Integrative Analysis of m⁶A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in...

There is growing evidence to demonstrate that the epigenetic regulation of immune characteristics, especially for N6-methyladenosine (m⁶A) RNA methylation. However, how m⁶A methylation is involved in lupus nephritis (LN) is still unclear. This study aimed to determine the role of m⁶A RNA methylation and their association with the immune microenvironment in LN.

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 m⁶A regulators. CIBERSORT was used to assess the abundance of infiltrating immunocytes. The m⁶A 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 m⁶A 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 m⁶A methylation markers. Lastly, the Nephroseq V5 tool was used to analyze the correlation between m⁶A markers and renal function.

We found that the expression of m⁶A regulators was more significantly different in the glomeruli in LN compared with tubulointerstitium and whole kidney tissue. We established an m⁶A regulator signature, comprised of METTL3, WTAP, YTHDC2, YTHDF1, FMR1, and FTO, that can easily distinguish LN and healthy individuals. Two distinct m⁶A modification patterns based on 18 m⁶A regulators were determined, with significant differences in m⁶A regulator expression, immune microenvironment, biological functional pathways, and clinical characteristics. Activated NK cells, most immune responses, and HLA genes had strong correlations with m⁶A regulators. Seven m⁶A markers were identified and demonstrated a meaningful correlation with GFR, indicating that they are potential prognostic biomarkers.

This study emphasized that m⁶A RNA methylation and the immune microenvironment are closely linked in LN. A better understanding of m⁶A modification patterns provide a basis for the development of novel therapeutic options for LN.