ncRNA network pharmacology integrated with miRNA omics and experimental validation reveal the anti-autophagic effect of Xuefu Zhuyu Decoction in traumatic brain injury

  • J Ethnopharmacol. 2026 Sep 15:368:121852. doi: 10.1016/j.jep.2026.121852.
Yi Qiu  1 ,  Yao Chen  2 ,  Minghui Hu  3 ,  Wenxin Zhu  4 ,  Xin Guo  5 ,  Quan Chen  6 ,  Zhiqiang Yuan  7 ,  Zhiyan Sheng  8 ,  Xinyu Xiong  9 ,  Tao Tang  10 ,  Yang Wang  11 ,  Zhenyu Nie  12 ,  Teng Li  13
Affiliations
  • 1. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 2. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 3. National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China; Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China. Electronic address: [email protected].
  • 4. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 5. The First Affiliated Hospital Children's Medical Centre, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, PR China. Electronic address: [email protected].
  • 6. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 7. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 8. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 9. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 10. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
  • 11. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China; FuRong Laboratory, Changsha, 410078, Hunan, PR China. Electronic address: [email protected].
  • 12. NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China; Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China. Electronic address: [email protected].
  • 13. Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; National Clinical Research Center for Geriatric Disease (Xiangya Hospital), Xiangya Hospital, Central South University, Changsha, 410008, P.R. China. Electronic address: [email protected].
PMID: 42119634 DOI: 10.1016/j.jep.2026.121852
Abstract

Ethnopharmacological relevance: Traumatic brain injury (TBI) is a major cause of death and long-term disability in humans. Xuefu Zhuyu Decoction (XFZYD) has potential therapeutic effects on TBI, but its molecular mechanism involving non-coding RNAs (ncRNAs) remains unclear.

Aim of the study: To elucidate the mechanism of XFZYD, this study proposed an integrated ncRNA-based network pharmacology (ncRNP) strategy, combined with multi-omics analysis, in vivo and in vitro experiments. Unlike traditional network pharmacology which primarily focuses on protein-coding targets, the ncRNP strategy shifts the regulatory perspective to the transcriptional level, specifically targeting the herb-compound-ncRNA axis to bridge the gap between Traditional Chinese medicine (TCM) multi-component synergy and epigenetic regulation.

Materials and methods: The ncRNP framework was established through four integrated modules: 1) construction of herbal-ncRNA regulatory networks; 2) high-throughput miRNA profiling of TBI mice; 3) multi-omics integration to identify core "herb-miRNA-pathway" nodes; and 4) experimental validation. Male C57BL/6J TBI mice were treated with different doses of XFZYD, and their neurological functions were examined. The ncRNP integrative strategy was established and used in XFZYD. Electron microscopy, western blotting, qRT-PCR, and immunofluorescence were further performed to confirm the anti-autophagy effects of XFZYD by miR-323-3p.

Results: XFZYD treatment significantly improved neurological deficits and reduced neuronal loss and Apoptosis. By implementing the ncRNP strategy which filters pharmacological targets through the lens of differential ncRNA expression, we identified a unique profile of 5 potential miRNAs. Through bioinformatics analysis and validation, miR-323-3p was selected as the key miRNA. We further confirmed that XFZYD normalized the pathological over-activation of Autophagy after TBI by upregulating miR-323-3p, and subsequently suppressed the excessive activation of the AMPK/ULK1/Beclin-1 signaling axis. Overexpression of miR-323-3p directly inhibited the AMPK-dependent Autophagy and restored cellular homeostasis.

Conclusions: XFZYD alleviates TBI-induced neuronal injury by rebalancing the miR-323-3p/AMPK-mediated autophagic flux. The established ncRNP strategy represents a methodological advancement over traditional network pharmacology by incorporating ncRNA-mediated epigenetic signatures, providing a more comprehensive and high-resolution framework for deciphering the complex pharmacological basis of TCM.

Keywords
Autophagy; Herbs; Neuroprotection; Omics; miRNA; ncRNA network pharmacology.
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