Transcriptomics and Network Pharmacology Reveal Anti-Inflammatory and Anti-Oxidative Stress Mechanisms of Qingxuan Runmu Yin in Dry Eye Disease

Shanshan Zhao,1,* Jiadi Wang,1,2,* Ying Liu,1 Xi Hu,1 Chenhao Gu,1 Jing Yao1,2 1Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150000, People’s Republic of China; 2Ophthalmology Department, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150000, People’s Republic of China*These authors contributed equally to this workCorrespondence: Jing Yao, Ophthalmology Department, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, 26 Heping Road, Xiangfang District, Harbin, Heilongjiang, 150000, People’s Republic of China, Tel +451-82111401, Email [email protected]: Dry eye disease (DED) is a multifactorial chronic disorder of the ocular surface, characterized by reduced tear secretion, tear film instability, and inflammation. Oxidative stress is pivotal in DED pathogenesis. Qingxuan Runmu Yin (QRY) has shown substantial clinical efficacy in managing DED. This study aims to elucidate the molecular mechanisms underlying the antioxidant and anti-inflammatory effects of QRY in DED.Methods: A benzalkonium chloride (BAC)-induced DED mouse model was established to evaluate QRY’s protective effects on the ocular surface. RNA sequencing identified differentially expressed genes (DEGs, fold change > 1.5, P < 0.05) among control, untreated DED, and QRY-treated DED mice. Transcriptomic analysis of DEGs was conducted. The active ingredients and targets of the ten Chinese herbal medicines in QRY were obtained from the TCMSP and TCMIP databases, whereas DED and oxidative stress-related genes were identified from the DisGeNET, OMIM, and GeneCards databases. A Chinese herbal medicine-active ingredient-target-disease network was constructed. The key pathways and targets of QRY against DED were investigated through transcriptomics and network pharmacology, and experimental validation was performed.Results: QRY alleviated ocular surface damage in DED mice by repairing goblet cells, improving corneal damage, enhancing tear secretion, and reducing inflammatory factors and reactive oxygen species (ROS). Combined transcriptomic and network pharmacology analyses indicated that QRY reduced oxidative stress in DED by inhibiting pathways such as NF-κB and TNF. In vitro, QRY improved the survival of human corneal epithelial (HCE) cells damaged by oxidative stress. It inhibited the NF-κB signaling pathway and reduced levels of the pro‑inflammatory cytokines IL‑1β, IL‑6, and TNF‑α. In addition, QRY lowered ROS levels and enhanced superoxide dismutase (SOD) activity.Conclusion: This study is the first to demonstrate that QRY mitigates ocular surface inflammation and oxidative stress in DED, providing a scientific foundation for its clinical application. Keywords: dry eye disease, oxidative stress, inflammation, transcriptomics, network pharmacology, qingxuan runmu yin (QRY)