Single-Cell RNA Sequencing Reveals the Pathogenic Relevance of Intracranial Atherosclerosis in Blood Blister-Like Aneurysms

The integration of scRNA-seq with microarray and in-vivo experiments facilitates a comprehensive elucidation of the molecular mechanisms underlying endothelial cell involvement in myocardial infarction

Myocardial infarction (MI) remains a major global health challenge, with endothelial cell function playing a crucial role in its progression. Advances in single-cell RNA sequencing (scRNA-seq) have enhanced our understanding of MI pathogenesis. This study aims to identify key genes within endothelial cells using scRNA-seq data and validate them through microarray data and in vivo models elucidate their role in the progression of MI. ScRNA-seq and microarray datasets relevant to MI were obtained from the GEO database. The Seurat package was used for data pre-processing and marker gene identification. Endothelial cell subpopulations were characterised using the hdWGCNA package, while intercellular interactions with fibroblasts were assessed using CellChat. Key genes were identified using comprehensive bioinformatics techniques such as scCODE, FindMarkers and protein-protein interaction (PPI) analysis, with validation from microarray data and in vivo experiments (WB, qPCR, immunofluorescence) in the model of MI. The analysis via scRNA-seq revealed 16 distinct cell clusters encompassing 7 unique cell types. Endothelial cells were categorized into 8 subpopulations by hdWGCNA; notably, Endothelial Cells-2 exhibited significant interactions with fibroblasts mediated by PDGF, PROS, and GAS signaling pathways. Integration of hdWGCNA, scCODE and FindMarkers, 10 key genes were identified, which were subsequently refined to DBP, NR1D1, and TEF following PPI analysis. These genes demonstrated marked downregulation the progression of MI, as confirmed by subsequent in vivo experiments. This study highlights the crucial roles of DBP, NR1D1, and TEF in MI development, providing a basis for future research on endothelial cell function in cardiovascular disease.

Single-cell analysis reveals the implication of vascular endothelial cell-intrinsic ANGPT2 in human intracranial aneurysm

AIMS

While previous single-cell RNA sequencing (scRNA-seq) studies have attempted to dissect intracranial aneurysm (IA), the primary molecular mechanism for IA pathogenesis remains unknown. Here, we uncovered the alterations of cellular compositions, especially the transcriptome changes of vascular endothelial cells (ECs), in human IA.

METHODS AND RESULTS

We performed scRNA-seq to compare the cell atlas of sporadic IA and the control artery. The transcriptomes of 43 462 cells were profiled for further analysis. In general, IA had increased immune cells (T/NK cells, B cells, myeloid cells, mast cells, neutrophils) and fewer vascular cells (ECs, vascular smooth muscle cells, and fibroblasts). Based on the obtained high-quantity and high-quality EC data, we found genes associated with angiogenesis in ECs from IA patients. By EC-specific expression of candidate genes in vivo, we observed the involvement of angpt2a in causing cerebral vascular abnormality. Furthermore, an IA zebrafish model mimicking the main features of human IA was generated through targeting pdgfrb gene, and knockdown of angpt2a alleviated the vascular dilation in the IA zebrafish model.

CONCLUSION

By performing a landscape view of the single-cell transcriptomes of IA and the control artery, we contribute to a deeper understanding of the cellular composition and the molecular changes of ECs in IA. The implication of angiogenic regulator ANGPT2 in IA formation and progression, provides a novel potential therapeutical target for IA interventions.

A comprehensive proteomic analysis reveals novel inflammatory biomarkers in intracranial aneurysms

