Gene Expression Profiles in Human Ruptured and Unruptured Intracranial Aneurysms

Dysregulated Genes and Signaling Pathways in the Formation and Rupture of Intracranial Aneurysm

Intracranial aneurysm (IA) has the potential to rupture. Despite scientific advances, we are still not in a position to screen patients for IA and identify those at risk of rupture. It is critical to comprehend the molecular basis of disease to facilitate the development of novel diagnostic strategies. We used transcriptomics to identify the dysregulated genes and understand their role in the disease biology. In particular, RNA-Seq was performed in tissue samples of controls, unruptured IA, and ruptured IA. Dysregulated genes (DGs) were identified and analyzed to understand the functional aspects of molecules. Subsequently, candidate genes were validated at both transcript and protein level. There were 314 DGs in patients with unruptured IA when compared to control samples. Out of these, SPARC and OSM were validated as candidate molecules in unruptured IA. PI3K-AKT signaling pathway was found to be an important pathway for the formation of IA. Similarly, 301 DGs were identified in the samples of ruptured IA when compared with unruptured IAs. CTSL was found to be a key candidate molecule which along with Hippo signaling pathway may be involved in the rupture of IA. We conclude that activation of PI3K-AKT signaling pathway by OSM along with up-regulation of SPARC is important for the formation of IA. Further, regulation of Hippo pathway through PI3K-AKT signaling results in the down-regulation of YAP1 gene. This along with up-regulation of CTSL leads to further weakening of aneurysm wall and its subsequent rupture.

Multiomics integrated analysis and experimental validation identify TLR4 and ALOX5 as oxidative stress-related biomarkers in intracranial aneurysms

BACKGROUND

Intracranial aneurysm (IA) is a severe cerebrovascular disease, and effective gene therapy and drug interventions for its treatment are still lacking. Oxidative stress (OS) is closely associated with the IA, but the key regulatory genes involved are still unclear. Through multiomics analysis and experimental validation, we identified two diagnostic markers for IA associated with OS.

METHODS

In this study, we first analyzed the IA dataset GSE75436 and conducted a joint analysis of oxidative stress-related genes (ORGs). Differential analysis, functional enrichment analysis, immune infiltration, WGCNA, PPI, LASSO, and other methods were used to identify IA diagnostic markers related to OS. Next, the functions of TLR4 and ALOX5 expression in IA and their potential targeted therapeutic drugs were analyzed. We also performed single-cell sequencing of patient IA and control (superficial temporal artery, STA) tissues. 23,342 cells were captured from 2 IA and 3 STA samples obtained from our center. Cell clustering and annotation were conducted using R software to observe the distribution of TLR4 and ALOX5 expression in IAs. Finally, the expression of TLR4 and ALOX5 were validated in IA patients and in an elastase-induced mouse IA model using experiments such as WB and immunofluorescence.

RESULTS

Through bioinformatics analysis, we identified 16 key ORGs associated with IA pathogenesis. Further screening revealed that ALOX5 and TLR4 were highly expressed to activate a series of inflammatory responses and reduce the production of myocytes. Methotrexate (MTX) may be a potential targeted drug. Single-cell analysis revealed a notable increase in immune cells in the IA group, with ALOX5 and TLR4 primarily localized to monocytes/macrophages. Validation through patient samples and mouse models confirmed high expression of ALOX5 and TLR4 in IAs.

CONCLUSIONS

Bioinformatics analysis indicated that ALOX5 and TLR4 are the most significant ORGs associated with the pathogenesis of IA. Single-cell sequencing and experiments revealed that the high expression of ALOX5 and TLR4 are closely related to IA. These two genes are promising new targets for IA therapy.

Temporal Changes on Postgadolinium MR Vessel Wall Imaging Captures Enhancement Kinetics of Intracranial Atherosclerotic Plaques and Aneurysms

BACKGROUND AND PURPOSE

Analysis of vessel wall contrast kinetics (ie, wash-in/washout) is a promising method for the diagnosis and risk-stratification of intracranial atherosclerotic disease plaque (ICAD-P) and the intracranial aneurysm walls (IA-W). We used black-blood MR imaging or MR vessel wall imaging to evaluate the temporal relationship of gadolinium contrast uptake kinetics in ICAD-Ps and IA-Ws compared with normal anatomic reference structures.

MATERIALS AND METHODS

Patients with ICAD-Ps or IAs who underwent MR vessel wall imaging with precontrast, early postcontrast (5-15 minutes), and delayed postcontrast (20-30 minutes) 3D T1-weighted TSE sequences were retrospectively studied. ROIs of a standardized diameter (2 mm) were used to measure the signal intensities of the cavernous sinus, pituitary infundibulum, temporalis muscle, and choroid plexus. Point ROIs were used for ICAD-Ps and IA-Ws. All ROI signal intensities were normalized to white matter signal intensity obtained using ROIs of 10-mm diameter. Measurements were acquired on precontrast, early postcontrast, and delayed postcontrast 3D T1 TSE sequences for each patient.ajnr;45/9/1206/T1T1T1Table 1:MR-VWI parameters for ICAD-Ps and IAsParameterValueSequence3D TSEScan planeAxialFOV (mm)160TR/TE (ms)800/28-32BW (Hx/pixel)370θ120Acceleration2ETL42Matrix acquisition0.5 mm ×0.5 mmMatrix recon0.5 mm ×0.5 mmNo. of slices/thick120/0.5Note:-FOV indicates field of view; TR, the repetition time; TE, the echo time; BW, bandwidth; ETL, echo train length; Matrix recon, matrix reconstruction.

RESULTS

Ten patients with 17 symptomatic ICAD-Ps and 30 patients with 34 IA-Ws were included and demonstrated persisting contrast uptake (P < .001) of 7.21% and 10.54% beyond the early phase (5-15 minutes postcontrast) and in the delayed phase (20-30 minutes postcontrast) on postcontrast MR vessel wall imaging. However, normal anatomic reference structures including the pituitary infundibulum and cavernous sinus demonstrated a paradoxical contrast washout in the delayed phase. In both ICAD-Ps and IA-Ws, the greatest percentage of quantitative enhancement (>70%-90%) occurred in the early phase of postcontrast imaging, consistent with the rapid contrast uptake kinetics of neurovascular pathology.

CONCLUSIONS

Using standard MR vessel wall imaging techniques, our results demonstrate the effects of gadolinium contrast uptake kinetics in ICAD-Ps and IA-Ws with extended accumulating enhancement into the delayed phase (> 15 minutes) as opposed to normal anatomic reference structures that conversely exhibit decreasing enhancement. Because these relative differences are used to assess qualitative patterns of ICAD-P and IA-W enhancement, our findings highlight the importance of standardizing acquisition time points and MR vessel wall imaging protocols to interpret pathologic enhancement for the risk stratification of cerebrovascular pathologies.

Identifying novel risk genes in intracranial aneurysm by integrating human proteomes and genetics

Genome-wide association studies (GWAS) have become increasingly popular for detecting numerous loci associated with intracranial aneurysm (IA), but how these loci function remains unclear. In this study, we employed an integrative analytical pipeline to efficiently transform genetic associations and identify novel genes for IA. Using multidimensional high-throughput data, we integrated proteome-wide association studies (PWAS), transcriptome-wide association studies (TWAS), Mendelian randomization (MR) and Bayesian co-localization analyses to prioritize genes that can increase IA risk by altering their expression and protein abundances in the brain and blood. Moreover, single-cell RNA sequencing (scRNA-seq) of the circle of Willis was performed to enrich filtered genes in cells, and gene set enrichment analysis (GSEA) was conducted for each gene using bulk RNA-seq data for IA. No significant genes with cis-regulated plasma protein levels were proven to be associated with IA. The protein abundances of five genes in the brain were found to be associated with IA. According to cellular enrichment analysis, these five genes were expressed mainly in the endothelium, fibroblasts and vascular smooth muscle cells. Only three genes, CNNM2, GPRIN3 and UFL1, passed MR and Bayesian co-localization analyses. While UFL1 was not validated in confirmation PWAS as it was not profiled, it was validated in TWAS. GSEA suggested these three genes are associated with the cell cycle. In addition, the protein abundance of CNNM2 was found to be associated with IA rupture (based on PWAS, MR and co-localization analyses). Our findings indicated that CNNM2, GPRIN3 and UFL1 (CNNM2 correlated with IA rupture) are potential IA risk genes that may provide a broad hint for future research on possible mechanisms and therapeutic targets for IA.

Decoding the Cell Atlas and Inflammatory Features of Human Intracranial Aneurysm Wall by Single-Cell RNA Sequencing

BACKGROUND

Intracranial aneurysm (IA) is common and occasionally results in life-threatening hemorrhagic strokes. However, the cell architecture and inflammation in the IA dome remain less understood.

