Integrative Analysis of MA 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 (mA) RNA methylation. However, how mA methylation is involved in lupus nephritis (LN) is still unclear. This study aimed to determine the role of mA 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 mA regulators. CIBERSORT was used to assess the abundance of infiltrating immunocytes. The mA 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 mA 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 mA methylation markers. Lastly, the Nephroseq V5 tool was used to analyze the correlation between mA markers and renal function.

Results: We found that the expression of mA regulators was more significantly different in the glomeruli in LN compared with tubulointerstitium and whole kidney tissue. We established an mA regulator signature, comprised of , , , , , and , that can easily distinguish LN and healthy individuals. Two distinct mA modification patterns based on 18 mA regulators were determined, with significant differences in mA regulator expression, immune microenvironment, biological functional pathways, and clinical characteristics. Activated NK cells, most immune responses, and HLA genes had strong correlations with mA regulators. Seven mA markers were identified and demonstrated a meaningful correlation with GFR, indicating that they are potential prognostic biomarkers.

Conclusion: This study emphasized that mA RNA methylation and the immune microenvironment are closely linked in LN. A better understanding of mA modification patterns provide a basis for the development of novel therapeutic options for LN.