Molecular mechanism and natural drug screening for ferroptosis-targeted therapy in rheumatoid arthritis

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 and performed network topology analysis. Then, using DAVID Bioinformatics Resources 6.8, we conducted Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses to explore biological functions and signaling pathways. Finally, the SymMap platform was used to identify natural medicines, and the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was used to find small molecule compounds and corresponding targets for molecular docking analysis. RESULTS AND CONCLUSION: Two datasets, GSE55457 and GSE55235, were identified from the GEO database, and 340 common differentially expressed targets were obtained via limma analysis. A total of 487 ferroptosis-related targets were collected from the FerrDb platform, and 17 common targets related to ferroptosis and rheumatoid arthritis were obtained after intersection. A protein interaction network was constructed using the 17 common targets, containing 16 target proteins and 33 interactions. Core targets such as EGFR, AR, MAPK8, CDKN1A, JUN, ATM, and EGR1 occupied important positions in the network. Five core targets (EGFR, AR, MAPK8, CDKN1A, and JUN) were identified as key ferroptosis-related targets in rheumatoid arthritis. GO and KEGG enrichment analyses showed that treating rheumatoid arthritis via the ferroptosis pathway may be related to DNA binding processes and SMAD2/3 signaling pathways. Molecular docking results showed that natural small molecule compounds such as progesterone, estradiol, and quercetin could form good binding with core targets, providing new directions for drug development and research in rheumatoid arthritis.

1. Introduction

Rheumatoid arthritis (RA) is a common chronic immune-mediated disease that can cause dysfunction of various immune cells and signaling networks, leading to uncontrolled inflammation and joint damage [1-2]. Clinical manifestations include joint swelling, stiffness, and synovial inflammation with cartilage and bone destruction [3]. Inadequate treatment can result in cumulative joint damage and irreversible disability [4]. Current therapeutic strategies primarily include disease-modifying antirheumatic drugs, glucocorticoids, and nonsteroidal anti-inflammatory drugs, which modulate immunity and inflammation [5-6]. However, the pathogenesis remains unclear, and some patients do not respond to existing treatments. Moreover, corticosteroids, NSAIDs, and antirheumatic drugs have considerable adverse effects [7], sometimes life-threatening [8]. Natural small-molecule drugs, with their multi-target, low toxicity, and wide availability, have become an important research direction for RA treatment. Therefore, exploring the pathogenesis of RA, identifying key gene targets, and discovering potential traditional Chinese medicine components are of great significance for clinical diagnosis and therapy.

Ferroptosis is a unique form of programmed cell death that is iron-dependent and associated with lipid peroxidation and iron metabolism dysregulation. It has been implicated in various diseases, including RA. This study employs bioinformatics methods to investigate the molecular mechanisms of ferroptosis in RA and to screen for natural compounds that may target ferroptosis, offering new avenues for RA treatment.