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Sanchez S, Chimenti MS, Lu Y, Sagues E, Gudino A, Dier C, Hasan D, Samaniego EA. Modulation of the Immunological Milieu in Acute Aneurysmal Subarachnoid Hemorrhage: The Potential Role of Monocytes Through CXCL10 Secretion. Transl Stroke Res 2024:10.1007/s12975-024-01259-4. [PMID: 38780865 DOI: 10.1007/s12975-024-01259-4] [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: 04/12/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Emerging evidence indicates that aneurysmal subarachnoid hemorrhage (aSAH) elicits a response from both innate and adaptive immune systems. An upregulation of CD8 + CD161 + cells has been observed in the cerebrospinal fluid (CSF) after aSAH, yet the precise role of these cells in the context of aSAH is unkown. CSF samples from patients with aSAH and non-aneurysmal SAH (naSAH) were analyzed. Single-cell RNA sequencing (scRNAseq) was performed on CD8 + CD161 + sorted samples from aSAH patients. Cell populations were identified using "clustering." Gene expression levels of ten previously described genes involved in inflammation were quantified from aSAH and naSAH samples using RT-qPCR. The study focused on the following genes: CCL5, CCL7, APOE, SPP1, CXCL8, CXCL10, HMOX1, LTB, MAL, and HLA-DRB1. Gene clustering analysis revealed that monocytes, NK cells, and T cells expressed CD8 + CD161 + in the CSF of patients with aSAH. In comparison to naSAH samples, aSAH samples exhibited higher mRNA levels of CXCL10 (median, IQR = 90, 16-149 vs. 0.5, 0-6.75, p = 0.02). A trend towards higher HMOX1 levels was also observed in aSAH (median, IQR = 12.6, 9-17.6 vs. 2.55, 1.68-5.7, p = 0.076). Specifically, CXCL10 and HMOX1 were expressed by the monocyte subpopulation. Monocytes, NK cells, and T cells can potentially express CD8 + CD161 + in patients with aSAH. Notably, monocytes show high levels of CXCL10. The elevated expression of CXCL10 in aSAH compared to naSAH indicates its potential significance as a target for future studies.
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Affiliation(s)
| | | | - Yongjun Lu
- Department of Neurology, University of Iowa, Iowa, IA, USA
| | - Elena Sagues
- Department of Neurology, University of Iowa, Iowa, IA, USA
| | - Andres Gudino
- Department of Neurology, University of Iowa, Iowa, IA, USA
| | - Carlos Dier
- Department of Neurology, University of Iowa, Iowa, IA, USA
| | - David Hasan
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Edgar A Samaniego
- Department of Neurology, University of Iowa, Iowa, IA, USA.
- Department of Neurosurgery, University of Iowa, Iowa, IA, USA.
- Department of Radiology, University of Iowa, Iowa, IA, USA.
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2
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Kumar M, Patel K, Chinnapparaj S, Sharma T, Aggarwal A, Singla N, Karthigeyan M, Singh A, Sahoo SK, Tripathi M, Takkar A, Gupta T, Pal A, Attri SV, Bansal YS, Ratho RK, Gupta SK, Khullar M, Vashishta RK, Mukherjee KK, Grover VK, Prasad R, Chatterjee A, Gowda H, Bhagat H. Dysregulated Genes and Signaling Pathways in the Formation and Rupture of Intracranial Aneurysm. Transl Stroke Res 2023:10.1007/s12975-023-01178-w. [PMID: 37644376 DOI: 10.1007/s12975-023-01178-w] [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: 09/19/2022] [Revised: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/31/2023]
Abstract
Intracranial aneurysm (IA) has the potential to rupture. Despite scientific advances, we are still not in a position to screen patients for IA and identify those at risk of rupture. It is critical to comprehend the molecular basis of disease to facilitate the development of novel diagnostic strategies. We used transcriptomics to identify the dysregulated genes and understand their role in the disease biology. In particular, RNA-Seq was performed in tissue samples of controls, unruptured IA, and ruptured IA. Dysregulated genes (DGs) were identified and analyzed to understand the functional aspects of molecules. Subsequently, candidate genes were validated at both transcript and protein level. There were 314 DGs in patients with unruptured IA when compared to control samples. Out of these, SPARC and OSM were validated as candidate molecules in unruptured IA. PI3K-AKT signaling pathway was found to be an important pathway for the formation of IA. Similarly, 301 DGs were identified in the samples of ruptured IA when compared with unruptured IAs. CTSL was found to be a key candidate molecule which along with Hippo signaling pathway may be involved in the rupture of IA. We conclude that activation of PI3K-AKT signaling pathway by OSM along with up-regulation of SPARC is important for the formation of IA. Further, regulation of Hippo pathway through PI3K-AKT signaling results in the down-regulation of YAP1 gene. This along with up-regulation of CTSL leads to further weakening of aneurysm wall and its subsequent rupture.
