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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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Hamper M, Schmidt-Kastner R. Sleep Disorder Kleine-Levin Syndrome (KLS) Joins the List of Polygenic Brain Disorders Associated with Obstetric Complications. Cell Mol Neurobiol 2023; 43:3393-3403. [PMID: 37553546 DOI: 10.1007/s10571-023-01391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
Kleine-Levin Syndrome is a rare neurological disorder with onset typically during adolescence that is characterized by recurrent episodes of hypersomnia, behavioral changes, and cognitive abnormalities, in the absence of structural changes in neuroimaging. As for many functional brain disorders, the exact disease mechanism in Kleine-Levin Syndrome is presently unknown, preventing the development of specific treatment approaches or protective measures. Here we review the pathophysiology and genetics of this functional brain disorder and then present a specific working hypothesis. A neurodevelopmental mechanism has been suspected based on associations with obstetric complications. Recent studies have focused on genetic factors whereby the first genome-wide association study (GWAS) in Kleine-Levin Syndrome has defined a linkage at the TRANK1 locus. A Gene x Environment interaction model involving obstetric complications was proposed based on concepts developed for other functional brain disorders. To stimulate future research, we here performed annotations of the genes under consideration for Kleine-Levin Syndrome in relation to factors expected to be associated with obstetric complications. Annotations used data-mining of gene/protein lists related to for hypoxia, ischemia, and vascular factors and targeted literature searches. Tentative links for TRANK1, four additional genes in the TRANK1 locus, and LMOD3-LMO2 are described. Protein interaction data for TRANK1 indicate links to CBX2, CBX4, and KDM3A, that in turn can be tied to hypoxia. Taken together, the neurological sleep disorder, Kleine-Levin Syndrome, shows genetic and mechanistic overlap with well analyzed brain disorders such as schizophrenia, autism spectrum disorder and ADHD in which polygenic predisposition interacts with external events during brain development, including obstetric complications.
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Affiliation(s)
- Michael Hamper
- Florida Atlantic University (FAU), CE Schmidt College of Medicine, Boca Raton, FL, USA
| | - Rainald Schmidt-Kastner
- Florida Atlantic University (FAU), CE Schmidt College of Medicine, Boca Raton, FL, USA.
- Dept. Clinical Neurosciences, CE Schmidt College of Medicine, Florida Atlantic University (FAU), 777 Glades Road, Boca Raton, FL, 33431, USA.
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Ren Y, YaneYang, Lu Q, Wang Q, Lu G, Wei Y, Zhou J. Transcription factor cellular promoter 2 is required for upstream binding protein 1 -mediated angiogenesis. Gene Expr Patterns 2023; 48:119308. [PMID: 36889372 DOI: 10.1016/j.gep.2023.119308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/22/2022] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
OBJECTIVE Angiogenesis is a key process of repairing tissue damage, and it is regulated by the delicate balance between anti-angiogenesis factors. In the present study, we investigate whether transcription factor cellular promoter 2 (TFCP2) is required for upstream binding protein 1 (UBP1)-mediated angiogenesis. METHODS Levels of UBP1 and TFCP2 in human umbilical vein endothelial cells (HUVECs) are detected by quantitative polymerase chain reaction (q-PCR) and Western blotting (WB). Effects of UBP1 on angiogenesis and migration are detected by tube-like network formation on matrigel assay and scratch assay. The interaction between UBP1 and TFCP2 is predicted and verified by STRING and Co-immunoprecipitation (Co-IP). RESULTS Firstly, the UBP1 expression level was up-regulated in the stimuli of vascular endothelial growth factor (VEGF) in HUVECs, and the knockdown of UBP1 inhibited angiogenesis and migration of HUVECs. Then, UBP1 interacted with TFCP2. Besides, the TFCP2 expression level was up-regulated in VEGF-stimulated HUVECs. Furthermore, knockdown of TFCP2 inhibited angiogenesis and migration in VEGF-stimulated HUVECs, and down-regulation of UBP1 enhanced the inhibition. CONCLUSION TFCP2 also plays a key role in UBP1 mediated angiogenesis of HUVECs stimulated by VEGF. These findings will provide a new theoretical basis for the treatment of angiogenic diseases.
