LN is the most common severe complication of SLE and contributes significantly to mortality in this disease[21, 22]. Despite currently available aggressive treatments, up to 50% of patients progress to end-stage renal disease within 5 years of diagnosis [21, 22]. As previously noted, most research and therapeutic target in clinical practice focus almost exclusively on glomerular pathology. More and more researches support the importance of tubulointerstitial inflammation in determining prognosis and patient outcomes[23–25]. Thus, kidney involvement in LN can affect either glomerular or tubulointerstitial compartments as well as combinations thereof. Here we used the bioinformatics analysis to identify the hub genes in glomerular and tubulointerstitial of LN. The hub genes could be used to elucidate the pathogenesis of this disease, and might be important biomarkers and/or therapeutic targets for LN.
In our study, microarray dataset was used to identify the DEGs in both glomerular and tubulointerstitial of LN, and total of 351 DEGs (250 upregulated and 101 downregulated) and 129 DEGs (104 upregulated and 25 downregulated) were identified in glomerular and tubulointerstitial, respectively. Next, we predicted the DEGs functions based on GO and KEGG pathway enrichment analysis. Based on the PPI network, 14 DEGs, including 13 up-regulated and 1 down-regulated genes were recognized as hub genes. Unexpectedly, GO analysis of the 14 hub genes showed that all these 14 genes were enriched in the type I IFN related terms. It is well documented that the type I IFN signature is a feature of LN. Increased level of IFN in serum of patients with SLE was already described 40 years ago and were later identified as type I IFN. IFN is important in both the inflammatory process and development of damage in LN. Kidney biopsies of patients with SLE showed increased expression of IFN-inducible genes[27–30] and plasmacytoid dendritic cells accumulate in glomeruli of patients with active disease.
Type I IFN, as a central mediator in the pathogenesis of LN, may activate innate and adaptive immunity and intrarenal pathogenic mechanisms. Both direct and indirect effects of IFNs result from induction of a subset of genes, called IFN stimulated genes. The 13 up-regulated genes including IFITM1, IFIT1, IFI6, IFITM3, ISG15, MX2, XAF1, IFIT3, IFIT2, RSAD2, OAS1, IFI27, MX1, were almost IFN-inducible genes. The demonstration of a broad IFN-I–induced gene transcript signature in SLE PBMCs emerged from several laboratories[32, 33]. Recent data from epigenetic analyses of hypomethylated genome sites support activation of many genes related to type I IFN signaling in SLE patients. IFIT1 is the first gene described as a candidate gene for SLE, and may function by activating Rho proteins through interaction with Rho/Rac guanine nucleotide exchange factor. Wang J, et al. have found that IFIT3 is one of the genes that contributes to the overactive cGAS/STING signaling pathway in human SLE monocytes. IFITM1 were found to be up-regulated in platelets from SLE patients compared with healthy volunteers. The ISG15 mRNA level was higher in whole blood cell counts of SLE patients when compared with the disease control and healthy control groups and ISG15 expression correlated with lymphocytopenia in active SLE patients. The epigenome-wide DNA methylation study in lupus showed significant hypomethylation of differentially methylated sites was associated with several interferon-related genes, including MX1, IFI44L, IFIT1, RSAD2 and IRF7 in PBMCs. However, the role of IFITM3 and XAF1 in SLE/LN has not been reported. In our study, XAF1 was found to be upregulated in both glomerular and tubulointerstitial of LN based on dataset GSE32591. Additionally, the clinical manifestation detection showed the XAF1 expression could be associated with proteinuria in the lupus mouse model. Therefore, we speculated that XAF1 participants in the progression of LN, and may be a novel biomarker and therapeutic target for LN.
XAF1, a novel IFN stimulated gene, was identified in gene array studies in IFN-sensitive melanoma cells (WM9). XAF1 was discovered in a yeast two hybrid studies as a XIAP (X-linked inhibitor of apoptosis protein) -interacting protein and seemed to function as a negative regulator of members of the IAP (inhibitor of apoptosis protein) family. Overexpression of XAF1 resulted in neutralization of XIAP’s ability to inhibit cell death. It is well known that, XAF1 as a proapoptotic tumor suppressor is always inactivated in multiple human cancers. XAF1 was identified ubiquitously in all normal adult and fetal tissues but was present in very low levels in a variety of cancer cell lines[41–45]. Both IFN-α2 and IFN-β were found to induce XAF1 transcription. Type I IFN may therefore inhibit XIAP function by the induction of XAF1, and then negatively regulate the inhibitor of apoptosis. XAF1 was upregulated in whole peripheral blood from the Sjögren's syndrome patients compared with controls. However, there have been no research about the role of XAF1 in SLE/LN progression. In this study, the immunostaining results showed that XAF1 was upregulated in the kidneys of LN compared with IgAN, and the XAF1 expression was associated with pathological type and the proteinuria. According to these results, it should be concluded that up-regulation and activation of XAF1 was specifically in LN and may participant in the progresses of LN. Moreover, the expression level of XAF1 was increased in Class V + IV LN and Class V LN compared to Class IV LN, respectively. The histopathologic class of LN was depended on the nature and exposure site of the autoantigens, immune complexes and complement cause injury in different compartments of the glomerulus. Subendothelial immune complex and complement deposits cause vascular obstruction by endothelial cells (LN classes III and IV). Meanwhile, Subepithelial immune complex and complement deposits injure podocytes (membranous LN class V), which promotes massive proteinuria and podocyte injure. Therefore, we speculated that the expression of XAF1 might be induced by the subepithelial immune complex deposits in lupus kidney tissue and associated with podocyte injure. Meanwhile, the expression of XAF1 was positive correlation with quantitative 24 h proteinuria, which indicated that XAF1 may be implicated in the kidney filtration barrier and tubular reabsorption dysfunction.