1
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Cyr Y, Bozal FK, Barcia Durán JG, Newman AAC, Amadori L, Smyrnis P, Gourvest M, Das D, Gildea M, Kaur R, Zhang T, Wang KM, Von Itter R, Schlegel PM, Dupuis SD, Sanchez BF, Schmidt AM, Fisher EA, van Solingen C, Giannarelli C, Moore KJ. The IRG1-itaconate axis protects from cholesterol-induced inflammation and atherosclerosis. Proc Natl Acad Sci U S A 2024; 121:e2400675121. [PMID: 38564634 PMCID: PMC11009655 DOI: 10.1073/pnas.2400675121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Atherosclerosis is fueled by a failure to resolve lipid-driven inflammation within the vasculature that drives plaque formation. Therapeutic approaches to reverse atherosclerotic inflammation are needed to address the rising global burden of cardiovascular disease (CVD). Recently, metabolites have gained attention for their immunomodulatory properties, including itaconate, which is generated from the tricarboxylic acid-intermediate cis-aconitate by the enzyme Immune Responsive Gene 1 (IRG1/ACOD1). Here, we tested the therapeutic potential of the IRG1-itaconate axis for human atherosclerosis. Using single-cell RNA sequencing (scRNA-seq), we found that IRG1 is up-regulated in human coronary atherosclerotic lesions compared to patient-matched healthy vasculature, and in mouse models of atherosclerosis, where it is primarily expressed by plaque monocytes, macrophages, and neutrophils. Global or hematopoietic Irg1-deficiency in mice increases atherosclerosis burden, plaque macrophage and lipid content, and expression of the proatherosclerotic cytokine interleukin (IL)-1β. Mechanistically, absence of Irg1 increased macrophage lipid accumulation, and accelerated inflammation via increased neutrophil extracellular trap (NET) formation and NET-priming of the NLRP3-inflammasome in macrophages, resulting in increased IL-1β release. Conversely, supplementation of the Irg1-itaconate axis using 4-octyl itaconate (4-OI) beneficially remodeled advanced plaques and reduced lesional IL-1β levels in mice. To investigate the effects of 4-OI in humans, we leveraged an ex vivo systems-immunology approach for CVD drug discovery. Using CyTOF and scRNA-seq of peripheral blood mononuclear cells treated with plasma from CVD patients, we showed that 4-OI attenuates proinflammatory phospho-signaling and mediates anti-inflammatory rewiring of macrophage populations. Our data highlight the relevance of pursuing IRG1-itaconate axis supplementation as a therapeutic approach for atherosclerosis in humans.
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Affiliation(s)
- Yannick Cyr
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Fazli K. Bozal
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | | | - Alexandra A. C. Newman
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Letizia Amadori
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Panagiotis Smyrnis
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Morgane Gourvest
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Dayasagar Das
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Michael Gildea
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Ravneet Kaur
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Tracy Zhang
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Kristin M. Wang
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Richard Von Itter
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - P. Martin Schlegel
- Department of Anesthesiology and Intensive Care, School of Medicine and Health, Technical University of Munich, Munich81675, Germany
| | - Samantha D. Dupuis
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Bernard F. Sanchez
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Ann Marie Schmidt
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
- Division of Endocrinology, Diabetes and Metabolism, New York University Langone Health, New York, NY10016
| | - Edward A. Fisher
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY10016
| | - Coen van Solingen
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
| | - Chiara Giannarelli
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Kathryn J. Moore
- Cardiovascular Research Center, New York University Grossman School of Medicine, New York, NY10016
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY10016
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2
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Eberhardt N, Noval MG, Kaur R, Amadori L, Gildea M, Sajja S, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. Nat Cardiovasc Res 2023; 2:899-916. [PMID: 38076343 PMCID: PMC10702930 DOI: 10.1038/s44161-023-00336-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 12/19/2023]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present increased risk for ischemic cardiovascular complications up to 1 year after infection. Although the systemic inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques remains unknown. Here we report that SARS-CoV-2 viral RNA is detectable and replicates in coronary lesions taken at autopsy from severe COVID-19 cases. SARS-CoV-2 targeted plaque macrophages and exhibited a stronger tropism for arterial lesions than adjacent perivascular fat, correlating with macrophage infiltration levels. SARS-CoV-2 entry was increased in cholesterol-loaded primary macrophages and dependent, in part, on neuropilin-1. SARS-CoV-2 induced a robust inflammatory response in cultured macrophages and human atherosclerotic vascular explants with secretion of cytokines known to trigger cardiovascular events. Our data establish that SARS-CoV-2 infects coronary vessels, inducing plaque inflammation that could trigger acute cardiovascular complications and increase the long-term cardiovascular risk.
