1.TCMHTI: a Transformer-based herb-target interaction prediction model for Qingfu Juanbi Decoction in rheumatoid arthritis
Zhenzhong LIANG ; Changsong DING
Digital Chinese Medicine 2025;8(2):206-218
[Objective] :
To predict the potential targets of Qingfu Juanbi Decoction (青附蠲痹汤, QFJBD) in treating rheumatoid arthritis (RA) using an improved Transformer model and investigate the network pharmacological mechanisms underlying QFJBD’s therapeutic effects on RA.
Methods:
First, a traditional Chinese medicine herb-target interaction (TCMHTI) model was constructed to predict herb-target interactions based on Transformer improvement. The performance of the TCMHTI model was evaluated against baseline models using three metrics: area under the receiver operating characteristic curve (AUC), precision-recall curve (PRC), and accuracy. Subsequently, a protein-protein interaction (PPI) network was built based on the predicted targets, with core targets identified as the top nine nodes ranked by degree values. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the targets predicted by TCMHTI and the targets identified through network pharmacology method for comparison. Then, the results were compared. Finally, the core targets predicted by TCMHTI were validated through molecular docking and literature review.
Results:
The TCMHTI model achieved an AUC of 0.883, PRC of 0.849, and accuracy of 0.818, predicting 49 potential targets for QFJBD in RA treatment. Nine core targets were identified: tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, IL-10, IL-17A, cluster of differentiation 40 (CD40), cytotoxic T-lymphocyte-associated protein 4 (CTLA4), IL-4, and signal transducer and activator of transcription 3 (STAT3). The enrichment analysis demonstrated that the TCMHTI model predicted 49 targets and enriched more pathways directly associated with RA, whereas classical network pharmacology identified 64 targets but enriched pathways showing weaker relevance to RA. Molecular docking demonstrated that the active molecules in QFJBD exhibit favorable binding energy with RA targets, while literature research further revealed that QFJBD can treat RA through 9 core targets.
Conclusion
The TCMHTI model demonstrated greater accuracy than traditional network pharmacology methods, suggesting QFJBD exerts therapeutic effects on RA by regulating targets like TNF-α, IL-1β, and IL-6, as well as multiple signaling pathways. This study provides a novel framework for bridging traditional herbal knowledge with precision medicine, offering actionable insights for developing targeted TCM therapies against diseases.
2.Design and Implementation of Germplasm Resources Information System for Chinese Medicines
Wei LIU ; Changsong DING ; Yang LIANG
Chinese Journal of Information on Traditional Chinese Medicine 2017;24(5):5-7
Germplasm Resources Information System for Chinese Medicines (GRIS-CM) is designed and realized for improving the management efficiency of the germplasm resources for Chinese materia medica. The system integrates and analyzes the germplasm resources data, realizes information management of the germplasm resources for Chinese materia medica, and provides better services for scientific research institutions, governments, enterprises and medicinal herb growers. It contains 3 databases and 13 function modules, including the basic information base, literature library and gene bank. GRIS-CM can help manage the related data of germplasm resources for Chinese materia medica, and is better for data integration, analysis and statistics to find the rules and patterns. GRIS-CM provides flexible data comparison and visualization functions, and has significant practical value and research value.
3.TCM Data Management Based on Object Characteristics under the Background of Big Data
Changsong DING ; Haoyu QU ; Shiwen WU
Chinese Journal of Information on Traditional Chinese Medicine 2016;23(9):10-14
Targeting the problem that it is difficult for traditional data management mode to effectively manage TCM information, this article analyzed from the aspect of object characteristics of TCM information resources and summarized that the reason lies in the TCM information resources with big data 4V features, proposed strategies for TCM information resource management based on big data technology, and expounded the feasibility.
4.Laparoscopic cholecystectomy in gallbladder calculi incarceration
Yiwei ZHOU ; Junrong DING ; Changsong MA ; Jianhua GUO
International Journal of Surgery 2009;36(8):518-520
Objective To evaluate the feasibility,safety and operation timing of laparoscopic cholecys-tectomy in treatment of gallbladder calculi incarceration. Methods The data of 280 cases of gallbladder stone incarceration performed by LC were retrospectively analyzed. Results Eight out of 280 cases were converted to open cholecystectomy. The successful rate of LC was 97. 1%. There were no complications such as bile and intestinal injury. Conclusion LC for gallbladder calculi incarceration is safe and feasible as long as operators have skilled technique and make right decisions on operation timing.
