Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice

Yali Yuan,1,2,* Hairong Hu,1,* Zhongmei Sun,3,* Wenting Wang,4 Zhibin Wang,1 Mengyu Zheng,5 Yunqi Xing,1 Wenji Zhang,1 Muyuan Wang,1 Xinyu Lu,1 Yitong Li,1 Chengtao Liang,1 Zhengdao Lin,1 Chune Xie,6 Junxiang Li,1 Tangyou Mao1 1Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China; 2Hebei North University, Zhangjiakou, Hebei, People’s Republic of China; 3Tianjin Nankai Hospital, Tianjin, People’s Republic of China; 4Beitaipingzhuang Community Health Service Center, Beijing, People’s Republic of China; 5King’s College, London, UK; 6Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, People’s Republic of China*These authors contributed equally to this workCorrespondence: Tangyou Mao; Junxiang Li, Email [email protected]; [email protected]: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.Purpose: We aimed to probe the mechanism of QCWZD for the treatment of IBD.Methods: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.Results: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3+CD4+IL-17+ (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-κB, TNF-α and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.Conclusion: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD. Keywords: intestinal bowel disease, Qingchang Wenzhong Decoction, microbial homeostasis, Th17 cells, mucosal immunity