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Bioinformatic identification and validation of autophagy-related genes in rheumatoid arthritis

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Abstract

Objectives

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disorder characterized by progressive synovial inflammation and joint destruction, with a largely unknown etiology. Studies have suggested that autophagy and its expression may be involved in the pathogenesis of RA; however, autophagy-related genes in RA are still largely unidentified. Therefore, in this study, we aimed to identify and validate autophagy-related genes in RA.

Methods

We identified differentially expressed autophagy-related genes between patients with RA and healthy individuals using gene expression profiles in the GSE55235 dataset and R software. Subsequently, correlation analysis, protein–protein interaction, gene ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were carried out using these differentially expressed autophagy-related genes. Finally, our results were validated by examining the expression of differentially expressed autophagy-related hub genes in clinical samples using qRT-PCR.

Results

We identified 52 potential autophagy-related genes in RA based on bioinformatic analyses. Ten hub genes, CASP8, CTSB, TNFSF10, FADD, BAX, MYC, FOS, CDKN1A, GABARAPL1, and BNIP3, were validated to be differentially expressed and may serve as valuable prognostic markers and new potential therapeutic targets for RA via the regulation of autophagy.

Conclusions

Our results may help improve the understanding of RA pathogenesis. Autophagy-related genes in RA could be valuable biomarkers for diagnosis and prognosis and they might be exploited clinically as therapeutic targets in the future.

Key Points

• CASP8, CTSB, TNFSF10, FADD, BAX, MYC, FOS, CDKN1A, GABARAPL1, and BNIP3 may be autophagy-related hub genes correlated with the pathogenesis of RA.

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Funding

This study was supported by the National Nature Science Foundation of China (grant number 82071752).

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Author notes

  1. Dan-dan Fan and Peng-yu Tan contributed equally to this work.

Authors and Affiliations

  1. Rheumatology and Clinical Immunology, ZhuJiang Hospital, Southern Medical University, Guangzhou, 510285, People’s Republic of China

    Dan-dan Fan, Peng-yu Tan, Li Jin, Yuan Qu & Qing-hong Yu

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  1. Dan-dan Fan
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Contributions

Q-h Y and D-d F designed the experiments; D-d F and P-y T collected and analyzed the data; L J and P-y T collected the clinical samples and performed the molecular experiments; D-d F wrote the manuscript; Q-h Yu and Y Q revised this paper.

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Correspondence to Qing-hong Yu.

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Fan, Dd., Tan, Py., Jin, L. et al. Bioinformatic identification and validation of autophagy-related genes in rheumatoid arthritis. Clin Rheumatol 42, 741–750 (2023). https://doi.org/10.1007/s10067-022-06399-2

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  • DOI: https://doi.org/10.1007/s10067-022-06399-2

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