Abstract
Background
Kawasaki disease (KD) is a systemic vasculitis that predominantly occurs in children, but the pathogenesis of KD remains unclear. Here, we explored key genes and underlying mechanisms potentially involved in KD using bioinformatic analyses.
Material/Methods
The shared differentially expressed genes (DEGs) in KD compared to control samples were identified using the microarray data from the Gene Expression Omnibus Series (GSE) 18606, GSE68004, and GSE73461. Analyses of the functional annotation, protein-protein interaction (PPI) network, microRNA-target DEGs regulatory network, and immune cell infiltration were performed. The expression of hub genes before and after intravenous immunoglobulin (IVIG) treatment in KD was further verified using GSE16797.
Results
A total of 195 shared DEGs (164 upregulated and 31 downregulated genes) were identified between KD and healthy controls. These shared DEGs were mainly enriched in immune and inflammatory responses. Ten upregulated hub genes (ITGAX, SPI1, LILRB2, MMP9, S100A12, C3AR1, RETN, MAPK14, TLR5, MYD88) and the most significant module were identified in the PPI network. There were 309 regulatory relationships detected within 70 predicted microRNAs and 193 target DEGs. The immune cell infiltration analysis showed that monocytes, neutrophils, activated mast cells, and activated natural killer cells had relatively high proportions and were significantly more infiltrated in KD samples. Six hub genes of ITGAX, LILRB2, C3AR1, MAPK14, TLR5, and MYD88 were markedly downregulated after IVIG treatment for KD.
Conclusions
Our study identified the candidate genes and associated molecules that may be related to the KD process, and provided new insights into potential mechanisms and therapeutic targets for KD.
Keywords: Databases, Genetic; Diagnosis; Mucocutaneous Lymph Node Syndrome
Background
Kawasaki disease (KD), also called mucocutaneous lymph node syndrome, is an acute, self-limited febrile illness of unknown causes that predominantly affects children below 5 years of age [1]. It is a multisystem disorder characterized by acute vasculitis in small and medium-sized arteries, especially in coronary arteries [2]. This disease is more markedly prevalent in children in Japan (annual incidence 264.8/100 000 in 2012), whereas the incidence was estimated to be 19/100 000 in the USA and 8.4/100 000 in the UK in children below 5 years of age [3,4]. As reported, the incidence of KD is 2.5 times higher in Asians and Pacific Islanders and 1.5 times higher in Blacks compared to Whites [4]. The course of KD needs more attention since nearly 25% of people with KD, if left untreated, will experience vascular complications such as coronary artery aneurysm (CAA), thromboembolism, stenosis, or even sudden death [5]. KD has been reported as the leading cause of acquired heart diseases in children in developed countries [5]. Although timely treatment with intravenous immunoglobulin (IVIG) reduces the risk of CAA, some children who do not respond to IVIG are still at considerable risks of developing coronary artery damage [6]. In addition, the lack of specific diagnostic tests and biomarkers for KD make early diagnosis and treatment challenging. Therefore, KD remains an important focus of research and it is extremely important to perform detailed exploration of the etiopathogenesis of KD and to further improve healthcare for this population.
The etiology of KD has been studied extensively, but the exact pathogenic factors or triggering agents for KD are still unidentified, and the underlying mechanisms for initiation and progression of KD remain largely unknown. Recently, it has been suggested that KD involves the complex interplay of infectious triggers and genetic susceptibility followed by an abnormal immune response [5]. A large number of candidate pathogens has been tested and discarded. Some case reports linked KD with viral agents; however, no specific infectious agent has been shown to be consistently and causally associated with KD [6]. Genetic factors also increase susceptibility to KD, as suggested by differences in incidence of KD among races [6]. Moreover, KD occurs as a consequence of a dysregulated immune system, which involves the activation and infiltration of the arterial wall by cells of both the innate and adaptive immune systems [7]. Recent studies have found that several genes are closely associated with the KD process [8–10], indicating that genetic alterations may play a critical role in the development of KD.
In this study, we identified the shared differentially expressed genes (DEGs) and underlying pathways in acute KD compared to healthy control samples among 3 GSE datasets by using an integrated bioinformatic analysis. Base on the shared DEGs, analyses of functional annotation, protein-protein interaction (PPI) network, microRNA (miRNA)-DEGs network construction, and immune cell infiltration were performed. We also verified the hub gene expression in KD before and after IVIG treatment. With these analyses, we hope to identify biomarkers for early KD detection and provide potential therapeutic targets for KD.
Material and Methods
Microarray Data Resources
The microarray data of GSE18606, GSE68004, and GSE73461 comparing gene expression in whole-blood samples between acute KD and healthy controls were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) to screen out DEGs involved in KD. Another GSE16797 dataset was also obtained from the GEO database and used to validate the hub gene expression before and after IVIG treatment in acute KD patients. Detailed information on these datasets is shown in Table 1. Study flowchart is shown in Figure 1A.
Table 1.