METHODS AND RESULTS

Single-cell RNA sequencing was performed on ruptured and unruptured human IA domes for delineating the cell atlas, gene expression perturbations, and inflammation features. Two external bulk mRNA sequencing-based data sets and serological results of 126 patients were collected for validation. As a result, a total of 21 332 qualified cells were captured. Vascular cells, including endothelial cells, smooth muscle cells, fibroblasts, and pericytes, were assigned in extremely sparse numbers (4.84%), and were confirmed by immunofluorescence staining. Pericytes, characterized by ABCC9 and HIGD1B, were identified in the IA dome for the first time. Abundant immune cells were identified, with the proportion of monocytes/macrophages and neutrophils being remarkably higher in ruptured IA. The lymphocyte compartment was also thoroughly categorized. By leveraging external data sets and machine learning algorithms, macrophages were robustly associated with IA rupture, irrespective of their polarization status. The single nucleotide polymorphism rs2280543, which is identified in East Asian populations, was associated with macrophage metabolic reprogramming through regulating TALDO1 expression.

CONCLUSIONS

This study provides insights into the cellular architecture and inflammatory features in the IA dome and may enlighten novel therapeutics for unruptured IA.

ADORA3: A Key Player in the Pathogenesis of Intracranial Aneurysms and a Potential Diagnostic Biomarker

BACKGROUND

The effects of genes on the development of intracranial aneurysms (IAs) remain to be elucidated, and reliable blood biomarkers for diagnosing IAs are yet to be established. This study aimed to identify genes associated with IAs pathogenesis and explore their diagnostic value by analyzing IAs datasets, conducting vascular smooth muscle cells (VSMC) experiments, and performing blood detection.

METHODS

IAs datasets were collected and the differentially expressed genes were analyzed. The selected genes were validated in external datasets. Autophagy was induced in VSMC and the effect of selected genes was determined. The diagnostic value of selected gene on the IAs were explored using area under curve (AUC) analysis using IAs plasma samples.

RESULTS

Analysis of 61 samples (32 controls and 29 IAs tissues) revealed a significant increase in expression of ADORA3 compared with normal tissues using empirical Bayes methods of "limma" package; this was further validated by two external datasets. Additionally, induction of autophagy in VSMC lead to upregulation of ADORA3. Conversely, silencing ADORA3 suppressed VSMC proliferation and autophagy. Furthermore, analysis of an IAs blood sample dataset and clinical plasma samples demonstrated increased ADORA3 expression in patients with IA compared with normal subjects. The diagnostic value of blood ADORA3 expression in IAs was moderate when analyzing clinical samples (AUC: 0.756). Combining ADORA3 with IL2RB or CCR7 further enhanced the diagnostic ability for IAs, with the AUC value over 0.83.

CONCLUSIONS

High expression of ADORA3 is associated with IAs pathogenesis, likely through its promotion of VSMC autophagy. Furthermore, blood ADORA3 levels have the potential to serve as an auxiliary diagnostic biomarker for IAs.

Transcription factor CEBPB mediates intracranial aneurysm rupture by inflammatory and immune response

INTRODUCTION

Genetic factors play a major part in mediating intracranial aneurysm (IA) rupture. However, research on the role of transcription factors (TFs) in IA rupture is rare.

AIMS

Bioinformatics analysis was performed to explore the TFs and related functional pathways involved in IA rupture.

RESULTS

A total of 63 differentially expressed transcription factors (DETFs) were obtained. Significantly enriched biological processes of these DETFs were related to regulation of myeloid leukocyte differentiation. The top 10 DETFs were screened based on the MCC algorithm from the protein-protein interaction network. After screening and validation, it was finally determined that CEBPB may be the hub gene for aneurysm rupture. The GSEA results of CEBPB were mainly associated with the inflammatory response, which was also verified by the experimental model of cellular inflammation in vitro.

CONCLUSION

The inflammatory and immune response may be closely associated with aneurysm rupture. CEBPB may be the hub gene for aneurysm rupture and may have diagnostic value. Therefore, CEBPB may serve as the diagnostic signature for RIAs and a potential target for intervention.

Treatment of aneurysmal artery with PED: A case report

RATIONALE

Pipeline embolization devices are a new treatment for intracranial aneurysms, especially irregular, giant aneurysms.

PATIENT CONCERNS

A 48-year-old female patient presented with a headache in the frontal part for 3 weeks.

DIAGNOSES

Cerebral computed tomographic angiography and magnetic resonance angiography showed a saccular aneurysm in the right internal carotid artery that wrapped the parent artery. Digital subtraction angiography provided images with 1 large saccular internal carotid aneurysm.

INTERVENTIONS

The patient was treated by flow diverter stent and coil embolization and dual antiplatelet therapy with aspirin and ticagrelor in the ICU and was discharged after 10 days without complications.

OUTCOMES

One year after interventional therapy, repeated digital subtraction angiography showed no recurrence of aneurysm and embolization well, and the patient reported improvement in neurological symptoms.

LESSONS

Aneurysmal parent artery is a rare phenomenon. The combination of flow diverter stents and coil embolization to treat cases with large saccular aneurysms has important clinical significance and this may provide a reference for clinical treatment of aneurysmal parent artery.

The Role and Therapeutic Implications of Inflammation in the Pathogenesis of Brain Arteriovenous Malformations

Brain arteriovenous malformations (bAVMs) are focal vascular lesions composed of abnormal vascular channels without an intervening capillary network. As a result, high-pressure arterial blood shunts directly into the venous outflow system. These high-flow, low-resistance shunts are composed of dilated, tortuous, and fragile vessels, which are prone to rupture. BAVMs are a leading cause of hemorrhagic stroke in children and young adults. Current treatments for bAVMs are limited to surgery, embolization, and radiosurgery, although even these options are not viable for ~20% of AVM patients due to excessive risk. Critically, inflammation has been suggested to contribute to lesion progression. Here we summarize the current literature discussing the role of the immune system in bAVM pathogenesis and lesion progression, as well as the potential for targeting inflammation to prevent bAVM rupture and intracranial hemorrhage. We conclude by proposing that a dysfunctional endothelium, which harbors the somatic mutations that have been shown to give rise to sporadic bAVMs, may drive disease development and progression by altering the immune status of the brain.

Common mechanisms of physiological and pathological rupture events in biology: novel insights into mammalian ovulation and beyond

Ovulation is a cyclical biological rupture event fundamental to fertilisation and endocrine function. During this process, the somatic support cells that surround the germ cell undergo a remodelling process that culminates in breakdown of the follicle wall and release of a mature egg. Ovulation is driven by known proteolytic and inflammatory pathways as well as structural alterations to the follicle vasculature and the fluid-filled antral cavity. Ovulation is one of several types of systematic remodelling that occur in the human body that can be described as rupture. Although ovulation is a physiological form of rupture, other types of rupture occur in the human body which can be pathological, physiological, or both. In this review, we use intracranial aneurysms and chorioamniotic membrane rupture as examples of rupture events that are pathological or both pathological and physiological, respectively, and compare these to the rupture process central to ovulation. Specifically, we compared existing transcriptomic profiles, immune cell functions, vascular modifications, and biomechanical forces to identify common processes that are conserved between rupture events. In our transcriptomic analysis, we found 12 differentially expressed genes in common among two different ovulation data sets and one intracranial aneurysm data set. We also found three genes that were differentially expressed in common for both ovulation data sets and one chorioamniotic membrane rupture data set. Combining analysis of all three data sets identified two genes (Angptl4 and Pfkfb4) that were upregulated across rupture systems. Some of the identified genes, such as Rgs2, Adam8, and Lox, have been characterised in multiple rupture contexts, including ovulation. Others, such as Glul, Baz1a, and Ddx3x, have not yet been characterised in the context of ovulation and warrant further investigation as potential novel regulators. We also identified overlapping functions of mast cells, macrophages, and T cells in the process of rupture. Each of these rupture systems share local vasoconstriction around the rupture site, smooth muscle contractions away from the site of rupture, and fluid shear forces that initially increase and then decrease to predispose one specific region to rupture. Experimental techniques developed to study these structural and biomechanical changes that underlie rupture, such as patient-derived microfluidic models and spatiotemporal transcriptomic analyses, have not yet been comprehensively translated to the study of ovulation. Review of the existing knowledge, transcriptomic data, and experimental techniques from studies of rupture in other biological systems yields a better understanding of the physiology of ovulation and identifies avenues for novel studies of ovulation with techniques and targets from the study of vascular biology and parturition.

Integrative analysis of multi-omics data to identify three immune-related genes in the formation and progression of intracranial aneurysms

OBJECTIVE AND DESIGN

The prevalence of intracranial aneurysms (IAs) has increased globally. We performed bioinformatics analysis to identify key biomarkers associated with IA formation.

METHODS AND RESULTS

We conducted a comprehensive analysis combined with multi-omics data and methods to identify immune-related genes (IRGs) and immunocytes involved in IAs. Functional enrichment analyses showed enhanced immune responses and suppressed organizations of extracellular matrix (ECM) during aneurysm progression. xCell analyses showed that the abundance of B cells, macrophages, mast cells, and monocytes significantly increased from levels in control to unruptured aneurysms and to ruptured aneurysms. Of 21 IRGs identified by overlapping, a three-gene (CXCR4, S100B, and OSM) model was constructed through LASSO logistic regression. The diagnostic ability of the three biomarkers in discriminating aneurysms from the control samples demonstrated a favorable diagnostic value. Among the three genes, OSM and CXCR4 were up-regulated and hypomethylated in IAs, while S100B was down-regulated and hypermethylated. The expression of the three IRGs was further validated by qRT-PCR and immunohistochemistry and mouse IA model using scRNA-seq analysis.

