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Feng Y, Zhang H, Dai S, Li X. Aspirin treatment for unruptured intracranial aneurysms: Focusing on its anti-inflammatory role. Heliyon 2024; 10:e29119. [PMID: 38617958 PMCID: PMC11015424 DOI: 10.1016/j.heliyon.2024.e29119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
Intracranial aneurysms (IAs), as a common cerebrovascular disease, claims a worldwide morbidity rate of 3.2%. Inflammation, pivotal in the pathogenesis of IAs, influences their formation, growth, and rupture. This review investigates aspirin's modulation of inflammatory pathways within this context. With IAs carrying significant morbidity and mortality upon IAs rupture and current interventions limited to surgical clipping and endovascular coiling, the quest for pharmacological options is imperative. Aspirin's role in cardiovascular prevention, due to its anti-inflammatory effects, presents a potential therapeutic avenue for IAs. In this review, we examine aspirin's efficacy in experimental models and clinical settings, highlighting its impact on the progression and rupture risks of unruptured IAs. The underlying mechanisms of aspirin's impact on IAs are explored, with its ability examined to attenuate endothelial dysfunction and vascular injury. This review may provide a theoretical basis for the use of aspirin, suggesting a promising strategy for IAs management. However, the optimal dosing, safety, and long-term efficacy remain to be established. The implications of aspirin therapy are significant in light of current surgical and endovascular treatments. Further research is encouraged to refine aspirin's clinical application in the management of unruptured IAs, with the ultimate aim of reducing the incidence of aneurysms rupture.
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Affiliation(s)
- Yuan Feng
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Hongchen Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shuhui Dai
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
- National Translational Science Center for Molecular Medicine and Department of Cell Biology, Fourth Military Medical University, Xi'an, China
| | - Xia Li
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Ji H, Han Y, Danyang Jie, Yue Li, Hailan Yang, Sun H, You C, Xiao A, Liu Y. Decoding the biology and clinical implication of neutrophils in intracranial aneurysm. Ann Clin Transl Neurol 2024; 11:958-972. [PMID: 38317016 PMCID: PMC11021671 DOI: 10.1002/acn3.52014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
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.
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Affiliation(s)
- Hang Ji
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yujing Han
- Plevic Floor Disorders Centre, West China Tianfu HospitalSichuan UniversityNo. 3966, Tianfu AvenueChengduSichuanChina
| | - Danyang Jie
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yue Li
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Hailan Yang
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Haogeng Sun
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Chao You
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Anqi Xiao
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yi Liu
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
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Shi X, Wang T, Teng D, Hou S, Lin N. A mendelian randomization study investigates the causal relationship between immune cell phenotypes and cerebral aneurysm. Front Genet 2024; 15:1333855. [PMID: 38313677 PMCID: PMC10834707 DOI: 10.3389/fgene.2024.1333855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024] Open
Abstract
Background: Cerebral aneurysms (CAs) are a significant cerebrovascular ailment with a multifaceted etiology influenced by various factors including heredity and environment. This study aimed to explore the possible link between different types of immune cells and the occurrence of CAs. Methods: We analyzed the connection between 731 immune cell signatures and the risk of CAs by using publicly available genetic data. The analysis included four immune features, specifically median brightness levels (MBL), proportionate cell (PC), definite cell (DC), and morphological attributes (MA). Mendelian randomization (MR) analysis was conducted using the instrumental variables (IVs) derived from the genetic variation linked to CAs. Results: After multiple test adjustment based on the FDR method, the inverse variance weighted (IVW) method revealed that 3 immune cell phenotypes were linked to the risk of CAs. These included CD45 on HLA DR+NK (odds ratio (OR), 1.116; 95% confidence interval (CI), 1.001-1.244; p = 0.0489), CX3CR1 on CD14- CD16- (OR, 0.973; 95% CI, 0.948-0.999; p = 0.0447). An immune cell phenotype CD16- CD56 on NK was found to have a significant association with the risk of CAs in reverse MR study (OR, 0.950; 95% CI, 0.911-0.990; p = 0.0156). Conclusion: Our investigation has yielded findings that support a substantial genetic link between immune cells and CAs, thereby suggesting possible implications for future clinical interventions.
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Affiliation(s)
- Xingjie Shi
- Department of Neurosurgery, The Affiliated Chuzhou Hospital of Anhui Medical University, The First People’s Hospital of Chuzhou, Chuzhou, Anhui, China
| | - Tao Wang
- Department of Neurosurgery, Xishan People’s Hospital, Wuxi Branch of Zhongshan Hospital Affiliated to Southeast University, Wuxi, Jiangsu, China
| | - Da Teng
- Department of General Surgery, The Affiliated Chuzhou Hospital of Anhui Medical University, The First People’s Hospital of Chuzhou, Chuzhou, Anhui, China
| | - Shiqiang Hou
- Department of Neurosurgery, The Affiliated Chuzhou Hospital of Anhui Medical University, The First People’s Hospital of Chuzhou, Chuzhou, Anhui, China
| | - Ning Lin
- Department of Neurosurgery, The Affiliated Chuzhou Hospital of Anhui Medical University, The First People’s Hospital of Chuzhou, Chuzhou, Anhui, China
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Tutino VM, Fricano S, Chien A, Patel TR, Monteiro A, Rai HH, Dmytriw AA, Chaves LD, Waqas M, Levy EI, Poppenberg KE, Siddiqui AH. Gene expression profiles of ischemic stroke clots retrieved by mechanical thrombectomy are associated with disease etiology. J Neurointerv Surg 2023; 15:e33-e40. [PMID: 35750484 PMCID: PMC9789205 DOI: 10.1136/neurintsurg-2022-018898] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Determining stroke etiology is crucial for secondary prevention, but intensive workups fail to classify ~30% of strokes that are cryptogenic. OBJECTIVE To examine the hypothesis that the transcriptomic profiles of clots retrieved during mechanical thrombectomy are unique to strokes of different subtypes. METHODS We isolated RNA from the clots of 73 patients undergoing mechanical thrombectomy. Samples of sufficient quality were subjected to 100-cycle, paired-end RNAseq, and transcriptomes with less than 10 million unique reads were excluded from analysis. Significant differentially expressed genes (DEGs) between subtypes (defined by the Trial of Org 10 172 in Acute Stroke Treatment) were identified by expression analysis in edgeR. Gene ontology enrichment analysis was used to study the biologic differences between stroke etiologies. RESULTS In all, 38 clot transcriptomes were analyzed; 6 from large artery atherosclerosis (LAA), 21 from cardioembolism (CE), 5 from strokes of other determined origin, and 6 from cryptogenic strokes. Among all comparisons, there were 816 unique DEGs, 174 of which were shared by at least two comparisons, and 20 of which were shared by all three. Gene ontology analysis showed that CE clots reflected high levels of inflammation, LAA clots had greater oxidoreduction and T-cell processes, and clots of other determined origin were enriched for aberrant platelet and hemoglobin-related processes. Principal component analysis indicated separation between these subtypes and showed cryptogenic samples clustered among several different groups. CONCLUSIONS Expression profiles of stroke clots were identified between stroke etiologies and reflected different biologic responses. Cryptogenic thrombi may be related to multiple etiologies.