Gene expression datasets used in this study.
| Dataset | Year | Country | Platform | Samples |
|---|---|---|---|---|
| GSE18606 | 2009 | USA | GPL 6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F | Whole blood from 20 acute KD (before treatment) and 9 healthy controls |
| GSE68004 | 2012 | USA | GPL570 Illumina HumanHT-12 V4.0 expression beadchip | Whole blood from 76 acute complete KD and 37 healthy controls |
| GSE73461 | 2018 | UK | GPL10558 Illumina HumanHT-12 V4.0 expression beadchip | Whole blood from 78 acute KD and 55 healthy controls |
| GSE16797 | 2010 | Japan | GPL570 Affymetrix Human Genome U133 Plus 2.0 Array | Whole blood from IVIG-responsive KDs, 6 pre-IVIG and 6 post-IVIG treatment |
Figure 1.
Study flowchart and Venn diagram. (A) The GSE datasets and bioinformatic analyses used in this study. (B) Venn diagram showing the 195 shared DEGs in GSE18606, GSE68004, and GSE73461.
Identification of DEGs
Raw gene expression data were read and processed using affy package (version 1.50.0) in R software (version 4.0.1) [11]. Gene probes were annotated using an annotation profile provided by the platform, and unmatched probes were discarded. When multiple probes matched one gene symbol, the average values of probes were calculated as the final expression of the gene. DEGs between KD and control samples in each GSE dataset were screened out using Linear Models for Microarray (Limma) package (Version 3.30.3) in R, and the threshold was defined as |log2(foldchange)| >1 and P<0.05. DEGs were labeled as upregulated and downregulated. The significance of DEGs in each dataset was exhibited in a volcano plot using ggplot2 in R. To visualize the shared DEGs among the 3 datasets, the online tool Bioinformatics & Evolutionary Genomics (http://bioinformatics.psb.ugent.be/webtools/Venn/) was used to draw Venn diagrams. Further, the differences in shared DEGs are shown in heatmaps created using pheatmap in R.
Functional Annotation
Biological functions of the shared DEGs were explored with the Gene Ontology (GO) [12] and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses [13] using the online tool Database for Annotation, Visualization, and integrated discovery (DAVID) (Version 6.8; https://david.ncifcrf.gov/home.jsp) [14]. The GO terms included biological process (BP), cellular component (CC), and molecular function (MF). Significant GO and KEGG pathways with the thresholds of count ≥2 and P<0.05 were selected for further analysis.
Protein–Protein Interaction (PPI) Network
The PPI network among shared DEGs was constructed using the Search tool for the retrieval of interacting genes/proteins (STRING) database (Version 11.0; www.string-db.org) [15], and a PPI score (medium confidence) ≥0.4 was defined as the cutoff value. The network was then visualized using Cytoscape (Version 3.7.1; www.cytoscape.org) [16]. The degree of each node, considered as the significance of DEGs-encoded protein in the network, was calculated using the cytoHubba plugin in Cytoscape [17]. DEGs with the top 10 highest degrees were selected as hub genes. Moreover, the Molecular Complex Detection (MCODE) plugin in Cytoscape was used to identify significant modules in the network [18], and the parameters were set as follows: Degree Cutoff=2, Node Score Cutoff=0.2, K-Core=2, Max. Depth=100. The most common and largest module was defined as MCODE score >5.
Construction of miRNA-target DEGs Regulatory Networks
The potential miRNAs of shared DEGs were predicted based on miRTarBase using Enrichr (http://amp.pharm.mssm.edu/Enrichr/) [19] with the threshold of P<0.05. A regulatory network between predicted miRNA and target DEGs was constructed using Cytoscape.
Immune Cell Infiltration Analysis
CIBERSORT is a recently developed algorithm used for sensitive and specific quantification of the relative levels of 22 human immune cell phenotypes within a complex gene expression mixture (https://cibersort.stanford.edu) [20]. Normalized expression profiles of shared DEGs in all the KD and control samples among the 3 datasets were extracted and used to calculate the immune infiltration scores. The samples were screened according to P<0.05, and the percentage of each type of immune cells in samples (immune infiltration score) was calculated using the CIBERSORT algorithm. The deviations of immune infiltration in each sample are shown in a stacked bar chart, while the differences in immune infiltration levels of each immune cell type between control and KD groups are shown in a violin graph generated via R software.
Validation of Hub Gene Expression in KD Before and After IVIG Treatment
To investigate if key genes would be differently expressed before and after IVIG treatment in KD, we validated the hub gene expression among pre- and post-IVIG samples using another GSE16797 dataset. Box charts were plotted using GraphPad prism (Version 8.0.2).
Results
Identification of DEGs in KD
A total of 195 shared DEGs were identified in the whole blood of acute KD pediatric patients (before treatment) compared to control samples (Figure 1B), including 164 upregulated and 31 downregulated genes. The foldchange and significance of DEGs in each dataset are shown in Figure 2. The heatmap of the shared DEGs indicated that these genes could easily distinguish KD from controls (Figure 3), suggesting that they may play a critical role in the development of KD.
Figure 2.
Volcano plots showing the DEGs in each GSE dataset. The x-axis was log2 (foldchange) and y-axis was −log10 (P value) in volcano plots. The red dots indicate upregulated genes, and green dots indicate downregulated genes.
Figure 3.