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Affiliation(s)
- Yanyan Ren
- Department of Neurology, Liaocheng Third People's Hospital, No. 62 Weiyu Road, Dongchangfu District, Liaocheng, Shandong, 252000, China
| | - YaneYang
- The Second Department of Neurology, Gaotang People's Hospital, North of Provincial Road No.520 and West of Binhu Road, Gaotang County, Liaocheng, Shandong, 252800, China
| | - Qingbo Lu
- Department of Emergency, Ningyang First People's Hospital, No. 872, Jinyang Street, Ningyang County, Tai'an, Shandong, 271400, China
| | - Qiang Wang
- Department of Neurosurgery, Gaoqing People's Hospital, Gaoqing People's Hospital of Zibo City, Shandong, 256300, China
| | - Gentao Lu
- The Third Department of Neurology, Ningyang First People's Hospital, No.872 Jinyang Road, Ningyang County, Tai'an, Shandong, 271400, China
| | - Yanli Wei
- Department of Respiratory and Critical Care, First Hospital of Zibo City, No.4 Emeishan East Road, Boshan District, Zibo City, Shandong, 255200, China
| | - Jiaqi Zhou
- Department of Traditional Chinese Medicine, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, 213017, China; Department of Traditional Chinese Medicine, The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, 213017, China.
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Gallego I, Villate-Beitia I, Saenz-Del-Burgo L, Puras G, Pedraz JL. Therapeutic Opportunities and Delivery Strategies for Brain Revascularization in Stroke, Neurodegeneration, and Aging. Pharmacol Rev 2022; 74:439-461. [PMID: 35302047 DOI: 10.1124/pharmrev.121.000418] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/25/2022] Open
Abstract
Central nervous system (CNS) diseases, especially acute ischemic events and neurodegenerative disorders, constitute a public health problem with no effective treatments to allow a persistent solution. Failed therapies targeting neuronal recovery have revealed the multifactorial and intricate pathophysiology underlying such CNS disorders as ischemic stroke, Alzheimeŕs disease, amyotrophic lateral sclerosis, vascular Parkisonism, vascular dementia, and aging, in which cerebral microvasculature impairment seems to play a key role. In fact, a reduction in vessel density and cerebral blood flow occurs in these scenarios, contributing to neuronal dysfunction and leading to loss of cognitive function. In this review, we provide an overview of healthy brain microvasculature structure and function in health and the effect of the aforementioned cerebral CNS diseases. We discuss the emerging new therapeutic opportunities, and their delivery approaches, aimed at recovering brain vascularization in this context. SIGNIFICANCE STATEMENT: The lack of effective treatments, mainly focused on neuron recovery, has prompted the search of other therapies to treat cerebral central nervous system diseases. The disruption and degeneration of cerebral microvasculature has been evidenced in neurodegenerative diseases, stroke, and aging, constituting a potential target for restoring vascularization, neuronal functioning, and cognitive capacities by the development of therapeutic pro-angiogenic strategies.
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Affiliation(s)
- Idoia Gallego
- NanoBioCel Research Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P); Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine, Institute of Health Carlos III, Madrid, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.); and Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.)
| | - Ilia Villate-Beitia
- NanoBioCel Research Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P); Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine, Institute of Health Carlos III, Madrid, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.); and Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.)
| | - Laura Saenz-Del-Burgo
- NanoBioCel Research Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P); Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine, Institute of Health Carlos III, Madrid, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.); and Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.)
| | - Gustavo Puras
- NanoBioCel Research Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P); Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine, Institute of Health Carlos III, Madrid, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.); and Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.)
| | - José Luis Pedraz
- NanoBioCel Research Group, Laboratory of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P); Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine, Institute of Health Carlos III, Madrid, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.); and Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain (I.G., I.V.-B., L.S.-B., G.P., J.L.P.)
