Identification and validation of novel biomarkers for cold-dampness syndrome of rheumatoid arthritis based on integration of multiple bioinformatics methods.
10.19540/j.cnki.cjcmm.20231105.401
- Author:
Tao LI
1
;
Wen-Jia CHEN
1
;
Yan-Qiong ZHANG
1
;
Wei LIU
2
;
Na LIN
1
;
Xue-Ting LIU
1
Author Information
1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China.
2. First Teaching Hospital of Tianjin University of Traditional Chinese Medicine Tianjin 300193, China.
- Publication Type:Journal Article
- Keywords:
cold-dampness syndrome;
gene set enrichment analysis;
proteasome 26S subunit,ATPase 2;
rheumatoid arthritis;
transcriptomics;
weighted correlation network analysis
- MeSH:
Humans;
Arthritis, Rheumatoid/drug therapy*;
Biomarkers/metabolism*;
Medicine, Chinese Traditional;
Gene Expression Profiling/methods*;
Computational Biology;
Gene Regulatory Networks;
ATPases Associated with Diverse Cellular Activities/therapeutic use*;
Proteasome Endopeptidase Complex/therapeutic use*
- From:
China Journal of Chinese Materia Medica
2023;48(24):6721-6729
- CountryChina
- Language:Chinese
-
Abstract:
This study aims to identify the novel biomarkers of cold-dampness syndrome(RA-Cold) of rheumatoid arthritis(RA) by gene set enrichment analysis(GSEA), weighted gene correlation network analysis(WGCNA), and clinical validation. Firstly, transcriptome sequencing was carried out for the whole blood samples from RA-Cold patients, RA patients with other traditional Chinese medicine(TCM) syndromes, and healthy volunteers. The differentially expressed gene(DEG) sets of RA-Cold were screened by comparison with the RA patients with other TCM syndromes and healthy volunteers. Then, GSEA and WGCNA were carried out to screen the key DEGs as candidate biomarkers for RA-Cold. Experimentally, the expression levels of the candidate biomarkers were determined by RT-qPCR for an independent clinical cohort(not less than 10 cases/group), and the clinical efficacy of the candidates was assessed using the receiver operating characteristic(ROC) curve. The results showed that 3 601 DEGs associated with RA-Cold were obtained, including 106 up-regulated genes and 3 495 down-regulated genes. The DEGs of RA-Cold were mainly enriched in the pathways associated with inflammation-immunity regulation, hormone regulation, substance and energy metabolism, cell function regulation, and synovial pannus formation. GSEA and WGCNA showed that recombinant proteasome 26S subunit, ATPase 2(PSMC2), which ranked in the top 50% in terms of coefficient of variation, representativeness of pathway, and biological modules, was a candidate biomarker of RA-Cold. Furthermore, the validation results based on the clinical independent sample set showed that the F1 value, specificity, accuracy, and precision of PSMC2 for RA-Cold were 70.3%, 61.9%, 64.5%, and 81.3%, respectively, and the area under the curve(AUC) value was 0.96. In summary, this study employed the "GSEA-WGCNA-validation" integrated strategy to identify novel biomarkers of RA-Cold, which helped to improve the TCM clinical diagnosis and treatment of core syndromes in RA and provided an experimental basis for TCM syndrome differentiation.