Heatmaps of the shared DEGs in the 3 datasets. The expression of the 195 shared DEGs among KD and controls in each dataset are shown via heatmap. The x-axis represents different samples, and y-axis represents different genes. The red boxes indicate upregulated genes, and blue boxes indicate downregulated genes.
A detailed list of shared DEGs is shown in Supplementary Table 1.
Functional Enrichment Analyses of Shared DEGs
The GO and KEGG enrichment analyses revealed that the BP of shared DEGs were mainly enriched in immune and inflammatory responses, and cell surface receptor signaling pathway; the CC were mainly existed in extracellular exosome and plasma membrane; and the MF were mostly enriched in receptor activity (Figure 4A–4C). Meanwhile, the significantly enriched KEGG pathways of shared DEGs included osteoclast differentiation, hematopoietic cell lineage, tumor necrosis factor signaling pathway, and immune-related diseases (Figure 4D). The top 10 results of GO-BP and KEGG enrichment analyses are shown in Supplementary Tables 2 and 3.
Figure 4.
GO and KEGG enrichment analyses of shared DEGs. GO enrichment analyses of top 10 most significantly enriched biological process (A), cellular component (B), and molecular function (C) of the shared DEGs, and the top 10 enriched KEGG pathways of the shared DEGs (D).
PPI Network Analysis
A total of 157 nodes and 555 interactional pairs were included in the PPI network (Figure 5A). After calculating degrees via cytoHubba, DEGs with the top 10 highest degrees were selected as hub genes, including ITGAX, SPI1, LILRB2, MMP9, S100A12, C3AR1, RETN, MAPK14, TLR5, and MYD88. They were all significantly upregulated in KD and their functions are summarized in Table 2. Further, the most significant module in the PPI network with 23 nodes and 126 edges was identified (MCODE score=11.4), and the hub genes of ITGAX, RETN, and LILRB2 were also included (Figure 5B).
Figure 5.
PPI network and the most significant module. Upregulated genes are marked in red and downregulated genes are marked in blue in the PPI network (A). The most significant module in PPI network was also identified (B).
Table 2.
The hub genes in Kawasaki disease.
| Hub genes | Full name | Degrees in PPI | Functions |
|---|---|---|---|
| ITGAX | Integrin alpha-X | 34 | A receptor for fibrinogen. Mediates cell-cell interaction during inflammatory responses |
| SPI1 | Spi-1 proto-oncogene | 29 | A transcriptional activator specifically involved in the differentiation or activation of macrophages or B cells |
| LILRB2 | Leukocyte immunoglobulin-like receptor subfamily B member 2 | 27 | Receptor for class I MHC antigens. Recognizes a broad spectrum of HLA. Involved in immune response and the development of tolerance |
| MMP9 | Matrix metalloproteinase-9 | 24 | Mediates local proteolysis of extracellular matrix. Plays a role in leukocyte migration, chemotaxis, and inflammation and contributes to unstable atherosclerotic plaques |
| S100A12 | S100 calcium-binding protein A12 | 22 | A calcium-, zinc-, and copper-binding protein that regulates inflammatory processes and immune response. |
| C3AR1 | Complement component 3a receptor 1 | 20 | Receptor for anaphylatoxin C3a. Mediates chemotaxis, granule enzyme release and superoxide anion production |
| RETN | Resistin | 20 | A kind of adipokine that links obesity to diabetes and promotes chemotaxis, inflammation, and atherosclerosis |
| MAPK14 | Mitogen-activated protein kinase 14 | 19 | One of the 4 p38 MAPKs. Plays a key role in cellular responses evoked by proinflammatory cytokines and leads to direct activation of transcription factors |
| TLR5 | Toll-like receptor 5 | 18 | Pattern recognition receptor on cell surface. Participates in activation of innate immunity and inflammation |
| MYD88 | Myeloid differentiation primary response protein | 17 | Adapter protein involved in the Toll-like receptor and IL-1 receptor signaling pathway in innate immune response |
miRNA-target DEGs Regulatory Network Analysis
In the miRNA-target DEGs network, there were 309 regulatory relationships detected within 263 nodes, including 70 predicted miRNAs and 193 DEGs (Figure 6). The top 3 most significant miRNAs were hsa-miR-34a-5p (P=1.08E-05), has-miR-122-3p (P=7.82E-04) and has-miR-548ah-5p (P=0.001), respectively.
Figure 6.
Predicted miRNA-target DEGs regulatory network. Regulatory network between predicted miRNA and target DEGs. The red dots indicate DEGs and yellow dots indicate miRNAs. The blue lines indicate miRNA-DEGs pairs.
Immune Cell Infiltration Analysis
The differences in immune infiltration between the KD and control samples were analyzed by the CIBERSORT algorithm. As a result, the 22 subtypes of immune cells were both detected in KD and controls, and the immunocyte composition of the entire cohort is summarized via a box plot in Figure 7A. The violin plot indicated that 17 types of immune cells were differentially infiltrated between KD and controls (Figure 7B). Specifically, plasma cells, γδ T cells, activated natural killer (NK) cells, monocytes, resting dendritic cells (DCs), resting and activated mast cells, and neutrophils had higher infiltration in KD samples, while naïve B cells, naïve CD4 T cells, resting and activated memory CD4 T cells, resting NK cells, M1 and M2 macrophages, activated DCs, and eosinophils had relatively lower infiltration in KD than that in the control group. Of note, the monocytes, neutrophils, activated mast cells, and activated NK cells had relatively high proportions and were significantly more infiltrated in KD samples, suggesting that they may play a central role in the pathogenesis of acute KD.