CONCLUSION

The present study demonstrated heightened immune response and suppressed ECM organization in aneurysm formation and rupture. The three-gene immune-related signature (CCR4, S100B, and OSM) model may facilitate IA diagnosis and prevention.

Transcriptomic Studies on Intracranial Aneurysms

Intracranial aneurysm (IA) is a relatively common vascular malformation of an intracranial artery. In most cases, its presence is asymptomatic, but IA rupture causing subarachnoid hemorrhage is a life-threating condition with very high mortality and disability rates. Despite intensive studies, molecular mechanisms underlying the pathophysiology of IA formation, growth, and rupture remain poorly understood. There are no specific biomarkers of IA presence or rupture. Analysis of expression of mRNA and other RNA types offers a deeper insight into IA pathobiology. Here, we present results of published human studies on IA-focused transcriptomics.

A two-stage hybrid gene selection algorithm combined with machine learning models to predict the rupture status in intracranial aneurysms

An IA is an abnormal swelling of cerebral vessels, and a subset of these IAs can rupture causing aneurysmal subarachnoid hemorrhage (aSAH), often resulting in death or severe disability. Few studies have used an appropriate method of feature selection combined with machine learning by analyzing transcriptomic sequencing data to identify new molecular biomarkers. Following gene ontology (GO) and enrichment analysis, we found that the distinct status of IAs could lead to differential innate immune responses using all 913 differentially expressed genes, and considering that there are numerous irrelevant and redundant genes, we propose a mixed filter- and wrapper-based feature selection. First, we used the Fast Correlation-Based Filter (FCBF) algorithm to filter a large number of irrelevant and redundant genes in the raw dataset, and then used the wrapper feature selection method based on the he Multi-layer Perceptron (MLP) neural network and the Particle Swarm Optimization (PSO), accuracy (ACC) and mean square error (MSE) were then used as the evaluation criteria. Finally, we constructed a novel 10-gene signature (YIPF1, RAB32, WDR62, ANPEP, LRRCC1, AADAC, GZMK, WBP2NL, PBX1, and TOR1B) by the proposed two-stage hybrid algorithm FCBF-MLP-PSO and used different machine learning models to predict the rupture status in IAs. The highest ACC value increased from 0.817 to 0.919 (12.5% increase), the highest area under ROC curve (AUC) value increased from 0.87 to 0.94 (8.0% increase), and all evaluation metrics improved by approximately 10% after being processed by our proposed gene selection algorithm. Therefore, these 10 informative genes used to predict rupture status of IAs can be used as complements to imaging examinations in the clinic, meanwhile, this selected gene signature also provides new targets and approaches for the treatment of ruptured IAs.

m6A regulator–mediated RNA methylation modification patterns and immune microenvironment infiltration characterization in patients with intracranial aneurysms

Background

The role of epigenetic modulation in immunity is receiving increased recognition—particularly in the context of RNA N6-methyladenosine (m6A) modifications. Nevertheless, it is still uncertain whether m6A methylation plays a role in the onset and progression of intracranial aneurysms (IAs). This study aimed to establish the function of m6A RNA methylation in IA, as well as its correlation with the immunological microenvironment.

Methods

Our study included a total of 97 samples (64 IA, 33 normal) in the training set and 60 samples (44 IA, 16 normal) in the validation set to systematically assess the pattern of RNA modifications mediated by 22 m6A regulators. The effects of m6A modifications on immune microenvironment features, i.e., immune response gene sets, human leukocyte antigen (HLA) genes, and infiltrating immune cells were explored. We employed Lasso, machine learning, and logistic regression for the purpose of identifying an m6A regulator gene signature of IA with external data validation. For the unsupervised clustering analysis of m6A modification patterns in IA, consensus clustering methods were employed. Enrichment analysis was used to assess immune response activity along with other functional pathways. The identification of m6A methylation markers was identified based on a protein–protein interaction network and weighted gene co-expression network analysis.

Results

We identified an m6A regulator signature of IGFBP2, IGFBP1, IGF2BP2, YTHDF3, ALKBH5, RBM15B, LRPPRC, and ELAVL1, which could easily distinguish individuals with IA from healthy individuals. Unsupervised clustering revealed three m6A modification patterns. Gene enrichment analysis illustrated that the tight junction, p53 pathway, and NOTCH signaling pathway varied significantly in m6A modifier patterns. In addition, the three m6A modification patterns showed significant differences in m6A regulator expression, immune microenvironment, and bio-functional pathways. Furthermore, macrophages, activated T cells, and other immune cells were strongly correlated with m6A regulators. Eight m6A indicators were discovered—each with a statistically significant correlation with IA—suggesting their potential as prognostic biological markers.

Conclusion

Our study demonstrates that m6A RNA methylation and the immunological microenvironment are both intricately correlated with the onset and progression of IA. The novel insight into patterns of m6A modification offers a foundation for the development of innovative treatment approaches for IA.

Identification of Potential Core Genes for the Rupture of Intracranial Aneurysms by a Bioinformatics Analysis

Background: Previous studies, using autopsy and angiography, have shown that 3.6–6% of the population have intracranial aneurysms, and the rupture of aneurysm can lead to brain dysfunction or even death in patients.

Methods: To explore potential preventional target genes for the ruptured of aneurysm, we analyze three gene expression datasets (GSE13353, GSE15629 and GSE54083) derived from the GEO database. We confirm DEGs associated with the unrupture of aneurysms by R package. DAVID version provides functional classification and annotation analyses of associated genes, including GO and KEGG pathway. PPI of these DEGs is analyzed based on the string database and visualized by Cytoscape software. DEGs are verified by qRT-PCR using samples isolated from the patients.

Results: 249 overlapping DEGs, including 96 up-regulated genes and 153 down-regulated genes are screened using the Venn diagram webtool. The GO term and KEGG pathways analysis results indicate that these DEGs are mainly enriched in protein phosphorylation, apoptotic process and inflammatory response in the BP term and focal adhesion, thyroid hormone signaling pathway, ErbB signaling pathway, cytokine-cytokine receptor interaction and some disease processes in the KEGG pathways. 6 candidates are confirmed by Cytoscape software and qRT-PCR, including APP, JUN, GSK3B, ErbB2, PPBP and THBS1.

Conclusions: Our data and previous studies show that ErbB2 and THBS1 are crucial to prevent aneurysm rupture, while APP, JUN, GSK3B and PPBP performs the opposite role, and further experiments are needed to verify these findings.

Investigation of molecular regulation mechanism under the pathophysiology of subarachnoid hemorrhage

This study aimed to investigate the molecular mechanism under the pathophysiology of subarachnoid hemorrhage (SAH) and identify the potential biomarkers for predicting the risk of SAH. Differentially expressed mRNAs (DEGs), microRNAs, and lncRNAs were screened. Protein-protein interaction (PPI), drug-gene, and competing endogenous RNA (ceRNA) networks were constructed to determine candidate RNAs. The optimized RNAs signature was established using least absolute shrinkage and selection operator and recursive feature elimination algorithms. A total of 124 SAH-related DEGs were identified, and were enriched in inflammatory response, TNF signaling pathway, and others. PPI network revealed 118 hub genes such as TNF, MMP9, and TLR4. Drug-gene network revealed that chrysin targeted more genes, such as TNF and MMP9. JMJD1C-AS-hsa-miR-204-HDAC4/SIRT1 and LINC01144-hsa-miR-128-ADRB2/TGFBR3 regulatory axes were found from ceRNA network. From these networks, 125 candidate RNAs were obtained. Of which, an optimal 38 RNAs signatures (2 lncRNAs, 1 miRNA, and 35 genes) were identified to construct a Support Vector Machine classifier. The predictive value of 38 biomarkers had an AUC of 0.990. Similar predictive performance was found in external validation dataset (AUC of 0.845). Our findings provided the potential for 38 RNAs to serve as biomarkers for predicting the risk of SAH. However, their application values should be further validated in clinical.

Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture

The prevalence of intracranial aneurysm (IA) is increasing, and the consequences of its rupture are severe. This study aimed to reveal specific, sensitive, and non-invasive biomarkers for diagnosis and classification of ruptured and unruptured IA, to benefit the development of novel treatment strategies and therapeutics altering the course of the disease. We first assembled an extensive candidate biomarker bank of IA, comprising up to 717 proteins, based on altered proteins discovered in the current tissue and serum proteomic analysis, as well as from previous studies. Mass spectrometry assays for hundreds of biomarkers were efficiently designed using our proposed deep learning-based method, termed DeepPRM. A total of 113 potential markers were further quantitated in serum cohort I (n = 212) & II (n = 32). Combined with a machine-learning-based pipeline, we built two sets of biomarker combinations (P6 & P8) to accurately distinguish IA from healthy controls (accuracy: 87.50%) or classify IA rupture patients (accuracy: 91.67%) upon evaluation in the external validation set (n = 32). This extensive circulating biomarker development study provides valuable knowledge about IA biomarkers.

