Comprehensive bioinformatics analysis revealed potential key genes and pathways underlying abdominal aortic aneurysm

Identification and Experimental Validation of NETosis-Mediated Abdominal Aortic Aneurysm Gene Signature Using Multi-omics, Machine Learning, and Mendelian Randomization

Abdominal aortic aneurysm (AAA) is a life-threatening disorder with limited therapeutic options. Neutrophil extracellular traps (NETs) are formed by a process known as "NETosis" that has been implicated in AAA pathogenesis, yet the roles and prognostic significance of NET-related genes in AAA remain poorly understood. This study aimed to identify key AAA- and NET-related genes (AAA-NETs-RGs), elucidate their potential mechanisms in contributing to AAA, and explore potential therapeutic compounds for AAA therapy. Through bioinformatics analysis of multiomics and machine learning, we identified six AAA-NETs-RGs: DUSP26, FCN1, MTHFD2, GPRC5C, SEMA4A, and CCR7, which exhibited strong diagnostic potential for predicting AAA progression, were significantly enriched in pathways related to cytokine-cytokine receptor interaction and chemokine signaling. Immune infiltration analysis revealed a causal association between AAA-NETs-RGs and immune cell infiltration. Cell-cell communication analysis indicated that AAA-NETs-RGs predominantly function in smooth muscle cells, B cells, T cells, and NK cells, primarily through cytokine and chemokine signaling. Gene profiling revealed that CCR7 and MTHFD2 exhibited the most significant upregulation in AAA patients compared to non-AAA controls, as well as in in vitro AAA models. Notably, genetic depletion of CCR7 and MTHFD2 strongly inhibited Ang II-induced phenotypic switching, functional impairment, and senescence in vascular smooth muscle cells (VSMCs). Based on AAA-NETs-RGs, molecular docking analysis combined with the Connectivity Map (CMap) database identified mirdametinib as a potential therapeutic agent for AAA. Mirdametinib effectively alleviated Ang II-induced phenotypic switching, biological dysfunction, and senescence. These findings provide valuable insights into understanding the pathophysiology of AAA and highlight promising therapeutic strategies targeting AAA-NETs-RGs.

IRF8 Drives Conventional Type 1 Dendritic Cell Differentiation and CD8+ T Cell Activation to Aggravate Abdominal Aortic Aneurysm Development

Abdominal aortic aneurysm (AAA) is the most common true aneurysm worldwide, and recent studies suggest that dendritic cells (DCs) play a key role in its development, though the specific subtypes and underlying mechanisms remain unclear. In this study, the role of interferon regulatory factor 8 (IRF8) in AAA is investigated by focusing on its effect on the differentiation of DC precursors into conventional type 1 dendritic cells (cDC1s). It is found significant infiltration of HLA-DR+ IRF8+ cells in human AAA tissue samples. In mice, DC-specific overexpression of Irf8 exacerbates aneurysm expansion following periadventitial elastase application, while DC-specific Irf8 deletion attenuates AAA development. Batf3-/- mice, which lack cDC1s, exhibit AAA characteristics similar to the Irf8-deleted mice. Additionally, an increased population of activated CD8+ T cells is observed in the DC-Irf8 overexpressed mice, while the DC-Irf8 deletion mice show a decrease in these cells. Blocking antigen cross-presentation to CD8+ T cells also reduces AAA progression. Tissue microarray analysis of human aortic samples further confirms a correlation between IRF8 expression and AAA development. These findings suggest that IRF8 activation promotes cDC1 differentiation, leading to the recruitment of CD8+ T cells, which contribute to aortic wall destruction and AAA formation.

Identification of endoplasmic reticulum stress-associated lncRNAs influencing inflammation and VSMC function in abdominal aortic aneurysm