Figure 7.
Immune cell infiltration analysis of the shared DEGs showing the infiltration levels of 22 immune cell subtypes in KD and controls. (A) Stacked bar chart showing deviations of immune infiltration in each control or KD sample among the 3 datasets. (B) Violin plot showing differences in proportions of each immune cell type between control and KD groups. * P<0.05, ** P<0.01, *** P<0.001, ns: not significant.
Validation of Hub Gene Expression in KD Before and After IVIG Treatment
We focused on the effect of IVIG of hub gene expression in KD patients. The results showed that, out of the 10 hub genes, 6 genes were differentially expressed among pre- and post-IVIG KD samples, including ITGAX, LILRB2, C3AR1, MAPK14, TLR5, and MYD88. These genes were originally upregulated in acute KD as compared with control, while after IVIG infusion, they were markedly downregulated and back to normal levels (Figure 8). This indicated that these 6 hub genes were closely related to immune and inflammatory responses in KD and might be potential therapeutic targets for IVIG treatment.
Figure 8.
Validation of the hub gene expression changes in KD before and after IVIG treatment. Expression of the identified 10 hub genes in pre- and post-IVIG treatment KD were compared using GSE16797, and 6 genes were significantly downregulated after IVIG. (A) ITGAX. (B) LILRB2. (C) C3AR1. (D) MAPK14. (E) TLR5. (F) MYD88. The x-axis shows different groups and y-axis shows a log2 transformation of gene expression. * P<0.05, ** P<0.01.
Discussion
It is reported that not only infectious stimulus and immune responses are responsible for the occurrence of KD, but that genetic susceptibility also plays an essential role [2]. In Japan, there is a 10-fold higher risk of KD in siblings of patients with KD than in the general population and a 2-fold higher risk in those with parental history of KD [21]. These differences in the family and races suggest that genetic factors might be involved in the pathogenesis of KD. Previous studies have found that single-nucleotide polymorphisms (SNPs) in multiple genes are associated with KD and disease outcome (such as aneurysm formation and response to IVIG), including 1,4,5-triphosphate 3-kinase (ITPKC), caspase-3 (CASP3), B lymphocyte kinase (BLK), CD40, and human leukocyte antigen (HLA) [8–10]. Genetic variants in transforming growth factor (TGF)-β pathways also contributes to increased risk of aneurysm formation in European patients [22]. In addition to polymorphisms and mutations, altered gene expression is also a promoter in KD [23]; however, mechanisms linking the genetic alterations with KD progression are still poorly elucidated and require more investigation.
With the aid of the large open-sourced GEO database, bioinformatic analyses based on gene microarray profiles have been used to reveal the key hub genes and potential therapeutic targets of multiple diseases. However, related investigations in KD based on gene and molecular levels are still lacking. Herein, we obtained the genome-wide expression data in whole-blood samples of patients with acute KD and in controls using 3 different GSE datasets, and performed an integrated analysis. As a result, 195 shared DEGs were screened out and they were mainly enriched in immune and inflammatory responses. The identified 10 hub genes were all significantly upregulated in KD. Some of them have been found to be closely related to KD, while the function of the other genes in KD warrants further research. We also detected potential miRNAs involved in KD, analyzed the immune cell infiltration in KD samples, and validated the hub gene expression after IVIG treatment. All these data may help us better understand the etiology of KD.
The 10 hub genes (ITGAX, SPI1, LILRB2, MMP9, S100A12, C3AR1, RETN, MAPK14, TLR, MYD88) are closely related to immunomodulation and inflammation. Of these, integrin alpha-X (ITGAX) is a receptor for fibrinogen and mediates cell-cell interaction during inflammation. Spi-1 proto-oncogene (SPI1) is a transcriptional activator mainly involved in the differentiation, activation, and migration of macrophages or B cells. Leukocyte immunoglobulin-like receptor subfamily B member 2 (LILRB2) is the receptor for class I MHC antigens, which recognizes a broad spectrum of HLA and can be involved in immune response. Matrix metalloproteinase-9 (MMP9) is a member of the MMPs family that degrades extracellular matrix components and plays a key role in both inflammation and tissue remodeling processes. S100 calcium-binding protein A12 (S100A12) belongs to the S100 protein family and regulates a variety of inflammatory responses. Complement component 3a receptor 1 (C3AR1) is the receptor for chemotactic anaphylatoxin C3a. Resistin (RETN) is an adipokine that links obesity to diabetes and promotes inflammation and atherogenesis. Mitogen-activated protein kinase 14 (MAPK14) mediates cellular responses evoked by proinflammatory cytokines and causes direct activation of transcription factors. Toll-like receptor 5 (TLR5) is the pattern recognition receptor on the cell surface that mediates innate immunity and inflammation. Myeloid differentiation primary response protein (MYD) is the adapter protein involved in Toll-like receptor and interleukin (IL)-1 receptor signaling pathways in immune responses. We assumed that these hub genes may play a key role in the pathogenesis of KD; however, this hypothesis needs to be verified in future studies. Still, some pilot studies have explored the association of MMP9, S100A12, C3, RETN, and TLR5 with KD progression.