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Affiliation(s)
- Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Maria Gabriela Noval
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Michael Gildea
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Dayasagar Das
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Burak Cilhoroz
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - O’Jay Stewart
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Andrea Vasquez Guillen
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan D. Newman
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Maldonado
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Caron Rockman
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Winthrop Hospital, Long Island School of Medicine, New York, NY, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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3
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Eberhardt N, Noval MG, Kaur R, Sajja S, Amadori L, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Gildea M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. bioRxiv 2023:2023.08.14.553245. [PMID: 37645908 PMCID: PMC10461985 DOI: 10.1101/2023.08.14.553245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
COVID-19 patients present higher risk for myocardial infarction (MI), acute coronary syndrome, and stroke for up to 1 year after SARS-CoV-2 infection. While the systemic inflammatory response to SARS-CoV-2 infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques to locally promote inflammation remains unknown. Here, we report that SARS-CoV-2 viral RNA (vRNA) is detectable and replicates in coronary atherosclerotic lesions taken at autopsy from patients with severe COVID-19. SARS-CoV-2 localizes to plaque macrophages and shows a stronger tropism for arterial lesions compared to corresponding perivascular fat, correlating with the degree of macrophage infiltration. In vitro infection of human primary macrophages highlights that SARS-CoV-2 entry is increased in cholesterol-loaded macrophages (foam cells) and is dependent, in part, on neuropilin-1 (NRP-1). Furthermore, although viral replication is abortive, SARS-CoV-2 induces a robust inflammatory response that includes interleukins IL-6 and IL-1β, key cytokines known to trigger ischemic cardiovascular events. SARS-CoV-2 infection of human atherosclerotic vascular explants recapitulates the immune response seen in cultured macrophages, including pro-atherogenic cytokine secretion. Collectively, our data establish that SARS-CoV-2 infects macrophages in coronary atherosclerotic lesions, resulting in plaque inflammation that may promote acute CV complications and long-term risk for CV events.
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4
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Amadori L, Calcagno C, Fernandez DM, Koplev S, Fernandez N, Kaur R, Mury P, Khan NS, Sajja S, Shamailova R, Cyr Y, Jeon M, Hill CA, Chong PS, Naidu S, Sakurai K, Ghotbi AA, Soler R, Eberhardt N, Rahman A, Faries P, Moore KJ, Fayad ZA, Ma’ayan A, Giannarelli C. Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. Nat Cardiovasc Res 2023; 2:550-571. [PMID: 37771373 PMCID: PMC10538622 DOI: 10.1038/s44161-023-00278-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/28/2023] [Indexed: 09/30/2023]
Abstract
The development of new immunotherapies to treat the inflammatory mechanisms that sustain atherosclerotic cardiovascular disease (ASCVD) is urgently needed. Herein, we present a path to drug repurposing to identify immunotherapies for ASCVD. The integration of time-of-flight mass cytometry and RNA sequencing identified unique inflammatory signatures in peripheral blood mononuclear cells stimulated with ASCVD plasma. By comparing these inflammatory signatures to large-scale gene expression data from the LINCS L1000 dataset, we identified drugs that could reverse this inflammatory response. Ex vivo screens, using human samples, showed that saracatinib-a phase 2a-ready SRC and ABL inhibitor-reversed the inflammatory responses induced by ASCVD plasma. In Apoe-/- mice, saracatinib reduced atherosclerosis progression by reprogramming reparative macrophages. In a rabbit model of advanced atherosclerosis, saracatinib reduced plaque inflammation measured by [18F] fluorodeoxyglucose positron emission tomography-magnetic resonance imaging. Here we show a systems immunology-driven drug repurposing with a preclinical validation strategy to aid the development of cardiovascular immunotherapies.