Comprehensive mass spectrometry for development of proteomic biomarkers of intracranial aneurysms

Protein biomarkers of intracranial aneurysm (IA) are essential for early detection and prediction of its rupture to facilitate the diagnosis and clinical management of the disease, monitor treatment response and detect recurrence. Here, we developed a comprehensive strategy for IA biomarker discovery by analyzing tissues from an animal model (n = 4) and serum from human patients (n = 60) using isobaric tandem mass tags-based quantitative proteomics. A total of 4811 and 562 proteins were identified from aneurysm tissue and serum samples, respectively. The 223 candidate protein biomarkers were further validated in an independent serum cohort (n = 30) by multiple reaction monitoring analysis. Combined with a logistic regression model, we built a diagnostic classifier P2 (FCN2 & RARRES2) to differentiate IA from healthy controls with accuracy of 93.3%, as well as a diagnostic classifier P7 (ADAM12, APOL3, F9, C3, CEACAM1, ICAM3, KLHDC7A) to classify ruptured IA from unruptured IA with accuracy of 95.0%. Taken together, our results suggest a valuable strategy for biomarker discovery and patient stratification in IA.

RNA Sequencing Data from Human Intracranial Aneurysm Tissue Reveals a Complex Inflammatory Environment Associated with Rupture

BACKGROUND

Intracranial aneurysm (IA) rupture leads to deadly subarachnoid hemorrhages. However, the mechanisms leading to rupture remain poorly understood. Altered gene expression within IA tissue is linked to the pathobiology of aneurysm development and progression. Here, we analyzed expression patterns of control tissue samples and compared them to those of unruptured and ruptured IA tissue samples using data from the Gene Expression Omnibus (GEO).

METHODS

FASTQ files for 21 ruptured IAs, 21 unruptured IAs, and 16 control tissue samples were accessed from the GEO database. DESeq2 was used for differential expression analysis in three comparisons: unruptured IA versus control, ruptured IA versus control, and ruptured versus unruptured IA. Genes that were differentially expressed in multiple comparisons were evaluated to find those progressively increasing/decreasing from control to unruptured to ruptured. Significance was tested by either analysis of variance/Gabriel or Brown-Forsythe/Games Howell (p < 0.05 was considered significant). We used additional RNA sequencing and proteomics datasets to evaluate if our differentially expressed genes (DEGs) were present in other studies. Bioinformatics analyses were performed with g:Profiler and Ingenuity Pathway Analysis.

RESULTS

In total, we identified 1768 DEGs, of which 318 were found in multiple comparisons. Unruptured versus control reflected vascular remodeling processes, while ruptured versus control reflected inflammatory responses and cell activation/signaling. When comparing ruptured to unruptured IAs, we found massive activation of inflammation, inflammatory responses, and leukocyte responses. Of the 318 genes in multiple comparisons, 127 were found to be significant in the multi-cohort correlation analysis. Those that progressively increased (70 genes) were associated with immune system processes, while those that progressively decreased (38 genes) did not return any gene ontology terms. Many of our DEGs were also found in the other IA tissue sequencing studies.

CONCLUSIONS

We found unruptured IAs relate more to remodeling processes, while ruptured IAs reflect more inflammatory and immune responses.

Identification of Hub Genes Associated with the Pathogenesis of Intracranial Aneurysm via Integrated Bioinformatics Analysis

BACKGROUND

At present, the pathogenesis of intracranial aneurysms (IA) remains unclear, which significantly hinders the development of novel strategies for the clinical treatment. In this study, bioinformatics methods were used to identify the potential hub genes and pathways associated with the pathogenesis of IA.

METHODS

The gene expression datasets of patients with intracranial aneurysm were downloaded from the Gene Expression Database (GEO), and the different data sets were integrated by the robust rank aggregation (RRA) method to identify the differentially expressed genes between patients with intracranial aneurysm and the controls. The functional enrichment analyses of the significant differentially expressed genes (DEGs) were performed and the protein-protein interaction (PPI) network was constructed; thereafter, the hub genes were screened by cytoHubba plug-in of Cytoscape, and finally sequencing dataset GSE122897 was used to verify the hub genes.

RESULTS

The GSE15629, GSE75436, GSE26969, and GSE6551 expression profiles have been included in this study, including 34 intracranial aneurysm samples and 26 control samples. The four datasets obtained 136 significant DEGs (45 up-regulated, 91 down-regulated). Enrichment analysis showed that the extracellular matrix structural constituent and the ECM-receptor interaction were closely related to the occurrence of IA. It was finally determined that eight hub genes associated with the development of IA, including VCAN, COL1A1, COL11A1, COL5A1, COL5A2, POSTN, THBS2, and CDH2.

CONCLUSION

The discovery of potential hub genes and pathways could enhance the understanding of the molecular mechanisms associated with the development of IA. These hub genes may be potential therapeutic targets for the management and new biomarker for the diagnosis of IA.

A Rare Variant of ANK3 Is Associated With Intracranial Aneurysm

Intracranial aneurysm (IA) is a cerebrovascular disorder in which abnormal dilation of a blood vessel results from weakening of the blood vessel wall. The aneurysm may rupture, leading to subarachnoid hemorrhage with severe outcomes. This study was conducted to identify the genetic factors involved in the etiology of IA. Whole-exome sequencing was performed in three IA-aggregate families to identify candidate variants. Further association studies of candidate variants were performed among sporadic cases and controls. Bioinformatic analysis was used to predict the functions of candidate genes and variants. Twenty variants were identified after whole-exome sequencing, among which eight were selected for replicative association studies. ANK3 c.4403G>A (p.R1468H) was significantly associated with IA (odds ratio 4.77; 95% confidence interval 1.94–11.67; p-value = 0.00019). Amino acid R1468 in ANK3 was predicted to be located in the spectrin-binding domain of ankyrin-G and may regulate the migration of vascular endothelial cells and affect cell–cell junctions. Therefore, the variation p.R1468H may cause weakening of the artery walls, thereby accelerating the formation of IA. Thus, ANK3 is a candidate gene highly related to IA.

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression

BACKGROUND

Genome-wide association studies have identified many single nucleotide polymorphisms (SNPs) associated with increased risk for intracranial aneurysm (IA). However, how such variants affect gene expression within IA is poorly understood. We used publicly-available ChIP-Seq data to study chromatin landscapes surrounding risk loci to determine whether IA-associated SNPs affect functional elements that regulate gene expression in cell types comprising IA tissue.

METHODS

We mapped 16 significant IA-associated SNPs to linkage disequilibrium (LD) blocks within human genome. Using ChIP-Seq data, we examined these regions for presence of H3K4me1, H3K27ac, and H3K9ac histone marks (typically associated with latent/active enhancers). This analysis was conducted in several cell types that are present in IA tissue (endothelial cells, smooth muscle cells, fibroblasts, macrophages, monocytes, neutrophils, T cells, B cells, NK cells). In cell types with significant histone enrichment, we used HiC data to investigate topologically associated domains (TADs) encompassing the LD blocks to identify genes that may be affected by IA-associated variants. Bioinformatics were performed to determine the biological significance of these genes. Genes within HiC-defined TADs were also compared to differentially expressed genes from RNA-seq/microarray studies of IA tissues.

RESULTS

We found that endothelial cells and fibroblasts, rather than smooth muscle or immune cells, have significant enrichment for enhancer marks on IA risk haplotypes (p < 0.05). Bioinformatics demonstrated that genes within TADs subsuming these regions are associated with structural extracellular matrix components and enzymatic activity. The majority of histone marked TADs (83% fibroblasts [IMR90], 77% HUVEC) encompassed at least one differentially expressed gene from IA tissue studies.

CONCLUSIONS

These findings provide evidence that genetic variants associated with IA risk act on endothelial cells and fibroblasts. There is strong circumstantial evidence that this may be mediated through altered enhancer function, as genes in TADs encompassing enhancer marks have also been shown to be differentially expressed in IA tissue. These genes are largely related to organization and regulation of the extracellular matrix. This study builds upon our previous (Poppenberg et al., BMC Med Genomics, 2019) by including a more diverse set of data from additional cell types and by identifying potential affected genes (i.e. those in TADs).

Identification of Circulating Gene Expression Signatures of Intracranial Aneurysm in Peripheral Blood Mononuclear Cells

Peripheral blood mononuclear cells (PBMCs) play an important role in the inflammation that accompanies intracranial aneurysm (IA) pathophysiology. We hypothesized that PBMCs have different transcriptional profiles in patients harboring IAs as compared to IA-free controls, which could be the basis for potential blood-based biomarkers for the disease. To test this, we isolated PBMC RNA from whole blood of 52 subjects (24 with IA, 28 without) and performed next-generation RNA sequencing to obtain their transcriptomes. In a randomly assigned discovery cohort of n = 39 patients, we performed differential expression analysis to define an IA-associated signature of 54 genes (q < 0.05 and an absolute fold-change ≥ 1.3). In the withheld validation dataset, these genes could delineate patients with IAs from controls, as the majority of them still had the same direction of expression difference. Bioinformatics analyses by gene ontology enrichment analysis and Ingenuity Pathway Analysis (IPA) demonstrated enrichment of structural regulation processes, intracellular signaling function, regulation of ion transport, and cell adhesion. IPA analysis showed that these processes were likely coordinated through NF-kB, cytokine signaling, growth factors, and TNF activity. Correlation analysis with aneurysm size and risk assessment metrics showed that 4/54 genes were associated with rupture risk. These findings highlight the potential to develop predictive biomarkers from PBMCs to identify patients harboring IAs.