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Affiliation(s)
- Vincent M Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
- Department of Mechanical and Aerospace Engineering, University at Buffalo School of Engineering and Applied Sciences, Buffalo, New York, USA
- Department of Biomedical Engineering, University at Buffalo School of Engineering and Applied Sciences, Buffalo, New York, USA
| | - Sarah Fricano
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Aichi Chien
- Department of Radiological Sciences, UCLA, Los Angeles, California, USA
| | - Tatsat R Patel
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Mechanical and Aerospace Engineering, University at Buffalo School of Engineering and Applied Sciences, Buffalo, New York, USA
| | - Andre Monteiro
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Hamid H Rai
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Adam A Dmytriw
- Neuroendovascular Program, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neuroradiology and Neurointervention, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lee D Chaves
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Elad I Levy
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
| | - Adnan H Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, New York, USA
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
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Transcriptomic Studies on Intracranial Aneurysms. Genes (Basel) 2023; 14:genes14030613. [PMID: 36980884 PMCID: PMC10048068 DOI: 10.3390/genes14030613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
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.
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6
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Poppenberg KE, Chien A, Santo BA, Baig AA, Monteiro A, Dmytriw AA, Burkhardt JK, Mokin M, Snyder KV, Siddiqui AH, Tutino VM. RNA Expression Signatures of Intracranial Aneurysm Growth Trajectory Identified in Circulating Whole Blood. J Pers Med 2023; 13:jpm13020266. [PMID: 36836499 PMCID: PMC9967913 DOI: 10.3390/jpm13020266] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
After detection, identifying which intracranial aneurysms (IAs) will rupture is imperative. We hypothesized that RNA expression in circulating blood reflects IA growth rate as a surrogate of instability and rupture risk. To this end, we performed RNA sequencing on 66 blood samples from IA patients, for which we also calculated the predicted aneurysm trajectory (PAT), a metric quantifying an IA's future growth rate. We dichotomized dataset using the median PAT score into IAs that were either more stable and more likely to grow quickly. The dataset was then randomly divided into training (n = 46) and testing cohorts (n = 20). In training, differentially expressed protein-coding genes were identified as those with expression (TPM > 0.5) in at least 50% of the samples, a q-value < 0.05 (based on modified F-statistics with Benjamini-Hochberg correction), and an absolute fold-change ≥ 1.5. Ingenuity Pathway Analysis was used to construct networks of gene associations and to perform ontology term enrichment analysis. The MATLAB Classification Learner was then employed to assess modeling capability of the differentially expressed genes, using a 5-fold cross validation in training. Finally, the model was applied to the withheld, independent testing cohort (n = 20) to assess its predictive ability. In all, we examined transcriptomes of 66 IA patients, of which 33 IAs were "growing" (PAT ≥ 4.6) and 33 were more "stable". After dividing dataset into training and testing, we identified 39 genes in training as differentially expressed (11 with decreased expression in "growing" and 28 with increased expression). Model genes largely reflected organismal injury and abnormalities and cell to cell signaling and interaction. Preliminary modeling using a subspace discriminant ensemble model achieved a training AUC of 0.85 and a testing AUC of 0.86. In conclusion, transcriptomic expression in circulating blood indeed can distinguish "growing" and "stable" IA cases. The predictive model constructed from these differentially expressed genes could be used to assess IA stability and rupture potential.
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Affiliation(s)
- Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Aichi Chien
- Department of Radiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Briana A. Santo
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Ammad A. Baig
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Andre Monteiro
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adam A. Dmytriw
- Neuroendovascular Program, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jan-Karl Burkhardt
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maxim Mokin
- Department of Neurosurgery, University of South Florida, Tampa, FL 33620, USA
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Correspondence: ; Tel.: +1-716-829-5400
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7
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Poppenberg KE, Chien A, Santo BA, Chaves L, Veeturi SS, Waqas M, Monteiro A, Dmytriw AA, Burkhardt JK, Mokin M, Snyder KV, Siddiqui AH, Tutino VM. Profiling of Circulating Gene Expression Reveals Molecular Signatures Associated with Intracranial Aneurysm Rupture Risk. Mol Diagn Ther 2023; 27:115-127. [PMID: 36460938 PMCID: PMC9924426 DOI: 10.1007/s40291-022-00626-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND Following detection, rupture risk assessment for intracranial aneurysms (IAs) is critical. Towards molecular prognostics, we hypothesized that circulating blood RNA expression profiles are associated with IA risk. METHODS We performed RNA sequencing on 68 blood samples from IA patients. Here, patients were categorized as either high or low risk by assessment of aneurysm size (≥ 5 mm = high risk) and Population, Hypertension, Age, Size, Earlier subarachnoid hemorrhage, Site (PHASES) score (≥ 1 = high risk). Modified F-statistics and Benjamini-Hochberg false discovery rate correction was performed on transcripts per million-normalized gene counts. Protein-coding genes expressed in ≥ 50% of samples with a q value < 0.05 and an absolute fold-change ≥ 2 were considered significantly differentially expressed. Bioinformatics in Ingenuity Pathway Analysis was performed to understand the biology of risk-associated expression profiles. Association was assessed between gene expression and risk via Pearson correlation analysis. Linear discriminant analysis models using significant genes were created and validated for classification of high-risk cases. RESULTS We analyzed transcriptomes of 68 IA patients. In these cases, 31 IAs were large (≥ 5 mm), while 26 IAs had a high PHASES score. Based on size, 36 genes associated with high-risk IAs, and two were correlated with the size measurement. Alternatively, based on PHASES score, 76 genes associated with high-risk cases, and nine of them showed significant correlation to the score. Similar ontological terms were associated with both gene profiles, which reflected inflammatory signaling and vascular remodeling. Prediction models based on size and PHASES stratification were able to correctly predict IA risk status, with > 80% testing accuracy for both. CONCLUSIONS Here, we identified genes associated with IA risk, as quantified by common clinical metrics. Preliminary classification models demonstrated feasibility of assessing IA risk using whole blood expression.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Aichi Chien
- Department of Radiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Briana A Santo
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Lee Chaves
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Sricharan S Veeturi
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Andre Monteiro
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Adam A Dmytriw
- Neuroendovascular Program, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jan-Karl Burkhardt
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Maxim Mokin
- Department of Neurosurgery, University of South Florida, Tampa, FL, USA
| | - Kenneth V Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Adnan H Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Vincent M Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, 875 Ellicott Street, Buffalo, NY, 14203, USA.
- Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA.
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, USA.
- Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY, USA.
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8
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Wang X, Wen D, You C, Ma L. Identification of the key immune-related genes in aneurysmal subarachnoid hemorrhage. Front Mol Neurosci 2022; 15:931753. [PMID: 36172261 PMCID: PMC9511034 DOI: 10.3389/fnmol.2022.931753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Subarachnoid hemorrhage (SAH) is a major cause of death and morbidity worldwide, often due to rupture of intracranial aneurysms (IAs). Immune infiltration and inflammatory activation play key roles in the process of aneurysmal SAH (aSAH). This study aimed to elaborate the immune infiltration and identify related biomarkers both in blood and tissue samples from patients with aSAH. Expression data of aSAH and healthy control samples were obtained from gene expression omnibus (GEO) database. Overall, a blood sample dataset GSE36791 and a tissue sample dataset GSE122897 were included. Differentially expressed genes (DEGs) between aSAH and healthy samples were explored. We applied GO biological and Gene Set Enrichment Analyses (GSEA) processes to access the functional enrichment. Then feature elimination algorithms based on random forest were used to screen and verify the biomarkers of aSAH. We performed three computational algorithms including Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), Microenvironment Cell Populations-counter (MCPcounter), and xcell to evaluate the immune cell infiltration landscape to identify the unique infiltration characteristics associated with rupturing. We found 2,220 DEGs (856 upregulated and 1,364 downregulated) in the original dataset. Functional analysis revealed most of these genes are enriched in immunological process, especially related with neutrophil response. Similar signaling pathway enrichment patterns were observed in tissue sample dataset and ClueGo. Analysis of immune microenvironment infiltration suggested neutrophils were abnormally upregulated in aSAH compared with those in the control group. Key gene SRPK1 was then filtered based on feature elimination algorithms, and transcription factor (TF) ZNF281 is assumed to participate in immunomodulation by regulating expression of SRPK1. Several immunomodulators such as CXCR1 and CXCR2 also appear to be involved in the progression of aSAH. In the present study, we performed a comprehensive stratification and quantification of the immune infiltration status of aSAH. By exploring the potential mechanism for aSAH based on several computational algorithms, key genes including SRPK1 and ZNF281 were filtered. This study may be of benefit to patients who are at high risk of suffering aSAH which allows for early diagnosis and potential therapy.
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Affiliation(s)
- Xing Wang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Dingke Wen
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Chao You
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
- West China Brain Research Centre, Sichuan University, Chengdu, China
- *Correspondence: Chao You Lu Ma
| | - Lu Ma
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Chao You Lu Ma
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Machine Learning and Intracranial Aneurysms: From Detection to Outcome Prediction. ACTA NEUROCHIRURGICA. SUPPLEMENT 2021; 134:319-331. [PMID: 34862556 DOI: 10.1007/978-3-030-85292-4_36] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Machine learning (ML) is a rapidly rising research tool in biomedical sciences whose applications include segmentation, classification, disease detection, and outcome prediction. With respect to traditional statistical methods, ML algorithms have the potential to learn and improve their predictive performance when fed with large data sets without the need of being specifically programmed. In recent years, this technology has been increasingly applied for tackling clinical issues in intracranial aneurysm (IA) research. Several studies attempted to provide reliable models for enhanced aneurysm detection. Convolutional neural networks trained with variable degrees of human interaction on data from diverse imaging modalities showed high sensitivity in aneurysm detection tasks, also outperforming expert image analysis. Algorithms were also shown to differentiate ruptured from unruptured IAs, with however limited clinical relevance. For prediction of rupture and stability assessment, ML was preliminarily shown to achieve better performance compared to conventional statistical methods and existing risk scores. ML-based complication and functional outcome prediction in the event of SAH have been more extensively reported, in contrast with periprocedural outcome investigation in unruptured IA patients. ML has the potential to be a game changer in IA patient management. Currently clinical translation of experimental results is limited.
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Danilov GV, Shifrin MA, Kotik KV, Ishankulov TA, Orlov YN, Kulikov AS, Potapov AA. Artificial Intelligence Technologies in Neurosurgery: a Systematic Literature Review Using Topic Modeling. Part II: Research Objectives and Perspectives. Sovrem Tekhnologii Med 2021; 12:111-118. [PMID: 34796024 PMCID: PMC8596229 DOI: 10.17691/stm2020.12.6.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
The current increase in the number of publications on the use of artificial intelligence (AI) technologies in neurosurgery indicates a new trend in clinical neuroscience. The aim of the study was to conduct a systematic literature review to highlight the main directions and trends in the use of AI in neurosurgery.
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Affiliation(s)
- G V Danilov
- Scientific Board Secretary; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia; Head of the Laboratory of Biomedical Informatics and Artificial Intelligence; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
| | - M A Shifrin
- Scientific Consultant, Laboratory of Biomedical Informatics and Artificial Intelligence; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
| | - K V Kotik
- Physics Engineer, Laboratory of Biomedical Informatics and Artificial Intelligence; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
| | - T A Ishankulov
- Engineer, Laboratory of Biomedical Informatics and Artificial Intelligence; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
| | - Yu N Orlov
- Head of the Department of Computational Physics and Kinetic Equations; Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 4 Miusskaya Sq., Moscow, 125047, Russia
| | - A S Kulikov
- Staff Anesthesiologist; N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
| | - A A Potapov
- Professor, Academician of the Russian Academy of Sciences, Chief Scientific Supervisor N.N. Burdenko National Medical Research Center for Neurosurgery, Ministry of Health of the Russian Federation, 16, 4 Tverskaya-Yamskaya St., Moscow, 125047, Russia
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Morel S, Bijlenga P, Kwak BR. Intracranial aneurysm wall (in)stability-current state of knowledge and clinical perspectives. Neurosurg Rev 2021; 45:1233-1253. [PMID: 34743248 PMCID: PMC8976821 DOI: 10.1007/s10143-021-01672-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/15/2021] [Accepted: 10/05/2021] [Indexed: 12/19/2022]
Abstract
Intracranial aneurysm (IA), a local outpouching of cerebral arteries, is present in 3 to 5% of the population. Once formed, an IA can remain stable, grow, or rupture. Determining the evolution of IAs is almost impossible. Rupture of an IA leads to subarachnoid hemorrhage and affects mostly young people with heavy consequences in terms of death, disabilities, and socioeconomic burden. Even if the large majority of IAs will never rupture, it is critical to determine which IA might be at risk of rupture. IA (in)stability is dependent on the composition of its wall and on its ability to repair. The biology of the IA wall is complex and not completely understood. Nowadays, the risk of rupture of an IA is estimated in clinics by using scores based on the characteristics of the IA itself and on the anamnesis of the patient. Classification and prediction using these scores are not satisfying and decisions whether a patient should be observed or treated need to be better informed by more reliable biomarkers. In the present review, the effects of known risk factors for rupture, as well as the effects of biomechanical forces on the IA wall composition, will be summarized. Moreover, recent advances in high-resolution vessel wall magnetic resonance imaging, which are promising tools to discriminate between stable and unstable IAs, will be described. Common data elements recently defined to improve IA disease knowledge and disease management will be presented. Finally, recent findings in genetics will be introduced and future directions in the field of IA will be exposed.
