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Latifi-Navid H, Barzegar Behrooz A, Jamehdor S, Davari M, Latifinavid M, Zolfaghari N, Piroozmand S, Taghizadeh S, Bourbour M, Shemshaki G, Latifi-Navid S, Arab SS, Soheili ZS, Ahmadieh H, Sheibani N. Construction of an Exudative Age-Related Macular Degeneration Diagnostic and Therapeutic Molecular Network Using Multi-Layer Network Analysis, a Fuzzy Logic Model, and Deep Learning Techniques: Are Retinal and Brain Neurodegenerative Disorders Related? Pharmaceuticals (Basel) 2023; 16:1555. [PMID: 38004422 PMCID: PMC10674956 DOI: 10.3390/ph16111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Neovascular age-related macular degeneration (nAMD) is a leading cause of irreversible visual impairment in the elderly. The current management of nAMD is limited and involves regular intravitreal administration of anti-vascular endothelial growth factor (anti-VEGF). However, the effectiveness of these treatments is limited by overlapping and compensatory pathways leading to unresponsiveness to anti-VEGF treatments in a significant portion of nAMD patients. Therefore, a system view of pathways involved in pathophysiology of nAMD will have significant clinical value. The aim of this study was to identify proteins, miRNAs, long non-coding RNAs (lncRNAs), various metabolites, and single-nucleotide polymorphisms (SNPs) with a significant role in the pathogenesis of nAMD. To accomplish this goal, we conducted a multi-layer network analysis, which identified 30 key genes, six miRNAs, and four lncRNAs. We also found three key metabolites that are common with AMD, Alzheimer's disease (AD) and schizophrenia. Moreover, we identified nine key SNPs and their related genes that are common among AMD, AD, schizophrenia, multiple sclerosis (MS), and Parkinson's disease (PD). Thus, our findings suggest that there exists a connection between nAMD and the aforementioned neurodegenerative disorders. In addition, our study also demonstrates the effectiveness of using artificial intelligence, specifically the LSTM network, a fuzzy logic model, and genetic algorithms, to identify important metabolites in complex metabolic pathways to open new avenues for the design and/or repurposing of drugs for nAMD treatment.
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Affiliation(s)
- Hamid Latifi-Navid
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
- Departments of Ophthalmology and Visual Sciences and Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Amir Barzegar Behrooz
- Department of Human Anatomy and Cell Science, University of Manitoba College of Medicine, Winnipeg, MB R3T 2N2, Canada;
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Saleh Jamehdor
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 6517838636, Iran;
| | - Maliheh Davari
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Masoud Latifinavid
- Department of Mechatronic Engineering, University of Turkish Aeronautical Association, 06790 Ankara, Turkey;
| | - Narges Zolfaghari
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Somayeh Piroozmand
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Sepideh Taghizadeh
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Mahsa Bourbour
- Department of Biotechnology, Alzahra University, Tehran 1993893973, Iran;
| | - Golnaz Shemshaki
- Department of Studies in Zoology, University of Mysore, Manasagangothri, Mysore 570005, India;
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil 5619911367, Iran;
| | - Seyed Shahriar Arab
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran;
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran; (H.L.-N.); (M.D.); (N.Z.); (S.P.); (S.T.); (Z.-S.S.)
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran 1666673111, Iran;
| | - Nader Sheibani
- Departments of Ophthalmology and Visual Sciences and Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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Joyce K, Fabra GT, Bozkurt Y, Pandit A. Bioactive potential of natural biomaterials: identification, retention and assessment of biological properties. Signal Transduct Target Ther 2021; 6:122. [PMID: 33737507 PMCID: PMC7973744 DOI: 10.1038/s41392-021-00512-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Biomaterials have had an increasingly important role in recent decades, in biomedical device design and the development of tissue engineering solutions for cell delivery, drug delivery, device integration, tissue replacement, and more. There is an increasing trend in tissue engineering to use natural substrates, such as macromolecules native to plants and animals to improve the biocompatibility and biodegradability of delivered materials. At the same time, these materials have favourable mechanical properties and often considered to be biologically inert. More importantly, these macromolecules possess innate functions and properties due to their unique chemical composition and structure, which increase their bioactivity and therapeutic potential in a wide range of applications. While much focus has been on integrating these materials into these devices via a spectrum of cross-linking mechanisms, little attention is drawn to residual bioactivity that is often hampered during isolation, purification, and production processes. Herein, we discuss methods of initial material characterisation to determine innate bioactivity, means of material processing including cross-linking, decellularisation, and purification techniques and finally, a biological assessment of retained bioactivity of a final product. This review aims to address considerations for biomaterials design from natural polymers, through the optimisation and preservation of bioactive components that maximise the inherent bioactive potency of the substrate to promote tissue regeneration.
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Affiliation(s)
- Kieran Joyce
- School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Georgina Targa Fabra
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Yagmur Bozkurt
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland.