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Affiliation(s)
- Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Claudia Calcagno
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Dawn M. Fernandez
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Simon Koplev
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicolas Fernandez
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Pauline Mury
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nayaab S Khan
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Yannick Cyr
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Minji Jeon
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Christopher A. Hill
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Peik Sean Chong
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sonum Naidu
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ken Sakurai
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Adam Ali Ghotbi
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Raphael Soler
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Adeeb Rahman
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Zahi A. Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Avi Ma’ayan
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Pathology; NYU Grossman School of Medicine, NYU Langone Health, New York, NY USA
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5
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Toner YC, Ghotbi AA, Naidu S, Sakurai K, van Leent MMT, Jordan S, Ordikhani F, Amadori L, Sofias AM, Fisher EL, Maier A, Sullivan N, Munitz J, Senders ML, Mason C, Reiner T, Soultanidis G, Tarkin JM, Rudd JHF, Giannarelli C, Ochando J, Pérez-Medina C, Kjaer A, Mulder WJM, Fayad ZA, Calcagno C. Systematically evaluating DOTATATE and FDG as PET immuno-imaging tracers of cardiovascular inflammation. Sci Rep 2022; 12:6185. [PMID: 35418569 PMCID: PMC9007951 DOI: 10.1038/s41598-022-09590-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/22/2022] [Indexed: 02/08/2023] Open
Abstract
In recent years, cardiovascular immuno-imaging by positron emission tomography (PET) has undergone tremendous progress in preclinical settings. Clinically, two approved PET tracers hold great potential for inflammation imaging in cardiovascular patients, namely FDG and DOTATATE. While the former is a widely applied metabolic tracer, DOTATATE is a relatively new PET tracer targeting the somatostatin receptor 2 (SST2). In the current study, we performed a detailed, head-to-head comparison of DOTATATE-based radiotracers and [18F]F-FDG in mouse and rabbit models of cardiovascular inflammation. For mouse experiments, we labeled DOTATATE with the long-lived isotope [64Cu]Cu to enable studying the tracer's mode of action by complementing in vivo PET/CT experiments with thorough ex vivo immunological analyses. For translational PET/MRI rabbit studies, we employed the more widely clinically used [68Ga]Ga-labeled DOTATATE, which was approved by the FDA in 2016. DOTATATE's pharmacokinetics and timed biodistribution were determined in control and atherosclerotic mice and rabbits by ex vivo gamma counting of blood and organs. Additionally, we performed in vivo PET/CT experiments in mice with atherosclerosis, mice subjected to myocardial infarction and control animals, using both [64Cu]Cu-DOTATATE and [18F]F-FDG. To evaluate differences in the tracers' cellular specificity, we performed ensuing ex vivo flow cytometry and gamma counting. In mice subjected to myocardial infarction, in vivo [64Cu]Cu-DOTATATE PET showed higher differential uptake between infarcted (SUVmax 1.3, IQR, 1.2-1.4, N = 4) and remote myocardium (SUVmax 0.7, IQR, 0.5-0.8, N = 4, p = 0.0286), and with respect to controls (SUVmax 0.6, IQR, 0.5-0.7, N = 4, p = 0.0286), than [18F]F-FDG PET. In atherosclerotic mice, [64Cu]Cu-DOTATATE PET aortic signal, but not [18F]F-FDG PET, was higher compared to controls (SUVmax 1.1, IQR, 0.9-1.3 and 0.5, IQR, 0.5-0.6, respectively, N = 4, p = 0.0286). In both models, [64Cu]Cu-DOTATATE demonstrated preferential accumulation in macrophages with respect to other myeloid cells, while [18F]F-FDG was taken up by macrophages and other leukocytes. In a translational PET/MRI study in atherosclerotic rabbits, we then compared [68Ga]Ga-DOTATATE and [18F]F-FDG for the assessment of aortic inflammation, combined with ex vivo radiometric assays and near-infrared imaging of macrophage burden. Rabbit experiments showed significantly higher aortic accumulation of both [68Ga]Ga-DOTATATE and [18F]F-FDG in atherosclerotic (SUVmax 0.415, IQR, 0.338-0.499, N = 32 and 0.446, IQR, 0.387-0.536, N = 27, respectively) compared to control animals (SUVmax 0.253, IQR, 0.197-0.285, p = 0.0002, N = 10 and 0.349, IQR, 0.299-0.423, p = 0.0159, N = 11, respectively). In conclusion, we present a detailed, head-to-head comparison of the novel SST2-specific tracer DOTATATE and the validated metabolic tracer [18F]F-FDG for the evaluation of inflammation in small animal models of cardiovascular disease. Our results support further investigations on the use of DOTATATE to assess cardiovascular inflammation as a complementary readout to the widely used [18F]F-FDG.
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Affiliation(s)
- Yohana C Toner
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Adam A Ghotbi
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Clinical Physiology, Nuclear Medicine and PET and Cluster for Molecular Imaging, Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Sonum Naidu
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ken Sakurai
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mandy M T van Leent
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stefan Jordan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Institute of Microbiology, Infectious Diseases and Immunology, Berlin, Germany
| | - Farideh Ordikhani
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Alexandros Marios Sofias
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Elizabeth L Fisher
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Maier
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cardiology and Angiology I, Faculty of Medicine, Heart Center Freiburg University, University of Freiburg, Freiburg, Germany
| | - Nathaniel Sullivan
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jazz Munitz
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Max L Senders
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Christian Mason
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Reiner
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Radiology and Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA
| | - Georgios Soultanidis
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason M Tarkin
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - James H F Rudd
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
- Cardiovascular Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jordi Ochando
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Transplant Immunology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Pérez-Medina
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine and PET and Cluster for Molecular Imaging, Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Willem J M Mulder
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Laboratory of Chemical Biology, Department of Biochemical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Zahi A Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Claudia Calcagno
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave, PO Box: 1234, New York, NY, 10029, USA.
- Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Hao K, Ermel R, Sukhavasi K, Cheng H, Ma L, Li L, Amadori L, Koplev S, Franzén O, d’Escamard V, Chandel N, Wolhuter K, Bryce NS, Venkata VRM, Miller CL, Ruusalepp A, Schunkert H, Björkegren JL, Kovacic JC. Integrative Prioritization of Causal Genes for Coronary Artery Disease. Circ Genom Precis Med 2022; 15:e003365. [PMID: 34961328 PMCID: PMC8847335 DOI: 10.1161/circgen.121.003365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Hundreds of candidate genes have been associated with coronary artery disease (CAD) through genome-wide association studies. However, a systematic way to understand the causal mechanism(s) of these genes, and a means to prioritize them for further study, has been lacking. This represents a major roadblock for developing novel disease- and gene-specific therapies for patients with CAD. Recently, powerful integrative genomics analyses pipelines have emerged to identify and prioritize candidate causal genes by integrating tissue/cell-specific gene expression data with genome-wide association study data sets. METHODS We aimed to develop a comprehensive integrative genomics analyses pipeline for CAD and to provide a prioritized list of causal CAD genes. To this end, we leveraged several complimentary informatics approaches to integrate summary statistics from CAD genome-wide association studies (from UK Biobank and CARDIoGRAMplusC4D) with transcriptomic and expression quantitative trait loci data from 9 cardiometabolic tissue/cell types in the STARNET study (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task). RESULTS We identified 162 unique candidate causal CAD genes, which exerted their effect from between one and up to 7 disease-relevant tissues/cell types, including the arterial wall, blood, liver, skeletal muscle, adipose, foam cells, and macrophages. When their causal effect was ranked, the top candidate causal CAD genes were CDKN2B (associated with the 9p21.3 risk locus) and PHACTR1; both exerting their causal effect in the arterial wall. A majority of candidate causal genes were represented in cross-tissue gene regulatory co-expression networks that are involved with CAD, with 22/162 being key drivers in those networks. CONCLUSIONS We identified and prioritized candidate causal CAD genes, also localizing their tissue(s) of causal effect. These results should serve as a resource and facilitate targeted studies to identify the functional impact of top causal CAD genes.
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Affiliation(s)
- Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Sema4, Stamford, CT
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ling Li
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Center for Doctoral Studies in Informatics and its Applications, Dept of Informatics, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Current affiliation: New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Oscar Franzén
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Valentina d’Escamard
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nirupama Chandel
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kathryn Wolhuter
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | - Nicole S. Bryce
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia,University of New South Wales, Faculty of Medicine and Health, Sydney, Australia
| | | | - Clint L. Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia,Department of Cardiology, Institute of Clinical Medicine, Tartu University
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY,Victor Chang Cardiac Research Institute, Darlinghurst, Australia,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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7
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Koplev S, Seldin M, Sukhavasi K, Ermel R, Pang S, Zeng L, Bankier S, Di Narzo A, Cheng H, Meda V, Ma A, Talukdar H, Cohain A, Amadori L, Argmann C, Houten SM, Franzén O, Mocci G, Meelu OA, Ishikawa K, Whatling C, Jain A, Jain RK, Gan LM, Giannarelli C, Roussos P, Hao K, Schunkert H, Michoel T, Ruusalepp A, Schadt EE, Kovacic JC, Lusis AJ, Björkegren JLM. A mechanistic framework for cardiometabolic and coronary artery diseases. Nat Cardiovasc Res 2022; 1:85-100. [PMID: 36276926 PMCID: PMC9583458 DOI: 10.1038/s44161-021-00009-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Coronary atherosclerosis results from the delicate interplay of genetic and exogenous risk factors, principally taking place in metabolic organs and the arterial wall. Here we show that 224 gene-regulatory coexpression networks (GRNs) identified by integrating genetic and clinical data from patients with (n = 600) and without (n = 250) coronary artery disease (CAD) with RNA-seq data from seven disease-relevant tissues in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study largely capture this delicate interplay, explaining >54% of CAD heritability. Within 89 cross-tissue GRNs associated with clinical severity of CAD, 374 endocrine factors facilitated inter-organ interactions, primarily along an axis from adipose tissue to the liver (n = 152). This axis was independently replicated in genetically diverse mouse strains and by injection of recombinant forms of adipose endocrine factors (EPDR1, FCN2, FSTL3 and LBP) that markedly altered blood lipid and glucose levels in mice. Altogether, the STARNET database and the associated GRN browser (http://starnet.mssm.edu) provide a multiorgan framework for exploration of the molecular interplay between cardiometabolic disorders and CAD.