Endoplasmic reticulum (ER) stress plays a critical role in the abdominal aortic aneurysm (AAA), a life-threatening disease characterized by inflammation, destructive remodeling, and vascular smooth muscle cells (VSMCs) dysfunction. The current therapy relies on surgical repair, but no effective pharmacological strategies are available to limit aneurysm progression. Long non-coding RNAs (lncRNAs) are essential factors in health and disease; however, their specific contribution to AAA development and its relationship with ER stress remain unexplored. Here, we have performed a whole-genome transcriptomic analysis characterizing the expression profile of lncRNAs in AAA. RNA sequencing was carried out in abdominal aorta from patients with AAA and healthy donors. We identified 6576 differentially expressed (DE)-mRNAs and 1283 DE-lncRNAs. Interestingly, bioinformatic analysis revealed a set of 368 DE-lncRNAs related to ER stress. The differential expression of the most induced lncRNAs (IL-21-AS1, ITPKB-IT, PCED1B-AS1, TCL-6, LINC00494, LINC00582, LINC00626, LINC00861, and LINC00892) was validated in a large cohort of patients with AAA. The ability of these selected lncRNAs to discriminate patients with AAA from healthy subjects was established by receiveroperating characteristic curves and logistic regression analysis. In human aortic VSMC and Jurkat T-cells, tunicamycin-induced ER stress triggered the expression of IL21-AS1, LINC00626, LINC00494, LINC00892, PCED1B-AS1, ITPKB-IT, and TCL-6, while tauroursodeoxycholic acid counteracted these effects. Finally, an integrated analysis of mRNA-lncRNA co-expression revealed the correlation between the selected lncRNAs and the DE-mRNAs involved in immune response and muscle contraction. Therefore, these DE-lncRNAs potentially implicated in the ER stress response, a pathological process in AAA, could be considered as potential therapeutic target to handle AAA.

In-depth computational analysis reveals the significant dysregulation of key gap junction proteins (GJPs) driving thoracic aortic aneurysm development

OBJECTIVE

Thoracic aortic aneurysm (TAA) represents an aortic pathology that is caused by the deranged integrity of the three layers of the aortic wall and is related to severe morbidity and mortality. Consequently, it is crucial to identify the biomarkers implicated in the pathogenesis and biology of TAA. The aim of the current computational study was to assess the differential gene expression profile of the gap junction proteins (GJPs) in patients with TAA to identify novel potential biomarkers for the diagnosis and treatment of this disease.

METHODS

We implemented bioinformatics methodology to construct the gene network of the GJPs family, evaluate their expression in pathologic aortic tissue excised from patients with TAA, and compare it with healthy controls. We also investigated the related biological functions and miRNA families.

RESULTS

We extracted raw data related to the transcriptomic profile of selected genes from a microarray dataset, incorporating 43 TAA and 43 healthy control samples. A total of 17 GJPs were evaluated. Eight GJPs (47%) were downregulated in TAA (GJA3, GJA9, GJA10, GJB1 GJC2, GJD2, GJD3, and GJD4). We also demonstrated the important correlations among the differentially expressed genes (DEGs). Four GJPs (GJA3, GJA9, GJC2, and GJD3) were associated with fair discrimination and calibration traits in predicting TAA presentation. Finally, we performed gene set enrichment analysis (GSEA) and identified the major biological functions and miRNA families (hsa-miR-5001-3p, hsa-miR-942-5p, hsa-miR-7113-3p, hsa-miR-6867-3p, and hsa-miR-4685-3p) associated with the DEGs.

CONCLUSION

These outcomes support the important role of certain gap junction proteins in the pathogenesis of TAA.

CXCL8 upregulation mediates inflammatory cell infiltration and accelerates abdominal aortic aneurysm progression

OBJECTIVE

To explore abdominal aortic aneurysm (AAA) pathogenesis and identify early diagnostic markers, providing a theoretical basis for novel preventive and therapeutic strategies.

METHODS

Gene expression profiles were retrieved from the Gene Expression Omnibus database (datasets: GSE7084, GSE47472, and GSE57691) comprising messenger RNA data from the aortic samples of 69 patients with AAA and 25 non-AAA controls. Data were merged and normalized; bioinformatics analysis was conducted on upregulated differentially expressed genes.

RESULTS

C-X-C motif chemokine ligand 8 (CXCL8) was prominently involved in regulating the chemokine signaling pathway. CXCL8 expression was significantly higher in the aortic walls of patients with AAA than that of controls. NLRP3, interleukin (IL)-18, and IL-1β expression levels were upregulated in patients with AAA and positively correlated with CXCL8 expression. CXCL8 may directly or indirectly interact with NLRP3.

CONCLUSIONS

CXCL8 was upregulated in patients with AAA and induced inflammatory cell infiltration and cytokine secretion. CXCL8-induced NLRP3 inflammasome regulation triggered pyroptosis in vascular smooth muscle cells, exacerbating inflammation and tissue damage in the aortic wall. This degeneration of the aortic media accelerated AAA progression.

