Supplementary Material for: Combined genetic association and differed expression analysis of UBE2L3 uncovers a genetic regulatory role of (immuno) proteasome in IgA Nephropathy

Introduction: IgA nephropathy (IgAN) is a leading cause of end-stage renal disease. The exact pathogenesis of IgAN is not well defined, but some genetic studies have led to a novel discovery that the (immuno) proteasome probably plays an important role in IgAN.
Methods: We firstly analyzed the association of variants in the UBE2L3 region with susceptibility to IgA nephropathy in 3495 patients and 9101 controls, and then analyzed the association between lead variant and clinical phenotypes in 1803 patients with regular follow-up data. The blood mRNA levels of members of the ubiquitin-proteasome system including UBE2L3 were analyzed in peripheral blood mononuclear cells (PBMCs) from 53 patients and 28 healthy controls. The associations between UBE2L3 and the expression levels of genes involved in Gd-IgA1 production were also explored.
Results: The rs131654 showed the most significant association signal in UBE2L3 region (OR 1.10, 95% CI 1.04-1.16, P = 2.29×10-3), whose genotypes were also associated with the levels of Gd-IgA1 (P = 0.04). The rs131654 was observed to exert cis-eQTL effects on UBE2L3 in various tissues and cell types, particularly in immune-cell types in multiple databases. The UBE2L3, LUBAC, and proteasome subunits were highly expressed in patients compared with healthy controls. High expression levels of UBE2L3 were not only associated with higher proteinuria (r = 0.34, P = 0.01) and lower eGFR (r = -0.28, P = 0.04), also positively correlated with the gene expression of LUBAC and other proteasome subunits. Additionally, mRNA expression levels of UBE2L3 were also positively correlated with IL-6 and RELA, but negatively correlated with the expression levels of the key enzyme in the process of glycosylation including C1GALT1 and C1GALT1C1.
Conclusion: In conclusion, by combined genetic association and differed expression analysis of UBE2L3, our data support a role of genetically conferred dysregulation of the (immuno) proteasome in regulating galactose-deficient IgA1 in the development of IgAN.