Increased expression and activity of a diverse set of MMPs have been demonstrated in acute KD [24]. The expression of MMP3 and MMP9, both known to mediate vascular smooth muscle cell (VSMC) migration and neointimal formation, are increased in patients with KD, and the circulating levels of these MMPs are correlated with the formation of CAAs in KD [25–27]. MMP9 also was reported to lead to elastin breakdown in a mouse model of KD [28]. Among the S100 protein family, serum concentrations of S100A12 are substantially higher in acute KD and decline after IVIG treatment [29–31], while in patients with giant CAAs, plasma S100A12 levels remain elevated, highlighting its potential utility as a biomarker to monitor long-term persistence of arteritis [30]. S100A12 also promotes vasculitis by stimulating monocytes to produce interleukin (IL)-1β, which directly induces coronary artery endothelial cell dysfunction [31]. Post-mortem studies have revealed that 73% of KD patients have acute kidney injury involving glomerulonephritis with deposition of IgA and complement C3 [32]. The deposition of C3 can enhance the damage of small and medium-sized vessels, particularly the coronary arteries [33]. C3a, along with its receptor, C3aR, can also induce a variety of vascular inflammation and remodeling [34]. As for resistin, it is reported that the circulating resistin levels are significantly higher in patients with KD and are correlated with the occurrence of CAAs [35]. Resistin also enhances inflammation by cross-talking with the nuclear factor-κB in a mouse coronary arteritis model [36]. The TLR5 is a key member of TLRs, which may stimulate the immunopathogenesis of KD and vasculitis [37]. Interestingly, we verified the hub gene expression in KD before and after IVIG treatment, and found that the hub genes of ITGAX, LILRB2, C3AR1, MAPK14, TLR5, and MYD88 were significantly downregulated after IVIG treatment. However, the mechanisms by which IVIG ameliorates KD and reduces the risk of CAAs remain unclear and warrant more studies, so as to identify high-risk patients of developing CAAs and to find new efficient therapeutics.
Immune responses are closely related to the pathogenesis of KD, involving activation and infiltration of both innate and adaptive immune cells. These cells can release proinflammatory cytokines such as IL-1β and TNF-α, and further enhance inflammation and promote necrotizing arteritis [38]. Their matric products also progressively obstruct the coronary lumen and induce a variety of cardiovascular lesions [38]. Consistently, we found that the monocytes, neutrophils, activated mast cells, and activated NK cells mainly compose the inflammatory infiltrate in KD samples and they were significantly upregulated compared with controls. These data indicate that these immune cell infiltrations play an important role in the progression of KD vasculitis.
miRNA is a class of small non-coding RNAs that regulate mRNA expression. Of human coding genes, 60–70% are estimated to be regulated by miRNAs, which are emerging as critical gene regulators in a host of cellular processes, including apoptosis, inflammation, and innate immune response [39]. Additionally, circulating miRNAs are easily detectable, relatively stable, and tissue-specific, making them attractive disease biomarkers [40]. Several studies have found that the miRNA profiles of serum exosome or coronary artery tissues are associated with acute KD, including miR-23a, miR-27b, miR-223, and miR-145 [41–42]. In the present study, we also identified 70 predicted miRNAs that may be potentially related to KD, of which hsa-miR-34a-5p had the most target DEGs and the most significant value. It is reported that miR-34a-5p can upregulate the IL-1β-mediated inflammatory process, while inhibiting miR-34a-5p attenuates the lipopolysaccharide-induced injury of endothelial cells [43,44]. We assumed that miR-34a-5p might serve as a diagnostic biomarker for KD. However, these predicted miRNAs have not been validated in a KD cohort and their functional roles require further experiments.
Several limitations should be acknowledged in this study. First, the shared DEGs in KD were identified via microarray data re-analysis. Further in vitro and in vivo validation experiments of cell lines and animal models are needed to reveal their specific functions in the pathogenesis of KD. Second, the incidence of KD varies based on ethnicity, but the KD samples of the GSE datasets were limited to patients from the USA, UK, and Japan, leading to a potential racial bias. Thus, our results may not be universally applicable and should be verified by international, multi-center, and large-scale studies. Third, the prognostic power of the identified DEGs of KD remains unclear. Therefore, the performance of these genes for risk stratification and outcomes prediction in KD patients warrants further investigations.
Conclusions
The present study identified the key genes and underlying mechanisms involved in Kawasaki disease, which may provide new perspectives to reveal the molecular pathogenesis of Kawasaki disease and develop potential diagnostic and therapeutic targets.
Supplementary Information
Supplementary Table 1.
