Five immune-gene-signatures participate in the development and pathogenesis of Kawasaki disease

Identification of hub biomarkers and immune-related pathways participating in the progression of Kawasaki disease by integrated bioinformatics analysis

BACKGROUND

Kawasaki disease (KD) is a systemic vasculitis that commonly affects children and its etiology remains unknown. Growing evidence suggests that immune-mediated inflammation and immune cells in the peripheral blood play crucial roles in the pathophysiology of KD. The objective of this research was to find important biomarkers and immune-related mechanisms implicated in KD, along with their correlation with immune cells in the peripheral blood.

MATERIAL/METHODS

Gene microarray data from the Gene Expression Omnibus (GEO) was utilized in this study. Three datasets, namely GSE63881 (341 samples), GSE73463 (233 samples), and GSE73461 (279 samples), were obtained. To find intersecting genes, we employed differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA). Subsequently, functional annotation, construction of protein-protein interaction (PPI) networks, and Least Absolute Shrinkage and Selection Operator (LASSO) regression were performed to identify hub genes. The accuracy of these hub genes in identifying KD was evaluated using the receiver operating characteristic curve (ROC). Furthermore, Gene Set Variation Analysis (GSVA) was employed to explore the composition of circulating immune cells within the assessed datasets and their relationship with the hub gene markers.

RESULTS

WGCNA yielded eight co-expression modules, with one hub module (MEblue module) exhibiting the strongest association with acute KD. 425 distinct genes were identified. Integrating WGCNA and DEGs yielded a total of 277 intersecting genes. By conducting LASSO analysis, five hub genes (S100A12, MMP9, TLR2, NLRC4 and ARG1) were identified as potential biomarkers for KD. The diagnostic value of these five hub genes was demonstrated through ROC curve analysis, indicating their high accuracy in diagnosing KD. Analysis of the circulating immune cell composition within the assessed datasets revealed a significant association between KD and various immune cell types, including activated dendritic cells, neutrophils, immature dendritic cells, macrophages, and activated CD8 T cells. Importantly, all five hub genes exhibited strong correlations with immune cells.

CONCLUSION

Activated dendritic cells, neutrophils, and macrophages were closely associated with the pathogenesis of KD. Furthermore, the hub genes (S100A12, MMP9, TLR2, NLRC4, and ARG1) are likely to participate in the pathogenic mechanisms of KD through immune-related signaling pathways.

Integration of scRNA-Seq and bulk RNA-Seq uncover perturbed immune cell types and pathways of Kawasaki disease

Introduction

Kawasaki disease (KD) is an acute febrile illness primarily affecting children and characterized by systemic inflammation and vasculitis that can lead to coronary artery complications. The aim of this study was to gain a comprehensive understanding of immune dysregulation in KD.

Methods

To this end, we employed integration of single-cell RNA sequencing (scRNA-Seq) and bulk RNA sequencing (bulk RNA-Seq) data. Furthermore, we conducted flow cytometry analysis for a cohort of 82 KD patients.

Results

Our analysis revealed significant heterogeneity within immune cell populations in KD patients, with distinct clusters of T cells, B cells, and natural killer (NK) cells. Importantly, CD4+ naïve T cells in KD patients were found to predominantly differentiate into Treg cells and Th2 cells, potentially playing a role in the excessive inflammation and vascular damage characteristic of the disease. Dysregulated signaling pathways were also identified, including the mTOR signaling pathway, cardiomyopathy pathway, COVID-19 signaling pathway, and pathways involved in bacterial or viral infection.

Discussion

These findings provide insights into the immunopathogenesis of KD, emphasizing the importance of immune cell dysregulation and dysregulated signaling pathways. Integration of scRNA-Seq and bulk RNA-Seq data offers a comprehensive view of the molecular and cellular alterations in KD and highlights potential therapeutic targets for further investigation. Validation and functional studies are warranted to elucidate the roles of the identified immune cell types and pathways in KD pathogenesis and to develop targeted interventions to improve patient outcomes.