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Chen X, Cheng C, Cheng W, Wang Y, Zuo X, Tang W, Yu Z, Yang Z, Wang Z, Zhu P, Huang W. Different Responses to Identical Trauma Between BALB/C and C57BL/6 Mice. Med Sci Monit 2021; 27:e928676. [PMID: 33621218 PMCID: PMC7911832 DOI: 10.12659/msm.928676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Different responses to identical trauma may be related to the genetic background of individuals, but the molecular mechanism is unclear. In this study we investigated the heterogeneity of trauma in mice and the potential biological explanations for the differences. Material/Methods Compared with other organs, the pathological response of the lung after injury is the earliest and most serious. We used C57BL/6 and BALB/C mice to explore the genetic background of different responses to trauma in the lung. We measured mortality rate, pulmonary microvascular permeability, and Cxcl15 gene expression in BALB/C and C57BL/6 mice before and after blast-wave injury. Microvascular permeability was measured using a fluorescent tracer, and Cxcl15 gene expression level and expression distribution were measured using fluorogenic probe quantitative polymerase chain reaction and northern blot. Results C57BL/6 mice showed lower mortality rates and pulmonary microvascular permeability than BALB/C mice after blast-wave injury; there was no significant difference in the permeability before blast-wave injury. The Cxcl15 gene was expressed specifically in the lung tissue of mice. The level of Cxcl15 expression in BALB/C mice was higher than in C57BL/6 mice before and after injury, and the variation trend of Cxcl15 expression level after injury was significantly different between BALB/C and C57BL/6 mice. Conclusions Our results indicated that BALB/C and C57BL/6 mice had significant heterogeneity in posttraumatic response in terms of mortality and degree of lung damage. The differences in genetic factors such as Cxcl15 may have played a role in this heterogeneity.
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Affiliation(s)
- Xiuying Chen
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
| | - Chang Cheng
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
| | - Wenchao Cheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (mainland)
| | - Yuhan Wang
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
| | - Xuzheng Zuo
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
| | - Weiju Tang
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
| | - Zhanyang Yu
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhihuan Yang
- Department 4, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China (mainland)
| | - Zhengguo Wang
- Department 4, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China (mainland)
| | - Peifang Zhu
- Department 4, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China (mainland)
| | - Wen Huang
- Department of Neurology, Second Affiliated Hospital of Army Medical University, Chongqing, China (mainland)
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Dos Santos TM, Righetti RF, Rezende BG, Campos EC, Camargo LDN, Saraiva-Romanholo BM, Fukuzaki S, Prado CM, Leick EA, Martins MA, Tibério IFLC. Effect of anti-IL17 and/or Rho-kinase inhibitor treatments on vascular remodeling induced by chronic allergic pulmonary inflammation. Ther Adv Respir Dis 2020; 14:1753466620962665. [PMID: 33357114 PMCID: PMC7768836 DOI: 10.1177/1753466620962665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background and aims: Expansion and morphological dysregulation of the bronchial vascular network occurs in asthmatic airways. Interleukin (IL) -17 and Rho-kinase (ROCK) are known to act in inflammation control and remodeling. Modulation of Rho-kinase proteins and IL-17 may be a promising approach for the treatment of asthma through the control of angiogenesis. Our objective was to analyze the effects of treatment with anti-IL17 and/or Rho-kinase inhibitor on vascular changes in mice with chronic allergic pulmonary inflammation. Methods: Sixty-four BALB/c mice, with pulmonary inflammation induced by ovalbumin were treated with anti-IL17A (7.5/µg per dose, intraperitoneal) and/or Rho-kinase inhibitor (Y-27632-10 mg/kg, intranasal), 1 h before each ovalbumin challenge (22, 24, 26, and 28/days). Control animals were made to inhale saline. At the end of the protocol, lungs were removed, and morphometric analysis was performed to quantify vascular inflammatory, remodeling, and oxidative stress responses. Results: Anti-IL17 or Rho-kinase inhibitor reduced the number of CD4+, CD8+, dendritic cells, IL-4, IL-5, IL-6, IL-10, IL-13, IL-17, Rho-kinase 1 and 2, transforming growth factor (TGF-β), vascular endothelial growth factor (VEGF), nuclear factor (NF)-KappaB, iNOS, metalloproteinase (MMP)-9, MMP-12, metalloproteinase inhibitor-1 (TIMP-1), FOXP-3, signal transducer and activator of transcription 1 (STAT1) and phospho-STAT1-positive cells, and actin, endothelin-1, isoprostane, biglycan, decorin, fibronectin and the collagen fibers volume fraction compared with the ovalbumin group (p < 0.05). The combination treatment, when compared with anti-IL17, resulted in potentiation of decrease in the number of IL1β- and dendritic cells-positive cells. When we compared the OVA-RHO inhibitor-anti-IL17 with OVA-RHO inhibitor we found a reduction in the number of CD8+ and IL-17, TGF-β, and phospho-STAT1-positive cells and endothelin-1 in the vessels (p < 0.05). There was an attenuation in the number of ROCK 2-positive cells in the group with the combined treatment when compared with anti-IL17 or Rho-kinase inhibitor-treated groups (p < 0.05). Conclusion: We observed no difference in angiogenesis after treatment with Rho-kinase inhibitor and anti-IL17. Although the treatments did not show differences in angiogenesis, they showed differences in the markers involved in the angiogenesis process contributing to inflammation control and vascular remodeling. The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Tabata M Dos Santos