Gene expression profiling of brain endothelial cells after experimental subarachnoid haemorrhage

Subarachnoid haemorrhage (SAH) is a type of hemorrhagic stroke that is associated with high morbidity and mortality. New effective treatments are needed to improve outcomes. The pathophysiology of SAH is complex and includes early brain injury and delayed cerebral ischemia, both of which are characterized by blood–brain barrier (BBB) impairment. We isolated brain endothelial cells (BECs) from mice subjected to SAH by injection of blood into the prechiasmatic cistern. We used gene expression profiling to identify 707 unique genes (2.8% of transcripts, 403 upregulated, 304 downregulated, 24,865 interrogated probe sets) that were significantly differentially expressed in mouse BECs after SAH. The pathway involving prostaglandin synthesis and regulation was significantly upregulated after SAH, including increased expression of the Ptgs2 gene and its corresponding COX-2 protein. Celecoxib, a selective COX-2 inhibitor, limited upregulation of Ptgs2 in BECs. In this study, we have defined the gene expression profiling of BECs after experimental SAH and provide further insight into BBB pathophysiology, which may be relevant to other neurological diseases such as traumatic brain injury, brain tumours, ischaemic stroke, multiple sclerosis, and neurodegenerative disorders.

Vascular Macrophages as Therapeutic Targets to Treat Intracranial Aneurysms

Aneurysmal subarachnoid hemorrhage (aSAH) is a highly fatal and morbid type of hemorrhagic strokes. Intracranial aneurysms (ICAs) rupture cause subarachnoid hemorrhage. ICAs formation, growth and rupture involves cellular and molecular inflammation. Macrophages orchestrate inflammation in the wall of ICAs. Macrophages generally polarize either into classical inflammatory (M1) or alternatively-activated anti-inflammatory (M2)-phenotype. Macrophage infiltration and polarization toward M1-phenotype increases the risk of aneurysm rupture. Strategies that deplete, inhibit infiltration, ameliorate macrophage inflammation or polarize to M2-type protect against ICAs rupture. However, clinical translational data is still lacking. This review summarizes the contribution of macrophage led inflammation in the aneurysm wall and discuss pharmacological strategies to modulate the macrophageal response during ICAs formation and rupture.

Protocatechuic acid attenuates cerebral aneurysm formation and progression by inhibiting TNF-alpha/Nrf-2/NF-kB-mediated inflammatory mechanisms in experimental rats

Our current research aims to examine whether protocatechuic acid (PCA) can be used as a therapeutic agent for the development of cerebral aneurysm (CA) and to elucidate the mechanisms behind this. We assessed the effects of PCA at 50 and 100 mg/kg on the activation of signaling pathways for tissue necrosis factor (TNF)-α/nuclear factor (NF)-κB/nuclear factor erythroid 2 (Nrf-2) on progression and development in an elastase-induced CA model, accompanied by a high-salt diet to induce hypertension. The expression of inflammatory cytokines, chemokines, tumor necrosis factor-α, interleukins (IL)-8, IL-17, IL-6, IL-1β, and matrix metalloproteinase (MMP)-2 and MMP-9 was analyzed by ELISA, western blot, and reverse transcriptase quantative polymerase chain reaction. The expression levels of antioxidant enzymes and translocation of Nrf-2 were also determined. The group treated with PCA demonstrated a significant (P < 0.05) decrease in the aneurysmal size in rats compared to the CA-induced group. We found that PCA treatment suppressed the invasion of macrophage and activation of TNF-α/NF-κB/Nrf-2 signaling pathways. There was a significant decrease (P < 0.05) in pro-inflammatory cytokine and chemokine levels in a dose-dependent manner. We found that PCA treatment exerts protective effects by suppressing the development and progression of CA through the inhibition of inflammatory responses in macrophages via TNF-α/NF-κB/Nrf-2 signaling pathways, thus demonstrating that PCA can act as a treatment for CA.

Endogenous animal models of intracranial aneurysm development: a review

The pathogenesis and natural history of intracranial aneurysm (IA) remains poorly understood. To this end, animal models with induced cerebral vessel lesions mimicking human aneurysms have provided the ability to greatly expand our understanding. In this review, we comprehensively searched the published literature to identify studies that endogenously induced IA formation in animals. Studies that constructed aneurysms (i.e., by surgically creating a sac) were excluded. From the eligible studies, we reported information including the animal species, method for aneurysm induction, aneurysm definitions, evaluation methods, aneurysm characteristics, formation rate, rupture rate, and time course. Between 1960 and 2019, 174 articles reported endogenous animal models of IA. The majority used flow modification, hypertension, and vessel wall weakening (i.e., elastase treatment) to induce IAs, primarily in rats and mice. Most studies utilized subjective or qualitative descriptions to define experimental aneurysms and histology to study them. In general, experimental IAs resembled the pathobiology of the human disease in terms of internal elastic lamina loss, medial layer degradation, and inflammatory cell infiltration. After the early 2000s, many endogenous animal models of IA began to incorporate state-of-the-art technology, such as gene expression profiling and 9.4-T magnetic resonance imaging (MRI) in vivo imaging, to quantitatively analyze the biological mechanisms of IA. Future studies aimed at longitudinally assessing IA pathobiology in models that incorporate aneurysm growth will likely have the largest impact on our understanding of the disease. We believe this will be aided by high-resolution, small animal, survival imaging, in situ live-cell imaging, and next-generation omics technology.

Comparative bioinformatics analysis between proteomes of rabbit aneurysm model and human intracranial aneurysm with label-free quantitative proteomics

Aims

This study aimed to find critical proteins involved in the development of intracranial aneurysm by comparing proteomes of rabbit aneurysm model and human aneurysms.

Methods

Five human intracranial aneurysm samples and 5 superficial temporal artery samples, and 4 rabbit aneurysm samples and 4 control samples were collected for protein mass spectrometry. Four human intracranial aneurysm samples and 4 superficial temporal artery samples, and 6 rabbit aneurysm samples and 6 control samples were used for immunochemistry.

Results

Proteomic analysis revealed 180 significantly differentially expressed proteins in human intracranial aneurysms and 716 significantly differentially expressed proteins in rabbit aneurysms. Among them, 57 proteins were differentially expressed in both species, in which 24 were increased and 33 were decreased in aneurysms compared to the control groups. Proteins were involved in focal adhesion and extracellular matrix‐receptor interaction pathways. We found that COL4A2, MYLK, VCL, and TAGLN may be related to aneurysm development.

Conclusion

Proteomics analysis provided fundamental insights into the pathogenesis of aneurysm. Proteins related to focal adhesion and extracellular matrix‐receptor interaction pathways play an important role in the occurrence and development of intracranial aneurysm.

Roles of inflammation in the natural history of intracranial saccular aneurysms

Aneurysmal subarachnoid hemorrhage is caused by intracranial aneurysm (IA) rupture and results in high rates of mortality and morbidity. Factors contributing to IA generation, growth and rupture can involve genetics, injury, hemodynamics, environmental factors, and inflammation, in which inflammatory factors are believed to play central roles in the whole natural history. Inflammatory reactions that contribute to IA development may involve synthesis of many functional proteins and expression of genes induced by changes of blood flow, external stimuli such as smoking, internal balance such as hormonal status changes, and blood pressure. Meanwhile, inflammatory reactions itself can evoke inflammatory cytokines release and aggregation such as MMPs, MCP-1, TNF-α and ZO-1, directly or indirectly promoting aneurysm growth and rupture. However, the details of these inflammatory reactions and their action on inflammatory chemokines are still unknown. Moreover, some agents with the function of anti-inflammation, lipid-lowering, antihypertension or inflammatory factor inhibition may have the potential benefit to reduce the risk of aneurysm development or rupture in a group of population despite the underlying mechanism remains unclear. Consequently, we reviewed the potential inflammatory responses and their mechanisms contributing to aneurysm development and rupture and sought intervention targets that may prevent IA rupture or generation.

Identification and validation of key genes mediating intracranial aneurysm rupture by weighted correlation network analysis

Background

Rupture of intracranial aneurysm (IA) is the leading cause of subarachnoid hemorrhage. However, there are few pharmacological therapies available for the prevention of IA rupture. Therefore, exploring the molecular mechanisms which underlie IA rupture and identifying the potential molecular targets for preventing the rupture of IA is of vital importance.

