2Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
Abstract
Background: Patients with rheumatoid arthritis (RA) have an increased risk of developing cardiovascular disease (CVD). However, the mechanisms underlying the comorbidity between RA and CVD remain poorly understood. This study aimed to identify the shared genes between RA and CVD and to explore their functional relationships.
Methods: Rheumatoid arthritis– and CVD-associated genes were obtained from the DisGeNET and Malacards databases, respectively. Shared genes between the 2 diseases were identified, and gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using WebGestalt and Cytoscape (v3.9.0). To further investigate potential molecular interactions, protein–protein interaction networks were constructed based on data from the STRING database. Finally, the in silico Tabula Muris single-cell transcriptomic dataset was used to assess the tissue-specific expression of candidate genes and evaluate their potential roles in specific tissues and cell types.
Results: A total of 108 genes were shared between RA and CVD, out of the 898 and 552 genes identified for each condition. Functional enrichment analysis showed that these shared genes were predominantly associated with inflammation and immune response–related pathways. Among them, 42 candidate genes were identified, of which 7 (i.e., IFNG, CCL5, CXCL10, FN1, EGFR, CXCL1, and CD44) were highlighted based on their strong connectivity and biological relevance. For validation, the validation, Tabula Muris single-cell transcriptomic dataset revealed that these genes were highly expressed in mouse cardiac tissues.
Conclusion: Seven shared genes associated with both RA and CVD were identified, which may contribute to the comorbidity between the 2 diseases.
Highlights
- To screen the rheumatoid arthritis (RA)– and cardiovascular disease (CVD)–associated genes, with the aim to investigate their comorbidity.
- Seven shared RA- and CVD-associated genes were responsible for the comorbidity of CVD and RA.
- Inflammation and immune responses were enriched in the shared genes.
Introduction
Rheumatoid arthritis (RA) and cardiovascular disease (CVD) have overlapping pathophysiologic mechanisms involving inflammation, immunity, and oxidative stress.1,
Although there is definite evidence for the shared mechanisms of RA and CVD, there is still a lack of studies at the molecular level. To date, the understanding of the genes associated with RA and CVD is still limited due to lacking of appropriate techniques and approaches. The increasing availability of large-scale genomic data, such as UK Biobank data, facilitates the investigation of CVD risk-related pathways among RA patients at the molecular level.7 Notably, recent Mendelian randomization (MR) studies have provided new insights into the causal relationships between RA and CVD.8,
To further investigate the molecular association between CVD and RA, disease-associated genes were systematically collected from the MalaCards and DisGeNET databases. Subsequently, functional enrichment analysis was conducted to identify the key biological processes and signaling pathways enriched in the shared genes, as well as their potential interactions. Finally, the potential hub genes were identified based on their central roles in the protein–protein interaction (PPI) network, which may be involved in the comorbidity of CVD and RA.
Methods
Selection of Rheumatoid Arthritis– and Cardiovascular Disease–Associated Genes from Databases
A flowchart of the study design is shown in Supplementary Figure 1. Rheumatoid arthritis– and CVD-associated genes were extracted from DisGeNET (
Functional and Pathway Enrichment Analyses
To explore the biological significance of the shared genes between RA and CVD, a series of functional annotation and pathway enrichment analyses were performed. Firstly, GO analysis was conducted using WebGestalt (
Hub gene selection was performed using ClueGO, CluePledia and CytoHubba.16,
To further investigate functional relationships among biological pathways, a pathway cross-talk analysis was conducted. Enriched KEGG pathways (
Identification of Candidate Genes Through Protein–Protein Interaction Network Analysis
We first mapped the RA-associated genes and CVD-associated genes into the PPI network, which yielded an RA-specific network and a CVD-specific network, respectively. To exclude the irrelevant interactions, the RA-specific network and CVD-specific network were merged into a combined network. Subsequently, the RA-specific network was compared with the CVD-specific network, followed by the extraction of the overlapping network. The Cytoscape software was utilized to calculate the node degree of the genes using the Network Analyzer.21,
Expression Analysis of Candidate Genes from databases
To explore the tissue and cell-type-specific expression patterns of the candidate genes, an in silico expression analysis was performed using the Tabula Muris database (
Results
Identification and Selection of Shared Genes
Rheumatoid arthritis– and CVD-associated genes were retrieved from the DisGeNET and Malacards databases using defined thresholds. Specifically, 290 RA-related genes and 210 CVD-related genes were retrieved from the MalaCards database, and 787 RA-related genes and 433 CVD-related genes from the DisGeNET databases (Supplementary Table 1). Among these genes, 108 shared genes were identified between RA and CVD (
Functional Annotation of the Shared Genes
Gene ontology (GO) enrichment analysis was then performed on the 108 genes, which showed that 10 GO biological processes were significantly enriched (Supplementary Table 2). Among these processes, immune responses were the most significant, followed by secretion by cells, leukocyte activation, and immune effector process.