Cellular Senescence Genes as Cutting-Edge Signatures for Abdominal Aortic Aneurysm Diagnosis: Potential for Innovative Therapeutic Interventions

Abdominal aortic aneurysm (AAA) is the most prevalent dilated arterial aneurysm that poses a significant threat to older adults, but the molecular mechanisms linking senescence to AAA progression remain poorly understood. This study aims to identify cellular senescence-related genes (SRGs) implicated in AAA development and assess their potential as therapeutic targets. Four hundred and twenty-nine differentially expressed genes (DEGs) were identified from the GSE57691 training set, and 867 SRGs were obtained. Through the intersection of DEGs with SRGs, 19 differentially expressed senescence-related genes (DESRGs) were uncovered. Functional enrichment analysis was performed to explore their biological roles in AAA. To identify hub genes, we applied machine learning algorithms, including LASSO, SVM-RFE and random forest. These hub genes were then validated in two independent datasets. In the initial validation cohort, significant differences in the expression levels of BTG2, ETS1, ID1 and ITPR3 were observed between the AAA and control groups. Receiver operating characteristic (ROC) analysis demonstrated a robust diagnostic performance. Further validation across different AAA stages (small, large and ruptured AAA) identified ETS1 and ITPR3 as potential diagnostic genes. Subsequently, the diagnostic relevance of ETS1 and ITPR3 was further validated in human serum samples and mouse models of AAA. In addition, single-cell RNA sequencing suggests that senescent endothelial cells play a pivotal role in AAA progression, we further confirmed the correlation between ETS1 and ITPR3 and senescent endothelial cells by WB, IF and RT-qPCR. In conclusion, our study reveals the pivotal role of cellular senescence in AAA progression and identifies ETS1 and ITPR3 as promising diagnostic biomarkers.

CRP deposition in human abdominal aortic aneurysm is associated with transcriptome alterations toward aneurysmal pathogenesis: insights from in situ spatial whole transcriptomic analysis

Background

We investigated the effects of C-reactive protein (CRP) deposition on the vessel walls in abdominal aortic aneurysm (AAA) by analyzing spatially resolved changes in gene expression. Our aim was to elucidate the pathways that contribute to disease progression.

Methods

AAA specimens from surgically resected formalin-fixed paraffin-embedded tissues were categorized into the AAA-high CRP [serum CRP ≥ 0.1 mg/dL, diffuse and strong immunohistochemistry (IHC); n = 7 (12 cores)] and AAA-low-CRP [serum CRP < 0.1 mg/dL, weak IHC; n = 3 (5 cores)] groups. Normal aorta specimens obtained during heart transplantation were used as the control group [n = 3 (6 cores)]. Spatially resolved whole transcriptomic analysis was performed, focusing on CD68-positive macrophages, CD45-positive lymphocytes, and αSMA-positive vascular smooth muscle cells.

Results

Spatial whole transcriptomic analysis revealed significant differential expression of 1,086, 1,629, and 1,281 genes between high-CRP and low-CRP groups within CD68-, CD45-, and αSMA-positive cells, respectively. Gene ontology (GO) analysis of CD68-positive macrophages identified clusters related to inflammation, apoptosis, and immune response, with signal transducer and activator of transcription 3 implicated across three processes. Notably, genes involved in blood vessel diameter maintenance were significantly downregulated in the high-CRP group. GO analysis of lymphocytes showed upregulation of leukocyte rolling and the apoptosis pathway, whereas, in smooth muscle cells, genes associated with Nuclear factor kappa B (NF-κB) signaling and c-Jun N-terminal Kinase (JNK) pathway were upregulated, and those related to blood pressure regulation were downregulated in the high-CRP group.

Discussion

CRP deposition was associated with significant transcriptomic changes in macrophages, lymphocytes, and vascular smooth muscle cells in AAA, suggesting its potential role in promoting pro-inflammatory and apoptotic processes, as well as contributing to the degradation of vascular structure and elasticity.

