Background
Worldwide, immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulopathy. Reportedly, 20–50% of adults who suffered with IgAN would progress to end-stage renal diseases [
1]. Therefore, it is pivotal for IgAN patients to identify predictors of prognosis. Numerous risk factors associated with IgAN progression have been reported. A study in Chinese population identifies three risk factors, including renal impairment, hypertension as well as advanced histological involvement [
2]. Besides, another study reveals that expressions of renal leukocyte infiltrations and cytokines, such as leukocyte common antigen (LCA), CD3, CD68 and interleukin-1Beta (IL1B), are highly correlated with IgAN [
3]. Currently, biochemical and genetic data indicate that aberrantly glycosylated IgA1 play significant roles in pathogenesis of IgAN [
4‐
6]. Moreover, alteration on the glycan structure of IgA1 causes the deposition of nephritogenic immune complexes, which induce resident mesangial cells proliferation and extracellular matrix proteins expression, and subsequently lead to the loss of glomerular function [
7]. Based on the pathogenesis, several biomarkers have been identified, such as levels of urinary secretory (sIgA) [
8], serum galactose-deficient immunoglobulin A1 (Gd-IgA1) [
9] and the tandem repeats polymorphism of
MUC20 gene [
10]. However, cellular events involved in the IgAN pathogenesis are unclear.
Recently, it is found that abnormality of IgAN disease is related to IgA immune system and peripheral blood leucocytes, especially the peripheral blood mononuclear cells [
11,
12]. Monocytes, a kind of the phagocytes that formed in bone marrow, can differentiate into macrophages and dendritic cells (DCs) in peripheral tissues. Monocytes have a crucial part in immune response and may contribute to the pathogenesis of IgAN [
13]. Thus, a guideline for target therapy of IgAN will be obtained through identifying gene alterations in monocytes of IgAN patients. Moreover, Cox et al. uncover that the altered genes in IgAN monocytes are mainly associated with apoptotic pathway and mitochondrial dysfunction [
13]. In particular, the expression of NADH: ubiquinone oxidoreductase core subunit S3 (NDUFS3) and TNF receptor superfamily member 1A (TNFRSF1A) proteins are upregulated, thus verifying the altered mitochondrial respiratory system and death receptor homeostasis. Additionally, the TNF expression in monocytes of IgAN patients are reduced compared with those in healthy blood donors (HBDs) [
13]. However, other critical genes and their interaction have not been investigated.
In the present study, we re-analyzed GSE58539 profiling using a more comprehensive bioinformatics. After identifying the differentially expressed genes (DEGs) in monocytes between IgAN patients and HBDs, functional enrichment and protein-protein interactions (PPIs) network analyses were carried out, followed by key nodes prediction of the network through four network centrality analyses. Notably, in order to reveal potential interactions of DEGs that involved in similar functions and pathways, gene functional interaction (FI) network and the module network analyses were performed based on gene expressions of each sample. The study aimed to further uncover the pathogenesis and progression of IgAN, and thus provide potential molecular biomarkers for the diagnosis and targeting therapy of IgAN.
Discussion
In the present study, a total of 72 crucial nodes in the PPI network were identified via re-analyzing the dataset GSE58539, which could well distinguish the IgAN and healthy samples. Among which, genes such as IL6, TNF, IL1B, PRKACA, and CCL20 were closely related to the following pathways: NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, hematopoietic cell lineage, apoptosis and Toll-like receptor signaling pathway. Moreover, 12 genes in the FI network belonged to the 72 identified key nodes, such as CCL20, HDAC10, FPR2 and PRKACA. Besides, the 12 genes were also the key genes in 4 module networks correlating with pathways of integration of energy metabolism (module a), GPCR-related pathways (module b), RNA binding-related pathways (module c), alcoholism and chromatin modifying enzymes (module d).
