Abstract: BACKGROUND: Current research in rheumatoid arthritis focuses on iron metabolism-related proteins and the effects of ferroptosis on immune cells. This study proposes new approaches to target ferroptosis in the treatment of rheumatoid arthritis from the perspective of traditional Chinese medicine. These approaches include developing new traditional Chinese medicine therapies, creating individualized treatment plans based on patients’ genes and biomarkers, optimizing therapeutic strategies, and improving symptoms. These strategies aim to facilitate early treatment and improve prognosis.
OBJECTIVE: Bioinformatics was applied to investigate the molecular mechanism of treating rheumatoid arthritis from the perspective of ferroptosis, and to screen potential traditional Chinese medicines and active ingredients, opening up a new way for the treatment of rheumatoid arthritis.
METHODS: The Gene Expression Omnibus database, maintained by the National Center for Biotechnology Information, is primarily used to store and share high-throughput gene expression, microarray, and sequencing data. The Gene Expression Omnibus database enables researchers to search and analyze genomic data related to various diseases. This study is based on publicly available summary statistics databases and does not require ethical approval. The Gene Expression Omnibus database was searched for datasets related to rheumatoid arthritis that met the screening criteria. The Sanger sequencing platform was then used to obtain the transcriptome data of rheumatoid arthritis. Finally, the limma algorithm was applied to screen the differentially expressed genes. Meanwhile, the ferroptosis-related gene set was extracted from the FerrDb database. Through integration analysis, we obtained the intersection of the differentially expressed genes and the ferroptosis-related genes. We constructed a protein interaction network using this intersection to study the topological structure characteristics of the network. Then, the screened potential targets were analyzed using the online analysis tool DAVID Bioinformatics Resources 6.8 by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis to explore their biological functions and signaling pathway characteristics. Finally, the SymMap platform was used to locate natural drugs. Molecular docking analysis was performed to find small molecule compounds corresponding to natural drugs and their targets using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform.
RESULTS AND CONCLUSION: (1) The Gene Expression Omnibus database was screened to identify two datasets, GSE55457 and GSE55235, and 340 common differentially expressed targets were obtained after limma differential analysis. Through the FerrDb platform, 487 ferroptosis-related targets were collected and intersected with the above common differentially expressed targets, yielding a total of 17 co-targets related to ferroptosis and rheumatoid arthritis. (2) The protein interaction network was constructed using 17 co-targets, containing 16 target proteins and 33 protein interactions. Among them, core targets such as EGFR, AR, MAPK8, CDKN1A, JUN, ATM and EGR1 occupied important positions in the network, and 5 core co-targets related to ferroptosis and rheumatoid arthritis were screened out through the network topological features, namely EGFR, AR, MAPK8, CDKN1A, and JUN. (3) Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the treatment of rheumatoid arthritis through the ferroptosis pathway may be associated with DNA binding process, cytoplasmic and nuclear SMAD2/3 signaling pathway, etc. (4) The results of SymMap platform and Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform show that natural small molecule compounds such as progesterone, estradiol and quercetin could form a good molecular docking with the core target, which provides a new direction for the development of a new direction for the development and research of new drugs for rheumatoid arthritis.

Key words: bioinformatics, ferroptosis, rheumatoid arthritis, natural pharmaceutical ingredients, progesterone, estradiol, quercetin