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR; Hospital Sirio-Libanes, São Paulo, Brazil
| | - Renato F Righetti
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR; Hospital Sirio-Libanes, São Paulo, Brazil
| | - Bianca G Rezende
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Elaine C Campos
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil; Hospital Sirio-Libanes, São Paulo, Brazil
| | - Leandro do N Camargo
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR. Hospital Sirio-Libanes, São Paulo, Brazil
| | - Beatriz M Saraiva-Romanholo
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil.,Department of Medicine, University City of São Paulo (UNICID), São Paulo, Brazil
| | - Silvia Fukuzaki
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Carla M Prado
- Department of Biosciences, Federal University os Sao Paulo, Santos, SP, Brazil
| | - Edna A Leick
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Milton A Martins
- Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Iolanda F L C Tibério
- Departamento de Clínica Médica, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 455- Sala 1210, São Paulo, SP 01246-903, Brazil
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Muqri F, Helkin A, Maier KG, Gahtan V. Thrombospondin-5 and fluvastatin promote angiogenesis and are protective against endothelial cell apoptosis. J Cell Biochem 2020; 121:4154-4165. [PMID: 32348623 DOI: 10.1002/jcb.29686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/09/2019] [Indexed: 01/03/2023]
Abstract
The thrombospondins (TSPs), multifunctional matricellular proteins, are known mediators of endothelial cell (EC) angiogenesis and apoptosis. TSP-1, an antiangiogenic molecule, is important in the progression of vascular disease, in part by inducing EC apoptosis. TSP-2, although less studied, also induces EC apoptosis and inhibits angiogenesis. The effects of TSP-5 are largely unexplored in ECs, but TSP-5 is believed to be protective against arterial disease. Statin drugs have been shown to have beneficial pleiotropic effects, including decreasing EC apoptosis, increasing angiogenesis, and blocking TSP signaling. We hypothesized TSP-5 will be proangiogenic and antiapoptotic, and statin pretreatment would reverse the proapoptotic and antiangiogenic phenotype of TSP-1 and TSP-2. ECs were exposed to serum-free medium, TSP-1, TSP-2, or TSP-5 with or without fluvastatin pretreatment. Quantitative real-time polymerase chain reaction was performed on 96 apoptosis and 96 angiogenesis-related genes using microfluidic card assays. Angiogenesis was measured using Matrigel assays, while apoptosis was measured by fluorescent caspase assay. TSP-5 suppressed apoptotic genes and had a mixed effect on the angiogenic genes; however, TSP-5 did not alter apoptois but was proangiogenic. Pretreatment with fluvastatin downregulated proapoptotic genes and apoptosis and upregulated proangiogenic genes and angiogenesis. Findings indicate TSP-5 and fluvastatin have a protective effect on ECs, being proangiogenic and reversing the antiangiogenic effects of TSP-1 and TSP-2. In conclusion, TSP-5 and fluvastatin may be beneficial for inducing angiogenesis in the setting of ischemia.
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Affiliation(s)
- Furqan Muqri
- Division of Vascular Surgery and Endovascular Services, SUNY Upstate Medical University, Syracuse, New York
- Department of Veterans Affairs, VA Healthcare Network Upstate, Syracuse, New York
| | - Alex Helkin
- Division of Vascular Surgery and Endovascular Services, SUNY Upstate Medical University, Syracuse, New York
- Department of Veterans Affairs, VA Healthcare Network Upstate, Syracuse, New York
| | - Kristopher G Maier
- Division of Vascular Surgery and Endovascular Services, SUNY Upstate Medical University, Syracuse, New York
- Department of Veterans Affairs, VA Healthcare Network Upstate, Syracuse, New York
| | - Vivian Gahtan
- Division of Vascular Surgery and Endovascular Services, SUNY Upstate Medical University, Syracuse, New York
- Department of Veterans Affairs, VA Healthcare Network Upstate, Syracuse, New York
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Hoang VT, Matossian MD, Ucar DA, Elliott S, La J, Wright MK, Burks HE, Perles A, Hossain F, King CT, Browning VE, Bursavich J, Fang F, Del Valle L, Bhatt AB, Cavanaugh JE, Flaherty PT, Anbalagan M, Rowan BG, Bratton MR, Nephew KP, Miele L, Collins-Burow BM, Martin EC, Burow ME. ERK5 Is Required for Tumor Growth and Maintenance Through Regulation of the Extracellular Matrix in Triple Negative Breast Cancer. Front Oncol 2020; 10:1164. [PMID: 32850332 PMCID: PMC7416559 DOI: 10.3389/fonc.2020.01164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Conventional mitogen-activated protein kinase (MAPK) family members regulate diverse cellular processes involved in tumor initiation and progression, yet the role of ERK5 in cancer biology is not fully understood. Triple-negative breast cancer (TNBC) presents a clinical challenge due to the aggressive nature of the disease and a lack of targeted therapies. ERK5 signaling contributes to drug resistance and metastatic progression through distinct mechanisms, including activation of epithelial-to-mesenchymal transition (EMT). More recently a role for ERK5 in regulation of the extracellular matrix (ECM) has been proposed, and here we investigated the necessity of ERK5 in TNBC tumor formation. Depletion of ERK5 expression using the CRISPR/Cas9 system in MDA-MB-231 and Hs-578T cells resulted in loss of mesenchymal features, as observed through gene expression profile and cell morphology, and suppressed TNBC cell migration. In vivo xenograft experiments revealed ERK5 knockout disrupted tumor growth kinetics, which was restored using high concentration Matrigel™ and ERK5-ko reduced expression of the angiogenesis marker CD31. These findings implicated a role for ERK5 in the extracellular matrix (ECM) and matrix integrity. RNA-sequencing analyses demonstrated downregulation of matrix-associated genes, integrins, and pro-angiogenic factors in ERK5-ko cells. Tissue decellularization combined with cryo-SEM and interrogation of biomechanical properties revealed that ERK5-ko resulted in loss of key ECM fiber alignment and mechanosensing capabilities in breast cancer xenografts compared to parental wild-type cells. In this study, we identified a novel role for ERK5 in tumor growth kinetics through modulation of the ECM and angiogenesis axis in breast cancer.
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Affiliation(s)
- Van T. Hoang
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Margarite D. Matossian
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Deniz A. Ucar
- Department of Genetics, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Steven Elliott
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Jacqueline La
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Maryl K. Wright
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hope E. Burks
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Aaron Perles
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Fokhrul Hossain
- Department of Genetics, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Connor T. King
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Valentino E. Browning
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Jacob Bursavich
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Fang Fang
- Medical Sciences, School of Medicine, Indiana University Bloomington, Bloomington, IN, United States
| | - Luis Del Valle
- Department of Pathology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Akshita B. Bhatt
- Department of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Jane E. Cavanaugh
- Department of Pharmacology, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Patrick T. Flaherty
- Department of Medicinal Chemistry, School of Pharmacy, Duquesne University, Pittsburgh, PA, United States
| | - Muralidharan Anbalagan
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Brian G. Rowan
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Melyssa R. Bratton
- Cellular and Molecular Biology Core, Xavier University, New Orleans, LA, United States
| | - Kenneth P. Nephew
- Medical Sciences, School of Medicine, Indiana University Bloomington, Bloomington, IN, United States
| | - Lucio Miele
- Department of Genetics, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Bridgette M. Collins-Burow
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Cancer Center, New Orleans, LA, United States
| | - Elizabeth C. Martin
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Matthew E. Burow
- Section of Hematology & Medical Oncology, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, United States
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Transcription Factor Prospero Homeobox 1 (PROX1) as a Potential Angiogenic Regulator of Follicular Thyroid Cancer Dissemination. Int J Mol Sci 2019; 20:ijms20225619. [PMID: 31717665 PMCID: PMC6888435 DOI: 10.3390/ijms20225619] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 01/25/2023] Open
Abstract
It is well known that Prospero homeobox 1 (PROX1) is a crucial regulator of lymphangiogenesis, that reprograms blood endothelial cells to lymphatic phenotype. However, the role of PROX1 in tumor progression, especially in angiogenesis remains controversial. Herein, we studied the role of PROX1 in angiogenesis in cell lines derived from follicular thyroid cancer (FTC: FTC-133) and squamous cell carcinoma of the thyroid gland (SCT: CGTH-W-1) upon PROX1 knockdown. The genes involved in angiogenesis were selected by RNA-seq, and the impact of PROX1 on vascularization potential was investigated using human umbilical vein endothelial cells (HUVECs) cultured in conditioned medium collected from FTC- or SCT-derived cancer cell lines after PROX1 silencing. The angiogenic phenotype was examined in connection with the analysis of focal adhesion and correlated with fibroblast growth factor 2 (FGF2) levels. Additionally, the expression of selected genes involved in angiogenesis was detected in human FTC tissues. As a result, we demonstrated that PROX1 knockdown resulted in upregulation of factors associated with vascularization, such as metalloproteinases (MMP1 and 3), FGF2, vascular endothelial growth factors C (VEGFC), BAI1 associated protein 2 (BAIAP2), nudix hydrolase 6 (NUDT6), angiopoietin 1 (ANGPT1), and vascular endothelial growth factor receptor 2 (KDR). The observed molecular changes resulted in the enhanced formation of capillary-like structures by HUVECs and upregulated focal adhesion in FTC-133 and CGTH-W-1 cells. The signature of selected angiogenic genes' expression in a series of FTC specimens varied depending on the case. Interestingly, PROX1 and FGF2 showed opposing expression levels in FTC tissues and seven thyroid tumor-derived cell lines. In summary, our data revealed that PROX1 is involved in the spreading of thyroid cancer cells by regulation of angiogenesis.
