.; Soundararajan, A.; Hepfer, R. G.; Kheyfets, B.; Hu, J.; Alshanqiti, I.; Raman, S.; Tosa, I.; Huh, J. T.; Yee, M.; Damon, B. J.; Wang, S.; Kim, Y. S.; Chung, M.-K.; Embree, M. C.; Lee, J. S.; Ye, T.; Yao, H.

doi:10.1101/2025.08.23.671843

bioRxiv · 10.1101/2025.08.23.671843

Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain

Chen, P.·Chai, J.·Soundararajan, A.·Hepfer, R. G.·Kheyfets, B.·Hu, J.·Alshanqiti, I.·Raman, S.·Tosa, I.·Huh, J. T.·Yee, M.·Damon, B. J.·Wang, S.·Kim, Y. S.·Chung, M.-K.·Embree, M. C.·Lee, J. S.·Ye, T.·Yao, H.

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Abstract

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating the intricate mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, we introduce a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically designed to overcome key challenges of immunostaining and optical clearing of intact joints. Coupled with large-field light sheet microscopy, our approach enables 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including mouse, rat, and pig. Our findings reveal 3D heterogeneous distributions of neurovascular networks and previously uncharacterized neurovascular pathways within joints. Using the proteoglycan 4 knockout (Prg4-/-) mouse model of joint degeneration, we identified significant alterations in joint-wide neurovascular architecture, highlighting neurovascular changes along degenerative processes. Furthermore, in a traumatic joint injury mouse model, we observed long-lasting pain behavior and a time-course 3D neurovascular remodeling preceding detectable joint morphological change, bridging microscale alterations with potential pain mechanisms. This platform offers a powerful tool for multiscale 3D analysis, enabling new insights into joint pathophysiology and intricate interplay among joint tissues.

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Chen, P., Chai, J., Soundararajan, A., Hepfer, R. G., Kheyfets, B., Hu, J., Alshanqiti, I., Raman, S., Tosa, I., Huh, J. T., Yee, M., Damon, B. J., Wang, S., Kim, Y. S., Chung, M.-K., Embree, M. C., Lee, J. S., Ye, T., Yao, H.. 2025-08-28. Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain. https://doi.org/10.1101/2025.08.23.671843

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