Single-nucleotide Polymorphism rs17860041 A/C in the Promoter of the PPIA Gene is Associated with Susceptibility to Kawasaki Disease in Chinese Children

Diagnostic model based on bioinformatics and machine learning to distinguish Kawasaki disease using multiple datasets

Background

Kawasaki disease (KD), characterized by systemic vasculitis, is the leading cause of acquired heart disease in children. Herein, we developed a diagnostic model, with some prognosis ability, to help distinguish children with KD.

Methods

Gene expression datasets were downloaded from Gene Expression Omnibus (GEO), and gene sets with a potential pathogenic mechanism in KD were identified using differential expressed gene (DEG) screening, pathway enrichment analysis, random forest (RF) screening, and artificial neural network (ANN) construction.

Results

We extracted 2,017 DEGs (1,130 with upregulated and 887 with downregulated expression) from GEO. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were significantly enriched in innate/adaptive immune response-related processes. Subsequently, the results of weighted gene co-expression network analysis and DEG screening were combined and, using RF and ANN, a model with eight genes (VPS9D1, CACNA1E, SH3GLB1, RAB32, ADM, GYG1, PGS1, and HIST2H2AC) was constructed. Classification results of the new model for KD diagnosis showed excellent performance for different datasets, including those of patients with KD, convalescents, and healthy individuals, with area under the curve values of 1, 0.945, and 0.95, respectively.

Conclusions

We used machine learning methods to construct and validate a diagnostic model using multiple bioinformatic datasets, and identified molecules expected to serve as new biomarkers for or therapeutic targets in KD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03557-y.

Association of miR-181c/d gene locus rs8108402 C/T polymorphism with susceptibility to Kawasaki disease in Chinese children

BACKGROUND

Kawasaki disease (KD) is an acute systemic vasculitis of unknown etiology. The rs8108402 C/T single nucleotide polymorphism (SNP) is located in the promoter region of miR-181-c/d gene and the intron of Nanos3 gene. The miR-181 family contributes to the pathogenesis of cardiovascular and inflammatory disorders, while Nanos3 is involved in DNA transcription regulation and cell proliferation. However, no studies have examined the association between miR-181c/d and Nanos3 polymorphisms and the susceptibility and progression of KD.

OBJECTIVE

The purpose of our study is to examine the association of miR-181c/miR-181d/Nanos3 gene locus rs8108402 C/T polymorphism with KD susceptibility, intravenous immunoglobulin (IVIG) responsiveness, and the development of coronary artery lesions (CAL).

METHODS

Peripheral blood specimens from 100 children with KD and 100 healthy children were collected. The polymorphism of rs8108402 C/T was detected using polymerase chain reaction-sequencing-based typing technique.

RESULTS

There were statistically significant differences in C and T allele frequency distributions between the KD group and healthy controls for the polymorphic site rs8108402 C/T (P = 0.002). The distribution of the genotypes CC, CT, and TT also presented statistical significant difference between the KD and control groups (P = 0.003). Compared to the rs8108402 C allele, the T allele was associated with increased KD susceptibility (OR = 2.080, 95% CI = 1.317∼3.283). However, there were no significant associations discovered between the rs8108402 C/T polymorphism and CAL formation or IVIG unresponsiveness in the study.

CONCLUSION

SNP rs8108402 C/T located in the miR-181c/d promoter and Nanos3 intronic region is associated with susceptibility to Kawasaki disease but not with the development of coronary artery lesions or IVIG unresponsiveness in Chinese children.

The Expression and Role of microRNA-133a in Plasma of Patients with Kawasaki Disease

Kawasaki disease (KD)), also known as mucocutaneous lymph node syndrome (MCLS), is an autoimmune and systemic vasculitis syndrome. Its etiology and pathogenesis are still unclear. microRNAs (miRNA), a novel class of small non-coding RNAs, regulate the expression of multiple protein-encoding genes at the post-transcriptional level. We intend to study the change of miRNA-133a in the plasma of patients with KD, explore the role of miRNA-133a on HUVEC and define the pathogenesis of vascular dysfunction in KD. miRNA-133a expression and the mRNA and protein expression of protein phosphatase 2 catalytic subunit alpha (PPP2CA) were assessed by RT-qPCR and Western blot, respectively. The PPP2CA mRNA 3'UTR was predicted to be the potential target of miRNA-133a by using the miRNA databases and verified by the luciferase assay. The plasmids of miRNA-133a mimics and inhibitors were transfected into HUVEC cells. The plasma soluble vascular endothelial cadherin (sVE-cadherin, the excised extracellular part of VE-cadherin) levels were investigated by ELISA. The results suggested that miRNA-133a was increased by 3.8 times in the acute KD group and by 2.7 times in the convalescent KD group compared with the control group (both P = .000). PPP2CA is the target gene of miRNA-133a and its expression was inhibited by miRNA-133a acting on PPP2CA mRNA 3'UTR (P = .013). The plasma sVE-cadherin levels in the acute KD groups were increased compared with the control group (P = .024). The ROC curve analysis showed that the expression of miRNA-133a segregate acute KD patients from convalescent KD patients and healthy children. Our results suggest that miRNA-133a might be a new biomarker for KD.