Inflammation is a complex factor in the pathogenesis of intracranial aneurysms (IA), but its specific cellular inflammatory factors remain uncertain. We collected two cohorts and measured the representation of vascular inflammation-related proteins using the Olink CVD II Vascular Inflammation Panel. We subsequently validated our findings using ELISA and RT-qPCR. Our proteomic analysis identified 11 vascular inflammation-related markers that were significantly differentially represented between the IA and control groups. These markers were implicated in leukocyte migration, immune response, triglyceride and lipoprotein metabolism, acute phase response, T cell regulation, and several key biological pathways, including PPAR, HIF-1, cytokine-cytokine interactions, and PI3K-AKT signaling. Further validation with ELISA and RT-qPCR confirmed the differential representation of IL6, PTX3, LPL, and OLR1 between the two groups. Notably, a combination marker incorporating these four factors demonstrated high diagnostic potential for the early detection of IA. Our study has identified a set of informative biomarkers (IL6, PTX3, LPL, and OLR1) that could be valuable for the early diagnosis of IA. Importantly, this is the first report of significantly elevated OLR1 representation in the plasma of IA patients. Further investigation into the role of OLR1 in the pathogenesis of IA is warranted. SIGNIFICANCE: This study significantly advances our understanding of the molecular mechanisms underlying intracranial aneurysm (IA) pathogenesis. By identifying a panel of novel biomarkers, including the previously unreported elevated expression of OLR1 in IA patients, we provide crucial insights into the inflammatory processes involved in aneurysm formation and development. These findings have important clinical implications, as the identified biomarkers could serve as valuable tools for early diagnosis and potentially targeted therapeutic interventions. Furthermore, the study highlights the complex interplay of inflammatory pathways in IA, suggesting that a multi-faceted approach may be necessary for effective management.

Phoenixin-14 inhibits the formation of cerebral aneurysms in rats by downregulating the p38/NF-κB signaling pathway

Cerebral aneurysms (CA) are a serious condition characterized by the bulging of a blood vessel in the brain, which can lead to rupture and life-threatening bleeding. The pathophysiology of CA involves complex processes, particularly inflammation and macrophage infiltration. Phoenixin-14 (PNX-14) is a neuropeptide with diverse biological effects, including roles in reproduction, energy homeostasis, and inflammation. Recent evidence has highlighted the therapeutic potential of PNX-14 in various conditions. Notably, PNX-14 has demonstrated neuroprotective effects in the central nervous system, and we hypothesized that it could also offer vascular protection in the context of CA. In this study, we demonstrate that serum PNX-14 levels are reduced in patients and rat models with CA compared to healthy controls. Our findings show that PNX-14 administration significantly reduces aneurysmal size in a rat model with left renal artery ligation. Furthermore, PNX-14 mitigates the inflammatory response by inhibiting the expression of IL-1β and MCP-1 at both the mRNA and protein levels in the Circle of Willis (COW) region. PNX-14 treatment also decreases the levels of MMP-2 and MMP-9 in the COW region. Mechanistically, PNX-14 suppresses macrophage infiltration and inhibits the activation of the p38/NF-κB signaling pathway. These findings suggest that PNX-14 could be a promising therapeutic agent for the prevention and treatment of CA.

Computational hemodynamic pathophysiology of internal carotid artery blister aneurysms

OBJECTIVE

Blister aneurysms of the internal carotid artery (ICA) are rare and are primarily documented in the literature through small series and case reports. The intraoperative observation of a hemorrhage in the artery wall proximal to the aneurysmal bulge led to the hypothesis that some of these aneurysms might develop in a retrograde manner.

METHODS

We developed software to reconstruct the ICA with and without Type I and II blister aneurysms using patients' imagery as input to simulate hemodynamic conditions before and after their formation. Kinematic blood flow data before and after aneurysm formation were obtained using a finite volume solver. We compared the wall shear stress (WSS) distribution of the arterial wall prior to aneurysm formation.

RESULTS

In two out of four cases, WSS was significantly elevated on the dorsal wall of the supraclinoid segment of the ICA at the distal part of the future site of the aneurysm sac, suggesting that the aneurysm sac may ultimately develop in a retrograde fashion. Once the structural changes have been initiated, WSS gradient (WSSG) was significantly elevated at the proximal and distal boundaries of the bulging aneurysmal pouch. Low WSS and high WSSG at the proximal part of the aneurysm sac seem to contribute to the extension of the proximal intramural hematoma observed during blister aneurysm surgery.

CONCLUSIONS

By enabling assessment of the impact of elevated WSS and its gradient, our computational pipeline supports the hypothesis that the development of blister aneurysms may occur either in a retrograde or anterograde fashion.