Methods

We used the Gene Expression Omnibus (GEO) datasets GSE13353, GSE15629, and GSE54083 in our study. The 3 datasets were merged and normalized. Differentially expressed gene (DEG) screening and weighted correlation network analysis (WGCNA) were conducted. The co-expression patterns between ruptured IA samples and unruptured IA samples were compared. Then, the DEGs were mapped into the whole co-expression network of ruptured IA samples, and a DEG co-expression network was generated. Molecular Complex Detection (MCODE) (http://baderlab.org/Software/MCODE) was used to identify key genes based on the DEG co-expression network. Finally, key genes were validated using another GEO dataset (GSE122897), and their potential diagnostic values were shown using receiver operating characteristic (ROC) analysis.

Results

In our study, 49 DEGs were screened while 8 and 6 gene modules were detected based on ruptured IA samples and unruptured IA samples, respectively. Pathways associated with inflammation and immune response were clustered in the salmon module of ruptured IA samples. The DEG co-expression network with 35 nodes and 168 edges was generated, and 14 key genes were identified based on this DEG co-expression network. The gene with the highest degree in the key gene cluster was CXCR4. All key genes were validated using GSE122897, and they all showed the potential diagnostic value in predicting IA rupture.

Conclusions

Using a weighted gene co-expression network approach, we identified 8 and 6 modules for ruptured IA and unruptured IA, respectively. After that, we identified the hub genes for each module and key genes based on the DEG co-expression network. All these key genes were validated by another GEO dataset and might serve as potential targets for pharmacological therapies and diagnostic markers in predicting IA rupture. Further studies are needed to elucidate the detailed molecular mechanisms and biological functions of these key genes which underlie the rupture of IA.

Identification of potential key pathways, genes and circulating markers in the development of intracranial aneurysm based on weighted gene co-expression network analysis

Background: Intracranial aneurysm (IA) is a disease resulted from weak brain control, characterized by local expansion or dilation of brain artery. This study aimed to construct a gene co-expression network by Weighted Gene Correlation Network Analysis (WGCNA) to explore the potential key pathways and genes for the development of IA.Method: Six IA-related gene expression data sets were downloaded from the Gene Expression Omnibus (GEO) database for identifying differentially expressed genes (DEGs). WGCNA was used to identify modules associated with IA. Functional enrichment analysis was used to explore the potential biological functions. ROC analysis was used to find markers for predicting IA.Results: Purple, greenyellow and yellow modules were significantly associated with unruptured intracranial aneurysms, while blue and turquoise modules were significantly associated with ruptured intracranial aneurysms. Functional modules significantly related to IA were enriched in Ribosome, Glutathione metabolism, cAMP signalling pathway, Lysosome, Glycosaminoglycan degradation and other pathways. CD163, FCEREG, FPR1, ITGAM, NLRC4, PDG, and TYROBP were up-regulated ruptured intracranial aneurysms and serum, these genes were potential circulating markers for predicting IA rupture.Conclusions: Potential IA-related key pathways, genes and circulating markers were identified for predicting IA rupture by WGCNA analysis.

Characteristics of circulating monocytes at baseline and after activation in patients with intracranial aneurysm

Intracranial aneurysm (IA) is a bulging of blood vessels around the brain that is often asymptomatic but may cause severe complications and death if ruptured. Macrophage-mediated immune responses can contribute to the development of IA. During homeostasis and inflammation, circulating monocytes can infiltrate the vasculature, where they develop into macrophages, and modulate immune responses. Based on the expression of CD14 and CD16, total circulating monocytes can be distinguished into three main subsets, including the CD14⁺CD16^- classical monocytes, the CD14⁺CD16⁺ intermediate monocytes, and the CD14^loCD16⁺⁺ non-classical monocytes. In this study, we found that frequencies of CD14⁺CD16^- classical monocytes were significantly lower in IA patients than in healthy controls, while the frequencies of CD14⁺CD16⁺ intermediate monocytes and CD14^loCD16⁺⁺ non-classical monocytes were significantly higher in IA patients than in healthy controls. The frequencies of CD14⁺CD16⁺ intermediate monocytes were further elevated in IA-ruptured patients compared to those in IA-unruptured patients. Compared to classical monocytes, intermediate monocytes and non-classical monocytes presented higher TNF-α and IL-1β expression. When cocultured with autologous naive CD4 T cells, intermediate and non-classical monocytes preferentially promoted the expression of TBX21 and RORC over the expression of FOXP3 in CD4 T cells. Inhibition of TNF-α and IL-1β slightly reduced TBX21 expression and markedly reduced RORC expression, and at the same time significantly increased FOXP3 expression in CD4 T cells. Overall, this study demonstrated that the monocytes were dysregulated in IA patients in a manner that favored the development of proinflammatory responses.

Genetic Profiles Related to Pathogenesis in Sporadic Intracranial Aneurysm Patients

BACKGROUND

Intracranial aneurysm (IA) represents a cerebrovascular disorder that featured by dilation or bulging of the weakened blood vessel wall. When it ruptures, an IA leads to subarachnoid hemorrhage with high disability and mortality rates. Despite the numerous studies focusing on IA ruptures, little research on IA pathogenesis has been reported. In this study, we aimed to reveal key genes related to IA formation.

METHODS

Four datasets from Gene Expression Omnibus data were downloaded, normalized, and separated into the IA group and the normal vessel control group for analyses. We screened for differentially expressed genes (DEGs) between groups and conducted functional enrichment, pathway enrichment, and gene set enrichment analysis analyses among significant DEGs.

RESULTS

according to our analyses, significant DEGs majorly associate with smooth muscle system and the complement system. Among all DEGs, 5 down-regulated genes (MYH11, CNN1, MYOCD, ACTA1, and LMOD1) and 3 up-regulated genes (C1QB, C3AR1, and VSIG4) are most relevant in IA formation.

CONCLUSIONS

Key DEGs identified in this study are related to IA pathogenesis. Among identified DEGs, LMOD1 is the most significant and merits more attention.

Gene Expression in Intracranial Aneurysms-Comparison Analysis of Aneurysmal Walls and Extracranial Arteries with Real-Time Polymerase Chain Reaction and Immunohistochemistry

BACKGROUND

This study was aimed at evaluating the gene expression levels of 4 genes in the intracranial aneurysm wall and comparing them with extracranial arteries. The analysis was done using real-time polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC). Also, a correlation of the differential genetic expression was done with various patient clinical and radiologic factors.

METHODS

The quantitative assessment of ribonucleic acid levels was done with RT-PCR and was validated with IHC. The genes studied were collagen 1A2 (COL1A2), tissue inhibitor of metalloproteinase 4 (TIMP4), cathepsin B (CTSB), and alpha-1 antitrypsin (α-1 AT). The analysis was done on 24 aneurysm sacs and superficial temporal/occipital artery samples from patients undergoing surgical clipping.

RESULTS

The mean fold change of COL1A2 in the aneurysm sample was 8.89, that of TIMP4 was 10.16, that of CTSB was 1.02, and that of α-1 AT was 1.46 when compared with normal control vessel on PCR. On semiquantitative IHC, COL1A2 was 94.44%, α-1 AT was 77.8% overexpressed, CTSB was positive in 50%, and the expression of TIMP4 was 94.4% underexpressed in aneurysmal walls. There was no statistically significant correlation between patient profile and gene expression.

CONCLUSIONS

On RT-PCR and IHC analysis, COL1A2 and α-1 AT were overexpressed, CTSB was marginally overexpressed, and TIMP4 had equivocal expression in the aneurysmal sac when compared with the normal extracranial vessel. This is the first study of its kind in the Indian population with the largest sample size on live human patients.

Microenvironment of ruptured cerebral aneurysms discovered using data driven analysis of gene expression

BACKGROUND

It is well known that ruptured intracranial aneurysms are associated with substantial morbidity and mortality, yet our understanding of the genetic mechanisms of rupture remains poor. We hypothesize that applying novel techniques to the genetic analysis of aneurysmal tissue will yield key rupture-associated mechanisms and novel drug candidates for the prevention of rupture.

METHODS

We applied weighted gene co-expression networks (WGCNA) and population-specific gene expression analysis (PSEA) to transcriptomic data from 33 ruptured and unruptured aneurysm domes. Mechanisms were annotated using Gene Ontology, and gene network/population-specific expression levels correlated with rupture state. We then used computational drug repurposing to identify plausible drug candidates for the prevention of aneurysm rupture.

RESULTS

Network analysis of bulk tissue identified multiple immune mechanisms to be associated with aneurysm rupture. Targeting these processes with computational drug repurposing revealed multiple candidates for preventing rupture including Btk inhibitors and modulators of hypoxia inducible factor. In the macrophage-specific analysis, we identify rupture-associated mechanisms MHCII antigen processing, cholesterol efflux, and keratan sulfate catabolism. These processes map well onto several of highly ranked drug candidates, providing further validation.

CONCLUSIONS

Our results are the first to demonstrate population-specific expression levels and intracranial aneurysm rupture, and propose novel drug candidates based on network-based transcriptomics.