The Immunologic Profiles of Kawasaki Disease Triggered by Mycoplasma pneumoniae Infection

OBJECTIVE

We compared the immunologic characteristics of mycoplasma pneumoniae-triggered Kawasaki disease (MP-KD) with Kawasaki disease (KD) not associated with mycoplasma pneumoniae (MP), with mycoplasma pneumoniae-triggered Henoch-Schönlein purpura (MP-HSP), and with healthy controls.

METHODS

Complement levels, cellular and humoral immunity were assessed in KD, in MP-KD, in MP-HSP, and in healthy children.

RESULTS

Of 622 children with KD, 74 had MP-KD. Complement C3 and CD4/CD8 ratio were significantly increased in MP-KD compared to KD. C3, C4, and the ratio of CD4/CD8 in the MP-KD group were higher than those in the MP-HSP group. IgA and CD56 were lower in the MP-KD group than the MP-HSP group.

CONCLUSIONS

Both C3 and polyclonal CD4+ T lymphocytes may be activated in the patients with MP-KD.

Identification of Hub Biomarkers and Immune and Inflammation Pathways Contributing to Kawasaki Disease Progression with RT-qPCR Verification

BACKGROUND

Kawasaki disease (KD) is characterized by a disordered inflammation response of unknown etiology. Immune cells are closely associated with its onset, although the immune-related genes' expression and possibly involved immune regulatory mechanisms are little known. This study aims to identify KD-implicated significant immune- and inflammation-related biomarkers and pathways and their association with immune cell infiltration. Patients and Methods. Gene microarray data were collected from the Gene Expression Omnibus database. Differential expression analysis, weighted gene coexpression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) regression, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were used to find KD hub markers. GSEA was used to assess the infiltration by 28 immune cell types and their connections to essential gene markers. Receiver operating characteristic (ROC) curves were used to examine hub markers' diagnostic effectiveness. Finally, hub genes' expressions were validated in Chinese KD patients by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

RESULTS

One hundred and fifty-one unique genes were found. Among 10 coexpression modules at WGCNA, one hub module exhibited the strongest association with KD. Thirty-six overlapping genes were identified. Six hub genes were potential biomarkers according to LASSO analysis. Immune infiltration revealed connections among activated and effector memory CD4+ T cells, neutrophils, activated dendritic cells, and macrophages. The six hub genes' diagnostic value was shown by ROC curve analysis. Hub genes were enriched in immunological and inflammatory pathways. RT-qPCR verification results of FCGR1B (P < 0.001), GPR84 (P < 0.001), KREMEN1 (P < 0.001), LRG1 (P < 0.001), and TDRD9 (P < 0.001) upregulated expression in Chinese KD patients are consistent with our database analysis.

CONCLUSION

Neutrophils, macrophages, and activated dendritic cells are strongly linked to KD pathophysiology. Through immune-related signaling pathways, hub genes such as FCGR1B, GPR84, KREMEN1, LRG1, and TDRD9 may be implicated in KD advancement.

Bioinformatic analysis of underlying mechanisms of Kawasaki disease via Weighted Gene Correlation Network Analysis (WGCNA) and the Least Absolute Shrinkage and Selection Operator method (LASSO) regression model

BACKGROUND

Kawasaki disease (KD) is a febrile systemic vasculitis involvingchildren younger than five years old. However, the specific biomarkers and precise mechanisms of this disease are not fully understood, which can delay the best treatment time, hence, this study aimed to detect the potential biomarkers and pathophysiological process of KD through bioinformatic analysis.

METHODS

The Gene Expression Omnibus database (GEO) was the source of the RNA sequencing data from KD patients. Differential expressed genes (DEGs) were screened between KD patients and healthy controls (HCs) with the "limma" R package. Weighted gene correlation network analysis (WGCNA) was performed to discover the most corresponding module and hub genes of KD. The node genes were obtained by the combination of the least absolute shrinkage and selection operator (LASSO) regression model with the top 5 genes from five algorithms in CytoHubba, which were further validated with the receiver operating characteristic curve (ROC curve). CIBERSORTx was employed to discover the constitution of immune cells in KDs and HCs. Functional enrichment analysis was performed to understand the biological implications of the modular genes. Finally, competing endogenous RNAs (ceRNA) networks of node genes were predicted using online databases.