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Affiliation(s)
- Sandrine Morel
- Department of Pathology and Immunology, Faculty of Medicine, Centre Medical Universitaire, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Neurosurgery Division, Department of Clinical Neurosciences, Faculty of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Philippe Bijlenga
- Neurosurgery Division, Department of Clinical Neurosciences, Faculty of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Brenda R Kwak
- Department of Pathology and Immunology, Faculty of Medicine, Centre Medical Universitaire, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
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12
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Tutino VM, Fricano S, Frauens K, Patel TR, Monteiro A, Rai HH, Waqas M, Chaves L, Poppenberg KE, Siddiqui AH. Isolation of RNA from Acute Ischemic Stroke Clots Retrieved by Mechanical Thrombectomy. Genes (Basel) 2021; 12:genes12101617. [PMID: 34681010 PMCID: PMC8536169 DOI: 10.3390/genes12101617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Mechanical thrombectomy (MT) for large vessel acute ischemic stroke (AIS) has enabled biologic analyses of resected clots. While clot histology has been well-studied, little is known about gene expression within the tissue, which could shed light on stroke pathophysiology. In this methodological study, we develop a pipeline for obtaining useful RNA from AIS clots. A total of 73 clot samples retrieved by MT were collected and stored in RNALater and in 10% phosphate-buffered formalin. RNA was extracted from all samples using a modified Chemagen magnetic bead extraction protocol on the PerkinElmer Chemagic 360. RNA was interrogated by UV–Vis absorption and electrophoretic quality control analysis. All samples with sufficient volume underwent traditional qPCR analysis and samples with sufficient RNA quality were subjected to next-generation RNA sequencing on the Illumina NovaSeq platform. Whole blood RNA samples from three patients were used as controls, and H&E-stained histological sections of the clots were used to assess clot cellular makeup. Isolated mRNA was eluted into a volume of 140 µL and had a concentration ranging from 0.01 ng/µL to 46 ng/µL. Most mRNA samples were partially degraded, with RNA integrity numbers ranging from 0 to 9.5. The majority of samples (71/73) underwent qPCR analysis, which showed linear relationships between the expression of three housekeeping genes (GAPDH, GPI, and HPRT1) across all samples. Of these, 48 samples were used for RNA sequencing, which had moderate quality based on MultiQC evaluation (on average, ~35 M reads were sequenced). Analysis of clot histology showed that more acellular samples yielded RNA of lower quantity and quality. We obtained useful mRNA from AIS clot samples stored in RNALater. qPCR analysis could be performed in almost all cases, while sequencing data could only be performed in approximately two-thirds of the samples. Acellular clots tended to have lower RNA quantity and quality.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY 14260, USA
- Correspondence: ; Tel.: +1-716-829-5400; Fax: +1-716-854-1850
| | - Sarah Fricano
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Kirsten Frauens
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Tatsat R. Patel
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY 14260, USA
| | - Andre Monteiro
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Hamid H. Rai
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Lee Chaves
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (S.F.); (K.F.); (T.R.P.); (A.M.); (H.H.R.); (M.W.); (L.C.); (K.E.P.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
- Department of Radiology, University at Buffalo, Buffalo, NY 14260, USA
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13
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Li Y, Qin J. A Two-Gene-Based Diagnostic Signature for Ruptured Intracranial Aneurysms. Front Cardiovasc Med 2021; 8:671655. [PMID: 34485395 PMCID: PMC8414364 DOI: 10.3389/fcvm.2021.671655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Ruptured intracranial aneurysm (IA) is a disease with high mortality. Despite the great progress in treating ruptured IA, methods for risk assessment of ruptured IA remain limited. Methods: In this study, we aim to develop a robust diagnostic model for ruptured IA. Gene expression profiles in blood samples of 18 healthy persons and 43 ruptured IA patients were obtained from the Gene Expression Omnibus (GEO). Differential expression analysis was performed using limma Bioconductor package followed by functional enrichment analysis via clusterProfiler Bioconductor package. Immune cell compositions in ruptured IA and healthy samples were assessed through the CIBERSORT tool. Protein-protein interaction (PPI) was predicted based on the STRING database. Logistic regression model was used for the construction of predictive model for distinguishing ruptured IA and healthy samples. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed to validate the gene expression between the ruptured IA and healthy samples. Results: A total of 58 differentially expressed genes (DEGs) were obtained for ruptured IA patients compared with healthy controls. Functional enrichment analysis showed that the DEGs were enriched in biological processes related to neutrophil activation, neutrophil degranulation, and cytokine-cytokine receptor interaction. Notably, immune analysis results proved that the rupture of IA might be related to immune cell distribution. We further identified 24 key genes as hub genes using the PPI networks. The logistic regression model trained based on the 24 key genes ultimately retained two genes, i.e., IL2RB and CCR7, which had great potential for risk assessment for rupture of IA. The RT-qPCR further validated that compared with the healthy samples, the expression levels of IL2RB and CCR7 were decreased in ruptured IA samples. Conclusions: This study might be helpful for cohorts who have a high risk of ruptured IA for early diagnosis and prevention of the disease.
