SLE is one of the most common systemic autoimmune diseases that seriously endangers human health. There are many factors causing the pathogenesis of SLE, among which the abnormal expression of important genes may contribute to lupus pathogenesis by participating in critical pathways, including immune complex processing, type I interferon producing, toll-like receptor signaling, and so on [37]. However, the accurate mechanism of SLE caused these microenvironmental factors has not been completely elucidated, so more attention should be paid to the detection and evaluation of the expression level of lupus - related genes in lupus researches. In present study, we are committed to discover possible SLE - causing molecules, and 257 DEGs (30 up-regulated genes and 227 down-regulated genes) are screened out from GSE50772 expression dataset. They certainly has laid a foundation for our subsequent analyses, and that may be able to illuminate the initiation and progression of SLE.
Considering that multiple organs or systems involvement caused by autoantibodies is the feature of SLE, we performed tissue - specific expression analysis on DEGs. As revealed by the result, the most highly enriched system is the hematologic/immune system, which is in line with the pathogenesis and clinical manifestations of SLE, and this seems to explain the underlying molecular mechanisms of a self-aimed immune response in SLE patients. Besides, skin/skeletal muscle system, respiratory system, digestive system, urinary and reproductive systems are also enriched by DEGs. Some studies have also suggested that ANXA3 [38, 39], TCN1 [40], C1QC [41], AREG [42] and COL17A1 [43] are associated with respiratory injury. ALOX15B [44] may be related to kidney diseases as reported in the literature. ADM [45] and S100P [46] possibly play important roles in lesions of the reproductive system. And changes in expression of OLFM4 [47], CYP4F3 [48], HP [49], ORM1 [50], ANG [51], LRG1 [52], C15orf48 [53], KRT23 [54] and ARG1 [55] are involved with digestive system diseases. Even some of them have been thought to be classic markers of a particular tissue injury. While whether those tissue - specific DEGs above-mentioned are essential for the development of complications of SLE remains inconclusive, and we postulate that the abnormal expression of those genes probably can indicate organ involvement in SLE patients. However, in our results, there are other relatively common organs and tissues that are not significantly enriched by DEGs, such as the central nervous system, cardiovascular and circulatory systems. Limited gene expression microarray data with insufficient samples may be a by-no-means negligible cause.
In order to understand disease machinery more deeply and to visualize the overview of the functional connections between all DEGs, we constructed PPI networks, the vital tools for analysis by identifying subnetworks or modules that display specific topology and/or functional characteristics [56]. Afterwards, on the basis of DEGs’ PPI networks, the top 20 hub genes (CXCL1, CAMP, HP, PTX3, ARG1, ELANE, LCN2, RETN, MMP8, SLPI, PGLYRP1, LTF, OLFM4, ORM1, TCN1, LRG1, CRISP3, CHI3L1, MMP9 and DEFA4) were selected. According to cluster analysis results on them, it is obvious that most hub genes are up-expressed in SLE patients, while relatively low-expressed in normal subjects, which highlights the importance and representativeness of these hub genes in SLE disease. And further functional enrichment analysis on them manifests that immune system processes are dominant. Furthermore, 13 hub genes verified by Immport database are thought to be immune-related genes as expected, namely CXCL1, CAMP, PTX3, ARG1, ELANE, LCN2, RETN, SLPI, PGLYRP1, LTF, ORM1, MMP9 and DEFA4. The result exactly supports the idea that these 20 hub genes probably play essential roles in immune-related pathways which can trigger autoimmune dysfunction in patients, and resulting in the pathogenesis and development of SLE.
