1
|
Zhang Y, Wang H, Oliveira RHM, Zhao C, Popel AS. Systems biology of angiogenesis signaling: Computational models and omics. WIREs Mech Dis 2021; 14:e1550. [PMID: 34970866 PMCID: PMC9243197 DOI: 10.1002/wsbm.1550] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/10/2023]
Abstract
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their cellular signal transduction, activation, proliferation, differentiation, as well as their intercellular communication. The coordinated execution and integration of such complex signaling programs is critical for physiological angiogenesis to take place in normal growth, development, exercise, and wound healing, while its dysregulation is critically linked to many major human diseases such as cancer, cardiovascular diseases, and ocular disorders; it is also crucial in regenerative medicine. Although huge efforts have been devoted to drug development for these diseases by investigation of angiogenesis‐targeted therapies, only a few therapeutics and targets have proved effective in humans due to the innate multiscale complexity and nonlinearity in the process of angiogenic signaling. As a promising approach that can help better address this challenge, systems biology modeling allows the integration of knowledge across studies and scales and provides a powerful means to mechanistically elucidate and connect the individual molecular and cellular signaling components that function in concert to regulate angiogenesis. In this review, we summarize and discuss how systems biology modeling studies, at the pathway‐, cell‐, tissue‐, and whole body‐levels, have advanced our understanding of signaling in angiogenesis and thereby delivered new translational insights for human diseases. This article is categorized under:Cardiovascular Diseases > Computational Models Cancer > Computational Models
Collapse
Affiliation(s)
- Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebeca Hannah M Oliveira
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
2
|
Bradshaw EL, Spilker ME, Zang R, Bansal L, He H, Jones RDO, Le K, Penney M, Schuck E, Topp B, Tsai A, Xu C, Nijsen MJMA, Chan JR. Applications of Quantitative Systems Pharmacology in Model-Informed Drug Discovery: Perspective on Impact and Opportunities. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2019; 8:777-791. [PMID: 31535440 PMCID: PMC6875708 DOI: 10.1002/psp4.12463] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/19/2019] [Indexed: 12/15/2022]
Abstract
Quantitative systems pharmacology (QSP) approaches have been increasingly applied in the pharmaceutical since the landmark white paper published in 2011 by a National Institutes of Health working group brought attention to the discipline. In this perspective, we discuss QSP in the context of other modeling approaches and highlight the impact of QSP across various stages of drug development and therapeutic areas. We discuss challenges to the field as well as future opportunities.
Collapse
Affiliation(s)
| | - Mary E Spilker
- Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Richard Zang
- Genentech Inc., South San Francisco, California, USA
| | | | - Handan He
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey, USA
| | | | - Kha Le
- Agios, Cambridge, Massachusetts, USA
| | | | | | - Brian Topp
- Merck & Co., Inc, Kenilworth, New Jersey, USA
| | - Alice Tsai
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts, USA
| | | | | | - Jason R Chan
- Eli Lilly and Company, Indianapolis, Indiana, USA
| |
Collapse
|
3
|
Gorenjak V, Vance DR, Petrelis AM, Stathopoulou MG, Dadé S, Shamieh SE, Murray H, Masson C, Lamont J, Fitzgerald P, Visvikis-Siest S. Peripheral blood mononuclear cells extracts VEGF protein levels and VEGF mRNA: Associations with inflammatory molecules in a healthy population. PLoS One 2019; 14:e0220902. [PMID: 31419243 PMCID: PMC6697334 DOI: 10.1371/journal.pone.0220902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/25/2019] [Indexed: 01/09/2023] Open
Abstract
