Comparison of immune cells and diagnostic markers between spondyloarthritis and rheumatoid arthritis by bioinformatics analysis

Wang, Jiaqian; Xue, Yuan; Zhou, Liang

doi:10.1186/s12967-022-03390-y

Cited by 10 publications

(8 citation statements)

References 31 publications

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“…Quantitative real-time polymerase chain reaction (qRT-PCR) was carried out as the method previously described. 16 All experiments were performed independently in triplicate. Paired t -test and Mann–Whitney U -test were used to assess the significant differences between two groups.…”

Section: Methodsmentioning

confidence: 99%

New Classification of Rheumatoid Arthritis Based on Immune Cells and Clinical Characteristics

Wang,

Xue,

Zhou

2024

JIR

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Background Rheumatoid arthritis (RA) is a chronic systemic immune disease characterized by joint synovitis, but there are differences in clinical manifestations and serum test results among different patients. Methods This is a bioinformatics study. We first obtained the gene expression profile of RA and normal synovium from the database, and screened the differentially expressed immune related genes for enrichment analysis. Subsequently, we classified RA into three subtypes by unsupervised clustering of serum gene expression profiles based on immune enrichment scores. Then, the enrichment and clinical characteristics of different subtypes were analyzed. Finally, according to the infiltration of different subtypes of immune cells, diagnostic markers were screened and verified by qRT-PCR. Results C1 subtype is related to the increase of neutrophils, C-reactive protein and erythrocyte sedimentation rate, and joint pain is more significant in patients. C2 subtype is related to the expression of CD8+T cells and Tregs, and patients have mild joint pain symptoms. The RF value of C3 subtype is higher, and the expression of various immune cells is increased. CD4 T cells, NK cells activated, macrophages M1 and neutrophils are immune cells significantly infiltrated in synovium and serum of RA patients. IFNGR1, TRAC, IFITM1 can be used as diagnostic markers of different subtypes. Conclusion In this study, RA patients were divided into different immune molecular subtypes based on gene expression profile, and immune diagnostic markers were screened, which provided a new idea for the diagnosis and treatment of RA.

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Section: Methodsmentioning

confidence: 99%

New Classification of Rheumatoid Arthritis Based on Immune Cells and Clinical Characteristics

Wang,

Xue,

Zhou

2024

JIR

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“…Quantitative real-time polymerase chain reaction (qRT-PCR) was carried out as the method previously described. 21 Simply put, total RNA was extracted from tissues using TRIzol reagent (Beyotime, China) and reverse transcribed. qRT-PCR was performed on CFX connect real-time PCR detection system (Bio-Rad, USA).…”

Section: Methodsmentioning

confidence: 99%

Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles

Xue,

Zhou,

Wang

2023

Bone Joint Res

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AimsKnee osteoarthritis (OA) involves a variety of tissues in the joint. Gene expression profiles in different tissues are of great importance in order to understand OA.MethodsFirst, we obtained gene expression profiles of cartilage, synovium, subchondral bone, and meniscus from the Gene Expression Omnibus (GEO). Several datasets were standardized by merging and removing batch effects. Then, we used unsupervised clustering to divide OA into three subtypes. The gene ontology and pathway enrichment of three subtypes were analyzed. CIBERSORT was used to evaluate the infiltration of immune cells in different subtypes. Finally, OA-related genes were obtained from the Molecular Signatures Database for validation, and diagnostic markers were screened according to clinical characteristics. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to verify the effectiveness of markers.ResultsC1 subtype is mainly concentrated in the development of skeletal muscle organs, C2 lies in metabolic process and immune response, and C3 in pyroptosis and cell death process. Therefore, we divided OA into three subtypes: bone remodelling subtype (C1), immune metabolism subtype (C2), and cartilage degradation subtype (C3). The number of macrophage M0 and activated mast cells of C2 subtype was significantly higher than those of the other two subtypes. COL2A1 has significant differences in different subtypes. The expression of COL2A1 is related to age, and trafficking protein particle complex subunit 2 is related to the sex of OA patients.ConclusionThis study linked different tissues with gene expression profiles, revealing different molecular subtypes of patients with knee OA. The relationship between clinical characteristics and OA-related genes was also studied, which provides a new concept for the diagnosis and treatment of OA.Cite this article: Bone Joint Res 2023;12(12):702–711.

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“…All participants gave written informed consent. Quantitative real-time polymerase chain reaction (qRT-PCR) was carried out as the method previously described [15]. All experiments were performed independently in triplicate.…”

Section: Qrt-pcr Validationmentioning

confidence: 99%

New classification of rheumatoid arthritis based on immune cells and clinical characteristics

Wang

Zhou²,

Xue

2023

Preprint

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Background Rheumatoid arthritis (RA) is a chronic systemic immune disease characterized by joint synovitis, but the specific etiology is unknown, and the characteristic serum diagnostic markers are also lacking. Methods First, we obtained the gene expression profile of synovium to evaluate the infiltration of immune cells in synovium, and screened the differentially expressed immune related genes for enrichment analysis. Subsequently, we classified RA into three subtypes by unsupervised clustering of serum gene expression profiles based on immune enrichment scores. Then, the enrichment and clinical characteristics of different subtypes were analyzed. Finally, according to the infiltration of different subtypes of immune cells, diagnostic markers were screened and verified by qRT-PCR. Results C1 subtype is related to the increase of neutrophils, CRP and ESR, and joint pain is more significant in patients. C2 subtype is related to the expression of CD8+T cells and Tregs, and patients have mild joint pain symptoms. The RF value of C3 subtype is higher, and the expression of various immune cells is increased. The function of this subtype is enriched in a variety of immune system diseases. T cells CD4, NK cells activated, macrophages M1 and neutrophils are immune cells significantly infiltrated in synovium and serum of RA patients. IFNGR1, TRAC, IFITM1 can be used as diagnostic markers of different subtypes. Conclusion In this study, RA patients were divided into different immune molecular subtypes based on gene expression profile, and immune diagnostic markers were screened, which provided a new idea for the diagnosis and treatment of RA.

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Comparison of immune cells and diagnostic markers between spondyloarthritis and rheumatoid arthritis by bioinformatics analysis

Cited by 10 publications

References 31 publications

New Classification of Rheumatoid Arthritis Based on Immune Cells and Clinical Characteristics

New Classification of Rheumatoid Arthritis Based on Immune Cells and Clinical Characteristics

Classification of distinct osteoarthritis subtypes with different knee joint tissues by gene expression profiles

New classification of rheumatoid arthritis based on immune cells and clinical characteristics

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