RNA sequencing analysis revealed the induction of CCL3 expression in human intracranial aneurysms

Intracranial aneurysm (IA) is a socially important disease as a major cause of subarachnoid hemorrhage. Recent experimental studies mainly using animal models have revealed a crucial role of macrophage-mediated chronic inflammatory responses in its pathogenesis. However, as findings from comprehensive analysis of unruptured human IAs are limited, factors regulating progression and rupture of IAs in humans remain unclear. Using surgically dissected human unruptured IA lesions and control arterial walls, gene expression profiles were obtained by RNA sequence analysis. RNA sequencing analysis was done with read count about 60~100 million which yielded 6~10 billion bases per sample. 79 over-expressed and 329 under-expressed genes in IA lesions were identified. Through Gene Ontology analysis, ‘chemokine activity’, ‘defense response’ and ‘extracellular region’ were picked up as over-represented terms which included CCL3 and CCL4 in common. Among these genes, quantitative RT-PCR analysis using another set of samples reproduced the above result. Finally, increase of CCL3 protein compared with that in control arterial walls was clarified in IA lesions. Findings of the present study again highlight importance of macrophage recruitment via CCL3 in the pathogenesis of IA progression.

High-Throughput Data Reveals Novel Circular RNAs via Competitive Endogenous RNA Networks Associated with Human Intracranial Aneurysms

Background

Little is known about epigenetic regulation of intracranial aneurysms (IAs). Circular non-coding RNAs (circRNAs) play crucial roles in cardiovascular diseases, but they have received scant research attention regarding their relationship with IAs. This study aimed to explore new pathological mechanisms of IA through circRNA expression profiles and to provide novel therapeutic strategies.

Material/Methods

The comprehensive circRNA and mRNA expression profiles were detected by RNA-Seq in human IA walls and superficial temporal arteries (STAs). The RNA-Seq findings were validated by qRT-PCR. GO and KEGG analyses indicated the functions of these circRNAs. A competing endogenous RNA (ceRNA) network was constructed to reveal the circRNA-miRNA-mRNA relationship. Two newly discovered circRNAs were further detected in peripheral blood of IA patients and healthy people to clarify their expression patterns in the periphery.

Results

Many differentially expressed circRNAs are closely involved in immune/inflammatory response and cell adhesion/adherens junction. The novel circRNAs (hsa_circ_0072309 and hsa_circ_0008433) regulate DDR2 and MMP2, respectively, which are associated with SMC dysfunction and vascular injury through ceRNA. Moreover, we found differential expression of these 2 circRNAs in the peripheral blood of IA patients, and the expression pattern of hsa_circ_0072309 had central and peripheral consistency.

Conclusions

To the best of our knowledge, this is the first study to perform circRNA sequencing analysis of IAs. hsa_circ_0072309 and hsa_circ_0008433 are novel and pivotal circRNAs related to IAs. This study provides new insights into therapeutic targets and biomarkers for IA patients.

Tanshinone IIA attenuates cerebral aneurysm formation by inhibiting the NF‑κB‑mediated inflammatory response

The inflammatory response plays a vital role in cerebral aneurysm (CA) formation and progression. Tanshinone  IIA (Tan IIA) is one of the major active components of Chinese medicine Danshen (Salvia miltiorrhiza Bunge) and is widely used for the treatment of cardiovascular diseases, due to its anti‑inflammatory effects. The aim of the present study was to investigate whether Tan IIA can attenuate CA formation in rat models, and determine its underlying mechanisms. CAs were induced in rats surgically and through high‑salt diet treatments. The Tan IIA‑treated group displayed relatively mild symptoms, as compared with the control group. Tan IIA treatment reduced macrophage infiltration and nuclear factor (NF)‑κB activation in aneurysmal walls. Next, lipopolysaccharide (LPS)‑stimulated RAW 264.7 murine macrophage cells were used to examine the anti‑inflammatory effects of Tan IIA on macrophages. It was found that Tan IIA reversed LPS‑induced differentiation of RAW 264.7 cells and suppressed NF‑κB pathway activation. In conclusion, these findings demonstrated that Tan IIA can suppress CA formation by inhibiting inflammatory responses in macrophages.

Analysis of Peripheral Blood Cells' Transcriptome in Patients With Subarachnoid Hemorrhage From Ruptured Aneurysm Reveals Potential Biomarkers

BACKGROUND

Subarachnoid hemorrhage (SAH) is an uncommon disease. Considering ruptured intracranial aneurysms as the main cause of this disease and only a minority of the intracranial aneurysms will rupture sooner or later, to understand the underlying pathology or a specific gene expression profile of an impending ruptured intracranial aneurysm is of great importance.

METHODS

The transcriptome in peripheral blood cells of patients with SAH from ruptured aneurysm was compared with that of control patients suffering from headaches. The microarray dataset GSE36791 comprised 43 patients with SAH from ruptured aneurysms and 18 control patients. Differential expression analysis was performed with the R language packages to identify differentially expressed genes (DEGs). Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway database analysis were performed to identify significantly altered biological functions and pathways, respectively. The protein-protein interaction networks were constructed with information from the STRING database.

RESULTS

A total of 528 DEGs were identified, of which 311 were upregulated and 217 downregulated. Clustering analysis confirmed that these genes can distinguish ruptured aneurysm SAH patients from the control patients. The DEGs were mainly enriched for immune/inflammation response and related pathways. Among the DEGs, 8 genes (ARG1, MAPK14, RPS2, SPI1, FYN, CEBPB, FLOT1, and CD4) were identified as the key regulators in the Protein-Protein Interaction network. MAPK14, CEBPB, FLOT1, and CD4 might be potential biomarkers of SAH.

CONCLUSION

This study identified a range of DEGs SAH patients with ruptured aneurysms, which may enhance our current knowledge on this disease and may provide potential biomarkers of this disease.

Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysms

BACKGROUND

Intracranial aneurysms (IAs) are dangerous because of their potential to rupture and cause deadly subarachnoid hemorrhages. Previously, we found significant RNA expression differences in circulating neutrophils between patients with unruptured IAs and aneurysm-free controls. Searching for circulating biomarkers for unruptured IAs, we tested the feasibility of developing classification algorithms that use neutrophil RNA expression levels from blood samples to predict the presence of an IA.

METHODS

Neutrophil RNA extracted from blood samples from 40 patients (20 with angiography-confirmed unruptured IA, 20 angiography-confirmed IA-free controls) was subjected to next-generation RNA sequencing to obtain neutrophil transcriptomes. In a randomly-selected training cohort of 30 of the 40 samples (15 with IA, 15 controls), we performed differential expression analysis. Significantly differentially expressed transcripts (false discovery rate < 0.05, fold change ≥ 1.5) were used to construct prediction models for IA using four well-known supervised machine-learning approaches (diagonal linear discriminant analysis, cosine nearest neighbors, nearest shrunken centroids, and support vector machines). These models were tested in a testing cohort of the remaining 10 neutrophil samples from the 40 patients (5 with IA, 5 controls), and model performance was assessed by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (PCR) was used to corroborate expression differences of a subset of model transcripts in neutrophil samples from a new, separate validation cohort of 10 patients (5 with IA, 5 controls).

RESULTS

The training cohort yielded 26 highly significantly differentially expressed neutrophil transcripts. Models using these transcripts identified IA patients in the testing cohort with accuracy ranging from 0.60 to 0.90. The best performing model was the diagonal linear discriminant analysis classifier (area under the ROC curve = 0.80 and accuracy = 0.90). Six of seven differentially expressed genes we tested were confirmed by quantitative PCR using isolated neutrophils from the separate validation cohort.

CONCLUSIONS

Our findings demonstrate the potential of machine-learning methods to classify IA cases and create predictive models for unruptured IAs using circulating neutrophil transcriptome data. Future studies are needed to replicate these findings in larger cohorts.

Expression profile analysis of differentially expressed genes in ruptured intracranial aneurysms: In search of biomarkers

Intracranial aneurysms (IAs) result from the bulging of arterial walls secondary to several factors such as flow, vessel morphology, and genetics. Subarachnoid hemorrhage occurs when such walls rupture, leading to high disability and mortality. Despite numerous investigations pertaining to the relationship between geometric characteristics and IA rupture, only a few have obtained consistent results. This study aimed to further identify the potential genes associated with the pathogenesis of IAs, which may provide novel molecular biomarkers. We downloaded and reanalyzed six datasets, which were divided into four groups. IA walls and blood samples were screened for differentially expressed genes (DEGs); then, functional and pathway enrichment analyses were conducted. In total, 158 common DEGs were identified from Groups 1-3 and 396 genes (187 upregulated and 209 downregulated genes) were differentially expressed in Group 4. The functional analysis revealed that the DEGs were mainly associated with the major histocompatibility complex class II protein complex and antigen processing and presentation. Finally, we identified nine key genes, both in aneurysm tissue samples and blood samples, of which three were mostly associated with the progression and rupture of IAs. Bioinformatics was used to analyze the datasets of the ruptured IAs and identify potential biomarkers, which may provide information for the early detection and treatment of IAs.

Statin Therapy and Diabetes Do Not Affect Aneurysm Occlusion or Clinical Outcomes After Pipeline Embolization Device Treatment: A Preliminary Study

BACKGROUND

The effect of statins and diabetes on angiographic and clinical outcomes in aneurysms treated with pipelines has not been adequately reported. Our aim is to assess the effect of concurrent statin medications and diabetes mellitus (DM) on aneurysm occlusion status and outcomes in patients treated with the pipeline embolization device.

