Efficient detection of differentially methylated regions in the genome of patients with thoracic aortic dissection and association with MMP2 hypermethylation

Matrix metalloproteinases in aortic dissection

Aortic dissection, characterized by a high immediate mortality, is primarily caused by excessive bleeding within the walls of the aorta or a severe tear within the intimal layer of the aorta. Inflammation, as well as oxidative stress and the degradation of extracellular matrix (ECM), are significant factors in the development and occurrence of aortic dissection. Matrix metalloproteinases (MMPs) are pivotal enzymes responsible for degrading the ECM. Inflammatory factors and oxidants can interact with MMPs, indicating the potential significance of MMPs in aortic dissection. A substantial body of evidence indicates that numerous MMPs are significantly upregulated in aortic dissection, playing a critical role in ECM degradation and the pathogenesis of aortic dissection. Furthermore, targeting these enzymes has demonstrated potential in facilitating ECM restoration and reducing the incidence of aortic dissection. This review initially provides a brief overview of MMP biology before delving into their expression patterns, regulatory mechanisms, and therapeutic applications in aortic dissection. A profound comprehension of the catabolic pathways associated with aortic dissection is imperative for the future development of potential preventive or therapeutic bio-interventions for aortic dissection.

Biomarkers in aortic dissection: Diagnostic and prognostic value from clinical research

ABSTRACT

Aortic dissection is a life-threatening condition for which diagnosis mainly relies on imaging examinations, while reliable biomarkers to detect or monitor are still under investigation. Recent advances in technologies provide an unprecedented opportunity to yield the identification of clinically valuable biomarkers, including proteins, ribonucleic acids (RNAs), and deoxyribonucleic acids (DNAs), for early detection of pathological changes in susceptible patients, rapid diagnosis at the bedside after onset, and a superior therapeutic regimen primarily within the concept of personalized and tailored endovascular therapy for aortic dissection.

Epigenomics in aortic dissection: From mechanism to therapeutics

Aortic dissection (AD) has an unfavorable prognosis. It requires early diagnosis, appropriate treatment strategies, and suspicion to recognize symptoms; thus, it is commonly described as an acute aortic emergency. The clinical manifestations of painless AD are complex and variable. However, there is no effective treatment to prevent the progression of AD. Therefore, study of the molecular targets and mechanisms of AD to enable prevention or early intervention is particularly important. Although multiple gene mutations have been proposed as linked to AD development, evidence that multiple epigenetic elements are strongly associated is steadily increasing. These epigenetic processes include DNA methylation, N6-methyladenosine, histone modification, non-histone posttranslational modification, and non-coding RNAs (ncRNAs). Among these processes, resveratrol targeting Sirtuin 1 (SIRT1), 5-azacytidine (5azaC) targeting DNA methyltransferase (DNMT), and vitamin C targeting ten-eleven translocation 2 (Tet2) showed unique advantages in improving AD and vascular dysfunction. Finally, we explored potential epigenetic drugs and diagnostic methods for AD, which might provide options for the future.

Identification of pathological-related and diagnostic potential circular RNAs in Stanford type A aortic dissection

Introduction

Stanford type A aortic dissection (TAAD) is one of the lethal macrovascular diseases caused by the invasion of blood into the media layer of ascending aortic wall. Inflammation, smooth muscle dysfunction, and extracellular matrix (ECM) degradation were regarded as the major pathology in affected tissue. However, the expression pattern and its regulation especially through circular RNAs (circRNAs) as an overall characteristic of TAAD molecular pathology remain unclear.

Methods

We employed CIRCexplorer2 to identify circRNAs based on the RNA sequencing (RNA-seq) data of human ascending aortic tissues to systematically assess the role of circRNA in the massive alterations of gene expression in TAAD aortas. The key circRNAs were determined by LASSO model and functionally annotated by competing endogenous RNAs (ceRNA) network and co-analysis with mRNA profile. The expression level and diagnostic capability of the 4 key circRNAs in peripheral serum were confirmed by real-time polymerase chain reaction (RT-PCR).

Results

The 4 key circRNAs, namely circPTGR1 (chr9:114341075-114348445[-]), circNOX4 (chr11:89069012-89106660[-]), circAMN1 (chr12:31854796-31862359[-]) and circUSP3 (chr15:63845913-63855207[+]), demonstrated a high power to discriminate between TAAD and control tissues, suggesting that these molecules stand for a major difference between the tissues at gene regulation level. Functionally, the ceRNA network of circRNA-miRNA-mRNA predicted by the online databases, combining gene set enrichment analysis (GSEA) and cell component prediction, revealed that the identified circRNAs covered all the aspects of primary TAAD pathology, centralized with increasing inflammatory factors and cells, and ECM destruction and loss of vascular inherent cells along with the circRNAs. Importantly, we validated the high concentration and diagnostic capability of the 4 key circRNAs in the peripheral serum in TAAD patients.

Discussion

This study reinforces the vital status of circRNAs in TAAD and the possibility of serving as promising diagnostic biomarkers.

