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. 2025 Dec;63(6):5361-5382.
doi: 10.1007/s10528-024-10989-x. Epub 2024 Dec 10.

Exploration of the Regulatory Network of Programmed Cell Death Genes in Rheumatoid Arthritis Based on Blood-Derived circRNA Transcriptome Information and Single-Cell Multi-omics Data

Yuxuan Fang  1 , Nan Xu  1 , Jiacheng Shen  1 , Hongyi Chen  1 , Guoqing Li  2
Affiliations

Exploration of the Regulatory Network of Programmed Cell Death Genes in Rheumatoid Arthritis Based on Blood-Derived circRNA Transcriptome Information and Single-Cell Multi-omics Data

Yuxuan Fang et al. Biochem Genet. 2025 Dec.

Abstract

Programmed cell death (PCD) and circular RNA (circRNA) have been found to involve in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to explore PCD mechanisms and gene regulatory networks in RA. RA related to circRNA, mRNA and single-cell data sets were obtained from the GEO database. The limma package was used to screen differentially expressed circRNA and differentially expressed genes (DEGs) of RA. The PCD gene set from literature was intersected with the DEGs of RA to obtain PCD-related DEGs of RA. The ENCORI database was used to predict and construct a competing endogenous RNAs (ceRNA) regulatory network to obtain key circRNAs and PCD-related DEGs. Hub genes were identified from the key PCD-related DEGs in the ceRNA regulatory network through LASSO regression, and a diagnostic model was constructed based on these hub genes. The expression of hub genes in various cells and stages was analyzed using single-cell datasets. Finally, the expression of key circRNAs and hub genes in peripheral blood of RA patients and healthy individuals was verified by PCR. In this study, a total of 71 differential circRNAs and 221 DEGs in RA were obtained, and 23 PCD-related DEGs were identified. Through ceRNA regulatory network, three key circRNAs (hsa_circ_0001241, hsa_circ_0089761, and hsa_circ_0001654) and four hub PCD-related DEGs. Among them, TXN and RRAGD were highly expressed, and PARP1 and TXNIP were lowly expressed in RA. Single-cell analysis revealed that these genes were significantly differentially expressed in myeloid cell subpopulation. PCR results indicated that among the 7 key factors, the expression of hsa_circ_0001241, hsa_circ_0089761, TXN, and RRAGD in RA was consistent with the results of bioinformatics analysis. Hsa_circ_0001241, hsa_circ_0089761, TXN and RRAGD may be potential biomarkers for RA, and their interactions may have significant implications for the pathology of RA.

Keywords: Blood-derived circRNA; Gene regulatory network; Programmed cell death; Rheumatoid arthritis; Single-cell sequencing.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests. Ethical Approval: This study was conducted by the Declaration of Helsinki and approved by the Ethics Committee of the Ethics Committee of the Affiliated Hospital of Yangzhou University [2023-YKL10-(05)]. Informed Consent: All participants in this study provided written informed consent.

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