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Affiliation(s)
- Yuwang Li
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Jie Qin
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
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Characterization of Long Non-coding RNA Signatures of Intracranial Aneurysm in Circulating Whole Blood. Mol Diagn Ther 2021; 24:723-736. [PMID: 32939739 DOI: 10.1007/s40291-020-00494-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND OBJECTIVE Long non-coding RNAs (lncRNAs) may serve as biomarkers for complex disease states, such as intracranial aneurysms. In this study, we investigated lncRNA expression differences in the whole blood of patients with unruptured aneurysms. METHODS Whole blood RNA from 67 subjects (34 with aneurysm, 33 without) was used for next-generation RNA sequencing. Differential expression analysis was used to define a signature of intracranial aneurysm-associated lncRNAs. To estimate the signature's ability to classify aneurysms and to identify the most predictive lncRNAs, we implemented a nested cross-validation pipeline to train classifiers using linear discriminant analysis. Ingenuity pathway analysis was used to study potential biological roles of differentially expressed lncRNAs, and lncRNA ontology was used to investigate ontologies enriched in signature lncRNAs. Co-expression correlation analysis was performed to investigate associated differential protein-coding messenger RNA expression. RESULTS Of 4639 detected lncRNAs, 263 were significantly different (p < 0.05) between the two groups, and 84 of those had an absolute fold-change ≥ 1.5. An eight-lncRNA signature (q < 0.35, fold-change ≥ 1.5) was able to separate patients with and without aneurysms on principal component analysis, and had an estimated accuracy of 70.9% in nested cross-validation. Bioinformatics analyses showed that networks of differentially expressed lncRNAs (p < 0.05) were enriched for cell death and survival, connective tissue disorders, carbohydrate metabolism, and cardiovascular disease. Signature lncRNAs shared ontologies that reflected regulation of gene expression, signaling, ubiquitin processing, and p53 signaling. Co-expression analysis showed correlations with messenger RNAs related to inflammatory responses. CONCLUSIONS Differential expression in whole blood lncRNAs is detectable in patients harboring aneurysms, and reflects expression/signaling regulation, and ubiquitin and p53 pathways. Following validation in larger cohorts, these lncRNAs may be potential diagnostic targets for aneurysm detection by blood testing.
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Inflammatory Biomarkers and Intracranial Hemorrhage after Endovascular Thrombectomy. Can J Neurol Sci 2021; 49:644-650. [PMID: 34548113 DOI: 10.1017/cjn.2021.197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Intracranial hemorrhage after endovascular thrombectomy is associated with poorer prognosis compared with those who do not develop the complication. Our study aims to determine predictors of post-EVT hemorrhage - more specifically, inflammatory biomarkers present in baseline serology. METHODS We performed a retrospective review of consecutive patients treated with EVT for acute large vessel ischemic stroke. The primary outcome of the study is the presence of ICH on the post-EVT scan. We used four definitions: the SITS-MOST criteria, the NINDS criteria, asymptomatic hemorrhage, and overall hemorrhage. We identified nonredundant predictors of outcome using backward elimination based on Akaike Information Criteria. We then assessed prediction accuracy using area under the receiver operating curve. Then we implemented variable importance ranking from logistic regression models using the drop in Naegelkerke R2 with the exclusion of each predictor. RESULTS Our study demonstrates a 6.3% SITS (16/252) and 10.0% NINDS (25/252) sICH rate, as well as a 19.4% asymptomatic (49/252) and 29.4% (74/252) overall hemorrhage rate. Serologic markers that demonstrated association with post-EVT hemorrhage were: low lymphocyte count (SITS), high neutrophil count (NINDS, overall hemorrhage), low platelet to lymphocyte ratio (NINDS), and low total WBC (NINDS, asymptomatic hemorrhage). CONCLUSION Higher neutrophil counts, low WBC counts, low lymphocyte counts, and low platelet to lymphoycyte ratio were baseline serology biomarkers that were associated with post-EVT hemorrhage. Our findings, particularly the association of diabetes mellitus and high neutrophil, support experimental data on the role of thromboinflammation in hemorrhagic transformation of large vessel occlusions.
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Tutino VM, Lu Y, Ishii D, Poppenberg KE, Rajabzadeh-Oghaz H, Siddiqui AH, Hasan DM. Aberrant Whole Blood Gene Expression in the Lumen of Human Intracranial Aneurysms. Diagnostics (Basel) 2021; 11:diagnostics11081442. [PMID: 34441376 PMCID: PMC8392298 DOI: 10.3390/diagnostics11081442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 01/19/2023] Open
Abstract
The rupture of an intracranial aneurysm (IA) causes devastating hemorrhagic strokes. Yet, most IAs remain asymptomatic and undetected until they rupture. In the search for circulating biomarkers of unruptured IAs, we previously performed transcriptome profiling on whole blood and identified an IA-associated panel of 18 genes. In this study, we seek to determine if these genes are also differentially expressed within the IA lumen, which could provide a mechanistic link between the disease and the observed circulating gene expression patterns. To this end, we collected blood from the lumen of 37 IAs and their proximal parent vessels in 31 patients. The expression levels of 18 genes in the lumen and proximal vessel were then measured by quantitative polymerase chain reaction. This analysis revealed that the expression of 6/18 genes (CBWD6, MT2A, MZT2B, PIM3, SLC37A3, and TNFRSF4) was significantly higher in intraluminal blood, while the expression of 3/18 genes (ST6GALNAC1, TCN2, and UFSP1) was significantly lower. There was a significant, positive correlation between intraluminal and proximal expression of CXCL10, MT2A, and MZT2B, suggesting local increases of these genes is reflected in the periphery. Expression of ST6GALNAC1 and TIFAB was significantly positively correlated with IA size, while expression of CCDC85B was significantly positively correlated with IA enhancement on post-contrast MRI, a metric of IA instability and risk. In conclusion, intraluminal expression differences in half of the IA-associated genes observed in this study provide evidence for IA tissue-mediated transcriptional changes in whole blood. Additionally, some genes may be informative in assessing IA risk, as their intraluminal expression was correlated to IA size and aneurysmal wall enhancement.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14260, USA; (V.M.T.); (K.E.P.); (H.R.-O.); (A.H.S.)
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Yongjun Lu
- Department of Cardiovascular Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA;
| | - Daizo Ishii
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, 1616 JCP, 200 Hawkins Dr, Iowa City, IA 52242, USA;
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14260, USA; (V.M.T.); (K.E.P.); (H.R.-O.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Hamidreza Rajabzadeh-Oghaz
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14260, USA; (V.M.T.); (K.E.P.); (H.R.-O.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14260, USA; (V.M.T.); (K.E.P.); (H.R.-O.); (A.H.S.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14260, USA
| | - David M. Hasan
- Department of Neurosurgery, University of Iowa Hospitals and Clinics, 1616 JCP, 200 Hawkins Dr, Iowa City, IA 52242, USA;
- Correspondence: ; Tel.: +1-319-384-8669
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Tutino VM, Zebraski HR, Rajabzadeh-Oghaz H, Waqas M, Jarvis JN, Bach K, Mokin M, Snyder KV, Siddiqui AH, Poppenberg KE. Identification of Circulating Gene Expression Signatures of Intracranial Aneurysm in Peripheral Blood Mononuclear Cells. Diagnostics (Basel) 2021; 11:diagnostics11061092. [PMID: 34203780 PMCID: PMC8232768 DOI: 10.3390/diagnostics11061092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022] Open
Abstract
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.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
- Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY 14228, USA
- Correspondence: ; Tel.: +1-(716)-829-5400; Fax: +1-(716)-854-1850
| | - Haley R. Zebraski
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14228, USA;
| | - Hamidreza Rajabzadeh-Oghaz
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - James N. Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY 14203, USA;
| | - Konrad Bach
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33620, USA; (K.B.); (M.M.)
| | - Maxim Mokin
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33620, USA; (K.B.); (M.M.)