The pro-atherogenic effects and the underlying mechanisms of chronic bisphenol S (BPS) exposure in apolipoprotein E-deficient mice

Atherosclerosis (AS) and its related cardiovascular diseases (CVDs) remain the most frequent cause of morbidity and mortality worldwide. Researches showed that bisphenol A (BPA) exposure might exacerbate AS progression. However, as an analogue of BPA, little is known about the cardiovascular toxicity of bisphenol S (BPS), especially whether BPS exposure has the pro-atherogenic effects in mammals is still unknown. Here, we firstly constructed an apolipoprotein E knockout (ApoE-/-) mouse model and cultured cells to investigate the risk of BPS on AS and explore the underlying mechanisms. Results showed that prolonged exposure to 50 μg/kg body weight (bw)/day BPS indeed aggravated AS lesions both in the en face aortas and aortic sinuses of ApoE-/- mice. Moreover, BPS were found to be implicated in the AS pathological process: 1) stimulates adhesion molecule expression to promote monocyte-endothelial cells (ECs) adhesion with 3.6 times more than the control group in vivo; 2) increases the distribution of vascular smooth muscle cells (VSMCs) with 9.3 times more than the control group in vivo, possibly through the migration of VSMCs; and 3) induces an inflammatory response by increasing the number of macrophages (MACs), with 3.7 times more than the control group in vivo, and the release of inflammatory mediators. Furthermore, we have identified eight significant AS-related genes induced by BPS, including angiopoietin-like protein 7 (Angptl17) and lipocalin-2 (Lcn2) in ECs; matrix metalloproteinase 9 (Mmp13), secreted phosphoprotein 1 (Spp1), and collagen type II alpha 1 (Col2a1) in VSMCs; and kininogen 1 (Kng1), integrin alpha X (Itgax), and MAC-expressed gene 1 (Mpeg1) in MACs. Overall, this study firstly found BPS exposure could exacerbate mammalian AS and might also provide a theoretical basis for elucidating BPS and its analogues induced AS and related CVDs.

Landscape of epithelial cell subpopulations in the human esophageal squamous cell carcinoma microenvironment

Aims

We sought to reveal the landscape of epithelial cell subpopulations in the human esophageal squamous cell carcinoma microenvironment and investigate their parts on esophageal squamous carcinoma (ESCC) development.

Background

Epithelial cells play an important role in the occurrence and development of ESCC through multiple mechanisms. While the landscape of epithelial cell subpopulations in ESCC, remains unclear.

Objective

Exploring the role of epithelial cell subpopulations in ESCC progression.

Methods

Seurat R package was used for single-cell RNA sequencing (scRNA-seq) data filtering, dimensionality reduction, clustering and differentially expressed genes analysis. Cellmarker database was adopted for cell cluster annotation. Functional enrichment analysis was carried out by Gene Ontology (GO) analysis. InferCNV package was conducted for copy number variation (CNV) of epithelial cell subpopulations in all chromosomal regions. Pseudotime trajectory analysis was implemented for exploring differentiation trajectory of epithelial cells subgroups during the cancer progression. CellChat analysis was used for probing the interactions between epithelial cells and NK/T cells. cellular experiments were performed using Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR), Wound-Healing Assay and transwell.

Results

11 major cell subpopulations were identified in ESCC and adjunct tissues. Further reclassification of epithelial cells uncovered 4 subpopulations. Enrichment analysis revealed that highly expressed genes in 4 epithelial cell subpopulations were related to cell proliferation, immune response and angiogenesis. CNV analysis found that UBD + epithelial cells and GAS2L3+ epithelial cells had a higher proportion of CNV. Cell differentiation trajectories disclosed that KRT6C+ and GSTA1+ epithelial cells were in an intermediate state of differentiation, while UBD+ and GAS2L3+ epithelial cells are in an end state of differentiation during ESCC progression. Finally, we found that four epithelial cell subpopulations all inhibited NK/T cells through NECTIN2-TIGIT and CLEC2B-KLRB1. Low ATF3 and DDIT3 mRNA expression inhibited ESCC cell migration and invasion.

Conclusion

Here, we obtained a through epithelial cell atlas of ESCC at single-cell resolution, explored the role of epithelial cell in ESCC progression, and unveiled immunosuppressive signals to NK/T cells in promoting ESCC. Our findings expand the comprehension of epithelial cells and offer a theoretical guidance for future anti-epithelial cell treatment of ESCC.