Identification of CCR7 and CBX6 as key biomarkers in abdominal aortic aneurysm: Insights from multi-omics data and machine learning analysis

Abdominal aortic aneurysm (AAA) is a severe vascular condition, marked by the progressive dilation of the abdominal aorta, leading to rupture if untreated. The objective of this study was to identify key biomarkers and decipher the immune mechanisms underlying AAA utilising multi-omics data analysis and machine learning techniques. Single-cell RNA sequencing disclosed a heightened presence of macrophages and CD8-positive alpha-beta T cells in AAA, highlighting their critical role in disease pathogenesis. Analysis of cell-cell communication highlighted augmented interactions between macrophages and dendritic cells derived from monocytes. Enrichment analysis of differential expression gene indicated substantial involvement of immune and metabolic pathways in AAA pathogenesis. Machine learning techniques identified CCR7 and CBX6 as key candidate biomarkers. In AAA, CCR7 expression is upregulated, whereas CBX6 expression is downregulated, both showing significant correlations with immune cell infiltration. These findings provide valuable insights into the molecular mechanisms underlying AAA and suggest potential biomarkers for diagnosis and therapeutic intervention.

Age-Disturbed Vascular Extracellular Matrix Links to Abdominal Aortic Aneurysms

Abdominal aortic aneurysm (AAA) is a common but life-threatening vascular condition in men at an advanced age. However, the underlying mechanisms of age-increased incidence and mortality of AAA remain elusive. Here, we performed RNA sequencing (RNA-seq) of mouse aortas from males (young: 3-month, n = 4 vs old: 23-month, n = 4) and integrated with the data sets of human aortas (young: 20-39, n = 47 vs old: 60-79 years, n = 92) from GTEx project and the data set (GSE183464) for AAA to search for age-shifted aortic aneurysm genes, their relevant biological processes, and signaling pathways. Angiotensin II-induced AAA in mice was used to verify the critical findings. We found 1 001 genes transcriptionally changed with ages in both mouse and human. Most age-increased genes were enriched intracellularly and the relevant biological processes included mitochondrial function and translational controls, whereas the age-decreased genes were largely localized in extracellular regions and cell periphery and the involved biological processes were associated with extracellular matrix (ECM). Fifty-one were known genes for AAA and found dominantly in extracellular region. The common age-shifted vascular genes and known aortic aneurysm genes had shared functional influences on ECM organization, apoptosis, and angiogenesis. Aorta with angiotensin II-induced AAA exhibited similar phenotypic changes in ECM to that in old mice. Together, we present a conserved transcriptional signature for aortic aging and provide evidence that mitochondrial dysfunction and the imbalanced ribosomal homeostasis act likely as driven-forces for aortic aging and age-disturbed ECM is the substrate for developing AAA.

Transcriptomic Analysis of Tight Junction Proteins Demonstrates the Aberrant Expression and Function of Zona Occludens 2 (ZO-2) Protein in Stanford Type A Aortic Dissection

OBJECTIVE

Thoracic aortic aneurysm dissection (TAAD) represents a cardiac surgery emergency characterized by the disrupted integrity of the aortic wall and is associated with poor prognosis. In this context, the identification of biomarkers implicated in the pathobiology of TAAD is crucial. Our aim in the present original in silico study is to assess the differential gene expression profile of the tight junction proteins (TJPs) in patients with TAAD and to propose novel biomarkers for the diagnosis and prognosis of this disease.

METHODS

We implemented bioinformatics methodology in order to construct the gene network of the TJPs family, identify the differentially expressed genes (DEGs) in pathologic aortic tissue excised from patients with TAAD as compared to healthy aortic tissue, and assess the related biological functions and the associated miRNA families.

RESULTS

Data regarding the transcriptomic profile of selected genes were retrieved and incorporated from three microarray datasets, including 23 TAAD and 20 healthy control samples. A total of 32 TJPs were assessed. The zona occludens 2 (ZO-2) protein encoded by the gene TJP2 was significantly under-expressed in patients with TAAD compared to the control group (p = 0.009). ZO-2 was associated with fair discrimination and calibration traits in predicting the TAAD presentation. CpG islands of ZO-2 were demonstrated. No important difference was found regarding ZO-2 expression between aneurysmal non-dissected and healthy control aortic tissue. Finally, we performed gene set enrichment analysis (GSEA) and uncovered the major biological functions and miRNA families (hsa-miR-155-5p, hsa-miR-1-3p, hsa-miR-2118-5p, hsa-miR-4691-3p, and hsa-miR-1229-3p) relevant to ZO-2.

CONCLUSIONS

These outcomes demonstrated the important role of ZO-2 in the pathobiology of TAAD.