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Affiliation(s)
- Munish Kumar
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Shobia Chinnapparaj
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tanavi Sharma
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashish Aggarwal
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Navneet Singla
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhivanan Karthigeyan
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Apinderpreet Singh
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sushanta Kumar Sahoo
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manjul Tripathi
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aastha Takkar
- Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tulika Gupta
- Department of Anatomy, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arnab Pal
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Savita Verma Attri
- Pediatric Biochemistry, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yogender Singh Bansal
- Department of Forensic Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil K Gupta
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kumar Vashishta
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kanchan Kumar Mukherjee
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vinod Kumar Grover
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Hemant Bhagat
- Division of Neuro-anesthesia, Department of Anesthesia and Intensive Care, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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3
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Su J, Cao J, Yang H, Xu W, Liu W, Wang R, Huang Y, Wu J, Gao X, Weng R, Pu J, Liu N, Gu Y, Qian K, Ni W. Diagnosis of Unruptured Intracranial Aneurysm by High-Performance Serum Metabolic Fingerprints. SMALL METHODS 2023; 7:e2201486. [PMID: 36634984 DOI: 10.1002/smtd.202201486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Unruptured intracranial aneurysm (UIA) is a high-risk cerebrovascular saccular dilatation, the effective medical management of which depends on high-performance diagnosis. However, most UIAs are diagnosed incidentally during neurovascular imaging modalities, which are time-consuming and harmful (e.g., radiation). Serum metabolic fingerprints is a promising alternative for early diagnosis of UIA. Here, nanoparticle enhanced laser desorption/ionization mass spectrometry is applied to obtain high-performance UIA-specific serum metabolic fingerprints. Diagnostic performance with an area-under-the-curve (AUC) of 0.842 (95% confidence interval (CI): 0.783-0.891) is achieved by the constructed machine learning (ML) model, including ML algorithm selection and feature selection. Lactate, glutamine, homoarginine, and 3-methylglutaconic acid are identified as the metabolic biomarker panel, which showed satisfactory diagnosis (AUC of 0.812, 95% CI: 0.727-0.897) and effective growth risk assessment (p<0.05, two-tailed t-test) of UIAs. This work aims to promote the diagnostics of UIAs and metabolic biomarker screening for medical management.