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Affiliation(s)
- Simon Koplev
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marcus Seldin
- Departments of Medicine, Human Genetics and Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, CA, USA
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Raili Ermel
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Shichao Pang
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Sean Bankier
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Antonio Di Narzo
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vamsidhar Meda
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angela Ma
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Husain Talukdar
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Ariella Cohain
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oscar Franzén
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Giuseppe Mocci
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Omar A. Meelu
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiyotake Ishikawa
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carl Whatling
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anamika Jain
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Rajeev Kumar Jain
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
| | - Li-Ming Gan
- Early Clinical Development, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- New York University Cardiovascular Research Center, Department of Medicine, Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York University Langone Health, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Tom Michoel
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Arno Ruusalepp
- Department of Cardiac Surgery and the Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent’s Clinical School, University of NSW, Sydney, New South Wales, Australia
| | - Aldon J. Lusis
- Departments of Medicine, Human Genetics and Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
- Clinical Gene Networks AB, Stockholm, Sweden
- Correspondence and requests for materials should be addressed to Johan L. M. Björkegren.
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8
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Glicksberg BS, Amadori L, Akers NK, Sukhavasi K, Franzén O, Li L, Belbin GM, Ayers KL, Shameer K, Badgeley MA, Johnson KW, Readhead B, Darrow BJ, Kenny EE, Betsholtz C, Ermel R, Skogsberg J, Ruusalepp A, Schadt EE, Dudley JT, Ren H, Kovacic JC, Giannarelli C, Li SD, Björkegren JLM, Chen R. Correction to: Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. BMC Med Genomics 2019; 12:154. [PMID: 31684948 PMCID: PMC6829820 DOI: 10.1186/s12920-019-0573-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Nicholas K Akers
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Katyayani Sukhavasi
- Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Novum, 14157, Huddinge, Sweden
| | - Li Li
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Gillian M Belbin
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kristin L Ayers
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Khader Shameer
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Marcus A Badgeley
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ben Readhead
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bruce J Darrow
- Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Eimear E Kenny
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Raili Ermel
- Department of Cardiac Surgery, Tartu University Hospital, 1a Ludwig Puusepa Street, 50406, Tartu, Estonia
| | - Josefin Skogsberg
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden
| | - Arno Ruusalepp
- Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Health Policy and Research, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Hongxia Ren
- Department of Pediatrics, Herman B Wells Center for PediatricResearch, Center for Diabetes and Metabolic Diseases, Stark Neurosciences Research Institute, Indiana University, 635 Barnhill Dr., MS2049, Indianapolis, IN, 46202, USA
| | - Jason C Kovacic
- Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Shuyu D Li
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA.
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia. .,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden. .,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden.
| | - Rong Chen
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA.
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9
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Glicksberg BS, Amadori L, Akers NK, Sukhavasi K, Franzén O, Li L, Belbin GM, Ayers KL, Shameer K, Badgeley MA, Johnson KW, Readhead B, Darrow BJ, Kenny EE, Betsholtz C, Ermel R, Skogsberg J, Ruusalepp A, Schadt EE, Dudley JT, Ren H, Kovacic JC, Giannarelli C, Li SD, Björkegren JLM, Chen R. Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. BMC Med Genomics 2019; 12:108. [PMID: 31345219 PMCID: PMC6657044 DOI: 10.1186/s12920-019-0542-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Genetic loss-of-function variants (LoFs) associated with disease traits are increasingly recognized as critical evidence for the selection of therapeutic targets. We integrated the analysis of genetic and clinical data from 10,511 individuals in the Mount Sinai BioMe Biobank to identify genes with loss-of-function variants (LoFs) significantly associated with cardiovascular disease (CVD) traits, and used RNA-sequence data of seven metabolic and vascular tissues isolated from 600 CVD patients in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study for validation. We also carried out in vitro functional studies of several candidate genes, and in vivo studies of one gene. Results We identified LoFs in 433 genes significantly associated with at least one of 10 major CVD traits. Next, we used RNA-sequence data from the STARNET study to validate 115 of the 433 LoF harboring-genes in that their expression levels were concordantly associated with corresponding CVD traits. Together with the documented hepatic lipid-lowering gene, APOC3, the expression levels of six additional liver LoF-genes were positively associated with levels of plasma lipids in STARNET. Candidate LoF-genes were subjected to gene silencing in HepG2 cells with marked overall effects on cellular LDLR, levels of triglycerides and on secreted APOB100 and PCSK9. In addition, we identified novel LoFs in DGAT2 associated with lower plasma cholesterol and glucose levels in BioMe that were also confirmed in STARNET, and showed a selective DGAT2-inhibitor in C57BL/6 mice not only significantly lowered fasting glucose levels but also affected body weight. Conclusion In sum, by integrating genetic and electronic medical record data, and leveraging one of the world’s largest human RNA-sequence datasets (STARNET), we identified known and novel CVD-trait related genes that may serve as targets for CVD therapeutics and as such merit further investigation. Electronic supplementary material The online version of this article (10.1186/s12920-019-0542-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Nicholas K Akers
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Katyayani Sukhavasi
- Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Novum, 14157, Huddinge, Sweden
| | - Li Li
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Gillian M Belbin
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kristin L Ayers
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Khader Shameer
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Marcus A Badgeley
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ben Readhead
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bruce J Darrow
- Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Eimear E Kenny
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Raili Ermel
- Department of Cardiac Surgery, Tartu University Hospital, 1a Ludwig Puusepa Street, 50406, Tartu, Estonia
| | - Josefin Skogsberg
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden
| | - Arno Ruusalepp
- Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Health Policy and Research, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Hongxia Ren
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Stark Neurosciences Research Institute, Indiana University, 635 Barnhill Dr., MS2049, Indianapolis, IN, 46202, USA
| | - Jason C Kovacic
- Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Shuyu D Li
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA.