Screening of 195 shared DEGs in KD.
| DEGs | List of gene symbols |
|---|---|
| Downregulated (31) | LEF1, MAL, CLEC2D, ABLIM1, LBH, PTPN4, SAMD3, ZNF831, EPHX2, SGK223, CD2, STAT4, SKAP1, TGFBR3, BCL11B, CD8A, ADGRG1, TMEM204, CD96, GPR183, RORA, NELL2, CD3G, GZMH, LRRN3, KLRB1, IL7R, TARP, KLRG1, ZNF683, GZMK |
| Upregulated (164) | MCEMP1, ANXA3, MMP9, SOCS3, ALPL, MGAM, S100A12, NLRC4, CDK5RAP2, DYSF, ADGRG3, RETN, ADM, CEACAM1, TLR5, BPI, ST3GAL4, PGLYRP1, SLC22A4, CR1, LILRA5, SIPA1L2, LIMK2, FCGR1B, CA4, SIGLEC5, HIST2H2AC, LRG1, HK3, IFITM3, LMNB1, FOLR3, HIST2H2AA4, CYSTM1, IL18R1, PFKFB3, OSM, GYG1, MAPK14, ROPN1L, GRB10, ZNF438, ITGA2B, PYGL, PGD, ANPEP, CREB5, IRAK3, APOBR, IL1RN, CSF3R, HIST2H2BE, ATP9A, HIST1H2BD, CLEC4D, TCN1, MYL9, LCN2, UPP1, B4GALT5, SLC11A1, TNFAIP6, RNF24, CAMP, CST7, GADD45A, PROK2, HPSE, GK, CYP1B1, RGL4, ANKRD22, SBNO2, SMARCD3, PDLIM7, C3AR1, NCF4, DGAT2, SIGLEC9, RNASE2, SLC2A3, OSCAR, LTB4R, CDA, CEACAM3, FCAR, TREML1, STXBP2, NQO2, CCR1, NECTIN2, FLOT1, AGTRAP, ITGAX, PLBD1, DRAM1, CETP, PHC2, LILRA3, LPCAT2, GAS7, AIM2, S100A11, PSTPIP2, DHRS13, CRISPLD2, KCNJ2, PADI4, SPI1, CTSA, TSHZ3, STOM, LILRB3, APMAP, SHKBP1, CMTM2, FPR1, SORT1, LRPAP1, SIRPA, FES, RAB31, RALB, NACC2, FRAT1, CDC42EP3, MYD88, MSRB1, GAS6, NFKBIZ, LY96, LILRB2, POR, IER3, SLC12A9, ZNF467, SIGLEC10, TXN, CEBPB, FLOT2, HIST1H3F, CSTA, MLKL, CD55, TSPO, HSPA1A, ACER3, RAB24, FGR, PILRA, PLP2, LTBR, GRINA, ALOX5AP, SNX20, SIRPD, TMEM120A, PLIN3, IMPDH1, RAB27A, LILRA2, EIF4E3, CKLF, FKBP5 |
Supplementary Table 2.
The top 10 results of GO-BP enrichment analyses of the shared DEGs.
| GO-BP term | Count | Gene | P value |
|---|---|---|---|
| GO: 0006955~immune response | 23 | IFITM3, CCR1, CD96, IL1RN, CEBPB, SLC11A1, NCF4, OSM, LILRB2, CST7, LTB4R, FCAR, GZMH, TGFBR3, AIM2, CD8A, GPR183, BPI, LTBR, PGLYRP1, IL7R, FCGR1B, IL18R1 | 1.85E-09 |
| GO: 0007166~cell surface receptor signaling pathway | 17 | CCR1, CDA, SIGLEC9, KLRB1, LY96, CD3G, LILRB2, LILRB3, MAPK14, CD2, ADGRG3, ADGRG1, CD8A, IL7R, CLEC2D, MYD88, KLRG1 | 7.43E-08 |
| GO: 0045087~innate immune response | 20 | ZNF683, CR1, LY96, NLRC4, LILRA5, TREML1, FGR, CLEC4D, AIM2, FES, LCN2, S100A12, PADI4, PGLYRP1, TLR5, CD55, MYD88, CAMP, KLRG1, MSRB1 | 3.47E-07 |
| GO: 0006954~inflammatory response | 18 | CCR1, CEBPB, TNFAIP6, EPHX2, SLC11A1, FPR1, LY96, NLRC4, LTB4R, AIM2, NFKBIZ, C3AR1, PROK2, S100A12, LTBR, TLR5, MYD88, KLRG1 | 1.20E-06 |
| GO: 0007155~cell adhesion | 17 | CCR1, CD96, CSF3R, SIGLEC9, TNFAIP6, ITGA2B, SIGLEC10, CD2, ADGRG1, CEACAM1, ITGAX, CYP1B1, FLOT2, SIRPA, GAS6, NECTIN2, SIGLEC5 | 5.71E-05 |
| GO: 0006935~chemotaxis | 9 | CCR1, FES, FPR1, C3AR1, PROK2, CMTM2, PLP2, RNASE2, MAPK14 | 6.65E-05 |
| GO: 0050776~regulation of immune response | 10 | TREML1, CD96, SIGLEC9, KLRB1, CD8A, CD3G, LILRB2, CLEC2D, NECTIN2, OSCAR | 1.74E-04 |
| GO: 0002250~adaptive immune response | 9 | ZNF683, CLEC4D, GPR183, LILRB2, LILRB3, LILRA2, FCGR1B, LILRA3, SKAP1 | 2.54E-04 |
| GO: 0071222~cellular response to lipopolysaccharide | 8 | SBNO2, CEBPB, LCN2, TSPO, LILRB2, MAPK14, TLR5, CAMP | 2.71E-04 |
| GO: 0042742~defense response to bacterium | 8 | CEBPB, CLEC4D, ANXA3, SLC11A1, S100A12, NLRC4, TLR5, CAMP | 3.71E-04 |
Supplementary Table 3.