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 biology and clinical implication of neutrophils in intracranial aneurysm

OBJECTIVE

Abundant neutrophils have been identified in both ruptured and unruptured intracranial aneurysm (IA) domes, with their function and clinical implication being poorly characterized.

MATERIALS AND METHODS

We employed single-cell RNA sequencing (scRNA-Seq) datasets of both human and murine model, and external bulk mRNA sequencing datasets to thoroughly explore the features and functional heterogeneous of neutrophils infiltrating the IA dome.

RESULTS

We found that both unruptured and ruptured IA dome contain a substantial population of neutrophils, characterized by FCGR3B, G0S2, CSF3R, and CXCR2. These cells exhibited heterogeneity in terms of function and differentiation. Despite similar transcriptional activation, neutrophils in IA dome expressed a repertoire of gene programs that mimicked transcriptomic alterations observed from bone marrow to peripheral blood, showing self-similarity. In addition, the recruitment of neutrophils in unruptured IA was primarily mediated by monocytes/macrophages, and once ruptured, both neutrophils, and a specific subset of inflammatory smooth muscle cells (SMCs) were involved in the process. The receiver operator characteristic curve (ROC) analysis indicated that distinct neutrophil subclusters were associated with IA formation and rupture, respectively. By reviewing current studies, we found that neutrophils play a detrimental role to IA wall integrity through secreting specific ligands, ferroptosis driven by ALOX5AP and PTGS2, and the formation of neutrophil extracellular traps (NETs) mediated by PADI4.

INTERPRETATION

This study delineated the biology and potential clinical implications of neutrophils in IA dome and provided a reliable basis for future researches.

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.

Changes of serum MMP-9, NSE, MPO levels and prognostic influencing factors in patients with intracranial aneurysm undergoing interventional embolization at different treatment timing

Background

To analyzes the changes in serum levels of matrix metalloproteinase-9 (MMP-9), neuroenolase (NSE), myeloperoxidase (MPO) and prognostic factors in patients with intracranial aneurysm (IA) undergoing interventional embolization at different treatment times.

Methods

A retrospective analysis was made of 200 IA patients admitted to our department from January 2018 to June 2021 was performed. All patients underwent interventional embolization. According to the timing of surgery, the patients were divided into an early group (n=120, onset to surgery ≤72 h) and a delayed group (n=80, onset to surgery >72 h). The effect of embolization, complications and neurological deficit scale (NDS) scores were compared between the two groups. Serum MMP-9, NSE and MPO levels were compared before and after surgery, and the prognosis of all patients within 2 years after surgery was assessed by the Glasgow outcome scale (GOS) and divided accordingly into the good prognosis group (n=147) and the poor prognosis group (n=53) accordingly, and the prognostic factors influencing the patients were analyzed univariately and multifactorially.

Emerging applications of single-cell profiling in precision medicine of atherosclerosis

Atherosclerosis is a chronic, progressive, inflammatory disease that occurs in the arterial wall. Despite recent advancements in treatment aimed at improving efficacy and prolonging survival, atherosclerosis remains largely incurable. In this review, we discuss emerging single-cell sequencing techniques and their novel insights into atherosclerosis. We provide examples of single-cell profiling studies that reveal phenotypic characteristics of atherosclerosis plaques, blood, liver, and the intestinal tract. Additionally, we highlight the potential clinical applications of single-cell analysis and propose that combining this approach with other techniques can facilitate early diagnosis and treatment, leading to more accurate medical interventions.

Current understanding of macrophages in intracranial aneurysm: relevant etiological manifestations, signaling modulation and therapeutic strategies

Macrophages activation and inflammatory response play crucial roles in intracranial aneurysm (IA) formation and progression. The outcome of ruptured IA is considerably poor, and the mechanisms that trigger IA progression and rupture remain to be clarified, thereby developing effective therapy to prevent subarachnoid hemorrhage (SAH) become difficult. Recently, climbing evidences have been expanding our understanding of the macrophages relevant IA pathogenesis, such as immune cells population, inflammatory activation, intra-/inter-cellular signaling transductions and drug administration responses. Crosstalk between macrophages disorder, inflammation and cellular signaling transduction aggravates the devastating consequences of IA. Illustrating the pros and cons mechanisms of macrophages in IA progression are expected to achieve more efficient treatment interventions. In this review, we summarized the current advanced knowledge of macrophages activation, infiltration, polarization and inflammatory responses in IA occurrence and development, as well as the most relevant NF-κB, signal transducer and activator of transcription 1 (STAT1) and Toll-Like Receptor 4 (TLR4) regulatory signaling modulation. The understanding of macrophages regulatory mechanisms is important for IA patients' clinical outcomes. Gaining insight into the macrophages regulation potentially contributes to more precise IA interventions and will also greatly facilitate the development of novel medical therapy.