RESULTS

A total of 267 DEGs were analyzed between 153 KD patients and 92 HCs in the training set, spanning two modules according to WGCNA. The turquoise module was identified as the hub module, which was mainly enriched in cell activation involved in immune response, myeloid leukocyte activation, myeloid leukocyte mediated immunity, secretion and leukocyte mediated immunity biological processes; included type II diabetes mellitus, nicotinate and nicotinamide metabolism, O-glycan biosynthesis, glycerolipid and glutathione metabolism pathways. The node genes included ADM, ALPL, HK3, MMP9 and S100A12, and there was good performance in the validation studies. Immune cell infiltration analysis revealed that gamma delta T cells, monocytes, M0 macrophage, activated dendritic cells, activated mast cells and neutrophils were elevated in KD patients. Regarding the ceRNA networks, three intact networks were constructed: NEAT1/NORAD/XIST-hsa-miR-524-5p-ADM, NEAT1/NORAD/XIST-hsa-miR-204-5p-ALPL, NEAT1/NORAD/XIST-hsa-miR-524-5p/hsa-miR-204-5p-MMP9.

CONCLUSION

To conclude, the five-gene signature and three ceRNA networks constructed in our study are of great value in the early diagnosis of KD and might help to elucidate our understanding of KD at the RNA regulatory level.

The CCR1 and CCR5 C-C chemokine receptors in Penaeus vannamei are annexed by bacteria to attenuate shrimp survival

The C-C chemokine receptors (CCRs) family is involved in diverse pathophysiological processes in mammals, such as immune regulation and cancer, but their functions in invertebrates remain enigmatic. Here, two CCR homologs in Penaeus vannamei (designated PvCCR1 and PvCCR5) were characterized and found to share sequence homology with other CCRs and contain the conserved 7TM functional domain. Both PvCCR1 and PvCCR5 were constitutively expressed in healthy shrimp tissues, while their mRNA transcript levels were induced in hepatopancreas and hemocytes by Vibrio parahaemolyticus, Streptococcus iniae, and white spot syndrome virus. Notably, shrimp survival increased after knockdown of PvCCR1 and PvCCR5 followed by V. parahaemolyticus infection, indicating that PvCCR1 and PvCCR5 are annexed by the bacteria for their benefit, the absence of which attenuates the effects of the pathogen on shrimp survival. The present data indicate that PvCCR1 and PvCCR5 play key roles in the antimicrobial immune response and therefore vital for shrimp survival.

Kawasaki Disease and Coronary Artery Involvement: A Narrative Review

Kawasaki disease is a systemic vasculitis with a risk of developing coronary artery lesions if left untreated. Kawasaki disease can be diagnosed clinically with classical symptoms (conjunctivitis, rash, lymphadenopathy, mucositis, edema of hands and feet), but predicting the risk of developing coronary artery aneurysm remains challenging. The coronary sequelae of Kawasaki disease have significant morbidity and mortality and are the second most common cause of acquired cardiac disease in children. Several genetic and immune factors are involved in the inflammation of coronary artery lesions in Kawasaki disease. Inositol trisphosphate 3-Kinase (ITPKC), Foxp3+, circular RNAs, mannose-binding lectin 2 (MBL2), complement factor H (CFH), kininogen 1 (KNG1), serpin family C member 1 (SERPINC1) and fibronectin 1 (FN1) are the essential genes identified in the pathogenesis of coronary artery lesions in Kawasaki disease. The addition of methylprednisolone to a combination of aspirin and intravenous immunoglobulins and biological agents like anakinra, etanercept, infliximab, and immunosuppressants like cyclosporine prevents the occurrence of coronary artery aneurysms in Kawasaki disease. Since the coronary artery lesions form the second most common cause of acquired cardiac disease in children and the incidence of myocardial infarction is a late complication, the risk stratification for coronary artery aneurysms and follow-up protocols for the prevention of cardiac thrombosis were proposed by the American Heart Association in 2017.