In prior studies on 20 hub genes mentioned above, the aberrant expression levels of 15 genes have been investigated that they may have various and crucial influences for different processes of SLE development. Given the roles of five novel genes in SLE as shown in Table 4, several novel genes, including ORM1, SLPI, OLFM4, TCN1 and CRISP3 may also have diagnostic value in the condition. ORM1 (orosomucoid 1) is an acute phase plasma protein known to activate NFκB, p38 and JNK pathways in macrophages, and it has been reported in rheumatoid arthritis (RA) [57], sarcoidosis and other immune diseases [58]. In experimental autoimmune encephalomyelitis, SLPI (secretory leukocyte peptidase inhibitor) exerted potent pro-inflammatory actions by regulating T cell activity, a process that might benefit the patient [59]. OLFM4(olfactomedin 4) could mediate the autoimmune inflammatory responses of generalized pustular psoriasis, a severe inflammatory skin disease [60]. Low expression of TCNI (transcobalamin I) involved in innate immunity might be partly responsible for the pathogenesis of IgG4-related disease, due to impairments in the innate immune system [61]. Since CRISP3 (cysteine-rich secretory protein 3) was detected to be significantly elevated in RA, the researchers hypothesized that it was implicated in the development of RA [62]. In addition, using the GeneCards database, three novel hub genes (ORM1, SLPI, and TCN1) were confirmed to be potentially involved in the pathogenesis of SLE. Almost all of these genes, either high or low expression, are associated in the development of immune diseases. Consequently, chances are that the five hub genes play pivotal roles in the molecular mechanism of SLE pathogenesis, and we reasonably confer that these novel hub genes may be used as biomarkers to help improve the diagnostic rate of SLE and to provide valuable information for the evaluation of organ or system involvement.It is well known that miRNAs can interfere with the transcription and regulate gene expression [63]. Altered miRNA expression has been regarded as another important factor to the pathogenesis of immune-related diseases, such as SLE. And because of the nature of stability of miRNA, measuring effective miRNA levels may be conducive to disease detectionin [64]. In immune cells, aberrant miRNAs can disturb immune homeostasis, produce massive autoantibodies and induce autoimmunity [65]. Following GO terms, we performed miRNA mining and interaction network analysis. MiRNA hsa-let-7e-5p targeting at OLR1(oxidized low- density lipoprotein receptor 1) and IRS2 ( insulin receptor substrate 2) was identified. The miRNA let-7e is a member of the let-7 family, and it plays a key role in inhibiting or promoting inflammatory response by regulating cytokine expression in various inflammatory and autoimmune diseases [66]. In an animal experiment, down-regulating the expression of hsa-let-7e-5p and other two miRNAs, 17β-estradiol could amplify the activation of IFN-α signaling in B cells to contribute to the sex bias in SLE [67–69]. Moreover, as target genes of has-let-7e-5p in this study, OLR1 and IRS2 are down-regulated in SLE patients compared with non-SLE subjects. When it comes to biological processes, OLR1 is associated with inflammatory response, while ISR2 is related to positive regulation of cell proliferation. Regarding molecular function, OLR1 and IRS2 both participate in exerting protein binding. Recent studies show that OLR1 is an inflammation-induced receptor. Together with a host of other reactions, an increase in OLR1 can trigger the formation of neutrophil extracellular traps, which can promote systemic inflammation, vascular damage and lung injury. Elevated expression level of OLR1 has been recognized as a possible indicator of high risk of SLE - related cardiovascular disease [70, 71]. Targeted by MiR-203a, IRS2 regulates the proliferation and apoptosis of pancreatic β cell [72], which implies the expression of IRS2 is closely related to type 1 diabetes mellitus (T1DM), an autoimmune disease. These results rend us to speculate that has-let-7e-5p may be a potential molecule to induce and deteriorate the SLE even though there have been rare relevant studies are published on this subject. Thus, we propose that hsa-let-7e-5p probably acts as another novel latent biomarker of SLE, and we hope it could provide new insights into molecular mechanism underlying the development and progression SLE.
Additionally, since the GSE50772 is a public dataset, patient consent or ethics committee approval is not required, but the information on individuals’ age, gender and health status, as well as medication use, is absent, which appears to be an underlying limitation.