Pentraxin 3: A promising therapeutic target for cardiovascular diseases

Cardiovascular disease (CVD) is the primary global cause of death, and inflammation is a crucial factor in the development of CVDs. The acute phase inflammatory protein pentraxin 3 (PTX3) is a biomarker reflecting the immune response. Recent research indicates that PTX3 plays a vital role in CVDs and has been investigated as a possible biomarker for CVD in clinical trials. PTX3 is implicated in the progression of CVDs through mechanisms such as exacerbating vascular endothelial dysfunction, affecting angiogenesis, and regulating inflammation and oxidative stress. This review summarized the structure and function of PTX3, focusing on its multifaceted effects on CVDs, such as atherosclerosis, myocardial infarction, and hypertension. This may help in explaining the varying PTX3 functions and usage, as well as in utilizing target organs to manage diseases. Moreover, elucidating the opposite role of PTX3 in the cardiovascular system will demonstrate the therapeutic and predictive potential in human diseases.

The molecular landscape of neurological disorders: insights from single-cell RNA sequencing in neurology and neurosurgery

Single-cell ribonucleic acid sequencing (scRNA-seq) has emerged as a transformative technology in neurological and neurosurgical research, revolutionising our comprehension of complex neurological disorders. In brain tumours, scRNA-seq has provided valuable insights into cancer heterogeneity, the tumour microenvironment, treatment resistance, and invasion patterns. It has also elucidated the brain tri-lineage cancer hierarchy and addressed limitations of current models. Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis have been molecularly subtyped, dysregulated pathways have been identified, and potential therapeutic targets have been revealed using scRNA-seq. In epilepsy, scRNA-seq has explored the cellular and molecular heterogeneity underlying the condition, uncovering unique glial subpopulations and dysregulation of the immune system. ScRNA-seq has characterised distinct cellular constituents and responses to spinal cord injury in spinal cord diseases, as well as provided molecular signatures of various cell types and identified interactions involved in vascular remodelling. Furthermore, scRNA-seq has shed light on the molecular complexities of cerebrovascular diseases, such as stroke, providing insights into specific genes, cell-specific expression patterns, and potential therapeutic interventions. This review highlights the potential of scRNA-seq in guiding precision medicine approaches, identifying clinical biomarkers, and facilitating therapeutic discovery. However, challenges related to data analysis, standardisation, sample acquisition, scalability, and cost-effectiveness need to be addressed. Despite these challenges, scRNA-seq has the potential to transform clinical practice in neurological and neurosurgical research by providing personalised insights and improving patient outcomes.

Heterogeneity of macrophages in atherosclerosis revealed by single-cell RNA sequencing

Technology at the single-cell level has advanced dramatically in characterizing molecular heterogeneity. These technologies have enabled cell subtype diversity to be seen in all tissues, including atherosclerotic plaques. Critical in atherosclerosis pathogenesis and progression are macrophages. Previous studies have only determined macrophage phenotypes within the plaque, mainly by bulk analysis. However, recent progress in single-cell technologies now enables the comprehensive mapping of macrophage subsets and phenotypes present in plaques. In this review, we have updated and discussed the definition and classification of macrophage subsets in mice and humans using single-cell RNA sequencing. We summarized the different classification methods and perspectives: traditional classification with an updated scoring system, inflammatory macrophages, foamy macrophages, and atherosclerotic-resident macrophages. In addition, some special types of macrophages were identified by specific markers, including IFN-inducible and cavity macrophages. Furthermore, we discussed macrophage subset-specific markers and their functions. In the future, these novel insights into the characteristics and phenotypes of these macrophage subsets within atherosclerotic plaques can provide additional therapeutic targets for cardiovascular diseases.