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Zhao C, Isenberg JS, Popel AS. Human expression patterns: qualitative and quantitative analysis of thrombospondin-1 under physiological and pathological conditions. J Cell Mol Med 2018; 22:2086-2097. [PMID: 29441713 PMCID: PMC5867078 DOI: 10.1111/jcmm.13565] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/07/2018] [Indexed: 12/12/2022] Open
Abstract
Thrombospondin-1 (TSP-1), a matricellular protein and one of the first endogenous anti-angiogenic molecules identified, has long been considered a potent modulator of human diseases. While the therapeutic effect of TSP-1 to suppress cancer was investigated in both research and clinical settings, the mechanisms of how TSP-1 is regulated in cancer remain elusive, and the scientific answers to the question of whether TSP-1 expressions can be utilized as diagnostic or prognostic marker for patients with cancer are largely inconsistent. Moreover, TSP-1 plays crucial functions in angiogenesis, inflammation and tissue remodelling, which are essential biological processes in the progression of many cardiovascular diseases, and therefore, its dysregulated expressions in such conditions may have therapeutic significance. Herein, we critically analysed the literature pertaining to TSP-1 expression in circulating blood and pathological tissues in various types of cancer as well as cardiovascular and inflammation-related diseases in humans. We compare the secretion rates of TSP-1 by different cancer and non-cancer cells and discuss the potential connection between the expression changes of TSP-1 and vascular endothelial growth factor (VEGF) observed in patients with cancer. Moreover, the pattern and emerging significance of TSP-1 profiles in cardiovascular disease, such as peripheral arterial disease, diabetes and other related non-cancer disorders, are highlighted. The analysis of published TSP-1 data presented in this review may have implications for the future exploration of novel TSP-1-based treatment strategies for cancer and cardiovascular-related diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical EngineeringSchool of MedicineJohns Hopkins UniversityBaltimoreMDUSA
| | - Jeffrey S. Isenberg
- Division of Pulmonary, Allergy and Critical CareDepartment of MedicineHeart, Lung, Blood and Vascular Medicine InstituteUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Aleksander S. Popel
- Department of Biomedical EngineeringSchool of MedicineJohns Hopkins UniversityBaltimoreMDUSA
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11
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Wight TN. Provisional matrix: A role for versican and hyaluronan. Matrix Biol 2016; 60-61:38-56. [PMID: 27932299 DOI: 10.1016/j.matbio.2016.12.001] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/22/2016] [Accepted: 12/01/2016] [Indexed: 12/19/2022]
Abstract
Hyaluronan and versican are extracellular matrix (ECM) components that are enriched in the provisional matrices that form during the early stages of development and disease. These two molecules interact to create pericellular "coats" and "open space" that facilitate cell sorting, proliferation, migration, and survival. Such complexes also impact the recruitment of leukocytes during development and in the early stages of disease. Once thought to be inert components of the ECM that help hold cells together, it is now quite clear that they play important roles in controlling cell phenotype, shaping tissue response to injury and maintaining tissue homeostasis. Conversion of hyaluronan-/versican-enriched provisional matrix to collagen-rich matrix is a "hallmark" of tissue fibrosis. Targeting the hyaluronan and versican content of provisional matrices in a variety of diseases including, cardiovascular disease and cancer, is becoming an attractive strategy for intervention.
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Affiliation(s)
- Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, United States.
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Grzela K, Litwiniuk M, Krejner A, Zagorska W, Grzela T. Increased angiogenic factors in exhaled breath condensate of children with severe asthma - New markers of disease progression? Respir Med 2016; 118:119-121. [PMID: 27578480 DOI: 10.1016/j.rmed.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/03/2016] [Accepted: 08/07/2016] [Indexed: 11/17/2022]
Abstract
Asthma progression is associated with airway remodeling and neo-vascularization. However, role of angiogenesis in these changes remains unclear and available data still incomplete. In this pilot study we verify usefulness of proteome profiler assay in screening of angiogenesis-related factors in exhaled breath condensates (EBC) collected from children with asthma. EBC samples from patients with mild or severe asthma and healthy controls were tested using protein array. In EBC samples from patients with severe asthma we have found large quantities of several angiogenesis regulators, including thrombospondin (TSP)-1, angiogenin, dipeptidyl peptidase (DPP) IV, matrix metalloproteinase (MMP)-9 and its inhibitor TIMP-1. Small amounts of angiopoietin (Ang)-2 and vascular endothelial growth factor (VEGF) were also present. In contrast to them, in EBC from mild asthma group we have detected TSP-1 and small quantities of Ang-2. EBC samples from healthy controls contained only TSP-1. Our preliminary report suggests that, since increased amounts of angiogenesis-related factors in EBC seem to correlate with asthma severity, they may be considered as convenient non-invasive markers of disease progression. However, further research is necessary.