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Identification of dysregulated pathways and key genes in human retinal angiogenesis using microarray metadata. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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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
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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
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Latifi-Navid H, Soheili ZS, Samiei S, Sadeghi M, Taghizadeh S, Pirmardan ER, Ahmadieh H. Network analysis and the impact of Aflibercept on specific mediators of angiogenesis in HUVEC cells. J Cell Mol Med 2021; 25:8285-8299. [PMID: 34250732 PMCID: PMC8419159 DOI: 10.1111/jcmm.16778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022] Open
Abstract
Angiogenesis, inflammation and endothelial cells’ migration and proliferation exert fundamental roles in different diseases. However, more studies are needed to identify key proteins and pathways involved in these processes. Aflibercept has received the approval of the US Food and Drug Administration (FDA) for the treatment of wet AMD and colorectal cancer. Moreover, the effect of Aflibercept on VEGFR2 downstream signalling pathways has not been investigated yet. Here, we integrated text mining data, protein‐protein interaction networks and multi‐experiment microarray data to specify candidate genes that are involved in VEGFA/VEGFR2 signalling pathways. Network analysis of candidate genes determined the importance of the nominated genes via different centrality parameters. Thereupon, several genes—with the highest centrality indexes—were recruited to investigate the impact of Aflibercept on their expression pattern in HUVEC cells. Real‐time PCR was performed, and relative expression of the specific genes revealed that Aflibercept modulated angiogenic process by VEGF/PI3KA/AKT/mTOR axis, invasion by MMP14/MMP9 axis and inflammation‐related angiogenesis by IL‐6‐STAT3 axis. Data showed Aflibercept simultaneously affected these processes and determined the nominated axes that had been affected by the drug. Furthermore, integrating the results of Aflibercept on expression of candidate genes with the current network analysis suggested that resistance against the Aflibercept effect is a plausible process in HUVEC cells.
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Affiliation(s)
- Hamid Latifi-Navid
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Shahram Samiei
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mehdi Sadeghi
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Sepideh Taghizadeh
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ehsan Ranaei Pirmardan
- Ocular Tissue Engineering Research Center, Molecular Biomarkers Nano-Imaging Laboratory, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Radiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Bar H, Bang S. A mixture model to detect edges in sparse co-expression graphs with an application for comparing breast cancer subtypes. PLoS One 2021; 16:e0246945. [PMID: 33571253 PMCID: PMC7877669 DOI: 10.1371/journal.pone.0246945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/28/2021] [Indexed: 11/19/2022] Open
Abstract
We develop a method to recover a gene network's structure from co-expression data, measured in terms of normalized Pearson's correlation coefficients between gene pairs. We treat these co-expression measurements as weights in the complete graph in which nodes correspond to genes. To decide which edges exist in the gene network, we fit a three-component mixture model such that the observed weights of 'null edges' follow a normal distribution with mean 0, and the non-null edges follow a mixture of two lognormal distributions, one for positively- and one for negatively-correlated pairs. We show that this so-called L2 N mixture model outperforms other methods in terms of power to detect edges, and it allows to control the false discovery rate. Importantly, our method makes no assumptions about the true network structure. We demonstrate our method, which is implemented in an R package called edgefinder, using a large dataset consisting of expression values of 12,750 genes obtained from 1,616 women. We infer the gene network structure by cancer subtype, and find insightful subtype characteristics. For example, we find thirteen pathways which are enriched in each of the cancer groups but not in the Normal group, with two of the pathways associated with autoimmune diseases and two other with graft rejection. We also find specific characteristics of different breast cancer subtypes. For example, the Luminal A network includes a single, highly connected cluster of genes, which is enriched in the human diseases category, and in the Her2 subtype network we find a distinct, and highly interconnected cluster which is uniquely enriched in drug metabolism pathways.