Atlas of circulating immune cells in Kawasaki disease

Increasing evidence shows that the pathogenesis of Kawasaki disease (KD) is caused by abnormal and unbalanced innate and adaptive immune responses. However, the changes in and functions of adaptive immune cells in the peripheral blood of subjects with KD remain controversial. In this study, three different methods, CIBERSORT, Immune Cell Abundance Identifier (ImmuCellAI), and immune cell markers, were used to evaluate the proportions and abundances of immune cells in eight KD datasets (GSE9863, GSE9864, GSE18606, GSE63881, GSE68004, GSE73461, GSE73463, and GSE64486; a total of 1,251 samples). Compared with those in normal controls and convalescent KD samples, the proportions and abundances of innate immune cells such as neutrophils, monocytes, and macrophages in acute KD peripheral blood samples were significantly increased, while those of adaptive immune cells such as B and T cells were significantly decreased. The change tendencies of these immune cells were similar to those observed in other febrile illnesses but were more significant. However, in the coronary artery tissues of patients with convalescent KD, adaptive immune cells, especially B cells and CD8+ T cell subsets, were significantly increased. This result suggests that adaptive immune cells can be selectively recruited from peripheral blood into the coronary arteries. In addition, we found that elevated neutrophils in peripheral blood could be used as a biomarker to assist in the differential diagnosis of KD, but we did not find immune cells that could accurately predict intravenousimmunoglobulin (IVIG) responses in multiple datasets.

Patterns of Immune Infiltration and the Key Immune-Related Genes in Acute Type A Aortic Dissection in Bioinformatics Analyses

Background

Immune-inflammatory mechanisms contribute greatly to the complex process leading to type A aortic dissection (TAAD). This study aims to explore immune infiltration and key immune-related genes in acute TAAD.

Methods

ImmuCellAI algorithm was applied to analyze patterns of immune infiltration in TAAD samples and normal aortic vessel samples in the GSE153434 dataset. Differentially expressed genes (DEGs) were screened. Immune-related genes were obtained from overlapping DEGs of GSE153434 and immune genes of the ImmPort database. The hub genes were obtained based on the protein–protein interaction (PPI) network. The hub genes in TAAD were validated in the GSE52093 dataset. The correlation between the key immune-related genes and infiltrating immune cells was further analyzed.

Results

In the study, the abundance of macrophages, neutrophils, natural killer T cells (NKT cells), natural regulatory T cells (nTreg), T-helper 17 cells (Th17 cells) and monocytes was increased in TAAD samples, whereas that of dendritic cells (DCs), CD4 T cells, central memory T cells (Tcm), mucosa associated invariant T cells (MAIT cells) and B cells was decreased. Interleukin 6 (IL-6), C-C motif chemokine ligand 2 (CCL2) and hepatocyte growth factor (HGF) were identified and validated in the GSE52093 dataset as the key immune-related genes. Furthermore, IL-6, CCL2 and HGF were correlated with different types of immune cells.

Conclusion

In conclusion, several immune cells such as macrophages, neutrophils, NKT cells, and nTreg may be involved in the development of TAAD. IL-6, CCL2 and HGF were identified and validated as the key immune-related genes of TAAD via bioinformatics analyses. The key immune cells and immune-related genes have the potential to be developed as targets of prevention and immunotherapy for patients with TAAD.

