Integrated Transcriptomic Analysis Identifies a Ferroptosis-Related Gene Signature Underlying Macrophage Heterogeneity and Immune Dysregulation in Rheumatoid Arthritis Synovium
- 1Faculty of Medicine, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- 2Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
Abstract
Ferroptosis contributes to rheumatoid arthritis (RA), but the key regulators and their cell-specific functions in the synovial microenvironment remain incompletely understood. This study aimed to identify robust ferroptosis-associated biomarkers and define their cellular context through an integrated transcriptomic framework. Bulk synovial transcriptomic datasets were integrated using differential expression, weighted gene co-expression network analysis, and a curated ferroptosis gene set. Candidate genes were prioritized using three feature-selection algorithms and validated across twelve models. Immune infiltration, single-cell RNA sequencing, pseudotime, CellChat, and virtual gene perturbation analyses characterized their cellular and functional context. Six ferroptosis-related genes (AIM2, HCP5, CAPG, ALOX5, TYMS, and RUNX3) formed a diagnostic signature discriminating RA from healthy synovium (mean leakage-free test AUC 0.977 across five training-only re-derivations; 0.9375 in the primary split), with consistent leave-one-dataset-out and osteoarthritis-control validation. These genes linked to adaptive immune and ferroptosis-associated transcriptional programs. Single-cell analysis localized this transcriptional score to macrophages, where ferroptosis-signature-high macrophages occupied a central communication-network position and showed collagen-pathway enrichment; because RA and healthy samples were not fully independent of dataset origin, this finding is hypothesis-generating. Pseudotime analysis suggested progressive induction of these genes toward an inflammatory NF-κB/TNF/IL-17 terminal state, and virtual perturbation suggested convergence on mitochondrial oxidative phosphorylation networks that persisted after removing sex-chromosome genes, though residual sex-associated effects cannot be fully excluded. This study identifies a biologically interpretable ferroptosis-related gene signature and suggests ferroptosis-associated macrophage reprogramming may contribute to immune dysregulation in RA synovium. The single-cell findings are hypothesis-generating given the cohort design, while the diagnostic signature was supported by leakage-free, cross-cohort, and disease-specificity analyses, providing candidate biomarkers and therapeutic targets for RA.
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BibTeX
@article{liu2026integrated,
title = {{Integrated Transcriptomic Analysis Identifies a Ferroptosis-Related Gene Signature Underlying Macrophage Heterogeneity and Immune Dysregulation in Rheumatoid Arthritis Synovium}},
author = {Houchen Liu and Ruizhuo Zhang},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219552},
url = {https://www.mdpi.com/1422-0067/27/21/9552},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrated Transcriptomic Analysis Identifies a Ferroptosis-Related Gene Signature Underlying Macrophage Heterogeneity and Immune Dysregulation in Rheumatoid Arthritis Synovium
AU - Houchen Liu
AU - Ruizhuo Zhang
PY - 2026
DA - 2026/10/26
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219552
UR - https://www.mdpi.com/1422-0067/27/21/9552
AB - Ferroptosis contributes to rheumatoid arthritis (RA), but the key regulators and their cell-specific functions in the synovial microenvironment remain incompletely understood. This study aimed to identify robust ferroptosis-associated biomarkers and define their cellular context through an integrated transcriptomic framework. Bulk synovial transcriptomic datasets were integrated using differential expression, weighted gene co-expression network analysis, and a curated ferroptosis gene set. Candidate genes were prioritized using three feature-selection algorithms and validated across twelve models. Immune infiltration, single-cell RNA sequencing, pseudotime, CellChat, and virtual gene perturbation analyses characterized their cellular and functional context. Six ferroptosis-related genes (AIM2, HCP5, CAPG, ALOX5, TYMS, and RUNX3) formed a diagnostic signature discriminating RA from healthy synovium (mean leakage-free test AUC 0.977 across five training-only re-derivations; 0.9375 in the primary split), with consistent leave-one-dataset-out and osteoarthritis-control validation. These genes linked to adaptive immune and ferroptosis-associated transcriptional programs. Single-cell analysis localized this transcriptional score to macrophages, where ferroptosis-signature-high macrophages occupied a central communication-network position and showed collagen-pathway enrichment; because RA and healthy samples were not fully independent of dataset origin, this finding is hypothesis-generating. Pseudotime analysis suggested progressive induction of these genes toward an inflammatory NF-κB/TNF/IL-17 terminal state, and virtual perturbation suggested convergence on mitochondrial oxidative phosphorylation networks that persisted after removing sex-chromosome genes, though residual sex-associated effects cannot be fully excluded. This study identifies a biologically interpretable ferroptosis-related gene signature and suggests ferroptosis-associated macrophage reprogramming may contribute to immune dysregulation in RA synovium. The single-cell findings are hypothesis-generating given the cohort design, while the diagnostic signature was supported by leakage-free, cross-cohort, and disease-specificity analyses, providing candidate biomarkers and therapeutic targets for RA.
SN - 1422-0067
ER -