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia. .,Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden. .,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden.
| | - Rong Chen
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA.
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10
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Frades I, Readhead B, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK, Kovacic JC, Dudley JT, Giannarelli C, Björkegren JLM, Peter I. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy. Circ Genom Precis Med 2019; 12:e002390. [PMID: 31059280 DOI: 10.1161/circgen.118.002390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Antiretroviral therapy (ART) for HIV infection increases risk for coronary artery disease (CAD), presumably by causing dyslipidemia and increased atherosclerosis. We applied systems pharmacology to identify and validate specific regulatory gene networks through which ART drugs may promote CAD. METHODS Transcriptional responses of human cell lines to 15 ART drugs retrieved from the Library of Integrated Cellular Signatures (overall 1127 experiments) were used to establish consensus ART gene/transcriptional signatures. Next, enrichments of differentially expressed genes and gene-gene connectivity within these ART-consensus signatures were sought in 30 regulatory gene networks associated with CAD and CAD-related phenotypes in the Stockholm Atherosclerosis Gene Expression study. RESULTS Ten of 15 ART signatures were significantly enriched both for differential expression and connectivity in a specific atherosclerotic arterial wall regulatory gene network (AR-RGN) causal for CAD involving RNA processing genes. An atherosclerosis in vitro model of cholestryl ester-loaded foam cells was then used for experimental validation. Treatments of these foam cells with ritonavir, nelfinavir, and saquinavir at least doubled cholestryl ester accumulation ( P=0.02, 0.0009, and 0.02, respectively), whereas RNA silencing of the AR-RGN top key driver, PQBP1 (polyglutamine binding protein 1), significantly curbed cholestryl ester accumulation following treatment with any of these ART drugs by >37% ( P<0.05). CONCLUSIONS By applying a novel systems pharmacology data analysis framework, 3 commonly used ARTs (ritonavir, nelfinavir, and saquinavir) were found altering the activity of AR-RGN, a regulatory gene network promoting foam cell formation and risk of CAD. Targeting AR-RGN or its top key driver PQBP1 may help reduce CAD side effects of these ART drugs.
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Affiliation(s)
- Itziar Frades
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ben Readhead
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Institute for Next Generation Healthcare (B.R., J.T.D.), Icahn School of Medicine at Mount Sinai, New York, NY.,ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe (B.R.)
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Simon Koplev
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Husain A Talukdar
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (H.A.T., J.L.M.B.)
| | - Heidi M Crane
- Department of Medicine, University of Washington, Seattle (H.M.C., P.K.C.)
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle (H.M.C., P.K.C.)
| | - Jason C Kovacic
- Department of Medicine (J.C.K.), Icahn School of Medicine at Mount Sinai, New York, NY.,Cardiovascular Research Center (J.C.K., C.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Institute for Next Generation Healthcare (B.R., J.T.D.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Cardiovascular Research Center (J.C.K., C.G.), Icahn School of Medicine at Mount Sinai, New York, NY.,Precision Immunology Institute (C.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (H.A.T., J.L.M.B.)