The top 10 results of KEGG pathway analyses of the shared DEGs.
| KEGG term | Count | Gene | P value |
|---|---|---|---|
| hsa04380: Osteoclast differentiation | 11 | SOCS3, SPI1, NCF4, SIRPA, LILRB2, LILRB3, LILRA2, MAPK14, LILRA3, OSCAR, LILRA5 | 8.53E-06 |
| hsa04640: Hematopoietic cell lineage | 9 | CD2, CSF3R, CR1, CD8A, ANPEP, ITGA2B, CD3G, IL7R, CD55 | 1.85E-05 |
| hsa04668: TNF signaling pathway | 7 | SOCS3, CEBPB, MLKL, MAPK14, MMP9, IL18R1, CREB5 | 0.002972 |
| hsa05134: Legionellosis | 5 | CR1, NLRC4, TLR5, MYD88, HSPA1A | 0.003569 |
| hsa05321: Inflammatory bowel disease (IBD) | 4 | STAT4, RORA, TLR5, IL18R1 | 0.027762 |
| hsa05140: Leishmaniasis | 4 | CR1, NCF4, MAPK14, MYD88 | 0.036063 |
| hsa00500: Starch and sucrose metabolism | 3 | HK3, MGAM, PYGL | 0.036499 |
| hsa05152: Tuberculosis | 6 | CEBPB, CR1, ITGAX, MAPK14, CAMP, MYD88 | 0.04376 |
| hsa05034: Alcoholism | 6 | HIST2H2AA4, HIST1H3F, HIST1H2BD, HIST2H2BE, HIST2H2AC, CREB5 | 0.04376 |
| hsa05132: Salmonella infection | 4 | NLRC4, MAPK14, TLR5, MYD88 | 0.049876 |
Footnotes
Source of support: This work was supported by grants from the National Natural Science Foundation of China (81670415)
References
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Supplementary Table 1.
Screening of 195 shared DEGs in KD.
| DEGs | List of gene symbols |
|---|---|
| Downregulated (31) | LEF1, MAL, CLEC2D, ABLIM1, LBH, PTPN4, SAMD3, ZNF831, EPHX2, SGK223, CD2, STAT4, SKAP1, TGFBR3, BCL11B, CD8A, ADGRG1, TMEM204, CD96, GPR183, RORA, NELL2, CD3G, GZMH, LRRN3, KLRB1, IL7R, TARP, KLRG1, ZNF683, GZMK |
| Upregulated (164) | MCEMP1, ANXA3, MMP9, SOCS3, ALPL, MGAM, S100A12, NLRC4, CDK5RAP2, DYSF, ADGRG3, RETN, ADM, CEACAM1, TLR5, BPI, ST3GAL4, PGLYRP1, SLC22A4, CR1, LILRA5, SIPA1L2, LIMK2, FCGR1B, CA4, SIGLEC5, HIST2H2AC, LRG1, HK3, IFITM3, LMNB1, FOLR3, HIST2H2AA4, CYSTM1, IL18R1, PFKFB3, OSM, GYG1, MAPK14, ROPN1L, GRB10, ZNF438, ITGA2B, PYGL, PGD, ANPEP, CREB5, IRAK3, APOBR, IL1RN, CSF3R, HIST2H2BE, ATP9A, HIST1H2BD, CLEC4D, TCN1, MYL9, LCN2, UPP1, B4GALT5, SLC11A1, TNFAIP6, RNF24, CAMP, CST7, GADD45A, PROK2, HPSE, GK, CYP1B1, RGL4, ANKRD22, SBNO2, SMARCD3, PDLIM7, C3AR1, NCF4, DGAT2, SIGLEC9, RNASE2, SLC2A3, OSCAR, LTB4R, CDA, CEACAM3, FCAR, TREML1, STXBP2, NQO2, CCR1, NECTIN2, FLOT1, AGTRAP, ITGAX, PLBD1, DRAM1, CETP, PHC2, LILRA3, LPCAT2, GAS7, AIM2, S100A11, PSTPIP2, DHRS13, CRISPLD2, KCNJ2, PADI4, SPI1, CTSA, TSHZ3, STOM, LILRB3, APMAP, SHKBP1, CMTM2, FPR1, SORT1, LRPAP1, SIRPA, FES, RAB31, RALB, NACC2, FRAT1, CDC42EP3, MYD88, MSRB1, GAS6, NFKBIZ, LY96, LILRB2, POR, IER3, SLC12A9, ZNF467, SIGLEC10, TXN, CEBPB, FLOT2, HIST1H3F, CSTA, MLKL, CD55, TSPO, HSPA1A, ACER3, RAB24, FGR, PILRA, PLP2, LTBR, GRINA, ALOX5AP, SNX20, SIRPD, TMEM120A, PLIN3, IMPDH1, RAB27A, LILRA2, EIF4E3, CKLF, FKBP5 |
Supplementary Table 2.
