DNA methylation of IFI44L as a potential blood biomarker for childhood-onset systemic lupus erythematosus

Jingwei Wang; Xiqiang Dang; Xiaochuan Wu; Zhongyuan Xiang; Yongzhen Li; Yaqian Fu; Tian Shen

doi:10.1038/s41390-024-03135-1

DNA methylation of IFI44L as a potential blood biomarker for childhood-onset systemic lupus erythematosus

Pediatr Res. 2024 Mar 21. doi: 10.1038/s41390-024-03135-1. Online ahead of print.

Authors

Jingwei Wang^{1

2}, Xiqiang Dang^{1

2}, Xiaochuan Wu^{1

2}, Zhongyuan Xiang³, Yongzhen Li^{1

2}, Yaqian Fu⁴, Tian Shen^{5

6}

Affiliations

¹ Children's Medical Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
² Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
³ Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
⁴ Health Management Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
⁵ Children's Medical Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. shentian0215@csu.edu.cn.
⁶ Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. shentian0215@csu.edu.cn.

PMID: 38514858
DOI: 10.1038/s41390-024-03135-1

Abstract

Background: IFN-induced protein 44-like (IFI44L) promoter methylation has been demonstrated to serve as an effective blood diagnostic biomarker for adult-onset SLE. However, its utility as a diagnostic marker for childhood-onset SLE (cSLE) remains to be verified.

Methods: Initially, we conducted a differential analysis of gene methylation and mRNA expression patterns in cSLE whole blood samples obtained from the public GEO database to determine IFI44L gene expression and assess the methylation status at its CpG sites. Subsequently, we collected clinical whole blood samples from 49 cSLE patients and 12 healthy children, employing an HRM-qPCR-based IFI44L methylation detection technique to evaluate its diagnostic efficacy in pediatric clinical practice.

Results: A total of 26 hypomethylated, highly expressed genes in cSLE were identified by intersecting differentially expressed genes (DEGs) and differentially methylation genes (DMGs). GO enrichment analysis for these 26 genes indicated a robust association with type I IFN. Among the overlapping genes, IFI44L exhibited the most pronounced differential expression and methylation. In subsequent clinical validation experiments, IFI44L methylation was confirmed as an effective blood-based diagnostic biomarker for cSLE, achieving an AUC of 0.867, a sensitivity of 0.753, and a specificity of 1.000.

Conclusions: IFI44L methylation is a promising blood biomarker for cSLE.

Impact: IFI44L promoter methylation was reported to serve as a highly sensitive and specific diagnostic marker for adult-onset SLE. However, the diagnostic efficacy of IFI44L in childhood-onset SLE (cSLE) still remains to be confirmed. In this study, we utilized bioinformatics analysis and conducted clinical experiments to demonstrate that IFI44L methylation can also serve as a promising blood biomarker for cSLE. The findings of this study can facilitate the diagnosis of cSLE and broaden our understanding of its molecular mechanisms, with a particular focus on those related to type I interferons.