| | - Inga Peter
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
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11
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Rahman A, Amadori L, Kim-Schulze S, Mury P, Moss N, Li J, Pina C, Faries P, Merad M, Giannarelli C. Abstract 612: High Dimensional Single-Cell Intracellular Signaling Identifies CCL5 as a Potential Key Driver of Myeloid Cell Reprogramming in Atherosclerotic Patients. Arterioscler Thromb Vasc Biol 2017. [DOI: 10.1161/atvb.37.suppl_1.612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Atherosclerosis is a disease characterized by chronic inflammation. However, identifying new molecularly targeted interventions in human atherosclerosis has proven difficult. In this study, we used phosphoCyTOF to comprehensively characterize functional responses of peripheral immune populations in human atherosclerosis at the single-cell level. Healthy PBMCs were exposed to plasma of patients with atherosclerosis (n=20) or healthy donors (n=10) and the activation of major signaling pathways across all major immune subsets using 18 surface markers and 10 intracellular phospho-proteins. Using viSNE we visualized and defined 10 major immune cell populations: B cells, Basophils, CD1c DCs, CD4 T cells, CD8 T cells, CD14 and CD16 monocytes, NK cells, NKT cells, and pDCs. Next, we evaluated the relative expression of 10 phospho-proteins (IkBa, pCREB, pERK1/2, pMAPKAP2, pp38, pPLCg2, pS6, pSTAT1, pSTAT3, and pSTAT5) across this immunological map and visualized functional pathways that were differentially induced in response to plasma of atherosclerotic patients vs. healthy donors. Monocytes exhibited the greatest immune activation, showing increased phosphorylation of p38, MAPKAP2, ERK1/2, CREB and S6 in response to atherosclerotic plasma. To identify plasma cytokines responsible for this effect, we measured a panel of 41 cytokines and identified CCL5, CXCL10 (IP-10), CXCL1 (GRO), PDGF-AA and PDGF-BB as the most differentially expressed in atherosclerotic vs. healthy plasma. PhosphoCyTOF analysis showed that only CCL5 reproduced the phosphorylation pattern induced by atherosclerotic plasma in monocytes, an effect that was completely inhibited by a CCL5 blocking antibody (Fig. 1). These results suggest that CCL5 in plasma of patients with atherosclerotic disease drives specific innate immune cell signaling functions that mark the inflammatory response in atherosclerotic disease.
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Affiliation(s)
- Adeeb Rahman
- Icahn Sch of Medicine at Mount Sinai, New York, NY
| | | | | | - Pauline Mury
- Icahn Sch of Medicine at Mount Sinai, New York, NY
| | - Noah Moss
- Icahn Sch of Medicine at Mount Sinai, New York, NY
| | - Jennifer Li
- Icahn Sch of Medicine at Mount Sinai, New York, NY
| | | | - Peter Faries
- Icahn Sch of Medicine at Mount Sinai, New York, NY
| | - Miriam Merad
- Icahn Sch of Medicine at Mount Sinai, New York, NY
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12
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Schneider C, Kon N, Amadori L, Shen Q, Schwartz FH, Tischler B, Bossennec M, Dominguez-Sola D, Bhagat G, Gu W, Basso K, Dalla-Favera R. FBXO11 inactivation leads to abnormal germinal-center formation and lymphoproliferative disease. Blood 2016; 128:660-6. [PMID: 27166359 PMCID: PMC9709922 DOI: 10.1182/blood-2015-11-684357] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/22/2016] [Indexed: 12/14/2022] Open
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor that is required for the germinal center (GC) reaction and is implicated in lymphomagenesis. BCL6 protein stability is regulated by F-box protein 11 (FBXO11)-mediated ubiquitination and degradation, which is impaired in ∼6% of diffuse large B-cell lymphomas that carry inactivating genetic alterations targeting the FBXO11 gene. In order to investigate the role of FBXO11 in vivo, we analyzed GC-specific FBXO11 knockout mice. FBXO11 reduction or loss led to an increased number of GC B cells, to an altered ratio of GC dark zone to light zone cells, and to higher levels of BCL6 protein in GC B cells. B-cell receptor-mediated degradation of BCL6 was reduced in the absence of FBXO11, suggesting that FBXO11 contributes to the physiologic downregulation of BCL6 at the end of the GC reaction. Finally, FBXO11 inactivation was associated with the development of lymphoproliferative disorders in mice.