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Affiliation(s)
- Katarzyna Grzela
- Department of Paediatrics, Pneumonology and Allergology, Medical University of Warsaw, Poland
| | - Malgorzata Litwiniuk
- Department of Histology and Embryology, Medical University of Warsaw, Poland; Potgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Alicja Krejner
- Department of Histology and Embryology, Medical University of Warsaw, Poland
| | - Wioletta Zagorska
- Department of Paediatrics, Pneumonology and Allergology, Medical University of Warsaw, Poland
| | - Tomasz Grzela
- Department of Histology and Embryology, Medical University of Warsaw, Poland.
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13
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Guo S, Lok J, Zhao S, Leung W, Som AT, Hayakawa K, Wang Q, Xing C, Wang X, Ji X, Zhou Y, Lo EH. Effects of Controlled Cortical Impact on the Mouse Brain Vasculome. J Neurotrauma 2016; 33:1303-16. [PMID: 26528928 DOI: 10.1089/neu.2015.4101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Perturbations in blood vessels play a critical role in the pathophysiology of brain injury and neurodegeneration. Here, we use a systematic genome-wide transcriptome screening approach to investigate the vasculome after brain trauma in mice. Mice were subjected to controlled cortical impact and brains were extracted for analysis at 24 h post-injury. The core of the traumatic lesion was removed and then cortical microvesels were isolated from nondirectly damaged ipsilateral cortex. Compared to contralateral cortex and normal cortex from sham-operated mice, we identified a wide spectrum of responses in the vasculome after trauma. Up-regulated pathways included those involved in regulation of inflammation and extracellular matrix processes. Decreased pathways included those involved in regulation of metabolism, mitochondrial function, and transport systems. These findings suggest that microvascular perturbations can be widespread and not necessarily localized to core areas of direct injury per se and may further provide a broader gene network context for existing knowledge regarding inflammation, metabolism, and blood-brain barrier alterations after brain trauma. Further efforts are warranted to map the vasculome with higher spatial and temporal resolution from acute to delayed phase post-trauma. Investigating the widespread network responses in the vasculome may reveal potential mechanisms, therapeutic targets, and biomarkers for traumatic brain injury.
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Affiliation(s)
- Shuzhen Guo
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Josephine Lok
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts.,2 Department of Pediatrics, Massachusetts General Hospital , Harvard Medical School, Boston, Massachusetts
| | - Song Zhao
- 3 The Department of Spine Surgery, the First Hospital of Jilin University , Changchun, China
| | - Wendy Leung
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Angel T Som
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Kazuhide Hayakawa
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Qingzhi Wang
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Changhong Xing
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Xiaoying Wang
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Xunming Ji
- 4 Cerebrovascular Research Center, Department of Neurosurgery, Xuanwu Hospital, Capital Medical University , Beijing, China
| | - Yiming Zhou
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
| | - Eng H Lo
- 1 Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital , Harvard Medical School, Charlestown, Massachusetts
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Pomin VH, Mulloy B. Current structural biology of the heparin interactome. Curr Opin Struct Biol 2015; 34:17-25. [PMID: 26038285 DOI: 10.1016/j.sbi.2015.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/03/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
Abstract
Heparin is the best known therapeutically active carbohydrate. It can bind and regulate multiple functional proteins such as coagulation cofactors, chemokines, and growth factors. This versatility has led to the recently developed concept of the heparin interactome--a group of proteins that, as the name implies, interact with heparin. The heparin interactome is structurally and functionally diverse. Though natural ligands of this class of proteins may be any of the glycosaminoglycans however, their structural biology is generally studied using heparin as a model compound. NMR spectroscopy contributes significantly to structural investigations of the resultant complexes in solution. This review aims therefore at discussing the current status in structural biology of the molecular complexes formed between heparin and its protein partners through the current concept of the heparin interactome.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil.
| | - Barbara Mulloy
- Glycosciences Laboratory, Imperial College, Department of Medicine, Burlington Danes Building, Du Cane Road, London W12 0NN, UK.