Background Vascular endothelial growth factor (VEGF) is a signal protein, implicated in various physiological and pathophysiological processes together with other common inflammatory biomarkers. However, their associations have not yet been fully elucidated. In the present study, we investigated associations between VEGF and four specific VEGF mRNA isoforms with levels of 11 inflammation molecules, derived from peripheral blood mononuclear cells (PBMCs) extracts. Methods Healthy participants from the STANISLAS Family Study (n = 285) were included. Levels of VEGF (four mRNA isoforms and protein levels) and inflammatory molecules (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, INF-γ, TNF-α, MCP-1, EGF) were measured in PBMCs extracts. Multiple regression analyses were performed, adjusted for age and gender. Results The analyses revealed significant associations between VEGF protein levels and levels of IL-4 (β = 0.028, P = 0.013), MCP-1 (β = 0.015, P<0.0001) and EGF (β = 0.017, P<0.0001). Furthermore, mRNA isoform VEGF165 was associated with MCP-1 and IL-1α (P = 0.002 and P = 0.008, respectively); and mRNA isoform VEGF189 was associated with IL-4 and IL-6 (P = 0.019 and P = 0.034, respectively). Conclusions To our knowledge, the present study represents the first investigation that successfully demonstrates links between VEGF protein levels and inflammatory molecules levels derived from PBMCs extracts and identifies associations between specific VEGF mRNA isoforms and inflammatory molecules. Impact These findings provide novel insights that may assist in the development of new tissue and mRNA isoform specific measurements of VEGF levels, which may positively contribute to predicting the risk of common complex diseases and response of currently used anti-VEGF agents, and developing of novel targeted therapies for VEGF-related pathophysiology.
Collapse
Affiliation(s)
| | - Dwaine R. Vance
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | | | | | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Helena Murray
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | | | - John Lamont
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Peter Fitzgerald
- Randox Laboratories Limited, Crumlin, Co. Antrim, Northern Ireland, United Kingdom
| | - Sophie Visvikis-Siest
- Université de Lorraine, Inserm, IGE-PCV, Nancy, France
- Department of Internal Medicine and Geriatrics, CHU Technopôle Nancy-Brabois, Rue du Morvan, Vandoeuvre-lès-Nancy, France
- * E-mail:
| |
Collapse
|
4
|
Bazzazi H, Zhang Y, Jafarnejad M, Isenberg JS, Annex BH, Popel AS. Computer Simulation of TSP1 Inhibition of VEGF-Akt-eNOS: An Angiogenesis Triple Threat. Front Physiol 2018; 9:644. [PMID: 29899706 PMCID: PMC5988849 DOI: 10.3389/fphys.2018.00644] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/11/2018] [Indexed: 01/08/2023] Open
Abstract
The matricellular protein thrombospondin-1 (TSP1) is a potent inhibitor of angiogenesis. Specifically, TSP1 has been experimentally shown to inhibit signaling downstream of vascular endothelial growth factor (VEGF). The molecular mechanism of this inhibition is not entirely clear. We developed a detailed computational model of VEGF signaling to Akt-endothelial nitric oxide synthase (eNOS) to investigate the quantitative molecular mechanism of TSP1 inhibition. The model demonstrated that TSP1 acceleration of VEGFR2 degradation is sufficient to explain the inhibition of VEGFR2 and eNOS phosphorylation. However, Akt inhibition requires TSP1-induced phosphatase recruitment to VEGFR2. The model was then utilized to test various strategies for the rescue of VEGF signaling to Akt and eNOS. Inhibiting TSP1 was predicted to be not as effective as CD47 depletion in rescuing signaling to Akt. The model further predicts that combination strategy involving depletion of CD47 and inhibition of TSP1 binding to CD47 is necessary for effective recovery of signaling to eNOS. In all, computational modeling offers insight to molecular mechanisms involving TSP1 interaction with VEGF signaling and provides strategies for rescuing angiogenesis by targeting TSP1-CD47 axis.
Collapse
Affiliation(s)
- Hojjat Bazzazi
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Yu Zhang
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Mohammad Jafarnejad
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey S Isenberg
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brian H Annex
- Division of Cardiovascular Medicine, Department of Medicine, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|