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Affiliation(s)
- Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, United States of America
| | - Seojin Bang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, United States of America
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9
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Efthymiou G, Saint A, Ruff M, Rekad Z, Ciais D, Van Obberghen-Schilling E. Shaping Up the Tumor Microenvironment With Cellular Fibronectin. Front Oncol 2020; 10:641. [PMID: 32426283 PMCID: PMC7203475 DOI: 10.3389/fonc.2020.00641] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022] Open
Abstract
Normal tissue homeostasis and architecture restrain tumor growth. Thus, for a tumor to develop and spread, malignant cells must overcome growth-repressive inputs from surrounding tissue and escape immune surveillance mechanisms that curb cancer progression. This is achieved by promoting the conversion of a physiological microenvironment to a pro-tumoral state and it requires a constant dialog between malignant cells and ostensibly normal cells of adjacent tissue. Pro-tumoral reprogramming of the stroma is accompanied by an upregulation of certain extracellular matrix (ECM) proteins and their cognate receptors. Fibronectin (FN) is one such component of the tumor matrisome. This large multidomain glycoprotein dimer expressed over a wide range of human cancers is assembled by cell-driven forces into a fibrillar array that provides an obligate scaffold for the deposition of other matrix proteins and binding sites for functionalization by soluble factors in the tumor microenvironment. Encoded by a single gene, FN regulates the proliferation, motile behavior and fate of multiple cell types, largely through mechanisms that involve integrin-mediated signaling. These processes are coordinated by distinct isoforms of FN, collectively known as cellular FN (as opposed to circulating plasma FN) that arise through alternative splicing of the FN1 gene. Cellular FN isoforms differ in their solubility, receptor binding ability and spatiotemporal expression, and functions that have yet to be fully defined. FN induction at tumor sites constitutes an important step in the acquisition of biological capabilities required for several cancer hallmarks such as sustaining proliferative signaling, promoting angiogenesis, facilitating invasion and metastasis, modulating growth suppressor activity and regulating anti-tumoral immunity. In this review, we will first provide an overview of ECM reprogramming through tumor-stroma crosstalk, then focus on the role of cellular FN in tumor progression with respect to these hallmarks. Last, we will discuss the impact of dysregulated ECM on clinical efficacy of classical (radio-/chemo-) therapies and emerging treatments that target immune checkpoints and explore how our expanding knowledge of the tumor ECM and the central role of FN can be leveraged for therapeutic benefit.
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Affiliation(s)
| | - Angélique Saint
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France.,Centre Antoine Lacassagne, Nice, France
| | - Michaël Ruff
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
| | - Zeinab Rekad
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
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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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11
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Synergy Between Low Dose Metronomic Chemotherapy and the pH-centered Approach Against Cancer. Int J Mol Sci 2019; 20:ijms20215438. [PMID: 31683667 PMCID: PMC6862380 DOI: 10.3390/ijms20215438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
Low dose metronomic chemotherapy (MC) is becoming a mainstream treatment for cancer in veterinary medicine. Its mechanism of action is anti-angiogenesis by lowering vascular endothelial growth factor (VEGF) and increasing trombospondin-1 (TSP1). It has also been adopted as a compassionate treatment in very advanced human cancer. However, one of the main limitations of this therapy is its short-term effectiveness: 6 to 12 months, after which resistance develops. pH-centered cancer treatment (pHT) has been proposed as a complementary therapy in cancer, but it has not been adopted or tested as a mainstream protocol, in spite of existing evidence of its advantages and benefits. Many of the factors directly or indirectly involved in MC and anti-angiogenic treatment resistance are appropriately antagonized by pHT. This led to the testing of an association between these two treatments. Preliminary evidence indicates that the association of MC and pHT has the ability to reduce anti-angiogenic treatment limitations and develop synergistic anti-cancer effects. This review will describe each of these treatments and will analyze the fundamentals of their synergy.
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Sonawane AR, Weiss ST, Glass K, Sharma A. Network Medicine in the Age of Biomedical Big Data. Front Genet 2019; 10:294. [PMID: 31031797 PMCID: PMC6470635 DOI: 10.3389/fgene.2019.00294] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess the effect and impact of cellular heterogeneity and environmental perturbations on the observed phenotype. Marrying the two, network medicine with biomedical data provides a framework to build meaningful models and extract impactful results at a network level. In this review, we survey existing network types and biomedical data sources. More importantly, we delve into ways in which the network medicine approach, aided by phenotype-specific biomedical data, can be gainfully applied. We provide three paradigms, mainly dealing with three major biological network archetypes: protein-protein interaction, expression-based, and gene regulatory networks. For each of these paradigms, we discuss a broad overview of philosophies under which various network methods work. We also provide a few examples in each paradigm as a test case of its successful application. Finally, we delineate several opportunities and challenges in the field of network medicine. We hope this review provides a lexicon for researchers from biological sciences and network theory to come on the same page to work on research areas that require interdisciplinary expertise. Taken together, the understanding gained from combining biomedical data with networks can be useful for characterizing disease etiologies and identifying therapeutic targets, which, in turn, will lead to better preventive medicine with translational impact on personalized healthcare.
