RETRACTED ARTICLE: Correlations of SELE and SELP genetic polymorphisms with myocardial infarction risk: a meta-analysis and meta-regression

Identification and Analysis of DNA Methylation Inflammation-Related Key Genes in Intracerebral Hemorrhage

Inflammation and DNA methylation have been reported to play key roles in intracerebral hemorrhage (ICH). This study aimed to investigate new diagnostic biomarkers associated with inflammation and DNA methylation using a comprehensive bioinformatics approaches. GSE179759 and GSE125512 were collected from the Gene Expression Omnibus database, and 3222 inflammation-related genes (IFRGs) were downloaded from the Molecular Signatures Database. Key differentially expressed methylation-regulated and inflammation-related genes (DE-MIRGs) were identified by overlapping methylation-regulated differentially expressed genes (MeDEGs) between patients with ICH and control samples, module genes from weighted correlation network analysis, and IFRGs. Functional annotation of DE-MIRGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A protein-protein interaction (PPI) network was constructed to clarify the interrelationships between different DE-MIRGs. The key genes were categorized by least absolute shrinkage selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), and gene set enrichment analysis (GSEA). A total of 22 DE-MIRGs were acquired from 451 MeDEGs, 3222 IFRGs, and 302 module genes, and were mainly enriched in the GO terms of wound healing, blood coagulation, and hemostasis; and the KEGG pathways of PI3K/Akt signaling, focal adhesion, and regulation of actin cytoskeleton. A PPI network with 22 nodes and 87 edges was constructed based on the 22 DE-MIRGs, 11 of which were selected for key gene selection. Two 2 key genes (SELP and S100A4) were identified using LASSO and SVM-RFE. Finally, SELP was mainly enriched in cell morphogenesis involved in differentiation, cytoplasmic translation, and actin binding of GO terms, and the KEGG pathway including endocytosis, focal adhesion, and platelet activation. S100A4 was mainly enriched in GO terms including mitochondrial inner membrane; mitochondrial respirasome and lysosomal membrane; and the KEGG pathway of oxidative phosphorylation, regulation of actin cytoskeleton, and chemical carcinogenesis-reactive oxygen species. Twenty-two DE-MIRGs-associated inflammation and DNA methylation were identified between patients with ICH and normal controls, and two key genes (SELP and S100A4) were identified and regarded as biomarkers for ICH, which could provide the research foundation for further investigation of the pathological mechanism of ICH.

Genetic Analyses Identified a SALL4 Gene Mutation Associated with Holt-Oram Syndrome

Holt-Oram syndrome (HOS) is an autosomal dominant disorder, which is characterized by deformities of upper limbs and congenital heart defects. Alterations of TBX5 gene have been identified to be the leading cause of HOS, while some cases could not be explained by TBX5 mutations. In our study, we preliminarily diagnosed a newborn baby, who had Tetralogy of Fallot, thumb agenesis, facial dysplasia, and right ear canal malformation, as HOS. Chromosome microarray analyses showed no pathological deletions or replications of chromosome segments; whole exome sequencing screened out six candidate genes that were involved in cardiac diseases or syndromes among which SALL4 has been reported as HOS related gene. We evaluated the pathogenicity of SALL4 mutant sites by series of software. The results indicated that SALL4-M143V may be a polymorphism site, and SALL4-R418C could cause disease. HOPE and SWISS PDB viewer showed that SALL4-R418C leads to changes in amino acid properties, loss of protein hydrogen bond, and functional impact of SALL4 zinc finger domain. These results further confirmed the pathogenic significance of SALL4-R418C mutant. When genetic analyses coupled with bioinformatic analyses, we identified a SALL4 gene rare mutation which might contribute to a newborn with HOS. Although some doubts need to be further discussed and explored, our study deepened the understanding of phenotype difference among syndromes and role of SALL4 mutations in disease occurrence.