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Zhu QM, Hsu YHH, Lassen FH, MacDonald BT, Stead S, Malolepsza E, Kim A, Li T, Mizoguchi T, Schenone M, Guzman G, Tanenbaum B, Fornelos N, Carr SA, Gupta RM, Ellinor PT, Lage K. Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease. Commun Biol 2024; 7:87. [PMID: 38216744 PMCID: PMC10786878 DOI: 10.1038/s42003-023-05705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD.
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Affiliation(s)
- Qiuyu Martin Zhu
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Frederik H Lassen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bryan T MacDonald
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Stead
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edyta Malolepsza
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taibo Li
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taiji Mizoguchi
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Schenone
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaelen Guzman
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Tanenbaum
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajat M Gupta
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
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Berg P, Beuing O. Multiple intracranial aneurysms: a direct hemodynamic comparison between ruptured and unruptured vessel malformations. Int J Comput Assist Radiol Surg 2017; 13:83-93. [PMID: 28733907 DOI: 10.1007/s11548-017-1643-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/11/2017] [Indexed: 11/27/2022]
Abstract
PURPOSE Despite numerous studies addressing the rupture risk of intracranial aneurysms that have been published, the assessment thereof still remains challenging. Image-based simulations enable a precise prediction of patient-specific blood flow information. However, those approaches normally consider only small segments of the complete cerebral vasculature. METHODS To test the validity of the consideration of single aneurysms in one computational setup, domains of the complete anterior and posterior circulations with multiple intracranial aneurysms (MIA) were simulated. Six patients with MIA were investigated, while 3D surfaces of eleven unruptured and six ruptured aneurysms were segmented. The segmentations were used for the determination of morphological parameters and also for image-based blood flow simulations used to characterize the hemodynamic properties of each aneurysm. RESULTS In the geometric comparison, neck aspect ratios of unruptured and ruptured aneurysms did not differ significantly. In contrast, size ratios, aspect ratios, surface areas, volumes, and non-sphericity indices were significantly higher in the ruptured cases. The analysis of hemodynamic parameters demonstrated that in each patient, the ruptured aneurysm exhibited the lowest averaged wall shear stresses and highest oscillatory shears. Unstable flow was also detected in ruptured aneurysms based on increased oscillatory velocity. CONCLUSION In this small study involving patients with MIA, different morphologies and flow patterns were observed between ruptured and unruptured aneurysms. The analysis of the hemodynamics in such patients revealed a good agreement with studies that only considered single malformations. Additionally, complex flow patterns are detected in ruptured cases, which require deeper investigation.
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Affiliation(s)
- Philipp Berg
- Laboratory of Fluid Dynamics and Technical Flows, University of Magdeburg "Otto von Guericke", Universitätsplatz 2, 39106, Magdeburg, Germany.
| | - Oliver Beuing
- Institute of Neuroradiology, University Hospital Magdeburg, Leipziger Str. 44, 39120, Magdeburg, Germany
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Hendrix P, Foreman PM, Harrigan MR, Fisher WS, Vyas NA, Lipsky RH, Lin M, Walters BC, Tubbs RS, Shoja MM, Pittet JF, Mathru M, Griessenauer CJ. Association of Plasminogen Activator Inhibitor 1 (SERPINE1) Polymorphisms and Aneurysmal Subarachnoid Hemorrhage. World Neurosurg 2017; 105:672-677. [PMID: 28599907 DOI: 10.1016/j.wneu.2017.05.175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Genetic variations of the serine proteinase inhibitor family E member 1 (SERPINE1) gene, which encodes plasminogen activator inhibitor 1, correlate with serum levels of its product and are associated with thrombophilia and coronary atherosclerosis. Various SERPINE1 ;gene polymorphisms have been identified. However, only the functional 5G/4G polymorphism has been assessed in the context of aneurysmal subarachnoid hemorrhage (aSAH). We assessed associations of 6 SERPINE1 polymorphisms with the clinical sequelae of aSAH. METHODS From 2012 to 2015, patients with aSAH were prospectively enrolled into the CARAS (Cerebral Aneurysm Renin Angiotensin System) study at 2 major academic institutions. Blood samples were used to evaluate 6 common SERPINE1 single nucleotide polymorphisms via 5' exonuclease (Taqman) genotyping assays. RESULTS There was an association of the AA genotype of rs2227631 with the 4G/4G genotype and of the GG genotype of rs7242 with the AA genotype of rs2227684. In multivariable analysis, patients with the AA genotype of rs2227631 and 4G/4G genotype had an increased risk for developing delayed cerebral ischemia. Patients with the GG genotype of rs7242 and AA genotype of rs2227684 had a decreased risk for a poor functional outcome. CONCLUSIONS SERPINE1 gene polymorphisms were associated with delayed cerebral ischemia and functional outcome after aSAH. These associations may arise from alterations of plasminogen activator inhibitor 1 levels.
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Affiliation(s)
- Philipp Hendrix
- Department of Neurosurgery, Saarland University Medical Center and Saarland University Faculty of Medicine, Homburg/Saar, Germany.
| | - Paul M Foreman
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mark R Harrigan
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Winfield S Fisher
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nilesh A Vyas
- Department of Neurosciences, Inova Health System, Falls Church, Virginia, USA
| | - Robert H Lipsky
- Department of Neurosciences, Inova Health System, Falls Church, Virginia, USA; Department of Molecular Neuroscience, George Mason University, Fairfax, Virginia, USA
| | - Minkuan Lin
- Department of Molecular Neuroscience, George Mason University, Fairfax, Virginia, USA
| | - Beverly C Walters
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA; Department of Neurosciences, Inova Health System, Falls Church, Virginia, USA; Department of Molecular Neuroscience, George Mason University, Fairfax, Virginia, USA
| | - R Shane Tubbs
- Seattle Science Foundation, Seattle, Washington, USA
| | - Mohammadali M Shoja
- Neuroscience Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jean-Francois Pittet
- Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mali Mathru
- Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christoph J Griessenauer
- Department of Neurosurgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA; Department of Neurosurgery, Geisinger Health System, Danville, Pennsylvania, USA
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