5.Effect of Mailuoning injection on lower extremity diabetic atherosclerotic obliterans
Yiwei ZHOU ; Changsong MA ; Junrong DING ; Xiaoyan ZHAO
International Journal of Traditional Chinese Medicine 2011;33(8):684-685
Objective To observe the effect and safety of Mailuoning Injection(MLN) in treating patients with type 2 diabetes mellitus accompanying lower extremity atherosclerotic obliterans.Methods The selected patients were assigned by randomized digital table to a treated group (120 cases treated with MLN) and a control group (60 cases treated with alprostadil). The clinical efficacy was assessed after 4 weeks of treatment. Results The total effective rate in the treated group was 95.0%, better than that in the control group,83.3%(P<0.01).Conclusion MLN has the effect of activating blood circulation.dissolving stasis and dredging collaterals, reducing the formation of thrombi. MLN is effective and safe when applied in clinical practice for the treatment of lower extremity diabetic atherosclerotic obliterans.
6.Exploring the mechanism of action of acupuncture-targeted therapy for rheumatoid arthritis and identifying candidate traditional Chinese medicines
Mengya LI ; Yue CHEN ; Ning CHENG ; Haixin YOU ; Changsong DING
International Journal of Traditional Chinese Medicine 2024;46(6):764-772
Objective:Exploration on the mechanism of acupuncture-targeted therapy for rheumatoid arthritis and identification of candidate Chinese materia medica.Methods:Targets of acupuncture for RA were collected from related literature, and GSE205962 gene chips were obtained from GEO database. The weighted co-expression network (WGCNA) was constructed by screening differentially expressed genes using R 4.3.1. The collection targets were taken to intersect with the differential genes, and the common genes were obtained for high-throughput GO and KEGG enrichment. The Hub genes were screened by constructing protein interaction networks using the String database and Cytoscape 3.9.0 software. The CIBERSORT algorithm was used to explore the mechanisms of RA immune infiltration, and finally the Coremine Medical database was applied to predict Chinese materia medica.Results:A total of 8 key targets were selected (RHOA, JAK1, FYN, LCK, STAT1, STAT3, EGF, GATA3). The results of immune infiltration analysis showed that various immune cells were closely related to the biological processes of rheumatoid arthritis, including γδ T cells, monocytes, regulatory T cells, CD8 T cells, etc. Saposheikovize Radix, Cinnamomi Ramulus, Anemarrhenae Rhizoma, Dendrobii Caulis, Rehmannine Radix, Lonicerae Japonicae Flos, Pinelliae Rhizoma, Cimicifugae Rhizoma, Poria, Stephaniae Tetrandrae Radix were the 10 kinds of commonly used key Chinese materia medica in the treatment of RA.Conclusions:Acupuncture and moxibustion may treat RA by regulating RHOA, JAK1, FYN, LCK and other core targets. This study predicts that Chinese materia medica can be used as a source of drugs for the treatment of RA, and can provide new ideas for the combination of acupuncture and medicine for the treatment of RA.
7.Expert consensus on the diagnosis and treatment of severe and critical coronavirus disease 2019.
You SHANG ; Jianfeng WU ; Jinglun LIU ; Yun LONG ; Jianfeng XIE ; Dong ZHANG ; Bo HU ; Yuan ZONG ; Xuelian LIAO ; Xiuling SHANG ; Renyu DING ; Kai KANG ; Jiao LIU ; Aijun PAN ; Yonghao XU ; Changsong WANG ; Qianghong XU ; Xijing ZHANG ; Jicheng ZHANG ; Ling LIU ; Jiancheng ZHANG ; Yi YANG ; Kaijiang YU ; Xiangdong GUAN ; Dechang CHEN
Chinese Medical Journal 2022;135(16):1913-1916
Humans
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COVID-19
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Consensus
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SARS-CoV-2
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China