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
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Wu Y, Zheng J, Sun Y, Wang X, Zhao H, Qiu F, Zhang S, Jiang X, Yu X. Non-Coding RNAs as Circulating Biomarkers for the Diagnosis of Intracranial Aneurysm: A Systematic Review and Meta-Analysis. J Stroke Cerebrovasc Dis 2021; 30:105762. [PMID: 33813080 DOI: 10.1016/j.jstrokecerebrovasdis.2021.105762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Early diagnosis of intracranial aneurysm (IA) is arduous in the current situation, and no biomarker is available for the screening of IA. We here systematically evaluate the diagnostic value of circulating non-coding RNA (ncRNA) for the diagnosis of IA. METHODS We searched PubMed, Web of Science, Embase, Scopus and Cochrane Library databases from inception to June 2020. We included studies that investigated the diagnostic performance of circulating ncRNAs for the diagnosis of IA. We performed Random-effect meta-analyses for the diagnostic test accuracy to calculate pooled estimates. Subgroup analyses and sensitivity analyses were conducted to explore the source of heterogeneity. RESULTS Thirteen studies, including 1,105 patients and 28 ncRNAs, were included. The pooled sensitivity and specificity were 0.80 (95% confidence interval [CI], 0.76-0.83) and 0.80 (95% CI, 0.76-0.84), respectively, and the area under the hierarchical summary receiver operating characteristic curve was 0.87 (95% CI, 0.84-0.89). The pooled positive and negative likelihood ratios were 3.97 (95% CI, 3.17-4.98) and 0.25 (95% CI, 0.21-0.31), corresponding with a diagnostic odds ratio of 15.63 (95% CI, 10.41-23.47). Subgroup analyses revealed that the diagnostic accuracy of miRNA, lncRNA and circRNA were not significantly different (p > 0.05). Circulating ncRNAs showed higher diagnostic accuracy for patients with unruptured IA than those with ruptured IA (p = 0.0122). CONCLUSION Current evidence suggests that the circulating ncRNA test could be an effective method for universal IA screening. Future clinical studies need to confirm the diagnostic role of specific ncRNAs.
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Affiliation(s)
- Yuehui Wu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Jin Zheng
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Yun Sun
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Hongyang Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Feng Qiu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China
| | - Shuyuan Zhang
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, P R China; Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, P R China; Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, P R China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China.
| | - Xinyu Yu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan 430022, China.
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Zhang B, Lin L, Yuan F, Song G, Chang Q, Wu Z, Miao Z, Mo D, Huo X, Liu A. Clinical application values of neutrophil-to-lymphocyte ratio in intracranial aneurysms. Aging (Albany NY) 2021; 13:5250-5262. [PMID: 33526720 PMCID: PMC7950281 DOI: 10.18632/aging.202445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Inflammation plays an important role in the pathogenesis and growth of intracranial aneurysms (IAs). We investigated the clinical value of the neutrophil-to-lymphocyte ratio (NLR) as a marker of systemic subclinical inflammation in patients with IAs. Consecutive patients with IAs who underwent endovascular treatment (EVT) were enrolled in the study. The evaluation indicators were aneurysm size and rupture, a poor outcome at 3 to 6 months, and delayed cerebral ischemia (DCI) during hospitalization. In total, 532 patients with IAs underwent EVT (mean age, 54.0 years; 62.4% female). Among patients with ruptured IAs, those with a higher NLR had an increased risk of a poor outcome at 3 to 6 months and DCI during hospitalization than those with a lower NLR. A higher NLR was significantly more strongly associated with the size of unruptured aneurysms and aneurysm rupture than a lower NLR. The NLR and C-reactive protein concentration showed similar predictive ability for aneurysm size and treatment prognosis. The NLR was lower at discharge than admission for patients with ruptured IAs and DCI. An elevated NLR was significantly associated with the size of unruptured IAs, an increased risk of a poor outcome, and DCI in patients with ruptured IAs.
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Affiliation(s)
- Baorui Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China.,Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Lin Lin
- Department of Information Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Fei Yuan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China.,Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Guangrong Song
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China.,Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Qing Chang
- Department of Neurology, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, China
| | - Zhongxue Wu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China.,Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Zhongrong Miao
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Dapeng Mo
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Xiaochuan Huo
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Aihua Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China.,Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
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20
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Endogenous animal models of intracranial aneurysm development: a review. Neurosurg Rev 2021; 44:2545-2570. [PMID: 33501561 DOI: 10.1007/s10143-021-01481-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 12/13/2022]
Abstract
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.
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21
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Chu C, Xu G, Li X, Duan Z, Tao L, Cai H, Yang M, Zhang X, Chen B, Zheng Y, Shi H, Li X. Sustained expression of MCP-1 induced low wall shear stress loading in conjunction with turbulent flow on endothelial cells of intracranial aneurysm. J Cell Mol Med 2020; 25:110-119. [PMID: 33332775 PMCID: PMC7810920 DOI: 10.1111/jcmm.15868] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/30/2020] [Accepted: 08/24/2020] [Indexed: 12/28/2022] Open
Abstract
Shear stress was reported to regulate the expression of AC007362, but its underlying mechanisms remain to be explored. In this study, to isolate endothelial cells of blood vessels, unruptured and ruptured intracranial aneurysm (IA) tissues were collected from IA patients. Subsequently, quantitative real‐time PCR (qRT‐PCR), Western blot and luciferase assay were performed to investigate the relationships between AC007362, miRNAs‐493 and monocyte chemoattractant protein‐1 (MCP‐1) in human umbilical vein endothelial cells (HUVECs) exposed to shear stress. Reduced representation bisulphite sequencing (RRBS) was performed to assess the level of DNA methylation in AC007362 promoter. Accordingly, AC007362 and MCP‐1 were significantly up‐regulated while miR‐493 was significantly down‐regulated in HUVECs exposed to shear stress. AC007362 could suppress the miR‐493 expression and elevate the MCP‐1 expression, and miR‐493 was shown to respectively target AC007362 and MCP‐1. Moreover, shear stress in HUVECs led to the down‐regulated DNA methyltransferase 1 (DNMT1), as well as the decreased DNA methylation level of AC007362 promoter. Similar results were also observed in ruptured IA tissues when compared with unruptured IA tissues. In conclusion, this study presented a deep insight into the operation of the regulatory network of AC007362, miR‐493 and MCP‐1 upon shear stress. Under shear stress, the expression of AC007362 was enhanced by the inhibited promoter DNA methylation, while the expression of MCP‐1 was enhanced by sponging the expression of miR‐493.