METHODS

A retrospective review of our institution's database of aneurysms treated with the pipeline embolization device between 2013 and 2017 was conducted. We collected data about statin therapy status and intensity, and identified patients with a documented history of DM. Our primary outcome was aneurysm obliteration seen on digital subtracted angiography or magnetic resonance angiography at last follow-up.

RESULTS

We identified 151 patients with 182 aneurysms for this cohort, with a median radiographic follow-up time of 7.2 months (6.1-14.5). Thirty-nine patients were taking statins, and 112 patients did not receive statins. Log-rank tests revealed no statistically significant difference in occlusion rates between patients with and without statin therapy (P = 0.30). A history of DM was documented in 11 patients, with 14 aneurysms in total; 140 patients with 168 aneurysms had no history of DM. Similarly, there were no differences in occlusion rates between the diabetic and nondiabetic groups in multivariate analysis (P = 0.24). Only 2 patients showed significant in-stent stenosis on angiographic follow up, and both were diabetic.

CONCLUSIONS

Our analysis did not identify a statistically significant association between statin therapy or DM and higher occlusion rates or better outcomes after pipeline embolization. Diabetic patients may have a theoretic risk of significant in-stent stenosis.

Quantitative proteomics analysis of differentially expressed proteins in ruptured and unruptured cerebral aneurysms by iTRAQ

The underlying pathophysiological mechanisms involved in cerebral aneurysms rupture remain unclear. This study was performed to investigate the differentially expressed proteins between ruptured and unruptured aneurysms using quantitative proteomics. The aneurysmal walls of six ruptured aneurysms and six unruptured aneurysms were collected during the surgical operation. The isobaric tags for relative and absolute quantification (iTRAQ) were used to identify the differentially expressed proteins and western blotting was performed to validate the expression of the proteins of interest. Bioinformatics analysis of the differentially expressed proteins was also performed using the KEGG database and GO database. Between ruptured and unruptured aneurysms, 169 proteins were found differently expressed, including 74 up-regulated proteins and 95 down-regulated proteins with a fold change ≥ 2 and p value ≤ .05. KEGG pathway analysis revealed that phagosome, focal adhesion and ECM-receptor interaction were the most common pathways involved in aneurysm rupture. In addition, the differential expressions of ITGB3, CRABP1 and S100A9 were validated by western blotting. Through the iTRAQ method, we found that inflammatory responses and cell-matrix interactions may play a significant role in the rupture of cerebral aneurysms. These findings provide a basis for better understanding of pathophysiological mechanisms associated with aneurysm rupture.

BIOLOGICAL SIGNIFICANCE

Intracranial aneurysm is the leading cause of life-threating subarachnoid hemorrhage which can cause 45% patients die within 30 days and severe morbidity in long-term survivors. With a high prevalence ranging from 1% to 5% in general population, cerebral aneurysm has become a widespread health hazard over past decades. Though great advances have been achieved in the diagnosis and treatment of this disease, the underlying pathophysiological mechanisms of aneurysm rupture remains undetermined and a lot of uncertainty still exists surrounding the treatment of unruptured cerebral aneurysms. Clarifying the mechanism associated with aneurysm rupture is important for estimating the rupture risk, as well as the development of new treatment strategy. Some previous studies have analyzed the molecular differences between ruptured and unruptured IAs at gene and mRNA levels, but further comprehensive proteomic studies are relatively rare. Here we performed a comparative proteomics study to investigate the differentially expressed proteins between ruptured IAs (RIAs) and unruptured IAs (UIAs). Results of our present study will provide more insights into the pathogenesis of aneurysm rupture at protein level. With a better understanding of pathophysiological mechanisms associated with aneurysm rupture, some noninvasive treatment strategies may be developed in the future.

Integrated analysis of microarray data to identify the genes critical for the rupture of intracranial aneurysm

Intracranial aneurysm (IA) is a localized dilation of the blood vessel. The present study was designed to explore the mechanisms of rupture of IA. GSE13353 (including 11 ruptured and 8 unruptured IA samples) and GSE15629 (including 8 ruptured and 6 unruptured IA samples) were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) identified using limma and MetaDE packages were merged, and a protein-protein interaction (PPI) network analysis was performed using Cytoscape software. Pathway enrichment analysis was performed for the nodes of the PPI network using the fisher algorithm. The 100 most prominent genes in the network were designated candidate genes and a hierarchical clustering analysis was performed. The tune.svm function of e1071 package was used to construct a support vector machine (SVM) classifier, and the Candidate Cancer Gene Database was applied to analyze the characterization of gene-associated cancer. Furthermore, the genes involved in the SVM classifier were assessed via principal component analysis (PCA). In the ruptured samples, 1,292 DEGs and 1,029 DEGs separately were identified by limma and MetaDE packages. The 100 most prominent genes in the network included fibronectin 1 (FN1), amyloid β (A4) precursor protein (APP), nuclear RNA export factor 1 (NXF1) and signal transducer and activator of transcription 3 (STAT3). Pathway enrichment analysis identified that toll-like receptor 3 (TLR3) was enriched in the Toll-like receptor signaling pathway. A total of 15 genes (including FN1) were used to construct the SVM classifier. NXF1 was identified to be associated with Nervous System Cancer. PCA revealed that APP, NXF1 and STAT3 were the 3 principal components. TLR3, FN1, APP, NXF1 and STAT3 may affect the rupture of IA.

Circulating neutrophil transcriptome may reveal intracranial aneurysm signature

Background

Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs.

Methods

Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls. Samples from the two groups were paired based on demographics and comorbidities. RNA was extracted from isolated neutrophils and subjected to next-generation RNA sequencing to obtain differential expressions for identification of an IA-associated signature. Bioinformatics analyses, including gene set enrichment analysis and Ingenuity Pathway Analysis, were used to investigate the biological function of all differentially expressed transcripts.

Results

Transcriptome profiling identified 258 differentially expressed transcripts in patients with and without IAs. Expression differences were consistent with peripheral neutrophil activation. An IA-associated RNA expression signature was identified in 82 transcripts (p<0.05, fold-change ≥2). This signature was able to separate patients with and without IAs on hierarchical clustering. Furthermore, in an independent, unpaired, replication cohort of patients with IAs (n = 5) and controls (n = 5), the 82 transcripts separated 9 of 10 patients into their respective groups.

Conclusion

Preliminary findings show that RNA expression from circulating neutrophils carries an IA-associated signature. These findings highlight a potential to use predictive biomarkers from peripheral blood samples to identify patients with IAs.

Bioinformatic analysis of gene expression profiling of intracranial aneurysm

Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P-value <0.01 and |log₂ FC|≥1). Secondly, the database for annotation, visualization and integrated discovery software was utilized to perform pathway and functional enrichment analyses (false discovery rate ≤0.05). Finally, protein-protein interaction (PPI) network and sub-network clustering analyses were performed using the biomolecular interaction network database and ClusterONE software, respectively. Following this, a transcription factor regulatory network was identified from the PPI network. A total of 1,124 DEGs were identified, of which 989 were upregulated and 135 downregulated. Pathway and functional enrichment analyses revealed that the DEGs primarily participated in RNA splicing, functioning of the spliceosome, RNA processing and the mRNA metabolic process. Following PPI network analysis, 1 hepatocyte nuclear factor (HNF) 4A (transcription factor)-centered regulatory network and 5 DEG-centered sub-networks were identified. On analysis of the transcription factor regulatory network, 6 transcription factors (HNF6, HNF4A, E2F4, YY1, H4 and H31T) and a regulatory pathway (HNF6-HNF4-E2F4) were identified. The results of the present study suggest that activating transcription factor-5, Jun proto-oncogene, activator protein-1 transcription factor subunit, HNF6, HNF4 and E2F4 may participate in IA progression via vascular smooth muscle cell apoptosis, inflammation, vessel wall remodeling and damage and the tumor necrosis factor-β signaling pathway. However, further experimental studies are required to validate these predictions.

Association between polymorphism of SMAD3 gene and risk of sporadic intracranial arterial aneurysms in the Chinese Han population

Intracranial arterial aneurysms (IAAs) are locally abnormal dilations of the cerebral arteries and often result in subarachnoid hemorrhages (SAH). Genetic, molecular and cellular mechanisms of sporadic IAAs forms are poorly understood. In this study, we investigate the association between mothers against decapentaplegic homolog 3 (SMAD3) genotypes and the risk of sporadic intracranial arterial aneurysms among the Chinese Han population. A case-control study was conducted examining 330 IAA patients and 313 controls. There were eight single nucleotide polymorphisms of SMAD3 selected and genotyped using the polymerase chain reaction-ligase detection reaction (PCR-LDR) method. Our results indicated that SMAD3 rs1065080 polymorphism was associated with a risk of IAAs in a codominant model (GA vs GG, OR=1.433; 95% CI 1.030-1.994; P=0.032). In summary, we observed that SMAD3 rs1065080 single nucleotide gene polymorphisms were significantly associated with patient susceptibility to IAAs.