The cytokine encoded by
IL6 has great roles in inflammation and regulation of immune response [
29]. Toll-like receptors (TLRs) are major factors that initiate the immune reaction. Most TLRs promote immune response (including innate and adaptive) via inducing expression of proinflammatory cytokines [
30]. Increased TLRs, such as TLR-4, has been detected in circulating monocytes of patients with IgAN [
31]. Expression of IL6 protein is also increased in mouse proximal tubular epithelial cells, accompanying by the upregulation of
TLR4 mRNA [
32]. IL1B, encoded by
IL1B gene, is a member of interleukin 1 cytokine family and crucial for the regulation of inflammatory response [
33]. In response to the external infections, gene expressions of the proinflammatory cytokines (e. g.
IL1A,
IL1B and
IL6) are always upregulated simultaneously [
34,
35]. In particular,
IL1B is implicated in the
TLR-4 induced immune response in chronic pain [
36]. In our study,
IL6 and
IL1B were both downregulated and enriched in TLR signaling pathway. These results suggested that
IL6 and
IL1B might be co-regulated in TLR signaling pathway and contribute to the abnormality of the immune response in monocytes of IgAN patients.
TNF is a multifunctional proinflammatory cytokine. Reportedly, TNF expression is dramatically increased in
Mycoplasma penetrans-infected IgAN mice model, and the protein is proposed to involve in the induction of renal damage in IgAN [
37]. Moreover, levels of serum TNF receptors are also elevated in IgAN patients compared with healthy control [
38]. However, Cox et al. uncover that
TNF expression is obviously reduced in monocytes of IgAN patients, compared with those of HBDs [
13]. The finding indicates the downregulated TNF may lead to the monocytes apoptosis. Moreover, the inhibition of TNF-α is proposed as a causative factor of IgAN [
39]. Therefore, it might be speculated that the apoptosis of monocytes induced by downregulation of TNF contribute to IgAN progression.
CCL20 is a small cytokine that also involves in immune regulation and inflammation [
40]. Combination of CCL20 with CCR6 (the CCL20 receptor) cause the recruitment of leukocyte subsets, which finally promote immune-mediated kidney damage [
41]. Additionally,
CCL20 is one of the chemokines that take part in the host response to pathogens invasions by activating inflammatory cells, and it has the similar effects on monocytes [
42]. Therefore, the downregulated
CCL20 in monocytes of IgAN patients might cause alteration in immune response, and thereby influence the IgAN development.
Three novel genes, protein kinase, CAMP-dependent, catalytic, alpha (
PRKACA), formyl peptide receptor 2 (
FPR2) and histone deacetylase 10 (
HDAC10) were firstly predicted in monocytes of IgAN. PRKACA protein encoded by
PRKACA gene is one subunit of protein kinase A that participates in apoptosis. At present,
PRKACA amplification is served as a method for identifying genetic defect correlated with Cushing’s syndrome [
43]. Somatic mutations of
PRKACA have been detected in adenomas of the adrenal cortex [
44]. Moreover,
PRKACA mediates apoptosis-related signaling pathways in many cancer diseases, such as breast cancer and follicular thyroid cancer cells [
45,
46]. In the present study,
PRKACA was up-regulated and significantly enriched in apoptosis pathway, suggesting it might exert its function in monocytes via regulating apoptosis during IgAN progression.
FPR2 is known to activate the G-protein coupled receptor and N-formyl peptide receptor.
FPR2 is found in adipose tissues as a receptor for the pro-resolving mediators [
47], which contribute to the restoration of in adipose inflammation and treatment of obesity-related glomerulopathy [
48].
HDAC10, containing two catalytic sites, is highly expressed in numerous human tissues such as kidney [
49]. In lung cancer, decreased
HDAC10 is associated with the advanced stage and adverse outcome [
50]. However, there are rare reports on the relationship of IgAN and
HDAC10. In the current study,
FPR2 and
HDAC10 were hub up-regulated genes in both PPI network and FI network, implying they might co-function in monocytes of IgAN patients. One limitation of this study is the lack of expression validation. However, we will do more experiments to verify our conclusions once we collect the samples in the future.