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Affiliation(s)
- Cheng Chu
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Gang Xu
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xiaocong Li
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Zuowei Duan
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Lihong Tao
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Hongxia Cai
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Ming Yang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xinjiang Zhang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Bin Chen
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yanyu Zheng
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Hongcan Shi
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Xiaoyu Li
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
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22
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Zawy Alsofy S, Sakellaropoulou I, Nakamura M, Ewelt C, Salma A, Lewitz M, Welzel Saravia H, Sarkis HM, Fortmann T, Stroop R. Impact of Virtual Reality in Arterial Anatomy Detection and Surgical Planning in Patients with Unruptured Anterior Communicating Artery Aneurysms. Brain Sci 2020; 10:brainsci10120963. [PMID: 33321880 PMCID: PMC7763342 DOI: 10.3390/brainsci10120963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 01/20/2023] Open
Abstract
Anterior-communicating artery (ACoA) aneurysms have diverse configurations and anatomical variations. The evaluation and operative treatment of these aneurysms necessitates a perfect surgical strategy based on review of three-dimensional (3D) angioarchitecture using several radiologic imaging methods. We analyzed the influence of 3D virtual reality (VR) reconstructions versus conventional computed tomography angiography (CTA) scans on the identification of vascular anatomy and on surgical planning in patients with unruptured ACoA aneurysms. Medical files were retrospectively analyzed regarding patient- and disease-related data. Preoperative CTA scans were retrospectively reconstructed to 3D-VR images and visualized via VR software to detect the characteristics of unruptured ACoA aneurysms. A questionnaire was used to evaluate the influence of VR on the identification of aneurysm morphology and relevant arterial anatomy and on surgical strategy. Twenty-six patients were included and 520 answer sheets were evaluated. The 3D-VR modality significantly influenced detection of the aneurysm-related vascular structure (p = 0.0001), the recommended head positioning (p = 0.005), and the surgical approach (p = 0.001) in the planning of microsurgical clipping. Thus, reconstruction of conventional preoperative CTA scans into 3D images and the spatial presentation in VR models enabled greater understanding of the anatomy and pathology, provided realistic haptic feedback for aneurysm surgery, and influenced operation planning and strategy.
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Affiliation(s)
- Samer Zawy Alsofy
- Department of Medicine, Faculty of Health, Witten/Herdecke University, 58448 Witten, Germany;
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
- Correspondence:
| | - Ioanna Sakellaropoulou
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Makoto Nakamura
- Department of Neurosurgery, Academic Hospital Köln-Merheim, Witten/Herdecke University, 51109 Köln, Germany;
| | - Christian Ewelt
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Asem Salma
- Department of Neurosurgery, St. Rita’s Neuroscience Institute, Lima, OH 45801, USA;
| | - Marc Lewitz
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Heinz Welzel Saravia
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Hraq Mourad Sarkis
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Thomas Fortmann
- Department of Neurosurgery, St. Barbara-Hospital, Academic Hospital of Westfälische Wilhelms-University Münster, 59073 Hamm, Germany; (I.S.); (C.E.); (M.L.); (H.W.S.); (H.M.S.); (T.F.)
| | - Ralf Stroop
- Department of Medicine, Faculty of Health, Witten/Herdecke University, 58448 Witten, Germany;
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23
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Poppenberg KE, Li L, Waqas M, Paliwal N, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H, Tutino VM. Whole blood transcriptome biomarkers of unruptured intracranial aneurysm. PLoS One 2020; 15:e0241838. [PMID: 33156839 PMCID: PMC7647097 DOI: 10.1371/journal.pone.0241838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The rupture of an intracranial aneurysm (IA) causes devastating subarachnoid hemorrhages, yet most IAs remain undiscovered until they rupture. Recently, we found an IA RNA expression signature of circulating neutrophils, and used transcriptome data to build predictive models for unruptured IAs. In this study, we evaluate the feasibility of using whole blood transcriptomes to predict the presence of unruptured IAs. METHODS We subjected RNA from peripheral whole blood of 67 patients (34 with unruptured IA, 33 without IA) to next-generation RNA sequencing. Model genes were identified using the least absolute shrinkage and selection operator (LASSO) in a random training cohort (n = 47). These genes were used to train a Gaussian Support Vector Machine (gSVM) model to distinguish patients with IA. The model was applied to an independent testing cohort (n = 20) to evaluate performance by receiver operating characteristic (ROC) curve. Gene ontology and pathway analyses investigated the underlying biology of the model genes. RESULTS We identified 18 genes that could distinguish IA patients in a training cohort with 85% accuracy. This SVM model also had 85% accuracy in the testing cohort, with an area under the ROC curve of 0.91. Bioinformatics reflected activation and recruitment of leukocytes, activation of macrophages, and inflammatory response, suggesting that the biomarker captures important processes in IA pathogenesis. CONCLUSIONS Circulating whole blood transcriptomes can detect the presence of unruptured IAs. Pending additional testing in larger cohorts, this could serve as a foundation to develop a simple blood-based test to facilitate screening and early detection of IAs.
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Affiliation(s)
- Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Muhammad Waqas
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
| | - Nikhil Paliwal
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
- Department of Pediatrics, University at Buffalo, Buffalo, New York, United States of America
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurology, University at Buffalo, Buffalo, New York, United States of America
| | - Elad I. Levy
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
| | - John Kolega
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Hui Meng
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Vincent M. Tutino
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York, United States of America
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24
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Chen S, Yang D, Liu B, Wang L, Chen Y, Ye W, Liu C, Ni L, Zhang X, Zheng Y. Identification and validation of key genes mediating intracranial aneurysm rupture by weighted correlation network analysis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1407. [PMID: 33313152 PMCID: PMC7723540 DOI: 10.21037/atm-20-4083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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.
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Affiliation(s)
- Siliang Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Yang
- Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Wang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuexin Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Ye
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changwei Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Leng Ni
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobo Zhang
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehong Zheng
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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25
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Poppenberg KE, Tutino VM, Li L, Waqas M, June A, Chaves L, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm. J Transl Med 2020; 18:392. [PMID: 33059716 PMCID: PMC7565814 DOI: 10.1186/s12967-020-02550-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. Methods Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n = 94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n = 40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. Results Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC) = 0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. Conclusions We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Vincent M Tutino
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Biomedical Engineering, University of Buffalo, Buffalo, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Lu Li
- Department of Computer Science and Engineering, University of Buffalo, Buffalo, USA
| | - Muhammad Waqas
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Armond June
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Lee Chaves
- Department of Internal Medicine, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - James N Jarvis
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Kenneth V Snyder
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Elad I Levy
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Adnan H Siddiqui
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - John Kolega
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA. .,Department of Biomedical Engineering, University of Buffalo, Buffalo, USA. .,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA. .,Department of Mechanical & Aerospace Engineering, University At Buffalo, Buffalo, NY, USA.