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Affiliation(s)
- Abhijeet R. Sonawane
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA, United States
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Turner CJ, Badu-Nkansah K, Hynes RO. Endothelium-derived fibronectin regulates neonatal vascular morphogenesis in an autocrine fashion. Angiogenesis 2017; 20:519-531. [PMID: 28667352 PMCID: PMC5660148 DOI: 10.1007/s10456-017-9563-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/21/2017] [Indexed: 12/02/2022]
Abstract
Fibronectin containing alternatively spliced EIIIA and EIIIB domains is largely absent from mature quiescent vessels in adults, but is highly expressed around blood vessels during developmental and pathological angiogenesis. The precise functions of fibronectin and its splice variants during developmental angiogenesis however remain unclear due to the presence of cardiac, somitic, mesodermal and neural defects in existing global fibronectin KO mouse models. Using a rare family of surviving EIIIA EIIIB double KO mice, as well as inducible endothelial-specific fibronectin-deficient mutant mice, we show that vascular development in the neonatal retina is regulated in an autocrine manner by endothelium-derived fibronectin, and requires both EIIIA and EIIIB domains and the RGD-binding α5 and αv integrins for its function. Exogenous sources of fibronectin do not fully substitute for the autocrine function of endothelial fibronectin, demonstrating that fibronectins from different sources contribute differentially to specific aspects of angiogenesis.
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Affiliation(s)
- Christopher J Turner
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave, 76-361, Cambridge, MA, 02139, USA
- University of Suffolk, James Hehir Building, University Avenue, Ipswich, Suffolk, IP3 0FS, UK
| | - Kwabena Badu-Nkansah
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave, 76-361, Cambridge, MA, 02139, USA
- Duke University Medical Center, 307 Research Drive, Durham, NC, 27710, USA
| | - Richard O Hynes
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Ave, 76-361, Cambridge, MA, 02139, USA.
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Anderson JD, Johansson HJ, Graham CS, Vesterlund M, Pham MT, Bramlett CS, Montgomery EN, Mellema MS, Bardini RL, Contreras Z, Hoon M, Bauer G, Fink KD, Fury B, Hendrix KJ, Chedin F, El-Andaloussi S, Hwang B, Mulligan MS, Lehtiö J, Nolta JA. Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling. Stem Cells 2016; 34:601-13. [PMID: 26782178 DOI: 10.1002/stem.2298] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022]
Abstract
Mesenchymal stem cells (MSC) are known to facilitate healing of ischemic tissue related diseases through proangiogenic secretory proteins. Recent studies further show that MSC derived exosomes function as paracrine effectors of angiogenesis, however, the identity of which components of the exosome proteome responsible for this effect remains elusive. To address this we used high-resolution isoelectric focusing coupled liquid chromatography tandem mass spectrometry, an unbiased high throughput proteomics approach to comprehensively characterize the proteinaceous contents of MSCs and MSC derived exosomes. We probed the proteome of MSCs and MSC derived exosomes from cells cultured under expansion conditions and under ischemic tissue simulated conditions to elucidate key angiogenic paracrine effectors present and potentially differentially expressed in these conditions. In total, 6,342 proteins were identified in MSCs and 1,927 proteins in MSC derived exosomes, representing to our knowledge the first time these proteomes have been probed comprehensively. Multilayered analyses identified several putative paracrine effectors of angiogenesis present in MSC exosomes and increased in expression in MSCs exposed to ischemic tissue-simulated conditions; these include platelet derived growth factor, epidermal growth factor, fibroblast growth factor, and most notably nuclear factor-kappaB (NFkB) signaling pathway proteins. NFkB signaling was identified as a key mediator of MSC exosome induced angiogenesis in endothelial cells by functional in vitro validation using a specific inhibitor. Collectively, the results of our proteomic analysis show that MSC derived exosomes contain a robust profile of angiogenic paracrine effectors, which have potential for the treatment of ischemic tissue-related diseases.
