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Identification of potential biomarkers for systemic lupus erythematosus by integrated analysis of gene expression and methylation data

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Abstract

Introduction

Systemic lupus erythematosus (SLE) is a heterogeneous and chronic autoimmune disease. Aberrant DNA methylation occurs during various processes of SLE development regulating the mRNA expression of interrelated genes. This study aims to screen potential DNA methylation markers for SLE.

Methods

Gene expression and methylation datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between SLE patients and healthy controls were screened using the limma R package, and differentially methylated positions (DMPs) and regions (DMRs) were identified using dmpfinder and bumphunter (minfi). Additionally, the DNA methylation markers to distinguish SLE patients from healthy controls were explored through receiver operating characteristic (ROC) curves and logistic regression analyses. Finally, we validated the results of the bioinformatic analysis by pyrosequencing.

Results

In total, 91 DEGs, 90,092 DMPs, 15 DMRs, and 13 DMR-associated genes were identified. Through the integrative analysis of DEG- and DMR-associated genes, we identified five type I interferon (IFN)-related genes as key epigenetic-driven genes in SLE. GO enrichment analysis showed that the five SLE-associated epigenetic-driven genes were mainly enriched in the type I IFN signaling pathway involved in immune response and defense response to virus. Moreover, we identified two SLE-specific DNA methylation markers, three SLE without lupus nephritis (SLE-LN−)-specific DNA methylation markers, and two SLE with lupus nephritis (SLE-LN+)-specific DNA methylation markers by stepwise logistic regression.

Conclusions

Overall, our study demonstrates potential DNA methylation markers of SLE, SLE-LN−, and SLE-LN+, which may help the diagnosis, boost the development of new epigenetic therapy, and contribute to individualized treatment.

Key Points

• This study identified five type I IFN-related genes as key epigenetic-driven genes in SLE, which support the importance of the type I IFN pathway in the pathogenesis of SLE

• We identified novel DNA methylation biomarkers in SLE, SLE-LN−, and SLE-LN+ by a comprehensive analysis of bioinformatics methods and executed experimental validation, and binary logistic regression analysis showed that they have excellent potential

• These results may provide new insights into the biological mechanisms of SLE, and identify reliable biomarkers for SLE, SLE-LN−, and SLE-LN+, which may contribute to diagnosis and individualized treatment

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Data availability

The data that support the findings of this study are openly available in GEO (https://www.ncbi.nlm.nih.gov/geo/).

Abbreviations

SLE:

Systemic lupus erythematosus

PBMCs:

Peripheral blood mononuclear cells

GEO:

Gene Expression Omnibus

DEGs:

Differentially expressed genes

DMPs:

Differentially methylated positions

DMRs:

Differentially methylated regions

ROC:

Receiver operating characteristic

IFN:

Interferon

LN:

Lupus nephritis

FDR:

False discovery rate

GO:

Gene ontology

PPI:

Protein–protein interaction network

AUC:

Area under the curve

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Acknowledgements

We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript.

Funding

This work was supported by the National Natural Science Foundation of China [grant number 82073440] and the Medical Science and Technology Research Fund project of Guangdong Province [grant number A2019180].

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Authors and Affiliations

  1. Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, No. 1838, North Guangzhou Avenue, Guangzhou, 510515, China

    Wenjing Zhang, Guixin Liang, Huifeng Zhou, Xuedan Zeng, Zhiwen Zhang & Kuan Lai

  2. Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China

    Wenjing Zhang

  3. Guangzhou Institute of Dermatology, Guangzhou, 510030, China

    Xia Xu

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Contributions

WJZ, ZWZ, HFZ, and KL participated in the conception and design, KL and XX provided the administrative support, HFZ, XDZ, GXL, and ZWZ participated in the provision of study materials or patients, WJZ participated in the collection and assembly of data, and data analysis and interpretation. All authors participated in manuscript writing and final approval of manuscript.

Corresponding author

Correspondence to Kuan Lai.

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Ethics approval and consent to participate

This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Ethics Committee of Nanfang Hospital, Southern Medical University (Guangzhou, Guangdong, China).

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Informed consent was obtained from all individual participants included in the study.

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All authors consent to the publication of this work.

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The authors declare no competing interests.

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Wenjing Zhang and Guixin Liang have contributed equally to this work and share the first authorship.

Supplementary Information

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ESM 3

The mRNA expression of key epigenetic-driven genes (IFI44L, IFI44, IFT1, MX1 and USP18) was reversely correlated with the methylation status of the CpG sites in PBMCs(PNG 392 kb)

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Zhang, W., Liang, G., Zhou, H. et al. Identification of potential biomarkers for systemic lupus erythematosus by integrated analysis of gene expression and methylation data. Clin Rheumatol 42, 1423–1433 (2023). https://doi.org/10.1007/s10067-022-06495-3

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