Applying multi-omics techniques to the discovery of biomarkers for acute aortic dissection

Acute aortic dissection (AAD) is a cardiovascular disease that manifests suddenly and fatally. Due to the lack of specific early symptoms, many patients with AAD are often overlooked or misdiagnosed, which is undoubtedly catastrophic for patients. The particular pathogenic mechanism of AAD is yet unknown, which makes clinical pharmacological therapy extremely difficult. Therefore, it is necessary and crucial to find and employ unique biomarkers for Acute aortic dissection (AAD) as soon as possible in clinical practice and research. This will aid in the early detection of AAD and give clear guidelines for the creation of focused treatment agents. This goal has been made attainable over the past 20 years by the quick advancement of omics technologies and the development of high-throughput tissue specimen biomarker screening. The primary histology data support and add to one another to create a more thorough and three-dimensional picture of the disease. Based on the introduction of the main histology technologies, in this review, we summarize the current situation and most recent developments in the application of multi-omics technologies to AAD biomarker discovery and emphasize the significance of concentrating on integration concepts for integrating multi-omics data. In this context, we seek to offer fresh concepts and recommendations for fundamental investigation, perspective innovation, and therapeutic development in AAD.

DNA methylation alternation in Stanford- A acute aortic dissection

Background

Acute aortic dissection (AAD) is a life-threatening cardiovascular disease. Recent studies have shown that DNA methylation may be associated with the pathological mechanism of AAD, but the panorama of DNA methylation needs to be explored.

Methods

DNA methylation patterns were screened using Infinium Human Methylation 450 K BeadChip in the aortic tissues from 4 patients with Stanford-A AAD and 4 controls. Gene enrichment was analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO). DNA methylation levels of candidate genes were determined by pyrosequencing in the replication cohort including 16 patients with AAD and 7 controls. Protein expression level of candidate gene was assessed by Western blot.

Results

A total of 589 differentially methylated positions including 315 hypomethylated and 274 hypermethylated positions were found in AAD group. KEGG analysis demonstrated that differentially methylated position-associated genes were enriched in MAPK signaling pathway, TNF signaling pathway and apoptosis pathway, et al. GO analysis demonstrated that differentially methylated position-associated genes were enriched in protein binding, angiogenesis and heart development et al. The differential DNA methylation in five key genes, including Fas, ANGPT2, DUSP6, FARP1 and CARD6, was authenticated in the independent replication cohort. The protein expression level of the Fas was increased by 1.78 times, indicating the possible role of DNA methylation in regulation of gene expression.

Conclusion

DNA methylation was markedly changed in the aortic tissues of Stanford-A AAD and associated with gene dysregulation, involved in AAD progression.

Supplementary Information

The online version contains supplementary material available at10.1186/s12872-022-02882-5.

Identification of Molecular Regulatory Features and Markers for Acute Type A Aortic Dissection

BACKGROUND

Acute type A aortic dissection (ATAAD) is one of the most lethal cardiovascular diseases, and its molecular mechanism remains unclear.

METHODS

Differentially expressed genes (DEGs) between ATAAD and control were detected by limma R package in GSE52093, GSE153434, GSE98770, and GSE84827, respectively. The coexpression network of DEGs was identified by the WGCNA package. Enrichment analysis was performed for module genes that were positively correlated with ATAAD using clusterProfiler R package. In addition, differentially methylated markers between aortic dissection and control were identified by ChAMP package. After comparing with ATAAD-related genes, a protein-protein interaction (PPI) network was established based on the STRING database. The genes with the highest connectivity were identified as hub genes. Finally, differential immune cell infiltration between ATAAD and control was identified by ssGSEA.

RESULTS

From GSE52093 and GSE153434, 268 module genes were obtained with consistent direction of differential expression and high correlation with ATAAD. They were significantly enriched in T cell activation, HIF-1 signaling pathway, and cell cycle. In addition, 2060 differentially methylated markers were obtained from GSE84827. Among them, 77 methylation markers were ATAAD-related DEGs. Using the PPI network, we identified MYC, ITGA2, RND3, BCL2, and PHLPP2 as hub genes. Finally, we identified significantly differentially infiltrated immune cells in ATAAD.

CONCLUSION

The hub genes we identified may be regulated by methylation and participate in the development of ATAAD through immune inflammation and oxidative stress response. The findings may provide new insights into the molecular mechanisms and therapeutic targets for ATAAD.

Cardiac ECM: Its Epigenetic Regulation and Role in Heart Development and Repair

The extracellular matrix (ECM) is the non-cellular component in the cardiac microenvironment, and serves essential structural and regulatory roles in establishing and maintaining tissue architecture and cellular function. The patterns of molecular and biochemical ECM alterations in developing and adult hearts depend on the underlying injury type. In addition to exploring how the ECM regulates heart structure and function in heart development and repair, this review conducts an inclusive discussion of recent developments in the role, function, and epigenetic guidelines of the ECM. Moreover, it contributes to the development of new therapeutics for cardiovascular disease.