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Affiliation(s)
- Johnathon D Anderson
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Henrik J Johansson
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Calvin S Graham
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Mattias Vesterlund
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Missy T Pham
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Charles S Bramlett
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Elizabeth N Montgomery
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Matt S Mellema
- Surgical and Radiological Sciences, Department of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Renee L Bardini
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Zelenia Contreras
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Madeline Hoon
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Gerhard Bauer
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Kyle D Fink
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Brian Fury
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Kyle J Hendrix
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
| | - Frederic Chedin
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, USA
| | - Samir El-Andaloussi
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Billie Hwang
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Michael S Mulligan
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Janne Lehtiö
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jan A Nolta
- Stem Cell Program, Department of Internal Medicine, University of California Davis, Davis, California, USA
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15
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Schmidt-Kastner R. Genomic approach to selective vulnerability of the hippocampus in brain ischemia–hypoxia. Neuroscience 2015; 309:259-79. [DOI: 10.1016/j.neuroscience.2015.08.034] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/12/2015] [Accepted: 08/17/2015] [Indexed: 01/06/2023]
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16
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Systems biology of ion channels and transporters in tumor angiogenesis: An omics view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2647-56. [DOI: 10.1016/j.bbamem.2014.10.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/09/2014] [Accepted: 10/20/2014] [Indexed: 01/19/2023]
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17
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Bender RJ, Mac Gabhann F. Dysregulation of the vascular endothelial growth factor and semaphorin ligand-receptor families in prostate cancer metastasis. BMC SYSTEMS BIOLOGY 2015; 9:55. [PMID: 26341082 PMCID: PMC4559909 DOI: 10.1186/s12918-015-0201-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 08/20/2015] [Indexed: 01/01/2023]
Abstract
Background The vascular endothelial growth factor (VEGF) family is central to cancer angiogenesis. However, targeting VEGF as an anti-cancer therapeutic approach has shown success for some tumor types but not others. Here we examine the expression of the expanded VEGF family in prostate cancer, including the Semaphorin (Sema) family members that compete with VEGFs for Neuropilin binding and can themselves have pro- or anti-angiogenic activity. Results First, we used multivariate statistical methods, including partial least squares and clustering, to examine VEGF/Sema gene expression variability in previously published prostate cancer microarray datasets. We show that unlike some cancers, such as kidney cancer, primary prostate cancer is characterized by both a down-regulation of the pro-angiogenic members of the VEGF family and a down-regulation of anti-angiogenic members of the Sema family. We found pro-lymphangiogenic signatures, including the genes encoding VEGFC and VEGFD, associated with primary tumors that ultimately became aggressive. In contrast to primary prostate tumors, prostate cancer metastases showed increased expression of key pro-angiogenic VEGF family members and further repression of anti-angiogenic class III Sema family members. Given the lack of success of VEGF-targeting molecules so far in prostate cancer, this suggests that the reduction in anti-angiogenic Sema signaling may potentiate VEGF signaling and even promote resistance to VEGF-targeting therapies. Inhibition of the VEGF ‘accelerator’ may need to be accompanied by promotion of the Sema ‘brake’ to block cancer angiogenesis. To leverage our mechanistic understanding, and to link multigene expression changes to outcomes, we performed individualized computational simulations of competitive VEGF and Sema receptor binding across many tumor samples. The simulations suggest that loss of Sema expression promotes angiogenesis by lowering plexin signaling, not by potentiating VEGF signaling via relaxation of competition. Conclusions The combined analysis of bioinformatic data with computational modeling of ligand-receptor interactions demonstrated that enhancement of angiogenesis in prostate cancer metastases may occur through two different routes: elevation of VEGFA and reduction of class 3 Semaphorins. Therapeutic inhibition of angiogenesis in metastatic prostate cancer should account for both of these routes. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0201-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R Joseph Bender
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Feilim Mac Gabhann
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.
