Neural Regeneration Research ›› 2026, Vol. 21 ›› Issue (10): 4954-4964.doi: 10.4103/NRR.NRR-D-25-01391

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Multi-omics prediction of key proteases regulating scar formation and neural repair after spinal cord injury

Huan Jian1, 2, #, Jiahao Ren1, #, Jiawei Du1, #, Kailin Wu1, Shen Liu1, Yuanting Zhao2, *, Hengxing Zhou1, 3, 4, 5, *, Shiqing Feng1, 3, 4, 6, *   

  1. 1Department of Orthopedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China; 
    2Department of Spine Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, Shaan Province, China; 
    3Department of Orthopedics, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China; 
    4Shandong University Center for Orthopedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China; 
    5Center for Reproductive Medicine, Shandong University, Jinan, Shandong Province, China; 
    6Department of Orthopedics, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
  • Online:2026-10-15 Published:2026-06-15
  • Contact: Yuanting Zhao, PhD, doczhaoyuanting@126.com; Hengxing Zhou, PhD, zhouhengxing@sdu.edu.cn; Shiqing Feng, PhD, sqfeng@tmu.edu.cn.
  • Supported by:
    This study was supported by the National Natural Science Foundation of China, Nos. 82372413, 81972073 (both to HZ); Tianjin Municipal Science and Technology Commission’s Diverse Funds Research Program, No. 21JCYBJC00920 (to SL); and the National Key Research and Development Project of Stem Cell and Transformation Research, No. 2019YFA0112100 (to SF).

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Abstract: Neurological injury is often accompanied by extensive infiltration of macrophages along with activation of fibroblasts and endothelial cells. The activity of these cells is associated with elevated levels of various proteases, which contribute to the hydrolysis of multiple proteins, disrupt the extracellular matrix, and further promote the migration of immune cells into uninjured neural tissue. In this study, we combined single-cell sequencing with bulk RNA sequencing data from spinal cord injury to identify up-regulated protease-related differentially expressed genes post-injury. Using gene set variation analysis, least absolute shrinkage and selection operator regression, and random forest methods, we identified adamalysins, serine proteases, and matrix metalloproteinases as key protease types. Weighted gene co-expression network analysis combined with machine learning algorithms helped predict critical protease genes involved in spinal cord injury. Immune infiltration and single-cell analyses were applied to identify cell types enriched in proteases and their spatial localization. Molecular docking and in vivo and in vitro assays using a mouse model of spinal cord injury were used to validate potential drug interactions. We identified Mmp12 and Adam17 as key effectors regulating injury progression, and determined that macrophages, fibroblasts, and monocytes are the primary cells mediating the functions of core proteinases after injury. Subsequent in vivo and in vitro experiments demonstrated that selective inhibition of key protease activity with marimastat reduced axonal demyelination and fibrous scar formation after spinal cord injury, thereby promoting the recovery of neurological function. Our study identified the key proteases that regulate spinal cord injury repair along with their mechanisms of action, and verified that inhibiting these proteases effectively alleviates scar formation and inflammatory cell infiltration, providing novel therapeutic targets for the treatment of spinal cord injury. 

Key words: bulk RNA sequencing, fibrous scar, machine learning analysis, neuroimmunology, neuroinflammation, neurological function, protease, single-cell RNA sequencing, spinal cord injury, therapeutic drug