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Morjen M, Honoré S, Bazaa A, Abdelkafi-Koubaa Z, Ellafi A, Mabrouk K, Kovacic H, El Ayeb M, Marrakchi N, Luis J. PIVL, a snake venom Kunitz-type serine protease inhibitor, inhibits in vitro and in vivo angiogenesis. Microvasc Res 2014; 95:149-56. [PMID: 25173589 DOI: 10.1016/j.mvr.2014.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/17/2014] [Accepted: 08/21/2014] [Indexed: 12/22/2022]
Abstract
Development and homeostasis of the vascular system requires integrin-promoting endothelial cell adhesion, migration and survival. Nowadays, integrins represent potential targets for pharmacological agents and open new avenues for the control of metastatic spread in the treatment of tumor malignancies. We have already reported that PIVL, a serine protease inhibitor isolated from Macrovipera lebetina venom, displays an anti-tumor effect through interference with integrin receptor function. Here, we report that PIVL inhibits human vascular endothelial cell adhesion and migration onto fibrinogen and fibronectin in a dose-dependent manner without any cytotoxicity. Furthermore, we show that PIVL increases microtubule dynamic instability in HMEC-1 transfected with EGFP-tagged α-tubulin. Using Matrigel™ and chick chorioallantoic membrane assays, we demonstrate that PIVL exhibits a strong anti-angiogenic effect both in vitro and in vivo. Interestingly, results herein reveal that the potent anti-angiogenic properties of PIVL are mediated by its RGD-like motif ((41)RGN(43)).
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Affiliation(s)
- Maram Morjen
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Tunisia.
| | - Stéphane Honoré
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, UMR_S 911, Marseille, France; APHM, Hôpital Timone, Service Pharmacie, Marseille, France
| | - Amine Bazaa
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Tunisia
| | | | - Ameneallah Ellafi
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Tunisia
| | - Kamel Mabrouk
- Equipe CROPS, Institut de Chimie Radicalaire - UMR 7273, Université d'Aix-Marseille, Site de Saint Jérôme, Av. Escadrille Normandie Niemen, 13397 Marseille, France
| | - Hervé Kovacic
- APHM, Hôpital Timone, Service Pharmacie, Marseille, France
| | - Mohamed El Ayeb
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Tunisia
| | - Naziha Marrakchi
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Tunisia; Faculté de Médecine de Tunis, Tunisia
| | - José Luis
- APHM, Hôpital Timone, Service Pharmacie, Marseille, France
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Logsdon EA, Finley SD, Popel AS, Mac Gabhann F. A systems biology view of blood vessel growth and remodelling. J Cell Mol Med 2013; 18:1491-508. [PMID: 24237862 PMCID: PMC4190897 DOI: 10.1111/jcmm.12164] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022] Open
Abstract
Blood travels throughout the body in an extensive network of vessels – arteries, veins and capillaries. This vascular network is not static, but instead dynamically remodels in response to stimuli from cells in the nearby tissue. In particular, the smallest vessels – arterioles, venules and capillaries – can be extended, expanded or pruned, in response to exercise, ischaemic events, pharmacological interventions, or other physiological and pathophysiological events. In this review, we describe the multi-step morphogenic process of angiogenesis – the sprouting of new blood vessels – and the stability of vascular networks in vivo. In particular, we review the known interactions between endothelial cells and the various blood cells and plasma components they convey. We describe progress that has been made in applying computational modelling, quantitative biology and high-throughput experimentation to the angiogenesis process.
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Affiliation(s)
- Elizabeth A Logsdon
- Institute for Computational Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Bateman JF, Rowley L, Belluoccio D, Chan B, Bell K, Fosang AJ, Little CB. Transcriptomics of wild-type mice and mice lacking ADAMTS-5 activity identifies genes involved in osteoarthritis initiation and cartilage destruction. ACTA ACUST UNITED AC 2013; 65:1547-60. [PMID: 23436205 DOI: 10.1002/art.37900] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 02/05/2013] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To identify changes in gene expression in mice with osteoarthritis (OA) in order to explore the mechanisms of the disease. METHODS Gene expression profiling was performed in cartilage from mice with surgically induced OA. We used wild-type (WT) mice and Adamts5Δcat mice, in which ADAMTS-5 activity is lacking and aggrecan loss and cartilage erosion are inhibited, to distinguish gene expression changes that are independent of ADAMTS-5 activity and cartilage breakdown. Mechanical instability was introduced into the knee joints of 10-week-old male mice via surgical destabilization of the medial meniscus (DMM). Cartilage from the developing lesion in the destabilized medial meniscus and corresponding regions in sham-operated joints was harvested by microdissection at 1, 2, and 6 weeks postsurgery, and RNA was extracted, amplified, and hybridized to whole-genome microarrays. RESULTS Several previously identified OA-related genes, including Ptgs2, Crlf1, and Inhba, and novel genes, such as Phdla2 and Il11, were up-regulated in both WT mice and Adamts5Δcat mice, indicating that they are independent of ADAMTS-5 activity. The altered expression of other genes, including Col10a1, the sentinel marker of cartilage hypertrophy, and Wnt/β-catenin pathway genes, required ADAMTS-5 activity. Cell death pathway genes were dysregulated, and Tp53, Foxo4, and Xbp1 endoplasmic reticulum-stress transcriptional networks were activated. Analysis of degradome genes identified up-regulation of many proteases, including Mmp3, Capn2, and the novel cartilage proteases Prss46 and Klk8. Comparison with other studies identified 16 genes also dysregulated in rat and human OA as priorities for study. CONCLUSION We have identified, for the first time, several genes that have an ADAMTS-5-independent role in OA, identifying them as possible OA initiation candidates. This work provides new insights into the sequence of gene dysregulation and the molecular basis of cartilage destruction in OA.