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Affiliation(s)
- Jiabin Su
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Heng Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wanshan Liu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yida Huang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiao Wu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinjie Gao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Ruiyuan Weng
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ning Liu
- School of Electronics Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yuxiang Gu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei Ni
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
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4
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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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Lu T, He Y, Liu Z, Ma C, Chen S, Jia R, Duan L, Guo C, Liu Y, Guo D, Li T, He Y. A machine learning-derived gene signature for assessing rupture risk and circulatory immunopathologic landscape in patients with intracranial aneurysms. Front Cardiovasc Med 2023; 10:1075584. [PMID: 36844725 PMCID: PMC9950511 DOI: 10.3389/fcvm.2023.1075584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Background Intracranial aneurysm (IA) is an uncommon but severe subtype of cerebrovascular disease, with high mortality after aneurysm rupture. Current risk assessments are mainly based on clinical and imaging data. This study aimed to develop a molecular assay tool for optimizing the IA risk monitoring system. Methods Peripheral blood gene expression datasets obtained from the Gene Expression Omnibus were integrated into a discovery cohort. Weighted gene co-expression network analysis (WGCNA) and machine learning integrative approaches were utilized to construct a risk signature. QRT-PCR assay was performed to validate the model in an in-house cohort. Immunopathological features were estimated using bioinformatics methods. Results A four-gene machine learning-derived gene signature (MLDGS) was constructed for identifying patients with IA rupture. The AUC of MLDGS was 1.00 and 0.88 in discovery and validation cohorts, respectively. Calibration curve and decision curve analysis also confirmed the good performance of the MLDGS model. MLDGS was remarkably correlated with the circulating immunopathologic landscape. Higher MLDGS scores may represent higher abundance of innate immune cells, lower abundance of adaptive immune cells, and worse vascular stability. Conclusions The MLDGS provides a promising molecular assay panel for identifying patients with adverse immunopathological features and high risk of aneurysm rupture, contributing to advances in IA precision medicine.
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Affiliation(s)
- Taoyuan Lu
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Yanyan He
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chi Ma
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Song Chen
- Translational Research Institute, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Rufeng Jia
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Lin Duan
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yiying Liu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dehua Guo
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China
| | - Tianxiao Li
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China,Tianxiao Li,
| | - Yingkun He
- Department of Cerebrovascular Disease and Neurosurgery, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Henan International Joint Laboratory of Cerebrovascular Disease, Henan Provincial NeuroInterventional Engineering Research Center, Henan Engineering Research Center of Cerebrovascular Intervention Innovation, Zhengzhou, China,*Correspondence: Yingkun He,
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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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Kamińska J, Tylicka M, Dymicka-Piekarska V, Mariak Z, Matowicka-Karna J, Koper-Lenkiewicz OM. Canonical NF-κB signaling pathway and GRO-α/CXCR2 axis are activated in unruptured intracranial aneurysm patients. Sci Rep 2022; 12:21375. [PMID: 36494512 PMCID: PMC9734124 DOI: 10.1038/s41598-022-25855-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Activation of the nuclear factor kappa-B (NF-κB) stimulates the production of pro-inflammatory molecules involved in the formation of intracranial aneurysms (IA). The study aimed to assess the NF-κB p65 subunit and the GRO-α chemokine and its receptor CXCR2 concentrations in unruptured intracranial aneurysm patients (UIA, n = 25) compared to individuals without vascular changes in the brain (n = 10). It was also analyzed whether tested proteins are related to the size and number of aneurysms. Cerebrospinal fluid (CSF) and serum protein levels were measured using the ELISA method. Median CSF and serum NF-κB p65 concentrations were significantly lower, while median CSF GRO-α and CXCR2 concentrations were significantly higher in UIA patients compared to the control group. CSF and serum NF-κB p65 concentrations negatively correlated with the number of aneurysms. In UIA patients the median GRO-α concentration was two-fold and CXCR2 almost four-fold higher in CSF compared to the serum value. CSF GRO-α concentration positively correlated with the size of aneurysms.Significantly decreased CSF NF-κB p65 and significantly increased CSF GRO-α and its CXCR2 receptor concentrations in UIA patients compared to the control group may altogether suggest that the canonical NF-κB signaling pathway is activated and its target pro-inflammatory genes are highly expressed in UIA patients. However, to unequivocally assess the involvement of the classical NF-κB pathway with the participation of the NF-κB p65 subunit and the GRO-α/CXCR2 axis in the formation of IA, further in vivo model studies are needed.
