Integrative Analysis of m(6)A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis

BACKGROUND: There is growing evidence to demonstrate that the epigenetic regulation of immune characteristics, especially for N6-methyladenosine (m(6)A) RNA methylation. However, how m(6)A methylation is involved in lupus nephritis (LN) is still unclear. This study aimed to determine the role of m(6)A RNA methylation and their association with the immune microenvironment in LN. METHODS: In total, 87 glomeruli (73 LN, 14 living healthy donors), 110 tubulointerstitium (95 LN, 15 living healthy donors), and 21 kidney whole tissue samples (14 LN, 7 controls) were included in our research to evaluate the expression levels of m(6)A regulators. CIBERSORT was used to assess the abundance of infiltrating immunocytes. The m(6)A regulator gene signature for LN was identified using LASSO-logistic regression and verified with external data. Consensus clustering algorithms were used for the unsupervised cluster analysis of m(6)A modification patterns in LN. Single-sample gene-set enrichment analysis and gene set variation analysis algorithms were employed to assess the activity of immune responses and other functional pathways. Weighted gene co-expression network analysis and protein-protein interaction networks were used to identify m(6)A methylation markers. Lastly, the Nephroseq V5 tool was used to analyze the correlation between m(6)A markers and renal function. RESULTS: We found that the expression of m(6)A regulators was more significantly different in the glomeruli in LN compared with tubulointerstitium and whole kidney tissue. We established an m(6)A regulator signature, comprised of METTL3, WTAP, YTHDC2, YTHDF1, FMR1, and FTO, that can easily distinguish LN and healthy individuals. Two distinct m(6)A modification patterns based on 18 m(6)A regulators were determined, with significant differences in m(6)A regulator expression, immune microenvironment, biological functional pathways, and clinical characteristics. Activated NK cells, most immune responses, and HLA genes had strong correlations with m(6)A regulators. Seven m(6)A markers were identified and demonstrated a meaningful correlation with GFR, indicating that they are potential prognostic biomarkers. CONCLUSION: This study emphasized that m(6)A RNA methylation and the immune microenvironment are closely linked in LN. A better understanding of m(6)A modification patterns provide a basis for the development of novel therapeutic options for LN.