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Affiliation(s)
- John F Bateman
- Murdoch Childrens Research Institute and University of Melbourne, Parkville, Victoria, Australia.
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Minchenko D, Ratushna O, Bashta Y, Herasymenko R, Minchenko O. The Expression of <i>TIMP</i>1, <i>TIMP</i>2, <i>VCAN</i>, <i>SPARC</i>, <i>CLEC</i>3<i>B</i> and <i>E</i>2<i>F</i>1 in Subcutaneous Adipose Tissue of Obese Males and Glucose Intolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/cellbio.2013.22006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the angiome: a global angiogenesis protein interaction network. Physiol Genomics 2012; 44:915-24. [PMID: 22911453 DOI: 10.1152/physiolgenomics.00181.2011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Angiogenesis is the formation of new blood vessels from pre-existing microvessels. Excessive and insufficient angiogenesis have been associated with many diseases including cancer, age-related macular degeneration, ischemic heart, brain, and skeletal muscle diseases. A comprehensive understanding of angiogenesis regulatory processes is needed to improve treatment of these diseases. To identify proteins related to angiogenesis, we developed a novel integrative framework for diverse sources of high-throughput data. The system, called GeneHits, was used to expand on known angiogenesis pathways to construct the angiome, a protein-protein interaction network for angiogenesis. The network consists of 478 proteins and 1,488 interactions. The network was validated through cross validation and analysis of five gene expression datasets from in vitro angiogenesis assays. We calculated the topological properties of the angiome. We analyzed the functional enrichment of angiogenesis-annotated and associated proteins. We also constructed an extended angiome with 1,233 proteins and 5,726 interactions to derive a more complete map of protein-protein interactions in angiogenesis. Finally, the extended angiome was used to identify growth factor signaling networks that drive angiogenesis and antiangiogenic signaling networks. The results of this analysis can be used to identify genes and proteins in different disease conditions and putative targets for therapeutic interventions as high-ranked candidates for experimental validation.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA.
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Burgess JK, Weckmann M. Matrikines and the lungs. Pharmacol Ther 2012; 134:317-37. [PMID: 22366287 DOI: 10.1016/j.pharmthera.2012.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 02/03/2012] [Indexed: 01/09/2023]
Abstract
The extracellular matrix is a complex network of fibrous and nonfibrous molecules that not only provide structure to the lung but also interact with and regulate the behaviour of the cells which it surrounds. Recently it has been recognised that components of the extracellular matrix proteins are released, often through the action of endogenous proteases, and these fragments are termed matrikines. Matrikines have biological activities, independent of their role within the extracellular matrix structure, which may play important roles in the lung in health and disease pathology. Integrins are the primary cell surface receptors, characterised to date, which are used by the matrikines to exert their effects on cells. However, evidence is emerging for the need for co-factors and other receptors for the matrikines to exert their effects on cells. The potential for matrikines, and peptides derived from these extracellular matrix protein fragments, as therapeutic agents has recently been recognised. The natural role of these matrikines (including inhibitors of angiogenesis and possibly inflammation) make them ideal targets to mimic as therapies. A number of these peptides have been taken forward into clinical trials. The focus of this review will be to summarise our current understanding of the role, and potential for highly relevant actions, of matrikines in lung health and disease.
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Affiliation(s)
- Janette K Burgess
- Cell Biology, Woolcock Institute of Medical Research, Sydney, NSW, Australia.
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Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS. Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis. PLoS One 2011; 6:e24887. [PMID: 21931866 PMCID: PMC3172305 DOI: 10.1371/journal.pone.0024887] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 08/23/2011] [Indexed: 02/06/2023] Open
Abstract
Angiogenesis is important for many physiological processes, diseases, and also regenerative medicine. Therapies that inhibit the vascular endothelial growth factor (VEGF) pathway have been used in the clinic for cancer and macular degeneration. In cancer applications, these treatments suffer from a “tumor escape phenomenon” where alternative pathways are upregulated and angiogenesis continues. The redundancy of angiogenesis regulation indicates the need for additional studies and new drug targets. We aimed to (i) identify novel and missing angiogenesis annotations and (ii) verify their significance to angiogenesis. To achieve these goals, we integrated the human interactome with known angiogenesis-annotated proteins to identify a set of 202 angiogenesis-associated proteins. Across endothelial cell lines, we found that a significant fraction of these proteins had highly perturbed gene expression during angiogenesis. After treatment with VEGF-A, we found increasing expression of HIF-1α, APP, HIV-1 tat interactive protein 2, and MEF2C, while endoglin, liprin β1 and HIF-2α had decreasing expression across three endothelial cell lines. The analysis showed differential regulation of HIF-1α and HIF-2α. The data also provided additional evidence for the role of endothelial cells in Alzheimer's disease.
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Affiliation(s)
- Corban G Rivera
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
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