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Affiliation(s)
- Joanna Kamińska
- grid.48324.390000000122482838Department of Clinical Laboratory Diagnostics, Medical University of Białystok, 15A Jerzego Waszyngtona St., 15-269 Białystok, Poland
| | - Marzena Tylicka
- grid.48324.390000000122482838Department of Biophysics, Medical University of Białystok, Białystok, Poland
| | - Violetta Dymicka-Piekarska
- grid.48324.390000000122482838Department of Clinical Laboratory Diagnostics, Medical University of Białystok, 15A Jerzego Waszyngtona St., 15-269 Białystok, Poland
| | - Zenon Mariak
- grid.48324.390000000122482838Department of Neurosurgery, Medical University of Białystok, Clinical Hospital of the Medical University of Białystok, Białystok, Poland
| | - Joanna Matowicka-Karna
- grid.48324.390000000122482838Department of Clinical Laboratory Diagnostics, Medical University of Białystok, 15A Jerzego Waszyngtona St., 15-269 Białystok, Poland
| | - Olga Martyna Koper-Lenkiewicz
- grid.48324.390000000122482838Department of Clinical Laboratory Diagnostics, Medical University of Białystok, 15A Jerzego Waszyngtona St., 15-269 Białystok, Poland
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9
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Li Q, Wang P, Yuan J, Zhou Y, Mei Y, Ye M. A two-stage hybrid gene selection algorithm combined with machine learning models to predict the rupture status in intracranial aneurysms. Front Neurosci 2022; 16:1034971. [PMID: 36340761 PMCID: PMC9631203 DOI: 10.3389/fnins.2022.1034971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/30/2022] [Indexed: 07/31/2023] Open
Abstract
An IA is an abnormal swelling of cerebral vessels, and a subset of these IAs can rupture causing aneurysmal subarachnoid hemorrhage (aSAH), often resulting in death or severe disability. Few studies have used an appropriate method of feature selection combined with machine learning by analyzing transcriptomic sequencing data to identify new molecular biomarkers. Following gene ontology (GO) and enrichment analysis, we found that the distinct status of IAs could lead to differential innate immune responses using all 913 differentially expressed genes, and considering that there are numerous irrelevant and redundant genes, we propose a mixed filter- and wrapper-based feature selection. First, we used the Fast Correlation-Based Filter (FCBF) algorithm to filter a large number of irrelevant and redundant genes in the raw dataset, and then used the wrapper feature selection method based on the he Multi-layer Perceptron (MLP) neural network and the Particle Swarm Optimization (PSO), accuracy (ACC) and mean square error (MSE) were then used as the evaluation criteria. Finally, we constructed a novel 10-gene signature (YIPF1, RAB32, WDR62, ANPEP, LRRCC1, AADAC, GZMK, WBP2NL, PBX1, and TOR1B) by the proposed two-stage hybrid algorithm FCBF-MLP-PSO and used different machine learning models to predict the rupture status in IAs. The highest ACC value increased from 0.817 to 0.919 (12.5% increase), the highest area under ROC curve (AUC) value increased from 0.87 to 0.94 (8.0% increase), and all evaluation metrics improved by approximately 10% after being processed by our proposed gene selection algorithm. Therefore, these 10 informative genes used to predict rupture status of IAs can be used as complements to imaging examinations in the clinic, meanwhile, this selected gene signature also provides new targets and approaches for the treatment of ruptured IAs.
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Affiliation(s)
- Qingqing Li
- School of Medical Information, Wannan Medical College, Wuhu, Anhui, China
- Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, Anhui, China
| | - Peipei Wang
- School of Medical Information, Wannan Medical College, Wuhu, Anhui, China
- Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, Anhui, China
| | - Jinlong Yuan
- Department of Neurosurgery, Yijishan Hospital of Wannan Medical College, Wannan Medical College, Wuhu, Anhui, China
| | - Yunfeng Zhou
- Department of Radiology, Yijishan Hospital of Wannan Medical College, Wannan Medical College, Wuhu, Anhui, China
| | - Yaxin Mei
- School of Medical Information, Wannan Medical College, Wuhu, Anhui, China
- Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, Anhui, China
| | - Mingquan Ye
- School of Medical Information, Wannan Medical College, Wuhu, Anhui, China
- Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, Anhui, China
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10
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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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11
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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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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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15
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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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