Correlation Analysis of Anti-Cardiolipin Antibody/D Dimer/C-Reactive Protein and Coronary Artery Lesions/Multiple-Organ Damage in Children With Kawasaki Disease

Aim: Kawasaki disease (KD) is a systemic vasculitis with unknown etiology. In addition to cardiovascular system involvement, it can also have other multiple organs involved. This study is aimed at investigating the correlation between anti-cardiolipin antibody (ACA)/D dimer/C reactive protein (CRP) and coronary artery lesions (CAL)/multiple-organ lesions in children with KD. Methods: Retrospective analysis was performed in 284 KD/IKD patients from May 2015 to April 2016. Among them, 175 were males (61.6%), with average age of 2 years and 5 months old. Patients were divided into ACA+ group and ACA- group, elevated D dimer group (DDE) and normal D dimer group (DDN), and coronary artery injury (CAL) group and non-coronary artery injury (NCAL) group. Results: ACA was most likely tested positive in younger KD children (p < 0.05). ACA+ and hypoproteinemia were correlated with CAL, thrombocytosis, and granulocytopenia (p < 0.05-0.01). Levels of cTnI and CK in the CAL group were significantly higher than those in the NCAL group (p < 0.05). CAL was more frequently detected in younger patients and patients with prolonged fever, later IVIG treatment, and elevated CRP over 100 mg/l, but there was no statistically significant difference (all p > 0.05). In the KD with DDE group, the incidence of granulopenia, thrombocytosis, myocardial damage, cholestasis, hypoproteinemia, and aseptic urethritis was significantly higher than that in the KD with DDN group (p < 0.05-0.01). However, elevated D dimer was not associated with CAL. CRP elevation was highly correlated with D dimer, but not with CAL. Conclusion: Higher incidence of CAL and myocardial damage occurred in KD patients with positive ACA and hypoproteinemia. In the current study, ACA was only tested for positive and negative, which is a limitation to this study. To further elucidate the association, ACA titers would establish its significance in drawing a conclusion for the significance of ACA in CAL and myocardial damages. In addition, higher incidence of CAL occurred in younger patients. The higher D dimer was associated with increased multiple-organ damage (MOD). CRP was closely correlated with D dimer, but not correlated with ACA and CAL.

Five immune-gene-signatures participate in the development and pathogenesis of Kawasaki disease

Objective

To screen for immune genes that play a major role in Kawasaki disease and to investigate the pathogenesis of Kawasaki disease through bioinformatics analysis.

Methods

Kawasaki disease‐related datasets GSE18606, GSE68004, and GSE73461 were downloaded from the Gene Expression Omnibus database. Three microarrays were integrated and standardized to include 173 Kawasaki disease samples and 101 normal samples. The samples were analyzed using CIBERSORT to obtain the infiltration of 22 immune cells and analyze the differential immune cells in the samples and correlations. The distribution of the samples was analyzed using principal component analysis (PCA). Immune‐related genes were downloaded, extracted from the screened samples and analyzed for differential analysis (different expression genes [DEG]) and weighted gene co‐expression network analysis (WGCNA). We constructed coexpression networks, and used the cytohobbe tool in Cytoscape to analyze the coexpression networks and select the immune genes that played a key role in them.

Results

Immune cell infiltration analysis showed that B cells naive, T cells CD8, natural killer (NK) cells activated, and so forth were highly expressed in normal samples. T cells CD4 memory activated, monocytes, neutrophils, and so forth were highly expressed in Kawasaki disease samples. PCA results showed a significant difference in the distribution of normal and Kawasaki disease samples. From the screened samples, 97 upregulated and 103 downregulated immune‐related genes were extracted. WGCNA analysis of DEG yielded 10 gene modules, of which the three most relevant to Kawasaki disease were red, yellow, and gray modules. They were associated with cytokine regulation, T‐cell activation, presentation of T‐cell receptor signaling pathways, and NK cell‐mediated cytotoxicity. CXCL8, CCL5, CCR7, CXCR3, and CCR1 were identified as key genes by constructing a coexpression network.

Conclusion

Our study shows that we can distinguish normal samples from Kawasaki disease samples based on the infiltration of immune cells, and that CXCL8, CCL5, CCR7, CXCR3, and CCR1 may play important roles in the development of Kawasaki disease.