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26
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Li M, Dong X, Chen S, Wang W, Yang C, Li B, Liang D, Yang W, Liu X, Yang X. Genetic polymorphisms and transcription profiles associated with intracranial aneurysm: a key role for NOTCH3. Aging (Albany NY) 2020; 11:5173-5191. [PMID: 31339861 PMCID: PMC6682524 DOI: 10.18632/aging.102111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022]
Abstract
Intracranial aneurysm (IA) incidence is about 1~2%. However, the specific mechanisms of IA onset and development need further study. Our objective was to discover novel IA-related genes to determine possible etiologies further. We performed next-generation sequencing on nineteen Chinese patients with familial IA and one patient with sporadic IA. We obtained mRNA expression data of 129 samples from Gene Expression Omnibus (GEO) and made statistical computing to discover differentially expressed genes (DEGs). The screened IA-related gene NOTCH3 was determined by bioinformatic data mining. We verified the IA-related indicators of NOTCH3. Association was found between IA and the NOTCH3 SNPs rs779314594, rs200504060 and rs2285981. Levels of NOTCH3 mRNA were lower in IA tissue than in control tissue, but higher in peripheral blood neutrophils from IA patients than in neutrophils from controls. Levels of NOTCH3 protein were lower in IA tissue than in cerebral artery tissue. NOTCH3 also decreased the expression of angiogenesis factors in human umbilical vein endothelial cells. Variation in NOTCH3 and alteration of its expression in cerebral artery or neutrophils may contribute to IA. Our findings also describe a bioinformatic-experimental approach that may prove useful for probing the pathophysiology of other complex diseases.
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Affiliation(s)
- Mengqi Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China.,Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xinlong Dong
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China
| | - Shi Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China.,Department of Neurosurgery, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou 350007, China
| | - Weihan Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China
| | - Chao Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China
| | - Bochuan Li
- Collaborative Innovation Center of Tianjin for Medical Epigenetics and Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin 300052, China
| | - Degang Liang
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Weidong Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China
| | - Xiaozhi Liu
- Department of Neurosurgery, Tianjin Fifth Central Hospital, Tianjin 300450, China
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China.,Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China
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Poppenberg KE, Jiang K, Li L, Sun Y, Meng H, Wallace CA, Hennon T, Jarvis JN. The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches. Arthritis Res Ther 2019; 21:230. [PMID: 31706344 PMCID: PMC6842535 DOI: 10.1186/s13075-019-2010-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/23/2019] [Indexed: 01/09/2023] Open
Abstract
Background The response to treatment for juvenile idiopathic arthritis (JIA) can be staged using clinical features. However, objective laboratory biomarkers of remission are still lacking. In this study, we used machine learning to predict JIA activity from transcriptomes from peripheral blood mononuclear cells (PBMCs). We included samples from children with Native American ancestry to determine whether the model maintained validity in an ethnically heterogeneous population. Methods Our dataset consisted of 50 samples, 23 from children in remission and 27 from children with an active disease on therapy. Nine of these samples were from children with mixed European/Native American ancestry. We used 4 different machine learning methods to create predictive models in 2 populations: the whole dataset and then the samples from children with exclusively European ancestry. Results In both populations, models were able to predict JIA status well, with training accuracies > 74% and testing accuracies > 78%. Performance was better in the whole dataset model. We note a high degree of overlap between genes identified in both populations. Using ingenuity pathway analysis, genes from the whole dataset associated with cell-to-cell signaling and interactions, cell morphology, organismal injury and abnormalities, and protein synthesis. Conclusions This study demonstrates it is feasible to use machine learning in conjunction with RNA sequencing of PBMCs to predict JIA stage. Thus, developing objective biomarkers from easy to obtain clinical samples remains an achievable goal.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo, Buffalo, NY, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA.,Department of Neurosurgery, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Carol A Wallace
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Teresa Hennon
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo, Buffalo, NY, USA. .,Pediatric Rheumatology Research, Clinical & Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14203, USA.
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28
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Poppenberg KE, Jiang K, Tso MK, Snyder KV, Siddiqui AH, Kolega J, Jarvis JN, Meng H, Tutino VM. Epigenetic landscapes suggest that genetic risk for intracranial aneurysm operates on the endothelium. BMC Med Genomics 2019; 12:149. [PMID: 31666072 PMCID: PMC6821037 DOI: 10.1186/s12920-019-0591-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genetics play an important role in intracranial aneurysm (IA) pathophysiology. Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are linked to IA but how they affect disease pathobiology remains poorly understood. We used Encyclopedia of DNA Elements (ENCODE) data to investigate the epigenetic landscapes surrounding genetic risk loci to determine if IA-associated SNPs affect functional elements that regulate gene expression and if those SNPs are most likely to impact a specific type of cells. METHODS We mapped 16 highly significant IA-associated SNPs to linkage disequilibrium (LD) blocks within the human genome. Within these regions, we examined the presence of H3K4me1 and H3K27ac histone marks and CCCTC-binding factor (CTCF) and transcription-factor binding sites using chromatin immunoprecipitation-sequencing (ChIP-Seq) data. This analysis was conducted in several cell types relevant to endothelial (human umbilical vein endothelial cells [HUVECs]) and inflammatory (monocytes, neutrophils, and peripheral blood mononuclear cells [PBMCs]) biology. Gene ontology analysis was performed on genes within extended IA-risk regions to understand which biological processes could be affected by IA-risk SNPs. We also evaluated recently published data that showed differential methylation and differential ribonucleic acid (RNA) expression in IA to investigate the correlation between differentially regulated elements and the IA-risk LD blocks. RESULTS The IA-associated LD blocks were statistically significantly enriched for H3K4me1 and/or H3K27ac marks (markers of enhancer function) in endothelial cells but not in immune cells. The IA-associated LD blocks also contained more binding sites for CTCF in endothelial cells than monocytes, although not statistically significant. Differentially methylated regions of DNA identified in IA tissue were also present in several IA-risk LD blocks, suggesting SNPs could affect this epigenetic machinery. Gene ontology analysis supports that genes affected by IA-risk SNPs are associated with extracellular matrix reorganization and endopeptidase activity. CONCLUSION These findings suggest that known genetic alterations linked to IA risk act on endothelial cell function. These alterations do not correlate with IA-associated gene expression signatures of circulating blood cells, which suggests that such signatures are a secondary response reflecting the presence of IA rather than indicating risk for IA.
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Affiliation(s)
- Kerry E Poppenberg
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Michael K Tso
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kenneth V Snyder
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Radiology, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Adnan H Siddiqui
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Radiology, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - John Kolega
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Pediatrics, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Hui Meng
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY, USA
| | - Vincent M Tutino
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA. .,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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