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Affiliation(s)
| | - Ning Kon
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Letizia Amadori
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | | | - Marion Bossennec
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Govind Bhagat
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Wei Gu
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
- Department of Microbiology and Immunology, Columbia University, New York, NY
- Department of Genetics and Development, Columbia University, New York, NY
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13
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Paganotto MC, Amadori L, Di Donato N, Mauloni M, Busacchi P. Use of a preventive sling surgery for the simultaneous correction of latent stress urinary incontinence during the cystocele repair: two year follow-up. Minerva Ginecol 2013; 65:319-326. [PMID: 23689175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
AIM The aim of this paper was to assess the feasibility and utility of adding a preventive trans obturatory tape (TOT) during the same intervention for anterior prolapse repair, in patients with masked urinary incontinence and massive cystocele. METHODS A retrospective trial was conducted in a Tertiary care University Hospital. Ninety-nine women with a massive cystocele (Ba ≥2 cm of pelvic organ prolapse quantification) and an occult stress urinary incontinence were recruited from 2004 to 2010: 53 women were subjected to an anterior fascial reconstruction alone while 46 underwent the same intervention with the addition of TOT. Patients were also asked to rate their overall quality of life, using the International Consultation on Incontinence Modular Questionnaire-Lower Urinary Tract Symptoms Quality Of Life (ICIQ-LUTSqol). All patients were assessed at one, six, twelve and twenty-four months of follow-up. Statistical analysis was performed with SPSS 15.0 software; SPSS inc., Chicago IL, USA was performed using the Chi-square test with Fisher's post-hoc correction. RESULTS At 24 month follow-up the rate of appearance of stress urinary incontinence at the urogynecological examination, was higher in the group without TOT (81% vs. 19%, P=0.004). In terms of overall quality of life, significantly higher rates of satisfaction have been reported by the group treated with additional TOT (P=0.006). CONCLUSION The addition of TOT during the anterior prolapse correction seems to give a greater durability to the correction, resulting, in the long term, in a lower rate of urinary symptoms onset (first latency) and in a better quality of life compared to the traditional anterior colporrhaphy alone.
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Affiliation(s)
- M C Paganotto
- Department of Gynecology and Pathophysiology of Human Reproduction, Policlinico S. Orsola-Malpighi University Hospital, Alma Mater Studiorum-University of Bologna, Bologna, Italy
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14
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Cardi M, Muttillo IA, Amadori L, Barillari P, Sammartino P, Arnone F, Signorelli C, Bolognese A. [Intravenous omeprazole versus ranitidine in the treatment of hemorrhagic duodenal ulcer: a prospective randomized study]. Ann Chir 1997; 51:136-9. [PMID: 9297869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This prospective randomized trial compares the results of i.v. omeprazole and i.v. ranitidine in 45 patients admitted as an emergency with an endoscopic diagnosis of bleeding duodenal ulcer. The patients were randomized to receive i.v. omeprazole, 40 mg bolus followed by 80 mg/day by continuous infusion for 3 days (group A), or ranitidine 50 mg i.v. bolus followed by 400 mg/day i.v., continuous infusion for 3 days (group B). Follow-up endoscopy on day 4 demonstrated successful therapy, except when more than 4 units of blood/day had to be transfused to maintain hemoglobin level above 10 g/l. Bleeding stopped in 20/21 patients in group A (95.2%), and in 17/24 patients in group B (70.80%) (p < 0.05). From the results of the study, it can be concluded that intravenous omeprazole seems to be effective in the control of bleeding duodenal ulcer.
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Affiliation(s)
- M Cardi
- I Istituto di Clinica Chirurgica, S.S. Chirurgia d'Urgenza 3, Università Degli Studi di Roma La Sapienza, Policlinico Umberto I, Roma, Italy
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15
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Cardi M, Muttillo IA, Amadori L, Petroni R, Mingazzini P, Barillari P, Lisi D, Bolognese A. Superiority of laparoscopy compared to ultrasonography in diagnosis of widespread liver diseases. Dig Dis Sci 1997; 42:546-8. [PMID: 9073137 DOI: 10.1023/a:1018895009305] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The aim of the study was to compare the results of ultrasonography (US) and laparoscopy in a series of 210 patients referred to our institution for the diagnosis of widespread liver diseases. Among 205 patients, laparoscopy revealed cirrhosis in 114, chronic widespread disease in 70 (chronic persistent hepatitis in 21, chronic active hepatitis in 28, steatosis in 14, acute hepatitis in 5, fibrosis in 2), and absence of liver disease in 21. Four of these cases had minor complications. A corroborative diagnosis was obtained in 122 patients (59.5%). Overall sensitivity of US was 84% with a low specificity due to the high rate of false negatives. From the results of this study we conclude that laparoscopy is a safe and essential diagnostic tool in the final diagnosis of widespread liver diseases and that US is not a reliable screening method because of its incidence of false negatives.
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Affiliation(s)
- M Cardi
- I Instituto di Clinica Chirurgica, Dipartimento Biopatologia Umana, Cattedra Gastroenterologia, Università La Sapienza di Roma, Italy
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16
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Gatti AM, Amadori L. [Changes in color over time]. Attual Dent 1986; 2:51, 53. [PMID: 3461817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Gatti AM, Amadori L. [Composite resins: absorption test in a simulated liquid]. Mondo Odontostomatol 1985; 27:45-9. [PMID: 3866946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Gatti A, Amadori L. [Identification of P10, a composite resin for posterior restorations]. Dent Cadmos 1985; 53:63, 65, 68-70. [PMID: 3860420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Gatti A, Amadori L. [Testing the retention of composite materials]. Riv Odontostomatol Implantoprotesi 1984:107-8. [PMID: 6399363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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