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18
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Chu LH, Annex BH, Popel AS. Computational drug repositioning for peripheral arterial disease: prediction of anti-inflammatory and pro-angiogenic therapeutics. Front Pharmacol 2015; 6:179. [PMID: 26379552 PMCID: PMC4548203 DOI: 10.3389/fphar.2015.00179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/10/2015] [Indexed: 12/17/2022] Open
Abstract
Peripheral arterial disease (PAD) results from atherosclerosis that leads to blocked arteries and reduced blood flow, most commonly in the arteries of the legs. PAD clinical trials to induce angiogenesis to improve blood flow conducted in the last decade have not succeeded. We have recently constructed PADPIN, protein-protein interaction network (PIN) of PAD, and here we combine it with the drug-target relations to identify potential drug targets for PAD. Specifically, the proteins in the PADPIN were classified as belonging to the angiome, immunome, and arteriome, characterizing the processes of angiogenesis, immune response/inflammation, and arteriogenesis, respectively. Using the network-based approach we predict the candidate drugs for repositioning that have potential applications to PAD. By compiling the drug information in two drug databases DrugBank and PharmGKB, we predict FDA-approved drugs whose targets are the proteins annotated as anti-angiogenic and pro-inflammatory, respectively. Examples of pro-angiogenic drugs are carvedilol and urokinase. Examples of anti-inflammatory drugs are ACE inhibitors and maraviroc. This is the first computational drug repositioning study for PAD.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Brian H Annex
- Division of Cardiovascular Medicine, Department of Medicine and Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine Charlottesville, VA, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University Baltimore, MD, USA
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Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS. PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. Physiol Genomics 2015; 47:331-43. [PMID: 26058837 DOI: 10.1152/physiolgenomics.00125.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 06/04/2015] [Indexed: 11/22/2022] Open
Abstract
Peripheral arterial disease (PAD) results from an obstruction of blood flow in the arteries other than the heart, most commonly the arteries that supply the legs. The complexity of the known signaling pathways involved in PAD, including various growth factor pathways and their cross talks, suggests that analyses of high-throughput experimental data could lead to a new level of understanding of the disease as well as novel and heretofore unanticipated potential targets. Such bioinformatic analyses have not been systematically performed for PAD. We constructed global protein-protein interaction networks of angiogenesis (Angiome), immune response (Immunome), and arteriogenesis (Arteriome) using our previously developed algorithm GeneHits. The term "PADPIN" refers to the angiome, immunome, and arteriome in PAD. Here we analyze four microarray gene expression datasets from ischemic and nonischemic gastrocnemius muscles at day 3 posthindlimb ischemia (HLI) in two genetically different C57BL/6 and BALB/c mouse strains that display differential susceptibility to HLI to identify potential targets and signaling pathways in angiogenesis, immune, and arteriogenesis networks. We hypothesize that identification of the differentially expressed genes in ischemic and nonischemic muscles between the strains that recovers better (C57BL/6) vs. the strain that recovers more poorly (BALB/c) will help for the prediction of target genes in PAD. Our bioinformatics analysis identified several genes that are differentially expressed between the two mouse strains with known functions in PAD including TLR4, THBS1, and PRKAA2 and several genes with unknown functions in PAD including EphA4, TSPAN7, SLC22A4, and EIF2a.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland;
| | - Chaitanya G Vijay
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Brian H Annex
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Joel S Bader
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland; High-Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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20
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Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells. PLoS One 2014; 9:e110871. [PMID: 25329517 PMCID: PMC4199761 DOI: 10.1371/journal.pone.0110871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Angiogenesis involves stimulation of endothelial cells (EC) by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the “angiome”) could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A). We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME) show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC) and human microvascular EC (MEC). The results show that VEGFR1–VEGFR2 levels are more closely coupled than VEGFR1–VEGFR3 or VEGFR2–VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.
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21
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Finley SD, Chu LH, Popel AS. Computational systems biology approaches to anti-angiogenic cancer therapeutics. Drug Discov Today 2014; 20:187-97. [PMID: 25286370 DOI: 10.1016/j.drudis.2014.09.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/05/2014] [Accepted: 09/29/2014] [Indexed: 01/06/2023]
Abstract
Angiogenesis is an exquisitely regulated process that is required for physiological processes and is also important in numerous diseases. Tumors utilize angiogenesis to generate the vascular network needed to supply the cancer cells with nutrients and oxygen, and many cancer drugs aim to inhibit tumor angiogenesis. Anti-angiogenic therapy involves inhibiting multiple cell types, molecular targets, and intracellular signaling pathways. Computational tools are useful in guiding treatment strategies, predicting the response to treatment, and identifying new targets of interest. Here, we describe progress that has been made in applying mathematical modeling and bioinformatics approaches to study anti-angiogenic therapeutics in cancer.