Protein–Protein Interaction Network Construction for Shared Genes
A total of 6 gene modules (i.e., module 1-6) were generated after mapping all the shared genes onto the PPI network (
Hub Genes Selection from the Interaction Network
As shown in
Pathway Enrichment of Rheumatoid Arthritis– and Cardiovascular Disease–Associated Genes
Pathway enrichment analysis revealed 69 significant pathways for RA and 48 for CVD (Supplementary Table 3). After overlapping these enriched pathways, 40 shared pathways were obtained (Supplementary Table 4). Some of the shared pathways were associated with the T cell receptor signaling pathway, B cell receptor signaling pathway, chemokine signaling pathway, and leukocyte trans-endothelial migration. In addition, others were associated with signaling transmission, such as the Janus kinase/signal transducer and activator of transcriptio (JAK-STAT) signaling pathway, mitogen-activated protein kinases (MAPK) signaling pathway, the cytokine-cytokine receptor interaction, as well as the endocrine system and cancer-related pathways.
Pathway Cross-Talk Between Rheumatoid Arthritis and Cardiovascular Disease
Among the 40 shared pathways, 38 shared at least 3 genes with at least 1 other pathway and were included in the cross-talk analysis. Subsequently, a pathway interaction network was constructed based on shared genes to explore the underlying biological processes. In total, 52 out of the 108 shared genes were mapped to this network, resulting in 90 nodes and 734 edges (
Selection of Candidate Genes Associated with Rheumatoid Arthritis and Cardiovascular Disease
All RA- and CVD-associated genes were mapped onto a PPI network, generating 957 nodes (540 RA-associated and 417 CVD-associated) and 9272 edges (2425 RA-associated and 6747 CVD-associated). Subsequently, a combined network including 867 nodes and 8973 edges was established to identify genes potentially linked to both diseases. According to the node degree, 42 candidate genes that were directly linked to the shared genes were selected with a score of 20 or more (
Expression Analysis of Candidate Genes from Databases
In this section, tissue- and cell-specific expression analyses of the 21 novel candidate genes were performed. All 21 novel candidate genes were RA-associated, suggesting that these genes may be involved in the molecular mechanisms of CVD. As shown in
Discussion
In this study, the 108 shared genes between CVD and RA were systematically analyzed. Functional enrichment analyses revealed that these shared genes are involved in immune responses, inflammatory signaling, cytokine activity, and lipid metabolism. Among them, inflammation-related and immune signaling pathways were particularly prominent. Based on degree centrality in the PPI network, 42 candidate genes were identified, of which 7 (i.e.,
Rheumatoid arthritis has been consistently associated with an elevated risk of CVD, which is a leading cause of mortality in this population.23 This may be attributed to the chronic inflammatory state characteristic of RA, which is marked by elevated levels of circulating inflammatory mediators and endothelial dysfunction.24,
Chronic inflammation is a central feature in the pathogenesis of both RA and CVD.27 Lipid abnormalities, particularly the impaired atheroprotective function of high-density lipoprotein, are recognized as key contributors to the increased risk of atherosclerotic cardiovascular disease in RA patients.28 Consistently, the shared gene modules in the PPI network encompassed interleukin signaling, cytokine-cytokine receptor interaction, and pathways regulating inflammation resolution. Additionally, pathways related to lipid metabolism and arachidonic acid were significantly enriched, supporting evidence that altered lipid profiles and inflammatory lipoproteins contribute to the pathogenesis of CVD in RA patients.29,
To elucidate key molecular players bridging RA and CVD, we constructed a combined PPI network was constructed and candidate genes were identified based on their connectivity to shared disease-associated genes. Notably, 7 candidate genes that were found showed a direct link to at least 9 genes, including
Notably,
These 7 candidate genes represent potential molecular links between CVD and RA and may serve as future therapeutic targets. However, it is important to note that these findings are based on bioinformatics and in silico predictions. Functional validation is needed through experimental models and clinical cohorts to confirm causality and therapeutic relevance. In particular, interventions targeting
There are some limitations in this study. First, the analysis relied on publicly available databases, which may introduce biases or incomplete gene annotations. Second, the current human interactome is still not complete, and there might be some errors despite significant improvement in the quality of PPI databases. Third, the functional roles of candidate genes require further experimental validation, such as gene knockout or overexpression studies.
Conclusion
This study identified 108 shared genes between CVD and RA, with enrichment analyses highlighting their roles in immune and inflammatory processes. Among these, 7 candidate genes were considered as potential key mediators in the shared pathogenic mechanisms. These findings provide new insights into common molecular mechanisms and may offer promising targets for future diagnostic or therapeutic strategies.
Supplementary Materials
Footnotes
References
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