The top 10 results of GO-BP enrichment analyses of the shared DEGs.
| GO-BP term | Count | Gene | P value |
|---|---|---|---|
| GO: 0006955~immune response | 23 | IFITM3, CCR1, CD96, IL1RN, CEBPB, SLC11A1, NCF4, OSM, LILRB2, CST7, LTB4R, FCAR, GZMH, TGFBR3, AIM2, CD8A, GPR183, BPI, LTBR, PGLYRP1, IL7R, FCGR1B, IL18R1 | 1.85E-09 |
| GO: 0007166~cell surface receptor signaling pathway | 17 | CCR1, CDA, SIGLEC9, KLRB1, LY96, CD3G, LILRB2, LILRB3, MAPK14, CD2, ADGRG3, ADGRG1, CD8A, IL7R, CLEC2D, MYD88, KLRG1 | 7.43E-08 |
| GO: 0045087~innate immune response | 20 | ZNF683, CR1, LY96, NLRC4, LILRA5, TREML1, FGR, CLEC4D, AIM2, FES, LCN2, S100A12, PADI4, PGLYRP1, TLR5, CD55, MYD88, CAMP, KLRG1, MSRB1 | 3.47E-07 |
| GO: 0006954~inflammatory response | 18 | CCR1, CEBPB, TNFAIP6, EPHX2, SLC11A1, FPR1, LY96, NLRC4, LTB4R, AIM2, NFKBIZ, C3AR1, PROK2, S100A12, LTBR, TLR5, MYD88, KLRG1 | 1.20E-06 |
| GO: 0007155~cell adhesion | 17 | CCR1, CD96, CSF3R, SIGLEC9, TNFAIP6, ITGA2B, SIGLEC10, CD2, ADGRG1, CEACAM1, ITGAX, CYP1B1, FLOT2, SIRPA, GAS6, NECTIN2, SIGLEC5 | 5.71E-05 |
| GO: 0006935~chemotaxis | 9 | CCR1, FES, FPR1, C3AR1, PROK2, CMTM2, PLP2, RNASE2, MAPK14 | 6.65E-05 |
| GO: 0050776~regulation of immune response | 10 | TREML1, CD96, SIGLEC9, KLRB1, CD8A, CD3G, LILRB2, CLEC2D, NECTIN2, OSCAR | 1.74E-04 |
| GO: 0002250~adaptive immune response | 9 | ZNF683, CLEC4D, GPR183, LILRB2, LILRB3, LILRA2, FCGR1B, LILRA3, SKAP1 | 2.54E-04 |
| GO: 0071222~cellular response to lipopolysaccharide | 8 | SBNO2, CEBPB, LCN2, TSPO, LILRB2, MAPK14, TLR5, CAMP | 2.71E-04 |
| GO: 0042742~defense response to bacterium | 8 | CEBPB, CLEC4D, ANXA3, SLC11A1, S100A12, NLRC4, TLR5, CAMP | 3.71E-04 |
Supplementary Table 3.
The top 10 results of KEGG pathway analyses of the shared DEGs.
| KEGG term | Count | Gene | P value |
|---|---|---|---|
| hsa04380: Osteoclast differentiation | 11 | SOCS3, SPI1, NCF4, SIRPA, LILRB2, LILRB3, LILRA2, MAPK14, LILRA3, OSCAR, LILRA5 | 8.53E-06 |
| hsa04640: Hematopoietic cell lineage | 9 | CD2, CSF3R, CR1, CD8A, ANPEP, ITGA2B, CD3G, IL7R, CD55 | 1.85E-05 |
| hsa04668: TNF signaling pathway | 7 | SOCS3, CEBPB, MLKL, MAPK14, MMP9, IL18R1, CREB5 | 0.002972 |
| hsa05134: Legionellosis | 5 | CR1, NLRC4, TLR5, MYD88, HSPA1A | 0.003569 |
| hsa05321: Inflammatory bowel disease (IBD) | 4 | STAT4, RORA, TLR5, IL18R1 | 0.027762 |
| hsa05140: Leishmaniasis | 4 | CR1, NCF4, MAPK14, MYD88 | 0.036063 |
| hsa00500: Starch and sucrose metabolism | 3 | HK3, MGAM, PYGL | 0.036499 |
| hsa05152: Tuberculosis | 6 | CEBPB, CR1, ITGAX, MAPK14, CAMP, MYD88 | 0.04376 |
| hsa05034: Alcoholism | 6 | HIST2H2AA4, HIST1H3F, HIST1H2BD, HIST2H2BE, HIST2H2AC, CREB5 | 0.04376 |
| hsa05132: Salmonella infection | 4 | NLRC4, MAPK14, TLR5, MYD88 | 0.049876 |