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Affiliation(s)
- Stacey D Finley
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA.
| | - Liang-Hui Chu
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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22
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Davidsen PK, Herbert JM, Antczak P, Clarke K, Ferrer E, Peinado VI, Gonzalez C, Roca J, Egginton S, Barberá JA, Falciani F. A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. Genome Med 2014; 6:59. [PMID: 25228925 PMCID: PMC4165371 DOI: 10.1186/s13073-014-0059-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/24/2014] [Indexed: 01/03/2023] Open
Abstract
Background A relatively large percentage of patients with chronic obstructive pulmonary disease (COPD) develop systemic co-morbidities that affect prognosis, among which muscle wasting is particularly debilitating. Despite significant research effort, the pathophysiology of this important extrapulmonary manifestation is still unclear. A key question that remains unanswered is to what extent systemic inflammatory mediators might play a role in this pathology. Cigarette smoke (CS) is the main risk factor for developing COPD and therefore animal models chronically exposed to CS have been proposed for mechanistic studies and biomarker discovery. Although mice have been successfully used as a pre-clinical in vivo model to study the pulmonary effects of acute and chronic CS exposure, data suggest that they may be inadequate models for studying the effects of CS on peripheral muscle function. In contrast, recent findings indicate that the guinea pig model (Cavia porcellus) may better mimic muscle wasting. Methods We have used a systems biology approach to compare the transcriptional profile of hindlimb skeletal muscles from a Guinea pig rodent model exposed to CS and/or chronic hypoxia to COPD patients with muscle wasting. Results We show that guinea pigs exposed to long-term CS accurately reflect most of the transcriptional changes observed in dysfunctional limb muscle of severe COPD patients when compared to matched controls. Using network inference, we could then show that the expression profile in whole lung of genes encoding for soluble inflammatory mediators is informative of the molecular state of skeletal muscles in the guinea pig smoking model. Finally, we show that CXCL10 and CXCL9, two of the candidate systemic cytokines identified using this pre-clinical model, are indeed detected at significantly higher levels in serum of COPD patients, and that their serum protein level is inversely correlated with the expression of aerobic energy metabolism genes in skeletal muscle. Conclusions We conclude that CXCL10 and CXCL9 are promising candidate inflammatory signals linked to the regulation of central metabolism genes in skeletal muscles. On a methodological level, our work also shows that a system level analysis of animal models of diseases can be very effective to generate clinically relevant hypothesis. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0059-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter K Davidsen
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK ; School of Immunity and Infection, University of Birmingham, Birmingham, UK
| | - John M Herbert
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK
| | - Philipp Antczak
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK
| | - Kim Clarke
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK
| | - Elisabet Ferrer
- Department of Pulmonary Medicine, Hospital Clinic, University of Barcelona, Barcelona, Spain ; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Victor I Peinado
- Department of Pulmonary Medicine, Hospital Clinic, University of Barcelona, Barcelona, Spain ; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ; Biomedical Research Networking Center on Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Constancio Gonzalez
- Biomedical Research Networking Center on Respiratory Diseases (CIBERES), Barcelona, Spain ; Department of Biochemistry and Molecular Biology and Physiology, University of Valladolid, Valladolid, Spain
| | - Josep Roca
- Department of Pulmonary Medicine, Hospital Clinic, University of Barcelona, Barcelona, Spain ; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ; Biomedical Research Networking Center on Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Stuart Egginton
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joan A Barberá
- Department of Pulmonary Medicine, Hospital Clinic, University of Barcelona, Barcelona, Spain ; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ; Biomedical Research Networking Center on Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Francesco Falciani
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool, Crown Street, L69 7ZB Liverpool, UK
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Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev 2013; 23:611-21. [PMID: 24238873 PMCID: PMC3866044 DOI: 10.1016/j.gde.2013.10.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/04/2013] [Accepted: 10/09/2013] [Indexed: 02/06/2023]
Abstract
A prime objective of genomic medicine is the identification of disease-causing mutations and the mechanisms by which such events result in disease. As most disease phenotypes arise not from single genes and proteins but from a complex network of molecular interactions, a priori knowledge about the molecular network serves as a framework for biological inference and data mining. Here we review recent developments at the interface of biological networks and mutation analysis. We examine how mutations may be treated as a perturbation of the molecular interaction network and what insights may be gained from taking this perspective. We review work that aims to transform static networks into rich context-dependent networks and recent attempts to integrate non-coding RNAs into such analysis. Finally, we conclude with an overview of the many challenges and opportunities that lie ahead.
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Affiliation(s)
- Hannah Carter
- Institute for Genomic Medicine and Department of Medicine, University of California, San Diego, 9500 Gillman Drive, La Jolla, CA 92093, United States
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24
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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: 98] [Impact Index Per Article: 8.9] [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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